Dr. Bharti Ghude Wadekar and Mr.

Sahil Selot

Glossary on
Genetics

First Edition

JPS, Scientific Publications, India

 Glossary Book

GLOSSARY OF
GENETICS

Editors
Dr. Bharti Ghude Wadekar
Faculty of Department of Microbiology (Interdisciplinary), ZSCT’s Thakur College
of Science, Kandivali (E), Mumbai University, Mumbai, Maharashtra, India

Mr. Sahil Selot

Department of Microbiology (Interdisciplinary), ZSCT’s Thakur College of Science,
Kandivali (E), Mumbai University, Mumbai, Maharashtra, India

Published by

JPS Scientific Publications

India

i
Copyright©2022 by JPS Scientific Publications. All Rights Reserved

Published by

JPS Scientific Publications, Tamil Nadu, India.

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ii
 ABOUT THE EDITOR – Dr. Bharti Ghude Wadekar

Dr. Bharti Ghude Wadekar is currently working as an Assistant Professor in the department of
Microbiology (ID), ZSCT’s Thakur Shyamnarayan Degree College, Kandivali (E), Mumbai
University, Mumbai. She is IQAC Coordinator of TSDC, Mumbai. She has completed M.Sc.
from Sardar Patel College, Chandrapur, R.T.M. Nagpur University, Maharashtra. She received
her Ph.D. Degree in the year 2019 from Dr. Babasaheb Ambedkar Marathwada University,
Aurangabad, Maharashtra. She is the first DST, WOS-A FELLOW (2014-2018) of Department
of Microbiology, Dr. Babasaheb Ambedkar Marathwada University, and Maharashtra. She has
published 2 chapter, 3 books, 43 Research articles in National and International Journals. She has
participated in 10 National and International Conferences. She has attended above 100
webinars/workshops and 20 FDPs organized by other institutes. She has organized about 45
National Level Webinars, MCQ competitions, Workshops and 3 Conferences in the year 2021-
23. Her Three Germany Patent Published and granted, one Indian Patent published. She is a life
member of Indian Microbiologist Society. She got Best Paper Presentation Award in International
E-Conference on “Study of Microbiomes” ZSCT’s Thakur Shyamnarayan Degree College,
Kandivali East, Mumbai, Tilak Maharashtra Vidyapeeth, Pune, MS and Microbiologist Society,
India. She awarded as a 50 Highly Effective Teachers of 2022 by Education connect plus,
HYPEDGE. She received Indian Women Talent Award, NIRGIA brand Promotors, India. She
got “Global Best Researcher Award 2022” in recognition & appreciation of her contribution in key
areas and working position, by Management of MSSPM’s, Lalbahadur Shastri Sr. College Partur
(MS), MES’s, Arts Commerce and Science College, Sonai (MS) and Yuvraja’s College Mysuru,
Karnataka. Global Youth ICON Award-2022, International Council for Education, Research and
Training, 12th Aug. 2022. Most Inspiring Innovator Award, in IndoSingapore International
Conference on Sciences, Agriculture, Engineering, and Management ISICSAEM2022 held at
Rathinam College of Arts and Science, Coimbatore, Tamilnadu, India on August 13, 2022. She
got Research Excellence Award 2022, by InSc Institute of Scholars. Her specialization is in the
different subjects name as Biostatistics, Environmental Microbiology, Fermentation technology,
Bioprocess Technology, Genetics Bioinstrumentation, and Molecular biology.

iii
 ABOUT THE EDITOR – Mr. Sahil Selot

Sahil Naaz Selot is Currently Student of Second Year in Department of Microbiology in

ZSCT’s Thakur Shamnaarayan Degree College, Kandivali East Mumbai 400101 Maharashtra,
India. His interest in a Microbiology field. This field developed his inner and hidden talent like
Research and Content writing. His 5 research paper published in the International Journal of
Advanced Research Science, Communication and Technology Journal (IJARSCT).

iv
 Contents
Chapter Title Page Number
A 1
B 34
C 60
D 125
E 165
F 189
G 200
H 225
I 262
J 280
K 282
L 286
M 298
N 319
O 331
P 335
Q 371
R 371
S 406
T 435
U 458
V 462
W 466
X 468
Y 472
Z 474

v
Glossary of Genetics 1

identities in the posterior abdomen.

A The ABD-B regulation of the
pigmentation evolved through the
• AAA PROTEINS - The AAA
gain of the ABD-B binding sites in
proteins are the members of the
a specific cis-regulatory element of
larger AAA+ superfamily, are a
a yellow gene through a common
family of enzymatic machines
ancestor of the sexually dimorphic
which are involved in diverse
species. Within the melanogaster
cellular functions ranging from the
species group, the male-specific
DNA repair and replication to the
pigmentation has subsequently
organelle biogenesis, membrane
been lost by at least three different
trafficking, transcriptional
mechanisms, including the
regulation, and the protein quality
mutational inactivation of a key
control. The AAA proteins were
ABD-B binding site in one lineage.
defined as the ATPases associated
The ABD-B Gene generally
with the various cellular activities,
activates the pigmentation process
but this definition disguises the
in the Drosophila Melanogaster.
breadth and the importance of their
• ABSORBANCE OF DNA - The
functions and the common
Absorbance of the DNA is a
structures and the mechanisms of
technique which is It based on the
the action that underlie their
principles that the nucleic acids
activities.
absorb ultraviolet (UV) light at a
• ABDOMINAL-A GENE (Adb-A)
specific wavelength. For example,
DROSOPHILA - The Hox genes
the pure DNA samples, the
are the genes which encode the
maximum absorbance occurs over
transcription factors that can
a broader peak at around 260 nm,
generate the segmental diversity
but at 280 nm it only absorbs about
during the Drosophila
half as much UV light compared to
melanogaster development. In the
the 260 nm. The difference in the
overlapping expression domains of
20 nm plays a greater role in this
the abd-A and the Abd-B in the
technique.
early pupal abdominal epithelia,
• AMINOPURINE - The 2-
both the genes have essential roles.
Aminopurine, a purine analog of
While the Abd-A is required for
the guanine and the adenine, is a
the cell proliferation, the Abd-B
fluorescent molecular marker used
determines the segmental identity.
in the nucleic acid research. It most
• ABDOMINAL-B GENE (Adb-B)
commonly pairs with the thymine
DROSOPHILA - The Abdominal-
as an adenine-analogue, but can
B (Abd-B) gene of the Drosophila
also pair with the cytosine as a
Melanogaster controls the
guanine-analogue,. For this reason
specification of the segment
it is sometimes used in the

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
laboratory for the mutagenesis.
The 2-aminopurine is able to form
the Watson–Crick base pair with
the thymine, so it maintains the
structure of B-form of the DNA.
An oligonucleotide is synthesized
with a regular incorporation of
multiple number of 2-aminopurine,
which is then hybridized with a
complementary strand to form a
double-stranded substrate.
• AMINOACYL TRNA
SYNTHETASE - The aminoacyl-
tRNA synthetase (aaRS or the
ARS), also called as the tRNA-
ligase, is an enzyme that attaches
the appropriate amino acid onto its
corresponding tRNA. This is done
through catalyzing the
transesterification of the specific
cognate amino acid or through its
precursor to one of all its
compatible cognate tRNAs to form
the aminoacyl-tRNA. In the
humans, the 20 different types of
aa-tRNA are made by the 20
different aminoacyl-tRNA
synthetases, one for each amino
acid of the genetic code. This is
sometimes called as the "charging"
or "loading" the tRNA with an
amino acid. Once the tRNA is
charged, the ribosome can transfer
the amino acid from the tRNA
onto the growing peptide,
according to the available genetic
code. The Aminoacyl tRNA
therefore plays an important role in
the RNA translation, the
expression of the genes to create
the proteins.
© 2022 by JPS Scientific Publications, India
2
• ACTIVATOR ELEMENTS - A
transcriptional activator is a
protein which acts as a
transcription factor that increases
the rate of the transcription of a
gene or a set of the genes. These
Activators are considered to have a
positive control over the gene
expression, as they can function to
promote the gene transcription
and, in some of the cases they are
required for the transcription of the
genes to occur.
• ACCEPTOR SITES - This are the
sites or the location at which the
aminoacyl tRNA binds with the
ribosome during the protein
synthesis. The RNA splicing is an
part of the eukaryotic genes
expression. In the RNA Splicing
the Introns are eliminated and the
Exons are joined together.
• ACETYL CO-A - The Acetyl Co-
A ( Acetyl coenzyme A) is a
molecule which take part in many
of the biochemical reactions of the
Carbohydrates, proteins, etc. It’s
chemical formula is CH3CO. The
Acetyl Co-A plays a major role in
the production of the energy during
Fasting or Starving. The Acetyl
Co-A gives Acetyl group to the
Citric acid cycle (Kreb’s cycle).
• ACTIN FILAMENTS - The actin
filaments are the protein filaments
which are found in the cytoplasm
of the eukaryotic cells that form the
major part of the cytoskeleton. It is
an part of the Microfilaments. The
Actin filaments form a network
that provides the mechanical
Glossary of Genetics
support to determines the cell
shape and allows the movement of
the cell surface, thereby helping the
cells to migrate, engulf particles
and cells and divide.
• A COMPLEX ACRIDINE - The
Acridine orange is a fluorescent
dye. The Acridine Orange binds to
the genetic material and can
differentiate between the
deoxyribonucleic acid (DNA ) and
the ribonucleic acid (RNA ). The
Acridine Orange gives colour and
differentiate compound’s. The
Acridine Orange is known for it’s
property like Mutating the DNA.
• ACTIVATED MOLECULE -
The Gene activators are facilitated
or mediated through the binding
factors Such as the ABA
responsive elements. A activator
increases the rate of the
transcription of the gene or set of
the genes. A gene transcription is
kicked off when the proteins called
as the transcription factors bind to
the two key bits of the DNA, an
enhancer and a promoter.
• ACTIVATED STATE The -
process of activating the genes on
and off is known as the gene
regulation. It can occur at any
point during the gene expression,
but most commonly occurs at the
level of the transcription (when the
information in a gene’s DNA is
passed to the mRNA). In the
Activated State The gene is in it’s
utmost capacity for the regulation.
© 2022 by JPS Scientific Publications, India
3
• ACTIVATING REGION OF
CAP - The CAP stands for the
Catabolite Activator Protein. It
exists as Homodimer in the
solution. Each subunit of the CAP
is composed of a ligand-binding
domain at the N-terminus and a
DNA-binding domain at the C-
terminus. It activates the protein
Transcription through the Protein
Protein interaction through α-
subunit of the RNA Polymerase.
• ACTIVATION ENERGY - The
Activation energy is a minimum
amount of the energy required for
all the chemical and the biological
reactions. It is necessary to attain a
minimum amount of energy to
denaturate the DNA at certain
temperature.
• ACTIVATOR BYPASS
EXPERIMENT - The “activator-
bypass” experiment is performed in
the yeast and the bacteria, which
have played an important role in
formulating the idea that many
transcriptional activators work by
recruiting the transcriptional
machinery to the promoter. It takes
place in both the eukaryotes and
the prokaryotes but in case of the
prokaryotes, it takes place in the
cytoplasm and in the eukaryotes, it
takes place in the nucleus.
• ACTIVE SITE - The Active sites
are the regions which are usually
present on the surface of the
enzymes especially when the
modelled is nature during the
evolution that either catalyse a
reaction or are responsible for the
Glossary of Genetics
substrate binding. The Active sites
are the region of an enzyme where
the substrate molecules bind and
undergoes a chemical reaction.
• ACYCLOVIR - The Acyclovir
(ACV), is an antiviral drug which
is active in the treatment of the oral
and the genital Herpes infections.
It has been evaluated for the
mutagenic and the carcinogenic
potential in a battery of in vitro and
in vivo short-term assays The
Acyclovir triphosphate a drug
which inhibits the viral DNA
polymerase and the replication of
the viral DNA processes. It is
effective against the replicating
virus but does not eliminate the
latent virus.
• ACYL BOND - Thee Aminoacyl-
tRNAs are the biologically active
substrates which are used in the
protein synthesis using the peptide
bond formation. It is tRNA to
which the amino acids are
chemically bonded. A tRNA
molecule is an “L” shaped
structure which are joined together
by hydrogen bonds between the
bases in the different parts of the
tRNA sequence.
• ACYL – HOMISERINE
LACTONES - The Acyl
homoserine lactones are one of the
most important intercellular
signaling molecules which is used
by many of the bacteria to monitor
their population density in the
quorum-sensing control of the gene
expression. These signals are
© 2022 by JPS Scientific Publications, India
4
generally used by the gram
negative bacteria. These are signals
are also called as the Autoinducers.
These signals are synthesized by
the members of the LuxI family of
the proteins
• ADAPTOR HYPOTHESIS OF
CRICK - The Crick, in his adaptor
hypothesis, proposed that the small
RNA molecules would be the
adaptors that could be charged
with the amino acids by the certain
specific enzymes and that could
identify the codons of the mRNA
by base-pairing. Each amino acids
is attached to it’s own specific
“adaptor” piece of the nucleic acid
through an enzyme catalysed
reaction.
• ADAPTOR PROTEIN - The
Adaptor proteins are the proteins
which contain a series of protein-
binding sites that link the
respective interaction partners to
the each other and facilitate the
generation of the larger signaling
complexes. They form the short-
lived complexes with the other
proteins to the transduce
membrane activation signals to the
major cytoplasmic signaling
pathways. Some of the examples
are the MYD88, Grb2 and the
SHC1.
• ADENINE BASE PAIR - The
base-pairing rules are such that the
adenine can only be hybridize to
the thymine. It is a base in the ATP
which helps to phosphorylize the
molecules. It is present in both the
Glossary of Genetics
DNA and the RNA. Adenine is a
type of the purines.
• ADAR - It stands as adenosine
deaminase acting on the RNA.
These are the enzymes that
catalyze the chemical conversion
of the adenosines to the inosines in
the double-stranded RNA
(dsRNA) substrates. The ADAR
gene provides the instructions for
making a protein called as the
RNA-specific adenosine deaminase
1. This protein is involved in the
changes made in the ribonucleic
acid (RNA).
• ADENINE BINDING TO
THYMINE - In the DNA, the
adenine base pair binds to the
thymine base pair the via two
hydrogen bonds which plays a role
in assisting in stabilizing the
nucleic acid structures. The
Adenine is one of the two purines
nucleobases which is utilized in the
process of forming nucleotides of
the nucleic acids. This relationship
between the Adenine and the
Thymine is as called as the
complementary base paring.
• ADENOSINE DEAMINASE -
The ADA is the gene which
provides the instructions for
producing the enzyme adenosine
deaminase. It is a type of the
genetic disease which is caused by
the defect in the genes. The ADA
deficiency is a type of the inherited
disease which damages the
immune system and causes the
several combined
immunodeficiency (SCID).
© 2022 by JPS Scientific Publications, India
5
• ADENOVIRUS - The
Adenoviruses are the medium-
sized, non-enveloped viruses with
an icosahedral nucleocapsid
containing a double-stranded DNA
genome. The Adenovirus is the
most efficient gene delivery system
in a broad range of the cell and all
types of the tissue. The
Adenoviruses are also used for the
gene therapy and as vaccines to
express as the foreign antigens. The
genetic expression from the
adenoviruses is transient where the
DNA is free within the host cell’s
nucleus where it can be
transcribed, but upon the cell
division these genes will not be
replicated.
• ATF 1:- The Cyclic AMP-
dependent transcription factor
ATF-1 is a protein that in the
humans is encoded by the ATF1
gene. This gene encodes an
activating transcription factor,
which belongs to the ATF
subfamily and bZIP (basic-region
leucine zipper) family. It influences
the cellular physiologic processes
by regulating the expression of the
downstream target genes, which
are related to the growth, survival,
and the other cellular activities.
This protein is phosphorylated at
the serine 63 in its kinase-inducible
domain by the serine/threonine
kinases, cAMP-dependent protein
kinase A, calmodulin-dependent
protein kinase I/II, mitogen- and
stress-activated protein kinase and
the cyclin-dependent kinase 3 (cdk-
Glossary of Genetics
3). Its phosphorylation enhances its
transactivation and the
transcriptional activities, and
enhances the cell transformation.
The Fusion of this gene and the
FUS on the chromosome 16 or the
EWSR1 on the chromosome 22
induced by the translocation
generates chimeric proteins in the
angiomatoid fibrous histiocytoma
and clear cell sarcoma. This gene
has a pseudogene on the
chromosome 6.
• ADENYLATION OF AMINO
ACID - The Adenylylation, is also
called as the AMPylation, which is
a process in which an adenosine
monophosphate (AMP) molecule
is covalently attached to the amino
acid using a chain of a protein. It
is used to regulate the enzyme
activity via the post translational
process and it is used to produce
the unstable intermediates of the
protein, peptide or the amino acid
which allows the reactions that are
not thermodynamically not
favoured. The ADENYLATION
of the amino acid is an reversible
process.
• ADULT MUSCULAR
DYSTROPHY - The Muscular
dystrophy is a group of more than
30 inherited genetic diseases which
cause the progressive weakness and
loss of the muscle mass. In the
muscular dystrophy, the abnormal
genes interfere with the production
of the proteins such as the tubulin
needed to form healthy muscle.
These conditions are a type of the
© 2022 by JPS Scientific Publications, India
6
myopathy, a disease of the skeletal
muscles.
• AFFINITY
CHROMATOGRAPHY - It is a
separation method which is based
on a specific binding interaction
between an immobilized ligand
and its binding partner. Examples
include the antibody/antigen
binding. It is a type of the liquid
chromatography for the separation,
purification or the specific analysis
of the sample components.
• AGAROSE GEL
ELECTROPHORESIS - The
Agarose gel electrophoresis is a
method of the gel electrophoresis
which is used in the biochemistry,
molecular biology, genetics, and
the clinical chemistry. The
Electrophoresis is used to separate
the nucleic acids or the proteins on
the basis of the size and/or the
charge. In the agarose gel
electrophoresis, one of the two
buffers is used:- 1)Tris-Acetate–
EDTA (TAE) or the 2)Tris-Borate–
EDTA (TBE). TBE has a higher
buffering capacity than the TAE.
• AGING - The Aging is related to
the accumulation of the genetic
mutations which are not repaired
or replaced. A gene called as the
GATA6 regulates the aging of the
human mesenchymal
stem/stromal cells. Only about
30% of these genes may be directly
involved in the aging process. It is
known that the mutations
specifically in the mitochondrial
DNA are the cause of the aging.
Glossary of Genetics
• AGROBACTERIUM
TUMEFACEINS - The
Agrobacterium tumefaciens is also
known as the Agrobacterium
radiator. It is the casual agent of
the crown gall disease in over 140
species of the eudicots .It is a
special type of the phytopathogen.
It also causes the tumour in the
plant cells. It is a naturally
occurring soil bacterium. It is a
gram negative bacteria and the rod
shaped cells.
• AGROBACTERIUM
TUMEFACIENS
CHROMOSOME MAKEUP - It
consists of the one circular and the
one linear chromosome and the
two circular plasmid. Here the
DNA is carried on the large
plasmid called as the tumour
inducing or the Ti plasmid which
are susceptible to the plant cells.
The Ti plasmid Has two
components 1) T-DNA and 2) the
vir region. The Ti plasmid plays a
role of the cloning vector.
• ALANINE - The Alanine is an α-
amino acid which is used in the
biosynthesis of the proteins. It
carries an amino group and a
carboxylic acid both attached to
the central carbon atom which also
carries a methyl group. The
Alanine strengthens the immune
system and helps the body to use
sugars. The Alanine is produced
from the pyruvate by process
known as the transamination.
© 2022 by JPS Scientific Publications, India
7
• ALIGNMENT TOOLS - The
Alignment is a way of arranging
the protein or the DNA sequences
to identify the regions of the
similarity which may be a
consequence of the evolutionary
relationships between the
sequences. The Clustal Omega is a
multiple sequence alignment tool
which is best used for the aligning
similar sequence regions between
the three or the more RNA, DNA
or the protein sequences.
• ALKYLATION OF DNA - The
DNA alkylation is a process which
is refers to the addition o the f alkyl
groups to the specific bases,
resulting in the alkylation products
such as the O2‐alkylthymine which
cause the DNA mutations. The
Alkylation is a result of the
endogenous compounds,
environmental agents and the
alkylating drugs such as the
methylnitrosourea, tobacco-specific
nitrosamine.
• ALLOLACTOSE - The
Allolactose is a disaccharide
compound which is similar to the
lactose. It can be arise from the
occasional transglycosylation of
the lactose by the β-galactosidase.
It is used to preform activities such
as binding to the lac repressor,
stopping repression, and allowing
the transcription of the lacZ and
the related genes. In the absence of
the lactose Allolactose prevents the
process of the transcription. It is a
positive regulator.
Glossary of Genetics
• ALLOSTERIC MODEL OF
TERMINATION - The model
suggests that the termination
occurs due to the structural change
in the RNA polymerase unit after
binding to or the losing some of its
associated proteins, making it
separated from the DNA strand
after the signal. Here the
transcription and the translation
process terminates.
TheTranscription process
termination occurs when the
transcribing RNA polymerase
releases the DNA template and the
nascent RNA. Translation process
termination occurs when the
ribosome encounters a stop codon
(UAG, UAA, or the UGA) in the
A site.
• ALLOSTERIC REGULATION -
The Allosteric regulation is the
regulation of an enzyme by binding
an effector molecule at the site
other than the enzyme’s active site.
The site to which the effector binds
is known as the allosteric site or the
regulatory site. They can be
positive (activating) causing an
increase of the enzyme activity or
the negative (inhibiting) causing a
decrease of the enzyme activity.
Aspartate Transcarbamoylase,
Glucokinase, Acetyl-CoA
Carboxylase are the examples of
the allosteric enzymes.
• ALLOSTERIC - The Allostery is
a process where a binding event
take place at one site of a biological
macromolecule that affects the
binding activity at another distinct
© 2022 by JPS Scientific Publications, India
8
functional site which enables the
regulation of the corresponding
function. Commonly it is refers to
regulation at the distant sites. The
fundamental role of the allostery in
the cellular function is to
underscores its relevance to the
disease.
• Α-CARBON OF AMINO ACID -
The alpha carbon (α-carbon) is a
carbon which connects the amino
group to the acid carboxyl group
giving the amino acids their name.
It is the backbone carbon next to
the carbonyl carbon. The alpha
carbon also serves as the point of
the attachment for the sidechains
of the amino acids used in the
protein building. The Glycine is
the only amino acid with no
sidechain.
• Α-CTD - The C-terminal domain
of the alpha subunit is often
involved in the process of the
transcriptional regulation through
the RNA polymerase. It is also
important in assembling the
polymerase and positive control of
the transcription initiation. It is
also involved in the process of the
attachment to the spliceosome for
the RNA splicing. It is made of the
heptad repeats of the amino acids.
• Α-HELIX -
The alpha helix is a common motif
in the secondary structure of the
proteins and it is a right hand-helix
conformation in which the every
backbone N−H group hydrogen is
bonds to the backbone C=O group
of the amino acid which are
Glossary of Genetics
located at four residues earlier
along the protein sequence. It is a
description of how the main chain
of a protein is arranged in the
space. The alpha helix is a rod-like
structure whose inner section is
formed by a tightly coiled main
chain, with its side chains
extending outward in a helical
array.
• ALTERNATIVE SPLICING -
The Alternative splicing is a
process of selecting the different
types of the combinations of the
splice sites within a messenger
RNA precursor to produce the
variably spliced mRNAs. It is a
molecular mechanisms that
modifies the pre-mRNA construct
prior to the translation process.
This process can produce a
diversity of the mRNAs from a
single gene by arranging the coding
sequences i.e exons from the
recently spliced RNA transcripts
into the different combinations.
• AMES TEST - The Ames test is a
test which is widely employed
method that uses a bacteria to test
whether a given chemical can
cause the mutations in the DNA of
the test organism. More formally,
it is a biological assay to assess the
mutagenic potential of the
chemical compounds. It is one of
the most common test for the
mutations and it enables the
screening of the various chemicals.
The Test combines a bacterial
mutation assay with a simulation
of the mammalian metabolism to
© 2022 by JPS Scientific Publications, India
9
produce a highly sensitive test for
the mutagenic chemicals in the
environment.
• AMINO ACIDS RESIDUES -
The Amino acids residue is the
unique part of the amino acids
which is left over when the
identical features of the amino
acids are removed. The amino
acids are called as the residues
because they are involved in the
protein building, structure and the
regulation are leaked after a
protein is formed. Some of the
amino acid residues in the peptide
molecules such as the Cysteine,
Methionine, Tryptophan, Histidine
and the Tyrosine could be a subject
to the oxidation in the process of
the peptide synthesis, and be
transformed to their oxidized
counterparts. The oxidation
process could be mediated by the
air, or the another oxidant species.
• AMIDE BOND - The Amide
bond is also referred to as an
peptide bond it is formed between
the α-nitrogen atom of one amino
acid and the carbonyl carbon of a
second amino acid. This bonds are
the most prevalent structures
which are found in the organic
molecules and the various
biomolecules such as the proteins,
DNA, RNA and the peptides. This
bonds are covalent in the nature.
Amide bond represent a very vast
and the important functional group
in the organic chemistry and also
finds a wide variety of the use,
Glossary of Genetics
especially in the living systems and
the medicines.
• AMINOACYL SYNTHETASES
- An aminoacyl-t-RNA synthetase
which is also called as the t-RNA-
ligase which is an enzyme that
attaches the appropriate amino
acid onto its corresponding t-RNA.
It done by catalyzing the tran-
sesterification of a specific cognate
amino acid or its precursor to one
of all its compatible cognate
tRNAs to form an aminoacyl-
tRNA. They are generally
considered as the “housekeepers”
because they are involved in the
mechanism of the protein synthesis
whose primary function is to
catalyze the aminoacylation of the
transfer RNAs. Aminoacyl-t-RNA
synthetases are universally
distributed enzymes that catalyze
the esterification of a t-RNA to its
cognate amino acid.
• AMINOACYL T-RNA
BINDING TO A SITE OF
RIBOSOME - T-RNA molecules
are the molecules which bind to
the ribosome in a solvent-
accessible channel at the subunit
interface. The Amino acid t-RNA
in a ternary complex binds to the
ribosome in the A/T state i.e the
anticodon of the Amino acid t-
RNA can interact with the
messenger RNA (mRNA) codon in
the ribosomal A-site, while the
CCA end (to which the amino acid
is bound) is retained wit the EF-Tu
and is unavailable for the peptide
bond formation. At one of the end
© 2022 by JPS Scientific Publications, India
10
the t-RNA has an anticodon o the
3’-UAC-5’ which binds to a codon
in an mRNA that has a sequence
of the 5’-AUG-3’ through the
complementary base pairing. The
other end of the tRNA carries the
amino acid methionine
(Met)specified by the mRNA
codon AUG.
• AMINOACYL T-RNA
SYNTHESASES - An aminoacyl-
tRNA synthetase which is also
called as the tRNA-ligase, is an
enzyme that attaches the
appropriate amino acid onto its
corresponding tRNA. It does so by
catalyzing the transesterification
process of a specific amino acid or
its precursor to one of all its
compatible cognate tRNAs to form
an aminoacyl-tRNA. In the
eukaryotic organisms cells, these
enzymes are found in the free form
or in the form of the multi-tRNA
synthetase complex (MSC). It
produces the tRNA molecules with
their CCA three prime ends
covalently. It catalyzes the AMP----
ADP----ATP exchange reactions,
indicating the labile covalent
enzyme-amino-acid intermediates.
• ACTIVATORS - The
transcriptional activator is a
protein (transcription factor) that
increases the transcription of a
gene or the set of genes. The
Activators are considered to have
the positive control over the gene
expression, as they function to
promote the gene transcription
and, in some cases, are required for
Glossary of Genetics
the transcription of the genes to
occur. Most of the activators are
the DNA-binding proteins that
bind to the enhancers or the
promoter-proximal elements. The
DNA site bound by the activator is
referred to as the “activator-
binding site”. The part of the
activator that makes the protein–
protein interactions with the
general transcription machinery is
referred to as the “activating
region” or the “activation
domain”. Most of the activators
function by binding the sequence-
specifically to a regulatory DNA
site located near a promoter and
making the protein–protein
interactions with the general
transcription machinery i.e the
RNA polymerase and the general
transcription factors, thereby
facilitating the binding of the
general transcription machinery to
the promoter. Other activators help
to promote the gene transcription
by triggering the RNA polymerase
to release from the promoter and
proceed along the DNA. At times,
the RNA polymerase can pause
shortly after leaving the promoter,
activators also function to allow
these “stalled” RNA polymerases
to continue the transcription.
• AMINOPEPTIDASES - The
Aminopeptidases are the group
enzymes which catalyzes the
cleavage of the amino acids from
the amino terminus of the proteins
or the peptides. They remove the
N-terminal amino acids of the
© 2022 by JPS Scientific Publications, India
11
target substrates by sequential
cleavage of one amino acid residue
at a time. They are widely
distributed throughout the animal
and the plant kingdoms and are
mainly found in the subcellular
organelles, in the cytosol, and as
the membrane components. For
eg. the Membrane-bound
aminopeptidases in the small
intestine break down the peptides
and the dipeptides into the amino
acids. They are the group of the
hydrolases enzymes and are also
known as the brush border
enzymes. The Aminopeptidase is
also an exopeptidase and which
will remove the amino acids from
the amino terminal end of a
peptide chain. It is a
complementary to the
carboxypeptidase, which will
cleave the peptide chain and
remove the amino acids from the
carboxyl terminal.
• ANAPHASE - The Anaphase is
the stage of the mitosis after the
process of the metaphase, when the
replicated chromosomes are split
and the newly-copied
chromosomes are moved to the
opposite poles of the cell. After the
separation of the sister chromatids,
the chromosome movement occurs
in the two steps 1) Anaphase A, in
which the chromosomes move
towards the spindle poles 2)
Anaphase B, in which the spindle
poles move away from the each
other. In the process of the
anaphase the sister chromatids
Glossary of Genetics
separate from the each other and
are pulled towards the opposite
ends of the cell. The protein which
is named as the “glue” which holds
the sister chromatids together is
broken down thus allowing them
to separate. Each is now its own
chromosome. The chromosomes of
the each pairs are then pulled
towards the opposite ends of the
cell.
• ARRESTIN BETA 1 - The
Arrestin, beta 1, which is also
known as the ARRB1, is a protein
which in the humans is encoded by
the ARRB1 gene. Arrestin beta 1 is
a cytosolic protein and acts as a
cofactor in the beta-adrenergic
receptor kinase (BARK) mediated
desensitization of the beta-
adrenergic receptors. Besides the
central nervous system, it is
expressed at the high levels in the
peripheral blood leukocytes, and
thus the BARK/beta-arrestin
system is believed to play a major
role in regulating the receptor-
mediated immune functions.
Alternatively spliced transcripts
encoding the different isoforms of
the arrestin beta 1 have been
described, however, their exact
functions are not yet known.
• ARRESTIN BETA 2 - Beta-
arrestin-2, which is also known as
the arrestin beta-2, is an
intracellular protein that in the
humans is encoded by the ARRB2
gene. The Arrestin beta 2, like
arrestin beta 1, was shown to
inhibit the beta-adrenergic receptor
© 2022 by JPS Scientific Publications, India
12
function in vitro. It is expressed at
the high levels in the central
nervous system and may play a
role in the regulation of the
synaptic receptors. Besides the
brain, a cDNA for the arrestin beta
2 was isolated from the thyroid
gland, and thus it may also be
involved in the hormone-specific
desensitization of the TSH
receptors. Multiple alternatively
spliced transcript variants have
been found for this gene, but the
full-length nature of some of the
variants has not been defined. The
protein may interact with the
agonist DOI in the 5-HT2A
receptor signaling. The Arrestin
beta 2 is crucial for the
development of the tolerance to the
morphine and the other opioids.
• ADREGENIC RECEPTOR - The
adrenergic receptors or the
adrenoceptors are a class of the
protein-coupled receptors that are
targets of the many catecholamines
like the norepinephrine
(noradrenaline) and the
epinephrine (adrenaline) produced
by the body, but also many
medications like the beta blockers,
beta-2 (β2) agonists and the alpha-2
(α2) agonists, which are used to
treat the high blood pressure and
the asthma. Many cells have these
receptors, and the binding of a
catecholamine to the receptor will
generally stimulate the sympathetic
nervous system (SNS). The SNS is
responsible for the fight-or-flight
response, which is triggered by the
Glossary of Genetics
experiences such as the exercise or
the fear-causing situations. This
response dilates pupils, increases
heart rate, mobilizes energy, and
diverts blood flow from non-
essential organs to the skeletal
muscle. These effects together tend
to increase the physical
performance momentarily
• AND GATE - An AND gate
integrates the two inputs into an
output. The genetic AND gate is
based on the general regulation
mechanism of the transcription in a
bacteria. The output is the
transcription of a gene of a bacteria
which is dually regulated by the
inputs of the two small molecules.
It is a basic digital logic gate which
implements the logical conjunction
from the mathematical logic –
AND gate behaves according to
the truth table. A HIGH output
results are produced only if all the
inputs to the AND gate are HIGH.
If not all inputs to the AND gate
are HIGH, LOW output results
will be produced.
• ANFINSEN EXPERIMENT -
The Christian Anfinsen an
American biochemist scientist who
studied about the enzyme
ribonuclease, which divides the
RNA into smaller components. In
the 1961 in one of his experiments,
Anfinsen proved that the sequence
of the amino acids in itself
determines the way the chain folds
itself and that no additional genetic
information is required in this
© 2022 by JPS Scientific Publications, India
13
process. It shows that the native
structure of the ribonuclease A will
form following the denaturation
provided that the oxidation is
prevented. Therefore, it’s protein is
intrinsically capable of finding the
lowest-energy conformation. They
cleaved the disulfide bonds of
RNase with the aim of finding out
that if the bonds were related to its
catalytic functions or not. A
chemical known as the beta
mercaptoethanol was used in the
tiny amount to catalyze the
breaking of the incorrect disulfide
bonds.
• ANNOTATIONS - The DNA
annotation or the genome
annotation is the process of
identifying the locations of the
genes and all the coding regions in
a genome and determining what
those genes do in that regions. An
annotation is a note added by way
of explanation or commentary.
The Genes of a eukaryotic genome
can be annotated using various
annotation tools such as the the
FINDER. A modern annotation
pipeline can be support a user-
friendly web interface and software
containerization such as the
MOSGA. This annotation are
stored in the genomic databases
such as the Mouse Genome
Informatics, FlyBase, and the
WormBase. It consists of the two
main steps 1) Identifying the
elements on the genome through a
process called as the gene
prediction and 2) Attaching all the
Glossary of Genetics
biological information to these
elements.
• ANTENNAPEDIA COMPLEX -
The Antennapedia is a type of the
Hox gene which was first
discovered by the Walter Jacob
Gehring in the Drosophila
melanogaster which controls the
formation of the legs during the
development.The Loss-of-
functions of the mutations in the
regulatory region of this gene result
in the development of the second
leg pair into the ectopic antennae.
By gaining the contrast of the
function alleles convert the
antennae into the ectopic legs. The
Hox genes encode the
homeodomain transcription
factors. The ANT-C controls the
identity of segments that contribute
to the head and the anterior thorax.
The Antennapedia were also
discovered, which cause the
reverse transformation (leg-to-
antenna).A family of the genes
called the Hox genes are also
involved in the controlling of the
formation of the somites.
• ANTIBODIES - The Antibodies
are the proteins and the proteins
are encoded by the genes. The
Antibody diversity therefore poses
a special genetic problem. The
diversity of the antibodies is
determined by a mechanism called
as the gene restructuring. The
genes in the heavy chain variable
region of an antibody are divided
into the 3 regions named as 1) VH
gene regions, 2) DH gene regions,
© 2022 by JPS Scientific Publications, India
14
and 3) JH gene regions. There are
about 1000 different VH, 10
different DH, and the 4 different
JH heavy-chain genes. There are
about 200 VH and the 6 JH light-
chain genes. Each gene family
consists of the multiple DNA
coding sequences called as exons
which are separated by noncoding
sequences called as introns. The
immune system creates billions of
the different types of the antibodies
with a limited number o the genes
by process of the rearranging DNA
segments during the B cell
development, prior to the antigen
exposure. There are only 5 types
of the heavy chain constant regions
in the antibodies (immunoglobulin)
and according to the these types,
they are classified into the IgG,
IgM, IgA, IgD, and IgE. They are
distributed and function differently
in the body.
• ANTICANCER AGENTS - The
Antineoplastic agents that are also
known as the anticancer agents are
well known to cause the significant
direct hepatotoxicity when given in
the moderate to the high doses
particularly when they are used in
the myeloablation before the
hematopoietic cell transplantation
process includes various drugs like
the busulfan, melphalan,
cyclophosphamide, dacarbazine,
cytarabine, fluorouracil,
carboplatin. The main groups of
the anticancer agents includes the
Alkylating and the alkylating-like
agents, Antimetabolites and the
Glossary of Genetics
Antitumour antibiotics. There are
more than 100 anticancer drugs
have been discovered and are
approved by the FDA.The
Anticancer Drugs are also used to
the Eliminate cancer cells, Shrink
the tumor, Prevent the the cancer
from spreading and Relieve
symptoms from the cancer. The
anticancer drugs kill the cancer
cells by stopping them from
growing and multiplying. If the
cells can’t grow and multiply, they
usually die. Some chemotherapy
drugs also works during a specific
stage of the cell cycle.
• ANTICODON – CODON
PAIRING - An anticodon is a
three-base sequence which is
paired with a specific amino acid.
It Describes the pairing between
the mRNA codons and the
complementary tRNA anticodons
that allows the tRNA molecules to
recognize the codons and add the
correct amino acids to a growing
polypeptide chain. The anticodon
sequence is complementary to the
mRNA, using the base pairs in the
anti-parallel direction. These
interaction mimics the codon-
anticodon pairing in translation but
can occurs in the absence of the
ribosome. It binds at an area away
from the triplet to an amino acid
that is specific for that particular
anticodon.
• ANTIGEN – ANTIBODY
COMPLEX - An immune
complex, sometimes also called as
antigen-antibody complex or
© 2022 by JPS Scientific Publications, India
15
antigen-bound antibody, is a
molecule formed from the binding
of multiple antigens to antibodies.
The bound between antigen and
antibody complex acts as an
unitary object, effectively an
antigen of its own with a specific
epitope. The epitopes of antigen
reacts with the paratopes of
antibody forming the antigen-
antibody complex, Which acts like
lock and key mechanism and it’s
study is called as “serology”. After
an antigenic challenge, the
antibodies are secreted by the
differentiated B cells also called as
plasma cells. The Antibodies have
2 predominant roles that involves
the specific binding of antigens to
launch an immune response, along
with the activation of other
components of the immune system
to fight against the pathogens.
• ANTIPARALLEL
ORIENTATION OF DNA - The
DNA is composed of the two
strands of nucleotides which are
held together by the hydrogen
bonding. The strands of the DNA
runs from the 5' to 3' and run in the
antiparallel, or opposite directions
from one another. DNA strands
are antiparallel in the nature
because of the presence of the
hydrogen bond. The Hydrogen
bond binds the complementary
bases i.e purine and the
pyrimidine. They have opposite
chemical polarity or stated another
way their sugar-phosphate
Glossary of Genetics
backbones run in the opposite
directions.
• ANTISENSE RNA - The
Antisense RNA which is also
referred to as the antisense
transcript, natural antisense
transcript or the antisense
oligonucleotide, is a single
stranded RNA that is
complementary to a protein coding
messenger RNA with which it
hybridizes, and thereby blocks its
translation process into the protein.
It is a Small pieces of the RNA that
can bind to a specific molecules of
the RNA and block the cell’s
ability to use the RNA to make a
protein or work in the other ways.
Antisense RNA can be used to
block the production of the
proteins which is needed for the
growth of the cell. The Antisense
RNA is synthesized by the in-vitro
transcription process using a highly
specific DNA-dependent RNA
polymerases enzyme which is
derived from the bacteriophages
such as the SP6, T7, and T3
polymerases. The Trans-acting
small non-coding RNAs are
usually encoded in the intergenic
regions on the chromosome and
controls the translation or
degradation of their target
mRNAs. Generally, the each trans-
acting non-coding RNA has
multiple target mRNAs and binds
near the ribosomal binding site of
the target mRNAs. It is called as
antisense because its sequence of
© 2022 by JPS Scientific Publications, India
16
nucleotides is the complement of
message sense.
• APETALA 2 - The Apetala 2
(AP2) is a gene and a member of a
large family of the transcription
factors, the AP2/EREBP family.
In the Arabidopsis thaliana AP2
plays a role in the ABC model of
the flower development. It was
originally thought that this family
of the proteins was plant-specific;
however the recent studies have
shown that the apicomplexans,
including the causative agent of the
malaria, Plasmodium falciparum
encode a related set of the
transcription factors, called as the
ApiAP2 family. In the A. thaliana
transcription factor RAV1 the N-
terminal AP2 domain binds the 5'-
CAACA-3' sequence, while the C-
terminal highly conserved B3
domain binds the 5'-CACCTG-3'
sequence. The DNA is constantly
subject to the mutations, which can
cause a complete shift in the
function of the protein due to the
malformed protein, causing the
diseases in some of the cases.
• ATAC – SEQ - The ATAC-seq
(Assay for the Transposase-
Accessible Chromatin using
sequencing) is a technique used in
the molecular biology to assess the
genome-wide chromatin
accessibility. The ATAC-seq is a
faster and more sensitive analysis
of the epigenome than the DNase-
seq or the MNase-seq. The ATAC-
Seq analysis is used to investigate a
number of the chromatin-
Glossary of Genetics
accessibility signatures. The most
common use is the nucleosome
mapping experiments, but it can be
applied to the mapping
transcription factor binding sites,
adapted to map the DNA
methylation sites, or combined
with the sequencing techniques.
• ABORTIVE SYNTHESIS - The
Abortive initiation, also known as
the abortive transcription, is an
early process of the genetic
transcription in which the RNA
polymerase binds to a DNA
promoter and enters into the cycles
of synthesis of the short mRNA
transcripts which are released
before the transcription complex
leaves the promoter. This process
occurs in both the eukaryotes and
the prokaryotes. The Abortive
initiation is typically studied in the
T3 and the T7 RNA polymerases
in the bacteriophages and in the E.
coli. There are no widely accepted
functions for the resulting
truncated RNA transcripts.
However, a study in the year 1981
found evidence that there was a
relationship between the amount of
the abortive transcripts produced
and the time until the long RNA
strands are successfully produced.
When the RNA polymerase
undergoes the abortive
transcription in the presence of the
ATP, UTP, and GTP, a complex is
formed that has a much lower
capacity for the abortive recycling
and a much higher rate of the
© 2022 by JPS Scientific Publications, India
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synthesis of the full-length RNA
transcript
• AMPHIPHYSIN - The
Amphiphysin is a protein that in
the humans is encoded by the
AMPH gene. This gene encodes a
protein associated with the
cytoplasmic surface of the synaptic
vesicles. A subset of the patients
with the stiff person syndrome who
were also affected by the breast
cancer are positive for the
autoantibodies against this protein.
The Alternate splicing of this gene
results in the two transcript
variants encoding the different
isoforms. The Additional splice
variants have been described, but
their full length sequences have not
been determined. The
Amphiphysin is a brain-enriched
protein with an N-terminal lipid
interaction, dimerisation and
membrane bending BAR domain,
a middle clathrin and the adaptor
binding domain and a C-terminal
SH3 domain. In the brain, its
primary function is thought to be
the recruitment of the dynamin to
the sites of the clathrin-mediated
endocytosis.
• ANTITERMINATION -
Antitermination is the process in
the prokaryotic cell’s to fix the
premature termination of RNA
synthesis during the transcription
of RNA. It occurs when the
enzyme RNA polymerase ignores
the signal of termination and
continues the elongating its
transcript until a second signal is
Glossary of Genetics
reached. It provides a mechanism
where one or more genes at the
end of an operon can be switched
either on or off, depending on the
polymerase either recognizing or
not recognizing the termination
signal. Here When the levels of
Trp and charged tRNATrp are
high, the ribosome completes the
synthesis of the leader peptide, the
terminator forms and RNAP is
released. Antitermination process
is used by some phages to regulate
the progression from one stage of
gene expression to the next
generation.
• ANTIVIRAL AGENTS - •
Antiviral agents are the drugs
which areapproved by the Food
and Drug Administration (FDA)
for the treatment or control of viral
infections. They target the stages in
the viral life cycle. Antiviral drugs
are a class of medication which is
used for treating viral infections.
Most of the antivirals target
specific viruses, while a broad-
spectrum antiviral is effective
against a wide range of viruses.
Unlike most of the antibiotics,
antiviral drugs do not destroy their
target pathogen instead they inhibit
its further development process.
Antiviral resistance can be defined
by a decreased susceptibility to a
drug caused by the changes in viral
genotypes. In cases of antiviral
resistance, the drugs are either
diminished or no effectiveness
against their target virus. The issue
inevitably remains a major obstacle
© 2022 by JPS Scientific Publications, India
18
to the antiviral therapy as it has
developed to almost all specific
and effective antimicrobials,
including the antiviral agents. The
Viruses use the host’s cells to
replicate and this makes it difficult
to find the targets for the drug that
would interfere with the virus
without also harming the host
organism’s cells. Moreover, the
major difficulty in developing the
vaccines and anti-viral drugs is due
to the viral variation. Natural
viricides are produced by some of
the plants such as eucalyptus and
Australian tea trees.
APOBEC-1 - Apolipoprotein B
mRNA editing enzyme, catalytic
polypeptide 1 which is also known
as C-U editing enzyme. The
APOBEC-1 is a protein that in
humans is encoded by the
APOBEC1 gene. This gene also
encodes the member of the
APOBEC protein family and the
cytidine deaminase enzyme family.
The encoded proteins forms a
multiple-protein RNA editing
holoenzyme with APOBEC1
complementation factor. This
holoenzyme is also involved in the
editing process of cytosine-to-
uracil. It has been linked with
cholesterol control, cancer
development and inhibition of viral
replication. Its function relies on
introducing a stop codon into
apolipoprotein B (ApoB) mRNA,
which alters the lipid metabolism
in the gastrointestinal tract. The
editing mechanism is a highly
Glossary of Genetics
specific process. The A1’s
deamination of the cytosine base
yields the uracil, which creates a
stop codon in the mRNA. It has
been linked with both positive and
negative health effects. However
the A1 is currently found only at
extremely low levels in the human
organs such as liver and intestine,
while it is highly expressed in the
rodents. In the humans, the A1 is
found exclusively in
gastrointestinal epithelial cells.
• APOBEC-3G - APOBEC3G
(apolipoprotein B mRNA editing
enzyme, catalytic subunit 3G) is a
human enzyme which is encoded
by the APOBEC3G gene that
belongs to the APOBEC
superfamily of proteins. This
family of proteins has been
suggested to play an important role
in the innate anti-viral immunity
Process. APOBEC3G also belongs
to the family of cytidine
deaminases that catalyze the
deamination of cytidine to uridine
in the single stranded DNA
substrate. The C-terminal domain
of the A3G renders the catalytic
activity, several NMR and crystal
structures which explains the
substrate specificity and catalytic
activity. APOBEC3G exerts the
innate antiretroviral immune
activity against the retroviruses
most notably HIV by interfering
with proper replication. However
the lentiviruses such as HIV have
evolved the Viral infectivity factor
(Vif) protein in order to counteract
© 2022 by JPS Scientific Publications, India
19
this effect. Vif interacts with the
APOBEC3G and triggers the
ubiquitination and degradation of
APOBEC3G via the proteasomal
pathway. On the other hand the
foamy viruses produce an
accessory protein Bet (P89873)
which impairs the cytoplasmic
solubility of APOBEC3G proteins.
The two ways of inhibition are
distinct from the each other, but
they can replace each other in vivo
process.
• APOTOSIS - Apoptosis is a form
of programmed cell death which
occurs in the multicellular
organisms. The Biochemical events
lead to the characteristic cell
changes and death. These changes
also includes blebbing, cell
shrinkage, nuclear fragmentation,
chromatin condensation, DNA
fragmentation, and mRNA decay.
It is a type of cell death in which a
series of molecular steps occurs in
a cell which leads to its death. This
is one of the method the body uses
to get rid of unneeded or abnormal
cells. The process of apoptosis may
also be blocked in cancer cells.
This is also called as programmed
cell death. It occurs normally
during the development and aging
and as a homeostatic mechanism
to maintain cell populations in
tissues. Apoptosis can also occurs
as a defense mechanism such as in
the immune reactions or when cells
are damaged by disease or noxious
agents
Glossary of Genetics 20

• APTAMER - Aptamers are the commonly known as “bad

special class of nucleic acids
molecules that are beginning to be
investigated for the clinical use.
These small RNA/DNA molecules
can form secondary and tertiary
structures capable of specifically
binding proteins or other cellular
targets they are essentially a
chemical equivalent of antibodies.
Aptamers are the single-stranded
oligonucleotides which folds into
the defined architectures and bind
to the targets such as proteins. In
binding proteins they often inhibit
the protein–protein interactions
and thereby may elicit therapeutic
effects such as antagonism.They
are isolated via SELEX
(Systematic Evolution of Ligands
by Exponential Enrichment),
which is an evolutionary process
that involves the use of iterative
rounds of selection and
amplification before sequencing
and aptamer characterization. The
aptamers can be used for the
molecular recognition of their
respective targets. Aptamers have
been successfully used for the
pathogen recognition, cancer
recognition, monitoring the
environmental contamination, and
as stem cell markers.
• APOLIOPOPROTEIN-B-GENE
- Apolipoprotein B (ApoB) is a
protein that in humans which is
encoded by the APOB gene. It is
the primary apolipoprotein of
chylomicrons, VLDL, Lp, IDL,
and LDL particles (LDL—
cholesterol”) which is mainly
responsible for carrying the fat
molecules including cholesterol
around the body to all cells within
all tissues. While all the functional
roles of ApoB within the particles
remain somewhat unclear, it is the
primary organizing protein
component of the particles and is
absolutely required for the
formation of these particles. What
is also clear is that the ApoB on the
LDL particle acts as a ligand for
LDL receptors in various cells
throughout the body. The High
levels of ApoB are related to heart
disease. Hypobetalipoproteinemia
is a genetic disorder which can be
caused by a mutation in the ApoB
gene, APOB.
Abetalipoproteinaemia is a
disorder which is usually caused by
a mutation in the MTP gene.
Mutations in the gene APOB100
can also cause familial
hypercholesterolemia, a hereditary
form of metabolic disorder
hypercholesterolemia.
• araBAD OPERON - The L-
arabinose operon, which is also
called as araBAD operon, is a gene
sequence encoding enzymes which
is needed for the catabolism of
arabinose to xylulose 5-phosphate,
an intermediate of the pentose
phosphate pathway. It has the
both positive and negative
regulation. It encodes for three
metabolic enzymes that are
required for the metabolism of L-

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
arabinose. The three metabolic
enzymes are AraB, AraA, and
AraD—that are required for
Escherichia coli to utilize the sugar
arabinose. These genes are not
normally expressed in E. Coli. The
L-arabinose operon has been
commonly used in the protein
expression system, as the araBAD
promoter can also be used for the
producing targeted expression
under tight regulation. By fusing
the araBAD promoter to a gene of
interest, the expression of the target
gene can also be solely regulated
by arabinose. For eg, the pGLO
plasmid contains a green
fluorescent protein gene under the
control of the PBAD promoter,
allowing GFP production to be
induced by arabinose.
• ARABIDOPSIS THALIANA
CHROMOSOME MAKEUP -
The Arabidopsis thaliana genome
was sequenced in 2000 by the
Arabidopsis Genome Initiative
(AGI) program. The genome has
total five chromosomes and a total
size of approximately 135-
megabases. It consists of
approximately 570 tandem copies
of a heterogeneous 9900-base-pair
repeat units. It possesses a
relatively small, genetically
tractable genome that can be easily
manipulated through your genetic
engineering more easily and
rapidly than any other plant
genome.
© 2022 by JPS Scientific Publications, India
21
• ARABINOSE - The Arabinose is
an aldopentose – a
monosaccharide and is a five-
carbon sugar which is found
widely in the nature and can be
serve as a sole carbon source in the
many bacteria. The protein
products from the three genes
(araB, araA, and araD) are needed
for the arabinose degradation in
members of the Enterobacteriaceae
family. In the presence of the
arabinose, the AraC protein
promotes the binding of the RNA
polymerase to the promoter, which
causes the transcription of the GFP
gene into the messenger RNA
(mRNA), followed by the
translation of this mRNA into the
GFP. This process is called as the
gene expression. For the
biosynthetic reasons, most of the
saccharides are almost always
more than the abundant in nature
as the “D”-form or the structurally
analogous to the D-glyceraldehyde.
Arabinose acts as an allosteric
regulator for the AraC, changing
which the DNA sites can binds to
and how it forms a dimer. The
arabinose is the sugar that gets
catabolized by the proteins of the
AraBAD operon. The highest
amount concentrations of the L-
Arabinose are found in the instant
coffee, wine and the sake.
• ARC REPRESSOR - The Arc
repressor, is involved in the switch
system between the lysis and the
lysogeny process of the Salmonella
bacteriophage P22. It does not
Glossary of Genetics
belong to any of the known classes
of the DNA-binding proteins. The
Mutagenesis studies show that the
DNA-binding regionsis located in
the 15 N-terminal amino-acid
residues. The Arc dimer from an
extensive set of the interproton-
distance data obtained from 1H
NMR spectroscopy is 3 note that there are also so many
dimensional structure. A intra- and
inter-monomer nuclear Overhauser
effects (NOEs) cannot be
distinguished for a symmetric
dimer.
• ARCHAEOGLOBUS
FLUGIDUS - The Archaeoglobus
fulgidus is a type of the sulphur-
metabolizing organism. It is also
Known as the Archaeoglobales
anaerobes, most of which are
hyperthermophiles. These
hyperthermophilic marine sulphate
reducers are the only distantly
related to other bacterial sulphate
reducers and grow at very high
temperatures. Most of these
archaeoglobales are found in the
hydrothermal environments such
as the hot springs, oil wells, and
the hydrothermal vents.
Archaeoglobus species also forms
the iron sulphide which is known
to be a major cause of corrosion of
the steel and iron in both the oil
and the gas processing systems.
Their genome is a single and
circular chromosome of 2,178,400
base pairs with an 48.5% G+C
content. There are two regions of
high G+C content which contains
the genes for ribosomal RNAs,
© 2022 by JPS Scientific Publications, India
22
proteins that are involved in the
biosynthesis process of the hemAB,
along with the several other
transporters. There are also other
three regions of the low G+C
content. The organism has a
predicted total of 2,436 coding
sequences. It is also important to
gene duplications in the genome
and the duplicated proteins are not
identical.
• ARCHITECTURAL PROTEINS
- The Architectural proteins are the
proteins which mediate the
interactions between the distant
sequences in the genome. The Two
well-characterized functions of the
architectural protein interactions
includes the tethering of the
enhancers to the promoters and
bringing together the Polycomb-
containing sites to facilitate the
silencing process. The nature of
which the sequences interact with
the genome-wide appears to be
determined by the orientation of
the architectural protein binding
sites as well as the number and
identity of the architectural
proteins present there. Ultimately
a long range of the chromatin
interactions result in the formation
of the loops within the chromatin
fibers. The number of the
architectural proteins which are
characterized in the mammals is
not as extensive as in the
Drosophila. Multiple lines of
evidence indicate that CTCF and
cohesin are the mediators of the
Glossary of Genetics
chromatin interactions and thus
the architectural proteins.
Functional studies of the
architectural proteins evaluating
the function of CTCF and cohesin
in the chromatin looping within
the individual genomic loci were
the first studies to indicate these
proteins are regulators of the
chromatin interactions. More
recently, the CTCF and cohesin
depletion studies have shown that
loss of these architectural proteins
reduces the genome-wide
chromatin interaction.
• ARGONAUTE FAMILY - The
Argonaute protein family, which
was first discovered for its
evolutionarily conserved stem cell
function plays a central role in the
RNA silencing processes as
essential components of the RNA-
induced silencing complex. The
RISC is also responsible for the
gene silencing phenomenon known
as the RNA interference. The
highly conserved Argonaute
protein family members play a
central role in the regulation of the
gene expression networks and
orchestrating the establishment and
the maintenance of the cell identity
throughout the entire life cycle, as
well as in the several human
disorders, including the cancers.
The Argonaute proteins bind the
different classes of the small non-
coding RNAs, including the
themicroRNAs, small interfering
RNAs and the Piwi-interacting
RNA. Small RNAs guide the
© 2022 by JPS Scientific Publications, India
23
Argonaute proteins to their specific
targets through the sequence
complementarity, which then leads
to the mRNA cleavage, translation
inhibition, and/or the initiation of
the mRNA decay. In the humans,
there are eight AGO family
members, some of the which are
investigated intensively.
• AT-AC SPLICEOSOME - The
spliceosome precisely removes the
introns from the pre-mRNA to
generate the mature messages
(mRNA), a process which is also
referred to as the pre-mRNA
splicing. The spliceosome is also
important essential for the cell
function and defective pre-mRNA
splicing causes disease. It is a large
RNA-protein complex that
catalyses the removal of the introns
from the nuclear pre-mRNA. A
wide range of the biochemical and
the genetical studies shows that the
spliceosomes comprises of the
three major RNA-protein subunits
which are known as the U1, U2
and U4/U6. The snRNAs in the
spliceosome binds to the donor
sites and branch signals and bring
the ends of the exons together.
During the process of the splicing
the introns are removed from the
pre-mRNA by the spliceosome and
the exons are spliced back together
by the enzyme ligase. The
Constitutive splicing is the process
of the intron removal and the exon
ligation of the majority of the
exons in the order in which they
appear in a gene. Alternative
Glossary of Genetics 24

splicing is a deviation from this agarose or the polyacrylamide—

preferred sequence where the chemically modified to introduce
certain exons are skipped resulting the reactive functional groups with
in the various forms of the mature which the ligand can react, forming
mRNA. the stable covalent bonds.
• AFFINITY • AT HOOKS - The AT-hook are
CHROMATOGRAPHY - The the DNA-binding motif which are
Affinity chromatography is a present in many of the proteins,
method of separating the including the high mobility group
biomolecule from a mixture, based proteins, DNA-binding proteins
on a highly specific from the plants and the hBRG1
macromolecular binding protein, a central ATPase of the
interaction between the human switching/sucrose non-
biomolecule and the another fermenting remodeling complex.
substance. The specific type of the This motif consists of a conserved,
binding interaction depends on the palindromic sequences which is
biomolecule of the interest; antigen also known as the core sequence of
and the antibody, enzyme and the the proline-arginine-glycine-
substrate, receptor and the ligand, arginine-proline, although some of
or the protein and the nucleic acid. the AT-hooks contain only a single
The binding interactions are very proline in the core sequence. AT-
frequently exploited for the hooks also includes a variable
isolation of the various number of the positively charged
biomolecules. The affinity lysine and arginine residues on the
chromatography is very useful for either side of the core sequence.
its high selectivity and the The AT-hook binds to the minor
resolution of the separation, groove of the adenine-thymine
compared to the other (AT) rich DNA, hence the AT in
chromatographic methods. The the name. The rest of the name is
Affinity chromatography has an derived from a predicted
advantage of specific binding asparagine/aspartate “hook” in the
interactions between the analyte of earliest AT-hooks. The structural
the interest which is normally studies using the NMR determined
dissolved in the mobile phase, and that a DNA-bound AT-hook
a binding partner or the ligand adopted a crescent or the hook
which is immobilized on the shape around the minor groove of
stationary phase. In a typical a target DNA strand. HMGA
affinity chromatography proteins contains the three AT-
experiment, the ligand is attached hooks, although some of the
to a solid, insoluble matrix— proteins contain as many as 30.
usually a polymer such as the The optimal binding sequences for

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
the AT-hook proteins are repeats of
the form although the optimal
binding sequences for the core
sequence of the AT-hook are the
AAAT and the AATT.
• ATP - The Adenosine 5′-
triphosphate also abbreviated as
the ATP and usually expressed
without the 5′-, is an important
“energy molecule” found in the all
life forms. Specifically, it is a
coenzyme that works with the
enzymes such as the ATP
triphosphatase to transfer the
energy to cells by releasing its
phosphate groups. ATP captures
the chemical energy obtained from
the breakdown of the food
molecules and releases it to fuel the
other cellular processes. The
Adenosine triphosphate is the
source of the energy which is use
and storage at the cellular level.
The structure of the ATP is a
nucleoside triphosphate, consisting
of a nitrogenous base (adenine)
and a ribose sugar, and the three
serially bonded phosphate groups.
The main energy source for the
cellular metabolism is the glucose,
which is the catabolized in the
three subsequent processes—
glycolysis, tricarboxylic acid cycle
(TCA or Krebs cycle), and finally
the oxidative phosphorylation—to
produce the ATP. The ATP plays
an critical role in the transport of
the macromolecules such as the
proteins and lipids into and out of
the cell. The hydrolysis of the ATP
provides the required energy for
© 2022 by JPS Scientific Publications, India
25
the active transport mechanisms to
carry such molecules across a
concentration gradient.
• ATPase - The ATPases are the
class of enzymes which catalyzes
the decomposition of The ATP
into The ADP and a free
phosphate ion or the inverse
reaction. This dephosphorylation
reaction also releases the energy,
which the enzyme harnesses to
drive the other chemical reactions
that would not otherwise occur.
This process is widely used in all
the known forms of The life.
Transmembrane ATPases import
the metabolites necessary for the
cell metabolism and export the
toxins, wastes, and other solutes
that can hinder cellular processes.
An important example is the
sodium-potassium exchanger that
maintains the cell membrane
potential. ATPase is genetically
conserved in the animals therefore,
the cardenolides which are toxic
steroids produced by the plants that
act on the ATPases, make general
and effective animal toxins that act
dose dependently. Proton
ATPases are used by the cells to
transport the protons against the
electrochemical gradient by
harnessing the energy of The ATP
hydrolysis. Because the ATP is
hydrolyzed, the type of The
transport is referred to as active
transport. One of the use of a
proton ATPase is to acidify a
cellular compartment, such as a
lysosome.
Glossary of Genetics
• ATTENUATION - The
Attenuation is a proposed
mechanism of control in some of
the bacterial operons which results
in the premature termination of the
transcription and is based on the
fact that in the bacteria, the
transcription and the translation
both proceed simultaneously. The
stop signal which is referred to as
the attenuator, which prevents the
proper function of the ribosomal
complex, stopping the process.
During the attenuation process the
ribosome becomes stalled in the
attenuator region in the mRNA
leader. Depending on the
metabolic conditions, the
attenuator either stops the
transcription at that point or allows
to read-through to the structural
gene part of the mRNA and
synthesis of the appropriate
protein. The Attenuation is a
regulatory feature which is found
throughout the Archaea and the
Bacteria causing the premature
termination of the transcription.
Attenuators are the 5’-cis acting
regulatory regions which folds into
the one of the two alternative RNA
structures which determine the
success of the the transcription.
The folding is modulated by a
sensing mechanism producing
either a Rho-independent
terminator which resulting in
interrupted transcription and a
non-functional RNA product, or
an anti-terminator structure, which
© 2022 by JPS Scientific Publications, India
26
results in a functional RNA
transcript.
• ATP-BINDING MOTIF - The
ATP-binding motif is a 250-residue
sequence within an ATP-binding
protein’s primary structure. The
binding motif is associated with a
protein’s structure and/or the
function. The ATP is a molecule of
energy, and can be a coenzyme,
and can also involved in a number
of the biological reactions. The
ATP is proficient at interacting
with the other molecules through a
binding site. The ATP binding site
is the environment in which the
ATP catalytically actives the
enzyme and, as a result, is
hydrolyzed to the ADP. The
binding of the ATP causes a
conformational change to the
enzyme to which it is interacting
with. The ATP binding sites,
which may be the representative of
an ATP binding motif, are present
in many proteins which require an
input of the energy. Such sites acts
as the membrane transporters,
microtubule subunits, flagellum
proteins, and the various
hydrolytic and the proteolytic
enzymes. The ATP molecule binds
to the connecting point of each
subunit of the dimer, indicating
that the ATP is in close proximity
to both the subunits during the
catalysis. The two binding motifs
that ATP directly interacts with is
the residues from the Walker A
motif which is located on one of
the subunits, and the residues from
Glossary of Genetics
the C binding motif which is
located on the other subunit.
• AUG CODON - The start codon
is the first codon of a messenger
RNA which transcript the script
translated by a ribosome. The start
codon always codes for the
methionine in the eukaryotes and
in the Archaea and a N-
formylmethionine in the bacteria,
mitochondria and the plastids. The
most common start codon is the
AUG (ATG in the corresponding
DNA sequence). The codon AUG
codes for the methionine and
serves as an initiation site. The first
AUG in an mRNA’s coding region
is where the translation process
into the protein begins. The other
start codons listed by the GenBank
are very rare in the eukaryotes and
they generally codes for the
Met/fMet. The historical basis for
the designating the stop codons as
the amber, ochre and opal is
described in an autobiography by
the South African genetics
biologists Sydney Brenner and in a
historical article by the former
American Representative Bob
Edgar. The start codon also sets
the reading frame instead of the
continuing to move down the
mRNA transcript one base at a
time, the ribosome now reads the
mRNA codons consecutively,
three bases at a time. The
sequence of the triplet codon
determines which amino acid is
added next to the growing protein.
When the ribosome reaches a stop
© 2022 by JPS Scientific Publications, India
27
codon, it falls off the mRNA, and
the protein is complete. There are
three variations of the stop codon
i.e UGA, UAA, and UAG.
• AURORA B-KINASE - The
Aurora kinase B is a protein that
functions in the attachment of the
mitotic spindle to the centromere
region. The Aurora kinase B was
identified in the humans by a
polymerase chain reaction screen
for the kinases that are
overexpressed in the cancers. In
the same year, rat Aurora kinase B
was also identified in a screen
designed to find the kinases that
altered the S. Cerevisiae
proliferation when they were
overexpressed. Chromosomal
segregation during the mitosis
process as well as meiosis is
regulated by the enzymes kinases
and the phosphatases. The Aurora
kinases associate with the
microtubules during
thechromosome movement and
segregation. Aurora kinase B
localizes to microtubules near the
kinetochores, specifically to the
specialized microtubules called
which is called as the K-fibers, and
vAurora kinase A (MIM 603072)
localizes to the centrosomes. In
the cancerous cells, the over-
expression of these enzymes causes
the unequal distribution ofv genetic
information, creating aneuploid
cells, a hallmark of the cancer.
• AUTOINDUCERS - The term
“autoinduction” was first coined in
the year 1970, when it was first
Glossary of Genetics
observed that the bioluminescent
marine bacterium Vibrio fischeri
produced by a luminescent enzyme
known as the luciferase only when
the cultures had reached a
threshold population density.
Autoinducers are the signaling
molecules that are produced in the
response to the changes in a cell-
population density. As the density
of the quorum sensing bacterial
cells increases so does the
concentration of the autoinducer
also increases. Detection of the
signal molecules by the bacteria
acts as the stimulation which leads
to the altered gene expression once
the minimal threshold is reached.
Autoinducers comes in a number
of the different forms depending on
the species, but the effect that they
have is very similar in many of the
cases. Autoinducers also allows the
bacteria to communicate both
within and between the different
species. This communication alters
the gene expression and allows the
bacteria to mount coordinated
responses to their environments, in
a manner that is comparable to the
behavior and signaling in the
higher organisms.
• AUTORADIOGRAPH - An
autoradiograph is the image on an
x-ray film or the nuclear emulsion
produced by the pattern of the
decay emissions e.g., beta particles
or gamma rays from a distribution
of a radioactive substance.
Alternatively, the autoradiograph
is also available as a digital image
© 2022 by JPS Scientific Publications, India
28
which is also called as the digital
autoradiography, due to the recent
development of the scintillation gas
detectors or the rare earth
phosphorimaging systems. The
film or the emulsion is also
apposed to the labeled tissue
section to obtain the
autoradiograph which is also called
an autoradiogram. The auto- prefix
in the machine indicates that the
radioactive substance is within the
sample, as distinguished from the
case of the like historadiography or
the microradiography, in which the
sample is marked using an external
source. Some of the
autoradiographs can be examined
by microscopically for localization
of silver grains such as on the
interiors or exteriors of cells or
organelles in which the process is
termed as the micro-
autoradiography. For example,
the micro-autoradiography was
also used to examine whether the
atrazine was being metabolized by
the hornwort plant or by the
epiphytic microorganisms in the
biofilm layer surrounding the
plant.
• AVERY OSWALD THEORY -
In the year 1930 a very simple
experiment a molecular biologists
from Canada Oswald Avery’s
group showed that the DNA was
the “transforming principle. When
the DNA isolated from one strain
of the bacteria, DNA was able to
transform the another strain and
confer the characteristics onto that
Glossary of Genetics
second strain. Oswald Theodore
Avery studied the strains of the
pneumococcus of the genus
Streptococcus in the US in the first
half of the twentieth century. This
bacterium causes the disease called
as the pneumonia, it is also a
common cause of the death at the
turn of the twentieth century. In
the 1944 in one of his research
paper, Avery along with the his
colleagues Colin Munro MacLeod
and Maclyn McCarty
demonstrated that the
deoxyribonucleic acid, or DNA,
instead of the protein, formed the
material of heritable
transformation in the bacteria.
Avery helped the untangle some of
the relationships between genes
and the developmental processes
DNA was carrying the hereditary
information. The Oswald Avery
and his colleagues from the
Rockefeller Institute in the New
York published the first evidence
that the genes are made of the
DNA. Their discovery was
received with a mixture of the
enthusiasm, suspicion and the
perplexity.
• AZIDOTHYMIDINE - The
Zidovudine (ZDV), which is also
known as The azidothymidine
(AZT), is an antiretroviral
medication used to prevent and
treat the HIV/AIDS. It is generally
recommended for the use in
combination with The other
antiretrovirals medicines. It may be
used to prevent the mother-to-child
© 2022 by JPS Scientific Publications, India
29
spread of The HIV/AIDs during
the birth or after a needlestick
injury or the other potential
exposure. It is sold both by itself
and the together as the
lamivudine/zidovudine and
abacavir/lamivudine/zidovudine.
It can be used by mouth or by the
slow injection into a vein.
Zidovudine also has an
antibacterial properties, though it is
not routinely used in the clinical
settings. It acts on the bacteria with
a mechanism of action which is
still not fully explained. Promising
the results from in vitro and in vivo
studies showed that the efficacy of
the AZT also against the
multidrug-resistant gram-negative
bacteria, including the mcr-1
carrying and the metallo-β-
lactamase producing isolates
especially in combination with the
other active agents such as the
fosfomycin, colistin and the
tigecycline. AZT is not that potent
enough to prevent all the HIV
replication and may only slow the
replication process of the virus and
the progression of the disease.
Prolonged AZT treatment can lead
to the HIV developing resistance to
the AZT by the mutation of its
reverse transcriptase. To slow the
development of resistance,
physicians can generally
recommend that the AZT be given
in combination with the another
reverse-transcriptase inhibitor and
an antiretroviral medicines from
the another group, such as a
Glossary of Genetics
protease inhibitor, non-nucleoside
reverse-transcriptase inhibitor, or
the integrase inhibitor; this type of
therapy is known as the HAART i.
E Highly Active Anti Retroviral
Therapy.
• ANTITERMINATION - The
Antitermination is the prokaryotic
cell’s aid to fix the premature
termination of the RNA synthesis
during the transcription process of
the RNA. It occurs when the RNA
polymerase ignores the termination
signal and still it continues to
elongating its transcript until a
second signal is reached. The
Antitermination provides
mechanism whereby one or more
than one genes at the end of an
operon can be switched either on
or off, depending on the
polymerase either recognizing or
not recognizing the termination
signal.
• Antitermination is used by some of
the phages to regulate the
progression from one stage of the
gene expression to the next. The
lambda gene N, codes for an
antitermination protein (pN) that is
necessary to allow the RNA
polymerase to read through the
terminators that are located at the
ends of the immediate early genes.
Another antitermination protein,
pQ, is required later in the phage
infection. pN and pQ act on the
RNA polymerase as it passes
through the specific sites. These
sites are located at the different
30
relative positions in their respective
transcription units.
• ANTIPARALLEL
ORIENTATION - In the field of
biochemistry, the two biopolymers
are called as antiparallel if they run
parallel to the each other but with
the opposite directionality or
alignments. An example is the two
complementary strands of a DNA
double helix, which run in the
opposite directions alongside of the
each other. The importance of an
antiparallel DNA double helix
structure is because of the its
hydrogen bonding between the
a complementary nitrogenous base
pairs. If the DNA structure were to
be parallel, the hydrogen bonding
would not be able to possible, as
the base pairs would not be paired
in the possible known way. The
four base pairs are the adenine,
guanine, cytosine, and the
thymine, where the adenine
complements thymine, and the
guanine complements the cytosine.
Transcription would be an another
problem if the DNA structure were
to be parallel, making no sense of
the information being read from
the DNA. This would further lead
to the production of the incorrect
proteins. Many of the proteins may
adopt a beta sheet as part of their
secondary structure. In the beta
sheets, sections of a single
polypeptide may run side-by-side
and antiparallel to the each other,
to allow for the hydrogen bonding
between their backbone chains.
© 2022 by JPS Scientific Publications, India
Glossary of Genetics
The Beta sheets can also be either a
parallel or the anti-parallel
secondary structure. However, an
anti-parallel beta sheet is
significantly more stable than a
parallel structure due to their well
aligned H-bonds, which are at a
90° angle.
• ACTIVATOR SYNERGISM -
Most of the eukaryotic promoters
contain the binding sites for the
several different transcription
factors, which often act as
synergistically. Mechanistically,
synergy is ascribed either to
cooperative DNA-binding of the
factors to the promoter or to y
some type of the “multiple
contact” mechanism in which the
each activator performs a different
task in stimulating the transcription
machinery. The yeast activators
Gal4 and the Put3 bind to the
DNA cooperatively in vivo and
can activate the transcription
synergistically from the certain
synthetic promoters. Normally, the
Gal4 and Put3 bind to completely
different promoters and activate
the physiologically unrelated sets
of rye genes and it is extremely
unlikely that they have evolved
direct protein-protein contacts.
These studies add to a growing
body of the evidence that binding
of the proteins to the nearby sites
in the chromatin is intrinsically
cooperative and suggest that many
examples of the synergy ascribed to
multiple contact mechanisms may
© 2022 by JPS Scientific Publications, India
31
instead involve the non-traditional
cooperative DNA-binding.
• AUTONOMOUS AND NON
AUTONOMOUS
TRANSPOSONS - Both the class
1 and the class 2 TEs can be either
termed as the autonomous or the
nonautonomous. The Autonomous
TEs can move on their own, while
the nonautonomous elements
require the presence of the other
TEs in order to move. This is
because the nonautonomous
elements lack the gene for the
transposase or the reverse
transcriptase that is needed for
their transposition, so they must
“borrow” these proteins from the
another element in order to move.
Ac elements, for example, are the
autonomous because they can
move on their own, whereas the
Ds elements are the
nonautonomous because they
require the presence of the Ac in
order to transpose.
• ANTI DOUBLE STRANDED
DNA ANTIBODIES - The Anti-
double stranded DNA (Anti-
dsDNA) antibodies are a group of
rye anti-nuclear antibodies (ANA)
that target rye antigen of which is
the double stranded DNA. Rye
Blood tests such as the enzyme-
linked immunosorbent assay
(ELISA) and the
immunofluorescence are routinely
performed to detect the anti-
dsDNA antibodies in the
diagnostic laboratories. They are
highly diagnostic of the systemic
Glossary of Genetics
lupus erythematosus (SLE) and are
implicated in the pathogenesis of
the lupus nephritis. The Anti-
dsDNA antibodies are incredibly
specific for the SLE, with studies
quoting nearly 100%, and are
therefore used in the diagnosis of
rye SLE. Higher titres of the anti-
dsDNA antibodies are more
suggestive of rye SLE and lower
titres can be found in the people
without the disease. In contrast to
the high specificity, estimates of
around 25-85% have been observed
for the sensitivity of the anti-
dsDNA in the SLE. Therefore,
presence of the anti-dsDNA
antibodies are suggestive of the
SLE, however an absence of the
antibodies does not rule out the
disease. The levels of the
circulating anti-dsDNA antibodies
fluctuate with the disease activity
in the SLE. The increases in the
titres of the antibodies can coincide
with, or even precede an increase
of the disease activity. For this
reason the titres are serially
monitored by the clinicians to
assess the disease progression.
Titres are monitored more often in
the cases of more active lupus than
that of rye less active lupus at the
intervals of the 1–3 months and the
6–12 months, respectively.
• ARS OPERON - In the field of the
molecular biology, the ars operon
is an operon found in the several
bacterial taxon. It is required for
the detoxification of the arsenate,
arsenite, and the antimonite. This
© 2022 by JPS Scientific Publications, India
32
system transports the arsenite and
the antimonite out of the cell. The
pump is composed of the two
polypeptides, the products of the
arsA and arsB genes. This two-
subunit enzyme produces the
resistance to the arsenite and the
antimonite. The Arsenate,
however, must first be reduced to
the arsenite before it is extruded. A
third gene, arsC, expands the
substrate specificity to allow for the
arsenate pumping and the
resistance. The ArsC is an
approximately 150-residue arsenate
reductase that uses the reduced
glutathione (GSH) to convert the
arsenate to arsenite with a redox
active cysteine residue in the active
site. The ArsC forms an active
quaternary complex with the GSH,
arsenate, and glutaredoxin 1
(Grx1). The three ligands must be
present simultaneously for the
reduction to occur.
• ALTERNATIVE SPLICING -
The Alternative splicing is the
process of selecting the different
combinations of the splice sites
within a messenger RNA precursor
(pre-mRNA) to produce the
variably spliced mRNAs. These
multiple mRNAs can encode the
proteins that vary in their sequence
and the activity, and yet arise from
a single gene. The Alternative
splicing is an important
mechanism in the developmental
and in the cell-type specific control
of the gene expression, and as a
Glossary of Genetics 33

mechanism for increasing the

proteome diversity. It is found in
nearly all the eukaryotic organisms
that carry out the standard nuclear
pre-mRNA splicing, including the
animals, plants and in some of the
cases of the fungi. The Alternative
splicing is modulated by many
proteins which interact with a large
array of the splicing enhancer and
the splicing suppressor sequences.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
B mammalian
• BISTABLE SWITCH - The
Bistable switches are the
fundamental regulatory elements
of the complex systems, ranging
from the electronics to the living
cells. These are Designed as the
genetic toggle switches have been
constructed from pairs of the
natural transcriptional repressors
wired to the inhibit one another.
Bistability is a key for
understanding the basic
phenomena of the cellular
functioning, such as the decision-
making processes in the cell cycle
progression, the cellular
differentiation, and the apoptosis.
It is also involved in the loss of the
cellular homeostasis associated
with the early events in the cancer
onset and in the prion diseases as
well as in the origin of the new
species. Bistability can also be
generated by a positive feedback
loop with an ultrasensitive
regulatory step. Positive feedback
loops, such as the simple X
activates the Y and Y activates the
X motif, essentially link the output
signals to their input signals and
also have been noted to be an very
important regulatory motif in the
cellular signal transduction because
the positive feedback loops can
create the switches with an all-or-
nothing The Studies have also
shown that the numerous
biological systems, such as the
© 2022 by JPS Scientific Publications, India
34
Xenopus oocyte maturation,
calcium
transduction, and the polarity in
signal
the budding yeast, incorporate the
multiple positive feedback loops
with the different time scales (slow
and fast). Having multiple linked
positive feedback loops with the
different time scales (“dual-time
switches”) allows for (a) increased
regulation: two switches that have
independent changeable activation
and deactivation times; and (b)
noise filtering.
• BACTERIAL ARTIFICIAL
CHROMOSOME - A bacterial
artificial chromosome (BAC) is an
engineered DNA molecule that is
used to clone the DNA sequences
in the bacterial cells for e g E. Coli.
BACs are often used in the
connection with the DNA
sequencing. Segments of an
organism’s DNA, ranging from
100,000 to about 300,000 base
pairs, can be inserted into the
BACs. BACs are a DNA construct,
based on the functional fertility
plasmid (or F-plasmid), which is
used for the transforming and
cloning process in the bacteria,
usually in the bacteria E. Coli. The
F-plasmids play a crucial role
because they contain the partition
genes that promote the even
distribution of the plasmids after
the bacterial cell division. The
bacterial artificial chromosome’s
are usually insert in the size of
150–350 kbp. A similar cloning
vector which called as the PAC has
Glossary of Genetics
also been produced from the DNA
of the P1 bacteriophage. The BACs
are often used to sequence the
genome of the organisms in the
genome projects, for e.g the
Human Genome Project. A short
piece of the organism’s DNA is
amplified as an insert in the BACs,
and then sequenced.
• BACTERIOPHAGE MU - The
Bacteriophage Mu, which is also
known as the mu phage or the mu
bacteriophage, is a muvirus the
first of its kind to be identified of
the family Myoviridae which has
been shown to the cause of the
genetic transposition. It is of
particular importance as its
discovery in the Escherichia coli by
the Larry Taylor was among the
first observations of the insertion
elements in a genome. This
discovery opened up the world to
an investigation of the transposable
elements and their effects on a
wide variety of the organisms.
While the Mu was specifically
involved in the several distinct
areas of the research such as
including the E. Coli, maize, and
the HIV. The wider implications of
the transposition and the insertion
transformed the entire field of the
genetics. The Mu acts as a useful
organism to elucidate the process
of HIV integration, eventually
leading to the HIV integrase
inhibitors such as the raltegravir.
The Phage Mu is non enveloped,
with a head and a tail. The head
has an icosahedral structure of
© 2022 by JPS Scientific Publications, India
35
about 54 nm in the width. The
neck is like knob-like, and the tail
is a contractile with a base plate
and the six short terminal fibers.
The genome has been fully
sequenced and consists of 36,717
nucleotides, coding for the 55
proteins.
• BACTERIOPHAGE P22 - The
Salmonella virus P22 is a
bacteriophage in the Podoviridae
family that infects the Salmonella
typhimurium. Like many of the
phages, it has been used in the
molecular biology to induce the
mutations in a cultured bacteria
and to introduce the foreign
genetic material. P22 has been
used in the generalized
transduction and is an important
tool for investigating the
Salmonella genetics. The P22
shares many of the similarities in a
genetic structure and regulation
with the bacteriophage λ. It is a
temperate double stranded DNA
phage as well as a lambdoid phage
since it carries the control of the
gene expression regions and an
early operons similar to those of
the bacteriophage λ. However, the
genes which encode the proteins
that build the virion are different
from those of the bacteriophage λ.
The P22 has a 60 nm diameter
icosahedral virion head and a short
tail. This virion morphology puts
theP22 in the formal Podoviridae
group. The Traditionally, P22 is
associated with the viruses with the
similar genomic transcription
Glossary of Genetics
patterns and the life cycles
including the bacteriophage λ and
all the other of the lambdoid
phages. However, this relatedness
seems to be overestimated. The
Other relatives with the similar
short-tailed morphology and DNA
homology in the protein genes of
the virion include the
bacteriophages λ and the
Ε34.Many Podoviridae, for
example phages T7 and Φ29, share
the few DNA similarities with the
P22, even though their virion
morphologies are similar.
• BACTERIAL GROWTH - The
Bacterial growth is the proliferation
of the bacterium into two daughter
cells, in a process called as the
binary fission. Providing no event
occurs, the resulting daughter cells
are genetically identical to the
original cell. Hence, the bacterial
growth occurs. Both the daughter
cells from the division do not
necessarily survive. However, if the
surviving number exceeds unity on
the average, the bacterial
population undergoes the
exponential growth. The
measurement of the exponential
bacterial growth curve in the batch
culture was traditionally a part of
the training of all the
microbiologists; the basic means
requires the bacterial enumeration
(cell counting) by the direct and
individual (microscopic, flow
cytometry), direct and bulk
(biomass), indirect and individual
(colony counting), or indirect and
© 2022 by JPS Scientific Publications, India
36
bulk (most probable number,
turbidity, nutrient uptake) of the
methods. The Models reconcile
theory with the measurements.
There are different phases in the
bacteria growth, such as the lag
phase, log phase, stationary phase,
and the death phase.
• BACTERIOPHAGE SPO1 - The
Bacteriophage SPO1 is one of a
group of the large, lytic, tailed
bacteriophages of the Bacillus
subtilis, which contain the
hydroxymethyluracil (hmUra) in
the place of thymine in their DNA.
It was isolated from the soil. The
unique genome sequence of the
SPO1 is about 132,562 bp, and the
DNA packaged in the virion i.e in
the chromosome has about 13,185
bp terminal redundancy, giving a
total of the 145,747 bp. There are
about 204 protein coding genes and
about the five tRNA genes. About
69% of the encoded proteins show
no similarity to any previously
known protein of SPO1. There are
about 107 probable transcription
promoters most of them are the
members of the promoter classes
identified in earlier studies, but
there also have class of
transcription promoter that has the
same sequence as the host sigma K
promoters. There are three genes
encoding potential new
transcription factors, one of which
is a distant homologue of the host
sigma factor K. There are also
about 75 probable transcription
Glossary of Genetics
terminator structures. Promoters
and the terminators are generally
located between the genes. There
are complete genome sequences
available for about five additional
phages of the Gram-positive hosts
that are similar to the SPO1 in the
genome size and in the
composition and organization of
the genes. There is a pattern
similar to what has been noted in
the phage T4 and its relatives, in
which there is a minimal successful
of the horizontal exchange of the
genes among a “core” set of the
genes that includes most of the
virion structural genes and some
genes of the DNA metabolism, but
there is extensive horizontal
transfer of genes over the
remainder of the gene.
• BACTERIOPHAGE PM2 -
The bacteriophage PM2 is a
marine double stranded DNA
studied since 1968, is the type of
organism of the family
Corticoviridae, infecting the two
gram-negative organisms of
Pseudoalteromonas species. The
virion contains a membrane
underneath an icosahedral protein
capsid composed of the two
structural proteins. The purified
major capsid of the protein P2,
appears as a trimer, and the
receptor binding protein P1,
appears as a monomer. The C-
terminal part of the P1 is distal and
is responsible for the receptor
binding activity. The rest of the
structure of the proteins are
© 2022 by JPS Scientific Publications, India
37
associated with the internal
phospholipid membrane enclosing
the viral genome. This internal
particle is designated with the lipid
core. The overall structural
organization of the phage PM2
resembles that of the dsDNA
bacteriophage PRD1, the type
organism of the family known as
the Tectiviridae. The PM2, is the
only virion isolate in the family of
the Corticoviridae, is the first
bacteriophage for which the
presence of the lipids in the virion
was firmly demonstrated in the
studies. It is a type of lytic virus,
infecting the two
Pseudoalteromonas species i.e of
the marine gram-negative
Pseudoalteromonas espejiana
BAL-31 originally known as the
Pseudomonas sp. Strain BAL-31,
isolated along with the virus and
the Pseudoalteromonas sp. Strain
ER72M2. The PM2 genome is a
very highly supercoiled circular
double-stranded DNA (dsDNA)
molecule with the highest number
of the negative supercoils i.e −51
observed in a natural molecule.
The organization of the genes and
the transcriptional regulation of the
operons in the genome have been
determined. The 10,079-bp
genome replicates via a mechanism
known as the rolling-circle
mechanism while associated with
the host cytoplasmic membrane.
The viral lipids are derived from
the host cell membrane during the
assembly process, and the
Glossary of Genetics
composition is around ∼64%
phosphatidylglycerol, ∼27%
phosphatidylethanolamine, ∼8%
neutral lipids, and the small
amounts of the
asylphosphatidylglycerol.
• BACTERIOPHAGE T4 - The
Escherichia virus T4 is a species of
the bacteriophages that infect the
bacteria known as the Escherichia
coli bacteria. It is a double-
stranded DNA virus in the
subfamily Tevenvirinae from the
family known as the Myoviridae.
The T4 bacteriophage is capable of
undergoing only a lytic lifecycle
and not the lysogenic lifecycle. The
species was formerly named as the
T-even bacteriophage, a name
which also encompasses, among
the other strains or isolates the
Enterobacteria phage T2, the
Enterobacteria phage T4 and the
Enterobacteria phage T6. The T4
virus is a double-stranded DNA
and has a genome about 169 kbp
long and also encodes about 289
proteins. The T4 genome is
normally terminally redundant.
Upon the DNA replication, the
long multi-genome length
concatemers are also formed,
perhaps by a rolling circle
mechanism of the
replication.When they are
packaged, the concatemer is cut at
the unspecific positions of the same
length, leading to the several
genomes that represent the circular
permutations of the original. The
T4 genome bears like eukaryote-
© 2022 by JPS Scientific Publications, India
38
like intron sequences. The T4 is a
relatively large virus, at
approximately about 90 nm wide
and about 200 nm long. Most of
the viruses range from 25 to 200
nm in length. The DNA genome is
held in an icosahedral head, also
known as the capsid. The T4’s tail
is hollow so that it can pass its
nucleic acid into the cell it is
infecting after the attachment. The
Myoviridae phages like T4 have a
complex contractile tail structures
with a large number of the proteins
involved in the tail assembly and
the function. The tail fibres are also
important in recognizing the host
cell surface receptors, so they can
determine if a bacterium is within
the virus’s host range.
• BACTERIOPHAGE T7 - The
Bacteriophage T7 or the T7 phage
is a bacteriophage, or a virus that
infects the bacteria. It also infects
most of the strains of the
Escherichia coli and also relies on
these hosts to propagate. The
Bacteriophage T7 has a lytic life
cycle, meaning that it destroys the
cell it infects. It also possesses the
several properties that make it an
ideal phage for the
experimentation like its
purification and the concentration
have produced consistent values in
the chemical analyses or it can be
rendered the noninfectious by the
exposure to the UV light and it can
be also used in phage display to
clone the RNA binding proteins.
The T7 grows on the rough strains
Glossary of Genetics
of the Escherichia coli i.e. those
without the full-length O-antigen
polysaccharide on their surface,
and some of the other enteric
bacteria, but close relatives also
infect the smooth and even the
capsulated strains. The E. Coli is
more resistant to the T7 than to
some of the other similar phages.
The T7 virus has a complex
structural symmetry, with a capsid
of the phage that is icosahedral
(twenty faces) with an inner
diameter of about 55 nm and a tail
about 19 nm in diameter and about
28. 5 nm long attached to the
capsid. The ejection of the proteins
from the capsid upon the infection
causes the virus to change the
structure when it enters into the
cell.
• BAITS - The Baits are the
oligonucleotides that retrieve the
specific RNA species or the
genomic DNA fragments of
interest for the sequencing. The
desired DNA or the RNA
molecules hybridize with the baits,
and the others do not. This forms
the basis of a powerful selection
method that lets you to focus your
sequencing efforts. The baits are
manufactured by the Agilent that
the are biotinylated RNA
oligonucleotides. Currently, the
eArray supports a bait length of
around 120 nucleotides. In the
eArray, a single bait is a nucleotide
sequence that is associated with a
unique Bait ID and the species.
Although the final product is
© 2022 by JPS Scientific Publications, India
39
supplied by the Agilent is a kit of
the biotinylated RNA
oligonucleotides. The Agilent first
creates the DNA oligonucleotides,
and the later transcribes these into
the RNA. Thus, the bait sequences
in the eArray are specified in the
terms of DNA bases (A, C, G, T).
Additional annotation can also be
included with the baits, such as the
associated genomic interval, the
chromosomal location, the gene
symbols, and the accession
numbers. For the SureSelect
Target Enrichment application
type, the bait sequences can be in
the either sense (+) or antisense (–)
orientation, and the libraries can
contain the baits in the either or
both the rientations.
• BALANCER CHROMOSOME -
The Balancer chromosomes or
simply the balancers are the type of
the genetically engineered
chromosome which are used in the
laboratory biology for the
maintenance of the recessive lethal
or the sterile mutations within the
living organisms without the
interference from the natural
selection. Since such the
mutations are viable only in the
heterozygotes, they cannot be
stably maintained through the
successive generations and
therefore they can continually lead
to the production of the wild-type
organisms, which can be prevented
by replacing the homologous wild-
type chromosome with a balancer.
In this capacity, the balancers are
Glossary of Genetics
crucial for the genetics research on
the model organisms such as
Drosophila melanogaster, the
common fruit fly, for which the
stocks cannot be archived (e.g.
frozen). They can also be used in
the forward genetics screens to
specifically identify the recessive
lethal (or sterile) mutations. For
that the reason, the balancers are
also used in the other model
organisms, most notably the
nematode worm Caenorhabditis
elegans and the mouse models.
The Typical balancer
chromosomes are designed to carry
the recessive lethal mutations
themselves, thereby eliminating the
homozygotes which do not carry
the desired mutation and which
suppress the meiotic recombination
with their homologs, which
prevents de novo creation of the
wild-type chromosomes and also
carry the dominant genetic
markers, which can help to identify
the rare recombinants and are
useful for the screening purposes.
• BAM GENE - The β-amylase
(BAM) gene family is named for
the catalytic members’ ability to
hydrolyze the starch into the
maltose units. However, the family
also contains the proteins that are
catalytically inactive, and have
additional domains, or are not
localized with a specific starch
substrate. The Bam is especially
attractive as a target of the GSC
differentiation factors because the
current evidence indicates that the
© 2022 by JPS Scientific Publications, India
40
bam is both necessary and
sufficient for th cystoblast
differentiation. The bam gene is
mutually exclusive for both
transcriptional or post-
transcriptional mechanisms as the
primary regulators of the bam
expression in the GSCs and in the
cystoblasts. The bam transcription
is active in the young germ cells
but is repressed specifically in the
GSCs. The Activation depends on
a 50 bp fragment that carries at
least one germ cell-specific
enhancer element. A non-
overlapping 18 bp sequence carries
the transcriptional silencer that
prevents the bam gene expression
in the GSC. The Promoters lacking
this silencer cause the bam gene
expression in the GSC and
concomitant GSC loss. Thus,
asymmetry of the GSC division
can be reduced to identifying the
mechanism that selectively
activates the silencer element in the
GSCs.
• BAND SHIFT ASSAY - An
electrophoretic mobility shift assay
(EMSA) or the mobility shift
electrophoresis which is also
referred as a band shift assay, is a
common affinity electrophoresis
technique that is used to study the
protein–DNA or protein–RNA
interactions. This procedure can
determine if a protein or mixture of
the proteins is capable of binding
to a given DNA or the RNA
sequence, and can sometimes
indicate that if more than one
Glossary of Genetics
protein molecule is involved in the
binding complex. Band shift shift
assays are often performed in vitro
concurrently with the DNase
footprinting, the primer extension,
and the promoter-probe
experiments when studying the
transcription initiation, DNA gang
replication, DNA repair or the
RNA processing and maturation,
as well as the pre-mRNA splicing.
Although the precursors can be
found in the earlier literature, most
of the current assays are based on
the methods described by the
scientists named as the Garner and
Revzin and Fried and Crothers. A
mobility shift assay is the
electrophoretic separation of a
protein–DNA or protein–RNA
mixture on a polyacrylamide
agarose gel for a short period. The
speed at which the different
molecules move through the gel is
determined by their size and
charge, and to a lesser extent, also
their shape. The control lane
(DNA probe without protein
present) will contain a single band
corresponding to the unbound
DNA or the RNA fragment.
However, assuming that the
protein is capable of binding to the
fragment, the lane with a protein
that binds present will contain the
another band that represents the
larger and less mobile complex of
the nucleic acid probe bound to the
protein which is ‘shifted’ up on the
gel.
© 2022 by JPS Scientific Publications, India
41
• BINDING SITES - A binding site
is the region on a macromolecule
la such as a protein that binds to
the another molecule with the
specificity. The binding partner of
the macromolecule is often referred
to as the ligands. The Ligands may
include the other proteins which
resulting in a protein-protein
interaction, or the enzyme
substrates, the second messengers,
hormones, or the allosteric
modulators. The binding event is
often, but not the always,
accompanied by a conformational
change that can alters the protein’s
function. The Binding to protein
binding sites is most often
reversible i.e transient and non-
covalent, but can also be covalent
reversible or the irreversible. The
Enzymes incur catalysis by binding
the more strongly to the transition
states than the substrates and the
products. At the catalytic binding
site, the several different
interactions may act upon the
substrate. These range from the
electric catalysis, acid and the base
catalysis, covalent catalysis, and
the metal ion catalysis. These
interactions decrease the activation
energy of a chemical reaction by
providing the favorable
interactions to stabilize the high
energy molecule. Enzyme binding
allows for the closer proximity and
exclusion of the substances
irrelevant to the reaction. Side
reactions are also then discouraged
by this specific binding. The Types
Glossary of Genetics
of enzymes that can perform these
actions include the enzymes such
as oxidoreductases, transferases,
hydrolases, lyases, isomerases, and
ligases. For the instance, the
transferase hexokinase catalyzes
the phosphorylation of glucose to
make glucose-6-phosphate. The
Active site residues of the
hexokinase allow for the
stabilization of the glucose
molecule in the active site and spur
the onset of an alternative pathway
of favorable interactions,
decreasing the activation energy.
• BASE ANALOGS - The Base
analogues are the molecules that
can substitute for the normal bases
in the nucleic acids. Usually, the
substitution of a base analogue will
result in the altered base pairings
and the structural changes that
affect the DNA replication and the
transcription process of the genes.
Examples of the base analogues
include the 5-bromouracil, the 2-
aminopurine,the 6-
mercaptopurine, and the
acycloguanosine. Since the 5-
bromouracil can pair with either
the adenine or the guanine, it also
affects the base pairing during the
DNA replication, which leads to
the mutations. An analogue of the
adenine, 2-aminopurine, which
also causes the mutations in a
similar way since it can pair with
either the T or the C. 5-
Bromouracil is used to treat the
neoplasms in the form of its
nucleoside, 5-bromo-2-deoxy-
© 2022 by JPS Scientific Publications, India
42
uridine. 6-Mercaptopurine is an
analogue of the hypoxanthine and
it inhibits the purine nucleotide
synthesis and it’s metabolism. The
6-Mercaptopurine is used to treat
the acute leukemia.
Acycloguanosine which is also
called as the acyclovir is an
analogue of the guanine and is one
of the most commonly used
antiviral drugs. It is an effective
treatment for the herpes simplex
virus infection. Also, the base
analogues can inhibit the DNA
synthesis by inhibiting the certain
enzymes. For example, the 5-
fluorouracil is a thymine analogue
that inhibits the thymidylate
synthases, which is a key enzyme
in the thymine synthesis. Because
it inhibits the DNA synthesis. The
5-fluorouracil is used in the
treatment of some of the cancers,
and it belongs to the family of the
drugs which are called as the
antimetabolites.
• BASE EXCISION REPAIR - The
Base excision repair (BER) is a
type of the cellular mechanism,
which is studied in the fields of the
biochemistry and the genetics, that
repairs the damaged DNA
throughout the cell cycle. It is
responsible primarily for removing
the small, non-helix-distorting base
lesions from the genome. The
related nucleotide excision repair
pathway repairs the highly bulky
helix-distorting lesions. The BER is
important for removing the
damaged bases that could
Glossary of Genetics
otherwise cause the mutations by
mispairing or lead to breaks in the
DNA during the replication
process. The BER is initiated by
the DNA glycosylases, which
recognize and remove the specific
damaged or the inappropriate
bases, forming the AP sites. These
are then cleaved by an enzyme
known as AP endonuclease. The
resulting single-strand break can
then be processed by either the
short-patch where a single
nucleotide is replaced or the long-
patch BER where 2–10 new
nucleotides are synthesized. The
Single bases in the DNA can be
chemically damaged by a variety of
the mechanisms, the most
common ones being the
deamination, oxidation, and
alkylation. These modifications
can affect the ability of the base to
the hydrogen-bond, resulting in the
incorrect base-pairing, and as a
consequence, mutations in the
DNA. For example, the
incorporation of the adenine across
from 8-oxoguanine (right) during
the DNA replication causes a G:C
base pair to be mutated to the T:A.
Other examples of the base lesions
repaired by the BER include:
Oxidized bases, Alkylated bases,
Deaminated bases.
• BASE FLIPPING - The DNA
base flipping, which is also known
as the nucleotide flipping, is a
mechanism in which a single
nucleotide base, or the nucleobase,
is rotated outside the nucleic acid
© 2022 by JPS Scientific Publications, India
43
double helix. This occurs when a
nucleic acid-processing enzyme
needs the access to the base to
perform the work on it, such as its
excision for the replacement with
the another base during the DNA
repair. It was first observed in the
1994 using the X-ray
crystallography in a
methyltransferase enzyme
catalyzing the methylation of a
cytosine base in the DNA. Since
then, it has been shown to be used
by the different enzymes in many
biological processes such as the
DNA methylation, various DNA
repair mechanisms, and the DNA
replication. It can also occur in the
RNA double helices or in the
DNA:RNA intermediates formed
during the RNA transcription. The
DNA base flipping occurs by the
breaking of the hydrogen bonds
between the bases and unstacking
the base from its neighbors. This
could occur through an active
process, where an enzyme binds to
the DNA and then facilitates
rotation of the base, or a passive
process, where the base rotates out
spontaneously, and this state is
recognized and bound by the
enzyme. It can be detected using
the X-ray crystallography, the
NMR spectroscopy, the
fluorescence spectroscopy, or the
hybridization probes.
• BASE PAIRING - A base pair
(bp) is a fundamental unit of the
double-stranded nucleic acids
consisting of the two nucleobases
Glossary of Genetics
bound to the each other by the
hydrogen bonds. They form the
building blocks of the DNA double
helix and contribute to the folded
structure of both the DNA and the
RNA. Dictated by the specific
hydrogen bonding patterns, the
“Watson–Crick” base pairs i.e
guanine–cytosine and the adenine–
thymine allows the DNA helix to
maintain a regular helical structure
that is subtly dependent on its
nucleotide sequence. The
complementary nature of this
based-paired structure provides a
redundant copy of the genetic
information encoded within the
each strand of the DNA. The
regular structure and the data
redundancy provided by the DNA
double helix make the DNA well
suited to the storage of the genetic
information, while the base-pairing
between the DNA and the
incoming nucleotides provides the
mechanism through which the
DNA polymerase replicates the
DNA and RNA polymerase
transcribes the DNA into the
RNA. Many of the DNA-binding
proteins can recognize a specific
base-pairing patterns that identify
the particular regulatory regions of
the genes. The size of an individual
gene or an organism’s entire
genome is often measured in the
base pairs because the DNA is
usually a double-stranded. Hence,
the number of the total base pairs is
equal to the number of the
nucleotides in one of the strands
© 2022 by JPS Scientific Publications, India
44
with the exception of the non-
coding single-stranded regions of
the telomeres. The haploid human
genome (23 chromosomes) is
estimated to be about the 3.2
billion bases long and to contain
20,000–25,000 distinct protein-
coding genes. A kilobase (kb) is a
unit of the measurement in the
molecular biology which is equal
to the 1000 base pairs of the DNA
or the RNA. The total number of
the DNA base pairs on the Earth is
estimated at 5.0×1037 with a
weight of about 50 billion tonnes.
In comparison, the total mass of
the biosphere has been estimated to
be as much as the 4 TtC (trillion
tons of carbon).
• BEHAVIOR MUTATIONS - A
behaviour mutation is a genetic
mutation that alters the genes that
control the way in which an
organism behaves, causing their
behavioural patterns to change. A
mutation is a change or the error in
the genomic sequence of a cell. It
can occur during the meiosis or the
replication of the DNA, as well as
due to ionizing or the UV
radiation, transposons, mutagenic
chemicals, viruses and a number of
the other factors. The Mutations
usually (but not always) result in a
change in an organisms fitness.
These changes are largely
deleterious, having a negative
effect on the fitness, however, they
can also be neutral and even very
advantageous. The Behaviour
mutations have important
Glossary of Genetics
implications on the nature of the
evolution of the animal behaviour.
They can help us understand how
different forms of the behaviour
evolve, especially behaviour which
can seem strange or out of the
place. In the other cases, they can
help us understand how important
patterns of the behaviour were able
to arise – on the back of a simple
gene mutation.
• 5 BROMOURACIL - The 5-
Bromouracil (5-BrU, 5BrUra, or
br5Ura) is a brominated derivative
of the uracil that acts as an
antimetabolite or the base analog,
substituting for the thymine in the
DNA, and can induce the DNA
mutation in the same way as the 2-
aminopurine. It is used mainly as
an experimental mutagen, but its
deoxyriboside derivative (5-bromo-
2-deoxy-uridine) is used to treat the
neoplasms. Thus the 5-BrU
induces a point mutation via the
base substitution. This base pair
will change from an A-T to a G-C
or from a G-C to an A-T after a
number of the replication cycles,
depending on whether the 5-BrU is
within the DNA molecule or is an
incoming base when it is enolized
or the ionized.
• BRANCH MIGRATION - The
Branch migration is the process by
which the base pairs on the
homologous DNA strands are
consecutively exchanged at the
Holliday junction, moving the
branch point up or the down the
DNA sequence. The Branch
© 2022 by JPS Scientific Publications, India
45
migration is the second step of the
genetic recombination, following
the exchange of the two single
strands of the DNA between the
two homologous chromosomes.
The process is random, and the
branch point can be displaced in
the either direction on the strand,
influencing the degree of which the
genetic material is exchanged. The
Branch migration can also be seen
in the DNA repair and in the
replication, when filling in the gaps
in the sequence. It can also be seen
when a foreign piece of the DNA
invades the strand.
• BOVINE PANCREATIC
RIBONUCLEASE - The Bovine
pancreatic ribonuclease, also often
referred to as the vovine pancreatic
ribonuclease A or simply the
RNase A, is a pancreatic
ribonuclease enzyme that cleaves
the single-stranded RNA. The
Bovine pancreatic ribonuclease is
one of the classic model systems of
the protein science. The two Nobel
Prizes in the Chemistry have been
awarded in recognition of the work
on the bovine pancreatic
ribonuclease. In 1972, the Prize
was awarded to the Christian
Anfinsen for his work on the
protein folding and to the Stanford
Moore and William Stein for their
work on the relationship between
the protein's structure and its
chemical mechanism. In 1984, the
Prize was awarded to the Robert
Bruce Merrifield for the
development of the chemical
Glossary of Genetics
synthesis of the proteins. The
RNase A is a relatively small
protein. It can be characterized as a
two-layer protein with a deep cleft
for the binding ofthe RNA
substrate. The first layer is
composed of the three residues
from the N-terminal half of the
protein. The second layer consist of
three β-hairpins arranged in the
two β-sheets.
• BASE STACKING - The Base
stacking is a common arrangement
of the nucleobases found in the
three dimensional structure of the
nucleic acids. The Bases or the
base pairs are the planar, and these
planes stack at the contact distance
which is about 3.4 Angstrom,
excluding the water and the
maximizing Van der Waals
interactions. In the terms of the
structural stability of the nucleic
acids in the aqueous solution, the
stacking interactions of the bases
play a larger role than the
hydrogen bonds formed by the
bases. There are various examples
of the base stacking such as the
DNA double helix:
• In double-stranded DNA, the
bases from the two strands pair up
to form the base pairs, which are
stacked along the helix axis of the
double strand. Zooming in to a
detailed view of the G:C base pair,
the extent of the stacking contacts
are thereby determined by the
sequence. G:C base pairs
contribute more to the thermal
stability of the DNA than the A:T
© 2022 by JPS Scientific Publications, India
46
base pairs because they stack
better.
• RNA kissing loops: The Loops on
the two separate RNA pieces are
held together by the stacking
interactions i.e between thr base
pairs and the hydrogen bonds i.e
within the base pairs.
• RNA single strand bound to a
protein: In this the complex of
RNA bound to a protein, some of
the stacking interactions are the
disrupted by the amino acid side
chains such as the arginine,
histidine and the tyrosine
intercalating between the adjacent
bases.
• BASIC HELIX-LOOP-HELIX
PROTEINS - The basic helix–
loop–helix is a protein structural
motif that characterizes one of the
largest families of the dimerizing
transcription factors. The word
“basic” does not refer to
complexity but to the chemistry of
the motif because the transcription
factors in general contain the basic
amino acid residues in order to
facilitate the DNA binding. The
bHLH transcription factors are
often very important in the
development or the cell activity.
For one, the BMAL1-Clock which
is also called as the ARNTL is a
core transcription complex in the
molecular circadian clock. Other
genes, like the c-Myc and the HIF-
1, have been linked to the cancer
due to their effects on the cell
growth and their metabolism. The
bHLH transcription factors are the
Glossary of Genetics
heterodimeric in nature and their
activity is often highly regulated by
the dimerization of the subunits.
One of the subunit’s expression or
the availability is often very
controlled, whereas the other
subunit is very constitutively
expressed. Many of the known
regulatory proteins, such as the
Drosophila extramacrochaetae
protein, have the helix-loop-helix
structure but they lack the basic
region, making them unable to
bind to the DNA on their own.
They are, however, able to form
the heterodimers with proteins that
have the bHLH structure, and
inactivate their abilities as the
transcription factors. The bHLH
proteins typically bind to a
consensus sequence called an E-
box, or the CANNTG. The
canonical E-box is CACGTG
which is palindromic in the nature,
however some of the bHLH
transcription factors, notably those
of the bHLH-PAS family, bind to
the related non-palindromic
sequences, which are similar to the
E-box. The bHLH TFs may
homodimerize or the
heterodimerize with the other
bHLH TFs and form a large
variety of the dimers, each one
with the specific functions.
• BLAST - In the field of the
biogenetic the BLAST which is
known as the basic local alignment
search tool is an algorithm and the
program for comparing the
primary biological sequence
© 2022 by JPS Scientific Publications, India
47
information, such as the amino-
acid sequences of the proteins or
the nucleotides of the DNA and/or
the RNA sequences. A BLAST
search enables a researcher to
compare a subject protein or the
nucleotide sequence which is alled
a query with a library or the
database of the sequences, and the
identify database sequences that
resemble the query sequence above
a certain threshold. The BLAST
finds a similar sequences, by
locating the short matches between
the two sequences. This process of
finding the similar sequences is
called as the seeding. It is after this
first match that BLAST begins to
make the local alignments. While
attempting to find the similarity in
the sequences, the sets of the
common letters, known as the
words, are very important. If a
BLAST was being conducted
under the normal conditions, the
word size would be of 3 letters. In
this case, using the given stretch of
the letters, the searched words
would be the GLK, LKF, KFA.
The heuristic algorithm of the
BLAST locates all the common
three-letter words between the
sequence of the interest and the hit
sequence or sequences from the
database. This result will then be
used to build an alignment. After
making the words for the sequence
of interest, the rest of the words are
also assembled. These words must
satisfy a requirement of having a
score of at least the threshold T,
Glossary of Genetics
when compared by using a scoring
matrix. One of the most commonly
used scoring matrix for the BLAST
searches is the BLOSUM62.
• BASIC LEUCINE ZIPPER - A
leucine zipper or the leucine
scissors is a common three-
dimensional structural motif which
are present in the proteins. They
were first described by the
Landschulz and collaborators in
the year 1988, when they found
that an enhancer binding protein
had a very characteristic of about
30-amino acid segment and the
display of these amino acid
sequences on an idealized alpha
helix revealed a periodic repetition
of the leucine residues at every
seventh position over a distance
covering the eight helical The
polypeptide segments containing
these periodic arrays of the leucine
residues were proposed to exist in
an alpha-helical conformation and
the leucine side chains from one
alpha helix interdigitate with those
from the alpha helix of a second
polypeptide, facilitating the
dimerization. The leucine zippers
are a dimerization motif of the
bZIP i.e the Basic-region leucine
zipper a class of the eukaryotic
transcription factors. The bZIP
domain is about 60 to 80 amino
acids in length with a highly
conserved DNA binding basic
region and a more diversified
leucine zipper dimerization
region.The localization of the
leucines are very critical for the
© 2022 by JPS Scientific Publications, India
48
DNA binding to the proteins. The
Leucine zippers are present in the
both eukaryotic and the
prokaryotic regulatory proteins, but
are mainly a feature of the
eukaryotes. They can also be
annotated simply as the ZIPs, and
the ZIP-like motifs have been
found in the proteins other than the
transcription factors and are
thought to be one of the general
protein modules for the protein–
protein interactions.
• BCNU - It is a drug which is used
alone or with the other drugs to
treat the certain types of the brain
tumors, Hodgkin lymphoma, and
the non-Hodgkin lymphoma and
the prednisone to treat the multiple
myeloma. It is also being studied
in the treatment of the other types
of the cancer. The BCNU damages
the cell’s DNA and may also kill
the cancer cells. It is a type of
alkylating agent and a type of
nitrosourea which is also called as
the BiCNU and carmustine. When
treated with the BCNU the
majority of the primary cells in all
the 4 tumors had near-diploid
chromosome numbers and all were
resistant to concentrations of the
BCNU. Following the in vitro
cultivation, the cells from the
tumors retained their 2n modal
chromosome number with little
change in the complexity of the
karyotype. In contrast, the tumors
demonstrated a more unstable
genome. The Karyotyping
demonstrated additional ploidy
Glossary of Genetics
changes and new marker
chromosomes in the tumors. The
colony forming assay (CFA)
performed on the in vitro
cultivated cells demonstrated little
change in the sensitivity to the
BCNU in the tumors. The modal
chromosome number and the
BCNU sensitivity followed a
similar pattern in the 30 clones that
were isolated; 21 clones with near-
diploid and pseudodiploid
chromosome numbers were all
resistant to BCNU. The
karyotypes of the hyperdiploid
clones were more complex, they
were contained 5 or more ploidy
changes and/or had the marker
chromosomes. These studies
confirm the association of diploidy
and BCNU-resistance in the freshly
resected malignant gliomas.
• BDNF - The BDNF stands for the
brain derived neurotrophic factor.
The BDNF gene provides the
instructions for making the protein
found in the brain and in the spinal
cord which is called as the brain-
derived neurotrophic factor. This
protein promotes the survival of
the nerve cells called as neurons by
playing a vital role in the growth,
maturation (differentiation), and in
the maintenance of these cells. In
the brain, the BDNF protein is
active at the connections between
the nerve cells (synapses), where
the cell-to-cell communication
occurs. The synapses can change
and adapt over time in the
response to experience, a containing all the eight are referred
© 2022 by JPS Scientific Publications, India
49
characteristic called as synaptic
plasticity. The BDNF protein helps
to regulate the synaptic plasticity,
which is important for the learning
and memory. The BDNF protein is
found in the regions of the brain
that control the eating, drinking,
and the body weight, the protein
likely contributes to the
management of these functions.
This gene encodes a member of the
nerve growth factor family of the
proteins. Alternative splicing
results in the multiple transcript
variants, at least one of the which
encodes a preproprotein that is
proteolytically processed to
generate the mature protein.
Binding of this protein to its
cognate receptor promotes the
neuronal survival in the adult
brain. Expression of this gene is
reduced in the Alzheimer’s,
Parkinson’s, and in the
Huntington’s disease patients. This
gene may play a role in the
regulation of the stress response
and in the biology of the mood
disorders.
• B-COMPLEX - The B vitamins
are a class of the water-soluble
vitamins that play an important
roles in the cell metabolism and in
the synthesis of the red blood cells.
Though these vitamins share the
similar names (B1, B2, B3, etc.),
they are chemically very distinct
compounds that often coexist in
the same type of the foods. In the
general, dietary supplements
Glossary of Genetics
to as a vitamin B complex.
Individual B vitamin supplements
are referred to by the specific
number or name of the each
vitamin, such as the B1 for the
thiamine, B2 for the riboflavin, and
B3 for the niacin. Some of them
are more commonly recognized by
the name than by number, for
example the pantothenic acid,
biotin, and the folate. The Each B
vitamin is either a cofactor
(generally a coenzyme) for key
metabolic processes or is a
precursor needed to make one and
is thus an the essential nutrient.
The B vitamins are found in the
highest abundance in the meat,
eggs, and in the dairy products.
The Processed carbohydrates such
as the sugar and the white flour
tend to have lower B vitamin than
their unprocessed counterparts. For
this reason, it is required by law in
many of the countries that the B
vitamins such as thiamine,
riboflavin, niacin, and folic acid be
added back to white flour after the
processing. This is referred to as
the “enriched flour” on the food
labels. The B vitamins are
particularly concentrated in the
meat such as turkey, tuna and in
the liver.
• BWS SYNDROME - The BWS
stands for the Beckwith–
Wiedemann syndrome. It is an
overgrowth disorder usually
present at the time of the birth,
characterized by an increased risk
of the childhood cancer and the
© 2022 by JPS Scientific Publications, India
50
certain congenital features. A
minority cases of the BWS are very
familial, meaning that a close
relative may also have BWS, and
parents of an affected child may be
at very increased risk of having the
other children with the BWS.
While the children with the BWS
are at increased risk of childhood
cancer, most of the children with
BWS do not develop the cancer
and the vast majority of the
children who do develop cancer
can be treated successfully. The
Beckwith-Wiedemann syndrome is
a growth disorder variably
characterized by the neonatal
hypoglycemia, macrosomia,
macroglossia, hemihyperplasia,
omphalocele, embryonal tumors,
hepatoblastoma, neuroblastoma,
and the rhabdomyosarcoma,
visceromegaly, adrenocortical
cytomegaly, renal abnormalities,
and the ear creases/pits. It is
considered a clinical spectrum, in
which the affected individuals may
have many of these features or may
have only one or the two of the
clinical features. Early death may
also occur from the complications
of the prematurity, hypoglycemia,
cardiomyopathy, macroglossia, or
the tumors. The Macroglossia and
macrosomia are generally present
at the birth but may have the
postnatal onset. The Growth rate
slows around the age seven to eight
years. Hemihyperplasia may also
affect the segmental regions of the
body or the selected organs and the
Glossary of Genetics
tissues. A provisional diagnosis of
the BWS based on the clinical
assessment may be confirmed by
the molecular or the cytogenetic
testing.
• BEADLE GEORGE
EXPERIMENT - The famous
scientists such as the George Wells
Beadle and the Edward Lawrie
Tatum’s 1941 article “ The Genetic
Control of the Biochemical
Reactions in the Neurospora”
detailed their experiments on how
the genes regulated the chemical
reactions, and how the chemical
reactions in turn affected the
development in the organism. The
Beadle and the Tatum
experimented on the Neurospora, a
type of the bread mold, and they
concluded that the mutations to the
genes affected the enzymes of the
organisms, a result that the
biologists later generalized to the
proteins, not just the enzymes.
The Beadle and Tatum’s
experiments provided an early link
between the genetics and in the
field of the molecular biology.
Their final hypothesis supported
the one gene-one enzyme
hypothesis and they also confirmed
that the arginine pathway and then
was the restated as the one gene-
one polypeptide hypothesis. The
Beadle and Tatum reasoned that it
should be possible to induce the
mutations, or the changes in the
genes, that “broke” the specific
enzymes and thus the specific
pathways that is needed for the
© 2022 by JPS Scientific Publications, India
51
growth on the minimal medium.
A Neurospora line with such
mutation would grow normally on
the complete medium, but would
also lose the ability to survive on
the minimal medium. The Beadle
and Tatum exposed the
Neurospora spores to the radiation
i.e x-ray, UV, or neutron to make
the new mutations. After a few
genetic cleanup steps, they took the
descendants of the irradiated
spores and grew them individually
in the test tubes containing the
complete medium. Once the each
spore had established a growing
colony, a small piece of the colony
was transferred into the another
tube containing a minimal
medium.
• B- GALACTOSIDASE - The β-
galactosidase, which is also called
as the lactase, beta-gal or the β-gal,
is a family of the glycoside
hydrolase enzymes that catalyzes
the hydrolysis of the β-galactosides
into the monosaccharides through
the breaking of a glycosidic bond.
Β-galactosides includes the
carbohydrates containing galactose
where the glycosidic bond lies
above the galactose molecule. The
Substrates of different β-
galactosidases include the
ganglioside GM1,
lactosylceramides, lactose, and
various other types of
glycoproteins. The β-galactosidase
is an exoglycosidase which
hydrolyzes the β-glycosidic bond
formed between a galactose and its
Glossary of Genetics
organic moiety. It may also cleave
the fucosides and the arabinosides
but with very much lower
efficiency. It is an essential enzyme
in the human body. Deficiencies in
the protein can result in the
galactosialidosis or the Morquio B
syndrome. In E. Coli, the lacZ
gene is the structural gene for the β-
galactosidase, which is present as
the part of the inducible system lac
operon which is activated in the
presence of lactose when the
glucose level is very low. The β-
galactosidase synthesis stops when
the glucose levels are sufficient. Β-
galactosidase is an important for
the organisms as it is a key
provider in the production of the
energy and a source of thecarbons
through the break down of the
lactose to the galactose and the
glucose. It is also important for the
lactose intolerant community as it
is responsible for making the
lactose-free milk and the other
dairy products. Many of the adult
humans lack the lactase enzyme,
which has the same function of tge
beta-gal, so they are not able to
properly digest the dairy products.
Beta-galactose is also used in such
dairy products as yogurt, sour
cream, and some cheeses which
are treated with the enzyme to
break down any of the lactose
before thr human consumption
• B-GLOBULIN GENE - The HBB
(Hemoglobin Subunit Beta) is a
Protein Coding gene. The Diseases
is associated with the HBB
© 2022 by JPS Scientific Publications, India
52
including the Sickle Cell Anemia
and the Beta-Thalassemia, which
dominant Inclusion Body Type.
The Mutations in the globin genes
cause the thalassemias. The Beta
thalassemia affects one or the both
of the β-globin genes. These
mutations result in the impaired
synthesis of the β-globin protein
portion, a component of the Hb,
thus causing the anaemia. The
genetic defect usually is a missense
or the nonsense mutation in the β-
globin gene, although the
occasional defects due to the gene
deletions of the β-globin gene and
the surrounding regions also have
been reported. In the beta
thalassemia minor one of the β-
globin genes is defective. The
defect can be a complete absence of
the β-globin protein i.e. beta-zero
thalassemia or a reduced synthesis
of the β-globin protein i.e. beta-plus
thalassemia. Among its the related
pathways are Response to the
elevated platelet cytosolic Ca2+
and the Budding the and
maturation of the HIV virion. The
gene Ontology (GO) annotations
related to this gene include the iron
ion binding and the oxygen
binding. An important paralog of
this gene is the HBD. The HBB is
involved in the oxygen transport
from the lung to the various
peripheral tissues. The HBB
HUMAN LVV-hemorphin-7
potentiates the activity of the
bradykinin, causing a decrease in
the blood pressure. The Functions
Glossary of Genetics
is it acts an endogenous inhibitor
of the enkephalin-degrading
enzymes such as the DPP3, and as
a selective antagonist of the P2RX3
receptor which is involved in the
pain signaling, these properties
implicate it as a regulator of the
pain and the inflammation.
• B-SANDWHICH - The Beta-
sandwich, or the β-sandwich are
the domains consisting of the 80 to
350 amino acids which occur
commonly in the proteins. They
are characterized by the two
opposing antiparallel beta sheets
(β-sheets). The number of the
strands found in such domains
may differ from one protein to the
another. The β-sandwich domains
are subdivided in a variety of the
different folds. The
immunoglobulin-type fold found in
the antibodies (Ig-fold) consists of a
sandwich arrangement of 7 and 9
antiparallel β-strands arranged in
the two β-sheets. The jelly-roll
topology is also found in the
carbohydrate binding proteins such
as the concanavalin A and various
lectins, in the collagen binding
domain of the Staphylococcus
aureus Adhesin and in the modules
that bind the fibronectin as found
in the tenascin. The L-type of the
lectin domain is a variation of the
jelly roll fold. The C2 domain in its
typical version (PKC-C2) is a β-
sandwich composed of the 8 beta-
strands (β-strands).
© 2022 by JPS Scientific Publications, India
53
• B-STRAND - The Beta sheets
consist of the beta strands (β-
strands) which is connected
laterally by at least two or the three
backbone hydrogen bonds, forming
a generally twisted and pleated
sheet. A β-strand is a stretch of
polypeptide chain typically about 3
to 10 amino acids long with the
backbone in an extended
conformation. The supramolecular
association of the β-sheets has been
implicated in the formation of the
fibrils and the protein aggregates
observed in the amyloidosis,
notably the Alzheimer’s disease.
The majority of the β-strands are
arranged as the adjacent to the
other strands and also form an
extensive network of hydrogen
bond network with their
neighbours in which the N−H
groups in the backbone of one of
the strand establish hydrogen
bonds with the C=O groups in the
backbone of the adjacent In the
fully extended β-strand, the
successive side chains point
straight up and straight down in an
alternating pattern. The Adjacent
β-strands in a β-sheet are aligned so
that their Cα atoms are adjacent
and their side chains point in the
same direction. The “pleated”
appearance of the β-strands arises
from the tetrahedral chemical
bonding at the Cα atom.
• B-THALASSEMIA - The Beta
thalassemias (β thalassemias) are a
group of the inherited blood
disorders. They are the forms of
Glossary of Genetics
the thalassemia caused by the
reduced or the absent synthesis of
the beta chains of the hemoglobin
that result in the variable outcomes
ranging from the severe anemia to
the clinically asymptomatic
individuals. The Global annual
incidence is estimated at one in
100,000. The Beta thalassemias
occur due to the malfunctions in
the hemoglobin subunit beta or the
HBB. The severity of the disease
depends on the nature of the
mutation. The HBB blockage over
the time leads to the decreased
beta-chain synthesis. The body’s
inability to construct the new beta-
chains leads to the
underproduction of the HbA i.e
adult hemoglobin. The Reductions
in the HbA available overall to fill
the red blood cells in turn leads to
the microcytic anemia. The
Microcytic anemia ultimately
develops in respect to the
inadequate HBB protein for the
sufficient red blood cell
functioning. Due to the this factor,
the patient may also require the
blood transfusions to make up for
the blockage in the beta-chains.
The Repeated blood transfusions
cause the severe problems
associated with the iron overload.
• BICOID MRNA - The Bicoid
mRNA is actively localized to the
anterior of the fruit fly egg during
the oogenesis process along with
the microtubules by the motor
protein which is known as the
dynein, and it is retained there
© 2022 by JPS Scientific Publications, India
54
through the association with the
cortical actin. The Translation of
the bicoid is regulated by its 3′
UTR and it begins after the egg
deposition. The Diffusion and the
convection within the syncytium
produce an exponential gradient of
the Bicoid protein within roughly
one hour, after which the Bicoid
nuclear concentrations remain
approximately constant through
the cellularization. An alternative
model proposes that the formation
of a bicoid mRNA gradient in the
embryo along with the cortical
microtubules which then serves as
template for the translation of the
Bicoid protein to form the Bicoid
protein gradient. The Bicoid
protein represses the translation of
the caudal mRNA and enhances
the transcription of the anterior gap
genes including the hunchback,
orthodenticle, and the buttonhead.
• BICOID PROTEIN - The
Homeotic protein bicoid is
encoded by the bcd maternal effect
gene in the Drosophilia. The
Homeotic protein bicoid
concentration gradient patterns the
anterior-posterior (A-P) axis during
the Drosophila embryogenesis.
The Bicoid was the first protein
demonstrated to act as a
morphogen. Although the bicoid is
important for the development of
the Drosophila and the other
higher dipterans it is absent from
most of the other insects, where its
role is accomplished by the other
genes. The Bicoid is one of the few
Glossary of Genetics 55

proteins which uses its own extracellular polymers that

homeodomain to bind both the facilitate the attachment and the
DNA and RNA targets to regulate matrix formation, resulting in the
their transcription and the alteration in the phenotype of the
translation, respectively. The organisms with respect to the
nucleic acid-binding homeodomain growth rate and the gene
of the Bicoid has been solved by transcription. The Biofilm
the NMR. The Bicoid contains an formation is an important
arginine-rich motif that is similar to biological concept in the
the one found in the HIV protein environmental microbiology,
REV and is also essential for its where in the microbial cells adapt
nucleic acid binding. The Bicoid to the multicellular lifestyle by
protein gradient formation is one formation of the biofilm during
of the earliest steps in the fruit fly which the bacterial cells are self-
embryo A-P patterning. The proper immobilized in the extracellular
spatial expression of the polymeric matrix. It provides an
downstream genes relies on the insight into the concept of the
robustness of this gradient to the biofilm formation by the
common variations between the microorganisms
embryos, including in the number traditionally/naturally and in the
of maternally-deposited bicoid bioelectrochemical systems. The
mRNAs and in the egg size. The dynamics of the biofilm formation,
Comparative phylogenetic and the changes in the gene expression due
experimental evolution studies to biofilm, the regulatory
suggest that an inherent mechanisms, and the factors
mechanism for the robust associated with the biofilm
generation of a scaled Bicoid formation on the electrode surface
protein gradient. Mechanisms that were known. The importance of
have been proposed to effect this the electrogenic bacteria in the
scaling include the non-linear biofilm formation and the
degradation of the Bicoid,the differences with the nonconducting
nuclear retention as a size- biofilms are also debated. The
dependent regulator of the Bicoid changes in the gene expression in
protein’s effective diffusion the electrogenic model bacteria
coefficient, and scaling of the such as the Shewanella oneidensis
cytoplasmic streaming. MR-1 and the Geobacter
• BIOLFILM FORMATION - The sulfurreducens during the electron
Biofilm formation is a process transfer to the electrode were
whereby the microorganisms specially mentioned.
irreversibly attach to and grow on a
surface and also produce the

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
• BITHORAX COMPLEX - The
Bithorax complex (BX-C) is one of
the two Drosophila melanogaster
homeotic gene complexes, which is
ocated on the right arm of the
chromosome 3. It is responsible for
the the differentiation of the
posterior two-thirds (posterior
thorax and each abdominal
segment) of the fly by the
regulation of the three genes within
the complex i. E the Ultrabithorax
(Ubx), the abdominal A (abd-A),
and the Abdominal B (Abd-B). A
complete deletion of this complex
results in the posterior segments of
the Drosophila embryo becoming
the copies of the second thoracic
segment. The gene complex is
located on the right arm of the
chromosome 3 alongside the other
homeotic gene complex, the
Antennapedia (Antp) complex. It
is over about 300 kb long and
contains about nine distinct cis-
regulatory domains. The three
transcription units, Ubx, abd-A,
and the Abd-B, are spread out
evenly on the complex. A mutant
embryo with a triple knock-out of
the Ubx, abd-A, and Abd-B has a
phenotype that is identical to that
of an embryo with a complete BX-
C deletion, suggesting that the
three transcription units are the
only functional protein-coding
units in the complex. This was
confirmed when the entire complex
was eventually sequenced in the
year 1995. Only about 1.4% of the
© 2022 by JPS Scientific Publications, India
56
BX-C sequence codes for the
proteins.
• BIVALENT ATTACHMENT - A
bivalent is the one pair of the
chromosomes (sister chromatids)
in a tetrad. A tetrad is the
association of a pair of the
homologous chromosomes (4 sister
chromatids) physically held
together by at least one DNA
crossover. This physical
attachment allows for the
alignment and the segregation of
the homologous chromosomes in
the first meiotic division. The
formation of a bivalent occurs
during the first division of the
meiosis. In most of the organisms,
the each replicated chromosome
elicits the formation of the DNA
double-strand breaks during the
leptotene phase. These breaks are
repaired by the homologous
recombination, that uses the
homologous chromosome as a
template for the repair. The search
for the homologous target, helped
by the numerous proteins
collectively referred as the
synaptonemal complex, cause the
two homologs to pair, between the
leptotene and the pachytene phases
of the meiosis I. The Resolution of
the DNA recombination
intermediate into a crossover
exchanges the DNA segments
between the two homologous
chromosomes at a site called a
chiasma. This physical strand
exchange and the cohesion
between the sister chromatids
Glossary of Genetics
along the each chromosome ensure
robust pairing of the homologs in
the diplotene phase. The structure,
visible by microscopy, is called as a
bivalent.
• BLEOMYCIN - The Bleomycin is
a medication which is used to treat
the cancer. This includes the
Hodgkin’s lymphoma, the non-
Hodgkin’s lymphoma, the
testicular cancer, the ovarian
cancer, and the cervical cancer
among the others. It is typically
used with the other cancer
medications, it can be given
intravenously, by the injection into
a muscle or under the skin. It may
also be administered inside the
chest to help prevent the recurrence
of a fluid around the lung due to
the cancer however the talc is
better for this. The Common side
effects include the fever, weight
loss, vomiting, and the rash. A
severe type of the anaphylaxis may
also occur. It may also cause the
inflammation of the lungs that can
result in the lung scarring. The
Chest X-rays every couple of the
weeks are recommended to check
for this. The Bleomycin may cause
harm to the baby if used during the
pregnancy. It is believed to
primarily work by the preventing
the synthesis of the DNA. The
Bleomycin was discovered in the
year 1962. It is on the World
Health Organization’s List of
Essential Medicines.It is also
available as a generic medication.It
© 2022 by JPS Scientific Publications, India
57
is made by the bacterium
Streptomyces verticillus.
• BmrR - The Bovine
papillomaviruses (BPV) are a
paraphyletic group of the DNA
viruses of the subfamily
Firstpapillomavirinae of the
Papillomaviridae that are common
in the cattle. All the BPVs have a
circular double-stranded DNA
genome. The Infection causes the
warts i.e the papillomas and the
fibropapillomas of the skin and the
alimentary tract, and more rarely
cancers of the alimentary tract and
the urinary bladder. They are also
thought to cause the skin tumour
equine sarcoid in the horses and
the donkeys. The BPVs have been
used as a model for studying the
papillomavirus molecular biology
and also for dissecting the
mechanisms by which this group of
the viruses cause cancer. The
BPVs are the small non-enveloped
viruses with an icosahedral capsid
around 50–60 nm in the diameter.
The capsid is formed of the L1 and
L2 structural proteins, with the L1
C-terminus is exposed. All the
BPVs have a circular double-
stranded DNA genome of about
7.3–8.0 kb. The genetic
organisation of those BPVs which
have been sequenced is broadly
similar to the other
papillomaviruses. The open
reading frames (ORFs) are all
located on the one strand, and are
divided into the early and the late
regions. The early region encodes
Glossary of Genetics
the nonstructural proteins of E1 to
E7. There are the three viral
oncoproteins, such as the E5, E6
and the E7, the BPVs of the
Xipapillomavirus group lack the
E6 oncoprotiens. The late region
encodes the sructural proteins L1
and L2. There is also a non-coding
long control region.
• BBP - The yeast splicing factor
BBP which is termed as the
branchpoint bridging protein
jnteracts directly with the pre-
mRNA at or very near the highly
conserved branchpoint sequence
which is UACUAAC within the
commitment complex. It is known
that the recombinant protein
recognizes the UACUAAC
sequence. Therefore, the BBP is
also an acronym for the
branchpoint binding protein. The
mammalian splicing factor SF1 is a
BBP ortholog (mBBP) and an E
complex component, and also has
the branchpoint sequence
specificity. The relative
conservation of this region in the
yeast and in the mammals
correlates well with the RNA-
binding differences between BBP
and mBBP, suggesting that the
BBP contributes to the branchpoint
sequence definition in both the
systems.
• BRCA2 - The BRCA2 is gene
which provides the instructions for
making a protein that acts as a
tumor suppressor. The Tumor
suppressor proteins helps to
prevent the cells from growing and
© 2022 by JPS Scientific Publications, India
58
dividing too rapidly or in an very
uncontrolled way. The BRCA2
protein is also involved in the
repairing damaged DNA. In the
nucleus of the many types of the
normal cells, the BRCA2 protein
interacts with the several other
proteins to mend the breaks in the
DNA. These breaks can be caused
by the natural and the medical
radiation or the other
environmental exposures, and they
also occur when the chromosomes
exchange genetic material in
preparation for the cell division.
By helping to repair the DNA, the
BRCA2 protein plays a very
critical role in maintaining the
stability of a cell’s genetic
information. The Researchers
suspect that the BRCA2 protein
has the additional functions within
the cells. For example, the protein
may also helps to regulate the
cytokinesis, which is the step in the
cell division when the fluid
surrounding the nucleus (the
cytoplasm) divides to form the two
separate cells. Researchers are
investigating the protein’s other
potential activities.
• BROMODOMAINS - A
bromodomain is an approximately
about 110 amino acid protein
domain that recognizes the
acetylated lysine residues, such as
those on the N-terminal tails of the
histones. The Bromodomains, as
the “readers” of the lysine
acetylation, are responsible in the
transducing the signal carried by
Glossary of Genetics 59

the acetylated lysine residues and chromosomal duplications or The

translating it into the various rearrangements that suppress the
normal or the abnormal crossing over. In addition, it also
phenotypes. Their affinity is define lethal as any mutation that
higher for the regions where the blocks the survival or the
multiple acetylation sites exist in reproduction. Phenotypes
the proximity. This recognition is associated with lethal mutations in
often a prerequisite for the protein- the Caenorhabditis elegans range
histone association and the from the egg or the larval lethality
chromatin remodeling. The to the adult sterility and the
domain itself adopts an all-α maternal effect lethality, and can
protein fold, a bundle of the four include the conditional effects such
alpha helices each separated by the as the temperature sensitivity. The
loop regions of the variable lengths number of the essential genes in
that form a hydrophobic pocket the C. Elegans (those identified by
that recognizes the acetyl lysine. lethal mutations) may range as
The role of the bromodomains in high as 7000 according to the
the translating a deregulated cell genetic estimates. Thus, the lethal
acetylome into the disease mutations constitute a rich source
phenotypes was recently unveiled of the information about the basic
by the development of the small biological processes in this
molecule bromodomain inhibitors. nematode. The balancer
This breakthrough discovery chromosomes are an essential and
highlighted that the bromodomain- the powerful part of a fly
containing proteins as key players geneticist’s toolbox. They are used
in the field of cancer biology, as to maintain the deleterious
well as the inflammation and the mutations in the stable stocks as
remyelination in the multiple well as to prevent the
sclerosis. The Small molecule recombination and follow the
inhibitors of the non-BET chromosomes in the genetic
bromodomain proteins such as the mating schemes.
BRD7 and the BRD9 have also
been developed.
• BALANCER - The Genetic
balancers are the genetic constructs
or the chromosomal
rearrangements that allow the
lethal or the sterile mutations to be
stably maintained in the
heterozygotes. The term balancer
primarily to refer to the

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
C
• CHROMODOMAIN - A
chromodomain which is also
known as the chromatin
organization modifier is a protein
structural domain of about 40–50
amino acid residues commonly
found in the proteins associated
with the remodeling and the
manipulation of the chromatin.
The domain is highly conserved
among both the plants and the
animals, and is represented in a
large number of the different
proteins in many of the genomes,
such as that of the mouse. Some of
the chromodomain-containing
genes have multiple alternative
splicing isoforms that omit the
chromodomain entirely. In the
mammals, the chromodomain-
containing proteins are responsible
for the aspects of the gene
regulation related to the chromatin
remodeling and formation of the
heterochromatin regions. The
chromodomain-containing proteins
also bind the methylated histones
and appear in the RNA-induced
transcriptional silencing complex.
In the histone modifications, the
chromodomains are very
conserved. They function by
identifying and binding to the
methylated lysine residues that
exist on the surface of the
chromatin proteins and thereby
regulate the gene transcription.
© 2022 by JPS Scientific Publications, India
60
•
CHROMOBACTERIUM - The
Chromosome mapping is a
technique which is used in the
autosomal DNA testing which
allows the test to determine which
segments of the DNA came from
the which ancestor. In order to
map the DNA segments on the
specific chromosomes it is
necessary to test a number of the
close family relatives. Ideally one
should test the both parents, one of
their children, and a number of the
first to the third cousins on both
the maternal and the paternal sides
of the family. Not everyone has
the close relatives available for the
testing or has the funds to pay for
the such testing. Caution should be
exercised when attempting to map
the smaller segments, and
particularly segments under the 15
cM because of the high false
positive rate.
• CHROMOSOME
CONFORMATION CAPTURES
- The Chromosome conformation
capture techniques which is often
abbreviated to the 3C technologies
or the 3C-based methods are a set
of the molecular biology methods
used to analyze the spatial
organization of chromatin in a cell.
These methods quantify the
number of the interactions between
genomic loci that are nearby in the
3-D space, but may be separated by
the many nucleotides in the linear
genome. Such interactions may
result from the biological
functions, such as the promoter-
Glossary of Genetics
enhancer interactions, or from the
random polymer looping, where
the undirected physical motion of
the chromatin causes the loci to
collide. The Interaction
frequencies may be analyzed
directly, or they may be converted
to the distances and used to
reconstruct the 3-D structures. The
chief difference between the 3C-
based methods is their scope. For
example, when using the PCR to
detect the interaction in a 3C
experiment, the interactions
between the two specific fragments
are quantified. In the contrast, Hi-
C quantifies interactions between
all the possible pairs of the
fragments simultaneously. Deep
sequencing of the material
produced by the 3C also produces
the genome-wide interactions
maps.
• CONDENSATION - The
Condensation is the change of the
state of the matter from the gas
phase into the liquid phase, and is
the reverse of the vaporization. The
word most often refers to the water
cycle. It can also be defined as the
change in the state of the water
vapor to the liquid water when in
contact with a liquid or the solid
surface or the cloud condensation
nuclei within the atmosphere.
When the transition happens from
the gaseous phase into the solid
phase directly, the change is called
as the deposition. It is initiated by
the formation of the
atomic/molecular clusters of that
© 2022 by JPS Scientific Publications, India
61
species within its gaseous volume
like rain drop or the snow flake
formation within the clouds or at
the contact between the such
gaseous phase and a liquid or the
solid surface. In the clouds, this
can be catalyzed by the water-
nucleating proteins, produced by
the atmospheric microbes, which
are capable of the binding gaseous
or the liquid water molecules.
• COMPLEMENTARY NATURE
OF G:C - In the field of molecular
biology, the complementarity
describes a relationship between th
two structures each following the
lock-and-key principle. In nature
the complementarity is the base
principle of the DNA replication
and the transcription as it is a
property shared between the two
DNA or RNA sequences, such that
when they are aligned antiparallel
to the each other, the nucleotide
bases at the each position in the
sequences will be complementary,
much like looking like in the
mirror and seeing the reverse of the
things. This complementary base
pairing allows the cells to copy the
information from one generation to
the another and even find and
repair the damage to the
information stored in the
sequences. The Complementarity
of the DNA strands in a double
helix make it possible to use one of
the strand as a template to
construct the other. This principle
plays an important role in the
Glossary of Genetics
DNA replication, setting the
foundation of the heredity by
explaining how the genetic
information can be passed down to
the next generation.
Complementarity is also utilized in
the DNA transcription, which
generates an RNA strand from a
DNA template. In addition to this,
the human immunodeficiency
virus, a single-stranded RNA virus,
also encodes an RNA-dependent
DNA polymerase (reverse
transcriptase) that uses the
complementarity to catalyze the
genome replication. The reverse
transcriptase can also switch
between the two parental RNA
genomes by copy-choice
recombination during the
replication.
• CO COMPLEMENT - The
Complement component 9 (C9) is
a MACPF protein which is
involved in the complement
system, which is a part of the
innate immune system.Once it is
activated, about 12-18 molecules of
the C9 polymerize to form the
pores in the target cell membranes,
causing the lysis and the cell death.
The C9 is one of the member of the
complement membrane attack
complex (MAC), which also
includes the complement
components such as C5b, C6, C7
and the C8. The formation of the
MAC occurs through the three
distinct pathways i.e the classical,
alternative, and the lectin
pathways. The Pore formation by
© 2022 by JPS Scientific Publications, India
62
the C9 is an important way that the
bacterial cells are killed during an
infection, and the target cell is
often covered in the multiple
MACs. The clinical impact of a
deficiency in C9 is an infection
with the gram-negative bacterium
known as Neisseria meningitidis.
The MAC formation starts with
the assembly of a tetrameric
complex with the complement
components such as the C6, C7,
C8, and the C5b. The final step of
the MAC on the target cell surfaces
involves the polymerization of the
C9 molecules bound to the C5b8
forming the C5b-9. The C9
molecules allow the cylindrical,
asymmetrical transmembrane
pores to form. The overall complex
belongs to the MAC/perforin-like
(MACPF)/CDC superfamily. The
pore formation involves binding
the of the C9 molecules to the
target membrane, membrane
molecules forming a pre-pore
shape, and conformational change
in the TMH1, the first
transmembrane region, and the
TMH2, the second transmembrane
region. The formations of the pores
leads to the killing of the foreign
pathogens and the infected host
cells.
• CAENORHABDITIS ELEGANS
- The Caenorhabditis elegans is a
free-living transparent nematode
which is about 1 mm in the length
that lives in the temperate soil
environments. It is the special type
species of its genus. The name is a
Glossary of Genetics
blend of the Greek caeno- (recent),
rhabditis (rod-like) and the Latin
elegans (elegant). The C. Elegans is
an unsegmented pseudocoelomate
and lacks the respiratory or the
circulatory systems. Most of these
nematodes are the hermaphrodites
and a few are the males. The Males
have a specialised tails for the
mating that include the spicules.
Using the C. Elegans as a model
organism for the investigation of
the primarily of neural
development in the animals. It is
one of the most simplest organisms
with the presence of the nervous
system. The neurons do not fire the
action potentials, and do not
express any voltage-gated sodium
channels. In the hermaphrodite,
this system comprises about 302
neurons the pattern of which has
been comprehensively mapped, in
what is known as a connectome,
and shown to be a very small-
world network.
• CELL DEATH PATHWAYS - In
the multicellular organisms, the
cell death is a very critical and
active process that maintains the
tissue homeostasis and eliminates
the potentially harmful cells. There
are three major types of the
morphologically distinct cell death,
1) apoptosis i.e type I cell death, 2)
autophagic cell death i.e type II,
and 3) necrosis i.e type III. All the
types three can be executed
through the distinct, and
sometimes through the
overlapping, signaling pathways
© 2022 by JPS Scientific Publications, India
63
that are engaged in response to the
specific stimuli. The Apoptosis is
triggered when the cell-surface
death receptors such as the Fas are
bound by their ligands i.e the
extrinsic pathway or when the
Bcl2-family proapoptotic proteins
cause the permeabilization of the
mitochondrial outer membrane i.e
the intrinsic pathway. Both of the
pathways converge on the
activation of the caspase protease
family, which is ultimately
responsible for the dismantling of
the cell. The Autophagy defines a
catabolic process in which the parts
of the cytosol and specific
organelles are engulfed by a
double-membrane structure, which
known as the autophagosome, and
eventually it is degraded. The
Autophagy is mostly a survival
mechanism; nevertheless, there are
a very few examples of autophagic
cell death in which the components
of the autophagic signaling
pathway actively promote cell
death. The Necrotic cell death is
characterized by the rapid loss of
the plasma membrane integrity.
This form of the cell death can be
result from the active signaling
pathways, the best characterized of
which is dependent on the activity
of the protein kinase RIP3.
• COOPERATIVE BINDING -
The Cooperative binding occurs in
the binding systems containing
more than one type, or the species,
of the molecule and in which one
Glossary of Genetics
of the partners is not the mono-
valent and can bind more than one
of the molecule of the other
species. In a system where one
molecule of the species A can bind
to the molecules of the species B.
The Species A is called the receptor
and the species B is called as the
ligand. The Binding can be
considered as the “cooperative” if
the binding of the first molecule of
the B to A changes the binding
affinity of the second B molecule,
making it more or less likely to be
bind. In the other words, the
binding of the B molecules to the
different sites on A do not
constitute mutually the
independent events. The
Cooperativity can be positive or
negative. The Cooperative binding
is observed in many biopolymers,
including the proteins and the
nucleic acids. The Cooperative
binding has been shown to be the
mechanism of the underlying a
large range of biochemical and the
physiological processes. In a living
cell, the ultrasensitive modules are
embedded in a bigger network with
the upstream and the downstream
components. This components can
may constrain the range of inputs
that the module will receive as well
as the range of the module’s
outputs that network will be able to
detect. The sensitivity of a modular
system is affected by these
restrictions. The dynamic range of
the limitations imposed by the
downstream components can
© 2022 by JPS Scientific Publications, India
64
produce the effective sensitivities
much larger than that of the
original module when considered
in the isolation.
• C11 PROTEIN - The cII also
known as the transcriptional
activator II which is a DNA-
binding protein and also an
important transcription factor in
the life cycle of the lambda phage.
It is encoded in the lambda phage
genome by the 291 base pair cII
gene. The cII plays a key role in
determining whether the
bacteriophage will incorporate its
genome into its host and lie
dormant i.e lysogeny, or replicate
and kill the host i.e lysis.
• CHARGAFF’S RULE - The
Chargaff’s rules state that the DNA
from any of the species of any
organism should have a 1:1
stoichiometric ratio of the purine
and the pyrimidine bases and,
more specifically, that the amount
of the guanine should be equal to
the cytosine and the amount of the
adenine should be equal to the
thymine. This pattern is found in
the both strands of the DNA.
• CO-OPERATIVITY - The
Cooperativity is a phenomenon
which is displayed by the systems
involving the identical or the near-
identical elements which acts
dependently of the each other
relative to a hypothetical standard
of the non-interacting system in
which the individual elements are
acting independently. It plays an
Glossary of Genetics
important role in the DNA bounds
to the proteins.
• CIRCULAR CHROMOSOME -
A circular chromosome is a
chromosome which is found in the
bacteria, archaea, mitochondria,
and chloroplasts, in the form of a
molecule of circular DNA, unlike
the linear chromosome which is
present in most of the eukaryotes.
The Cells that do contain
chromosomes with the DNA ends,
or the telomeres most of the
eukaryotes, have acquired the
elaborate mechanisms to overcome
these challenges. However, a
circular chromosome can also
provide the other challenges for the
cells. After the replication, the two
progeny circular chromosomes can
also sometimes remain in
interlinked or tangled, and they
must be resolved so that the each
cell inherits one complete copy of
the chromosome during the cell
division process. The
Chromosome replication proceeds
in the three major stages i.e
initiation, elongation and the
termination. The initiation stage
starts with the ordered assembly of
the “initiator” proteins at the origin
region of the chromosome, which
is called as the oriC. These
assembly stages are regulated to
ensure that the chromosome
replication occurs only once in the
each cell cycle. During the
elongation phase of the replication,
the enzymes that were assembled
at the oriC region during the
© 2022 by JPS Scientific Publications, India
65
initiation proceed along the each
arm (“replichore”) of the
chromosome, in the opposite
directions away from the oriC,
replicating the DNA to create the
two identical copies. This process
is known as the bidirectional
replication which is unique. The
entire assembly of the molecules
involved in the DNA replication
on each arm is called a “replisome.
At the forefront of the replisome is
a enzyme known as DNA helicase
that unwinds the two strands of the
DNA, creating a moving
“replication fork”. The two
unwound single strands of DNA
serve as the templates for the DNA
polymerase, which moves with the
helicase together with other
proteins to synthesise a
complementary copy of the each
strand. In this way, the two
identical copies of the original
DNA are created.
• CONJUGATION - The Bacterial
conjugation is the process in the
which transfer of the genetic
material between the bacterial cells
by a method known as the direct
cell-to-cell contact or by a bridge-
like connection between the two
cells. This takes place through a
pilus or a opening. It is a
parasexual mode of reproduction
in the bacteria. It is a mechanism
of the horizontal gene transfer as
are transformation and
transduction although these two
other mechanisms do not involve
the cell-to-cell contact. The
Glossary of Genetics
Classical example is of E.coli
bacterial conjugation which is
often regarded as the bacterial
equivalent of the sexual
reproduction or mating since it
involves the exchange of the
genetic material. However, it is not
sexual reproduction, since there is
no exchange of the gamete occurs,
and indeed no generation of a new
organism is produced, instead an
existing organism is transformed.
During the classical E.Coli
conjugation the donor cell provides
a conjugative or the mobilizable
genetic element that is most often a
plasmid or a transposon. Most
conjugative plasmids have systems
that ensuring that the recipient cell
does not already contain a similar
element. The genetic information
which is transferred is often
considered as beneficial to the
recipient. Benefits may include in
the forms of the antibiotic
resistance, xenobiotic tolerance or
the ability to use the new
metabolites.
• Cl GENE - The cI is a
transcription inhibitor of the
bacteriophage Lambda. It is also
known as the Lambda Repressor,
cI is also responsible for
maintaining the lysogenic life cycle
of the phage Lambda. This is
achieved when the two repressor
dimers bind cooperatively to the
adjacent operator sites on the
DNA. The Bacterial cells
harboring a lysogenic lambda
phage are also immune to the
© 2022 by JPS Scientific Publications, India
66
further infection by the lambda.
The cI repressor protein inhibits
the lytic development of any of the
additional infecting phage
particles. The region of the genome
that codes for the cI repressor
protein is importantly known as
the immunity region. It binds the
DNA in the helix-turn-helix
binding motif. It regulates the
transcription process of the cI
protein. The life cycle of the
lambda phages is controlled by the
cI and Cro proteins. The lambda
phage will remain in the lysogenic
state if the cI proteins predominate,
but will be transformed into the
lytic cycle if the cro proteins
predominate. The cI dimer may
bind to any of the three operators
i.e, OR1, OR2, and OR3, in the
ascending order OR1 > OR2 >
OR3. The Binding of a cI dimer to
OR1 enhances the binding of a
second cI dimer to the OR2, an
effect which is called as the
cooperativity. Thus, the OR1 and
the OR2 are almost always
simultaneously occupied by the cI.
Upon the formation of the
octamer, the cI dimers can may
cooperatively bind to the OL3 and
OR3, repressing the transcription
of the cI. This autonegative
regulation ensures a stable
minimum concentration of the
repressor molecule and, should
SOS signals arise, allows for the
more efficient prophage induction.
Glossary of Genetics
• CRO REPRESSOR - The Cro
repressor family is a family of the
repressor proteins in which is
found in the bacteriophage lambda
that includes the Cro repressor.
The lambda phage Cro repressor
binds to the DNA as a highly
flexible dimer structure. The crystal
structure of the lambda phage Cro
repressor reveals a HTH DNA-
binding protein with an alpha/beta
fold that differs from the other Cro
family members, possibly by an
evolutionary fold change method.
Most of the Cro proteins, such as
the Enterobacteria phage P22 Cro
and Bacteriophage 434 Cro, have
an all-alpha structure that is
thought to be ancestral to the
lambda Cro, where the fourth and
the fifth helices are replaced by a
beta-sheet, possibly as a result of
the secondary structure switching
rather than by nonhomologous
replacement. The Cro protein is an
effective and the specific repressor
of the RNA synthesis from the N
and the cro genes thus the Cro is
an autorepressor which regulates
its own synthesis. The Cro
repressor also serves as an
transcriptional activator of the
LEE in EHEC process during the
in vitro growth. The Cro repressor
also activates the expression of the
LEE gene espA in the C.
• CAF 1 - The CAF stands for the
Chromatin Assembly Factor 1
(CAF-1) which facilitates the
establishment of the facultative
heterochromatin during the
© 2022 by JPS Scientific Publications, India
67
pluripotency exit. During the
process of the chromatin
replication, the nucleosomes are
the first disassembled to allow the
DNA replication machinery to
access the DNA. Following the
DNA replication, the newly
synthesized DNA is assembled
into the nucleosomes in a process
that is tightly coupled to the
ongoing DNA replication. This
DNA replication-coupled the
nucleosome assembly is regulated
by the histone chaperones
including the Chromatin Assembly
Factor 1 (CAF-1), the classical
chaperone for the histones is H3-
H4. The CAF-1 consists of the
three subunits which are p150, p60
and the p48. The CAF-1 is
recruited to the DNA replication
forks through its interaction with
the proliferating cell nuclear
antigen (PCNA), the ring-shaped
homotrimer serving as the sliding
clamp for the DNA polymerases.
The CAF-1 interacts with the
PCNA mainly through the CAF-1
p150 subunit. For the instance, the
mutations in the CAF-1 and the
PCNA lead to the defects in the
transcriptional silencing at the
heterochromatin in the yeast. In
the mammalian cells, the CAF-1
interacts with the heterochromatin
protein 1 i.e HP1, and depletion of
the p150 and p60 subunits results
in the impairment of the
pericentromeric heterochromatin
centers in the mouse cells. In the
plants, the CAF-1 interacts with
Glossary of Genetics
the PRC2, the H3K27
methyltransferase, and it has been
proposed that the PRC2–CAF-1
interaction helps in maintaining
the H3K27me3-mediated silent
chromatin during the DNA
replication.
• CAGE - The Cap analysis gene
[removed]CAGE) is a gene
expression technique which is used
in the molecular biology to
produce a snapshot of the 5′ end of
the messenger RNA population in
a biological sample i.e the
transcriptome. The small fragments
from the very beginnings of the
mRNAs i.e 5’ ends of the capped
transcripts, are extracted, reverse-
transcribed to the cDNA, PCR
amplified (if needed) and then
sequenced. The CAGE was first
published by the Hayashizaki,
Carninci and the co-workers in the
year 2003. The CAGE has been
extensively used within the
FANTOM research projects. The
output of the CAGE is a set of the
short nucleotide sequences which
is often called as the tags in
analogy to the expressed sequence
tags with their observed counts.
The Copy numbers of the CAGE
tags provide a digital quantification
of the RNA transcript abundances
in the biological samples. Using a
reference genome, a researcher can
usually determine, with some
confidence, the original mRNA the
tag was extracted from. The
CAGE tags tend to start with an
extra guanine (G) that is not
© 2022 by JPS Scientific Publications, India
68
encoded in the genome, which is
attributed to the template-free 5′-
extension during the first-strand of
the cDNA synthesis or the reverse-
transcription of the cap itself.
When not corrected, this can
induce the erroneous mapping of
the CAGE tags, for instance to the
nontranscribed pseudogenes.On
the other hand, this addition of the
Gs was also utilised as a signal to
filter the more reliable TSS peaks.
• CHEMOTHERAPEUTIC
AGENTS - The Chemotherapeutic
agents, which is also referred to as
the antineoplastic agents, are used
to directly or indirectly inhibit the
uncontrolled growth and the
proliferation of the cancer cells.
They are classified according to
their mechanism of the action and
include the alkylating agents, the
antimetabolites, topoisomerase
inhibitors, antibiotics, mitotic
inhibitors, and the protein kinase
inhibitors. The Chemotherapy is
associated with a range of the
adverse effects such as the nausea,
vomiting, immunosuppression,
and the impaired growth of the
healthy cells, and some of the
agents increase the risk of the
secondary neoplasm development.
For some the chemotherapeutic
agents, specific detoxifying agents
can be administered to avert the
preventable side effects such as the
leucovorin after the application of
the methotrexate, after the
cyclophosphamide application.
The Chemotherapeutic agents are
Glossary of Genetics
the most active on the cells with a
high growth fraction, i.e. the cells
actively undergoing division such
as including the normal cells, such
as the epithelial or the bone
marrow cells, as well as the cancer
cells. The log-kill hypothesis is a
mathematical model of the
chemotherapeutic agent action,
according to the which a given
dose of a certain chemotherapeutic
agent eliminates a constant fraction
of the cancer cells regardless of the
tumor size.
• CANDIDA ALBICANS - The
Candida albicans is an
opportunistic pathogenic yeast that
is a most common member of the
human gut flora. It can also survive
outside the human body. It is
detected in the gastrointestinal
tract and in the mouth in about 40–
60% of the healthy adults. It is
usually a commensal organism, but
it can become the pathogenic in the
immunocompromised individuals
under a variety of the conditions. It
is one of the few species of the
genus Candida that causes the
human infection candidiasis,
which results from an overgrowth
of the fungus. The Candidiasis is,
for example, often observed in the
HIV-infected patients. The C.
Albicans is the most common
fungal species isolated from the
biofilms either formed on the
(permanent) implanted medical
devices or on human tissue. The C.
Albicans, C. Tropicalis, C tye .
parapsilosis, and the C. Glabrata
© 2022 by JPS Scientific Publications, India
69
are together responsible for the 50–
90% of all cases of the candidiasis
in the umans. A mortality rate of
about 40% has been reported for
the patients with the systemic
candidiasis due to the C. Albicans.
By one of the estimate, the invasive
candidiasis contracted in a hospital
causes around 2,800 to 11,200
deaths yearly in the US.
Nevertheless, these numbers may
not truly reflect the true extent of
damage this organism causes,
given new studies indicating that
the C. Albicans can cross the
blood–brain barrier in the mice.
• CREB - The CREB-TF (CREB,
cAMP response element-binding
protein) is a cellular transcription
factor. It binds to the certain DNA
sequences called as the cAMP
response elements (CRE), thereby
increasing or decreasing the
transcription of the genes. The
CREB was first described in the
year 1987 as a cAMP-responsive
transcription factor regulating the
somatostatin gene. The Genes
whose transcription is regulated by
the CREB include: c-fos, BDNF,
tyrosine hydroxylase, numerous
neuropeptides (such as
somatostatin, enkephalin, VGF,
corticotropin-releasing hormone),
and the genes involved in the
mammalian circadian clock
(PER1, PER2). The CREB is
closely related in the structure and
function to the CREM (cAMP
response element modulator) and
the ATF-1 (activating transcription
Glossary of Genetics
factor-1) proteins. The CREB
proteins are expressed in many
animals, including the humans.
The CREB has a well-documented
role in neuronal plasticity and
long-term memory formation in
the brain and has been shown to be
integral in the formation of the
spatial memory. The CREB
downregulation is implicated in the
pathology of the Alzheimer's
disease and increasing the
expression of the CREB is being
considered as a possible
therapeutic target for the
Alzheimer's disease. THE CREB
also has a role in the
photoentrainment in mammals.
• CREM - The cAMP responsive
element modulator is a protein that
in the humans is encoded by the
CREM gene, and it belongs to the
cAMP-responsive element binding
protein family. It has multiple
isoforms, which act either as the
repressors or the activators. The
CREB family is important for in
regulating transcription in response
to the various stresses, metabolic
and the developmental signals. The
CREM transcription factors also
play an important role in many of
the physiological systems, such as
the cardiac function, circadian
rhythms locomotion and the
spermatogenesis. This gene
encodes a bZIP transcription factor
that binds to the cAMP responsive
element found in many of the viral
and the cellular promoters. It is an
important component of the
© 2022 by JPS Scientific Publications, India
70
cAMP-mediated signal
transduction during the
spermatogenetic cycle, as well as
the other complex processes.
Alternative promoter and the
translation initiation site usage
allows this gene to exert the spatial
and the temporal specificity to the
cAMP responsiveness. Multiple
alternatively spliced transcript
variants encoding the several
different isoforms have been found
for this gene, with some of them
functioning as the activators and
some as the repressors of the
transcription.
• COMBINATORIAL CONTROL
- The Combinatorial gene
regulation provides a mechanism
by which the relatively small
numbers of the transcription
factors can control the expression
of a much larger number of the
genes with the finely tuned
temporal and the spatial patterns.
This is achieved by the
transcription factors assembling
into the complexes in a
combinatorial fashion,
exponentially increasing the
number of genes that they can
target. Such an arrangement also
increases the specificity and affinity
for the cis-regulatory sequences
required for the accurate target
gene expression. This is
Superimposed on this transcription
factor combinatorial arrangement
is the increasing realization that the
histone modification marks expand
the regulatory information, which
Glossary of Genetics 71

is interpreted by the histone readers expression system CAP-T was

and writers that are part of the developed. The CAP-T cells are
regulatory apparatus. The based on the original CAP cells
perspective of the plant and are additionally express as the
combinatorial gene regulation, the large T antigen of the simian virus
providing examples of the different 40 (SV40). The CAP-T cells
regulatory solutions and present a highly efficient transient
comparing them to the other expression system for enabling the
metazoans. It also provides a generation of the mg amounts of
mechanism to explain the the protein of interest for the early
complexity of the gene expression research and the development
patterns. A TF may be part of the within only two weeks from the
different protein complexes that gene to the product. Furthermore,
determine the different types of the the CAP-T cell produced the
regulation of the different targets. proteins whichs shows fully human
Therefore, a composition of a posttranslational modification
protein complex and not a TF per pattern, which was also observed
se, represents an input the leading for the original human CAP cells,
to the distinct gene expression the CAP-T cells were derived. The
patterns as an output. CAP technology based on the
• CAP CELLS - CAP which is CAP-T cells for the transient
termed as the CEVEC’s transfection and the CAP cells for
Amniocyte Production cells are an the stable protein production,
immortalized cell line based on the therefore provides a unique system
primary human amniocytes. They in which the whole process from
were generated by the transfection the early research to the production
of these primary cells with a vector of the therapeutic proteins can be
containing the functions E1 and run through with the same cell
pIX of the adenovirus 5. The CAP • CAPPING ENZYME - A capping
cells allow for the competitive enzyme (CE) is an enzyme that
stable production of the catalyzes the attachment of the 5’
recombinant proteins with the cap to the messenger RNA
excellent biologic activity and the molecules that are in the process of
therapeutic efficacy as a result of being synthesized in the cell
the authentic human nucleus during the first stages of
posttranslational modification. In the gene expression. The addition
order to gain the access to the of the cap occurs in a co-
benefits of the CAP technology transcriptionally manner, after the
also for early research, the target growing of the RNA molecule that
evaluation or the assay contains as little as about 25
development, the transient nucleotides. The enzymatic

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
reaction is catalyzed specifically by
the phosphorylated carboxyl-
terminal domain (CTD) of the
RNA polymerase II. The 5’ cap is
therefore specific to the RNAs
synthesized by this polymerase
rather than those synthesized by
the RNA polymerase I or the RNA
polymerase III. The Pre-mRNA
undergoes a series of modifications
– such as the 5’ capping, splicing
and the 3’ polyadenylation before
becoming the mature mRNA that
exits the nucleus to be translated
into the functional proteins and
capping of the 5’ end is the first of
the these modifications. The Three
enzymes, e RNA triphosphatase,
guanylyltransferase (or CE), and
the methyltransferase are involved
in the addition of the methylated 5’
cap to the mRNA.
• CA REPEATS - The CA
REPEATS are also termed as the
Microsatellite. They are a short
sequence of the DNA consisting of
the multiple repetitions of a set of
two to nine base pairs, used as a
genetic marker when individuals
differ in the number of the
repetitions. It is a highly
polymorphic segment of the DNA
composed of the repetitive
stretches of short sequences of 2–6
base pairs of the DNA, which serve
as genetic markers to the track
inheritance in the families. The
Microsatellites include the
dinucleotides, trinucleotides and
the tetranucleotides, repeated in
the tandem arrays throughout a
© 2022 by JPS Scientific Publications, India
72
genome. The human genome has a
50–100,000 microsatellite loci. The
most laborious part of developing
the (CA)n microsatellite repeats as
the genetic markers is constructing
the DNA clones to permit the
determination of sequences
flanking the microsatellites. When
the cosmids or the large-insert
phage clones are used as the
primary sources of the (CA)n
repeat markers, they have
traditionally been subcloned into
the plasmid vectors such as the
pUC18 or the M13 mp 18/19
cloning vectors to obtain the
fragments of suitable size for the
DNA sequencing. This unit
presents an alternative approach
whereby a set of the degenerate
sequencing primers that anneal
directly to the (CA)n
microsatellites can be used to
determine the sequences that are
inaccessible with the vector-derived
primers. Because the primers
anneal to the repeat and not to the
vector, they can be used with the
subclones containing inserts of the
several kilobases and should, in
theory, always give the sequence in
the regions directly flanking the
repeat. Degeneracy at the 3 end of
each of these primers prevents the
elongation of the primers that have
annealed out-of-the-register. The
most laborious part of developing
the (CA)n microsatellite repeats as
genetic markers is constructing the
DNA clones to permit.
Glossary of Genetics
• CAS PROTEINS - The clustered
regularly interspaced short
palindromic repeats (CRISPR) or
the Cas (CRISPR-associated
proteins) is a prokaryotic adaptive
immune system that is represented
in most of the archaea and many
Of the bacteria. Among the
currently known as the prokaryotic
defense systems, the CRISPR-Cas
genomic loci show the
unprecedented complexity and the
diversity. The Classification of the
CRISPR-Cas variants that would
capture their evolutionary
relationships to the maximum
possible extent is essential for the
comparative genomic and the
functional characterization of this
theoretically and practically
important for the system of
adaptive immunity. To this end, a
multipronged approach has been
developed that combines the
phylogenetic analysis of the
conserved Cas proteins with the
comparison of the gene repertoires
and the arrangements in the
CRISPR-Cas loci. This approach
led to the current classification of
the CRISPR-Cas systems into the
three distinct types and the ten
subtypes for each of the which
signature genes that have been
identified. Moreover, most of the
cas genes evolve very rapidly,
complicating the family assignment
for many of the Cas proteins and
the use of the family profiles for the
recognition of the CRISPR-Cas
subtype signatures. Further
© 2022 by JPS Scientific Publications, India
73
progress in the comparative
analysis of the CRISPR-Cas
systems requires the integration of
the most sensitive sequence
comparison tools, protein structure
comparison, and the refined
approaches for the comparison of
the gene neighbourhoods.
• CASSETTE EXON SPLICING -
The Cassette exon splicing, which
is also known as the exon skipping,
is the most prevalent form of the
alternative splicing in the human
genome and accounts for around
50 to 60 percent of all the
alternatively spliced events. A
cassette exon is a splicing event in
which an intervening exon
between the two other exons from
the mature mRNA sequence can
be either included or skipped in
order to generate the two distinct
protein isoforms. A number of the
recent discoveries have concluded
that the cassette exon is closely
associated with a broad range of
the human diseases such as the
renal cancer, the neuromuscular
diseases, and the hearing loss. The
Cassette exons have also been
employed as a therapeutic strategy
for producing the required proteins
for the genetic diseases such as the
congenital myasthenia syndrome.
Despite its importance, because of
its complexity, the cassette exon
mechanism is not fully understood,
and because of the limited
availability of accurate
computational tools, genome-wide
Glossary of Genetics
detection of the cassette exons
remains a major challenge.
• CATENATION - The word
catenation is the bonding of the
atoms of the same element into a
series, which is called as the chain.
A chain or a ring shape may be
open if its ends are not bonded to
each other i.e an open-chain
compound, or closed if they are
bonded in a ring i.e a cyclic
compound. The words to catenate
and catenation reflect the Latin
root catena, which is called as the
“chain”. The ability of an element
to catenate is primarily based on
the bond energy of the element to
itself, which decreases with more
the diffuse orbitals i.e those with
the higher azimuthal quantum
number overlapping to form the
bond. Hence, the carbon, with the
least diffuse valence shell p orbital
is capable of forming the longer p-p
sigma bonded chains of the atoms
than the heavier elements which
bond via the higher valence shell
orbitals. The Catenation ability is
also influenced by a range of the
steric and the electronic factors,
including the electronegativity of
the element in the question, the
molecular orbital n and the ability
to form the different kinds of the
covalent bonds.
• CATENANE - A catenane is a
mechanically-interlocked
molecular architecture consisting
of the two or more than two
interlocked macrocycles, i.e. a
molecule containing two or more
© 2022 by JPS Scientific Publications, India
74
intertwined rings. The interlocked
rings cannot be separated without
the breaking of the covalent bonds
of the macrocycles. The Catenane
is derived from the Latin catena
which means “chain”. They are
conceptually related to the other
mechanically interlocked
molecular architectures, such as
the rotaxanes, molecular knots or
the molecular Borromean rings.
Recently the terminology which is
called as “mechanical bond” has
been coined that describes the
connection between the
macrocycles of a catenane.
Catenanes have alsobeen
synthesised in the two different
ways 1) statistical synthesis and 2)
the template-directed synthesis. If
there are more than the one
recognition sites it is possible to
observe the different colors
depending on the recognition site
of the ring occupies and thus it is
possible to change the color of the
catenane solution by changing the
preferred recognition site.
Switching between the two sites
may be achieved by the use of the
chemical, electrochemical or even
visible by the light based methods.
The Catenanes have also been
synthesized by incorporating the
many functional units, including
the redox-active groups e.g. such as
the viologen,
TTF=tetrathiafulvalene),
photoisomerizable groups (e.g.
azobenzene), fluorescent groups
and the chiral groups. Some such
Glossary of Genetics
units have also been used to create
the molecular switches as described
above, as well as for the fabrication
of the molecular electronic devices
and the molecular sensors.
• CBP - The Cyclic adenosine
monophosphate Response Element
Binding protein Binding Protein i.e
CREB Binding protein, which is
also known as the CREBBP or the
CBP, is a coactivator encoded by
the CREBBP gene in the humans,
located on the chromosome 16p.
The CBP has intrinsic
acetyltransferase functions i.e it is
able to add the acetyl groups to the
both transcription factors as well as
the histone lysines, the latter of
which has been shown to alter the
chromatin structure making the
genes more accessible for the
transcription. This relatively
unique acetyltransferase activity is
also seen in the another
transcription enzyme, EP300
which is also called as the p300.
Together, they are known as the
p300-CBP coactivator family and
are known to associate with more
than the 16,000 genes in the
humans, however while these
proteins share many of the
structural features, emerging the
evidence suggests that the these
two co-activators may promote the
transcription of the genes with the
different biological The CBP alone
has been implicated in a wide
variety of the pathophysiologies
including the colorectal cancer as
well as head and the neck
© 2022 by JPS Scientific Publications, India
75
squamous cell carcinoma. In these
diseases, the association of the
CBP with β-catenin has been
shown to the promote cancer cell
proliferation and the disease
aggressiveness, whereas p300/ β-
catenin leads to the cell
differentiation and/ or the
apoptosis. The CBP has also been
shown to help the modulate liver
function via maintenance of the
energy homeostasis in the response
to changes in the cell nutrition
conditions by regulating the
activity of the transcription factors
and the genes responsible for the
lipogenesis and the
gluconeogenesis. The CBP is also
implicated in the etiologies of
several other diseases including the
hematologic malignancies and the
other solid tumors, diabetes,
schizophrenia, Alzheimer’s
Disease, depression, and many of
the other neurological conditions.
• CAUDOBACTER
CRESCENTUS - Caulobacter
crescentus is a type of the Gram-
negative, oligotrophic bacterium
which is widely distributed in the
fresh water lakes and the streams.
It is an important model organism
for studying the regulation of the
cell cycle, the asymmetric cell
division, and the cellular
differentiation. Caulobacter
daughter cells have the two very
different forms. The One daughter
is a mobile “swarmer” cell that has
a single flagellum at one cell pole
that provides the swimming
Glossary of Genetics
motility for the chemotaxis. The
other daughter, which called as the
“stalked” cell, has a tubular stalk
structure protruding from the one
pole that has an adhesive holdfast
material on its end, with which the
stalked cell can adhere to the
surfaces. The Swarmer cells
differentiate into the stalked cells
after a short period of the motility.
The Chromosome replication and
the cell division only occurs in the
stalked cell stage. It derives its
name from its crescent shape,
which is caused by the protein
which is called as crescentin. It is
an interesting organism to study
because it inhabits the nutrient-
poor aquatic environments. Their
ability to thrive in the low levels of
the nutrients is facilitated by its
dimorphic developmental cycle.
The swarmer cell has a flagellum
that protrudes from a single pole
and is unable to initiate the DNA
replication unless differentiated
into a stalked cell. The
differentiation process includes a
morphological transition
characterized by the ejection of its
flagellum and the growth of a stalk
at the same pole. The Stalked cells
can elongate and replicate their
DNA while growing a flagellum at
the opposite pole, giving rise to a
pre-divisional cell. Although the
precise function of stalks is still
being investigated, it is likely that
the stalks are involved in the
uptake of nutrients in the nutrient-
limited conditions.
© 2022 by JPS Scientific Publications, India
76
• CATH DATABASE - The CATH
Protein Structure Classification
database is a type of free, which is
publicly available online resource
that provides the information on
the evolutionary relationships of
the protein domains. It was
created in the mid-1990s by the
Professor Christine Orengo and his
colleagues including the Janet
Thornton and the David Jones and
continues to be developed by the
Orengo group at the University
College of London. The CATH
shares many broad features with
the SCOP resource, however there
are also many areas in which the
detailed classification differs
greatly. The Experimentally-
determined protein three-
dimensional structures are
obtained from the Protein Data
Bank and split into their
consecutive polypeptide chains,
where they are applicable. The
Protein domains are identified
within these chains using a mixture
of the automatic methods and the
manual curation. The domains are
then classified within the CATH
structural hierarchy at the Class
(C) level, domains are assigned
according to their secondary
structure content, i.e. all the alpha,
all beta, a mixture of alpha and
beta, or the little secondary
structure; at the Architecture (A)
level, information on the secondary
structure arrangement in the three-
dimensional space is used for the
assignment at the Topology/fold
Glossary of Genetics
(T) level, information on how the
secondary structure elements are
connected and are arranged is
used, assignments are made to the
Homologous superfamily (H) level
if there is good evidence that the
domains are related by the
evolution i.e. they are homologous.
• the tumors. However, no study has
• CBX - The CBXs are the
transcriptional repressors found in
the normal human cells that the
regulate cell senescence. Their
expression is downregulated in the
colon cancer, gastric cancer, and
the hepatocellular carcinoma. As a
kind of epigenetic regulatory
complex, the CBXs repress target
gene transcription by modifying
the chromatin. The eight known
CBX proteins in the human
genome are involved in the
heterochromatin regulation, gene
expression, and the developmental
programming. The CBX proteins
are divided into the two groups
according to their molecular
structure. The HP 1 group
including the CBX1/3/5 and the
Pc group including the
CBX2/4/6/7. Although the CBX
levels are significantly associated
with the cancer patient prognosis,
there is no consistent pattern
among the different family
members. The CBX1 can serve as a
target gene for the microRNA-205-
5p and thus participates in the
pituitary tumor progression, while
the CBX7 regulates the stem cell-
like properties of the gastric cancer
© 2022 by JPS Scientific Publications, India
77
cells through the p16 and AKT
pathways. However, the CBX
family has not been studied in
depth in the LUAD.The members
of the Chromobox (CBX) family
are very important epigenetic
regulatory molecules with the
critical biological roles in many of
been analyzed or been verified
their role in the lung
adenocarcinoma (LUAD). The
Gene Ontology pathway, receiver
operating characteristic curves, and
the tumor-infiltrating immune cell
analyses were used to clarify the
biological function of the CBX hub
molecules in the cell. The Paired
tumor samples and the lung
adenocarcinoma cell lines were
collected for the molecular
functional assays to validate the
results of the bioinformatics
analysis.
• cccDNA - The cccDNA which is
called as the covalently closed
circular DNA is a special type of
DNA structure that arises during
the propagation of the some viruses
in the cell nucleus and may remain
permanently there. It is a double-
stranded DNA that originates in a
linear form that is ligated by the
means of the DNA ligase to a
covalently closed ring. In most of
the cases, the transcription of viral
DNA can occur from the circular
form only. The cccDNA of viruses
is also known as the episomal
DNA or occasionally as a
minichromosome. The cccDNA
Glossary of Genetics
was first described in the
bacteriophages, but it was also
found in some of the cell cultures
where an infection of the DNA
viruses (Polyomaviridae) was
detected. The cccDNA is typical
of the Caulimoviridae and
Hepadnaviridae, including the
hepatitis B virus (HBV). The
cccDNA in the HBV is formed by
the conversion of the capsid-
associated relaxed circular DNA
which is also called as rcDNA.
Following the hepatitis B be triggered by the specific external
infections, cccDNA can remain
following clinical treatment in the
liver cells and can rarely reactivate.
The relative quantity of the
cccDNA present is an indicator for
the HBV treatment. The CccDNA
is able to form a stable
minichromosome in the nucleus of
the cells that are infected with a
particular virus associated with the
cccDNA. As part of the nucleus,
the cccDNA is also able to interact
with the histone and the non-
histone proteins to form the
structures similar to the chromatin.
In the same way as the host
chromatin, the cccDNA
transcription is also regulated
through the control of the two
enhancers and the four distinct
promoters. It also depends on the
multiple regulators including the
transcription factors, co-activators,
co-repressors and the chromatin
modifying enzymes. In addition,
the cccDNA can also serve as a
template for the viral replication
© 2022 by JPS Scientific Publications, India
78
and the DNA transcription for the
five viral RNAs which allows for
the production of the viral
antigens.
• CRE LOX RECOMBINATION -
The Cre-Lox recombination is a
site-specific recombinase
technology, used to carry out the
deletions, insertions, translocations
and the inversions at the specific
sites in the DNA of the cells. It
allows the DNA modification to be
targeted to the specific cell type or
stimulus. It is implemented both in
the eukaryotic and in the
prokaryotic systems. The Cre-lox
recombination system has been
particularly useful to help the
neuroscientists to study the brain in
which the complex cell types and
the neural circuits come together to
generate the cognition and the
behaviors. The system consists of a
single enzyme, Cre recombinase,
that recombines a pair of the short
target sequences called as the Lox
sequences. This system can be
implemented without inserting any
of the extra supporting proteins or
the sequences. The Cre enzyme
and the original Lox site called as
the LoxP sequence are derived
from the bacteriophage P1.
• CBFB - The Core-binding factor
subunit beta is a protein that in the
humans is encoded by the CBFB
gene. The protein which is encoded
by this gene is the beta subunit of a
heterodimeric core-binding
transcription factor belonging to
Glossary of Genetics
the PEBP2/CBF transcription
factor family which master-
regulates a host of the genes
specific to the hematopoiesis (e.g.
RUNX1) and the osteogenesis (e.g.
RUNX2). The beta subunit is a
non-DNA binding regulatory
subunit; it allosterically enhances
the DNA binding by the alpha
subunit as the complex binds to the
core site of the various enhancers
and the promoters, including the
murine leukemia virus,
polyomavirus enhancer, T-cell
receptor enhancers and the GM-
CSF promoters. The Alternative
splicing generates the two mRNA
variants, each encoding a distinct
carboxyl terminus. In some of the
cases, a pericentric inversion of the
chromosome 16 produces a
chimeric transcript consisting of
the N terminus of the core-binding
factor beta in a fusion with the C-
terminal portion of the smooth
muscle myosin heavy chain 11.
This chromosomal rearrangement
is associated with the acute
myeloid leukemia of the M4Eo
subtype. The two transcript
variants encoding the different
isoforms have been found for this
gene. The Mutations in the CBFB
are implicated in the cases of the
breast cancer.
• CHROMOSOME
SEGREGATION - The
Chromosome segregation is the
process in the eukaryotes by which
the two sister chromatids formed
© 2022 by JPS Scientific Publications, India
79
as a consequence of the DNA
replication, or the paired
homologous chromosomes,
separate from the each other and
migrate to the opposite poles of the
nucleus. This segregation process
occurs during both the mitosis and
the meiosis. The chromosome
segregation also occurs in the
prokaryotes. However, in contrast
to the eukaryotic chromosome
segregation, replication and the
segregation are not temporally
separated. Instead the segregation
occurs progressively following the
replication.
• CDNA LIBRARY - A cDNA
library is a combination of the
cloned cDNA (complementary
DNA) fragments inserted into a
collection of the host cells, which
constitute some portion of the
transcriptome of the organism and
are stored as the "library". The
cDNA is produced from the fully
transcribed mRNA found in the
nucleus and therefore contains
only the expressed genes of an
organism. Similarly, the tissue-
specific cDNA libraries can be
produced. In the eukaryotic cells
the mature mRNA is already
spliced, hence the cDNA produced
lacks the introns and can be readily
expressed in the nacterial cell.
While the information in the
cDNA libraries is a powerful and
useful tool since the gene products
are easily identified, the libraries
lack the information about the
Glossary of Genetics
enhancers, introns, and the other
regulatory elements found in a
genomic DNA library.
• CROSSOVER
RECOMBINATION - During the
meiosis, the crossovers occur at a
very high level, but the level of the
noncrossover recombinants is even
the higher. The biological rationale
for the existence of the latter events
is not yet known. It has been
suggested that a noncrossover-
specific pathway exists specifically
to mediate the chromosome
pairing.
• C RAF - The RAF proto-oncogene
serine/threonine-protein kinase,
also known as the proto-oncogene
c-RAF or simply the c-Raf or even
thevRaf-1, is an enzyme that in the
humans is encoded by the RAF1
gene. The c-Raf protein is a part of
the ERK1/2 pathway as a MAP
kinase (MAP3K) that functions the
downstream of the Ras subfamily
of the membrane associated
GTPases. The C-Raf is a member
of the Raf kinase family of the
serine/threonine-specific protein
kinases, from the TKL (Tyrosine-
kinase-like) group of the kinases.
Although the c-Raf is a very clearly
capable of mutating into an
oncogene in the experimental
settings, and even in a few human
tumors, its sister kinase B-Raf is
the true major player in the
carcinogenesis in the humans. The
Sorafenib was the first clinically
useful agent, that provides a
pharmacological alternative to
© 2022 by JPS Scientific Publications, India
80
treat the previously largely
untreatable malignancies, such as
the renal cell carcinoma and the
melanoma. Several other
molecules followed up such as the
vemurafenib, Regorafenib,
Dabrafenib, etc.
• CHROMATIN
IMMUNOPRECIPITATION -
The Chromatin
immunoprecipitation (ChIP) is a
type of the immunoprecipitation
experimental technique used to
investigate the interaction between
the proteins and the DNA in the
cell. It aims to determine whether
the specific proteins are associated
with the specific genomic regions,
such as the transcription factors on
the promoters or the other DNA
binding sites, and possibly define
the cistromes. The ChIP also aims
to determine the specific location
in the genome that various histone
modifications are associated with
indicating the target of the histone
modifiers. The ChIP is crucial for
the advancements in the field of
the epigenomics and learning more
about the epigenetic phenomena.
There are mainly two types of the
ChIP, primarily differing in the
starting chromatin preparation.
The first uses the reversibly cross-
linked chromatin sheared by the
sonication called as the cross-
linked ChIP (XChIP). The Native
ChIP (NChIP) uses the native
chromatin sheared by the
micrococcal nuclease digestion.
Glossary of Genetics
• CHROMOSOME
CONFORMATION CAPTURE -
The Chromosome conformation
capture techniques (often
abbreviated to as the 3C
technologies or the 3C-based
methods) are a set of the molecular
biology methods used to analyze
the spatial organization of the
chromatin in a cell. These methods
quantify the number of the
interactions between the genomic
loci that are nearby in the 3-D
space, but may be separated by
many of the nucleotides in the
linear genome. Such interactions
may result from the biological
functions, such as the promoter-
enhancer interactions, or from the
random polymer looping, where
undirected physical motion of the
chromatin causes the loci to
collide. The Interaction frequencies
may be analyzed directly, or they
may be converted to the distances
and used to reconstruct the 3-D
structures. The 3C methods have
led to a number of the biological
insights, including the discovery of
the new structural features of the
chromosomes, the cataloguing of
the chromatin loops, and increased
the inderstanding of the
transcriptional regulation
mechanisms (the disruption of
which can lead to the disease).
• CHROMATIN REMODELING -
The Chromatin remodeling is the
dynamic modification of the
chromatin architecture to allow the
access of the condensed genomic
© 2022 by JPS Scientific Publications, India
81
DNA to the regulatory
transcription machinery proteins,
and thereby control the gene
expression. Such remodeling is
principally carried out by the 1)
covalent histone modifications by
the specific enzymes, e.g. histone
acetyltransferases (HATs),
deacetylases, methyltransferases,
and kinases, and the 2) ATP-
dependent chromatin remodeling
complexes which either move,
eject or restructure the
nucleosomes. [1] Besides the
actively regulating gene expression,
dynamic remodeling of the
chromatin imparts an epigenetic
regulatory role in the several key
biological processes, egg cells
DNA replication and repair
apoptosis, chromosome
segregation as well as the
development and the pluripotency.
The Aberrations in the chromatin
remodeling proteins are found to
be associated with the human
diseases, including the cancer.
Targeting chromatin remodeling
pathways is currently evolving as a
major therapeutic strategy in the
treatment of the several cancers.
• COL1A1 - The Collagen, type I,
alpha 1, is also known as the alpha-
1 type I collagen, is a protein that
in the humans is encoded by the
COL1A1 gene. The COL1A1
encodes the major component of
the type I collagen, the fibrillar
collagen found in most of the
connective tissues, including the
cartilage. The Collagen is a protein
Glossary of Genetics
that strengthens and supports
many of the tissues in the body,
including the cartilage, bone,
tendon, skin and the white part of
the eye (sclera). The COL1A1 gene
produces a component of the type I
collagen, called as the pro-alpha1
chain. This chain combines with
the another pro-alpha1 chain and
also with a pro-alpha2nchain to
make a molecule of the type I
procollagen. These triple-stranded,
rope-like procollagen molecules
must be processed by the enzymes
outside the cell. Once these
molecules are processed, they
arrange themselves into the long,
thin fibrils that cross-link to one
another in the spaces around cells.
The cross-links result in the
formation of the very strong
mature type I collagen fibers. The
Collagenous function includes the
rigidity and the elasticity.
• CSR - The Immunoglobulin class
switching, also known as the
isotype switching, isotypic
commutation or the class-switch
recombination (CSR), is
biological mechanism that changes
a B cell's production of the
immunoglobulin from one type to
the another, such as the from the
isotype IgM to the isotype IgG.
During the this process, the
constant-region portion of the
antibody heavy chain is changed,
but the variable region of the heavy
chain stays the same (the terms
variable and the constant refer to
the changes or the lack thereof
82
between the antibodies that target
different epitopes). Since the
variable region does not change,
the class switching does not affect
the antigen specificity. Instead, the
antibody retains affinity for the
same antigens, but can interact
with the different effector
molecules. The Class switching
occurs after the activation of a
mature B cell via its membrane-
bound antibody molecule (or B cell
receptor) to generate the different
classes of the antibody, all with the
same variable domains as the
original antibody generated in the
immature B cell during the process
of the V(D)J recombination, but
possessing the distinct constant
domains in their heavy chains. The
native mature B cells produce both
the IgM and IgD, which are the
first two heavy chain segments in
the immunoglobulin locus. After
activation by the antigen, these B
cells proliferate.
• CHD SUBFAMILY - The
Chromodomain helicase DNA-
a binding (CHD) proteins is a
subfamily of the ATP-dependent
chromatin remodeling complexes.
All the remodelers fall under the
umbrella of the RNA/DNA
helicase superfamily 2. In the
yeast, the CHD complexes are
primarily responsible for the
nucleosome assembly and the
organization. These complexes
play an additional role in the
multicellular eukaryotes, assisting
© 2022 by JPS Scientific Publications, India
Glossary of Genetics
in the chromatin access and in the
nucleosome editing.
• CAM2KG - The
Calcium/calmodulin-dependent
protein kinase type II gamma chain
is an enzyme that in the humans is
encoded by the CAMK2G gene.
The product of this gene belongs to
the type of the Serine/Threonine
protein kinase family, and to the
Ca(2+)/calmodulin-dependent
protein kinase subfamily. The
Calcium signaling is crucial for the
several aspects of plasticity at the
glutamatergic synapses. In the
mammalian cells the enzyme is
composed of the four different
chains: alpha, beta, gamma, and
delta. The product of this gene is a
gamma chain. The Six
alternatively spliced variants that
encode the six different isoforms
have been characterized to the
date. The Additional alternative
splice variants that encode the
different isoforms have been
described, but their full-length
nature has not been determined.
• COVERAGE - The Coverage (or
depth) in the DNA sequencing is
the number of the unique reads
that include a given nucleotide in
the reconstructed sequence. The
Deep sequencing refers to the
general concept of aiming for the
high number of the unique reads of
each of the region of a sequence.
• CCCA-ADDING ENZYMES -
The CCA-adding enzyme which is
also known as the tRNA
nucleotidyltransferase which
© 2022 by JPS Scientific Publications, India
83
synthesizes and repairs the 3′-
terminal CCA sequence of the
tRNA. The eubacterial, eukaryotic,
and the archaeal CCA-adding
enzymes all of these share a single
active-site signature motif, which
identifies these enzymes as
belonging to the family known as
nucleotidyltransferase superfamily.
The mutations at the Asp-53 or
Asp-55 of the bacteria known as
Sulfolobus shibatae signature
sequence abolish addition of rye
both C and A, demonstrating that
a single active site is responsible for
the addition of both the
nucleotides. Mutations at the Asp-
106 and to a lesser extent, at the
Glu-173 and the Asp-215
selectively impaired the addition of
the A, but not C. The tRNA
acceptor stem remains fixed on the
surface of the CCA-adding enzyme
during the C and the A addition.
Taken together with this new type
of evidence that there is a single
active site for the catalysis, the data
suggest that the specificity of the
nucleotide addition is determined
by a process known as
collaborative templating as the
single active site catalyzes the
addition of each nucleotide, the
growing 3′-end of the tRNA would
progressively refold to create a
binding pocket for the addition of
the next nucleotide.
• CIRCULAR DNA - The Circular
DNA is DNA that forms a closed
loop and has no ends. The Circular
DNA molecules that are of the
Glossary of Genetics
great significance in the nature as
well as in the numerous
biotechnology applications are the
plasmids, which are widespread
among the bacteria. The Plasmids
are the small circular DNA
molecules consisting of just a few
genes to more than a hundred.
Among the important genes carried
in the plasmids are those coding for
the resistance to a wide range of
the antibiotics and the genes that
allow the plasmids to be
transferred to the other bacteria,
even to the other species of the
bacteria. The process of transfer of
the plasmid and the chromosomal
DNA from one bacterium to the
another is called as the
conjugation. Transfer of the
antibiotic resistance genes among
the bacteria in the nature has
created serious problems in the
treatment of the many infectious
diseases such as the tuberculosis,
gonorrhea, pneumonia,
staphylococcus, and others. The
widespread use of the antibiotics in
the agriculture and in the hospitals
has resulted in the selection and
evolution of the pathogenic
microorganisms that are resistant
to many, sometimes all, of the
antibiotics normally used to treat
infections by these
microorganisms. The Plasmids
also have been genetically
engineered in a multitude of ways
so that they can carry and express
the foreign genes in the bacteria.
For example, the genes coding for
© 2022 by JPS Scientific Publications, India
84
the human insulin and human
growth hormone have been
inserted into the plasmids which
are then reintroduced into the
bacteria such as E. Coli. The
genetically engineered bacteria are
then used as the biological factories
to produce the desired drugs.
• CD4 PROTEIN - In the field of
genetics the CD4 or the cluster of
the differentiation 4 is a type of
glycoprotein that serves as a co-
receptor for the T-cell receptor or
TCR. The CD4 is found on the
surface of the immune cells such as
the T helper cells, monocytes,
macrophages, and the dendritic
cells. It was discovered in the late
1970s and was originally known as
the leu-3. In the humans, the CD4
protein is encoded by the CD4
gene. The CD4+ T helper cells are
the white blood cells that are an
essential part of the human
immune system. They are often
referred to as the CD4 cells, T-
helper cells or the T4 cells. They
are also called as the helper cells
because one of their main roles is
to send the signals to the other
types of the immune cells,
including the CD8 killer cells,
which then destroy the infectious
particle. If the CD4 cells become
depleted, for example in the
untreated HIV infection, or the
following immune suppression
prior to a transplant, the body is
left vulnerable to a wide range of
the infections that it would
Glossary of Genetics
otherwise have been able to fight.
The CD4 is a co-receptor of the T
cell receptor and assists the latter in
communicating with the antigen-
presenting cells. The TCR complex
and the CD4 bind to the distinct
regions of the antigen-presenting
MHC class II molecule. The
extracellular D1 domain of the
CD4 binds to the β2 region of the
MHC class II. The resulting close
proximity between the TCR
complex and the CD4 allows the
tyrosine kinase Lck bound to the
cytoplasmic tail of CD4 to
phosphorylate tyrosine residues of
the immunoreceptor tyrosine
activation motifs on the
cytoplasmic domains of the CD3
to amplify the signal generated by
the TCR. The Phosphorylated
ITAMs on the CD3 recruit and
activate the SH2 domain-
containing the protein tyrosine
kinases (PTK), such as the ZAP70,
to further mediate the downstream
signalling through the tyrosine
phosphorylation. These signals
lead to the activation of the
transcription factors, including the
NF-κB, NFAT, AP-1, to promote
the T cell activation.
• C-COMPLEX - The c-complex
helps the body to make the
collagen, an important protein
used to make the skin, cartilage,
tendons, ligaments, and the blood
vessels. The Vitamin C is needed
for the healing wounds, and for
repairing and maintaining the
bones and the teeth. It also helps
© 2022 by JPS Scientific Publications, India
85
the body to absorb iron from the
nonheme sources. The C complex
is a powerful antioxidant, and it
also prevents the formation of the
free radicals in the body. The c-
complex plays an important role in
reducing the risk of chronic
disease. It also help to manage the
high blood pressure. It also lower
the risk of the heart disease. It also
reduce the blood uric acid levels
and help to prevent the gout
attacks. It helps to prevent the iron
deficiency and also boosts the
immunity. It Protects the memory
and thinking as your age.
• CDC6 - The Cdc6, or the cell
division cycle 6, is a protein in the
eukaryotic cells. The CDC6 is
mainly studied in the budding
yeast known as the Saccharomyces
cerevisiae (P09119). It is an
essential type of regulator of the
DNA replication and plays an
important roles in the activation
and in the maintenance of the
checkpoint mechanisms in the cell
cycle that coordinate the S phase
and the mitosis. It is a part of the
pre-replicative complex (pre-RC)
and is required for loading the
minichromosome maintenance
(MCM) proteins onto the DNA, an
essential step in the initiation of the
DNA synthesis. In addition, it is a
member of the family of the AAA+
ATPases and it is highly related to
the ORC1 both are the same
protein in the archaea. The CDC6
is an ATP binding protein and it is
also a member of the pre-
Glossary of Genetics
replicative complex (pre-RC)
together with the origin recognition
complex (ORC), Cdt1 and the
MCM complex (containing
MCM2-7p). The CDC6 assembles
after the ORC in an ATP
dependent manner and is required
for the loading the MCM proteins
onto the DNA. The
Reconstruction of the electron
microscope images showed that the
ORC-CDC6 complex forms a ring-
shaped structure with the similar
dimensions to those of the ring-
shaped MCM helicase. A near-
atomic resolution model of the
entire ORC-Cdc6-Cdt1-Mcm2-7
(OCCM) complex with the DNA
was assembled from the EM data.
It is thought that the CDC6-Cdt1
complex uses the ATP hydrolysis
to thread the DNA through the
central hole of the MCM
doughnut. Mutations in the
binding motif of the CDC6
strongly suggest that the ATP
binding and hydrolysis is essential
for its function. The minimal
requirement for the DNA binding
has been mapped within its 47-
amino acid sequence.
Furthermore, the Cdc6 indirectly
inhibits the activation of the
p34cdc2/CDC28 M phase kinase,
thus nuclear division is suppressed.
• CPEB - The CPEB, or the
cytoplasmic polyadenylation
element binding protein, is a highly
conserved RNA-binding protein
that promotes the elongation of the
polyadenine tail of the messenger
© 2022 by JPS Scientific Publications, India
86
RNA. The CPEB most commonly
activates the target RNA for the
translation, but can also act as a
repressor, dependent on its
phosphorylation state. In the
animals, the CPEB is expressed in
the several alternative splicing
isoforms that are specific to the
particular tissues and the functions,
including the self-cleaving
Mammalian CPEB3 ribozyme.
The CPEB was first identified in
the Xenopus oocytes and
associated with the meiosis, a role
has also been identified in the
spermatogenesis of the
Caenorhabditis elegans. The
CPEB is also involved in the
closed-loop regulation of the
mRNAs that keeps them inactive.
The closed-loop structure between
the 3’UTR and the 5’UTR inhibits
the translation. This has been
observed in the Xenopus laevis in
which the eIF4E bound to the 5’
cap interacts with the Maskin
bound to the CPEB on the 3’ UTR
creating the translationally inactive
transcripts
• CPSF - The Cleavage and the
polyadenylation specificity factor
(CPSF) is involved in the cleavage
of the 3’ signaling region from a
newly synthesized pre-messenger
RNA (pre-mRNA) molecule in the
process of the gene transcription.
It is the first type of the protein
which binds to the signaling region
near the cleavage site of the pre-
mRNA, to which the poly(A) tail
will be added by the polynucleotide
Glossary of Genetics
adenylyltransferase. The upstream
signaling region has the canonical
nucleotide sequence AAUAAA,
which is highly conserved across
the vast majority of the pre-
mRNAs. Another downstream
region which is called as the
second downstream signaling
region, located on the portion of
the pre-mRNA that is cleaved
before the polyadenylation,
consists of a GU-rich region
required for the efficient
processing.
• CODING REGION - The coding
region of a gene, also known as the
coding sequence (CDS), is the
portion of a gene's DNA or the
RNA that codes for the protein.
Studying the length, composition,
regulation, splicing, structures, and
the functions of the coding regions
compared to the non-coding
regions over the different species
and the time periods can provide a
significant amount of the
important information regarding
the gene organization and the
evolution of the prokaryotes and
the eukaryotes. This can further
assist in the mapping the human
genome and developing the gene
therapy. In the DNA, the coding
region is flanked by the promoter
sequence on the 5' end of the
template strand and the
termination sequence on the 3' end.
During the transcription, the RNA
Polymerase (RNAP) binds to the
promoter sequence and moves
along the template strand to the
© 2022 by JPS Scientific Publications, India
87
coding region. The RNAP then
adds the RNA nucleotides
complementary to the coding
region in order to form the mRNA,
substituting uracil in the place of
thymine. This continues until the
RNAP reaches the termination
sequence.[13]
• CRISPR - The CRISPR which is
termed as the clustered regularly
interspaced short palindromic
repeats is a family of the DNA
sequences found in the genomes of
the prokaryotic organisms such as
the bacteria and the archaea.
These sequences are derived from
the DNA fragments of the
bacteriophages that had previously
infected the prokaryote. They are
used to detect and destroy the
DNA from the similar
bacteriophages during the
subsequent infections. Hence these
sequences plays a very important
key role in the antiviral i.e. anti-
phage defense system of the
prokaryotes and provide a form of
the acquired immunity. The
CRISPR are found in the
approximately 50% of the
sequenced bacterial genomes and
nearly about 90% of the sequenced
archaea. The Cas9 or the
“CRISPR-associated protein 9” is
an enzyme which uses the CRISPR
sequences as a guide to recognize
and cleave the specific strands of
the DNA that are complementary
in nature to the CRISPR sequence.
Glossary of Genetics
• CAS 9 - The Cas9 (CRISPR
associated protein 9, formerly
called as the Cas5, Csn1, or the
Csx12) is a 160 kilodalton protein
which plays a vital and important
role in the immunological defense
of the certain bacteria against the
DNA viruses and the plasmids,
and is heavily utilized in the
genetic engineering applications.
Its main function is to cut the
DNA and thereby alter a cell’s
genome. More technically, the
Cas9 is a dual RNA-guided DNA
endonuclease enzyme associated
with the Clustered Regularly
Interspaced Short Palindromic
Repeats (CRISPR) which is a
adaptive immune system in the
Streptococcus pyogenes. The
S.Pyogenes utilizes the CRISPR to
memorize and the Cas9 to later
interrogate and cleave the foreign
DNA, such as the invading
bacteriophage DNA or the plasmid
DNA. The Cas9 performs this
interrogation by unwinding the
foreign DNA and checking for the
sites complementary to the 20
nucleotide spacer region of the
guide RNA (gRNA). If the DNA
substrate is complementary to the
guide RNA, the Cas9 cleaves the
invading DNA. In this sense, the
CRISPR-Cas9 mechanism has a
number of the parallels with the
RNA interference (RNAi)
mechanism in the eukaryotes.
• CRO REPRESSOR - In the field
of the molecular biology, the Cro
repressor family is a family of the
© 2022 by JPS Scientific Publications, India
88
repressor proteins in the
bacteriophage lambda that includes
the Cro repressor. The
Bacteriophage lambda encodes the
two repressors: the Cro repressor
that acts to turn off the early gene
transcription during the lytic cycle,
and the lambda or the cI repressor
required to maintain rye lysogenic
growth. Together the Cro and the
cI repressors form a helix-turn-
helix (HTH) superfamily. The
lambda Cro repressor binds to the
DNA as a highly flexible dimer.
The important crystal structure of
the lambda Cro repressor reveals a
HTH DNA-binding protein with
an alpha or the beta fold that
differs from the other Cro family
members, possibly by an
evolutionary fold change. Most of
the Cro proteins, such as the
Enterobacteria phage P22 Cro and
the Bacteriophage 434 Cro, have
an all-alpha structure that is
thought to be ancestral to the
lambda Cro, where the fourth and
the fifth helices are replaced by a
beta-sheet, possibly as a result of
the secondary structure switching
rather than by the nonhomologous
replacement.
• CROSSOVER REGION - The C-
reactive protein (CRP) is a
heritable biomarker of the systemic
inflammation that is commonly
elevated in the depressed patients.
Variants in the CRP gene that
influence the protein levels could
thus be associated with the
depression but this has the seldom
Glossary of Genetics
been examined, especially in the
elderly. The Center for the
Epidemiologic Studies Depression
scale or a diagnosis of the current
major depression based on the
Mini-International
Neuropsychiatric Interview and
according to the Diagnostic and
the Statistical Manual of the
Mental Disorders-IV criteria states
that this a very critical condition in
the aged people. The Five single-
nucleotide polymorphisms
spanning the CRP gene were
genotyped, and the circulating
levels of the high-sensitivity CRP
were also determined. The
Multivariable analyses adjusted for
the socio-demographic
characteristics, smoking, ischemic
pathologies, cognitive impairment
and the inflammation-related
chronic pathologies. The CRP gene
variants were associated with the
serum levels in a gender-specific
manner, but only rs1205 was found
to be nominally associated with
both an increased risk of DEP and
the lower circulating CRP levels in
the women. The Variants of the
CRP gene thus influence the
circulating CRP levels and appear
as the independent susceptibility
factors for the late-life depression.
• CDC13 - The Cdc13 is a single-
strand telomeric DNA-binding
protein that positively regulates the
yeast telomere replication by
recruiting the telomerase to the
chromosome termini through a site
on the Cdc13 that is eliminated by
© 2022 by JPS Scientific Publications, India
89
the cdc13-2 mutation. The Cdc13
has a separate role in the negative
regulation of the telomere
replication, based on the analysis
of a new mutation, Known as the
cdc13-5. Loss of this second
regulatory activity results in the
extensive elongation of the G
strand of the telomere by
telomerase, accompanied by a
reduced ability to coordinate the
synthesis of the C strand. Both the
cdc13-5 mutation and the DNA
polymerase α mutations which also
exhibit the elongated telomeres are
suppressed by the increased
expression of the Cdc13-interacting
protein Stn1, indicating that the
Stn1 coordinates action of the
lagging strand replication complex
with the regulatory activity of
CDC13. The association between
the Cdc13 and Stn1 is abolished by
the cdc13-2, the same mutation
that eliminates the interaction
between the Cdc13 and telomerase.
The Cdc13 participates in two
regulatory steps—first positive,
then negative—as a result of rye
successive binding of telomerase
and the negative regulator Stn1 to
overlapping sites on the Cdc13.
Thus, the Cdc13 coordinates
synthesis of the both strands of the
telomere by first recruiting the
telomerase and subsequently
limiting the G-strand synthesis by
the telomerase in response to the
C-strand replication.
• CDC45 - The CDC45 is a type of
protein that in humans is encoded
Glossary of Genetics
by the CDC45L gene. The protein
encoded by this gene was identified
by its strong similarity with the
Saccharomyces cerevisiae Cdc45,
an essential protein which is
required to the initiation of the
DNA replication. The Cdc45 is a
member of the highly conserved
multiprotein complex including the
Cdc6/Cdc18, the
minichromosome maintenance
proteins (MCMs) and the DNA
polymerase, which is important for
the early steps of the DNA
replication in the eukaryotes. This
protein has been shown to interact
with the MCM7 and the DNA
polymerase alpha. Studies of the
similar gene in the Xenopus
suggested that this protein plays a
pivotal role in the loading of the
DNA polymerase alpha onto the
chromatin. Multiple
polyadenlyation sites of this gene
are also reported.
• C-DNA - In the field of the
genetics, the complementary DNA
(cDNA) is the DNA synthesized
from a single-stranded RNA
e.g.messenger RNA (mRNA) or
the microRNA (miRNA)) template
in a reaction catalyzed by the
enzyme known as reverse
transcriptase. The cDNA is often
used to clone the eukaryotic genes
in the prokaryotes. When scientists
want to express a specific protein
in a cell that does not normally
express that protein i.e.
heterologous expression, they will
transfer the cDNA that codes for
© 2022 by JPS Scientific Publications, India
90
the protein to the recipient cell. In
the field of molecular biology, the
cDNA is also generated to analyze
the transcriptomic profiles in the
bulk tissue, single cells, or the
single nuclei in assays such as the
microarrays and the RNA-seq.
The cDNA is also produced
naturally by the retroviruses such
as the HIV-1, HIV-2, simian
immunodeficiency virus, etc. And
then integrated into the host’s
genome, where it creates a virus
known as provirus. The
Complementary DNA is often
used in the gene cloning or as the
gene probes or in the creation of a
cDNA library. When scientists
transfer a gene from one cell into
another cell in order to express the
new genetic material as a protein in
the recipient cell, the cDNA will be
added to the recipient rather than
the entire gene, because the DNA
for an entire gene may include tte
DNA that does not code for the
protein or that interrupts the
coding sequence of the protein e.g.
introns. The Partial sequences of
the cDNAs are often obtained as
the expressed sequence tags.
• CDK - The Cyclin-dependent
kinases (CDKs) are the families of
the protein kinases first discovered
for their role in regulating the cell
cycle. They are also involved in
regulating the transcription,
mRNA processing, and the
differentiation of the nerve cells.
They are present in all the known
eukaryotes, and their regulatory
Glossary of Genetics 91

function in the cell cycle has been CDK-activating kinase. The

evolutionarily conserved. In fact, Cyclin-CDK complexes
the yeast cells can proliferate phosphorylate substrates
normally when their CDK gene appropriate for the particular cell
has been replaced with the cycle phase. The Cyclin-CDK
homologous human gene. The complexes of earlier cell-cycle
CDKs are relatively very small phase help to activate the cyclin-
proteins, with the molecular CDK complexes in the later phase.
weights ranging from 34 to the 40
kDa, and contain little more than
the kinase domain. The CDK
• CDT1 - The CDT1 which is also
binds a regulatory protein called a
termed as the chromatin licensing
cyclin. Without the cyclin, CDK
and the DNA replication factor 1 is
has a very little kinase activity only
a protein that in the humans is
the cyclin-CDK complex is an
encoded by the CDT1 gene. It is a
active kinase but its activity can be
licensing factor that functions to
typically further modulated by the
limit the DNA from replicating
phosphorylation and the other
more than once per the cell cycle.
binding proteins, like p27. The
The protein is encoded by this gene
CDKs phosphorylate their
is a key licensing factor in the
substrates on serines and the
assembly of the pre-replication
threonines, so they are serine-
complexes (pre-RC), which occurs
threonine kinases. The consensus
during the G1 phase of the cell
sequence for the phosphorylation
cycle. In the assembly of the pre-
site in the amino acid sequence of a
RCs, origin recognition complexes
CDK substrate is [S/T*]PX[K/R],
(ORC1-6) recognize and bind to
where S/T* is the phosphorylated
the DNA replication origins. The
serine or the threonine, P is the
CDT1, along with the protein
proline, X is any amino acid, K is
CDC6, are then recruited to the
lysine, and R is the arginine. Most
forming pre-RC, followed by the
of the known cyclin-CDK
minichromosome maintenance
complexes regulate the progression
complexes (MCM2-7). The activity
through the cell cycle. The Animal
of the CDT1 during the cell cycle is
cells contain at least nine CDKs,
tightly regulated during the S phase
four of the which, CDK1, 2, 3, and
by the protein geminin, which
4, are directly involved in the cell
inhibits it, and by the SCFSKP2,
cycle regulation. In mammalian
which ubiquinates the protein to
cells, the CDK1, with its partners
tag it for the proteasomal
cyclin A2 and B1, alone can drive
degradation. This regulation is
the cell cycle. Another one, the
important in preventing the
CDK7, is involved indirectly as the
relicensing, thus ensuring that the

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
DNA is only replicated once per
the cell cycle. The DNA
replication factor CDT1 has been
shown to interact with the SKP2.
The Cdt1 is recruited by the origin
recognition complex in origin
licensing. The Null-mutations for
the CDT1 are lethal in the yeast
the spores undergo mitosis without
the DNA replication. The
overexpression of the CDT1 causes
the rereplication in H. Sapiens,
which activates the Chk1 pathway,
preventing entry into the mitosis.
• CHROMOSOME
REPLICATION – The
Chromosome replication is the key
event during the microbial cell
cycle that must be completed
before a cell divides. To reproduce
successfully, every cell must
replicate its chromosome(s) and
distinguish nascent sister
chromosomes from one to the
another. Each sister chromosome
must then be physically segregated
into one of the two new cells prior
to the completion of the cell
division. These are not the simple
tasks considering the large size of
the microbial genomes (0.2–5 mm)
and the extremely limited space
these genomes occupy (0.1–10
μm3). Yet, the errors (production
of chromosome-less cells) are very
rare (<10−5/cell division in the
Escherichia coli and in the
Saccharomyces cerevisiae. To
ensure a low error rate, the
microbial cells require the complex
and precise regulatory mechanisms
© 2022 by JPS Scientific Publications, India
92
for both properly time new rounds
of the replicative DNA synthesis
and orient newly synthesized DNA
with respect to the fixed
intracellular locations.
Chromosome replication is an
essential part of both the mitosis
and the meiosis. It ensures that
each of the daughter cell has the
correct number of the
chromosomes. To replicate the
DNA in the mitosis, each
chromosome replicates so that the
new chromosome is attached to the
original one at the centromere.
• CELL CYCLE CHECKPOINT -
The Cell cycle checkpoints are the
control mechanisms in the
eukaryotic cell cycle which ensure
its proper progression. The Each of
the checkpoint serves as a potential
termination point along the cell
cycle, during which the conditions
of the cell are assessed very well
with progression through the
various phases of the cell cycle
occurring only when the favorable
conditions are met. There are
many checkpoints in the cell cycle
process, but the three major ones
are the 1) the G1 checkpoint,
which is also known as the Start or
the restriction checkpoint or the
Major Checkpoint 2) the G2/M
checkpoint 3) and the metaphase-
to-anaphase transition which is
also known as the spindle
checkpoint. The Progression
through these checkpoints is
largely determined by the
activation of the cyclin-dependent
Glossary of Genetics
kinases by the regulatory protein
subunits which is called as the
cyclins, different forms of the
which are produced at each stage
of the cell cycle to control the
specific events that occur therein.
The DNA repair processes and the
cell cycle checkpoints have been
intimately linked with the cancer
due to their functions regulating
genome stability and the cell
progression, respectively. The
precise molecular mechanisms that
connect the dysfunctions in these
pathways to the onset of the
particular cancers are not well
understood in most of the cases.
The loss of the ATM has been
shown to precede the lymphoma
development presumably due to
excessive homologous
recombination, leading to the high
genomic instability. The
Disruption of the Chk1 in the mice
led significant misregulation of the
cell cycle checkpoints, an
accumulation of the DNA damage,
and an increased incidence of the
tumorigenesis. Perhaps most
famously, the single mutant
inheritance of the BRCA1 or
BRCA2 predisposes females
toward breast and the ovarian
cancers. The BRCA1 is known to
be required for the S and G2/M
transitions, and is involved in the
cellular response to the DNA
damage. The BRCA2 is believed to
be involved in the homologous
recombination and regulating the
S-phase checkpoint, and the
© 2022 by JPS Scientific Publications, India
93
mutations of the deficiencies in the
BRCA2 are strongly linked to the
tumorigenesis.
• CELL EXTRACT - The cell
extract-induced reprogramming of
the somatic cells is another method
of the integration-free generation of
the iPS cells. It has been shown
that nuclear and the cytoplasmic
extracts from the several cell types
elicit changes in the cell fate. The
procedure involves the reversible
permeabilization of a somatic cell,
exposure of the permeabilized cells
to the reprogramming extract, and
resealing of the cells. The cell
extract showed that the transient
exposure of the reversibly
permeabilized fibroblasts led to the
activation of the pluripotent stem
cells. However, the expression and
the precise timing of the other
genes involved in the cell-free-
extract-induced reprogramming
have not been addressed. The
exposure to mouse ESC extracts
induces the marked epigenetic
reprogramming in the NIH3T3
fibroblasts, including the
reactivation of the ESC-specific
gene expression. These
reprogrammed cells possess the
pluripotent stem cell-like
characteristics including the
multilineage differentiation
potential. The Cell extracts were
stored at the – 80 °C and
maintained at the 4 °C in the
autosampler of the
chromatographic system. The
stability in the experimental
Glossary of Genetics
conditions is assessed by analyzing
a QC sample corresponding to a
calibration point. It is injected at
least three times during the
experimental process i.e at the
beginning, the middle, and the end
of the experiment, and it is checked
that both the areas of the 15N
SRM transition pairs and the
14N/15N ratios of the analytes are
constant throughout the LC/ESI-
MS/MS acquisitions. We found
that the metabolites of the interest
in the cell extracts were stable in
the experimental conditions for at
least 72 h. Otherwise, the aliquots
of the 15N reference extracts are
stored at the – 80 °C and used for a
one-year period.
• COMPACTION - The
Compaction is the process in
which the large DNA molecule
undergoes a transition between an
elongated conformation and a very
compact form. In the nature, the
DNA compaction occurs to
package the genomic material
inside the tiny spaces such as the
viral capsids and the cell nuclei. In
vitro, several strategies exist to the
compact DNA. The regulated
compaction/decompaction can be
used to control the gene activity in
vitro, with a particular emphasis
on the use of the light to reversibly
control the gene expression. The
compaction is used as a way to
reversibly protect the DNA against
the chemical, biochemical, or the
mechanical stresses. The compact
DNA can be used as a
© 2022 by JPS Scientific Publications, India
94
nanostructure template to generate
the nanomaterials with a well-
defined size and the shape.
• COMPLEMENTARY BASE
PAIR - The Complementary base
pairing describes the manner in
which the nitrogenous bases of the
DNA molecules align with the
each other. The Complementary
base pairings are also responsible
for the double-helix structure of the
DNA. If you imagine yourself
looking at a closet with the four
pairs of the shoes that are all mixed
up, the complementary base
pairing would be the set of the
rules that you would use to know
which of the shoes go together. In
a similar way to which only the
correct two shoes will form a
working pair (you don’t want the
two left shoes or a black and a
brown one!), only some of the
nitrogenous bases of the DNA can
interact to form a stable DNA
molecule.
• CHIP ON CHIP - The ChIP-on-
chip (which is also known as the
ChIP-chip) is a technology that
combines the chromatin
immunoprecipitation (‘ChIP’) with
the DNA microarray (“chip”).
Like the regular, ChIP-on-ChIP is
used to investigate the interactions
between the proteins and the DNA
in vivo. Specifically, it allows the
identification of the cistrome, the
sum of the binding sites, for the
DNA-binding proteins on a
genome-wide basis. Whole-
genome analysis can be performed
Glossary of Genetics
to determine the locations of the
binding sites for almost any protein
of the interest. As the name of the
technique suggests, such proteins
are generally those operating in the
context of the chromatin. The most
prominent representatives of this
class are the transcription factors,
replication-related proteins, like the
origin recognition complex protein
(ORC), histones, their variants,
and the histone modifications. The
goal of the ChIP-on-ChIP is to
locate the protein binding sites that
may help to identify the functional
elements in the genome. Other
proteins allow the identification of
the promoter regions, enhancers,
repressors and the silencing
elements, insulators, boundary
elements, and sequences that
control the DNA replication. If
the histones are subject of the
interest, it is believed that the
distribution of the modifications
and their localizations may offer
the new insights into the
mechanisms of the regulation.
• CELL SURFACE RECEPTORS
- The Cell surface receptors or the
membrane receptors,
transmembrane receptors are the
receptors that are embedded in the
plasma membrane of the cells.
They act in the cell signaling by
receiving or binding to the
extracellular molecules. They are
very specialized integral membrane
proteins that allow the
communication between the cell
and the extracellular space. The
© 2022 by JPS Scientific Publications, India
95
extracellular molecules may be
hormones, neurotransmitters,
cytokines, growth factors, cell
adhesion molecules, or the
nutrients they react with the
receptor to induce the changes in
the metabolism and activity of a
cell. In the process of the signal
transduction, the ligand binding
affects a cascading chemical
change through the cell membrane.
Many membrane of the receptors
are the transmembrane proteins.
There are various kinds, including
the glycoproteins and the
lipoproteins. Hundreds of the
different receptors are known and
many more have yet to be studied.
The Transmembrane receptors are
typically classified based on their
tertiary i.e three-dimensional
structure. If the three-dimensional
structure is unknown, they can be
classified based on the membrane
topology. In the simplest receptors,
the polypeptide chains cross the
lipid bilayer once, while others,
such as the G-protein coupled
receptors, cross as many as seven
times. Each cell membrane can
have several kinds of the
membrane receptors, with varying
surface distributions. A single
receptor may also be differently
distributed at the different
membrane positions, depending on
the sort of the membrane and the
cellular function. The Receptors
are often clustered on the
membrane surface, rather than
evenly distributed.
Glossary of Genetics
• CELL-TO-CELL CONTACT -
The Cell–cell interaction refers to
the direct interactions between the
cell surfaces that play a crucial role
in the development and in the
function of the multicellular
organisms. These interactions
allow the cells to communicate
with each other in response to the
changes in their
microenvironment. This ability to
send and receive the signals is
essential for the survival of the cell.
The interactions between the cells
can be stable such as those made
through the cell junctions. These
junctions are involved in the
communication and in the
organization of the cells within a
particular tissue. Others are the
transient or the temporary such as
those between the cells of the
immune system or the interactions
involved in the tissue
inflammation. These types of the
intercellular interactions are
distinguished from the other types
such as those between the cells and
the extracellular matrix. The loss of
the communication between the
cells can result in the
uncontrollable cell growth and the
cancer. The Stable cell-cell
interactions are required for the cell
adhesion within a tissue and
controlling the shape and function
of the cells. The Tight junctions are
the multi-protein complexes that
hold the cells of a same tissue
together and prevent the
movement of the water and the
© 2022 by JPS Scientific Publications, India
96
water-soluble molecules between
cells. The Gap junctions are the
main site of the cell-cell signaling
or the communication that allow
the small molecules to diffuse
between the adjacent cells.
• CELLULOSE SYNTHASE -
The UDP-forming form of the
cellulose synthase is the main
enzyme that produces the
cellulose. Systematically, it is
known as the UDP-glucose,
(1→4)-β-D-glucan 4-β-D-
glucosyltransferase in the
enzymology. It catalyzes the
chemical reaction. This family of
enzymes is found in the bacteria
and in the plants alike. The Plant
members are usually known as the
CesA (cellulose synthase) or the
tentative CslA (cellulose synthase-
like), while the bacterial members
may additionally be known as the
BcsA (bacterial cellulose synthase)
or the CelA (simply “cellulose”).
The Plants acquired CesA from the
endosymbiosis event that produced
the chloroplast. This family
belongs to the glucosyltransferase
family 2 (GT2). The
Glycosyltransferases are involved
in the biosynthesis and hydrolysis
of the bulk of earth’s biomass.
There are known to be about seven
subfamilies in the plant CesA
superfamily,or ten in the combined
plant-algal superfamily. The
Urochordates are the only group of
the animals possessing this
enzyme, having acquired them by
the horizontal gene transfer more
Glossary of Genetics
than 530 million years ago. The
Cellulose is an aggregation of the
unbranched polymer chains made
of β-(1→4)-linked glucose residues
that makes up a large portion of
the primary and the secondary cell
walls. Although important for
plants, it is also synthesized by
most of the algae, some bacteria,
and some animals. Worldwide, 2 ×
1011 tons of the cellulose
microfibrils are produced, which
serves as a critical source of the
renewable biofuels and other
biological-based products, such as
the lumber, fuel, fodder, paper and
the cotton.
• CENP-A - The Centromere
protein A, which is also known as
the CENPA, is a protein which in
humans is encoded by the CENPA
gene. The CENPA is a histone H3
variant which is the critical factor
for determining the kinetochore
position(s) on each of the
chromosome in most of the
eukaryotes including the humans.
The CENPA is a protein which
epigenetically defines the position
of the centromere on each of the
chromosome, determining the
position of the kinetochore
assembly and the final site of the
sister chromatid cohesion during
the mitosis. The CENPA protein
is a histone H3 variant which
replaces one or both the canonical
H3 histones in a subset of the
nucleosomes within the
centromeric chromatin. The
CENPA has the greatest sequence
© 2022 by JPS Scientific Publications, India
97
divergence of the histone H3
variants, with just 48% similarity to
the canonical histone H3, and has
a highly diverged N-terminal tail
that lacks many well characterised
histone modification sites
including the H3K4, H3K9 and the
H3K27. The CENPA interacts
directly with the inner kinetochore
through the proteins including the
CENPC and the CENPN.
Through this interaction the
microtubules are able to accurately
segregate the chromosomes during
the mitosis. In most of the
eukaryotes CENPA is loaded into
the large domains of the highly
repetitive satellite DNA. The
position of the CENPA within the
satellite DNA are heritable at the
protein level through a purely
epigenetic mechanism.
• CENTRAL DOGMA - The
central dogma of the molecular
biology is an explanation of the
flow of genetic information within
a biological system. It is often
stated as the “DNA makes RNA,
and the RNA makes protein”,
although this is not its original
meaning. It was first stated by the
Francis Crick in the year 1957,
then published in the year 1958. It
deals with the detailed residue-by-
residue transfer of the sequential
information. It states that such
information cannot be transferred
back from the protein to either
protein or the nucleic acid. The
dogma is a framework for
understanding the transfer of the
Glossary of Genetics
sequence information between the
information-carrying biopolymers,
in the most common or the general
case, in living organisms. There
are 3 major classes of thebsuch
biopolymers: DNA and RNA
(both nucleic acids), and protein.
There are 3 × 3 = 9 conceivable
direct transfers of information that
can occur between these. The
dogma classes these into the 3
groups of the 3: three general
transfers i.e believed to occur
normally in the most of the cells,
two special transfers which is
known to occur, but only under
specific conditions in case of some
viruses or in a laboratory), and the
four unknown transfers (believed
never to occur). The general
transfers describe the normal flow
of the biological information,
DNA can be copied to the DNA
(DNA replication), DNA
information can be copied into
mRNA (transcription), and
proteins can be synthesized using
the information in mRNA as a
template (translation). The special
transfers describe, RNA being
copied from RNA (RNA
replication), DNA being
synthesised using an RNA
template (reverse transcription).
• CENTROMERE - The
centromere links a pair of the sister
chromatids together during the cell
division. This constricted region of
the chromosome connects the
sister chromatids, creating a short
arm (p) and a long arm (q) on the
© 2022 by JPS Scientific Publications, India
98
chromatids. During the mitosis,
spindle fibers attach to the
centromere via the kinetochore.
The physical role of the centromere
is to act as the site of the assembly
of the kinetochores – a highly
complex multiprotein structure that
is responsible for the actual events
of the chromosome segregation –
i.e. binding the microtubules and
signaling to the cell cycle
machinery when all the
chromosomes have adopted correct
attachments to the spindle, so that
it is safe for the cell division to
proceed and to completion and for
the cells to enter the anaphase.
There are, broadly speaking, two
types of centromeres.1) “Point
centromeres” bind to the specific
proteins that recognize the
particular DNA sequences with the
high efficiency. Any piece of the
DNA with the point centromere
DNA sequence on it will typically
form a centromere if present in the
appropriate species. 2) “Regional
centromeres” is the term coined to
describe the most centromeres,
which typically form on the regions
of the preferred DNA sequence,
but which can form on the other
DNA sequences as well. The
signal for the formation of a
regional centromere appears to be
epigenetic.
• CENTROSOME - The
centrosome is an organelle that
serves as the main microtubule
organizing center (MTOC) of the
animal cell, as well as a regulator
Glossary of Genetics
of the cell-cycle progression. The
centrosome provides structure for
the cell. The centrosome is thought
to have evolved only in the
metazoan lineage of the eukaryotic
cells. The Fungi and plants lack the
centrosomes and therefore use the
other structures to organize their
microtubules. Although the
centrosome has a key role in the
efficient mitosis in the animal cells,
it is not essential in certain fly and
in the flatworm species. The
Centrosomes are composed of the
two centrioles arranged at the right
angles to the each other, and
surrounded by a dense, highly
structured mass of the protein
termed as the pericentriolar
material (PCM). The PCM
contains the proteins responsible
for the microtubule nucleation and
the anchorin, including the γ-
tubulin, pericentrin and the ninein.
In general,the each centriole of the
centrosome is based on a nine-
triplet microtubule assembled in a
cartwheel structure, and contains
the centrin, cenexin and tektin. In
many of the cell types, the
centrosome is replaced by a cilium
during the cellular differentiation.
However, once the cell starts to
divide, the cilium is replaced again
by the centrosome.
• CGG TRIPLET REPEAT - The
CGG triplet repeat-binding protein
1 (CGGBP1) is a repetitive DNA-
binding transcription regulator
with the target sites at the CpG-
rich sequences such as the CGG
© 2022 by JPS Scientific Publications, India
99
repeats and the Alu-SINEs and the
L1-LINEs. The CGGBP1
mitigates the cytosine methylation
at the repetitive DNA sequences. It
also functions in the DNA
damage/repair and the telomere
metabolism. There are indications
that it may be involved in the
mRNA metabolism. The CGGBP1
ensures the CTCF occupancy
preferentially on repeats over the
canonical CTCF motifs, being a
regulator of the CTCF and its
binding sites in the interspersed
repeats. The CGGBP1/p20 is
known to bind to the
nonmethylated 5’-d(CGG)(n)-3’
trinucleotide repeats in the in the
promoter of the fragile X
messenger ribonucleoprotein 1
(FMR1/FMRP) gene, although it
seems not to have a direct effect on
the FMR1 transcription. The
Trinucleotide repeat disorders are
caused due to an abnormal number
of the triplet repeat sequences
either in the coding or the non-
coding regions and are a result of
the either maternal or the paternal
transmission.
• CHAIN TERMINATION - The
Chain termination is any chemical
reaction that ceases the formation
of the reactive intermediates in the
chain propagation step in the
course of the polymerization
process, effectively bringing it to a
halt. A method of the termination
that applies to all the polymer
reactions is the depletion of the
monomer. In the chain growth
Glossary of Genetics
polymerization, the two growing
chains can collide head to head
causing the growth of both of the
chains to stop. In the case of the
radical or the anionic
polymerization, the chain transfer
can occur where the radical are at
the end of the growing chain and
can also be transferred from the
chain to an individual monomer
unit causing a new chain to start
growing and the previous chain to
stop growing. With the step-
growth polymerization, the
reaction can also be terminated by
adding a monofunctional species
containing the same functionality
as one or more of the types of the
monomer used in the reaction.
• CHALCONE SYNTHASE - The
Chalcone synthase which is also
called as the naringenin-chalcone
synthase (CHS) is an enzyme
ubiquitous to the higher plants and
belongs to a family of the
polyketide synthase enzymes
(PKS) which is known as the type
III PKS. The Type III PKSs are
associated with the production of
the chalcones, a class of the
organic compounds found mainly
in the plants as the natural defense
mechanisms and as the synthetic
intermediates. The CHS was the
first type III of the PKS to be
discovered. It is the first committed
enzyme in the flavonoid
biosynthesis. The enzyme catalyzes
the conversion of the 4-coumaroyl-
CoA and the malonyl-CoA to the
naringenin chalcone. The CHS
© 2022 by JPS Scientific Publications, India
100
catalysis serves as the initial step
for the flavonoid biosynthesis. The
Flavonoids are important plant
secondary metabolites that serve
the various functions in the higher
plants. These include the
pigmentation, UV protection,
fertility, antifungal defense and the
recruitment of the nitrogen-fixing
bacteria. The CHS is believed to
act as a central hub for the
enzymes involved in the flavonoid
pathway. These enzymes interact
via the protein-protein
interactions.Through FLIM FRET,
it was shown that the CHS
interacts with the chalcone
isomerase (CHI), a consecutive
step enzyme, as well as the other
non-consecutive step enzymes
flavanone 3-hydroxylase (F3H),
dihydroflavonol 4-reductase
(DFR), and the flavonol synthase
I.
• CHAPERONE - In the field of the
molecular biology, the molecular
chaperones are the proteins that
assist in the conformational folding
or unfolding of the large proteins
or the macromolecular protein
complexes. There are a number of
the classes of the molecular
chaperones, all of the which
function to assist the large proteins
in the proper protein folding during
or after synthesis, and after the
partial denaturation. The
Chaperones are also involved in
the translocation of the proteins for
the proteolysis. The chaperones are
a type of assembly chaperones
Glossary of Genetics
which assist in the assembly of the
nucleosomes from the folded
histones and the DNA. One of the
major function of the molecular
chaperones is to prevent the
aggregation of the misfolded
proteins, thus many of the
chaperone proteins are classified as
the heat shock proteins, as the
tendency for the protein
aggregation is increased by the heat
stress. The majority of the
molecular chaperones do not
convey any of the steric
information for the protein folding,
and instead assist in the protein
folding by binding to and
stabilizing the folding
intermediates until the polypeptide
chain is fully translated. The
specific mode of the function of the
chaperones differs based on their
target proteins and the location.
Recent advances in single-molecule
analysis have brought insights into
the structural heterogeneity of the
chaperones, folding intermediates
and affinity of the chaperones for
the unstructured and the sructured
protein chains.
• CHARGAFF’S RULE - The
Chargaff’s rules state that the DNA
from any species of the any
organism should have a 1:1
stoichiometric ratio of the purine
and pyrimidine bases i.e.
A+G=T+C and, more specifically,
that the amount of the guanine
should be equal to cytosine and the
amount of the adenine should be
equal to the thymine. This pattern
© 2022 by JPS Scientific Publications, India
101
is found in both strands of the
DNA. This was discovered by the
Austrian-born chemist Erwin
Chargaff in the late 1940s. In most
of the bacterial genomes which are
generally 80-90% coding genes are
arranged in such a fashion that
approximately around 50% of the
coding sequence lies on the either
strand. The origin of the deviation
from the Chargaff’s rule in the
organelles has been suggested to be
a consequence of the mechanism of
the replication. During the
replication the DNA strands
separate. In the single stranded
DNA, the cytosine spontaneously
slowly deaminates to the adenosine
(a C to A transversion). The longer
the strands are separated the
greater the quantity of the
deamination. For the reasons that
are not yet clear the strands tend to
exist longer in the single form in
the mitochondria than in the
chromosomal DNA.
• CHROMATIN
IMMUNOPRECIPITATION -
The Chromatin
immunoprecipitation (ChIP) is a
type of the immunoprecipitation
experimental technique used to
investigate the interaction between
the proteins and the DNA in the
cell. It aims to determine whether
the specific proteins are associated
with the specific genomic regions,
such as the transcription factors on
the promoters or the other DNA
binding sites, and possibly define
the cistromes. The ChIP also aims
Glossary of Genetics
to determine the specific location
in the genome that the various
histone modifications are
associated with the indicating of
the target of the histone modifiers.
The ChIP is very crucial for the
advancements in the field of the
epigenomics and learning more
about the epigenetic phenomena.
There are mainly two types of the
ChIP, primarily differing in the
starting chromatin preparation.
The first uses the reversibly cross-
linked chromatin sheared by the
sonication called as the cross-
linked ChIP (XChIP). The Native
ChIP (NChIP) uses the native
chromatin sheared by the
micrococcal nuclease digestion.
The Large Scale assays using the
ChIP is challenging using the intact
model organisms. This is because
the antibodies have to be generated
for the each TF, or, alternatively,
the transgenic model organisms
expressing epitope-tagged TFs
need to be produced.
• CHIP ASSAY - The Chromatin
immunoprecipitation (ChIP)
assays is a technique which
identify the links between the
genome and the proteome by
monitoring the transcription
regulation through the histone
modification i. E epigenetics or the
transcription factor i.e DNA
binding interactions. The strength
of the ChIP assays is their ability to
capture a snapshot of the specific
protein i.e the DNA interactions
occurring in a system and to
© 2022 by JPS Scientific Publications, India
102
quantitate the interactions using
the quantitative polymerase chain
reaction (qPCR). The Chromatin
IP experiments require a variety of
the proteomics and the molecular
biology methods including the
crosslinking, cell lysis (protein–
DNA extraction), nucleic acid
shearing, antibody-based
immunoprecipitation, DNA
sample clean-up and the PCR. The
Additional techniques such as the
gel electrophoresis are usually used
during the optimization
experiments to validate the specific
steps. The technique involves the
cross-linking of the proteins with
the DNA, fragmentation, and the
preparation of the soluble
chromatin followed by the
immunoprecipitation with an
antibody recognizing the protein of
the interest. The basic steps in this
technique are the fixation,
sonication, immunoprecipitation,
and the analysis of the
immunoprecipitated DNA.
Although the ChIP is a very
versatile tool, the procedure
requires the optimization of the
reaction conditions.
• CHIP PROTEIN - A protein
microarray which is also called as
the protein chip is a high-
throughput method used to track
the interactions and the activities of
the proteins, and also to determine
their function, and determining
function on a large scale. Its main
advantage lies in the fact that the
large numbers of the proteins can
Glossary of Genetics
be tracked in parallel. The chip
consists of a support surface such
as a glass slide, nitrocellulose
membrane, bead, or the microtitre
plate, to which an array of capture
proteins is bound. The Probe
molecules, typically labeled with a
fluorescent dye, are added to the
array. Any of the reaction between
the probe and the immobilised
protein emits a signal which is
fluorescent in nature and it is read
by a laser scanner. The Protein
microarrays are rapid, automated,
economical, and highly sensitive,
consuming the small quantities of
samples and the reagents. The
concept and the methodology of
the protein microarrays was first
introduced and illustrated in the
antibody microarrays which is also
referred to as the antibody matrix
in the year 1983 in a scientific
publication and a series of the
patents. The high-throughput
technology behind the protein
microarray process was relatively
very easy to develop since it is
based on the technology developed
for the DNA microarrays, which
have become the most widely used
microarrays.
• CHIP SEQUENCING - The
ChIP-sequencing, which is also
known as the ChIP-seq, is a
method used to analyze the protein
interactions with the DNA. The
ChIP-seq combines the chromatin
immunoprecipitation (ChIP) with
the massively parallel DNA
sequencing to identify the binding
© 2022 by JPS Scientific Publications, India
103
sites of rye DNA-associated
proteins. It can be used to map the
global binding sites precisely for
any protein of the interest.
Previously, the ChIP-on-chip was
the most common technique
utilized to study these types of
protein–DNA relations. The ChIP-
seq is primarily used to determine
how the transcription factors and
the other chromatin-associated
proteins influence the phenotype-
affecting mechanisms.
Determining how the proteins
interact with the DNA to regulate
the gene expression is essential for
fully understanding many of the
biological processes and the disease
states. This epigenetic information
is complementary to the genotype
and the expression analysis. The
ChIP-seq technology is currently
seen primarily as an alternative to
the ChIP-chip which requires a
hybridization array. This
introduces some bias, as an array is
restricted to a fixed number of the
probes. Sequencing, by the
contrast, is thought to have a very
less bias, although the sequencing
bias of the different sequencing
technologies is not yet fully
understood.
• CHIP SEQUENCES ASSAY -
The Chromatin
immunoprecipitation (ChIP)
assays identify the links between
the genome and the proteome by
monitoring the transcription
regulation through the histone
modification (epigenetics) or the
Glossary of Genetics
transcription factor–DNA binding
interactions. By combining the
chromatin immunoprecipitation
(ChIP) assays with the sequencing,
the ChIP sequencing (ChIP-Seq) is
a powerful method for identifying
the genome-wide DNA binding
sites for the transcription factors
and the other proteins. Using the
ChIP seq assay, the DNA-protein
interactions are studied within the
context of the cell. The basic steps
in this technique are the fixation,
sonication, immunoprecipitation,
and the analysis of the
immunoprecipitated DNA.
Although the ChIP is a very
versatile tool, the procedure
requires the optimization of the
reaction conditions.
• CHROMATID - A chromatid is
one of the half of the duplicated
chromosome. Before the
replication, one chromosome is
composed of one DNA molecule.
In the replication, the DNA
molecule is copied, and the two
molecules are known as the
chromatids. During the later stages
of the cell division these
chromatids separate longitudinally
to become the individual
chromosomes. The Chromatid
pairs are normally genetically
identical, and said to be the
homozygous. However, if the
mutations occur, they will present
as the slight differences, in which
case they are the heterozygous.
The pairing of the chromatids
should not be confused with the
© 2022 by JPS Scientific Publications, India
104
ploidy of an organism, which is the
number of homologous versions of
a chromosome. The Chromatids
may be sister or the non-sister
chromatids. A sister chromatid is
the either one of the two
chromatids of the same
chromosome which is joined
together by a common centromere.
A pair of the sister chromatids is
called as the dyad. Once the sister
chromatids have separated i.e
during the anaphase of the mitosis
or the anaphase II of the meiosis
during the sexual reproduction,
they are again called as the
chromosomes, each having the
same genetic mass as one of the
individual chromatids that made
up its parent. The DNA sequence
of the two sister chromatids is
completely identical i.e apart from
very rare DNA copying errors.
• CHROMATIN ACCESSIBILITY
- The Chromatin accessibility, or
the physical access to the
chromatinized DNA, is a widely
studied characteristic of the
eukaryotic genome. As the active
regulatory DNA elements are
generally very ‘accessible’, the
genome-wide profiling of the
chromatin accessibility can be used
to identify the candidate regulatory
genomic regions in a tissue or in
the cell type. The Multiple
biochemical methods have been
developed to profile the chromatin
accessibility, both in the bulk and
at the single-cell level. Depending
on the method, the enzymatic
Glossary of Genetics
cleavage, transposition or the
DNA methyltransferases are used,
followed by the high-throughput
sequencing, providing a view of the
genome-wide chromatin
accessibility. It is an important
biochemical methods, as well as
the bioinformatics tools for
analysing and interpreting the
generated data, and insights into
the key regulators underlying the
developmental, evolutionary and
the disease processes. It requires
standards for data quality,
reproducibility and the deposition
used by the genomics community.
Although the chromatin
accessibility profiling is invaluable
to study the gene regulation, alone
it provides only a partial view of
this complex process. Orthogonal
assays facilitate the interpretation
of the accessible regions with
respect to the enhancer–promoter
proximity, functional transcription
factor binding and regulatory
function. This technological
improvements including the single-
molecule, multi-omics and spatial
methods will bring the further
insight into the secrets of the
genome regulation.
• CHRONIC LYMPHOCYTIC
LEUKEMIA - The Chronic
lymphocytic leukemia (CLL) is a
type of the cancer of the blood and
bone marrow the spongy tissue
inside bones where the blood cells
are made. The term “chronic” in
the chronic lymphocytic leukemia
comes from the fact that this
© 2022 by JPS Scientific Publications, India
105
leukemia typically progresses more
slowly than the other types of the
leukemia. The term “lymphocytic”
in the chronic lymphocytic
leukemia comes from the cells
affected by the disease a group of
the white blood cells called as the
lymphocytes, which help your
body to fight against the infection.
• CISPLATIN - The Cisplatin is a
chemotherapy medication which is
used to treat a number of the
cancers. These includes the
testicular cancer, ovarian cancer,
cervical cancer, breast cancer,
bladder cancer, head and neck
cancer, oesophageal cancer, lung
cancer, mesothelioma, brain
tumors and the neuroblastoma. It
is given by the injection into a vein.
The cisplatin is administered
intravenously as the short-term
infusion in the normal saline for
the treatment of the solid and
haematological malignancies. It is
used to treat the various types of
the cancers, including the
sarcomas, some carcinomas (e.g.
small cell lung cancer, squamous
cell carcinoma of the head and the
neck and the ovarian cancer),
lymphomas, bladder cancer,
cervical cancer, and the germ cell
tumors. The Cisplatin is
particularly effective against the
testicular cancer its adoption has
increased the cure rate from the
10% to the 85%. Although the
further trials are very necessary,
cisplatin has been studied with the
Auger therapy to increase the
Glossary of Genetics
therapeutic effects of the cisplatin,
without increasing the normal
tissue toxicities. The Common
side effects include the bone
marrow suppression, hearing
problems, kidney damage, and the
vomiting. Other serious side effects
include the numbness, trouble
walking, allergic reactions,
electrolyte problems, and the heart
disease. It’s Use during the
pregnancy can cause harm to the
developing foetus. The Cisplatin is
in the platinum-based
antineoplastic family of the
medications. It works in part by
binding to the DNA and inhibiting
its replication.
• CIS AND TRANS SPLICING -
In the cis-splicing, the U1 snRNP
base pairs with the 5’ splice site,
and the U2 snRNP base pairs with
the branchpoint near the 3’ splice
site. The intron is excised and the
two exons are then spliced
together. In the trans-splicing there
is no 5’ splice site on the pre-
mRNA for the U1 snRNP binding.
Instead, of the 5’ splice site is then
provided by the donor SL snRNP,
which can base pair with a
sequence in the outron, i.e the
region of the pre-mRNA between
the 5’ cap and the trans-splice site.
The SL exon is then spliced to the
first exon on the pre-mRNA. The
key difference between the cis and
the trans splicing is that the cis
splicing is an intramolecular
mechanism that removes the
introns and joins the exons that are
© 2022 by JPS Scientific Publications, India
106
within the same RNA transcript,
while the trans-splicing is an
intermolecular mechanism that
removes the introns or the outrons
and joins the exons that are not
within the same RNA
• CISTRON - A cistron is an
alternative term for the “gene”.
The word cistron is used to
emphasize that the genes exhibit a
specific behavior in a cis-trans test
distinct positions or loci within a
genome are the cistronic. For
example, suppose a mutation at a
chromosome position x is
responsible for the change in the
recessive trait in a diploid organism
where the chromosomes come in
the pairs. We say that the
mutation is the recessive because
the organism will exhibit the wild
type of the phenotype i.e the
ordinary trait, unless both the
chromosomes of a pair have the
mutation (homozygous mutation).
Similarly, suppose a mutation at
the another position y, is
responsible for the same recessive
trait. The positions of the x and the
y are then said to be within the
same cistron when an organism
that has the mutation at the x on
the one chromosome and has the
mutation at the position y on the
paired chromosome exhibits the
recessive trait even though the
organism is not homozygous for
the either mutation. When instead
the wild type trait is expressed, the
positions are said to belong to the
distinct cistrons / genes.
Glossary of Genetics
• CHROMOSOME JUMPING -
The Chromosome jumping is a
tool of the molecular biology that
is used in the physical mapping of
the genomes. It is related to the
several other tools used for the
same purpose, including the
chromosome walking. The
Chromosome jumping is used to
bypass the regions difficult to
clone, such as those containing the
repetitive DNA, that cannot be
easily mapped by the chromosome
walking, and is useful in moving
along a chromosome rapidly in
search of a particular gene. Unlike
the chromosome walking,
chromosome jumping is able to
start on one point of the
chromosome in order to traverse
the potential distant point of the
same chromosome without cloning
the intervening sequences. The
ends of a large DNA fragment is
the target cloning section of the
chromosome jumping while the
middle section gets removed by
sequences of the chemical
manipulations prior to the cloning
step. It Allows more rapid
movement through the genome
compared to other techniques,
such as the chromosome walking.
It is also Able to travel across the
chromosomal regions containing
the uncloneable sequences in the
bacterial hosts. This technique can
be used to generate the genomic
markers with the known
chromosomal locations. The
Combination of the jumping and
© 2022 by JPS Scientific Publications, India
107
the linking jumping libraries to
walking offers possibility of the
directional walking and might
allow the analysis of the longer
regions in the parallel mapping
strategies. It Reduces the
complexity of the libraries to be
screened and constructed of the
mammalian genome.
• CLASTOGEN - The clastogen is a
mutagenic agent that disturbs the
normal DNA related processes or
directly causes the DNA strand
breakages, thus causing the
deletion, insertion, or the
rearrangement of the entire
chromosome sections. These
processes are a form of the
mutagenesis which if left
unrepaired, or the improperly
repaired, which can lead to the
cancer. The Known clastogens
include the acridine yellow,
benzene, ethylene oxide, arsenic,
phosphine, mimosine, actinomycin
D, camptothecin, methotrexate,
methyl acrylate, resorcinol and the
5-fluorodeoxyuridine.
Additionally, the 1,2-
dimethylhydrazine is a very known
colon carcinogen and shows the
signs of the possessing clastogenic
activity. There are many of the
clastogens that are not listed here
and tteresearch is ongoing to
discover the new clastogens. Some
of the known clastogens only
exhibit the clastogenic activity in
the certain cell types, such as the
caffeine which exhibits the
clastogenic activity in the plant
Glossary of Genetics
cells. The Researchers are
interested in the clastogens for
researching the cancer, as well as
for the other human health
concerns such as the inheritability
of the clastogen effected paternal
germ cells that lead to the fetus
developmental defects.
• CLOCK PROTEINS - The
CLOCK which is termed as the
circadian locomotor output cycles
kaput is a gene encoding a basic
helix-loop-helix-PAS transcription
factor that is believed to affect both
the persistence and the period of
the circadian rhythms. The
CLOCK protein has been found to
play a ver central role as a
transcription factor in the circadian
pacemaker.In the Drosophila,
newly synthesized CLOCK (CLK)
is the hypophosphorylated in the
cytoplasm before entering into the
nucleus. Once in the nuclei, the
CLK is localized in the nuclear foci
and is later redistributed
homogeneously. The CYCLE
(CYC) which is also known as the
dBMAL for the BMAL1 ortholog
in the mammals dimerizes with the
CLK via their respective PAS
domains. This dimer then recruits
the co-activator CREB-binding
protein (CBP) and is further
phosphorylated. Once it is
phosphorylated, this CLK-CYC
complex binds to the E-box
elements of the promoters of the
period (per) and the timeless (tim)
via through its bHLH domain,
© 2022 by JPS Scientific Publications, India
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causing the stimulation of the gene
expression of the per and tim. A
large molar excess of the period
(PER) and the timeless (TIM)
proteins causes the formation of
the PER-TIM heterodimer which
prevents the CLK-CYC
heterodimer from binding to the E-
boxes of the per and tim,
essentially blocking the per and tim
transcription.
• CLONING - The Cloning is the
process of producing the individual
organisms with the identical or the
virtually identical DNA, either by
the natural or by the artificial
means. In the nature, some of the
organisms produce the clones
through the asexual reproduction.
In the field of biotechnology, the
cloning is the process of creating
the cloned organisms (copies) of
the cells and of the DNA fragments
(molecular cloning). The Cloning
is a natural form of the
reproduction that has allowed the
life forms to spread for the
hundreds of millions of the years.
It is a reproduction method used
by the plants, the fungi, and the
bacteria, and is also the way that
the clonal colonies reproduce
themselves. The Molecular cloning
refers to the process of making the
multiple molecules. The Cloning is
commonly used to amplify the
DNA fragments containing the
whole genes, but it can also be
used to amplify any of the DNA
sequence such as the promoters,
non-coding sequences and
Glossary of Genetics
randomly fragmented DNA. It is
used in a wide array of the
biological experiments and in the
practical applications ranging from
the genetic fingerprinting to the
large scale protein production.
Occasionally, the term cloning is
very misleadingly used to refer to
the identification of the
chromosomal location of a gene
associated with a particular
phenotype of the interest, such as
in the positional cloning process.
In practice, localization of the gene
to a chromosome or the genomic
region does not necessarily enable
one to the isolate or amplify the
relevant genomic sequence.
• CO-ACTIVATOR - A coactivator
is a type of the transcriptional
coregulator that binds to an
activator or a transcription factor
to increase the rate of the
transcription of a gene or set of the
genes. The activator contains a
DNA binding domain that binds
either to the DNA promoter site or
the specific DNA regulatory
sequence which is called an
enhancer. The Binding of the
activator-coactivator complex
increases the speed of the
transcription by recruiting the
general transcription machinery to
the promoter, therefore increasing
the gene expression. The use of
the activators and the coactivators
allows for the highly specific
expression of the certain genes
depending on the cell type and the
developmental stage. Some of the
© 2022 by JPS Scientific Publications, India
109
coactivators also have the histone
acetyltransferase (HAT) activity.
The HATs form the large
multiprotein complexes that
weaken the association of the
histones to the DNA by acetylating
the N-terminal histone tail. This
provides more space for the
transcription machinery to bind to
the promoter, therefore increasing
the gene expression. The
Activators are also found in the all
living organisms, but the
coactivator proteins are typically
only found in the eukaryotes
because they are very more
complex and they require a more
intricate mechanism for the gene
regulation. In the eukaryotes, the
coactivators are usually the
proteins that are localized in the
nucleus.
• COHESIN - The Cohesin is a
protein complex that mediates the
sister chromatid cohesion,
homologous recombination, and
the DNA looping. Cohesin is
formed of the SMC3, SMC1,
SCC1 and the SCC3 (SA1 or the
SA2 in the humans). The Cohesin
holds the sister chromatids together
after the DNA replication until the
anaphase when the removal of the
cohesin leads to separation of the
sister chromatids. The complex
forms a ring-like structure and it is
believed that the sister chromatids
are held together by the
entrapment inside the cohesin ring.
The Cohesin is a member of the
SMC family of the protein
Glossary of Genetics
complexes which includes the
Condensin, MukBEF and the
SMC-ScpAB. It is used to keep the
sister chromatids connected with
the each other during the
metaphase ensuring that during the
mitosis (and meiosis), each of the
sister chromatid segregates to the
opposite poles. Without the
cohesin, the cell would be unable
to control the sister chromatid
segregation since there would be
no way of ensuring whether the
spindle fiber attached on the each
sister chromatid is from a different
pole. It facilitates the spindle
attachment onto the chromosomes.
It facilitates the DNA repair by the
recombination method.
• CHROMATOGRAPHY - principally carried out by the 1)
Chromatography is a laboratory
technique for the separation of a
mixture into its various
components. The mixture is
dissolved in a fluid solvent which is
gas or a liquid) called the mobile
phase, which carries it through a
system which is a column, a
capillary tube, a plate, or a plane
sheet on which a material called
the stationary phase is fixed.
Because of the different
constituents of the mixture tends to
have the different affinities for the
stationary phase and are also
retained for the different lengths of
the time depending on their
interactions with its surface sites,
the constituents travel at the
different apparent velocities in the
mobile fluid, causing them to
© 2022 by JPS Scientific Publications, India
110
separate. The separation is based
on the differential partitioning
between the mobile and the
stationary phases. The Subtle
differences in a compound’s
partition coefficient result in the
differential retention on the
stationary phase and thus affect the
separation. The Chromatography
may be preparative or analytical.
• CHROMATIN REMODELING -
The Chromatin remodeling is the
dynamic modification of the
chromatin architecture to allow the
access of the condensed genomic
DNA to the regulatory
transcription machinery proteins,
and thereby the control of the gene
expression. Such remodeling is
covalent histone modifications by
the specific enzymes e.g. histone
acetyltransferases (HATs),
deacetylases, methyltransferases,
and the kinases, and the 2) ATP-
dependent chromatin remodeling
complexes which either move,
eject or restructure the
nucleosomes. Besides actively
regulating the gene expression, the
dynamic remodeling of the
chromatin imparts an epigenetic
regulatory role in several key
biological processes such as in egg
cells DNA replication and repair;
apoptosis; chromosome
segregation as well as in the
development and in the
pluripotency. The Aberrations in
the chromatin remodeling proteins
are found to be associated with the
Glossary of Genetics
human diseases, including the
cancer. Targeting the chromatin
remodeling pathways is currently
evolving as a major therapeutic
strategy in the treatment of the
several cancers.
• COILED COLI - A coiled coil is a
structural motif which is present in
the proteins in which 2–7 alpha-
helices are coiled together like the
strands of a rope. The Dimers and
the trimers are the most common
types. Many of the coiled coil-type
proteins are involved in the
important biological functions,
such as the regulation of the gene
expression e.g. transcription
factors. Notable examples are the
oncoproteins c-Fos and the c-Jun,
as well as the muscle protein
tropomyosin. The Coiled coils
usually contain a repeated pattern,
hxxhcxc, of the hydrophobic (h)
and the charged (c) amino-acid
residues, referred to as the heptad
repeat. The positions in the heptad
repeat are usually labeled as the
abcdefg, where a and d are the
hydrophobic positions, often being
occupied by the isoleucine, leucine,
or the valine. Folding of a
sequence with this repeating
pattern into an alpha-helical
secondary structure causes the
hydrophobic residues to be
presented as the ‘stripe’ that coils
very gently around the helix in the
left-handed fashion, forming an
amphipathic structure. The most
favorable way for the two such
helices to arrange themselves in the
© 2022 by JPS Scientific Publications, India
111
water-filled environment of the
cytoplasm is to wrap the
hydrophobic strands against the
each other sandwiched between the
hydrophilic amino acids. Thus, it
is the burial of the hydrophobic
surfaces that provides the
thermodynamic driving force for
the oligomerization.
• COLLINEARITY - The
Collinearity occurs when the
amino acid sequences in the
polypeptide correspond to the
codon sequences in the nucleic
acids, the 5′ end of the mRNA
matching with the NH2 end of the
polypeptide chain. Some of the
Drosophila genes, e.g. within the
ANTC (Antennapeadia complex,
chromosome 3-47.5) appear the
same sequence in the map as the
morphogenetic function they
control (lab, Pb, Dfd, Scr, Antp).
Similar collinearity has been
shown in the BXC (Bithorax
complex) Ultrabithorax segment.
The Collinearity is spelled with
two ls because derived from the
Latin word collineo. In the
homeotic complexes generally
there is an another “position
effect”, the products of the
relatively posterior acting genes
appear to be more abundant than
that of the anterior ones. The
Recent information indicates that
the collinearity is not completely
valid for the some/most parts of
the genome because the same
genetic elements are used
differently in the different contexts
Glossary of Genetics
of the genes and form an
interleaved or the modular
genomic.
• COLONY HYBRIDIZATION -
The Colony hybridization is a
method of selecting the bacterial
colonies with the desired genes
through a straightforward cloning
and the transfer process. The genes
of the interest have been added to a
bacterial plasmid previously
through the recombination,
allowing the genes from the other
organisms to be analyzed within a
bacterial colony. The overall
process involves a transfer of the
genetic material from one medium
to the another, typically using the
nitrocellulose filter paper, with the
intended goal of identifying and
isolating a specific type of the gene.
The radiographed RNA is used to
find the desired sequence within
the new bacterial colony and
essentially to “light it up” so that
the sequence can be identified for
the transfer. The most common
purpose of the colony
hybridization is to verify that a
certain DNA sequence was able to
successfully enter into a new cell,
meaning that the cells being
analyzed through this method are
the result of the recombination
between a specific piece of the
DNA and a bacterial. This method
was discovered by the scientists
Michael Grunstein and the David
S. Hogness.
• COM K - The comK is a positive
autoregulatory gene occupying a
© 2022 by JPS Scientific Publications, India
112
central position in the competence-
signal-transduction network. All
the regulatory routes identified in
this network converge at the level
of the comK expression. The
ComK protein is required for the
transcriptional induction of the
comK and the late competence
genes, which specify the
morphogenetic and the structural
proteins necessary for the
construction of the DNA-binding
and the uptake apparatus. The
ComK specifically binds to the
DNA fragments containing the
promoter and the upstream
sequences of the genes it affects
(comC, comE, comF, comG and
the comK). Using the portions of
the region upstream of the comC it
show that the ComK-binding
sequences are essential for the
expression of the competence.
Moreover, it demonstrate that the
presence of the ComK stimulates
the expression of the comF-lacZ
and the comG-lacZ translational
fusions in vivo in the Escherichia
coli. These results indicate that the
gene product of the comK is
identical to the previously inferred
to the competence transcription
factor (CTF).
• COMPARATIVE GENOMICS -
The Comparative genomics is a
field of the biological research in
which the genomic features of the
different organisms are compared.
The genomic features may also
include the DNA sequence, genes,
gene order, regulatory sequences,
Glossary of Genetics
and the other genomic structural
landmarks. In this branch of the
genomics, whole or the large parts
of the genomes resulting from the
genome projects are compared to
the study basic biological
similarities and the differences as
well as the evolutionary
relationships between the
organisms. The major principle of
the comparative genomics is that
the common features of the two
organisms will often be encoded
within the DNA that is
evolutionarily conserved between
them. Therefore, the comparative
genomic approaches start with
making some form of the
alignment of the genome sequences
and looking for the orthologous
sequences i.e the sequences that
share a very common ancestry, in
the aligned genomes and checking
to what extent those sequences are
conserved. Based on these, the
genome and the molecular
evolution are inferred and this may
in turn be put in the context of, for
example, the phenotypic evolution
or the population genetics.
• COMPLEMENTATION - In the
field of the genetics, the
complementation occurs when the
two strains of an organism with the
different types of the homozygous
recessive mutations that produce
the same mutant phenotype have
offspring that express the wild-type
phenotype when mated or crossed.
The Complementation will
ordinarily occur if the mutations
© 2022 by JPS Scientific Publications, India
113
are in the different genes i.e
intergenic complementation. The
Complementation may also occur
if the two mutations are at the
different sites within the same gene
i.e intragenic complementation,
but this effect is usually weaker
than that of the intergenic
complementation. In the case
where the mutations are in the
different genes, the each strain’s
genome supplies the wild-type of
the allele to the “complement” the
mutated allele of the other strain’s
genome. Since the mutations are
the recessive, the offspring will
display the wild-type phenotype. A
test known as the complementation
test (sometimes which is called as
the “cis-trans” test) can be used to
test whether the mutations in the
two strains are in the different
genes or not. The
Complementation ordinarily will
occur more weakly or not at all if
the mutations are in the same gene.
The convenience and the essence
of this test is that the mutations
that produce a phenotype can be
assigned to the different genes
without the exact knowledge of
what the gene product is doing on
a molecular level. The
complementation test was
developed by the American
geneticist Edward B. Lewis.
• COMPOSITE TRANSPOSON -
A composite transposon is very
similar in the function to the
simple transposons and in the
insertion sequence (IS) elements in
Glossary of Genetics
that it has the protein coding DNA
segments flanked by the inverted,
repeated sequences that can be
recognized by the transposase
enzymes. A composite
transposon, however, is flanked by
the two separate IS elements which
may or may not be the exact
replicas. Instead of the each the IS
element moving separately, the
entire length of the DNA spanning
from one IS element to the other is
transposed as the one complete
unit. The Composite transposons
will also often carry one or more
than one genes conferring the
antibiotic resistance. The DNA
arrangement forms a composite
transposon whose presence has
been confirmed by the complete
bovine genomic sequence where
the mobilized sequence may be
found on the bovine chromosome
15. It is likely that the similar
composite transposons exist in the
other bovine genomic regions and
the other mammalian genomes.
They could be detected with the
suitable algorithms.
• CONDENSIN - The Condensins
are the large protein complexes
that play a central role in the
chromosome assembly and in the
segregation during the mitosis and
the meiosis. Their subunits were
originally identified as the major
components of the mitotic
chromosomes assembled in the
Xenopus egg extracts. Many of the
eukaryotic cells possess the two
different types of the condensin
© 2022 by JPS Scientific Publications, India
114
complexes, known as the
condensin I and the condensin II,
each of the which is composed of
the five subunits. The Condensins
I and II share the same pair of the
core subunits, SMC2 and SMC4,
both belonging to a large family of
the chromosomal ATPases, known
as the SMC proteins (SMC stands
for the Structural Maintenance of
the Chromosomes). Each of the
complexes contains a distinct set of
the non-SMC regulatory subunits
known as the kleisin subunit and a
pair of the HEAT repeat subunits.
Both the complexes are large,
having a total molecular mass of
about 650-700 kDa. The core
subunits of the condensins (SMC2
and SMC4) are conserved among
all the eukaryotic species that have
been studied to the date. The non-
SMC subunits unique to the
condensin I are also conserved
among the eukaryotes, but the
occurrence of the non-SMC
subunits unique to the condensin II
is highly variable among the
species.
• CONFORMATIONAL
CHANGES IN PROTEINS - The
Structural fluctuations of the
proteins are often intimately
coupled to the biochemical
function. Indeed, the regulated
conformational changes control
diverse cellular processes, such as
the signal transduction, membrane
trafficking, vesicular transport and
the polypeptide chain elongation.
Key to the linkage of the structural
Glossary of Genetics
fluctuations and the functional
properties is the ability of alternate
conformations to the preferentially
interact with the different binding
partners at different times or the
locations. This spatiotemporal
modulation of the function through
the dynamics allows the eukaryotic
cells to manage a large number of
the essential cellular processes with
a limited number of the distinct
gene products. Perhaps the most
prominent examples of the proteins
that undergo the large-scale
conformational changes to regulate
the cell processes are the guanine
and the adenine nucleotide
triphosphatases (NTPases). These
ubiquitous enzymes function as the
conformational switches and
regulators fueled by the nucleotide
binding and the hydrolysis. There
are two classes of such proteins:
Ras-related G-proteins and the
kinases. The Guanine and the
adenine nucleotide
triphosphatases, such as the Ras
proteins and the protein kinases,
undergo a large conformational
changes upon the ligand binding in
the course of their functions.
• CHROMOSOME
CONFORMATIONAL
CAPTURE - The Chromosome
conformation capture techniques
which is often abbreviated to the
3C technologies or the 3C-based
methods are a set of the molecular
biology methods used to analyze
the spatial organization of the
chromatin in a cell. These
© 2022 by JPS Scientific Publications, India
115
methods quantify the number of
the interactions between the
genomic loci that are nearby in the
3-D space, but may be separated by
the many nucleotides in the linear
genome. Such interactions may
result from the biological
functions, such as the promoter-
enhancer interactions, or from the
random polymer looping, where
the undirected physical motion of
the chromatin causes the loci to
collide. The Interaction
frequencies may be analyzed
directly, or they may be converted
to the distances and used to
reconstruct the 3-D structures. The
chief difference between the 3C-
based methods is their scope. For
example, when using the PCR to
detect the interaction in a 3C
experiment, the interactions
between the two specific fragments
are then quantified. In contrast, the
Hi-C quantifies interactions
between all the possible pairs of the
fragments simultaneously. Deep
sequencing of the material
produced by the 3C also produces
the genome-wide interactions
maps.
• CONSENSUS SEQUENCE - In
the field of the molecular biology
and in the bioinformatics, the
consensus sequence or the
canonical sequence is the
calculated order of the most
frequent residues, either the
nucleotide or the amino acid,
found at the each position in a
sequence alignment. It serves as a
Glossary of Genetics
very simplified representation of
the viral population. It represents
the results of the multiple sequence
alignments in which the related
sequences are compared to the
each other and the similar
sequence motifs are then
calculated. Such information is
important when considering the
sequence-dependent enzymes such
as the RNA polymerase. A protein
binding site, which is represented
by a consensus sequence, may be a
short sequence of the nucleotides
which is found many to several
times in the genome and is thought
to play the same role in its different
locations. For example, many
transcription factors recognize the
particular patterns in the promoters
of the genes which they regulate.
In the same way, the restriction
enzymes usually have the
palindromic consensus sequences,
usually corresponding to the site
where they cut the DNA. The
Transposons act in much the same
manner in their identification of
the target sequences for the
transposition. Finally, the splice
sites or the sequences immediately
surrounding the exon-intron
boundaries can also be considered
as the consensus sequences.
• CSSR - The Site-specific
recombination, which is also
known as the conservative site-
specific recombination, is a type of
the genetic recombination in which
the DNA strand exchange takes
place between the segments
© 2022 by JPS Scientific Publications, India
116
possessing at least a certain degree
of the sequence homology. The
Enzymes known as a site-specific
recombinases (SSRs) perform the
rearrangements of the DNA
segments by recognizing and
binding to the short, specific DNA
sequences (sites), at which they
cleave the DNA backbone,
exchange the two DNA helices
involved, and rejoin the DNA
strands. In some of the cases the
presence of a recombinase enzyme
and the recombination sites is
sufficient for the reaction to
proceed further, in other systems a
number of the accessory proteins
and/or accessory sites are required.
Many of the different genome
modification strategies, among
these recombinase-mediated
cassette exchange (RMCE), an
advanced approach for the targeted
introduction of the transcription
units into the predetermined
genomic loci, rely on the SSRs.
The Site-specific recombination
systems are the highly specific, fast,
and efficient, even when faced with
the complex eukaryotic genomes.
They are employed naturally in a
variety of the cellular processes,
including the bacterial genome
replication, differentiation and the
pathogenesis, and the movement of
the mobile genetic elements. For
the same reasons, they present a
potential basis for the development
of the genetic engineering tools.
Glossary of Genetics
• CONSTITUTIVE EXPRESSION
- The Constitutively expressed
genes, that is, are the always “on”.
Even the given constitutive
expression, however, it is still
possible for an organism that is not
metabolizing to not to express
those genes. The Contrast
inducible as well as repressible or,
indeed the facultative genes. Note
that the constitutively expressed
genes often are known as the
housekeeping genes, that is,
playing the basic as well as the
continuously applicable roles in the
metabolism. Just because a gene is
always expressed, however, does
not mean that the level of its
expression, including the post-
transcriptionally or the post-
translationally, cannot be
modified.
• CONTIGS - A contig (from the
contiguous) is a set of the
overlapping DNA segments that
together represent a consensus
region of the DNA. In bottom-up
the sequencing projects, a contig
refers to the overlapping sequence
data, in top-down sequencing
projects, the contig refers to the
overlapping clones that form a
physical map of the genome that is
used to guide the sequencing and
the assembly. The Contigs can
thus refer to both the overlapping
DNA sequences and to the
overlapping physical segments
(fragments) contained in the clones
depending on the context. A
sequence contig is a continuous
© 2022 by JPS Scientific Publications, India
117
(not contiguous) sequence resulting
from the reassembly of the small
DNA fragments generated by the
bottom-up sequencing strategies.
The Contig can also refer to the
overlapping clones that form a
physical map of a chromosome
when the top-down or the
hierarchical sequencing strategy is
used. In this sequencing method, a
low-resolution map is made prior
to the sequencing in order to
provide a framework to guide the
later assembly of the sequence
reads of the genome. This map
identifies the relative positions and
overlap of the clones used for the
sequencing path that is used for the
sequencing.
• COOMASSIE BRILLIANT
BLUE - The Coomassie brilliant
blue is the name of the two similar
triphenylmethane dyes that were
developed for the use in the textile
industry but are now commonly
used for the staining proteins in the
analytical biochemistry. The
Coomassie brilliant blue G-250
differs from the Coomassie brilliant
blue R-250 by the addition of the
two methyl groups. The name
“Coomassie” is a registered
trademark of the Imperial
Chemical Industries. The Bradford
assay uses the spectral properties of
the Coomassie brilliant blue G-250
to estimate the amount of the
protein in a solution. A protein
sample is added to a solution of the
dye in the phosphoric acid and
ethanol. Under the acidic
Glossary of Genetics
conditions the dye is normally a
very brownish colour but on
binding to the protein the blue
form of the dye is then produced.
The optical absorbance of the
solution is measured at a
wavelength of the 595 nm.
However, among the
disadvantages of the method is its
variability of the color
development with the different
proteins the absorbance change per
unit mass of the proteins varies
with the type of the protein. On
binding to the protein, the
negatively charged Coomassie
brilliant blue G-250 dye molecule
will then give an overall negative
charge to the protein. This property
can be used to separate the proteins
or the protein complexes using the
polyacrylamide gel electrophoresis
under the non-denaturing
conditions in a technique called the
blue native PAGE. The mobility
of the complex in the
polyacrylamide gel will depend on
the size of the protein complex (i.e.
the molecular weight) and the
amount of the dye bound to the
protein.
• CORE AND LINEAR DNA -
The core DNA is the DNA that is
actually associated with the histone
octamer. This value is invariant
and is around 146 base pairs. The
core DNA forms the two loops
around the octamer, and this
permits the two regions that are
about 80 bp apart to be brought
into the close proximity. Thus, the
© 2022 by JPS Scientific Publications, India
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two sequences that are far apart
can interact with the same
regulatory protein to control the
gene expression. The DNA that is
between the each histone octamer
is called as the linker DNA and
can vary in the length from the 8 to
114 base pairs. This variation is the
species specific, but the variation in
the linker DNA length has also
been associated with the
developmental stage of the
organism or the specific regions of
the genome.
• CORE ENZYMES - The core
enzyme is a enzyme which consists
of the subunits of an enzyme that
are needed for the catalytic
activity, as in the core enzyme
RNA polymerase. An example of
the core enzyme is the RNA
polymerase enzyme without the
sigma factor (σ). This enzyme
consists of the only two alpha (2α),
one beta (β), one beta prime (β’)
and the one omega (ω). This is just
one example of a core enzyme.
The DNA Pol I can also be
characterized as having the core
and the holoenzyme segments,
where the 5’exonuclease can be
removed without destroying the
enzyme functionality.
• CORE HISTONE - The Core
histones play structural roles in the
chromatin assembly and in the
compaction by forming the
nucleosome. Each of the core
histones contain the histone fold
domain, composed of the three α-
helices connected by the two loops,
Glossary of Genetics
which allow the heterodimeric
interactions between the core
histones which is known as the
handshake motif. Additionally,
each of the core histone also
contains an N-terminal tail that is
subjected to a wide variety of the
PTMs. The core histone tails play
an important roles in the
nucleosome stability, and may
contribute to define the condensed
state of the chromatin fibre and the
higher order structures by
facilitating the nucleosome
assembly or the disassembly.
• CO SUPPRESSION - The
Cosuppression is a classical form
of the eukaryotic post-
transcriptional gene silencing. It
was first reported in the transgenic
petunia, where a sense transgene
meant to overexpress the host
Chalcone Synthase-A (CHS-A)
gene caused the degradation of the
homologous transcripts and the
loss of the flower pigmentation. In
the co-suppression, when a gene is
introduced by the transformation
into a cell, neither the resident nor
the transgene copy of the same
gene is expressed i.e the repeat-
induced gene silencing or
increasing the gene copy number
reduces the degree of the
expression. The co suppression
effect depends on the sequence
identity between the transgene and
the endogenous gene. Some cases
of the co-suppression resemble the
RNA interference the experimental
silencing of the genes by the
© 2022 by JPS Scientific Publications, India
119
introduction of the double-stranded
RNA, as the RNA seems to be
both an important initiator and a
target in these processes.
• CSTF - The Cleavage stimulatory
factor or the cleavage stimulation
factor (CstF or the CStF) is a
heterotrimeric protein, made up of
the proteins such as the CSTF1
(55kDa), CSTF2 (64kDa) and the
CSTF3 (77kDa), totalling about
200 kDa. It is type of factor which
is involved in the cleavage of the 3’
signaling region from a newly
synthesized pre-messenger RNA
(mRNA) molecule. The CstF is
recruited by the cleavage and the
polyadenylation specificity factor
(CPSF) and assembles into the
protein complex on the 3’ end to
promote the synthesis of the
functional polyadenine tail, which
results in the maturation of the
mRNA molecule which is ready to
be exported from the cell nucleus
to the cytosol for the amount of the
CstF in a cell is dependent on the
phase of the cell cycle, increasing
significantly during the transition
from the G0 phase to the S phase
in the mouse fibroblast and the
human splenic B cells.
• CTBP - The C-terminal-binding
protein 1 which is also known as
the CtBP1 is a protein that in the
humans is encoded by the CTBP1
gene. The CtBP1 is one of the two
CtBP proteins, the other protein
being is the CtBP2. The CtBP1
protein was originally identified as
the human protein that bound a
Glossary of Genetics
PLDLS motif in the C-terminus of
the adenovirus E1A proteins. It
and the related protein CTBP2
were later shown to function as the
transcriptional corepressors. That
is, regulatory proteins that bind to
the sequence-specific DNA-binding
proteins and help to turn the genes
off. The CtBPs do this by recruiting
the histone modifying enzymes
that add the repressive histone
marks and remove the activating
marks. The CtBP proteins can also
self-associate and presumably bring
together the gene regulatory
complexes. The CtBP1 is broadly
expressed from the embryo to the
adult, while the CtBP2 has a
somewhat more restricted pattern
of the expression. The CtBPs have
multiple biological roles and
appear to be the most important in
regulating the epithelial to the
mesenchymal transition, as well as
influencing the metabolism.
• CTCF - The Transcriptional
repressor CTCF which is also
known as the 11-zinc finger protein
or the CCCTC-binding factor is a
transcription factor that in the
humans is encoded by the CTCF
gene. The CTCF is involved in
many of the cellular processes,
including the transcriptional
regulation, insulator activity,
recombination and the regulation
of the chromatin architecture. The
primary role of the CTCF is
thought to be in regulating the 3D
structure of the chromatin. The
CTCF binds together the strands of
© 2022 by JPS Scientific Publications, India
120
the DNA, thus forming the
chromatin loops, and anchors the
DNA to the cellular structures like
the nuclear lamina. It also defines
the boundaries between the active
and the Heterochromatin DNA.
Since the 3D structure of the DNA
influences the regulation of the
genes, the CTCF’s activity
influences the expression of the
genes. The CTCF is thought to be
a primary part of the activity of the
insulators, sequences that block the
interaction between the enhancers
and the promoters. The CTCF
binding has also been both shown
to promote and repress the gene
expression. It is unknown whether
the CTCF affects the gene
expression solely through its
looping activity, or if it has some
other or the unknown activity.
• CTF - The Nuclear factor I (NF-I)
or the CCAAT box-binding
transcription factor (CTF) which is
also known as the TGGCA-
binding proteins are a family of the
vertebrate nuclear proteins which
recognise and bind, as the dimers,
the palindromic DNA sequence 5’-
TGGCANNNTGCCA-3’. This
family was first described for its
role in stimulating the initiation of
the adenovirus DNA replication.
In the vertebrates there are four
members known as the NFIA,
NFIB, NFIC, and the NFIX and
an orthologue from the
Caenorhabditis elegans has been
described, which is called as the
Nuclear factor I family protein
Glossary of Genetics
(NFI-I). The CTF/NF-I proteins
are individually capable of
activating the transcription and the
DNA replication, thus they
function by regulating the cell
proliferation and the
differentiation. They are involved
in the normal development and
have been associated with the
developmental abnormalities and
cancer in the humans. In a given
species, there are a large number of
the different CTF/NF-I proteins,
generated both by the alternative
splicing and by the occurrence of
four different genes. The
CTF/NF-1 proteins contain 400 to
600 amino acids.
• CTRNA - The Circulating tumor
RNA (ctRNA) in the blood is also
used to identify the mutations in
the genes of the interest, but
additionally, it also provides the
information about the relative
expression levels of the important
genes. The PD-L1 expression in
the ctRNA is isolated from the
various cancer types. The Tumors
inhibit the antitumor response by
modulating the immune
checkpoint proteins programmed
death ligand 1 (PD-L1) and its
cognate receptor PD1. The
expression of these genes has been
implicated in the evasion of the
immune response and the
resistance to the targeted therapies.
• CUR AND PASTE
TRANSPOSITION - The
mechanism by which the
conservative transposition occurs is
© 2022 by JPS Scientific Publications, India
121
called as the “cut-and-paste”
method, which involves the five
main steps:-
• The enzyme ransposase is bound
to the inverted repeated sequences
flanking the ends of the
transposon. The Inverted repeats
define the ends of the transposons
and provide the recognition sites
for the transposase to bind.
• The formation of the transposition
is a very complex mechanism. In
this step the DNA bends and folds
into a pre-excision synaptic
complex so the two transposases
enzymes can interact with each
other.
• The interaction of these
transponases activates the
complex. The transposase makes
the double stranded breaks in the
DNA and the transposon is fully
excised.
• The enzyme transposase locate,
recognize and then bind to the
target site within the target DNA.
• The Transposase creates the
aasdadad Double stranded break in
the DNA and integrates the
transposon into the target site.
Both the excision and the insertion
of the transposon leaves the single
or the double stranded gaps in the
DNA, which are repaired by the
host enzymes such as the DNA
polymerase.
• CUT GENE - The cut locus
encodes a homeobox protein that is
localized in the nuclei of a variety
of the tissues and is required for the
proper morphogenesis of those
Glossary of Genetics
tissues. The Cut protein is required
in the embryonic and the adult
external sensory organs, where its
absence results in the conversion of
the organs to the chordotonal
organs. The Expression of the cut
also occurs in the Malpighian
tubules, spiracles, central nervous
system, and a number of the other
tissues. The Gypsy transposon
insertions upstream of the cut
promoter block the expression in
the subsets of these tissues. The
effect of the gypsy insertions is
polar, with those the farthest from
the promoter affecting the very
fewest tissues. The hypothesis that
gypsy insertions block a series of
the tissue-specific enhancer
elements that are distributed over a
region of the 80 kb upstream of the
promoter predicts the location of
the enhancers for the cut
expression in each of the tissues in
which it is active in the embryos.
The DNA fragments from this
region drive expression of a
reporter gene in each of the
embryonic tissues in which the
endogenous cut gene is expressed.
• CYSTEINE – TRNA LIGASES -
In the field of the enzymology, a
cysteine—tRNA ligase is an
enzyme which catalyzes the
chemical reaction. This enzyme
belongs to the family of the ligases,
to be specific those forming the
carbon-oxygen bonds in the
aminoacyl-tRNA and the related
compounds. The systematic name
of this enzyme class is rye L-
© 2022 by JPS Scientific Publications, India
122
cysteine, tRNACys ligase (AMP-
forming). Other names in the
common use include the cysteinyl-
tRNA synthetase, cysteinyl-
transferRNA synthetase, cysteinyl-
transfer ribonucleate synthetase,
and the cysteine translase. This
enzyme participates in the cysteine
metabolism and in the aminoacyl-
trna biosynthesis.
• CYTIDINE DEAMINASE - The
Cytidine deaminase is an enzyme
that in the humans is encoded by
the CDA gene. This gene encodes
an enzyme involved in the
pyrimidine salvaging. The encoded
protein forms a tetramer which is
known as the homotetramer that
catalyzes the irreversible hydrolytic
deamination of the cytidine and
the deoxycytidine to the uridine
and the deoxyuridine, respectively.
It is one of the several deaminases
responsible for maintaining the
cellular pyrimidine pool. The
Mutations in this gene are
associated with the decreased
sensitivity to the cytosine
nucleoside analogue cytosine
arabinoside used in the treatment
of the certain childhood leukemias.
Most of the cytidine deaminases
act on the RNA, and the few that
act on the DNA require ssDNA. A
related activation-induced
(cytidine) deaminase (AID)
regulates rye antibody
diversification, especially the
process of the somatic
hypermutation.
Glossary of Genetics
• CYTOKINESIS - The Cytokinesis
is the part of the cell division
process during which the
cytoplasm of a single eukaryotic
cell divides into the two daughter
cells. The Cytoplasmic division
begins during or after the late
stages of the nuclear division in the
mitosis and in the meiosis. During
the cytokinesis the spindle
apparatus partitions and transports
the duplicated chromatids into the
cytoplasm of the separating
daughter cells. It thereby ensures
that the chromosome number and
the complement are maintained
from the one generation to the next
and that, except in the special
cases, the daughter cells will be
functional copies of the parent cell.
After the completion of the
telophase and the cytokinesis, each
of the daughter cell enters the
interphase of the cell cycle. The
Plant cytokinesis differs from the
animal cytokinesis, partly because
of the rigidity of the plant cell
walls.
• CYTOSINE ARABINOSIDE -
The Cytarabine, also known as the
cytosine arabinoside (ara-C), is a
type of the chemotherapy
medication used to treat the acute
myeloid leukemia (AML), acute
lymphocytic leukemia (ALL),
chronic myelogenous leukemia
(CML), and the non-Hodgkin’s
lymphoma. It is given by the
injection into a vein, under the
skin, or into the cerebrospinal
fluid. There is a liposomal
© 2022 by JPS Scientific Publications, India
123
formulation for which there is
tentative evidence of the better
outcomes in the lymphoma
involving the meninges. The
Cytarabine also possesses the
antiviral activity, and it has been
used for the treatment of the
generalised herpesvirus infection.
However, the cytarabine is not
very selective in this setting and
causes the bone marrow
suppression and the other severe
side effects. Therefore, the ara-C is
not a useful antiviral agent in the
humans because of its toxic profile.
The Cytarabine is also used in the
study of the nervous system to
control the proliferation of the glial
cells in the cultures, the amount of
the glial cells having an important
impact on the neurons.
• CIS-REGULATORY
SEQUENCES - The Cis-
regulatory elements (CREs) or the
Cis-regulatory modules (CRMs)
are the regions of the non-coding
DNA which regulate the
transcription of the neighboring
genes. The CREs are the vital
components of the genetic
regulatory networks, which in turn
control the morphogenesis, the
development of the anatomy, and
the other aspects of the embryonic
development, studied in the
evolutionary developmental
biology. The CREs are found in
the vicinity of the genes that they
regulate. The CREs typically
regulate the gene transcription by
binding to the transcription factors.
Glossary of Genetics 124

A single transcription factor may

bind to many CREs, and hence
control the expression of the many
genes (pleiotropy). The CRMs are
the stretches of the DNA, usually
100–1000 DNA base pairs in the
length, where a number of the
transcription factors can bind and
regulate the expression of the
nearby genes and regulate their
transcription rates. They are
labeled as the cis because they are
typically located on the same DNA
strand as the genes they control as
opposed to the trans, which refers
to the effects on the genes not
located on the same strand or
farther away, such as the
transcription factors. One cis-
regulatory element can regulate the
several genes, and conversely, one
gene can have several cis-
regulatory modules.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
D and the functional organization of
• DNM 1 - The Dynamin-1 is a
protein that in the humans is
encoded by the DNM1 gene. This
gene encodes a member of the
dynamin subfamily of the GTP-
binding proteins. The encoded
protein possesses unique
mechanochemical properties used
to tubulate and the sever
membranes, and is involved in the
clathrin-mediated endocytosis and
the other vesicular trafficking
processes. The Actin and the other
cytoskeletal proteins act as a
binding partners for the encoded
protein, which can also self-
assemble leading to the stimulation
of the GTPase activity. More than
sixty highly conserved copies of the
3' region of this gene are found
elsewhere in the genome,
particularly on the chromosomes Y
and 15. The Alternatively spliced
transcript variants encoding the
different isoforms have also been
described.
• DECODING CENTRE - The
decoding center of the ribosome
provides mRNA translation and
the fidelity of the codon--anticodon
interactions along with the mRNA
translocation in the course of the
protein biosynthesis. The three-
dimensional structure of the
ribosome decoding center is still
unknown. However, up to the now
a number of the direct and indirect
© 2022 by JPS Scientific Publications, India
125
experimental data on the structural
the decoding center have been
obtained.
• DNA SCRUNCHING - The
mechanism by which the RNA
polymerase moves along the DNA
strand during the abortive
initiation remained elusive. It had
been observed that the RNA
polymerase did not escape from
the promoter during the
transcription initiation, so it was
unknown how the enzyme could
read the DNA strand to transcribe
it without moving downstream.
Within the last decade, studies
have revealed that the abortive
initiation involves the DNA
scrunching, in which the RNA
polymerase remains stationary
while it unwinds and pulls
downstream the DNA into the
transcription complex to pass the
nucleotides through the
polymerase active site, thereby
transcribing the DNA without any
further This causes the unwound
DNA to accumulate within the
enzyme, hence the name DNA
"scrunching".
• DNA G - The DnaG is a type of
bacterial DNA primase which is
encoded by the dnaG gene. The
enzyme DnaG, and any of the
other DNA primase, synthesizes
the short strands of the RNA
known as the oligonucleotides
during the DNA replication. These
oligonucleotides are known as the
primers because they act as a
Glossary of Genetics
starting point for the DNA
synthesis. The DnaG catalyzes the
synthesis of the oligonucleotides
that are 10 to 60 nucleotides (the
fundamental unit of the DNA and
RNA) long, however most of the
oligonucleotides synthesized are 11
nucleotides. These RNA
oligonucleotides serve as the
primers, or the starting points, for
the DNA synthesis by the bacterial
DNA polymerase III (Pol III). The
DnaG is important in the bacterial
DNA replication because the DNA
polymerase cannot initiate the
synthesis of a DNA strand, but can
only add the nucleotides to a
preexisting strand. The DnaG
synthesizes a single RNA primer at
the origin of the replication. This
primer serves to the prime leading
strand DNA synthesis
• DNA CONDENSATION - The
DNA condensation refers to the
process of the compacting DNA
molecules in vitro or in vivo. The
Mechanistic details of the DNA
packing are essential for its
functioning in the process of the
gene regulation in the living
systems. The Condensed DNA
often has surprising properties,
which one would not predict from
the classical concepts of the dilute
solutions. Therefore, the DNA
condensation in vitro serves as a
model system for many processes
of the physics, biochemistry and
biology. In addition, the DNA
condensation has many potential
applications in the medicine and
© 2022 by JPS Scientific Publications, India
126
the biotechnology. In the viruses
and bacteriophages, the DNA or
the RNA is surrounded by a
protein capsid, sometimes further
enveloped by a lipid membrane.
The Double-stranded DNA is
stored inside the capsid in the form
of a spool, which can have the
different types of the coiling
leading to the different types of the
liquid-crystalline packing. This
packing can change from
hexagonal to the cholesteric to the
isotropic at the different stages of
the phage functioning.
• DNA OXIDATION - The DNA
oxidation is the process of the
oxidative damage of
deoxyribonucleic acid. As
described in detail by thr Burrows
et al. 8-oxo-2'-deoxyguanosine (8-
oxo-dG) is the most common
oxidative lesion observed in the
duplex DNA because the guanine
has a lower one-electron reduction
potential than the other
nucleosides in the DNA. The one
electron reduction potentials of the
nucleosides (in volts versus NHE)
are the guanine 1.29, adenine 1.42,
cytosine 1.6 and the thymine 1.7.
About 1 in the 40,000 guanines in
the genome are present as the 8-
oxo-dG under the normal
conditions. This means that the
>30,000 8-oxo-dGs may exist at
any given time in the genome of a
human cell. Another product of the
DNA oxidation is the 8-oxo-dA.
The 8-oxo-dA occurs at about 1/10
the frequency of the 8-oxo-dG.[2]
Glossary of Genetics
The reduction potential of the
guanine may be reduced by as
much as around 50%, depending
on the particular neighboring
nucleosides stacked next to it
within the DNA. The Excess DNA
oxidation is linked to the certain
diseases and the cancers, while the
normal levels of the oxidized
nucleotides, due to the normal
levels of the ROS, may be
necessary for the memory and
learning.
• DNASE-SEQ - The DNase-seq
(DNase I hypersensitive sites
sequencing) is a method in the
molecular biology used to identify
the location of the regulatory
regions, based on the genome-wide
sequencing of the regions sensitive
to the cleavage by the DNase I.
The DNase-seq requires some of
the downstream bioinformatics
analyses in order to provide the
genome-wide DNA footprints. The
computational tools proposed can
be categorized in the two classes:
segmentation-based and the site-
centric approaches. The
Segmentation-based methods are
based on the application of the
Hidden Markov models or the
sliding window methods to
segment the genome into the
open/closed chromatin region.
The Site-centric methods, on the
other hand, find the footprints
given the open chromatin profile
around the motif-predicted binding
sites, i.e. the regulatory regions
predicted using the DNA-protein
© 2022 by JPS Scientific Publications, India
127
sequence information (encoded in
the structures such as the Position
weight matrix).
• DHSs - In the field of genetics, the
DNase I hypersensitive sites
(DHSs) are the regions of the
chromatin that are sensitive to the
cleavage by the DNase I enzyme.
In these specific regions of the
genome, the chromatin has lost its
condensed structure, exposing the
DNA and making it more
accessible. This raises the
availability of the DNA to the
degradation by the enzymes, such
as the DNase I. These accessible
chromatin zones are functionally
related to the transcriptional
activity, since this remodeled state
is necessary for the binding of the
proteins such as the transcription
factors. Since the discovery of the
DHSs 30 years ago, they have been
used as the markers of the
regulatory DNA regions. These
regions have been shown to map
many types of the cis-regulatory
elements including the promoters,
enhancers, insulators, silencers and
the locus control regions. A high-
throughput measure of these
regions is available through the
DNase-Seq.
• DCE - The Downstream elements
are a newly appreciated class of the
core promoter elements of the
RNA polymerase II-transcribed
genes. The downstream core
element (DCE) was discovered in
the human beta-globin promoter,
and its sequence composition is
Glossary of Genetics
distinct from that of the
downstream promoter element
(DPE). The DCE is a bona fide
core promoter element present in a
large number of the promoters and
with the high incidence in the
promoters containing a TATA
motif. The Database analysis
indicates that the DCE is found in
the diverse promoters, supporting
its functional relevance in a variety
of the promoter contexts. The
DCE consists of the three
subelements, and the DCE
function is recapitulated in a
TFIID-dependent manner. The
Subelement 3 can function
independently of the other two and
shows a TFIID requirement as
well. The UV photo-cross-linking
results demonstrate that the
TAF1/TAF(II)250 interacts with
the DCE subelement DNA in a
sequence-dependent manner. The
downstream elements consist of at
least two types, those of the DPE
class and those of the DCE class;
they function via the different
DNA sequences and interact with
the different transcription
activation factors.
• DAM METHYLASE - The DNA
adenine methylase, (Dam
methylase) which is also known as
the site-specific DNA-
methyltransferase, modification
methylase, restriction-modification
system is an enzyme that adds a
methyl group to the adenine of the
sequence 5’-GATC-3’ in the newly
synthesized DNA. Immediately
© 2022 by JPS Scientific Publications, India
128
after the DNA synthesis, the
daughter strand remains the
unmethylated for a short period of
time. It is an orphan
methyltransferase that is not part of
a restriction-modification system
and regulates the gene expression.
This is a very large group of the
enzymes which is unique to the
prokaryotes and the
bacteriophages. The E. Coli DNA
adenine methyltransferase enzyme
(Dam), which is widely used for
the chromatin profiling technique,
DamID. In which the Dam is
fused to a DNA-binding protein of
the interest and expressed as a
transgene in a genetically tractable
model organism to identify the
protein binding sites.
• DELETION - In the field of the
genetics, a deletion which is also
called as the gene deletion,
deficiency, or the deletion
mutation, is a mutation or a
genetic aberration in which a part
of a chromosome or a sequence of
the DNA is left out during the
DNA replication. Any number of
the nucleotides can be deleted,
from a single base to an entire
piece of the chromosome. Some of
the chromosomes have fragile
spots where the breaks can occur
which result in the deletion of a
part of the chromosome. The
breaks can be induced by the heat,
viruses, radiations, and the
chemicals. When a chromosome
breaks, a part of it is deleted or lost,
the missing piece of the
Glossary of Genetics
chromosome is referred to as the
deletion or a deficiency. The
smallest single base deletion
mutations is occured by a single
base flipping in the template DNA,
followed by the template DNA
strand slippage, within the DNA
polymerase active site.
• DECATENATION - The
Decatenation is a crucial in the in
vivo reaction of the DNA
topoisomerases in the DNA
replication and is frequently used
in the in vitro drug screening.
Usually this reaction is monitored
using the kinetoplast DNA as a
substrate, although this assay has
several types of limitations. Here
we have engineered a substrate for
the Tn3 resolvase that generates a
singly-linked catenane that can
readily be purified from the DNA
substrate after restriction enzyme
digestion and centrifugation. This
catenated substrate can be used
with the high sensitivity in the
topoisomerase assays and in the
drug-inhibition assays. The DNA
topoisomerases are the enzymes
that modulate E DNA topology.
These essential enzymes catalyze
the interconversion between the
different topological forms of the
DNA and are categorized, on
evolutionary and the mechanistic
grounds, into two the types: I and
II. The two types are distinguished
by the number of the
phosphotyrosyl linkages
established in the covalent DNA–
protein complex. Type I enzymes
© 2022 by JPS Scientific Publications, India
129
form a single linkage, leading to
the transient single-stranded DNA
breaks, whereas the type II
topoisomerases form the transient
double-stranded breaks via the two
phosphotyrosyl linkages. The
reactions characteristic of the
topoisomerases include the
relaxation, supercoiling,
knotting/unknotting and the
catenation/decatenation of their
DNA substrates.
• DDE TRANSPOSES - The
Transposase proteins are necessary
for the efficient DNA
transposition. This domain is a
member of the DDE superfamily,
which contains the three
carboxylate residues that are
believed to be responsible for the
coordinating of the metal ions
which is needed for the catalysis.
The catalytic activity of this
enzyme involves the DNA
cleavage at a specific site followed
by a strand transfer reaction.
During the transposition
DD[E/D]-transposases undergo a
series of the conformational
changes. The structural features of
the DD[E/D]-transposases for
which the three-dimensional
structures are available and that
relate to the transposases, which
are being developed for the use in
the mammalian cells. Similar to
the other members of the
polynucleotidyl transferase family,
the catalytic domains of the
DD[E/D]-transposases share a
common feature: an RNase H-like
Glossary of Genetics
fold that draws three catalytically
active residues, the DDE motif,
into the close proximity. Beyond
this fold, the structures of the
catalytic domains vary
considerably, and the DD[E/D]-
transposases display marked
structural diversity within their
DNA-binding domains.
• DDK - The CDC7-DBF4 kinase
which is also known as the DDK,
initiates the DNA replication in the
eukaryotes by activating the
replicative MCM helicase. The
DDK has diverse and apparently
conflicting roles in the replication
checkpoint response in the various
organisms, but the underlying
mechanisms are very far from
settled. The human DDK
promotes the limited resection of
the newly synthesized DNA at the
stalled replication forks or the sites
of the DNA damage to initiate the
replication checkpoint signaling.
The DDK is also required for the
efficient fork restart and the G2/M
cell cycle arrest. The DDK exhibits
genetic interactions with the
ssDNA exonuclease EXO1 and the
phosphorylates EXO1 in vitro. The
EXO1 is also required for the
nascent strand degradation
following the exposure to HU, so
DDK might regulate the EXO1
directly. Lastly, the sublethal DDK
inhibition causes the various
mitotic abnormalities, which is
consistent with a checkpoint
deficiency. In summary, DDK has
a primary and previously
© 2022 by JPS Scientific Publications, India
130
undescribed role in the replication
checkpoint to promote the ssDNA
accumulation at the stalled forks,
which is required to initiate a
robust checkpoint response and the
cell cycle arrest to maintain the
genome integrity.
• DEACETYLATION OF
HISTONES - The Histone
acetylation and deacetylation are
the essential parts of the gene
regulation. These reactions are
typically catalysed by the enzymes
with “histone acetyltransferase”
(HAT) or the “histone deacetylase”
(HDAC) activity. The Acetylation
is the process where an acetyl
functional group is transferred
from the one molecule (in this
case, acetyl coenzyme A) to the
another. The Deacetylation is
simply the reverse reaction where
the acetyl group is removed from
the molecule. The Acetylated
histones, octameric proteins that
organize the chromatin into the
nucleosomes, the basic structural
unit of the chromosomes and
ultimately higher order structures,
represent a type of the epigenetic
marker within the chromatin. The
Acetylation removes the positive
charge on the histones, thereby
decreasing the interaction of the N
termini of histones with the
negatively charged phosphate
groups of the DNA. As a
consequence, the condensed
chromatin is transformed into a
more relaxed structure that is
associated with the greater levels of
Glossary of Genetics
the gene transcription. This
relaxation can be reversed by the
deacetylation catalyzed by the
HDAC activity. Relaxed,
transcriptionally active DNA is
referred to as the euchromatin.
More condensed (tightly packed)
DNA is referred to as the
heterochromatin. Condensation
can be brought about by the
processes including the
deacetylation and the methylation.
• DEAD BOX HELICASE - The
DEAD box proteins are involved
in an assortment of the metabolic
processes that typically involve the
RNAs, but in some of the cases
also the other nucleic acids. They
are highly conserved in the nine
motifs and can be found in the
most of the prokaryotes and the
eukaryotes, but not all. Many of
the organisms, including the
humans, contain the DEAD-box
(SF2) helicases, which are involved
in the RNA metabolism. The
DEAD box proteins were first
brought to attention in the late
1980s in a study that looked at a
group of the NTP binding sites that
were similar in the sequence to the
eIF4A RNA helicase sequence.
The results of this study showed
that these proteins (p68, SrmB,
MSS116, vasa, PL10, mammalian
eIF4A, yeast eIF4A) involved in
the RNA metabolism had several
common elements. There were
nine common sequences found to
be conserved amongst the studied
© 2022 by JPS Scientific Publications, India
131
species, which is an important
criterion of the DEAD box family.
• DEAMINATION - The
Deamination is the removal of an
amino group from a molecule. The
Enzymes that catalyse this reaction
are called as the deaminases. In the
human body, the deamination
primarily takes place in the liver,
however it can also occur in the
kidney. In situations of the excess
protein intake, the deamination is
used to break down the amino
acids for the energy. The amino
group is removed from the amino
acid and then converted to the
ammonia. The rest of the amino
acid is made up of mostly the
carbon and the hydrogen, and is
recycled or oxidized for the energy.
The Ammonia is toxic to the
human system, and enzymes
convert it to the urea or the ric acid
by the addition of the carbon
dioxide molecules (which is not
considered a deamination process)
in the urea cycle, which also takes
place in the liver. The Urea and
the uric acid can safely diffuse into
the blood and then be excreted in
the urine.
• DECODING CENTRE - The
decoding centre of the ribosome
provides the mRNA translation
and the fidelity of the codon—
anticodon interactions along with
the mRNA translocation in the
course of the protein biosynthesis.
The three-dimensional structure of
the ribosome decoding centre is
still very unknown. However, up to
Glossary of Genetics
now a number of the direct and the
indirect experimental data on the
structural and the functional
organization of the decoding centre
have been obtained. The Early
biochemical studies positioned the
decoding centre of the ribosome on
the small 30S ribosomal subunit at
the interface with the large 50S
subunit. This decoding centre
covers the parts of the 16S rRNA
that includes the nucleotides 1400–
1500 of helix 44 (h44), nucleotides
1050–1200 (h43), and the 530 loop
(h18).
• DEFORMED GENES - The
Deformed (Dfd) is a Drosophila
homeotic selector gene required for
the normal development of the
maxillary segment morphology in
the larval and the adult head.
Consistent with this function, the
Dfd transcripts are restricted to the
epidermal, mesodermal and the
neural cells in the embryonic
mandibular and in the maxillary
primordia. It has a far upstream
element in the Dfd sequences
which functions as an epidermal-
specific autoregulatory enhancer.
In a search through the 35 kb of the
Dfd sequences for the additional
transcriptional control elements,
we have identified a 3.2 kb DNA
fragment containing an enhancer
that mimics the expression of the
Dfd in the subesophageal ganglion
of the embryonic central nervous
system. This Neural autoregulatory
enhancer (NAE) maps in the large
Dfd intron just upstream of the
© 2022 by JPS Scientific Publications, India
132
homeobox exon and requires the
Dfd protein function for its full
activity. A 608 bp NAE
subfragment retains the regulatory
function that is principally
localized in the subesophageal
ganglion.
• DEGRADATIVE PATHWAYS
- The main degradation pathway
involves the acetic acid elimination
with the formation of the polyenes.
These may then undergo the
further oxidative changes. The
process of the elimination of the
acetic acid cannot be effectively
reduced with the stabilizers but the
stabilizers may reduce its
autocatalytic effect. Furthermore,
the thermooxidative changes can
be decreased by the use of the
antioxidants. The photolytic
degradation rate can be reduced by
the both HALS (e.g. Tinuvin 770)
and the UV absorber (e.g.,
benzophenones) but results are not
very encouraging because the
stabilizers are lost from the
material with a substantial rate.140
Cracking and yellowing was
observed when the EVAc was
exposed to the unfiltered radiation
from the mercury lamp
sandwitched between the two
layers of the quartz. The
Fluorinated ethylene-propylene
polymer, FEP, does not have
adhesion to the EVAc, which
affects its performance in the
photovoltaic modules. The so-
called cementable FEP has
adhesion to the EVAc but only
Glossary of Genetics
until it is exposed to artificial
weathering, especially to the
elevated humidity and the
temperature cycling. Addition of
the aluminum oxide helps to
maintain the adhesion between the
layers even after the extended
accelerated weathering.
• DEGENERACY OF GENETIC
CODE - The Degeneracy or the
redundancy of the codons is the
redundancy of the genetic code,
exhibited as the multiplicity of the
three-base pair codon
combinations that specify an
amino acid. The degeneracy of the
genetic code is what accounts for
the existence of the synonymous
mutations. These properties of the
genetic code make it more fault-
tolerant for the point mutations.
For example, in the theory, the
fourfold degenerate codons can
tolerate any point mutation at the
third position, although the codon
usage bias restricts this in practice
in many of the organisms the
twofold degenerate codons can
withstand silence mutation rather
than the Missense or the Nonsense
point mutations at the third
position. Since the transition
mutations (purine to the purine or
the pyrimidine to the pyrimidine
mutations) are more likely than the
transversion (purine to the
pyrimidine or the vice versa)
mutations, the equivalence of the
purines or that of the pyrimidines
at the twofold degenerate sites adds
a further fault-tolerance.
© 2022 by JPS Scientific Publications, India
133
• DELTA PROTEINS - The Delta
proteins activate the Notch
through a binding reaction that
depends on their extracellular
domains, but the intracellular (C-
terminal) domains of the Deltas
also have the significant functions.
All the classes of the vertebrates
possess a subset of the Delta
proteins with a conserved ATEV*
motif at their C termini. These
ATEV Deltas include the Delta1
and the Delta4 in the mammals
and the DeltaD and DeltaC in the
zebrafish. These Deltas are
associate with the membrane-
associated scaffolding proteins
MAGI1, MAGI2 and MAGI3,
through the direct interaction
between the C termini of the
Deltas and a specific PDZ domain
which is PDZ4 of the MAGIs. In
the cultured cells and in the subsets
of the cells in the intact of the
zebrafish embryo, DeltaD and the
MAGI1 are co-localized at the
plasma membrane. The interaction
and the co-localization can be
abolished by the injection of a
morpholino that blocks the mRNA
splicing reaction that gives the
DeltaD its terminal valine, on
which the interaction depends.
• DENATURATION - The
Denaturation is a process in which
the proteins or the nucleic acids
lose the quaternary structure,
tertiary structure, and the
secondary structure which is
present in their native state, by
application of the some external
Glossary of Genetics 134

stress or the compound such as a nucleoside residues, nucleotides

strong acid or the base, a and the nucleic acids, also suffer
concentrated inorganic salt, an from the depurination. The
organic solvent (e.g. alcohol or the Deoxyribonucleosides and their
chloroform), agitation and derivatives are substantially more
radiation or the heat. If the prone to the depurination than
proteins in a living cell are their corresponding ribonucleoside
denatured, this results in disruption counterparts. The Loss of the
of the cell activity and possibly cell pyrimidine bases (cytosine and the
death. The Protein denaturation is thymine) occurs by a similar
also a consequence of the cell mechanism, but at a substantially
death. The Denatured proteins can lower rate. When the depurination
exhibit a wide range of the occurs with the DNA, it leads to
characteristics, from the the formation of the apurinic site
conformational change and loss of and results in an alteration of the
the solubility to the aggregation structure. The Studies estimate that
due to the exposure of the as many as around 5,000 of the
hydrophobic groups. The loss of purines are lost this way each day
the solubility as a result of the in a typical human cell. In the
denaturation is called as the cells, one of the main causes of the
coagulation. The Denatured depurination is the presence of the
proteins lose their 3D structure and endogenous metabolites
therefore cannot do other function. undergoing the chemical reactions.
• DEPURINATION - The The Depurination is known to play
Depurination is a chemical a major role in the cancer
reaction of the purine initiation.
deoxyribonucleosides,
deoxyadenosine and the • DEOXYNUCLEOTIDE
deoxyguanosine, and the TRIPHOSPHATES - The
ribonucleosides, adenosine or the Deoxynucleotide triphosphates
guanosine, in which the β-N- (dNTPs) are the essential building
glycosidic bond is hydrolytically blocks of the nucleic acid
cleaved by releasing a nucleic base, molecules, and as such are the
adenine or the guanine, necessary components of the PCR
respectively. The second product mixes as no new (amplified) DNA
of the depurination of the could be generated without them.
deoxyribonucleosides and the The four individual
ribonucleosides is the sugar, 2’- deoxynucleotides which make up a
deoxyribose and ribose, DNA sequence (i.e.
respectively. More complex deoxyadenosine triphosphate,
compounds containing the dATP; deoxythymidine

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
triphosphate, dTTP; deoxycytosine
triphosphate, dCTP; and the
deoxyguanosine triphosphate,
dGTP) are usually added to the
PCR and the RT-PCR mixes in the
equimolar amounts, though if the
target DNA sequence to be PCR
amplified comprises mainly the
dATP/dTTP (AT ratio) or the
mainly dGTP/dCTP (GC ratio),
then the molar ratio of the dNTPs
added to the PCR mix may be
altered in order to take into
account this imbalance. The
dNTPs are usually purchased
either individually or as an
(equimolar) mix from the
commercial suppliers (e.g. Roche,
Promega, etc.), and are chemically
stable when stored in slightly
alkaline aqueous solutions at –
20°C. However, it should be noted
that the dNTPs are naturally acidic
in solution; hence working and
stock solutions may have to be
neutralized with the alkaline
compounds prior to the long-term
storage. The Neutralized dNTP
solutions are normally adjusted to
the 10 mM stock solutions by the
spectrophotometry, or by adding
the correct volume of the sterile
water to the lyophilized product
directly after its chemical synthesis.
• DORSOVENTRAL
PATTERNING - The
Dorsal/ventral (DV) patterning is
the process whereby the embryonic
cells assume the different types of
developmental fates as the function
of their position along an
© 2022 by JPS Scientific Publications, India
135
organism’s DV axis. In the
Drosophila embryo, the DV
patterning begins during the
oogenesis and is completed during
the early stages of the
embryogenesis. It requires the
cross-talk between the three signal
transduction pathways; such as the
epidermal growth factor (EGF)
receptor pathway, the Toll (Tl)
pathway, and the Decapentaplegic
(Dpp)/Short gastrulation (Sog)
pathway. The Drosophila oocyte
arises from the germline stem cells
present at the anterior tip of the
each ovariole. The Each ovary
contains the 16 such ovarioles,
which consist of the linear series of
the egg chambers that gradually
start maturing as they move from
the anterior to the posterior end of
the ovariole. The developing
oocyte in each of the egg chamber
is nourished by the 15 nurse cells
and is surrounded by a monolayer
follicle cell epithelium. The
Gurken (Grk), a transforming
growth factor (TGF)-α family
protein, is secreted from the one
side of the developing oocyte close
to its anterior end and then signals
via the endothelial growth factor
(EGF) receptor in the adjacent
follicle cells.
• DNA FOOTPRONTING - The
DNA footprinting is a method of
investigating the sequence
specificity of the DNA-binding
proteins in vitro. This technique
can be used to study the protein-
DNA interactions both outside and
Glossary of Genetics
within the cells. The regulation of
the transcription has been studied
extensively, and yet there is still
much that is unknown. The
Transcription factors and
associated proteins that bind the
promoters, enhancers, or the
silencers to drive or the repress the
transcription are the fundamental
to understanding the unique
regulation of by the individual
genes within the genome. The
Techniques like DNA footprinting
help to elucidate which proteins
bind to these associated regions of
the DNA and unravel the
complexities of the transcriptional
control. The in vivo footprinting is
a technique which is used to
analyze the protein-DNA
interactions that are occurring in a
cell at a given time point. The
DNase I can be used as a cleavage
agent if the cellular membrane has
been permeabilized. However the
most common cleavage agent used
is the UV irradiation because it
penetrates the cell membrane
without disrupting the cell state
and can thus capture the
interactions that are sensitive to the
cellular changes. Once the DNA
has been cleaved or damaged by
the UV, the cells can be lysed and
the DNA purified for analysis of a
region of the interest.
• DNA LOOPING - The DNA-
looping mechanisms are a part of
the networks which will regulate
all the aspects of the DNA
metabolism including the
© 2022 by JPS Scientific Publications, India
136
transcription, replication, and the
recombination. The DNA looping
is also involved in the regulation of
the transcriptional initiation in the
prokaryotic operons, including ara,
gal, lac, and deo, and in the phage
systems. The DNA looping is also
an important mechanism to
increase the affinity of the
regulatory molecules for their
cognate sites. It can also lead to the
suppression of the cell to the cell
variability.
• DNA COMPACTION - The
DNA condensation is a process
which is also refers to the process
of compacting the DNA molecules
in vitro or in vivo. Mechanistic
details of the DNA packing are
essential for its functioning in the
process of the gene regulation in
the living systems. Condensed
DNA often has the surprising
properties, which one would not
predict from the classical concepts
of the dilute solutions. Therefore,
the DNA condensation in vitro
serves as a model system for many
processes of physics, biochemistry
and biology. In addition, the DNA
condensation has also many
potential applications in medicine
and the biotechnology. Nowadays
the descriptions of a gene
regulation are based on the
approximations of the equilibrium
binding in the dilute solutions,
although it is clear that these
assumptions are in the fact violated
in the chromatin. The dilute-
solution approximation is violated
Glossary of Genetics
for the two reasons. First, the
chromatin content is far from being
the dilute, and second, the
numbers of the participating
molecules are sometimes so small,
that it does not make sense to talk
about the bulk concentrations of
the molecules. Further the
differences from the dilute
solutions arise due to the different
binding affinities of proteins to the
condensed and uncondensed
DNA. Thus in the condensed
DNA both the reaction rates can
be changed and their dependence
on the concentrations of the
reactants may become nonlinear.
• DNA BINDING REGIONS - The
DNA binding sites are the type of
binding sites found in the DNA
where other molecules may or may
not be bind. The enzyme RNA
polymerase, which makes a new
RNA molecule from a DNA
template, must attach to the DNA
of the gene. It attaches at a spot
called ass the promoter which is
the DNA binding site. A DNA-
binding domain (DBD) is an
independently folded protein
domain that contains at least one
structural motif that recognizes the
double- or the single-stranded
DNA.
• DSCAM GENE - DSCAM or the
Dscam are both abbreviations for
the Down syndrome cell adhesion
molecule. The DSCAM protein
structure is conserved with roughly
more than 20% of the amino acids
identity across the deuterostomes
© 2022 by JPS Scientific Publications, India
137
and the protostomes. It was first
identified in an effort to
characterize the proteins which are
located within the human
chromosome band 21q22, a region
which plays an important role in
the Down Syndrome. This gene is
a member of the immunoglobulin
superfamily of the cell adhesion
molecules and it is also involved in
the human central and the
peripheral nervous system
development. This gene is a
candidate for the Down syndrome
and the congenital heart disease.
• DNA HELICASE - The DNA
helicases are the enzymes which
were discovered in the E. Coli in
1976. This helicase was described
as a “DNA unwinding enzyme”
which is found to denature the
DNA duplexes in an ATP-
dependent reaction, without
detectably degrading the DNA.
The first eukaryotic DNA helicase
was discovered in the lily plant.
Since then, the DNA helicases
were also discovered and isolated
from the other bacteria, viruses,
yeast, flies, andv higher
eukaryotes. The enzyme DNA
helicase is used to separates the
two strands of the DNA double
helix. This forms a structure that is
called as r the eplication fork that
has the two exposed single strands.
Other enzymes which also called
as the DNA polymerases then use
each strand as a template to build a
new matching DNA strand.
Glossary of Genetics
• DNA BINDING - The DNA-
binding proteins are the proteins
that have the DNA-binding
domains and thus have a specific
or general affinity for a single- or
double-stranded DNA. The
Sequence-specific DNA-binding
proteins which generally interact
with the major groove of the B-
DNA, because it exposes the more
functional groups that identify a
base pair. However, there are
some known minor groove DNA-
binding ligands such as the
netropsin, the distamycin, the
Hoechst 33258, the pentamidine,
the DAPI and the others. Each
transcription factor binds to one of
the specific set of the DNA
sequences and activates or inhibits
the transcription of the genes that
have these sequences near their
promoters. The transcription
factors do this in two ways. Firstly,
they can bind the RNA polymerase
responsible for the transcription,
either directly or through the other
mediator proteins, this locates the
polymerase at the promoter and
allows it to begin with the
transcription. Alternatively, the
transcription factors can also bind
the enzymes that modify the
histones at the promoter. This
alters the accessibility of the DNA
template to the polymerase. These
DNA targets can occur throughout
an organism’s genome. Thus,
changes in the activity of one type
of transcription factor can affect
the thousands of the genes. Thus,
© 2022 by JPS Scientific Publications, India
138
these proteins are often the targets
of the signal transduction processes
that control the responses to the
environmental changes or the
cellular differentiation and the
development. The specificity of
these transcription factors
interactions with the DNA comes
from the proteins that makes
multiple contacts to the edges of
the DNA bases, allowing them to
read the DNA sequence. Most of
these base-interactions are made in
the major groove, where the bases
are most accessible.
• DGCR8 PROTEIN - The
microprocessor complex subunit
DGCR8 (DiGeorge syndrome
critical region 8) is a protein that is
present in the humans is encoded
by the DGCR8 gene. In the other
animals, particularly the common
model organisms Drosophila
melanogaster and the
Caenorhabditis elegans, the protein
is known as the Pasha (partner of
the Drosha). It is a very special
required component of the RNA
interference pathway. The subunit
DGCR8 is localized to the cell
nucleus and is required for the
microRNA (miRNA) processing. It
binds to the other subunit Drosha,
an RNase III enzyme, to form the
microprocessor complex that
cleaves a primary transcript known
as the pri-miRNA to a
characteristic stem-loop structure
which is known as a pre-miRNA,
which is then further processed to
the miRNA fragments by the
Glossary of Genetics
enzyme. The DGCR8 contains an
RNA-binding domain and is
thought to bind pri-miRNA to
stabilize it for the processing by the
Drosha. The DGCR8 is also
required for some types of the
DNA repair. Removal of the UV-
induced DNA photoproducts,
during the transcription coupled
nucleotide excision repair (TC-
NER), depends on the JNK
phosphorylation of the DGCR8 on
the serine 153.
• DICER PROTEIN - The Dicer,
which is also known as the
endoribonuclease Dicer or the
helicase with the RNase motif, is
an enzyme that in the humans is
encoded by the DICER1 gene.
Being part of the RNase III family,
the Dicer cleaves the double-
stranded RNA (dsRNA) and the
pre-microRNA (pre-miRNA) into
the short double-stranded RNA
fragments which is called as the
small interfering RNA and the
microRNA, respectively. These
fragments are approximately
around 20–25 base pairs long with
a two-base overhang on the 3′-end.
The Dicer facilitates the activation
of the RNA-induced silencing
complex (RISC), which is essential
for the RNA interference. The
RISC has a catalytic component
Argonaute, which is an
endonuclease capable of degrading
the messenger RNA (mRNA). The
Human dicer which is also known
as hsDicer or the DICER1 is
classified as a Ribonuclease III
© 2022 by JPS Scientific Publications, India
139
because it contains both the
helicase and the PAZ
(Piwi/Argonaute/Zwille)
domains. In the addition to these
domains, the hsDicer contains the
four other functional domains: two
RNaseIII domains and the two
double stranded RNA binding
domains (DUF283 and the
dsRBD).
• DIF SITES - The dif site is around
28bp sequence located within a
30kb region of the terminus which
is known as the “dif activity zone”
(DAZ) and is also involved in the
Chromosome Dimer Resolution
involving the XerCD. The dif
must be located in the terminus
region for the proper function and
may be functionally replaced by
the loxP if the Cre recombinase is
supplied in the trans. The XerC
binds the dif left half site while the
XerD binds the dif right half site-
these sites are not interchangeable.
• DIHYDROFOLATE
REDUCTASES - The
Dihydrofolate reductase, or the
DHFR, is an enzyme that reduces
the dihydrofolic acid to the
tetrahydrofolic acid, using the
NADPH as electron donor, which
can be converted to the kinds of the
tetrahydrofolate cofactors used in
the 1-carbon transfer chemistry. In
the humans, the DHFR enzyme is
encoded by the DHFR gene. It is
found in the q11→q22 region of
the chromosome 5. The Bacterial
species possess the distinct DHFR
enzymes which is based on their
Glossary of Genetics
pattern of binding the
diaminoheterocyclic molecules, but
the mammalian DHFRs are highly
very similar in nature. The
Dihydrofolate reductase converts
the dihydrofolate into the
tetrahydrofolate, a proton shuttle
required for the de novo synthesis
of the purines, thymidylic acid, and
the certain amino acids. While the
functional dihydrofolate reductase
gene has been mapped to the
chromosome 5, multiple intronless
processed pseudogenes or the
dihydrofolate reductase-like genes
have been identified on the
separate chromosomes. Since it is
found in all the organisms, the
DHFR has a critical role in
regulating the amount of the
tetrahydrofolate in the cell. The
Tetrahydrofolate and its derivatives
are essential for the purine and the
thymidylate synthesis, which are
important for the cell proliferation
and the cell growth.
• DIDEOXYNUCLEOTIDE - The
Dideoxynucleotides are the chain-
elongating inhibitors of the DNA
polymerase, which is used in the
Sanger method for the DNA
sequencing. They are also known
as the 2’,3’ because both the 2’ and
3’ positions on the ribose lack the
hydroxyl groups, and are
abbreviated as the ddNTPs
(ddGTP, ddATP, ddTTP and the
ddCTP). The Dideoxynucleotides
are useful in the sequencing of the
DNA in the combination with the
electrophoresis. A DNA sample
© 2022 by JPS Scientific Publications, India
140
that undergoes the PCR
(polymerase chain reaction) in a
mixture containing all the four
deoxynucleotides and one
dideoxynucleotide will produce the
strands of the length equal to the
position of the each base of the
type that complements the type
having a dideoxynucleotide
present. The taq polymerase used
in the PCR favors the ddGNTP,
that has been a pattern observed in
the various research. That is, each
nucleotide base of that particular
type has a probability of the being
bonded to not a deoxynucleotide
but rather a dideoxynucleotide,
which ends the chain elongation.
It is now common to use the
fluorescent dideoxynucleotides
such that each one of the four has a
different fluorescence that can be
detected by a sequencer that only
one reaction is needed.
• DIHYDROURIDINE - The
Dihydrouridine which is
abbreviated as the D, DHU, or the
UH2 is a pyrimidine nucleoside
which is the result of adding the
two hydrogen atoms to a uridine,
making it a fully saturated
pyrimidine ring with no remaining
double bonds. The D is found in
the tRNA and the rRNA molecules
as a nucleoside the corresponding
nucleobase is the 5, 6-
dihydrouracil. Since it is a non-
planar, the D disturbs the stacking
interactions in the helices and
destabilizes the RNA structure.
The D also stabilizes the C2’-endo
Glossary of Genetics
sugar conformation, which is more
flexible than the C3’-endo
conformation this effect is
propagated to the 5’-neighboring
residue. Thus, while the
pseudouridine and the 2’-O-
methylations stabilize the local
RNA structure, the D does the
opposite. The tRNAs of the
organisms that grow at a low
temperatures (psychrophiles) have
the high 5, 6-dihydrouridine levels
(40-70% more on average) which
provides the necessary local
flexibility of the tRNA at or below
the freezing point.
• DIRECT REPEATS - The Direct
repeats are a type of the genetic
sequence that consists of the two or
more than the two repeats of a
specific sequence. In the other
words, the direct repeats are the
nucleotide sequences which is
present in the multiple copies in
the genome. Generally, a direct
repeat occurs when a sequence is
repeated with the same pattern in a
downstream manner. There is no
inversion and the no reverse
complement associated with a
direct repeat. It may or may not
have the intervening nucleotides.
The nucleotide sequence written in
the bold characters signifies the
repeated sequence. The
Interspersed (or the dispersed)
DNA repeats (interspersed
repetitive sequences) are the copies
of the transposable elements
interspersed throughout the
genome. The Flanking (or the
© 2022 by JPS Scientific Publications, India
141
terminal) repeats (terminal repeat
sequences) are the sequences that
are repeated on the both ends of a
sequence, for example, the long
terminal repeats (LTRs) on the
retroviruses. The Direct terminal
repeats are in the same direction
and inverted terminal repeats are
opposite to each other in the
direction. The Tandem repeats
(tandem repeat sequences) are
repeated copies which lie adjacent
to the each other. These can also
be direct or the inverted repeats.
The ribosomal RNA and the
transfer RNA genes belong to the
class of the middle repetitive DNA.
• D-LOOP OF TRNA - The D-loop
in the tRNA contains the modified
nucleotide dihydrouridine. It is
composed of about 7 to 11 bases
and is closed by a Watson Crick
base pair. The TψC-loop which is
generally called as the T-loop,
contains the thymine, a base which
is usually found in the DNA and
the pseudouracil (ψ). The D-loop
and the T-loop form a tertiary
interaction in the tRNA. The D
loop contains the base which is
known as the dihydrouridine, for
which the arm is named. The D
loop’s main function is that of the
recognition. It is widely believed
that it acts as a recognition site for
the aminoacyl-tRNA synthetase,
an enzyme which is involved in the
aminoacylation of the tRNA
molecule. The D stem is also
believed to have a recognition role
Glossary of Genetics
in the tRNA although this has yet
to be verified.
• DMC1 - The DMC1 is a new
meiosis-specific yeast gene. The
Dmc1 protein is structurally
similar to the bacterial RecA
proteins. The dmc1 mutants are
defective in the reciprocal
recombination, accumulate double-
strand break (DSB) recombination
intermediates, fail to form the
normal synaptonemal complex
(SC), and arrest late in the meiotic
prophase. The dmc1 phenotypes
are consistent with a functional
relationship between the Dmc1
and the RecA, and thus eukaryotic
and prokaryotic mechanisms for
the homology recognition and the
strand exchange may be related.
The dmc1 phenotypes provide the
further evidence that
recombination and the SC
formation are interrelated
processes and are consistent with a
requirement for the DNA-DNA
interactions during the SC
formation. The dmc1 mutations
confer the prophase arrest.
Additional evidence suggests that
the arrest occurs at a meiosis-
specific cell cycle “checkpoint” in
response to a primary defect in the
prophase chromosome
metabolism. The DMC1 is
homologous to the yeast’s RAD51
gene, supporting the view that the
mitotic DSB repair has been
recruited for use in the meiotic
chromosome metabolism.
© 2022 by JPS Scientific Publications, India
142
• DNA ABSORBANCE - Before
using the DNA samples in the
analytical techniques, the quality
and the usability must be
determined through the DNA
quality indicators, which include
the DNA purity and the integrity.
The ratio of rye absorbance at 260
and 280 nm is used to assess the
DNA purity. A ratio of ∼1.8 is
generally accepted as the “pure”
for the DNA. If the ratio is
appreciably lower (≤1.6), it may
indicate the presence of the
proteins, phenol, or the other
contaminants that absorb strongly
at or near the 280   nm. To the
contrary, since the absorbance
readings cannot discriminate
between the DNA and the RNA,
the presence of the RNA can lead
to the ratio increasing and this
possibility must be considered to
avoid the DNA over
quantification. The 260/230 ratio
is widely used as a secondary
measure of the DNA purity. The
Expected 260/230 values for the
“pure” DNA are commonly within
the range between the 2.0 and 2.2.
If the ratio is appreciably lower
than the expected, it may indicate
the presence of the contaminants
that absorb at the 230 nm such as
the proteins, 8 guanidine HCL
(used for the DNA isolations),
EDTA, carbohydrates, lipids, salts,
or the phenol. Consequently, out
of the two DNA samples with the
same purity, the less concentrated
sample will show the lower
Glossary of Genetics
260/230 ratio because of the salts
absorbance at the 230 nm.
• DNA BARCODING - The DNA
barcoding is a method of the
species identification using a short
section of the DNA from a specific
gene or the genes. The premise of
the DNA barcoding is that, by
comparison with a reference library
of such DNA sections which is
also called as the “sequences”, an
individual sequence can be used to
uniquely identify an organism to
rye species, in the same way that a
supermarket scanner uses the
familiar black stripes of the UPC
barcode to identify an item in its
stock against its reference database.
These “barcodes” are sometimes
used in an effort to identify the
unknown species, parts of an
organism, or simply to catalogs as
many as taxa as possible, or to
compare with the traditional
taxonomy in an effort to determine
the species boundaries. The
Applications of the DNA
barcoding include the
identification of the new species,
safety assessment of the food,
identification and assessment of
the cryptic species, detection of the
alien species, identification of the
endangered and threatened species,
linking egg and the larval stages to
the adult species, securing
intellectual property rights for the
bioresources, framing global
management plans for the
conservation strategies and
elucidate feeding The DNA
© 2022 by JPS Scientific Publications, India
143
barcode markers can be applied to
the address basic questions in the
systematics, ecology, evolutionary
biology and the conservation,
including community assembly,
species interaction networks,
taxonomic discovery, and assessing
priority areas for the
environmental protection.
• DNA A - The DnaA is a protein
that activates the initiation of the
DNA replication in the bacteria. It
is a replication initiation factor
which promotes the unwinding of
the DNA at the oriC. The onset of
the initiation phase of rye DNA
replication is determined by the
concentration of the DnaA. The
DnaA accumulates during the
growth and then triggers the
initiation of the replication. The
Replication begins with the active
DnaA binding to the 9-mer (9-bp)
repeats upstream of the oriC. The
Binding of the DnaA leads to the
strand separation at the 13-mer
repeats. This binding causes the
DNA to loop in the preparation for
the melting open by the helicase
DnaB. The DnaA consists mainly
in two different forms, the active
ATP-form and the inactive ADP.
Immediately after a cell has
divided, the level of rye active
DnaA within the cell is very low.
Although the active form of the
DnaA requires the ATP, the
formation of the oriC/DnaA
complex and the subsequent DNA
unwinding does not require the
ATP hydrolysis.
Glossary of Genetics
• DNA B - The DnaB helicase is an
enzyme in the bacteria which
opens the replication fork during
the DNA replication. Although the
mechanism by which the DnaB
both couples the ATP hydrolysis to
the translocation along the DNA
and denatures the duplex is
unknown, a change in the
quaternary structure of the protein
involving the dimerisation of the
N-terminal domain has been
observed and may also occur
during the enzymatic Initially
when the DnaB binds to dnaA, it is
associated with the dnaC, a
negative regulator. After the DnaC
dissociates, DnaB binds the dnaG.
The DnaB helicase is the product
of the gene which is known as the
dnaB gene. The helicase enzyme
that is produced is a hexamer in
the E. Coli, as well as in many of
the other bacteria. The energy for
the DnaB activity is provided by
the NTP hydrolysis. The
Mechanical energy moves the
DnaB into the replication fork,
physically splitting it in to the half.
• DNA C - The dnaC is a loading
factor that complexes with the C-
terminus of the helicase dnaB and
inhibits it from the unwinding the
dsDNA at a replication fork. A
dnaB and the dnaC associate near
the dnaA bound origin for the each
of the ssDNA. One dnaB-dnaC
complex is oriented in the opposite
direction to the other dnaB-dnaC
complex due to the antiparallel
nature of the DNA. Because they
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are oriented in the opposite
directions, the one dnaB-dnaC
complex will complex with the
dnaA from the N-terminus of the
dnaB whereas the other dnaB-
dnaC complex will complex with
dnaA from the dnaC. After the
assembly of the dnaG onto the N-
terminus of the dnaB, dnaC is
released and the dnaB will be
allowed to begin the unwinding
dsDNA to make room for the
DNA polymerase III to begin the
synthesizing of the daughter
strands.
• DNA BINDING PROTEIN - The
DNA-binding proteins are the
proteins that have DNA-binding
domains and thus have a specific
or the general affinity for the
single- or the double-stranded
DNA. The Sequence-specific
DNA-binding proteins generally
interact with the major groove of
the B-DNA, because it exposes the
more functional groups that
identify a base pair. However,
there are some of the known minor
groove DNA-binding ligands such
as the netropsin, distamycin,
Hoechst 33258, pentamidine,
DAPI and the others. The DNA-
binding proteins include the
transcription factors which
modulate the process of the
transcription, various polymerases,
nucleases which cleave the DNA
molecules, and the histones which
are involved in the chromosome
packaging and the transcription in
the cell nucleus. DNA-binding
Glossary of Genetics
proteins can incorporate such as
the domains as the zinc finger, the
helix-turn-helix, and the leucine
zipper (among the many others)
that facilitate binding to the nucleic
acid. There are also more unusual
examples such as the transcription
activator like the effectors.
• DNA ALKYLATION - The DNA
alkylation damage can pose a very
serious threat to the genetic
integrity and the cellular survival.
To combat this damage, the cells
employ incredibly vast and the
elegant repair mechanisms,
including the excision of the
damaged nucleotides from DNA,
direct removal of the lesion
without the further modification of
the nucleotide or DNA, and a
bridging protein that connects the
DNA repair pathways. The
existence of these extensive and
creative mechanisms for the
cellular protection emphasizes the
importance of the DNA alkyl
lesion repair.
• DNA GYRASE - The DNA
gyrase, or simply the gyrase, is an
enzyme within the class of the
topoisomerase and is a subclass of
the type II topoisomerases that
reduces the topological strain in an
ATP dependent manner while the
double-stranded DNA is being
unwound by elongating the RNA-
polymerase or by the helicase in
front of the progressing replication
fork. The enzyme causes negative
supercoiling of the DNA or relaxes
the positive supercoils. It does so
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by looping the template so as to
form a crossing, then cutting one of
the double helices and passing the
other through it before releasing
the break, changing the linking
number by two in each of the
enzymatic step. This process
occurs in the bacteria, whose single
circular DNA is cut by the DNA
gyrase and the two ends are then
twisted around each other to form
the supercoils. The Gyrase is also
found in the eukaryotic plastids, it
has been found in the apicoplast of
the malarial parasite Plasmodium
falciparum and in the chloroplasts
of the several plants. The Bacterial
DNA gyrase is the target of the
many antibiotics, including the
nalidixic acid, novobiocin, and the
ciprofloxacin.
• DNA FINGERPRINTING - The
DNA profiling which is also called
as the DNA fingerprinting is the
process of the determining an
individual’s DNA characteristics.
The DNA analysis intended to
identify a species, rather than an
individual, is called as the DNA
barcoding. Discovered by the Sir
Alec Jeffreysy in the yeaar 1984,
DNA profiling is a forensic
technique in the criminal
investigations, comparing the
criminal suspects’ profiles to the
DNA evidence so as to assess the
likelihood of their involvement in
the crime. It is also used in the
paternity testing, and so as to
establish the immigration
eligibility, and in genealogical and
Glossary of Genetics
the medical research. The DNA
profiling has also been used in the
study of the animal and the plant
populations in the fields of the
zoology, botany, and in the
agriculture.
• DNA HAIRPIN - The Hairpin
DNA-functionalized the gold
nanoparticles (hAuNPs) which are
constructed of a 15 nm core gold
nanoparticle with covalently
attached the DNA hairpin beacons
via the gold–thiol bond formation.
The hAuNPs are taken up by the
cells nonspecifically and emit the
fluorescence upon the
hybridization with an intracellular
mRNA target. Each of the DNA
hairpin is constructed of a 5′
hexane thiol linker covalently
attached to a 10-thymine
extension, followed by a 30 base
hairpin recognition sequence and
the 3′ fluorophore. The first and
the last five bases of the
recognition sequence are
complementary resulting in a five-
base duplex stem. While in the
closed position, this construct
utilizes the fluorescence quenching
ability of the gold nanoparticle to
quench the fluorescent signal,
within the cytoplasm, binding of
the complementary mRNA
sequence to the hairpin DNA
(hDNA) which causes the 3′
fluorophore to extend beyond the
quenching range of the gold
nanoparticle resulting in the
emission of a fluorescent signal.
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• DNA HELICASE - The DNA
helicases were discovered in the E.
Coli in the year 1976. The helicase
was described as the “DNA
unwinding enzyme” that is “found
to denature the DNA duplexes in
the ATP-dependent reaction,
without detectably degrading”. The
Helicases are often used to separate
the strands of a DNA double helix
or a self-annealed RNA molecule
using the energy from the ATP
hydrolysis, a process characterized
by the breaking of the hydrogen
bonds between the annealed
nucleotide bases. They also
function to remove the nucleic
acid-associated proteins and the
catalyze homologous DNA
recombination. The Metabolic
processes of the RNA such as the
translation, transcription, ribosome
biogenesis, RNA splicing, RNA
transport, RNA editing, and the
RNA degradation are all facilitated
by the helicases. The Helicases
move incrementally along the one
nucleic acid strand of the duplex
with a directionality and
processivity specific to the each
particular enzyme.
• DYSTROPHIN - The Dystrophin
is a rod-shaped cytoplasmic
protein, and the vital part of a
protein complex that connects the
cytoskeleton of the muscle fiber to
the surrounding of the extracellular
matrix through the cell membrane.
This complex is variously known
as the costamere or the dystrophin-
associated protein complex
Glossary of Genetics
(DAPC). Many of the muscle
proteins, such as the α-
dystrobrevin, syncoilin, synemin,
sarcoglycan, dystroglycan, and the
sarcospan, colocalize with the
dystrophin at the costamere. It has
a molecular weight of abi 427 kDa.
The Dystrophin is coded for by the
DMD gene which is the largest
known human gene, covering
about 2.4 megabases (0.08% of the
human genome) at the locus Xp21.
The primary transcript in the
muscle measures about 2,100
kilobases and takes 16 hours to
transcribe the mature mRNA
measures about 14.0 kilobases. The
79-exon muscle transcript codes for
a protein around 3685 amino acid
residues. The Spontaneous or the
inherited mutations in the
dystrophin gene can cause the
different forms of the muscular
dystrophy, a disease characterized
by the progressive muscular
wasting. The most common of
these disorders caused by the
genetic defects in the dystrophin is
the Duchenne muscular dystrophy.
• DNA POLYMERASE
INTERACTION - The DNA
polymerases are the workhorses for
the replication of the genomic
information in the living cells but
more recently also for the
biotechnology applications such as
the polymerase chain reaction
(PCR) and the DNA sequencing.
In particular in the field of the
sequencing-by-synthesis (e.g. the
nanopore sequencing), massive
© 2022 by JPS Scientific Publications, India
147
efforts are currently being
undertaken to develop the working
principles for the faster, more
accurate and the consequently
more cost-effective assays designed
ultimately, to operate at the single
molecule level in the medical
applications. The Synthesis of the
leading DNA strand requires the
coordinated activity of the DNA
polymerase and the DNA helicase,
whereas the synthesis of the
lagging strand involves the
interactions of these proteins with
the DNA primase.
• DNA HELICASE LOADER -
The DnaC helicase loader (DnaC)
transfers the helicase to the
replication origins. The helicase
loaders belong to the two classes.
The ‘ring breakers’ break the
hexameric helicase to allow the
DNA to pass through. The ‘ring
makers’ assemble the helicase
monomers to the hexamers around
the DNA. It transfer the ring-
shaped replicative helicases onto
the DNA. They assort into the two
classes: ring breakers, which place
stabile hexameric rings on the
DNA via the transient gaps at the
subunit interfaces; and the helicase
makers, which assemble the
hexameric rings around DNA from
the monomeric helicase units.
• DNA LIGASE - The DNA ligase
is a specific type of enzyme, a
ligase, that facilitates the joining of
the DNA strands together by
catalyzing the formation of a
phosphodiester bond. It plays a
Glossary of Genetics
role in repairing the single-strand
breaks in the duplex DNA in the
living organisms, but some forms
such as the DNA ligase IV, may
specifically repair the double-
strand breaks (i.e. a break in both
of the complementary strands of
the DNA). The single-strand
breaks are repaired by the DNA
ligase using the complementary
strand of the double helix as a
template, with the DNA ligase
creating the final phosphodiester
bond to fully repair the DNA. The
DNA ligase is used in both the
DNA repair and the DNA
replication. In addition, the DNA
ligase has extensive use in the
molecular biology laboratories for
the recombinant DNA
experiments. The Purified DNA
ligase is used in the gene cloning to
join the DNA molecules together
to form the recombinant DNA.
• DNA LIGASE 4 - The DNA
ligase 4 is an enzyme that in the
humans is encoded by the LIG4
gene. The protein which is encoded
by this gene is an ATP-dependent
DNA ligase that joins the double-
strand breaks during the non-
homologous end joining pathway
of the double-strand break repair.
It is also essential for the V(D)J
recombination. The Lig4 forms a
complex with the XRCC4, and
further interacts with the DNA-
dependent protein kinase (DNA-
PK) and the XLF/Cernunnos,
which are also required for the
NHEJ. The Defects in this gene
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148
are the cause of the LIG4
syndrome. The yeast homolog of
the Lig4 is the Dnl4. In the
humans, the deficiency of DNA
ligase 4 results in a clinical
condition known as the LIG4
syndrome. This syndrome is
characterized by the cellular
radiation sensitivity, growth
retardation, developmental delay,
microcephaly, facial
dysmorphisms, increased
disposition to the leukemia,
variable degrees of the
immunodeficiency and the reduced
number of the blood cells.
• DNA METHYLTRANSFERASE
- In the field of biochemistry, the
DNA methyltransferase (which is
also known as the DNA MTase, or
the DNMT) family of the enzymes
catalyze the transfer of a methyl
group to the DNA. The DNA
methylation serves a wide variety
of the biological functions. All the
known DNA methyltransferases
use the S-adenosyl methionine
(SAM) as the methyl donor. At
least four differently active DNA
methyltransferases have been
identified in the mammals. They
are named as the DNMT1, two of
the isoforms transcribed from the
DNMT3a gene: DNMT3a1 and
the DNMT3a2, and the DNMT3b.
Recently, another enzyme which is
known as the DNMT3c has been
discovered specifically expressed in
the male germline of the mouse.
Glossary of Genetics
• DNA MICROARRAYS - The
DNA microarray which is also
commonly known as the DNA
chip or the biochip is a collection
of the microscopic DNA spots
attached to a solid surface. The
Scientists use the DNA
microarrays to measure the
expression levels of the large
numbers of the genes
simultaneously or to the genotype
multiple regions of a genome. Each
of the DNA spot contains the
picomoles (10−12 moles) of a
specific DNA sequence, known as
the probes (or reporters or oligos).
These can be a short section of a
gene or the other DNA element
that are used to hybridize a cDNA
or the cRNA which is also called
as the anti-sense RNA sample
under the high-stringency
conditions. The Probe-target
hybridization is usually detected
and quantified by the detection of
the fluorophore-, silver-, or the
chemiluminescence-labeled targets
to determine the relative
abundance of the nucleic acid
sequences in the target. The
original nucleic acid arrays were
the macro arrays approximately 9
cm × 12 cm and the first
computerized image based analysis
was published in the 1981. It was
invented by the Patrick O. Brown.
An example of its application is in
SNPs arrays for the
polymorphisms in the
cardiovascular diseases, cancer,
pathogens and in the GWAS
© 2022 by JPS Scientific Publications, India
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analysis. It is also used for the
identification of the structural
variations and the measurement of
the gene expression.
• DNA PHOTOLYASE - The
Photolyases are the DNA repair
enzymes that repair the damage
caused by the exposure to the
ultraviolet light. These enzymes
require the visible light from the
violet/blue end of the spectrum,
both for their own activationnand
for the actual DNA repair. The
DNA repair mechanism involving
the photolyases is called as the
photoreactivation. They mainly
convert the pyrimidine dimers into
a normal pair of the pyrimidine
bases. The Photolyases bind the
complementary DNA strands and
break the certain types of the
pyrimidine dimers that arise when
a pair of the thymine or the
cytosine bases on the same strand
of the DNA become covalently
linked. The bond length of this
dimerization is shorter than the
bond length of the normal B-DNA
structure which produces an
incorrect template for the
replication and the transcription.
The more of the common covalent
linkage involves the formation of
the cyclobutane bridge. The
Photolyases have a high affinity for
these lesions and reversibly bind
and convert them back to the
original bases.
• DNA PRIMASE - The DNA
primase is an enzyme which is
involved in the replication of the
Glossary of Genetics
DNA and is a type of the RNA
polymerase. The pimase catalyzes
the synthesis of a short RNA (or
the DNA in some of the living
organisms) segment called as the
primer complementary to a ssDNA
(single-stranded DNA) template.
After this elongation, the RNA
piece is removed by a 5’ to 3’
exonuclease and refilled with the
DNA. In the bacteria, the primase
binds to the DNA helicase forming
a complex which is called the
primosome. Rye Primase is
activated by the helicase where it
then synthesizes a short RNA
primer approximately 11 ±1
nucleotides long, to which a new
nucleotides can be added by the
DNA polymerase. The Archaeal
and rye eukaryote primases are the
heterodimeric proteins with one
large regulatory and the one
minuscule catalytic subunit. The
Primase is one of the most error
prone and the slow polymerases.
The Primases in the organisms
such as the E. Coli synthesize
around 2000 to 3000 primers at the
rate of the one primer per second.
• DNA POLYMERASE ALPHA -
The DNA polymerase alpha which
is also known as the Pol α is an
enzyme complex that is found in
the eukaryotes that is involved in
the initiation of the DNA
replication. The DNA polymerase
alpha complex consists of the 4
subunits: POLA1, POLA2,
PRIM1, and the PRIM2. The Pol α
has a very limited processivity and
© 2022 by JPS Scientific Publications, India
150
lacks the 3′ exonuclease activity for
the proofreading errors. Thus it is
not well suited to the efficiently
and the accurately copy long
templates. Instead it plays a more
limited role in the replication. The
Pol α is responsible for the
initiation of the DNA replication at
the origins of the replication (on
both the leading and lagging
strands) and during the synthesis of
the Okazaki fragments on the
lagging strand. Once the primase
has created the RNA primer, the
Pol α starts the replication
elongating the primer with around
~20 nucleotides.
• DNA POLYMERASE BETA -
The DNA polymerase beta, which
is also known as the POLB, is an
enzyme that is present in the
eukaryotes. In the humans, it is
encoded by the POLB gene. In the
eukaryotic cells, the DNA
polymerase beta (POLB) performs
the base excision repair (BER)
required for the DNA
maintenance, replication,
recombination, and the drug
resistance. The mitochondrial
DNA of rye mammalian cells is
constantly under the attack from
the oxygen radicals released during
the ATP production. The
Mammalian cell mitochondria
contain an efficient base excision
repair system employing the POLB
that removes some of the frequent
oxidative DNA damages. The
POLB thus has a key role in
maintaining the stability of the
Glossary of Genetics
mitochondrial genome. An
analysis of the fidelity of the DNA
replication by the polymerase beta
in the neurons from the young and
the very aged mice indicated that
the aging has no significant effect
on the fidelity of the DNA
synthesis by the polymerase beta.
This finding was considered to
provide the evidence against the
error catastrophe theory of the
aging.
• DNA POLYMERASE DELTA -
The DNA polymerase delta (DNA
Pol δ) is an enzyme complex which
is found in the eukaryotes that is
involved in the DNA replication
and in the repair. The DNA
polymerase delta complex consists
of the 4 subunits: POLD1,
POLD2, POLD3, and the POLD4.
The DNA Pol δ is an enzyme used
for both the leading and the lagging
strand synthesis. It exhibits the
increased processivity when
interacting with the proliferating
cell nuclear antigen (PCNA). As
well, the multisubunit protein
replication factor C, through its
role as the clamp loader for the
PCNA (which involves the
catalysing the loading of the
PCNA on to the DNA) is
important for the DNA Pol δ
function.
• DNA POLYMERASE EPILSON
- The DNA polymerase epsilon is a
member of the DNA polymerase
family of the enzymes which is
found in the eukaryotes. It is
composed of the following four
© 2022 by JPS Scientific Publications, India
151
subunits: POLE (central catalytic
unit), POLE2 (subunit 2), POLE3
(subunit 3), and the POLE4
(subunit 4). Recent evidence
suggests that it plays a major role
in the leading strand DNA
synthesis and in nucleotide and
also in the base excision repair.
Either the DNA polymerase
epsilon or the DNA polymerase
delta along with the DNA ligase
can be used to repair the UV-
damaged DNA. However, it is
found that the DNA polymerase
delta require the presence of the
both RFC and the PCNA in order
in the DNA repair. In addition, it
only produces the small amount of
the fractionated DNA ligated
products. The DNA polymerase
epsilon proves to be best suited for
the nucleotide excision repair. The
DNA polymerase epsilon is
independent of both the PCNA
and RFC, and produces mostly the
ligated DNA products. It is also
found that under one condition
where the DNA polymerase
epsilon require the PCNA and
RFC: nucleotide excision repair in
the presence of the single strand
binding protein RPA. The PCNA
and RFC function as anchor and
the direct DNA polymerase epsilon
onto the DNA template.
• DNA POLYMERASE 1 - The
DNA polymerase I (or the Pol I) is
an enzyme that participates in the
process of the prokaryotic DNA
replication. It was Discovered by
the Arthur Kornberg in the year
Glossary of Genetics
1956, it was the first known as the
DNA polymerase (and the first
known of any kind of the
polymerase). It was initially
characterized in the E. Coli and is
ubiquitous in the prokaryotes. In
the E. Coli and many other
bacteria, the gene that encodes the
Pol I is known as the polA. The E.
Coli Pol I enzyme is composed of
around 928 amino acids, and is an
example of a processive enzyme —
it can sequentially catalyze the
multiple polymerisation steps
without releasing any of the single-
stranded template. The
physiological function of the Pol I
is mainly to support the repair of
the damaged DNA, but it also
contributes to connecting the
Okazaki fragments by deleting the
RNA primers and replacing the
ribonucleotides with the DNA.
• DNA POLYMERASE ETA - The
DNA polymerase eta (Pol η), is a
protein that in the humans is
encoded by the POLH gene. The
DNA polymerase eta is a
eukaryotic DNA polymerase
involved in the DNA repair by the
translesion synthesis. The gene
encoding the DNA polymerase eta
is the POLH, which is also known
as the XPV, because loss of this
gene results in the disease known
as the xeroderma pigmentosum.
The Polymerase eta is particularly
important for allowing the accurate
translesion synthesis of the DNA
damage resulting from the
ultraviolet radiation or the UV.
© 2022 by JPS Scientific Publications, India
152
This gene encodes a member of the
Y family of the specialized DNA
polymerases. It copies the
undamaged DNA with a lower
fidelity than the other DNA-
directed polymerases. However, it
accurately replicates the UV-
damaged DNA, when the thymine
dimers are present, this polymerase
inserts the complementary
nucleotides in the newly
synthesized DNA, thereby
bypassing the lesion and
suppressing the mutagenic effect of
rye UV-induced DNA damage.
This polymerase is thought to be
involved in the hypermutation
during the immunoglobulin class
switch recombination process.
• DNA POLYMERASE I - The
DNA polymerase I (or the Pol I) is
an enzyme that participates in the
process of the prokaryotic DNA
replication. Discovered by the
Arthur Kornberg in the year 1956,
it was the first known as the DNA
polymerase (and the first known of
any kind of the polymerase). It was
initially characterized in the E.
Coli and is ubiquitous in the
prokaryotes. In the E. Coli and
many of the other bacteria, the
gene that encodes the Pol I is
known as the polA. The E. Coli
Pol I enzyme is composed of
around 928 amino acids, and is an
example of a processive enzyme it
can sequentially catalyze the
multiple polymerisation steps
without releasing any of the single-
stranded template. The
Glossary of Genetics
physiological function of the Pol I
is mainly to support the repair of
the damaged DNA, but it also
contributes to connecting the
Okazaki fragments by deleting the
RNA primers and replacing the
ribonucleotides with the DNA.
• DNA POLYMERASE 2 - The
The DNA polymerase II (which is
also known as the DNA Pol II or
the Pol II) is a prokaryotic DNA-
Dependent DNA polymerase
encoded by the PolB gene. The
DNA Polymerase II is an 89.9-kDa
protein and is a member of the B
family of the DNA polymerases. It
was originally isolated by the
Thomas Kornberg in the year
1970, and was characterized over
the next few years. The in vivo
functionality of rye Pol II is under
debate, yet consensus shows that
the Pol II is primarily involved as a
backup enzyme in the prokaryotic
DNA replication. The enzyme has
5′→3′ DNA synthesis capability as
well as the 3′→5′ exonuclease
proofreading activity. The DNA
Pol II interacts with the multiple
binding partners common with the
DNA Pol III in order to enhance
its fidelity and also it’s processivity.
• DNA POLYMERASE 3 - The
DNA polymerase III holoenzyme
is the primary enzyme complex
involved in the prokaryotic DNA
replication. It was discovered by
the Thomas Kornberg (son of the
Arthur Kornberg) and the Malcolm
Gefter in the year 1970. The
complex has high processivity (i.e.
© 2022 by JPS Scientific Publications, India
153
the number of the nucleotides
added per binding event) and,
specifically referring to the
replication of the E.coli genome,
works in conjunction with the four
other DNA polymerases (Pol I, Pol
II, Pol IV, and the Pol V). Being
the primary holoenzyme involved
in the replication activity, the
DNA Pol III holoenzyme also has
the proofreading capabilities that
corrects rye replication mistakes by
means of the exonuclease activity
reading 3’→5’ and synthesizing
5’→3’. The DNA Pol III is a
component of the replisome, which
is located at the replication fork.
The DNA polymerase III
synthesizes the base pairs at a rate
of around 1000 nucleotides per
second. The DNA Pol III activity
begins after the strand separation at
the origin of the replication.
Because the DNA synthesis cannot
start de novo, an RNA primer,
complementary to part of the
single-stranded DNA, is
synthesized by the primase (an
RNA polymerase).
• DNA POLYMERASE K - The
DNA polymerase kappa is an
DNA polymerase that in the
humans is encoded by the POLK
gene. It is involved in the
translesion synthesis. The DNA
polymerase (pol) kappa is a Y-
family translesion DNA
polymerase conserved throughout
all the domains of the life. The Pol
kappa is a specialized for the
ability to copy the DNA containing
Glossary of Genetics
the minor groove DNA adducts,
especially the N2-dG adducts, as
well as to extend Tte primer
termini containing the DNA
damage or the mismatched base
pairs. The Pol kappa generally
cannot copy the DNA containing
the major groove modifications or
the UV-induced photoproducts.
The Pol kappa can also copy the
structured or the non-B-form
DNA, such as the microsatellite
DNA, common fragile sites, and
the DNA containing G mammalian cells appear to favor
quadruplexes. Thus, the pol kappa
has roles both in the maintaining
and in compromising the genomic
integrity. The expression of the pol
kappa is altered in several different
cancer types, which can lead to the
genome instability. In addition,
many of the cancer-associated
single-nucleotide polymorphisms
have been reported in the POLK
gene, some of which are associated
with the poor survival and altered
the chemotherapy response.
Because of this, identifying
inhibitors of the pol kappa is an
active area of the research.
• DSB REPAIR - The double-strand
break repair model refers to the
various models of the pathways
that the cells undertake to repair
the double strand-breaks (DSB).
The DSB repair is an important
cellular process, as the
accumulation of the unrepaired
DSB could lead to the
chromosomal rearrangements,
tumorigenesis or even the cell
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154
death. In the human cells, there
are two main DSB repair
mechanisms, the Homologous
recombination (HR) and the non-
homologous end joining (NHEJ).
The HR relies on the undamaged
template DNA as reference to the
repair of the DSB, resulting in the
restoration of the original
sequence. The NHEJ modifies and
ligates the damaged ends regardless
of the homology. In terms of the
DSB repair pathway choice, most
the NHEJ rather than the HR. This
is because the employment of the
HR may lead to gene deletion or
the amplification in the cells which
contains the repetitive sequences.
In terms of repair models in the cell
cycle, the HR is only possible
during the S and G2 phases, while
the NHEJ can occur throughout
the whole process. These repair
pathways are all regulated by the
overarching the DNA damage
response mechanism. Besides the
HR and the NHEJ, there are also
other repair models which exists in
the cells. Some are categorized
under the HR, such as the
synthesis-dependent strain
annealing, break-induced
replication, and the single-strand
annealing; while others are an
entirely alternate repair model,
namely, the pathway
microhomology-mediated end
joining (MMEJ).
• DNA UNWIDING ELEMENT -
The DNA unwinding element
Glossary of Genetics
(DUE or the DNAUE) is the
initiation site for the opening of the
double helix structure of the DNA
at the origin of rye replication for
the DNA synthesis. It is A-T rich
and denatures easily due to its very
low helical stability, which allows
the single-strand region to be
recognized by the origin
recognition complex. The specific
unwinding of the DUE allows for
the initiation complex assembly at
the site of the replication on the
single-stranded DNA, as
discovered by the Huang
Kowalski. The DNA helicase and
the associated enzymes are now
able to bind to the unwound
region, creating the replication fork
start. The unwinding of this duplex
strand region is associated with a
very low free energy requirement,
due to the helical instability caused
by the specific base-stacking
interactions, in combination with
the counteracting supercoiling.
The Negative supercoiling allows
the DNA to be stable upon the
melting, driven by the reduction of
the torsional stress. Found in the
replication origins of both the
bacteria and the yeast, as well as
present in some of the mammalian
ones. It is found to be between the
30-100 bp long.
• DNASE FOOTPRINTING
ASSAY - The DNase footprinting
assay is a DNA footprinting
technique from the molecular
biology/biochemistry that detects
the DNA-protein interaction using
© 2022 by JPS Scientific Publications, India
155
the fact that a protein bound to the
DNA will often protect that the
DNA from the enzymatic
cleavage. This makes it possible to
locate the protein binding site on a
particular DNA molecule. The
method uses an enzyme, known as
the deoxyribonuclease (DNase, for
short), to cut the radioactively end-
labeled DNA, followed by the gel
electrophoresis to detect the
resulting cleavage pattern. The
cleavage pattern of the DNA in the
absence of a DNA binding protein,
typically referred to as the free
DNA, is compared to the cleavage
pattern of the DNA in the presence
of a DNA binding protein. If the
protein binds the DNA, the
binding site is protected from the
enzymatic cleavage. This
protection will result in a clear area
on the gel which is referred to as
the “footprint”. By varying the
concentration of the DNA-binding
protein, the binding affinity of the
protein can be estimated according
to the minimum concentration of
protein at which the footprint is
observed.
• DNA SEQUENCER - The DNA
sequencer is a scientific instrument
which is used to automate the
DNA sequencing process. Given a
sample of the DNA, a DNA
sequencer is used to determine the
order of the four bases: G
(guanine), C (cytosine), A
(adenine) and T (thymine). This is
then reported as the text string,
called as a read. Some of the DNA
Glossary of Genetics
sequencers can be also considered
as the optical instruments as they
analyze the light signals originating
from the fluorochromes attached to
the nucleotides. The Human
Genome Project spurred the
development of the cheaper, high
throughput and more accurate
platforms known as the Next
Generation Sequencers (NGS) to
sequence the human genome.
These include the 454, SOLiD and
the Illumina DNA sequencing
platforms. Next generation
sequencing machines have also
increased the rate of the DNA
sequencing substantially, as
compared with the previous Sanger
methods. The DNA samples can
be prepared automatically in as
little as about 90 mins, while a
human genome can be sequenced
at about 15 times coverage in a
matter of the days.
• DNA STRAND TRANSFER -
The two DNA strand transfer
reactions occur during the
retroviral reverse transcription. The
mechanism of the first, minus
strand strong-stop DNA, transfer
has been studied very intensively in
vitro with the human
immunodeficiency virus 1 reverse
transcriptase (HIV-1 RT) and a
model template-primer system
which is derived from the HIV-1
genome. The results reveal that
the HIV-1 RT alone can catalyze
the DNA strand transfer reactions.
The Two kinetically distinct
ribonuclease (RNase) H activities
© 2022 by JPS Scientific Publications, India
156
the associated with the HIV-1 RT
are required for the removal of the
RNA fragments annealed to the
nascent DNA strand.
Examination of the binding of the
DNA. The RNA duplex and the
single-stranded RNA to the HIV-1
RT during the strand transfer
supports a model where the
enzyme accommodates both of the
acceptor RNA template and the
nascent DNA strand before the
strand transfer event is completed.
The polymerase activity
incorporated additional bases
beyond the 5’ end of the RNA
template, resulting in a base
misincorporation upon the DNA
strand transfer. Such a process
occurring in vivo during the
retroviral homologous
recombination could contribute to
the hypermutability of the HIV-1
genome.
• DNA SUPERCOILED - The
DNA supercoiling refers to the
amount of the twist in a particular
DNA strand, which determines the
amount of the strain on it. A given
strand may be “positively
supercoiled” or the ‘”negatively
supercoiled” (more or the less
tightly wound). The amount of a
strand’s supercoiling affects a
number of the biological processes,
such as the compacting DNA and
regulating the access to the genetic
code (which strongly affects the
DNA metabolism and the possibly
gene expression). The Certain
enzymes, such as the
Glossary of Genetics
topoisomerases, change the
amount of the DNA supercoiling
to facilitate the functions such as
the DNA replication and the
transcription. The amount of the
supercoiling in a given strand is
described by a mathematical
formula that compares it to a
reference state known as the
“relaxed B-form” DNA. The DNA
supercoiling is important for the
DNA packaging within all the
cells. Because the length of the
DNA can be thousands of times
that of a cell, packaging this
genetic material into the cell or the
nucleus (in the eukaryotes) is a
very difficult feat. Supercoiling of
rye DNA reduces the space and
allows for the DNA to be
packaged. In the prokaryotes,
plectonemic supercoils are the
predominant, because of the
circular chromosome and relatively
small amount of the genetic
material. In the eukaryotes, the
DNA supercoiling exists on the
many levels of both the
plectonemic and the solenoidal
supercoils, with the solenoidal
supercoiling proving most effective
in the compacting of the he DNA.
The solenoidal supercoiling is
achieved with the histones to form
a 10 nm fiber. This fiber is further
coiled into a 30 nm fiber, and
further coiled upon the itself
numerous times more.
• DOCKING - In the field of the
molecular modeling, the docking is
a method which predicts the
© 2022 by JPS Scientific Publications, India
157
preferred orientation of one of the
molecule to a second when a
ligand and a target are bound to
each other to form a very stable
complex. The Knowledge of the
preferred orientation in turn may
be used to predict the strength of
the association or the binding
affinity between the two molecules
using, for example the scoring
functions. The associations
between the biologically relevant
molecules such as the proteins,
peptides, nucleic acids,
carbohydrates, and the lipids play a
central role in the signal
transduction. Furthermore, the
relative orientation of the two
interacting partners may affect the
type of the signal produced (e.g.,
agonism vs antagonism).
Therefore, the docking is very
useful for predicting both the
strength and the type of the signal
produced. The Molecular docking
is one of the most frequently used
methods in the structure-based
drug design, due to its ability to
predict the binding-conformation
of the very small molecule ligands
to the appropriate target binding
site. The Characterisation of the
binding behaviour plays an very
important role in the rational
design of the drugs as well as to
elucidate the fundamental
biochemical processes.
• DOMAIN SWAPPING - The
Domain swapping is a structural
phenomenon that plays an
important role in the mechanism of
Glossary of Genetics
the oligomerization of some of the
proteins. The monomer units in the
oligomeric structure become
entangled with the each other. It is
believed to play an important role
in the mechanism of the
oligomerization in the evolutionary
pathway of some of the proteins.
Some of the proteins remain
functional only in the oligomeric
state. There are almost 40 domain
swapped proteins studied so far by
the different research groups and
described in a systematic way. The
process of the domain swapping is
described as the domain of the one
subunit being replaced by the
identical domain of the other
subunit. The monomeric units in
the dimer or oligomer are always
extended to achieve the
intertwining with the other unit,
and this state of the monomer is
generally called as the “open
monomeric state” and the interface
is termed as the “open interface”.
On the other hand, the monomeric
state, which is not coupled with the
other molecule, is independent and
much more compact, and is
generally called as the “closed
monomeric state”, with the
interface being called as the
“closed interface”.
• DORMANCY CYCLING IN
ARABIDOPSIS - The molecular
regulation of the dormancy cycling
is still unknown, but an extensive
range of the mechanisms have been
identified in the laboratory
experiments. Using a targeted
© 2022 by JPS Scientific Publications, India
158
investigation of the gene
expression over the dormancy
cycle of the Arabidopsis seeds in
the field, we investigated how these
mechanisms are seasonally
coordinated. The Depth of the
dormancy and the gene expression
patterns were correlated with the
seasonal changes in the soil
temperature. The results were
consistent with the abscisic acid
(ABA) signaling linked to the deep
dormancy in the winter being
repressed in the spring concurrent
with the enhanced DELLA
repression of the germination as
depth of the dormancy decreased.
The Dormancy increased during
the winter as soil temperature
declined and the expression of the
ABA synthesis (NCED6) and the
gibberellic acid (GA) catabolism
(GA2ox2) genes increased.
• DSBCS - It is termed as the
Double-sideband suppressed-
carrier transmission (DSB-SC) and
it is a transmission in which the
frequencies produced by the
amplitude modulation (AM) are
symmetrically spaced above and
below the carrier frequency and the
carrier level is reduced to the
lowest practical level, ideally being
the completely suppressed. In the
DSB-SC modulation, unlike in the
AM, the wave carrier is not
transmitted, thus much of the
power is distributed between the
side bands, which implies an
increase of the cover in the DSB-
SC, compared to the AM, for the
Glossary of Genetics
same amount of power use. The
DSB-SC transmission is a special
case of the double-sideband
reduced carrier transmission. It is
used for the radio data systems.
This mode is frequently used in the
Amateur radio voice
communications, especially on the
High-Frequency bands.
• DOSAGE COMPENSATION -
The Dosage compensation is the
process by which the organisms
equalize the expression of the
genes between members of the
different biological sexes. Across
the species, the different sexes are
often characterized by the different
types and numbers of the sex
chromosomes. In order to
neutralize the large difference in
the gene dosage produced by the
differing numbers of the sex
chromosomes among the sexes,
various evolutionary branches have
acquired various methods to
equalize the gene expression
among the sexes. Because the sex
chromosomes contain the different
numbers of genes, different species
of the organisms have the
developed rye different
mechanisms to cope with this
inequality. Replicating the actual
gene is impossible true organisms
instead equalize the expression
from the each gene. For example,
in the humans, females (XX)
silence the transcription of the one
X chromosome of the each pair,
and transcribe all the information
from the other, expressed X
© 2022 by JPS Scientific Publications, India
159
chromosome. Thus, the human
females have the same number of
the expressed X-linked genes as do
the human males (XY), both the
sexes having essentially one X
chromosome per cell, from which
to transcribe and the express genes.
• DUTP DIPHOSPHATASE - In
the field of the enzymology, a dutp
diphosphatase is an enzyme that
catalyzes the chemical reaction.
This enzyme belongs to the family
of the hydrolases, specifically those
acting on the acid anhydrides in
the phosphorus-containing
anhydrides. The systematic name
of this enzyme class is the dUTP
nucleotidohydrolase. Other names
in the common use include the
deoxyuridine-triphosphatase,
dUTPase, dUTP pyrophosphatase,
desoxyuridine 5'-triphosphate
nucleotidohydrolase, and
desoxyuridine 5'-triphosphatase.
This enzyme participates in the
pyrimidine metabolism. This
enzyme has a dual function: on
one hand, it removes the dUTP
from the deoxynucleotide pool,
which reduces the probability of
this base being incorporated into
the DNA by the DNA
polymerases, while on the other
hand, it produces the dTTP
precursor dUMP. Lack or
inhibition of the dUTPase action
leads to the harmful perturbations
in the the nucleotide pool resulting
in the increased uracil content of
the DNA that activates a
Glossary of Genetics
hyperactive futile cycle of the
DNA repair.
• DOUBLE SEX GENE - The
Doublesex (dsx) is a gene that is
involved in the sex determination
system of the many insects
including the fruit fly Drosophila
melanogaster. The gene is
expressed in the both male and the
female flies and is subject to the
alternative splicing, producing the
protein isoforms dsxf in the
females and the longer dsxm in the
males. The production of the dsxf
is caused by the presence of the
female-specific version of the
transformer (tra) gene. In a sense,
the isoform of the dsx informs a
cell about the organism’s sex, for
instance, the female genitals only
develop if the dsxf is present. In the
conjunction with the gene fruitless,
the dsx also causes the differences
in the brain structure and the
behavior of the males and the
females. Although the details of the
sex determination differ in the
various species, there is a gene
related to the dsx in the vertebrates
(DMRT1) and in the nematodes
(MAB-3). All of these are the
transcription factors with a zinc
finger DNA-binding domain
(known as the DM domain) and
are involved in the sex-specific
differentiation
• DPE - In the field of the molecular
biology, a downstream promoter
element (DPE) is a core promoter
element. Like all the core
promoters, the DPE plays an
© 2022 by JPS Scientific Publications, India
160
important role in the initiation of
the gene transcription by the RNA
polymerase II. The DPE was first
described by the T. W. Burke and
the James T. Kadonaga in the
Drosophila melanogaster at the
University of the California, San
Diego in the year 1996. It is also
present in the other species
including the humans, but not in
the Saccharomyces cerevisiae.
Together with the initiator motif
(Inr), another core promoter
element, the DPE is recognized by
the transcription factor II D
(TFIID) subunits TAF6 and the
TAF9. It has been shown that the
DPE-dependent basal transcription
depends highly on the Inr (and vice
versa) and on the correct spacing
between the two elements. The
DPE consensus sequence was
originally thought to be
RGWCGTG, however more
recent studies have suggested it to
be the similar but the more general
sequence RGWYV(T). It is located
about 28–33 nucleotides
downstream of the transcription
start site.
• DPN - The Drosophila pan-neural
genes deadpan (dpn) and the
scratch (scrt) are expressed in most
or all the developing neural
precursor cells of the central
nervous system (CNS) and the
peripheral nervous system (PNS).
The Dpn also regulates tyesex-
determination by repressing the
sxl, the primary gene involved in
the sex differentiation. This is the
Glossary of Genetics
first demonstration that the Dpn is
a partner and the target of the
CK2, and raises the possibility that
its repressor functions might also
be regulated by the
phosphorylation. By itself, the dpn
cannot account for the
masculinizing effect of the
increased autosomal ploidy, the
effect that gave rise to the concept
of the X:A ratio. The Mutation of
the Dpn consensus binding site
from the asymmetric sequence 5’-
CACGCG-3’ to the palindromic
sequence 5’-CACGTG-3’ abolishes
the asymmetric inhibition. The
Loss of the deadpan results in the
reduced cell proliferation, while the
ectopic deadpan expression causes
the over-proliferation.
• DPP - The Decapentaplegic (Dpp)
is a key morphogen involved in the
development of the fruit fly
Drosophila melanogaster and it is
the first validated secreted
morphogen. It is known to be
necessary for the correct patterning
and the development of the early
Drosophila embryo and the fifteen
imaginal discs, which are the
tissues that will become the limbs
and the other organs and the
structures in the adult fly. It has
also been suggested that the Dpp
plays a important role in regulating
the growth and the size of the
tissues. The Flies with the
mutations in the decapentaplegic
fail to form these structures
correctly. The Dpp is the
Drosophila homolog of the
© 2022 by JPS Scientific Publications, India
161
vertebrate bone morphogenetic
proteins (BMPs), which are the
members of the TGF-β
superfamily, a class of the proteins
that are often associated with their
own specific signaling pathway.
Studies of Dpp in Drosophila have
led to the greater understanding of
the function and the importance of
their homologs in the vertebrates
like the humans.
• DSBs - The DNA double strand
breaks (DSB) are considered as the
most lethal form of the DNA
damage for the eukaryotic cells.
The DSB can either be properly
repaired, restoring the genomic
integrity, or the misrepaired
resulting in the drastic
consequences, such as the cell
death, genomic instability, and the
cancer. It is well established that
the exposure to the DSB-inducing
agents is associated with the
chromosomal abnormalities and
the leukemogenesis. The non-
homologous end joining (NHEJ)
pathway is considered as a major
route for the repair DSB in the
mammalian cells. Although the
mechanism(s) by which the repair
of the DSB lead to the leukemia
are poorly understood, recent
evidence is beginning to emerge
that a poorly defined and error-
prone branch of the NHEJ
pathway plays a very pivotal role
in this process.
• DNA MISMATCH REPAIR -
The DNA mismatch repair (MMR)
is a system for recognizing and
Glossary of Genetics
repairing the erroneous insertion,
deletion, and the mis-incorporation
of the bases that can arise during
the DNA replication and the
recombination, as well as repairing
some forms of the DNA damage.
The Mismatch repair is strand-
specific. During the DNA synthesis
the newly synthesised (daughter)
strand will commonly include the
errors. In order to begin the repair,
the mismatch repair machinery
distinguishes the newly synthesised
strand from the template
(parental). In the gram-negative
bacteria, the transient
hemimethylation distinguishes the
strands (the parental is methylated
and the daughter is not). However,
in the other prokaryotes and the
eukaryotes, the exact mechanism is
not yet clear. It is suspected that, in
the eukaryotes, the newly
synthesized lagging-strand DNA
transiently contains the nicks
(before being sealed by the DNA
ligase) and provides a signal that
directs the mismatch proofreading
systems to the appropriate strand.
The Recent work has shown that
nicks are sites for the RFC-
dependent loading of the
replication sliding clamp,
proliferating cell nuclear antigen
(PCNA), in an orientation-specific
manner, such that one face of the
donut-shape protein is juxtaposed
toward the 3'-OH end at the nick.
The Loaded PCNA then directs
the action of the MutLalpha
endonuclease to the daughter
© 2022 by JPS Scientific Publications, India
162
strand in the presence of a
mismatch and the MutSalpha or
the MutSbeta.
• DS ELEMENTS - The Ac/Ds
transposable controlling elements
was the first transposable element
system recognized in the maize.
The Ac Activator element is the
autonomous, whereas the Ds
Dissociation element requires an
additional Activator element to
transpose. The Ac was initially
discovered as the enabling a Ds
element to break the
chromosomes. Both the Ac and Ds
can also insert into the genes,
causing the mutants that may
revert to the normal on the
excision of the element. The
phenotypic consequence of the
Ac/Ds transposable element
includes the mosaic colours in the
kernels and the leaves in the maize.
The Genomic analysis of the maize
show that these elements, which
share the terminal 11 bp imperfect
inverted repeat sequences, have
much sequence heterogeneity, both
in the length and in the content.
They also include a class of the
DNA elements that do not
transpose in the presence of the Ac
element. The chromosome
breaking property has been shown
to come from the pairs of closely
positioned elements.
• DSRNA - The Double-stranded
RNA viruses (dsRNA viruses) are
a polyphyletic group of the viruses
that have double-stranded genomes
made of the ribonucleic acid. The
Glossary of Genetics
double-stranded genome is used to
transcribe the positive-strand of the
RNA by the viral RNA-dependent
RNA polymerase known as the
RdRp. The positive-strand of the
RNA may be used as the
messenger RNA (mRNA) which
can be translated into the viral
proteins by the host cell’s
ribosomes. The positive-strand of
the RNA can also be replicated by
the RdRp to create a new double-
stranded viral genome. The
Double-stranded RNA viruses are
classified in the two separate phyla
Duplornaviricota and the
Pisuviricota (specifically class
Duplopiviricetes), which are in the
kingdom Orthornavirae and realm
Riboviria. Both of the groups do
not share a common dsRNA virus
ancestor. The Double-stranded
RNA viruses evolved the two
separate times from the positive-
strand RNA viruses. In the
Baltimore classification system, the
dsRNA viruses belong to the
Group III. The Virus group
members vary widely in the host
range (animals, plants, fungi, and
bacteria), genome segment number
(one to twelve), and the virion
organization (T-number, capsid
layers, or turrets). The Double-
stranded RNA viruses include the
rotaviruses, which globally known
as a common cause of the
gastroenteritis in the young
children, and the bluetongue virus,
an economically significant
pathogen of the cattle and the
© 2022 by JPS Scientific Publications, India
163
sheep. The family Reoviridae is
the largest and the most diverse
dsRNA virus family in terms of the
host range.
• DYAD AXIS - In the field of the
genetics, the dyad symmetry refers
to the two areas of a DNA strand
whose base pair sequences are
inverted repeats of rye each other.
They are often described as the
palindromes. For example, the
following shows the dyad
symmetry between the sequences
GAATAC and the GTATTC
which are reverse complements of
the each other. Since the two
reverse complementary sequences
will fold and base-pair with the
each other, the sequence of rye
bases between them form a hairpin
loop. This structure is thought to
destabilize the binding of the RNA
polymerase enzyme to the DNA
(hence terminating the
transcription). The Dyad symmetry
is known to have a role in the rho
independent method of the
transcription termination in the E.
Coli. The Regions of the dyad
symmetry in the DNA sequence
stall the RNA polymerase enzyme
as it transcribes them.
• DNA GLYCOSYLASE - The
DNA glycosylases are a family of
the enzymes involved in the base
excision repair. The Base excision
repair is the mechanism by which
the damaged bases in the DNA are
removed and then replaced. The
DNA glycosylases catalyze the first
step of this process. The DNA
Glossary of Genetics 164

Glycosylases remove the damaged

nitrogenous base while leaving the
sugar-phosphate backbone intact,
creating an apurinic/apyrimidinic
site, which is commonly referred to
as an AP site. This is accomplished
by flipping the damaged base out
of the double helix followed by the
cleavage of the N-glycosidic bond.
The Glycosylases were first
discovered in the bacteria, and
have since been found in all
kingdoms of the life. In addition to
their role in the base excision
repair, the DNA glycosylase
enzymes have been implicated in
the repression of the gene silencing
in the A. thaliana, N. tabacum and
the other plants by the active
demethylation. The 5-
methylcytosine residues are excised
and then replaced with the
unmethylated cytosines allowing
the access to the chromatin
structure of the enzymes and the
proteins necessary for the
transcription and the subsequent
translation.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
E •
• E. coli REPLISOME - The
common method to study the
replisomes in vitro is to assemble
the replisome on the replication
fork substrate. The Replisome
studies often utilize a “rolling
circle” substrate which is a circular
duplex DNA with an break in the
one strand that has a 5′ single-
strand (ss) DNA tail. The inner
circle is the leading strand
template, and since a circle has no
end, the replisome can progress
very much around the circle
indefinitely, thus as the name
“rolling circle”. The leading strand
product is continuously displaced
from the circle to produce the long
ssDNA tail that serves as the
template for the primase and the
lagging strand DNA polymerase.
To assemble the E. Coli replisome
onto the minicircle replication fork,
the DnaB is allowed to slide over
the 5′ ssDNA tail, followed by the
Pol III* and the βclamp that load
onto the 3′ terminus of the circle.
This assembly step is performed in
the presence of only 2 dNTPs to
prevent the replisome movement.
Upon adding the dNTPs, rNTPs,
primase and the SSB the replisome
extends the 3′ terminus multiple
times around the circle, resulting in
a very long double-strand (ds)
DNA tail, the one strand is the
product of the leading polymerase
while the other strand is comprised
© 2022 by JPS Scientific Publications, India
165
of the lagging strand of Okazaki
fragments.
ETHIDIUM INTERCALATION
INTO DNA - The Ethidium
bromide is known as an intercalate
agent as it inserts itself between the
stacked bases of the DNA. The
ring structure of the ethidium
bromide resembles the rings of the
DNA bases and it is also
hydrophobic. The Ethidium
bromide is fluorescent and is
visible under the UV light. This
allows the DNA to be visualized.
• EVE GENE - The eve gene are
scientifically, are the collection of
the genes which is called as the
‘L0’ which are passed down
maternally through the
mitochondria which is also known
as ‘the powerhouse of the cell’ and
it is small bean-shaped structures in
our cells that convert the food into
energy used for powering the
bodily functions and the
biochemical reactions that keep us
alive. It is important to note that
the mitochondria have their own
DNA that carry this particular
‘Eve’/L0 genome. This more
commonly termed as the
mitochondrial DNA (mtDNA). It
is thus nicknamed the ‘Eve Gene’
as it is an inherited gene, paying
the reference to the story of
creation in the Genesis, the first
chapter of the Bible. The story of
the creation describes the Eve as
the first woman on the earth,
therefore in the essence she would
be the mother to us all. However,
Glossary of Genetics
this has not been scientifically
proven therefore, the term is used
only to refer to the most recent
female genetic ancestor of a
species.
• EUKARYOTIC ACTIVAING
REGIONS - The Eukaryotic
transcriptional activator are the
modular protein which are
typically comprises a sequence
specific DNA binding domain and
an activation region. The region
which helps to increase the rate of
the transcription are known as the
Enhancers.
• E.COLI GROWTH
CONDITION - The E. Coli can
also grow under a wide pH ranges.
The typical growth and
maintenance is performed at a
neutral pH of 7.0. Taking all the
optimal growth conditions into the
consideration i.e., 37°C, aeration,
pH of 7.0, a minimum doubling
time of 20 min should occur at
least. The growth and survival of
the E. Coli depends on a number
of the environmental factors such
as the temperature, pH, water
activity (aw) and the composition
of the food. The temperature range
for the growth of the E.Coli is
about 7–8°C to 46°C, with an
optimum temperature of around
35–40°C. There will not be any
effects of the visible light on the
growth of the E coli. However, you
should look the effect on the
orange juice and some of the anti-
oxidant produced from the juice
that can cause any effect to the
© 2022 by JPS Scientific Publications, India
166
E.coli. The acid limit for the E.
Coli growth is around pH 4.0–4. 5,
and all the known AR and ATR
systems only prolong survival of
the E. Coli cells under the acidic
conditions, but cannot support the
growth at pH 4.0–4.5. The
Escherichia coli is a metabolically
very versatile bacterium that is able
to grow in the presence and or in
absence of the oxygen. To achieve
this, it exploits a very flexible
biochemistry in which the aerobic
respiration is preferred to the
anaerobic respiration, which in
turn is preferred to the
fermentation.
• EXPRESSION VECTOR - The
expression vector, otherwise
known as an expression construct,
is usually a plasmid or the virus
designed for the gene expression in
the cells. The vector is used to
introduce a specific type of gene
into the target cell, and can
commandeer the cell's mechanism
for the protein synthesis to produce
the protein encoded by the gene.
The expression vectors are the
basic tools in the biotechnology for
the production of the proteins. The
vector is engineered to contain the
regulatory sequences that act as the
enhancer and the promoter regions
and lead to the efficient
transcription of the gene carried on
the expression vector. The goal of a
well-designed expression vector is
the efficient production of the
protein, and this may be achieved
by the production of the significant
Glossary of Genetics
amount of the stable messenger
RNA, which can then be translated
into the protein. The expression of
a protein may be tightly controlled,
and the protein is only produced in
the significant quantity when
necessary through the use of an
inducer, in some of the systems
however the protein may be
expressed constitutively. The
Escherichia coli is commonly used
as the host for the protein
production, but other cell types
may also be used. An example of
the use of the expression vector is
the production of the insulin,
which is used for the medical
treatments of the diabetes.
• EXTRACELLULAR MATRIX -
In the field of biology, the
extracellular matrix (ECM) is a
three-dimensional network
consisting of the extracellular
macromolecules and minerals,
such as the collagen, enzymes,
glycoproteins and the
hydroxyapatite that provide the
structural and the biochemical
support to the surrounding cells.
Because the multicellularity
evolved independently in the
different multicellular lineages, the
composition of the ECM varies
between the multicellular
structures; however, the cell
adhesion, cell-to-cell
communication and the
differentiation are common
functions of the ECM. The
extracellular matrix includes the
interstitial matrix and the basement
© 2022 by JPS Scientific Publications, India
167
membrane. The Interstitial matrix
is present between the various
animal cells. The Gels of the
polysaccharides and the fibrous
proteins fill the interstitial space
and act as a compression buffer
against the stress placed on the
ECM. The Basement membranes
are sheet-like depositions of the
ECM on which the various
epithelial cells rest. Each type of
the connective tissue in the animals
has a type of the ECM such as the
collagen fibers and bone mineral
comprise the ECM of the bone
tissue; reticular fibers and the
ground substance comprise the
ECM of the loose connective tissue
and the blood plasma is the ECM
of the The plant ECM includes the
cell wall components, like
cellulose, in addition to more the
complex signaling molecules.
Some single-celled organisms
adopt multicellular biofilms in
which the cells are embedded in an
ECM composed primarily of the
extracellular polymeric substances
(EPS).
• EF- TU SYNTHESIS - The
Elongation factor thermal unstable
Tu (EF-Tu) is a G protein which
catalyzes the binding of the
aminoacyl-tRNA to the A-site of
the ribosome inside the living cells.
The Structural and the biochemical
studies of EF-TU have described
the complex interactions needed to
effect the canonical function. It is a
prokaryotic elongation factor
which is responsible for catalyzing
Glossary of Genetics
the binding of an aminoacyl-tRNA
to the ribosome. It is a G-protein,
facilitates the selection and binding
of an aa-tRNA to the A-site of the
ribosome. EF-Tu is one of the most
abundant proteins found in the
bacteria’s often present as the 5%
of the total cell protein. The gene
encoding EF-Tu elongation factor
is called tuf, and many bacteria
have duplicate genes for this
protein. In addition to the
antibiotic-resistant mutants, some
of the mutants of the EF-Tu alter
the error frequency of translation.
• EUCHROMATIN - The
Euchromatin which is also called
as the “open chromatin” is a
lightly packed form of the
chromatin i.e DNA, RNA, and the
protein that is enriched in the
genes, and is often (but not always)
under the active transcription. The
euchromatin stands in contrast to
the heterochromatin, which is
tightly packed and it is less
accessible for the transcription.
About 92% of the human genome
is euchromatic. In the eukaryotes,
the euchromatin comprises the
most active portion of the genome
within the cell nucleus. In the
prokaryotes, the euchromatin is the
only form of the chromatin
present, this indicates that the
heterochromatin structure evolved
later along with the nucleus,
possibly as a mechanism to handle
the increasing genome size. The
Euchromatin participates in the
active transcription of the DNA to
© 2022 by JPS Scientific Publications, India
168
the mRNA products. The unfolded
structure allows the gene
regulatory proteins and the RNA
polymerase complexes to bind to
the DNA sequence, which can
then initiate the process of
transcription. It also take part in
the epigenetics which involves the
changes in the phenotype that can
be inherited without changing the
DNA sequence. This can occur
through many types of the
environmental interactions.
• ENHANCERS - In the field of
genetics, an enhancer is a short i.e
50–1500 bp region of the DNA
that can be bound by the proteins
(activators) to increase the
likelihood that transcription of a
particular gene will occur. These
proteins are usually referred to as
the transcription factors. The
Enhancers are the cis-acting. They
can be located up to the 1 Mbp
(1,000,000 bp) away from the gene,
upstream or the downstream from
the start site. There are hundreds of
thousands of the enhancers in the
human genome. They are found in
both the prokaryotes and in the
eukaryotes. The HACNS1 which is
also known as the CENTG2 and is
located in the Human Accelerated
Region is a gene enhancer “that
may have contributed to the
evolution of the uniquely
opposable human thumb, and
possibly also modifications in the
ankle or the foot that allow the
humans to walk on the two legs”.
An enhancer near the gene
Glossary of Genetics
GADD45g has been described that
may regulate the brain growth in
the chimpanzees and in the other
mammals, but not in the humans.
The GADD45G regulator in the
mice and in the chimps is active in
the regions of the brain where cells
that form the cortex, ventral
forebrain, and thalamus are located
and may suppress the further
neurogenesis.
• EPIGENETICS - The Epigenetics
is the study of how your behaviors
and environment can cause the
changes that affect the way your
genes work. Unlike the genetic
changes, the epigenetic changes are
reversible and do not change your
DNA sequences, but they can
change how your body reads a
DNA sequence. Several lifestyle
factors that have been identified
that might modify the epigenetic
patterns, such as the diet, obesity,
physical activity, tobacco smoking,
alcohol consumption,
environmental pollutants,
psychological stress, and working
on the night shifts. The altered
‘bad’ epigenetic defects that
accumulate in the cancer are
potentially reversible, and the
‘good’ epigenetic mechanisms
which may still operate in the
cancer stem cell driven contexts
could be promoted through the
inductive differentiation promoting
the signals.
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169
• EQUILIBRIUM CONSTANT -
The equilibrium constant of a
chemical reaction is the value of its
reaction quotient at the chemical
equilibrium, a state approached by
a dynamic chemical system after
the sufficient time has elapsed at
the which its composition has no
measurable tendency towards the
further change. For a given set of
the reaction conditions, the
equilibrium constant is
independent of the initial analytical
concentrations of the reactant and
the product species in the mixture.
Thus, given the initial composition
of a system, known equilibrium
constant values can be used to
determine the composition of the
system at the equilibrium.
However, the reaction parameters
like the temperature, solvent, and
the ionic strength may all influence
the value of the equilibrium
constant. A knowledge of the
equilibrium constants is essential
for the understanding of the many
chemical systems, as well as the
biochemical processes such as the
oxygen transport by the
hemoglobin in the blood and in the
acid–base homeostasis in the
human body. The Stability
constants, formation constants,
binding constants, association
constants and the dissociation
constants are all the types of the
equilibrium constants.
• EXON SHUFFLING - The Exon
shuffling is a molecular mechanism
for the formation of the new genes.
Glossary of Genetics
It is a process through which the
two or more exons from the
different types of genes can be
brought together ectopically, or the
same exon can be duplicated, to
create a very new exon-intron
structure. There are different
mechanisms through which the
exon shuffling occurs such as the
transposon mediated exon
shuffling, crossover during sexual
recombination of the parental
genomes and the illegitimate
recombination. The Exon
shuffling follows a certain splice
frame rules. The Introns can
interrupt the reading frame of a
gene by inserting a sequence
between the two consecutive
codons (phase 0 introns), between
the first and the second nucleotide
of a codon (phase 1 introns), or
between the second and the third
nucleotide of a codon (phase 2
introns). Additionally the exons
can be classified into the nine
different groups based on the phase
of the flanking introns. The
Symmetric exons are the only ones
that can be inserted into the
introns, undergo duplication, or be
deleted without changing the
reading frame.
• E2F - The E2F is a group of genes
that encodes a family of the
transcription factors (TF) in the
higher eukaryotes. The Three of
them are activators i.e the E2F1, 2
and E2F3a. The six others act as
the suppressors i.e E2F3b, E2F4-8.
All of them are involved in the cell
© 2022 by JPS Scientific Publications, India
170
cycle regulation and in the
synthesis of the DNA in the
mammalian cells. The E2Fs as TFs
bind to the TTTCCCGC (or slight
the variations of this sequence)
consensus binding site in the target
promoter sequence. The E2F
family members play a major role
during the G1/S transition in the
mammalian and in the plant cell
cycle. The DNA microarray
analysis reveals the unique sets of
the target promoters among the
E2F family members suggesting
that each of the protein has a
unique role in the cell cycle.
Among the E2F transcriptional
targets are the cyclins, CDKs,
checkpoints regulators, DNA
repair and the replication proteins.
Nonetheless, there is a great deal of
the redundancy among the family
members. The Mouse embryos
lacking the E2F1, E2F2, and one
of the E2F3 isoforms, can develop
normally when either E2F3a or the
E2F3b is expressed.
• ECTODODMAIN - An
ectodomain is the domain of a
membrane protein that extends
into the extracellular space i.et the
space outside a cell. The
Ectodomains are usually the parts
of the proteins that initiate the
contact with the surfaces, which
leads to the signal transduction.A
notable example of an ectodomain
is the S protein, commonly known
as the spike protein, of the viral
particle responsible for the
COVID-19 pandemic. The
Glossary of Genetics
ectodomain region of the spike
protein (S) is essential for the
attachment and in the eventual
entry of the viral protein into the
host cell. The Ectodomains play a
crucial part in the signaling
pathways of the viruses. In
perspective of the severe acute
respiratory syndrome corona virus
2 (SARS-Cov-2) these specific
ectodomains may detect the
antibody efficacy against the
SARS-Cov-2, in which the VN
titers can classify the eligible
plasma donors. The Protective
measures against the diseases and
the respiratory conditions can
further be advanced through the
ongoing research on the
ectodomains. The Ectodomain’s
play a crucial part in the signaling
pathways of the viruses.
• EDMAN DEGRADATION - The
Edman degradation, is developed
by the Pehr Edman, is a method of
sequencing the amino acids in a
peptide. In this method, the amino-
terminal residue is labeled and then
cleaved from the peptide without
disrupting the peptide bonds
between the other amino acid
residues. Since the Edman
degradation proceeds from the N-
terminus of the protein, it will not
work if the N-terminus has been
chemically modified (e.g. by the
acetylation or the formation of the
pyroglutamic acid). The
sequencing will stop if a non-α-
amino acid is encountered (e.g. the
isoaspartic acid), because the
© 2022 by JPS Scientific Publications, India
171
favored five-membered ring
intermediate is not able to be
formed. The edman degradation is
generally not useful to determine
the positions of the disulfide
bridges. It also requires the peptide
amounts of the 1 picomole or
above for the discernible results.
• EF-G - The EF-G (elongation
factor G, historically known as the
translocase) is a prokaryotic
elongation factor involved in the
protein translation. As a GTPase,
EF-G catalyzes the movement
(translocation) of the transfer RNA
(tRNA) and the messenger RNA
(mRNA) through the ribosome.
The EF-G catalyzes the
translocation of the tRNA and the
mRNA down the ribosome at the
end of the each round of the
polypeptide elongation. In this
process, the peptidyl transferase
center (PTC) has catalyzed the
formation of a peptide bond
between the amino acids, moving
the polypeptide chain from the P
site tRNA to the A site tRNA. The
50S and tyrv30S ribosomal
subunits are now allowed to rotate
relative to the each other by
approximately 7°. The subunit
rotation is coupled with the
movement of the 3’ ends of the
both tRNA molecules on the large
subunit from the A and the P sites
to the P and the E sites,
respectively, while the anticodon
loops remain unshifted. This
rotated ribosomal intermediate, in
which the first tRNA occupies a
Glossary of Genetics
hybrid A/P position and the
second tRNA occupies a hybrid
P/E position is a substrate for the
EF-G-GTP.
• EXPONENTIAL PHASE - The
Exponential growth is a process
that increases the quantity over the
time. It occurs when the
instantaneous rate of the change
(that is, the derivative) of a
quantity with respect to the time is
proportional to the quantity itself.
Described as a function, a quantity
undergoing the exponential growth
is an exponential function of the
time, that is, the variable
representing the time is the
exponent (in contrast to the other
types of the growth, such as the
quadratic growth). If the constant
of the proportionality is negative,
then the quantity decreases over
the time, and is said to be
undergoing the exponential decay
instead. In the case of a discrete
domain of the definition with the
equal intervals, it is also called as
the geometric growth or the
geometric decay since the function
values form a geometric
progression.
• EF-TS - The EF-Ts which is the
elongation factor thermo stable is
one of the prokaryotic elongation
factors. It is found in the human
mitochrondria as the TSFM. It is
similar to the eukaryotic EF-1B.
The EF-Ts serves as the guanine
nucleotide exchange factor for the
EF-Tu which is the elongation
factor thermo unstable, catalyzing
© 2022 by JPS Scientific Publications, India
172
the release of the guanosine
diphosphate from the EF-Tu. This
enables the EF-Tu to bind to a new
guanosine triphosphate molecule,
release EF-Ts, and go on to
catalyze the another aminoacyl
tRNA addition. The EF-Ts
functions as the guanine nucleotide
exchange factor, it catalyzes the
reaction of the EF-Tu*GDP
(inactive form) to the EF-Tu*GTP
(active). The EF-Tu (active) then
delivers the aminoacyl-tRNA to
the ribosome. Therefore, the EF-Ts
main role is recycling the EF-Tu
back to its active state in order to
complete the another elongation
cycle. The majority of this pathway
is performed through the
conformational changes of the EF-
Tu domain 1 which contains the
active site and the manipulation of
the switch 1 & 2 regions by the
ribosome and the tRNA. First, in
domain 1 of the EF-Tu the GTPase
activity site is blocked by a series of
the hydrophobic residues that
block the catalytic residue His 84
in the inactive form prior to
activation via EF-Ts.
• EFG - The Epidermal growth
factor (EGF) is a protein that
stimulates the cell growth and the
differentiation by binding to its
receptor, EGFR. The human EGF
is 6-kDa and it has 53 amino acid
residues and the three
intramolecular disulfide bonds.
The EGF, via binding to its
cognate receptor, results in the
cellular proliferation,
Glossary of Genetics
differentiation, and in the survival.
The Salivary EGF, which seems to
be regulated by the dietary
inorganic iodine, also plays an
important physiological role in the
maintenance of the oro-esophageal
and the gastric tissue integrity.
The biological effects of the
salivary EGF include the healing
of oral and the gastroesophageal
ulcers, inhibition of the gastric acid
secretion, stimulation of the DNA
synthesis as well as the mucosal
protection from the intraluminal
injurious factors such as the gastric
acid, bile acids, pepsin, and the
trypsin and to the physical,
chemical and the bacterial.
• EIF 1 - The Eukaryotic translation
initiation factor 1 (eIF1) is a
protein that in the humans is
encoded by the EIF1 gene. It is
related to the yeast SUI1. The eIF1
interacts with the eukaryotic small
(40S) ribosomal subunit and the
eIF3, and is a component of the
43S preinitiation complex (PIC).
The eIF1 and the eIF1A bind
cooperatively to the 40S to stabilize
an “open” conformation of the
preinitiation complex (PIC) during
the eukaryotic translation
initiation. The eIF1 binds to a
region near the ribosomal A-site in
the 40S subunit and functions in a
manner similar to the structurally
related to the bacterial counterpart
IF1. The function of the eIf1 has
some hidden aspects. However, in
all the eukaryotic cells initiation of
the mRNA translation starts with
© 2022 by JPS Scientific Publications, India
173
scanning via ribosomal 43S
preinitiation complexes starting
from the 5’ end of the mRNA.
Next, the induction via eIF1 and
eIF1A are needed to disclose the
conformation of the 40S subunit in
order to induce the DEAD-box
RNA helicase eIF4A, its cofactor
eIF4B, and the eIF4G activity.
• EIF 1A - The eIF1A (formerly
designated eIF-4C), is a
mammalian 17 kDa eukaryotic
initiation factor. It is essential for
the transfer of the initiator Met-
tRNAf (as the Met-
tRNAf.eIF2.GTP ternary complex)
to the 40 S ribosomal subunits in
the absence of the mRNA to form
the 40 S preinitiation complex (40
S.Met-tRNAf.eIF2.GTP).
Furthermore, the eIF1A acted
catalytically in this reaction to
mediate the highly efficient transfer
of the Met-tRNAf.eIF2.GTP
ternary complex to the 40 S
ribosomal subunits. The 40 S
complex formed was free of the
eIF1A indicating that its role in the
40 S preinitiation complex
formation is not to stabilize the
binding of the Met-tRNAf to the 40
S ribosomes. Additionally, the
eIF1A-mediated 40 S initiation
complex formed in the presence of
the AUG codon efficiently joined
60 S ribosomal subunits in an eIF5-
dependent reaction to form a
functional 80 S initiation complex.
In contrast to the other reports, we
found that the eIF1A plays no role
either in the subunit joining
Glossary of Genetics
reaction or in the generation of the
ribosomal subunits from the 80 S
ribosomes. The major function of
the eIF1A is to mediate the transfer
of the Met-tRNAf to the 40 S
ribosomal subunits to form the 40
S preinitiation complex.
• EIF 2 - The Eukaryotic Initiation
Factor 2 (eIF2) is a eukaryotic
initiation factor. It is required for
most forms of the eukaryotic
translation initiation. The eIF2
mediates the binding of the
tRNAiMet to the ribosome in a
GTP-dependent manner. The eIF2
is a heterotrimer consisting of an
alpha (also called as the subunit 1,
EIF2S1), a beta (subunit 2,
EIF2S2), and a gamma (subunit 3,
EIF2S3) subunit. Once the
initiation phase has completed, the
eIF2 is released from the ribosome
bound to GDP as an inactive
binary complex. To participate in
the another round of the
translation initiation, this GDP
must be exchanged for the GTP.
The eIF2 is an essential factor for
the protein synthesis that forms a
ternary complex (TC) with the
GTP and the initiator Met-
tRNAiMet. After the formation,
the TC binds the 40S ribosomal
subunit to form the 43S
preinitiation complex which is 43S
PIC. The 43S PIC assembly is
believed to be stimulated by the
initiation factors eIF1, eIF1A, and
the eIF3 complex according to in
vitro experiments. The 43S PIC
then binds the mRNA that has
© 2022 by JPS Scientific Publications, India
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previously been unwound by the
eIF4F complex. The 43S PIC and
the eIF4F proteins form a new 48S
complex on the mRNA, which
starts the searching process along
the mRNA for the start codon
(AUG). Upon the base pairing of
the AUG-codon with the Met-
tRNA, the eIF5 (which is a
GTPase-activating protei, or the
GAP) is recruited to the complex
and is induces eIF2 to hydrolyse its
GTP.
• EIF 2A - The Eukaryotic
translation initiation factor 2A
(eIF2A) is a protein that in the
humans is encoded by the EIF2A
gene. The eIF2A protein is not to
be confused with the eIF2α, a
subunit of the heterotrimeric eIF2
complex. Instead, the eIF2A
functions by a separate mechanism
in the eukaryotic translation. The
eIF2A is a 65 kDa protein that
catalyzes the formation of the
puromycin-sensitive 80S
preinitiation complexes. It may be
important for the translation
initiation mediated by the HCV
IRES under the stress conditions,
but this result has been debated.
• ERK - In the field of the
molecular biology, extracellular
signal-regulated kinases (ERKs) or
the classical MAP kinases are
widely expressed protein kinase
intracellular signalling molecules
that are involved in the functions
including the regulation of the
meiosis, mitosis, and the
postmitotic functions in the
Glossary of Genetics
differentiated cells. Many different
stimuli, including the growth
factors, cytokines, virus infection,
ligands for the heterotrimeric G
protein-coupled receptors,
transforming agents, and the
carcinogens, activate the ERK
pathway. The term, "extracellular
signal-regulated kinases", is
sometimes used as a synonym for
the mitogen-activated protein
kinase (MAPK), but has more
recently been adopted for a specific
subset of the mammalian MAPK
family. In the MAPK/ERK
pathway, the Ras activates c-Raf,
followed by the mitogen-activated
protein kinase kinase (abbreviated
as the MKK, MEK, or the
MAP2K) and then MAPK1/2.
The Ras is typically activated by
the growth hormones through the
receptor tyrosine kinases and the
GRB2/SOS, but may also receive
the other signals. ERKs are known
to activate many of the
transcription factors, such as the
ELK1, and some of the
downstream protein kinases. The
Disruption of the ERK pathway is
common in the cancers, especially
the Ras, c-Raf, and the receptors
such as the HER2.
• EIF 3 - The Eukaryotic initiation
factor 3 (eIF3) is a multiprotein
complex that functions during the
initiation phase of the eukaryotic
translation. It is essential for the
most forms of the cap-dependent
and the cap-independent
translation initiation. In the
© 2022 by JPS Scientific Publications, India
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humans, the eIF3 consists of the 13
nonidentical subunits (eIF3a-m)
with a combined molecular weight
of around 800 kDa, making it the
largest translation initiation factor.
The eIF3 complex is broadly
conserved across the eukaryotes,
but the conservation of the
individual subunits varies across
the organisms. For instance, while
most mammalian eIF3 complexes
are composed of the 13 subunits,
the budding yeast’s eIF3 has only
six subunits (eIF3a, b, c, g, i, j).
The eIF3 stimulates nearly all the
steps of the translation initiation.
The eIF3 also appears to
participate in other phases of the
translation, such as recycling,
where it promotes the splitting of
the post-termination ribosomes. In
specialized cases of the reinitiation
following the uORFs, eIF3 may
remain bound to the ribosome
through the elongation and
termination to promote the
subsequent initiation events.
Research has also indicated that
the eIF3 plays a role in the
programmed stop codon read
through in the yeast, by interacting
with the pre-termination
complexes and interfering with
decoding.
• EIF 3A - The Eukaryotic
translation initiation factor 3
subunit A (eIF3a) is a protein that
in the humans is encoded by the
EIF3A gene. It is one of the
subunits of the Eukaryotic
initiation factor 3 (eIF3) a
Glossary of Genetics
multiprotein complex playing
major roles in the translation
initiation in the eukaryotes.
• EIF 3B - The Eukaryotic
translation initiation factor 3
subunit B (eIF3b) is a protein that
in the humans is encoded by the
EIF3B gene. The EIF3B has been
shown to interact with the P70-S6
Kinase 1 and the EIF3A.
• EIF 4E - The Eukaryotic
translation initiation factor 4E,
which is also known as the eIF4E,
is a protein that in the humans is
encoded by the EIF4E gene. The
role of the eIF4E in the cancer was
established after the Lazaris-
Karatzas made the discovery that
overexpressing the If 4E causes the
tumorigenic transformation of the
fibroblasts. Since this initial
observation, numerous groups
have recapitulated these results in
the different cell lines. As a result,
the eIF4E activity is implicated in
the several cancers including the
cancers of the breast, lung, and the
prostate. In fact, the transcriptional
profiling of the metastatic human
tumors has revealed a distinct
metabolic signature wherein the
eIF4E is known to be consistently
up-regulated. Since the eIF4E is an
initiation factor that is relatively
low in the abundance, eIF4E is a
potential target for the
transcriptional control. The
Regulation of the eIF4E may be
achieved via the three distinct
mechanisms i.e the transcription,
© 2022 by JPS Scientific Publications, India
176
phosphorylation, and the
inhibitory proteins.
• EIF 4A - The eukaryotic initiation
factor-4A (eIF4A) family consists
of the 3 closely related proteins
EIF4A1, EIF4A2, and the
EIF4A3. These factors are required
for the binding of the mRNA to the
40S ribosomal subunits. In
addition these proteins are
helicases that function to unwind
the double-stranded RNA. The
Eukaryotic initiation factor
complex 2 (eIF2) forms a ternary
complex with the GTP and the
initiator Met-tRNA – this process
is regulated by the guanine
nucleotide exchange and
phosphorylation and serves as the
main regulatory element of the
bottleneck of the gene expression.
Before t translation can progress to
the elongation stage, a number of
the initiation factors must facilitate
the synergy of the ribosome and
the mRNA and ensure that the 5’
UTR of the mRNA is sufficiently
devoid of the secondary structure.
Binding in this way is facilitated by
the group 4 eukaryotic initiation
factors the eIF4F has implications
in the normal regulation of the
translation as well as the
transformation and progression of
the cancerous cells; as such, it
represents an interesting field of the
research.
• EIF 4B - The eukaryotic
translation initiation factor 4B is a
protein that in the humans is
encoded by the EIF4B gene. The
Glossary of Genetics
eIF4B has been shown to interact
with and stimulate the activity of
the eIF4A and bind to the eIF3
complex through the eIF3A
subunit. This interaction results in
the recruitment of the eukaryotic
small ribosomal subunit (40S) to
the mRNA which will in turn set
the stage for the later steps leading
to the elongation.
• EIF 5 - The Eukaryotic translation
initiation factor (eIF) 5 is crucial
for the assembly of the eukaryotic
preinitiation complex. This activity
is mediated by the ability of its C-
terminal HEAT domain to interact
with the eIF1, eIF2, and the eIF3
in the multifactor complex and
with the eIF4G in the 48S
complex. However, the binding
sites for these factors on the eIF5–
C-terminal domain (CTD) have
not been known. Here we present a
homology model for the eIF5-CTD
based on the HEAT domain of the
eIF2Bε. We show that the binding
site for the eIF2β is located in a
surface area containing the
aromatic and the acidic residues
(aromatic/acidic boxes), that the
binding sites for the eIF1 and the
eIF3c are located in a conserved
surface region of the basic residues,
and that the eIF4G binds the eIF5-
CTD at an interface overlapping
with the acidic area. Mutations in
these distinct eIF5 surface areas
impair GCN4 translational control
by disrupting the preinitiation
complex interactions. These results
indicate that the eIF5 HEAT
© 2022 by JPS Scientific Publications, India
177
domain is a critical nucleation core
for the preinitiation complex
assembly and the function.
• ELECTROPHORESIS
AGAROSE GEL - The Agarose
gel electrophoresis is a method of
the gel electrophoresis used in the
field of the biochemistry,
molecular biology, genetics, and
the clinical chemistry to separate a
mixed population of the
macromolecules such as the DNA
or the proteins in a matrix of the
agarose, which is one of the two
main components of the agar. The
proteins may be separated by the
charge and/or the size (isoelectric
focusing the agarose
electrophoresis is essentially size
independent), and the DNA and
the RNA fragments by the length.
The biomolecules are separated by
applying an electric field to move
the charged molecules through an
agarose matrix, and the
biomolecules are separated by the
size in the agarose gel matrix. The
agarose gel is easy to cast, has
relatively fewer charged groups,
and is particularly suitable for
separating the DNA of size range
most often encountered in the
laboratories, which accounts for
the popularity of its use. The
separated DNA may be viewed
with the stain, most commonly
under the UV light, and the DNA
fragments can be extracted from
the gel with relative ease. Most of
the agarose gels used are between
Glossary of Genetics
the 0.7–2% dissolved in a suitable
electrophoresis buffer.
• EMSA - The electrophoretic
mobility shift assay (EMSA) or the
mobility shift electrophoresis, also
referred to as a gel shift assay, gel
mobility shift assay, band shift
assay, or the gel retardation assay,
is a common affinity
electrophoresis technique used to
study the protein–DNA or the
protein–RNA interactions. This
procedure can determine if a
protein or the mixture of proteins is
capable of binding to a given DNA
or the RNA sequence, and can
sometimes indicate if more than
one protein molecule is involved in
the binding complex. The gel shift
assays are often performed in vitro
concurrently with the DNAse
footprinting, primer extension, and
the promoter-probe experiments
when studying the transcription
initiation, DNA gang replication,
DNA repair or the RNA
processing and the maturation, as
well as the pre-mRNA splicing.
Although the precursors can be
found in earlier literature, most of
the current assays are based on the
methods described by the Garner
and the Revzin and Fried and
Crothers.
• EMS - ThevEthyl
methanesulfonate (EMS) is a
mutagenic, teratogenic, and the
carcinogenic organic compound
with the formula C3H8SO3. It
produces the random mutations in
the genetic material by the
© 2022 by JPS Scientific Publications, India
178
nucleotide substitution, particularly
through the G:C to A:T transitions
induced by the guanine alkylation.
The EMS typically produces the
only point mutations. Due to its
potency and well understood
mutational spectrum, the EMS is
the most commonly used chemical
mutagen in the experimental
genetics. The Mutations induced
by the EMS exposure can then be
studied in the genetic screens or the
other assays. The ethyl group of
the EMS reacts with the guanine in
the DNA, forming the abnormal
base O6-ethylguanine. During the
DNA replication, the DNA
polymerases that catalyze the
process frequently place thymine,
instead of the cytosine, opposite
O6-ethylguanine.
• EZH 2 - The Enhancer of the zeste
homolog 2 (EZH2) is a histone-
lysine N-methyltransferase enzyme
encoded by the EZH2 gene, that
participates in the histone
methylation and, ultimately,
transcriptional repression. The
EZH2 catalyzes the addition of the
methyl groups to the histone H3 at
the lysine 27, by using the cofactor
S-adenosyl-L-methionine.
Methylation activity of the EZH2
facilitates heterochromatin
formation thereby silences the gene
function. The Remodeling of the
chromosomal heterochromatin by
the EZH2 is also required during
the cell mitosis. The EZH2 is the
functional enzymatic component
of the Polycomb Repressive
Glossary of Genetics
Complex 2 (PRC2), which is
responsible for the healthy
embryonic development through
the epigenetic maintenance of the
genes responsible for regulating the
development and the
differentiation. The EZH2 is
responsible for the methylation
activity of the PRC2, and the
complex also contains the proteins
required for the optimal function.
• ELL GENE - The RNA
polymerase II elongation factor
ELL is an enzyme that in the
humans is encoded by the ELL
gene. The ELL (gene) has been
shown to interact with the p53.
• ELONGATION FACTOR - The
Elongation factors are a set of
proteins that function at the
ribosome, during the protein
synthesis, to facilitate the
translational elongation from the
formation of the first to the last
peptide bond of a growing
polypeptide. Most of the common
elongation factors in the
prokaryotes are the EF-Tu, EF-Ts,
EF-G. The bacteria and the
eukaryotes use the elongation
factors that are largely homologous
to the each other, but with the
distinct structures and the different
research nomenclatures. The
Elongation is the most rapid step in
the translation. In the bacteria, it
proceeds at a rate of 15 to the 20
amino acids added per second
(about 45-60 nucleotides per
second). In the eukaryotes the rate
is about two amino acids per
© 2022 by JPS Scientific Publications, India
179
second (about 6 nucleotides read
per second). The Elongation
factors play a role in orchestrating
the events of this process, and in
ensuring the high accuracy
translation at these speeds.
• EMBRYONIC STEM CELLS -
The Embryonic stem cells (ESCs)
are the pluripotent stem cells
derived from the inner cell mass of
a blastocyst, which is an early-stage
pre-implantation embryo. The
Human embryos reach the
blastocyst stage 4–5 days post the
fertilisation, at which time they
consist of around 50–150 cells.
Isolating the inner cell mass
(embryoblast) using the
immunosurgery results in the
destruction of the blastocyst, a
process which raises the ethical
issues, including whether or not
embryos at the pre-implantation
stage have the same moral
considerations as embryos in the
post-implantation stage of the
development. The embryonic stem
cells of the inner cell mass are
pluripotent, meaning they are able
to differentiate to generate the
primitive ectoderm, which
ultimately differentiates during the
gastrulation into all the derivatives
of the three primary germ layers:
ectoderm, endoderm, and the
mesoderm. These germ layers
generate each of the more than
about 220 cell types in the adult
human body. When provided with
the appropriate signals, the ESCs
initially form the precursor cells
Glossary of Genetics
that in subsequently differentiate
into the desired cell types. The
Pluripotency distinguishes the
embryonic stem cells from the
adult stem cells, which are
multipotent and can only produce
a limited number of the cell types.
• ENDONUCLEASE HO - The
mating-type switching
endonuclease HO plays an
important and an central role in the
natural life cycle of the
Saccharomyces cerevisiae, but its
evolutionary origin is still very
unknown. The HO is a recent
addition to the yeast genomes,
present in only a few genera close
to the Saccharomyces. Here we
show that the HO is structurally
and phylogenetically related to a
family of the unorthodox homing
genetic elements found in the
Torulaspora and in the Lachancea
yeasts. These WHO elements
home into the aldolase gene FBA1,
replacing its 3' end each time they
try to integrate. They resemble
inteins but they operate by a
different mechanism that does not
require the protein splicing. We
show that a WHO protein cleaves
the Torulaspora delbrueckii FBA1
efficiently and in an allele-specific
manner, leading to the DNA repair
by the gene conversion or the
NHEJ. The DNA rearrangement
steps during the WHO element
homing are very similar to those
during the mating-type switching,
and indicate that the HO is a
domesticated WHO-like element.
© 2022 by JPS Scientific Publications, India
180
• END REPLICATION
PROBLEM -
The end replication problem
hypothesis proposes that the ends of
the linear DNA cannot be replicated
completely during the lagging strand
DNA synthesis. Although the idea has
been very widely accepted for
explaining the telomere attrition
during the cell proliferation, it has
never been directly demonstrated. In
order to take a biochemical approach
to understand how the linear DNA
ends are replicated, there have been
established a novel in vitro linear of
simian virus 40 DNA replication
system. In this system, terminally
biotin-labeled linear DNAs are
conjugated to the avidin-coated beads
and subjected to the replication
reactions. The Linear DNA was
efficiently replicated under the very
optimized conditions, and replication
products that had replicated using the
original DNA templates were
specifically analyzed by the purifying
bead-bound replication products. By
exploiting the system, we showed that
the leading strand is completely
synthesized to the end, the lagging
strand synthesis is still gradually halted
in the terminal around ∼500-bp
region, leaving 3′ overhangs. This
result is consistent with the
observations in the telomerase-
negative mammalian cells and
formally demonstrates the end
replication problem.
Glossary of Genetics
• ENDOSPERM - The
endosperm is a tissue produced
inside the seeds of most of the
flowering plants following the
double fertilization. It is
triploid (meaning there is three
chromosome sets per nucleus)
in most of the species, which
may be an auxin-driven. It
surrounds the embryo and
provides the nutrition in the
form of the starch, though it
can also contain the oils and
the protein. This can make
endosperm a source of the
nutrition in the animal diet. For
example, wheat endosperm is
ground into the flour for the
bread (the rest of the grain is
included as well in whole
wheat flour), while barley
endosperm is the main source
of the sugars for the beer
production. Other examples of
endosperm that forms the bulk
of the edible portion are the
coconut "meat" and the
coconut "water", and the corn.
Some of the plants, such as the
orchids, lack endosperm in
their seeds.
• ENERGY ACTIVATION -
The activation energy is the
minimum amount of the energy
that must be provided for the
compounds to result in a
chemical reaction. The
activation energy (Ea) of a
reaction is measured in the
joules per mole (J/mol),
kilojoules per mole (kJ/mol) or
© 2022 by JPS Scientific Publications, India
181
the kilocalories per mole
(kcal/mol). The Activation
energy can be thought of as the
magnitude of the potential
barrier (sometimes called as the
energy barrier) separating the
minima of the potential energy
surface pertaining to the initial
and the final thermodynamic
state. For a chemical reaction
to proceed at a reasonable rate,
the temperature of the system
should be high enough such
that there exists an appreciable
number of the molecules with
the translational energy equal
to or greater than the activation
energy. The term Activation
Energy was introduced in the
year 1889 by the Swedish
scientist Svante Arrhenius.
• ESEs - The Electrical status
epilepticus in sleep (ESES), a
childhood-onset epileptic
encephalopathy, is
characterized by the epilepsy,
cognitive regression, and
marked the activation of the
epileptiform activity during the
non-rapid eye movement
(NREM) sleep to produce an
electroencephalography (EEG)
pattern of the near-continuous
spike-wave discharges.
Different etiologies, both with
or without structural
abnormalities of the brain, have
been associated with the ESES.
Typically children, between the
2 and 12 years of age with a
peak between 3 and 5 years,
Glossary of Genetics
present with the infrequent
seizures (focal and/or
generalized) and stagnation or
regression of the development.
The existing treatment
paradigm is based on the
uncontrolled studies and case
series and primarily focused use
of the traditional antiepileptic
drugs (AEDs), including the
benzodiazepines,
corticosteroids, epilepsy
surgery, and the other non-
pharmacologic therapies, the
ketogenic diet. This activity
reviews the evaluation and
management of the ESES and
highlights the role of the
healthcare team in the
evaluating and treating the
patients with this condition.
• ENGRAILED - The engrailed
is a homeodomain transcription
factor which is involved in
many aspects of the
multicellular development.
First known for its role in the
arthropod embryological
development, working in the
consort with the Hox genes,
engrailed has been found to be
important in the other areas of
the development. It has been
identified in many of the
bilaterians, including the
arthropods, vertebrates,
echinoderms, molluscs,
nematodes, brachiopods, and
the polychaetes. It acts as a
"selector" gene, conferring a
specific identity to defined the
© 2022 by JPS Scientific Publications, India
182
areas of the body, and co-
ordinating the expression of the
downstream genes.
• ENU - The ENU, which is also
known as the N-ethyl-N-
nitrosourea (chemical formula
C3H7N3O2), is a highly potent
mutagen. For a given gene in
the mice, the ENU can induce
1 new mutation in every of the
700 loci. It is also toxic at the
high doses. Ever since the
discovery of the ENU as the
most potent mutagen by the
Russell. it has been used in
forward (phenotype based)
genetic screens with which one
can identify and study a
phenotype of the interest. The
screening process begins with
the mutagenising a male mouse
with the ENU. This is followed
by the systematic phenotypic
analysis of the progeny. The
progeny are assessed for the
behavioral, physiological or the
dysmorphological changes. The
abnormal phenotype is then
identified. The Identification of
the candidate gene is then
achieved by the positional
cloning of the mutant mice
with the phenotype of the
interest.
• ENHANCESOMES - An
enhanceosome is a protein
complex that assembles at an
enhancer region on the DNA
and it helps to regulate the
expression of a target gene.
Once the enhanceosome has
Glossary of Genetics 183

been formed, it recruits the are divided into the two

coactivators and the general categories, conformational
transcription factors to the epitopes and the linear
promoter region of the target epitopes, based on their
gene to begin the transcription. structure and the interaction
The effectiveness of this is with the paratope. The
dependent on the DNA Conformational and the linear
conformation. As a result, the epitopes interact with the
enhanceosome also recruits the paratope based on the 3-D
non histone architectural conformation adopted by the
transcription factors, which is epitope, which is determined by
called as the high-mobility the surface features of the
group (HMG) proteins, which involved epitope residues and
are responsible for regulating the shape or the tertiary
the chromatin structure. These structure of the other segments
factors do not bind to the of the antigen. A
enhancer, but instead are used conformational epitope is
to restructure the DNA to formed by the 3-D
ensure that the genes can be conformation adopted by the
accessed by the transcription interaction of the discontiguous
factors. amino acid residues. In
• EPITOPES - An epitope,which contrast, a linear epitope is
is also known as the antigenic formed by the 3-D
determinant, is the part of an conformation adopted by the
antigen that is recognized by interaction of the contiguous
the immune system, specifically amino acid residues. A linear
by the antibodies, B cells, or the epitope is not determined solely
T cells. The epitope is very by the primary structure of the
important because it is the involved amino acids. The
specific piece of the antigen to Residues that flank the such
which an antibody binds. The amino acid residues, as well as
part of an antibody that binds the more distant amino acid
to the epitope is called as the residues of the antigen affect
paratope. Although the the ability of the primary
epitopes are usually the non- structure residues to adopt the
self proteins, sequences derived epitope's 3-D conformation.
from the host that can be The 90% of epitopes are the
recognized (as in the case of the conformational.
autoimmune diseases) are also
known as the epitopes. The
epitopes of the protein antigens

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
• EGF - The Epidermal growth
factor (EGF) is a single
polypeptide of around 53
amino acid residues which is
involved in the regulation of
the cell proliferation. The Egf
exerts its effects in the target
cells by binding to the plasma
membrane located in the EGF
receptor. The EGF receptor is a
protein of transmembrane
tyrosine kinase. Binding of the
EGF to the receptor causes the
activation of the kinase and
subsequently of the receptor
autophosphorylation. The
autophosphorylation process is
essential for the interaction of
the receptor with the substrates.
These bind to the receptor by
the so-called as the SH2
domains. The signal
transduction pathways is
activated by the EGF include
the phosphatidylinositol
pathway, leading to the
activation of the protein kinase
C and to increase in the
intracellular Ca2+
concentration, and to the ras
pathway leading to the MAP
kinase activation. Recently the
cytoplasm has been implicated
as playing an important role in
the EGF induced signal
transduction. The EGF
receptor has been demonstrated
to be as an actin-binding
protein. In addition EGF
causes a rapid actin
depolymerisation and the
© 2022 by JPS Scientific Publications, India
184
formation of the membrane
ruffles. In particular these
membrane ruffles have been
shown to act as the first site of
the signal transduction after the
EGF binding, and thus may be
considered as the signal
transduction structures. Finally
the evidence has been presented
suggesting a positive role for
the EGF and/or the receptor in
the nucleus.
• E SITE - The E-site is the third
and the final binding site for the
t-RNA in the ribosome during
the translation, a part of the
protein synthesis. The "E"
stands for the exit, and is
accompanied by the P-site (for
the peptidyl) which is the
second binding site, and the A-
site (aminoacyl), which is the
first binding site. It is involved
in the cellular processes.
• ESS - An evolutionarily stable
strategy (ESS) is a strategy (or
the set of the strategies) that is
impermeable when adopted by
a population in adaptation to a
specific environment, that is to
say it cannot be displaced by an
alternative strategy (or set of
strategies) which may be novel
or the initially It was
Introduced by the john
Maynard Smith and the George
R. Price in the year 1972, it is
an important concept in the
behavioural ecology,
evolutionary psychology,
mathematical game theory and
Glossary of Genetics
the economics, with the
applications in the other fields
such as the anthropology,
philosophy and the political
science.
• EST - In the field of the
genetics, an expressed sequence
tag (EST) is a short sub-
sequence of the DNA
sequence. The ESTs may be
used to identify the gene
transcripts, and were
instrumental in the gene
discovery and in the gene-
sequence determination. The
identification of the ESTs has
proceeded rapidly, with
approximately around 74.2
million ESTs now available in
the public databases (e.g. the
GenBank 1 January 2013, all
species). The EST approaches
have largely been superseded
by the whole genome and the
transcriptome sequencing and
the metagenome sequencing.
An EST results from the one-
shot sequencing of a cloned
cDNA. The cDNAs used for
the EST generation are
typically individual clones from
a cDNA library. The resulting
sequence is a relatively low-
quality fragment whose length
is limited by the current
technology to approximately
around 500 to 800 nucleotides.
Because these clones consist of
the DNA that is
complementary to the mRNA,
the ESTs represent portions of
© 2022 by JPS Scientific Publications, India
185
the expressed genes. They may
be represented in the databases
as either the cDNA/mRNA
sequence or as the reverse
complement of the mRNA, the
template strand. One can map
the ESTs to the specific
chromosome locations using
the physical mapping
techniques, such as the
radiation hybrid mapping,
happy mapping, or the Fish.
Alternatively, if the genome of
the organism that originated
the EST has been sequenced,
one can align the EST sequence
to that genome using the
computer.
• ETHIDIUM BROMIDE - The
Ethidium bromide (or the
homidium bromide, chloride
salt homidium chloride) is an
intercalating agent commonly
used as the fluorescent tag
(nucleic acid stain) in the field
of the molecular biology
laboratories for the techniques
such as the agarose gel
electrophoresis. It is commonly
abbreviated as the EtBr, which
is also an abbreviation for the
bromoethane. To avoid the
confusion, some of the
laboratories have used the
abbreviation EthBr for this salt.
When exposed to the
ultraviolet light, it will fluoresce
with an orange colour,
intensifying almost 20-fold after
binding to the DNA. Under the
name homidium, it has been
Glossary of Genetics
commonly used since the 1950s
in the veterinary medicine to
treat the trypanosomiasis in the
cattle. The high incidence of
the antimicrobial resistance
makes this treatment
impractical in some of the
areas, where the related
isometamidium chloride is used
instead. Several science
commentators have alleged that
the ethidium bromide is safe.
• EUCHROMATIN - The
Euchromatin which is also
called as the "open chromatin"
is a lightly packed form of the
chromatin (DNA, RNA, and
protein) that is enriched in the
genes, and is often (but not
always) under the active
transcription. The Euchromatin
stands in contrast to the
heterochromatin, which is
tightly packed and less
accessible for the transcription.
92% of the human genome is
euchromatic. The Euchromatin
participates in the active
transcription of the DNA to the
mRNA products. The unfolded
structure allows the gene
regulatory proteins and the
RNA polymerase complexes to
bind to the DNA sequence,
which can then initiate the
transcription process. While
not all the euchromatin is
necessarily transcribed, as the
euchromatin is divided into the
transcriptionally active and the
inactive domains, the
© 2022 by JPS Scientific Publications, India
186
euchromatin is still generally
associated with the active gene
transcription. There is therefore
a direct link to how actively
productive a cell is and the
amount of the euchromatin that
can be found in its nucleus. It is
thought that the cell uses the
transformation from the
euchromatin into the
heterochromatin as a method of
the controlling gene expression
and the replication, since such
the processes behave differently
on the densely compacted
chromatin. This is known as
the 'accessibility hypothesis'.
One example of the constitutive
euchromatin that is 'always
turned on' is housekeeping
genes, which code for the
proteins needed for the basic
functions of cell survival.
• EXONUCLEASE - The
Exonuclease 1 is an enzyme
that in the humans is encoded
by the EXO1 gene. This gene
encodes a protein with the 5' to
3' exonuclease activity as well
as the RNase activity
(endonuclease activity cleaving
the RNA on the DNA/RNA
hybrid). It is similar to the
Saccharomyces cerevisiae
protein Exo1 which interacts
with the Msh2 and which is
involved in the DNA mismatch
repair and in the homologous
recombination. Alternative
splicing of this gene results in
the three transcript variants
Glossary of Genetics
encoding the two different
isoforms. The ExoI is essential
for the meiotic progression
through the metaphase I in the
budding yeast Saccharomyces
cerevisiae and in the mouse.
The Recombination during the
meiosis is often initiated by a
DNA double-strand break
(DSB). During the
recombination, sections of the
DNA at the 5' ends of the break
are cut away in a process called
as the resection. In the strand
invasion step that follows, an
overhanging 3' end of the
broken DNA molecule
"invades" the DNA of a
homologous chromosome that
is not broken, forming a
displacement loop (D-loop).
After the strand invasion, the
further sequence of events may
follow either of the two main
pathways leading to a crossover
(CO) or a non-crossover (NCO)
recombinant. The pathway
leading to a CO involves a
double Holliday junction
(DHJ) intermediate. The
Holliday junctions need to be
resolved for the CO
recombination to be completed.
• EXONUCLEASE 7 - The
enzyme exodeoxyribonuclease
VII (which is also called as the
EC 3.1.11.6, Escherichia coli
exonuclease VII, E. coli
exonuclease VII,
endodeoxyribonuclease VII,
exodeoxyribonuclease VII) is a
© 2022 by JPS Scientific Publications, India
187
bacterial exonuclease enzyme.
It is composed of the two
nonidentical subunits; one large
subunit and the 4 small ones,
that catalyses the
exonucleolytic cleavage in
either the 5′- to 3′- or 3′- to 5′-
direction to yield the nucleoside
5′-phosphates. The large
subunit also contains an N-
terminal OB-fold domain that
binds to the nucleic acids.
• EXONUCLEASE 3 - The
Exonuclease III (ExoIII) is an
enzyme that belongs to the
exonuclease family. The ExoIII
catalyzes the stepwise removal
of the mononucleotides from
the 3´-hydroxyl termini of the
double-stranded DNA. A
limited number of the
nucleotides are removed during
each of the binding event,
resulting in the coordinated
progressive deletions within the
population of the DNA
molecules. The preferred
substrates are blunt or the
recessed 3´-termini, although
the ExoIII also acts at nicks in
the duplex DNA to produce the
single-strand gaps. The enzyme
is not active on the single-
stranded DNA, and thus 3´-
protruding termini are resistant
to the cleavage. The degree of
the resistance depends on the
length of the extension, with
extensions 4 bases or longer
being essentially resistant to the
cleavage. This property is used
Glossary of Genetics 188

to produce the unidirectional and the RNA from the RNA:DNA

deletions from a linear hybrids in the 5'→3' direction. The
molecule with one resistant (3´- T7 Gene 6 Exonuclease is similar
overhang) and one susceptible to the Lambda Exonuclease in that
(blunt or 5´-overhang) it catalyzes the stepwise hydrolysis
terminus. The ExoIII activity of the duplex DNA from the 5'
depends partially on the DNA termini liberating the 5'
helical structure and displays mononucleotides. However, unlike
the sequence dependence the Lambda Exonuclease, the
(C>A=T>G). The ExoIII has enzyme has low processivity and it
also been reported to have the will remove both the 5'-hydroxyl
RNase H, 3´-phosphatase and and the 5'-phosphoryl termini. It
the AP-endonuclease activities. also degrades the RNA and the
• EXONUCLEASE 5 - The DNA from the RNA:DNA hybrids
Exonuclease 5 is a protein that in the 5'→3' direction but is unable
in the humans is encoded by to degrade either the double-
the EXO5 gene. The protein stranded or the single-stranded
which is encoded by this gene is RNA. This enzyme has been used
a single-stranded DNA for generating the single-stranded
(ssDNA)-specific exonuclease DNA templates for sequencing or
that can slide along the DNA the SNP analysis.
before cutting it. However, the
human replication protein A
binds the ssDNA and restricts
sliding of the encoded protein,
providing a 5'-directionality to
the enzyme. This protein
localizes to the nuclear repair
loci after the DNA damage.
• EXONUCLEASE 6:- The
T7 Gene 6 Exonuclease hydrolyzes
the duplex DNA non-processively
in the 5'→3' direction from both
the 5'-phosphoryl or 5'-hydroxyl
nucleotides by liberating the
oligonucleotides as well as the
mononucleotides, until about 50%
of the DNA is acid soluble. It also
degrades the nucleotides at the
gaps and nicks of the double-
stranded DNA from the 5'-termini

© 2022 by JPS Scientific Publications, India

Glossary of Genetics 189

transactions is a heterodimeric
F protein complex that affects the
eukaryotic RNA polymerase II
(Pol II) transcription elongation
• FEED FORWARD CONTROL -
both in vitro and in vivo. It was
The feed forward which is
discovered in the year 1998 as a
sometimes also written as the
factor purified from the human
feedforward is an element or the
cells that was essential for the
pathway within a system which is
productive, in vitro Pol II
also known as the control system
transcription on a chromatinized
that passes a controlling signal
DNA template. The FACT
from a internal source in its
consists of the 140 and 80
external environment to a load
kilodalton (kDa) subunits. The 140
which is present elsewhere in its
kDa subunit is encoded by the
external This is often a command
human gene SUPT16H, while the
signal from an external operator.
80 kDa subunit is encoded by the
The control system which has the
human gene SSRP1. Both of these
only feed-forward behavior
subunits in the yeast affect the Pol
responds to its control signal in a
II transcription elongation, and the
very pre-defined way without
purified human FACT binds
responding to the way the load
specifically to the
reacts it is in the contrast with a
mononucleosomes and the histone
system that also has its own
H2A/H2B dimer, but not to the
feedback, which can adjusts the
H3/H4 tetramer. The Co-
input to take the account of how it
immunoprecipitation assays with
affects the load, and also how the
the tagged recombinant proteins
load can itself may vary the load is
showed that the Spt16 subunit
also considered to belong to the
interacts with the H2A/H2B
external environment of the
dimers and the mononucleosomes,
system. In a feed-forward system,
but not with the H3/H4 tetramers,
the control variable adjustment is
whereas the SSRP1 subunit
not an error-based control. Instead
interacts only with the H3/H4
it is based on the knowledge about
tetramers and not
the process in the form of a
mononucleosomes. Deletion of the
mathematical model of the process
highly acidic C-terminus of the
and the knowledge about, or the
Spt16 does not prevent the Spt16
measurements of the process
from forming a stable complex
disturbances.
with the SSRP1, but it does
• FACT - The FACT (facilitates eliminate the interaction with the
chromatin transcription, mononucleosomes and ability to
sometimes facilitates the chromatin

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
stimulate the in vitro transcription
on the chromatinized templates.
• FACTORS FOR INVERSION
STIMULATION - The highly
abundant DNA binding protein
whose expression is strongly
correlated with the growth phase of
the bacteria. The protein plays a
role in the regulating of the DNA
topology and the activation of the
RIBOSOMAL RNA transcription.
It was originally identified as a
factor required for the inversion
stimulation by the Hin
recombinase of the
SALMONELLA and the Gin site-
specific recombinase of the
BACTERIOPHAGE MU.
• FELINE FOAMY VIRUS - The
Feline foamy virus or the Feline
syncytial virus (FeFV or FFV) is a
retrovirus and belongs to the family
Retroviridae and the subfamily
Spumaretrovirinae. It shares the
genus Felispumavirus with only
the Puma feline foamy virus. There
has been controversy on whether
the FeFV is nonpathogenic as the
virus is generally asymptomatic in
the affected cats and does not
cause the disease. However, some
of the changes in the kidney and
the lung tissue have been observed
over time in the cats affected with
the FeFV, which may or may not
be directly affiliated. This virus is
fairly common and the infection
rates gradually increase with a cat's
age.
• FAIRE SEQ - The FAIRE-Seq
(Formaldehyde-Assisted Isolation
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190
of the Regulatory Elements) is a
method in the molecular biology
used for the determining the
sequences of the DNA regions in
the genome associated with the
regulatory activity. The technique
was developed in the laboratory of
the Jason D. Lieb at the University
of the North Carolina, Chapel Hill.
In contrast to the DNase-Seq, the
FAIRE-Seq protocol doesn't
require the permeabilization of the
cells or the isolation of the nuclei,
and can analyse any type of the
cell. In a study of the seven diverse
human cell types, the DNase-seq
and the FAIRE-seq produced the
strong cross-validation, with each
of the cell type having around 1-2%
of the human genome as the open
chromatin.
• FMET - The N-
Formylmethionine (fMet, HCO-
Met, For-Met) is a derivative of the
amino acid methionine in which a
formyl group has been added to the
amino group. It is specifically used
for the initiation of the protein
synthesis from the bacterial and the
organellar genes, and may be
removed the post-translationally.
The fMet is a starting residue in the
synthesis of the proteins in the
bacteria, and, consequently, is
located at the N-terminus of the
growing polypeptide. The fMet is
delivered to the ribosome (30S) -
mRNA complex by a specialized
tRNA (tRNAfMet) which has a 3'-
UAC-5' anticodon that is capable
of binding with the 5'-AUG-3' start
Glossary of Genetics
codon located on the mRNA. The
fMet is thus coded by the same
codon as the methionine, however
the AUG is also the translation
initiation codon. When the codon
is used for the initiation, the fMet
is used instead of the methionine,
thereby forming the first amino
acid as the peptide chain is
synthesized.
• FERRITIN TRANSLATION -
The Translational regulation of the
ferritin mRNA depends on the two
distinctive features of the RNA: (1)
the conserved regulatory sequence
of the 28 nucleotides occurs in the
5' noncoding region (iron
'regulatory' or the 'responsive'
element, IRE) which interacts with
the cytoplasmic regulator proteins,
present in the animal cells, that
block the initiation sequences in
the 3' untranslated region can
modulate the translation when the
IRE is present. (2) The Ferritin
mRNA, either deregulated by the
iron induction in the cells or the
isolated from the cells (polyA+),
forms the initiation complexes
efficiently compared to the other
cellular mRNAs.
• FLP – FRT RECOMBINATION
- In the field of genetics, the Flp-
FRT recombination is a site-
directed recombination technology,
increasingly used to manipulate an
organism's DNA under controlled
conditions in vivo. It is analogous
to the Cre-lox recombination but
involves the recombination of the
sequences between the short
© 2022 by JPS Scientific Publications, India
191
flippase recognition target (FRT)
sites by the recombinase flippase
(Flp) derived from the 2 µ plasmid
of the baker's yeast Saccharomyces
cerevisiae. In the yeast, this
enzyme corrects the decreases in
the 2 µ plasmid copy number
caused by the rare missegregation
events. It does so by causing the
recombination between the two
inverted repetitions on the 2 µ
plasmid during DNA replication.
This changes the direction of the
one replication fork, causing the
multiple rounds of the copying in a
single initiation.
• FERRITIN - The Ferritin is a
universal intracellular protein that
stores the iron and releases it in a
controlled fashion. The protein is
produced by almost all the living
organisms, including the archaea,
bacteria, algae, higher plants, and
the animals. It is the primary
intracellular iron-storage protein in
both the prokaryotes and the
eukaryotes, keeping iron in a
soluble and the non-toxic form. In
the humans, it acts as a buffer
against the iron deficiency and the
iron overload. The ferritin is found
in most of the tissues as a cytosolic
protein, but small amounts are
secreted into the serum where it
functions as an iron carrier. The
Plasma ferritin is also an indirect
marker of the total amount of the
iron stored in the body hence,
serum ferritin is used as a
diagnostic test for the iron-
deficiency anemia. The Aggregated
Glossary of Genetics
ferritin transforms into a toxic form
of the iron called hemosiderin. The
Ferritin is a globular protein
complex consisting of the 24
protein subunits forming a hollow
nanocage with the multiple metal–
protein interactions. The Ferritin
that is not combined with the iron
is called as the apoferritin
• FAMALIAL ISOLATED
GROWTH HORMONES - The
isolated growth hormone
deficiency is a condition caused by
the severe shortage or absence of
the growth hormone. The Growth
hormone is a protein that is
necessary for the normal growth of
the body's bones and the tissues.
Because they do not have enough
of this hormone, people with the
isolated growth hormone
deficiency commonly experience a
failure to grow at the expected rate
and have the unusually short
stature. This condition is usually
apparent by the early childhood.
There are four types of the isolated
growth hormone deficiency
differentiated by the severity of the
condition, the gene involved, and
the inheritance pattern. The
Isolated growth hormone
deficiency type IA is caused by an
absence of the growth hormone
and is the most severe of all the
types. In people with type IA, the
growth failure is evident in the
infancy as the affected babies are
shorter than the normal at birth.
The People with the isolated
growth hormone deficiency type IB
© 2022 by JPS Scientific Publications, India
192
produce very low levels of the
growth hormone. As a result, type
IB is characterized by the short
stature. The Growth failure in
people with the type IB is usually
apparent in early to the mid-
childhood. The Individuals with
the isolated growth hormone
deficiency type II have very low
levels of the growth hormone and
the short stature that varies in the
severity. The growth failure in
these individuals is usually evident
in the early to the mid-childhood.
It is estimated that nearly half of
the individuals with the type II
have underdevelopment of the
pituitary gland (pituitary
hypoplasia). The Isolated growth
hormone deficiency type III is
similar to the type II in that the
affected individuals have very low
levels of the growth hormone and
the short stature that varies in the
severity. The Growth failure in the
type III is usually evident in the
early to the mid-childhood. People
with the type III may also have a
weakened immune system and are
prone to the frequent infections.
They produce very few B cells,
which are specialized and known
as the white blood cells that help to
protect the body against the
infection (agammaglobulinemia).
• F FACTORS - The F factor is a
100 kb of the duplex DNA with the
two replication-origin regions. The
oriV or the vegetative replication
region contains the two replication
origins, one of which is used for
Glossary of Genetics
the bidirectional maintenance
replication of the plasmid when it
is not being transferred to the
another cell. The oriT, the transfer
origin, promotes a special mode of
the unidirectional, single-(leading)
strand replication used during the
conjugative transfer of the F factor
to the another cell. This feature has
made the F factor useful to the
workers wishing to perform the
complementation and the
dominance tests with their gene in
a single copy replicon in the E.
coli. This allows creation of a state
of the article diploidy (also called
as the ‘merodiploidy’). Originally,
this was done by the isolation of
the F′ plasmids. The F factors that
have incorporated often large
segments of the DNA from the
bacterial chromosome by the
homologous recombination with
the chromosome.
• FGF - The Fibroblast growth
factors (FGFs) form a family of
generally the extracellular signaling
peptides, which are key regulators
of many of the biological processes
ranging from the cell proliferation
to the control of the embryonic
development in the metazoans.
Ever since the mitogenic activity of
the FGF-like factors was first
observed in the year 1939 and the
first FGF factor was isolated in the
1970s, a large number of the
members of this gene family have
been isolated and been
characterized in the different
metazoans. The FGFs are the
© 2022 by JPS Scientific Publications, India
193
small proteins (between 17 and
34 kDa) characterized by a
relatively well conserved central
domain of around 120 to 130
amino acids. This domain is
organized into the 12 antiparallel β
sheets forming a triangular
structure called as the beta trefoil.
In general, the FGFs function
through binding to a tyrosine
kinase receptor (FGFR) on the
surface of the cell membrane. The
Two FGF ligands bind a dimeric
receptor in the presence of the
heparan sulphate proteoglycan
(HSPG) allowing the
transphosphorylation and the
activation of the intracellular
tyrosine kinase domain of the
receptor. The Binding to the
FGFRs usually activates the
several intracellular cascades (i.e.,
Ras/MAPK, PI3K/Akt, and the
PLCγ/PKC) which may regulate
the transcription of the different
target genes.
• FIS - The fis is an E. coli gene
encoding the Fis (or the FIS)
protein. The regulation of this gene
is more complex than most of the
other genes in the E. coli genome,
as Fis is an important protein
which regulates the expression of
the other genes. It is supposed that
fis is regulated by the H-NS, IHF
and the CRP. It also regulates its
own [removed]autoregulation). Fis
is one of the most abundant DNA
binding proteins in the Escherichia
coli under the nutrient-rich growth
conditions. The Fis is a very
Glossary of Genetics
important small nucleotide-
associated protein which plays a
role in affecting the bacterial
chromosome structure and the
initiation of the DNA replication.
It is a nucleoid-associated protein
in the Escherichia coli that is
abundant during the early
exponential growth in the rich
medium but is in short supply
during the stationary phase. When
the stationary-phase cells are
subcultured into a rich medium,
Fis levels increase from the less
than the 100 to over 50,000 copies
per cell prior to the first cell
division. As cells enter the
exponential growth, nascent
synthesis is largely shut off, and the
intracellular Fis levels decrease as a
function of the cell division.
• 5 FLUOROURACIL - The
Fluorouracil (5-FU), sold under the
brand name Adrucil among the
others, is a cytotoxic chemotherapy
medication used to treat the
cancer. By the intravenous
injection it is used for the treatment
of the colorectal cancer,
oesophageal cancer, stomach
cancer, pancreatic cancer, breast
cancer, and the cervical cancer. As
a cream it is used for the actinic
keratosis, basal cell carcinoma, and
the skin warts. The Side effects of
the use by the injection are
common. They may include the
inflammation of the mouth, loss of
appetite, low blood cell counts,
hair loss, and the inflammation of
the skin. When used as a cream,
© 2022 by JPS Scientific Publications, India
194
irritation at the site of the
application usually occurs. The
Use of the either form in the
pregnancy may harm the baby.
The Fluorouracil is in the
antimetabolite and the pyrimidine
analog families of the medications.
• FLAGELLIN - The Flagellin is a
globular protein that arranges itself
in a hollow cylinder to form the
filament in a bacterial flagellum.
The flagellin has a mass of about
30,000 to 60,000 daltons. The
flagellin is the principal component
of the bacterial flagella, and is
present in the large amounts on
nearly all the flagellated bacteria.
The structure of the flagellin is
responsible for the helical shape of
the flagellar filament, which is
important for its proper function.
The flagellin is transported through
the center of the filament to the tip
where it polymerases
spontaneously into a part of the
filament. It is unfolded by the FliS
(P26608) flagellar secretion
chaperone during the transport.
The filament is made up of eleven
smaller "protofilaments", nine of
which contains the flagellin in the
L-type shape and the other two in
the R-type shape.
• FLANKING REGION - The 5′
flanking region is a region of the
DNA that is adjacent to the 5′ end
of the gene. The 5′ flanking region
contains the promoter, and may
also contain the enhancers or the
other protein binding sites. It is the
region of the DNA that is not
Glossary of Genetics
transcribed into the RNA. Not to
be confused with the 5′
untranslated region, this region is
not transcribed into the RNA or
translated into the functional
protein. These regions primarily
function in the regulation of the
gene transcription. The ′ flanking
regions are categorized between
the prokaryotes and the
eukaryotes. In the eukaryotes, the
5′ flanking region has a complex
set of the regulatory elements such
as the enhancers, silencers, and the
promoters. The primary promoter
element in the eukaryotes is the
TATA box. Other promoter
elements found in the eukaryotic 5′
flanking regions include the
initiator elements, downstream
core promoter element, CAAT
box, and the GC box. Whereas the
Prokaryotes only have the three
promoter elements, the two
elements are present at -35 and -10
nucleotides upstream of the
transcription start site, and the
third is directly upstream the
transcription start site.
• FLORESCENT LABELLING
OF DNA AND RNA - Several
procedures have been described for
the fluorescent labeling of the
DNA and the RNA. They are
based on the introduction of the
aldehyde groups by the partial
depurination of the DNA or the
oxidation of the 3'-terminal
ribonucleoside in the RNA by the
sodium periodate. The Fluorescent
labels with an attached hydrazine
© 2022 by JPS Scientific Publications, India
195
group are efficiently coupled with
the aldehyde groups and the
hydrazone bonds are stabilized by
the reduction with the sodium
cyanoborohydride. Alternatively,
the DNA can be quantitatively
split at the depurinated sites with
the ethylenediamine. The aldimine
bond between the aldehyde group
in the depurinated DNA or the
oxidized RNA and the
ethylenediamine is stabilized by
the reduction with the sodium
cyanoborohydride and the primary
amine group introduced at these
sites is used for the attachment of
the isothiocyanate or the
succinimide derivatives of the
fluorescent dyes. The labelling of
fluorescent DNA can be carried
out either in the solution or on a
reverse phase column. These
procedures provide the simple,
inexpensive methods of the
multiple DNA labeling and of
introducing one fluorescent dye
molecule per RNA, as well as the
quantitative DNA fragmentation
and incorporation of one label per
fragment. These methods of the
fluorophore attachment were
shown to be efficient for the use in
the hybridization of the labeled
RNA, DNA and the DNA
fragments with the oligonucleotide
microchips.
• FMET - The N-Formylmethionine
or the fmet is a derivative of the
amino acid methionine in which a
formyl group has been added to the
amino group. It is specifically used
Glossary of Genetics
for the initiation of the protein
synthesis from the bacterial and the
organellar genes, and may be
removed the post-translationally.
The fMet plays a very crucial part
in the protein synthesis of the
bacteria, mitochondria and the
chloroplasts. It is not used in the
cytosolic protein synthesis of the
eukaryotes, where the eukaryotic
nuclear genes are translated. It is
also not used by the Archaea. In
the human body, fMet is
recognized by the immune system
as the foreign material, or as an
alarm signal released by the
damaged cells, and stimulates the
body to fight against the potential
infection.
• FMRP - The clinical features of
the Fragile X mental retardation
syndrome are linked to the absence
of the set of the protein isoforms,
derived from the alternative
splicing of the Fragile X mental
retardation gene 1 (FMR1), and it
is collectively termed as the
FMRP. The FMRP is an RNA
binding protein that is part of a
ribonucleoprotein particle
associated to actively translating
the polyribosomes, and which can
shuttle between the nucleus and
the cytoplasm. The Two highly
homologous human proteins, the
FXR1P and the FXR2P, share the
same domain structure as the
FMRP, and probably also the
similar functions. The properties of
the FMRP suggested that it is
involved in the nuclear export,
© 2022 by JPS Scientific Publications, India
196
cytoplasmic transport, and/or
translational control of the target
mRNAs. In particular, it may play
a role in the regulation of the
protein synthesis at the
postsynaptic sites of the dendrites,
and in maturation of the dendritic
spines. Efforts are underway to
identify the putative specific
mRNA targets of the FMRP, and
study the effect of the FMRP
absence on the corresponding
proteins.
• FOXP1 - The Forkhead box
protein P1 is a protein that in the
humans is encoded by the FOXP1
gene. The FOXP1 is necessary for
the proper development of the
brain, heart, and the lung in the
mammals. It is a member of the
large FOX family of the
transcription factors. This gene
belongs to the subfamily P of the
forkhead box (FOX) transcription
factor family. The Forkhead box
transcription factors play an
important roles in the regulation of
the tissue- and cell type-specific
gene transcription during both the
development and the adulthood.
The Forkhead box P1 protein
contains both the DNA-binding-
and the protein-protein binding-
domains. This gene may act as a
tumor suppressor as it is lost in the
several tumor types and maps to a
chromosomal region reported to
contain a tumor suppressor
gene(s). Alternative splicing results
in the multiple transcript variants
encoding the different isoforms.
Glossary of Genetics
• FRAGILE X SYNDROME - The
Fragile X syndrome (FXS) is a
genetic disorder characterized by
the mild-to-moderate intellectual
disability. The average IQ in the
males with the FXS is under 55,
while about the two thirds of the
affected females are intellectually
disabled. The Physical features
may include a long and the narrow
face, large ears, flexible fingers,
and the large testicles. About a
third of those affected have features
of the autism such as the problems
with the social interactions and the
delayed speech. The Hyperactivity
is common, and the seizures occur
in about 10%. The Males are
usually more affected than the
females. This disorder and finding
of tbe fragile X syndrome has an X-
linked recessive inheritance. It is
typically caused by an expansion of
the CGG triplet repeat within the
FMR1 (fragile X messenger
ribonucleoprotein 1) gene on the X
chromosome. This results in the
silencing (methylation) of this part
of the gene and a deficiency of the
resultant protein (FMRP), which is
required for the normal
development of the connections
between the neurons. The
Diagnosis requires a genetic testing
to determine the number of the
CGG repeats in the FMR1 gene.
There is no cure. But the early
intervention is recommended, as it
provides the most opportunity for
developing the full range of the
skills.
© 2022 by JPS Scientific Publications, India
197
• FRASIER SYNDROME - The
Frasier syndrome is a urogenital
anomaly associated with the WT1
(Wilms tumor 1 gene) gene. Both
the males and the females can have
Frasier syndrome but their
presentations can be different. The
Affected females usually have the
normal genitalia and the gonads
and have only the features of the
impaired renal function, which
may not present until the early
childhood or even the adolescence.
Because the females do not have all
the features of the condition (e.g.
gonadal dysgenesis), females are
usually given the diagnosis of the
isolated nephrotic syndrome. The
Frasier syndrome in some of the
infants may therefore go
unrecognized until the affected
child presents with the signs of the
renal impairment and the further
testing is undertaken to evaluate
the cause. The Genetic screening
of the children experiencing
amenorrhea and the ateroid
resistant nephrotic syndrome can
diagnose the Fraiser syndrome
early, although the slow
progression of the renal failure
makes the diagnosis difficult.
• FUSION PROTEIN - The Fusion
proteins or the chimeric proteins
(literally, made of parts from the
different sources) are the proteins
created through the joining of the
two or more genes that originally
coded for the separate proteins.
The Translation of this fusion gene
results in a single or the multiple
Glossary of Genetics
polypeptides with the functional
properties derived from each of the
original proteins. The
Recombinant fusion proteins are
created artificially by the
recombinant DNA technology for
the use in the biological research or
the therapeutics. The Chimeric or
the chimera usually designate the
hbrid proteins made of the
polypeptides having the different
functions or the physico-chemical
patterns. The Chimeric mutant
proteins occur naturally when a
complex mutation, such as a
chromosomal translocation,
tandem duplication, or the
retrotransposition creates a novel
coding sequence containing the
parts of the coding sequences from
the two different genes. Naturally
occurring fusion proteins are
commonly found in the cancer
cells, where they may function as
the oncoproteins. The bcr-abl
fusion protein is a very well-known
example of the oncogenic fusion
protein, and is considered to be the
primary oncogenic driver of the
chronic myelogenous leukemia.
• FUSIDIC ACID - The Fusidic
acid, sold under the brand names
as the Busid among the others, is
an antibiotic that is often used as
topically in the creams and as the
eyedrops but may also be given
systemically as the tablets or the
injections. The global problem of
the advancing antimicrobial
resistance has led to a renewed
interest in its use recently. The
© 2022 by JPS Scientific Publications, India
198
Fusidic acid binds to the EF-G
after translocation and the GTP
(guanosine-5'-triphosphate)
hydrolysis. This interaction
prevents the necessary
conformational changes for the EF-
G release from the ribosome,
effectively blocking the protein
synthesis process. The Fusidic acid
can only bind to the EF-G in the
ribosome after the GTP hydrolysis.
Since the translocation is a part of
the elongation and the ribosome
recycling, the fusidic acid can
block either or both steps of the
protein synthesis.
• FLP RECOMBINASES - In the
field of the genetics, the Flp-FRT
recombination is a site-directed
recombination technology,
increasingly used to manipulate an
organism’s DNA under the
controlled conditions in vivo. It is
analogous to the Cre-lox
recombination but involves the
recombination of the sequences
between the short flippase
recognition target (FRT) sites by
the recombinase flippase (Flp)
derived from the 2 µ plasmid of the
baker’s yeast Saccharomyces
cerevisiae. In the yeast, this
enzyme corrects the decreases in
the 2 µ plasmid copy number
caused by the rare missegregation
events. It does so by causing the
recombination between the two
inverted repetitions on the 2 µ
plasmid during the DNA
replication. This changes the
Glossary of Genetics 199

direction of the one replication

fork, causing the multiple rounds
of the copying in a single initiation.
• Ftsk - The FtsK stands for the
“Filament temperature sensitive
mutant K”. It has about 1329
amino acid protein involved in the
bacterial cell division and
chromosome segregation. At the
high temperatures the mutant
bacterial cell fails to divide and the
long filaments develops instead. It
acts as the DNA pump, which
interacts with other cell division
proteins, and intervenes in the
regulation of the Xer
recombination process. It belongs
to the AAA (ATPase Associated
with the various cellular Activities)
superfamily and is present in most
of the bacterias. The phylogeny
tree of the FtsK ties back to the
split between the ssDNA and the
dsDNA which translocases where
TraB, FtsK, T4CPs and VirB4s
arise. Each of these shows the
structural similarities and the
parent branch of the FtsK arose
along with the other branches of
the TraB, TcpA, and FtsK. It has
been shown to be a part of the
divisome of bacteria and the couple
cell division with the resolution of
the dimers. It is thought to stabilize
the septum and aid in the
recruitment of the other proteins to
the site of the cell division.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
G through an N-glycosidic bond.
• GENETIC RECOMBINATION
- A genetic accommodation is
defined as a mechanism of the
evolution where a phenotype is
generated by either the mutations
or the environmental perturbation.
This phenotype adapts the change
by understanding the series of the
genetic changes.
• GENETIC CODE - The genetic
code is the set of the rules which is
used by the living cells to translate
the information encoded within the
genetic material into the proteins.
It is a four-letter code of the DNA
which is translated into the 20-
letter code of amino acids. The
genetic code can be expressed as
either the RNA or the DNA
codons. Since the genetic code is
shared by the diverse organisms so
they provides the important
evidence for the common origin of
life on the Earth. Each of the
genetic code is consists of the three
ribonucleotide letters, thus referred
to as a genetic code.
• GLYCOSIDIC BONDS - The
DNA molecules contain 5-
membered carbon rings called
which are called as the riboses that
are directly attached to the two
phosphate groups and a nucleobase
that contains the amino groups.
The nitrogen atoms from the
amino group in the nucleotides are
covalently linked to the anomeric
© 2022 by JPS Scientific Publications, India
200
carbon of the ribose sugar structure
Covalent bond that joins the
hemiacetal group of a saccharide
molecule and the hydroxyl group
of some organic compound or an
aldehyde or a ketone group on the
sugar can react with a hydroxyl
group on another sugar, this is
what is known as a glycosidic bond
(e.g alcohol). These bonds are the
primary form of energy storage in
the animal cells. They are the
bonds that compose the cellulose,
which makes up the woody parts
of the plants and the trees, and
chitin, which provides the tough
exoskeletons of the beetles, crabs,
lobsters and the fungi.
• GENOME SIZE – The Genome
size refers to the amount of the
DNA contained in a haploid
genome expressed either in terms
of the number of the base pairs i.e
kilobases (1 kb = 1000 bp), or the
megabases (1 Mb = 1 000 000 bp),
or as the mass of the DNA in the
picograms (1 pg = 10−12 g). The
Genome sizes of the
bacteriophages and the viruses
ranges from about 2 kb to over 1
Mb. In the diploid organisms, the
genome size is often used to
interchangeably with the term C-
value. Nuclear genome size is
mainly measured in eukaryotes
using either the densitometric
measurements of the Feulgen-
stained nuclei previously using
specialized machine known as the
densitometers, now more
Glossary of Genetics
commonly using computerized
image analysis or the flow
cytometry. In the prokaryotes,
pulsed field gel electrophoresis
method and complete genome
sequencing are the predominant
methods of the genome size
determination.
• GROWTH ASSAYS - The
Assaying effects of the putative
anticancer agents on the in vitro
growth and the survival of the
appropriate cell populations
represents a critical tool in their
pre-clinical evaluation
examination. Exposing the
multiple cell populations
simultaneously to a particular
agent in co-culture provides a data
complementary to the unitary with
the in vitro growth assays. The Co-
culture experiments have
importantly become more
logistically straightforward with
the recent development of the
vectors that are expressing
autofluorescent proteins, which
allows the permanent labeling of
the living cells and their progeny.
Thus, it has importantly become
practical to grow the two or more
cell populations side by side in the
co-culture, expose them
simultaneously to the anticancer
agents, and also track their
differential growth rate over the
time. Fink has also used the co-
cultures to model the differential
effect of the mismatch repair
(MMR) proficiency on in vivo and
in vitro cytotoxicity of cisplatin.
© 2022 by JPS Scientific Publications, India
201
The comparative growth assay was
also evaluated the extensively in a
model system of the two matched
cell lines by differing only in a
single gene alteration, which
namely in the presence of the an
intact mismatch repair (MMR)
hMLH1 gene. The assay was also
validated in a system of the two
cell lines by differing only in the
expression of the breast cancer
resistance protein (BRCP). The
hMLH1 gene belongs to the DNA
MMR system consisting of the
hMSH2, hMLH1, hPMS1,
hPMS2, and GTBP (hMSH6)
proteins which correct, on average,
99.9% of all the mismatches
occurring in the newly synthesized
strand. A functional deficiency of
the MMR system, found in 5% to
40% of the primary and metastatic
human cancers and in most
cancers of the patients with the
hereditary nonpolyposis colon
cancer (HNPCC) syndrome,
induces a resistance, not only
toward the alkylating agents as
originally proposed, but to a wide
variety of other the common
anticancer therapies as well.
• GROWTH CURVE - A growth
curve is an empirical model of the
evolution of a quantity over the
time phase. Growth curves are
widely used in the biology for
quantities such as the population
size or the biomass i.e in the
population ecology and
demography, for the population
growth analysis, individual body
Glossary of Genetics
height or biomass i.e in the
physiology, for the growth analysis
of the individuals. The Values for
the measured property can be
plotted on a graph as a function of
time. The Bacterial growth is the
proliferation of the bacterium into
two daughter cells, in a process
which is called as the binary
fission. Providing no event occurs,
the resulting daughter cells are
genetically identical to the original
cell. Hence, the bacterial growth
occurs. Both the daughter cells
from the division do not
necessarily survive. However, if the
surviving number exceeds the unity
on average, the bacterial
population undergoes the
exponential growth. The
measurement of an exponential
bacterial growth curve in the batch
culture was traditionally a part of
the training of all the
microbiologists the basic means
requires bacterial enumeration (cell
counting) by direct and individual
(microscopic, flow cytometry),
direct and the bulk (biomass),
indirect and individual (colony
counting), or the indirect and bulk
(most probable number, turbidity,
nutrient uptake) methods. In the
autecological studies, the growth of
bacteria or other microorganisms,
such as the protozoa, microalgae
or the yeasts in batch culture can
be modeled with the four different
phases i. E lag phase (A), log phase
or exponential phase (B),
© 2022 by JPS Scientific Publications, India
202
stationary phase (C), and the death
phase (D).
• GENE SILENCING - The Gene
silencing is the regulation of the
gene expression in a cell to prevent
the expression of a certain gene.
The Gene silencing can occur
during either the transcription or
translation and is often used in the
research. In particular, methods
used to silence genes are being
increasingly used to produce the
therapeutics to combat the cancer
and the other diseases, such as the
infectious diseases and the
neurodegenerative disorders. Gene
silencing is often considered the
same as the gene knockdown.
When the genes are silenced, their
expression is reduced. In contrast,
when the genes are knocked out,
they are completely erased from
the organism’s genome and, thus,
have no expression. The Gene
silencing is considered a gene
knockdown mechanism since the
methods used to silence the genes,
such as the RNAi, CRISPR, or the
siRNA, generally reduce the
expression of a gene by at least
70% but do not completely
eliminate it. The Methods using
gene silencing are often considered
better than the gene knockouts
since they allow the researchers to
study the essential genes that are
required for the animal models to
survive and cannot be removed. In
the addition, they provide a more
complete view on the development
of the diseases since the diseases
Glossary of Genetics
are generally associated with the
genes that have a reduced
expression.
• GEL FILTRATION
CHROMATOGRAPHY - The
Size-exclusion chromatography
(SEC), which is also known as a
molecular sieve chromatography,
is a chromatographic method in
which the molecules in solution are
separated by their size, and in
some of the cases by their
molecular weight. It is usually
applied to the large molecules or
the macromolecular complexes
such as the proteins and the
industrial polymers. Typically,
when an aqueous solution is used
to transport the sample through the
column, the technique is very
commonly known as the gel-
filtration chromatography, versus
the name given as the gel
permeation chromatography,
which is also used when an organic
solvent is used as a mobile phase.
The chromatography column is
packed with the fine, porous beads
which are commonly composed of
the dextran, agarose, or the
polyacrylamide polymers. The
pore sizes of these beads are used
to estimate the dimensions of the
macromolecules. The SEC is a
widely used polymer
characterization method because of
its ability to provide the good
molar mass distribution (Mw)
results for the polymers.
• GAP PHASES - The G1 phase,
gap 1 phase, or the growth 1 phase,
© 2022 by JPS Scientific Publications, India
203
is the first of the four phases of the
cell cycle that takes place in the
eukaryotic cell division. In this part
of the interphase, the cell
synthesizes the mRNA and
proteins in the preparation for the
subsequent steps leading to the
mitosis. The G1 phase ends when
the cell moves into the S phase of
rye interphase. Around 30 to 40
percent of the cell cycle time is
spent in the G1 phase. The G2
phase, Gap 2 phase, or the Growth
2 phase, is the third subphase of
the interphase in the cell cycle
directly preceding in the mitosis. It
follows the successful completion
of the S phase, during which the
cell’s DNA is replicated. The G2
phase ends with the onset of the
prophase, the first phase of rye
mitosis in which the cell’s
chromatin condenses into the
chromosomes.
• GENE DUPLICATION - The
Gene duplication or the
chromosomal duplication or the
gene amplification is a major
mechanism through which the new
genetic material is generated
during the molecular evolution. It
can be defined as any duplication
of a region of the DNA that
contains a gene. The Gene
duplications can arise as the
products of the several types of
errors in the DNA replication and
the repair machinery as well as
through the fortuitous capture by
the selfish genetic elements. The
common sources of the gene
Glossary of Genetics
duplications include the ectopic
recombination, retrotransposition
event, aneuploidy, polyploidy, and
the replication slippage. The
Duplications arise from an event
termed as the unequal crossing-
over that occurs during the meiosis
between the misaligned
homologous chromosomes. The
replication slippage is an error in
the DNA replication that can
produce the duplications of the
short genetic sequences. The
Polyploidy, or the whole genome
duplication is a product of the
nondisjunction during the meiosis
which results in the additional
copies of the entire genome. The
Aneuploidy occurs when the
nondisjunction at a single
chromosome results in an
abnormal number of the
chromosomes.
• GENE SEGREGATION - The
Principle of the Segregation
describes how the pairs of the gene
variants are separated into the
reproductive cells. The segregation
of the gene variants, called as the
alleles, and their corresponding
traits was first observed by the
Gregor Mendel in the year 1865.
Mendel was studying the genetics
by performing the mating crosses
in the pea plants. He crossed the
two heterozygous pea plants,
which means that the each plant
had two different types of the
alleles at a particular genetic
position. He also discovered that
the traits in the offspring of his
© 2022 by JPS Scientific Publications, India
204
crosses did not always match the
traits in the parental plants. This
meant that the pair of the alleles
encoding the traits in the each
parental plant had separated or
segregated from the one another
during the formation of the
reproductive cells. From his data,
Mendel formulated the Principle of
the Segregation. We now know
that the segregation of the genes
occurs during the meiosis in the
eukaryotes, which is a process that
produces the reproductive cells
called as the gametes.
• GENETIC ENGINEERING
APPLICATION - The Genetic
engineering has various
applications in the fields of the
medicine, research, industry and in
the agriculture and can be used on
a wide range of the plants, animals
and the microorganisms. In the
medicine, genetic engineering has
been used to mass-produce the
insulin, human growth hormones,
follistim for treating the infertility,
human albumin, monoclonal
antibodies, antihemophilic factors,
vaccines, and the many other types
of drugs. In the field of the
research, the organisms are
genetically engineered to discover
the functions of the certain types of
the genes. In the Industrial field,
it’s applications include the
transforming microorganisms such
as the bacteria or the yeast, or the
insect mammalian cells with a gene
coding for a useful protein. Mass
quantities of the protein can be
Glossary of Genetics
produced by growing the
transformed organism in the
bioreactors using the fermentation,
then purifying the protein. The
Genetic engineering is also used in
the agriculture to create the
genetically-modified crops or the
genetically-modified organisms.
• GAP GENE - The gap gene is a
type of the gene involved in the
development of the segmented
embryos of some of the arthropods.
The Gap genes are defined by the
effect of a mutation in that gene,
which causes the loss of the
contiguous body segments,
resembling a gap in the normal
body plan. Each of the gap gene,
therefore, is necessary for the
development of a section of the
organism. Once the gap genes had
been identified at the molecular
level it was found that the each gap
gene is expressed in a band in the
early embryo generally correlated
with the region that is absent in the
mutant. In the Drosophila the gap
genes encode the transcription
factors, and they directly control
the expression of the another set of
the genes involved in the
segmentation, the pair-rule genes.
The gap genes themselves are
expressed under the control of the
maternal effect genes such as the
bicoid and the nanos, and regulate
each other to achieve their precise
expression patterns.
• GRK 4 - The G protein-coupled
receptor kinase 4 (GRK4) is an
enzyme that in the humans is
© 2022 by JPS Scientific Publications, India
205
encoded by the GRK4 gene. This
gene encodes a member of the G
protein-coupled receptor kinase
subfamily of the Ser/Thr protein
kinase family, and is most similar
to the GRK5 and the GRK6. The
GRK4 is most expressed in the
testes, with low amounts in the
brain, kidney and the other tissues.
It has four alternatively-spliced
variants. The Polymorphisms in
the GRK4 gene have been linked
to the both genetic and the
acquired hypertension, acting in
the part through the kidney
dopamine receptors.
• GENE REGULATION IN
MOUSE - The Temporal and the
spatial control of the gene
expression in the mouse can be
achieved using the binary
transgenic systems, in which the
gene expression is controlled by the
interaction of an effector protein
product on a target transgene.
These interactions are controlled
by the crossing mouse lines, or by
the adding or removing an
exogenous inducer. The Binary
transgenic systems fall into the two
categories. One is based on the
transcriptional transactivation and
is well suited for the activating
transgenes in gain-of-function
experiments. The other is based on
the site-specific DNA
recombination and can also be
used to activate the transgenes or
to generate the tissue-specific gene
knockouts and the cell-lineage
markers.
Glossary of Genetics
• GRIFFITH EXPERIMENT - In
his experiment, Griffith used the
two strains of the pneumococcus
(Diplococcus pneumoniae)
bacteria which infect the mice – a
type III-S (smooth) which was the
virulent, and a type II-R (rough)
strain which was the nonvirulent.
The III-S strain which synthesized
a polysaccharide capsule that
protected itself from the host’s
immune system, which results in
the death of the host, while the II-
R strain which did not have the
that protective capsule and was
ultimately defeated by the host’s
immune system. In the
experiment, the bacteria from the
III-S strain were killed by the heat,
and their remains were added to
the II-R strain bacteria. While
neither the alone harmed the mice,
the combination was also able to
kill its host. Griffith was also able
to isolate both the live II-R and the
live III-S strains of the
pneumococcus from the blood of
these dead mice. The Griffith
concluded that the type II-R had
been “transformed” into the lethal
III-S strain by a principle which is
known as the “transforming
principle” that was somehow part
of the dead III-S strain bacteria.
• GCN4 - The Gcn4 is a
transcription factor and a “master
regulator” for the gene expression
which regulates rye close to one
tenth of the yeast genome. In a
study, the amino acid starvation
activated the transcription factor
© 2022 by JPS Scientific Publications, India
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Gcn4p, resulting in the
transcriptional induction of almost
all the genes involved in the amino
acid biosynthesis, including the
HIS4. Thus involvement of the
Gcn4 in the regulation of both the
histidinol dehydrogenase HIS4 and
rye interferon gamma hIFNγ was
hypothesised as a scenario
explaining the increased level of
the hIFNγ under the amino acid
starvation. The Gcn4 is a highly
conserved protein and its
mammalian homolog is known as
the activating transcription factor-4
(ATF4). The Overexpression of the
Gcn4 leads to the reduction in the
protein synthesis capacity which
contributes to the Gcn4-mediated
increase of the yeast lifespan. In
the budding yeast, deletion of the
Gcn4 prevents HIS4 from targeting
to the nuclear periphery upon the
transcriptional activation,
indicating that the Gcn4 is
necessary for the regulation of the
gene positioning and the
transcription.
• GENOMIC LIBRARY - The
genomic library is a collection of
the total genomic DNA from a
single organism. The DNA is
stored in a population of the
identical vectors, each containing a
different insert of the DNA. In
order to construct a genomic
library, the organism’s DNA is
extracted from the cells and then
digested with a restriction enzyme
to cut the DNA into the fragments
of a specific size. The DNA which
Glossary of Genetics
are cut into the fragments are then
inserted into the vector using the
enzyme DNA ligase. Next, the
vector DNA can be taken up by a
host organism – commonly a
population of the Escherichia coli
or the yeast – with each cell
containing only one vector
molecule. Using a host cell to
carry the vector allows for the easy
amplification and the retrieval of
the specific clones from the library
for the analysis. There are several
kinds of the vectors available with
the various insert capacities.
Generally, the libraries made from
the organisms with larger genomes
require the vectors featuring larger
inserts, thereby very fewer vector
molecules are needed to make the
library. The Genomic libraries are
commonly used for the sequencing
applications. They have played an
important role in the whole
genome sequencing of the several
organisms, including the human
genome and the several model
organisms.
• GENOMIC IMPRINTING - The
Genomic imprinting is an
epigenetic phenomenon that causes
the genes to be expressed or not,
depending on whether they are
inherited from the mother or the
father. The Genes can also be
partially imprinted. The partial
imprinting occurs when the alleles
from both the parents are
differently expressed rather than
the complete expression and the
complete suppression of one
© 2022 by JPS Scientific Publications, India
207
parent’s allele. The Forms of the
genomic imprinting have been
demonstrated in the fungi, plants
and the animals. There are about
150 imprinted genes known in the
mice and about half that in the
humans. As of 2019, about 260
imprinted genes have been
reported in the mice and 228 in the
humans. The Genomic imprinting
is an inheritance process which is
independent of the classical
Mendelian inheritance. It is an
epigenetic process that involves the
DNA methylation and the histone
methylation without altering the
genetic sequence. These epigenetic
marks are established
(“imprinted”) in the germline
(sperm or the egg cells) of the
parents and are maintained
through the mitotic cell divisions in
the somatic cells of an organism.
• GAP REPAIR - The Gap repair is
a fast and the efficient method for
assembling the recombinant DNA
molecules in the Saccharomyces
cerevisiae. This method produces a
circular DNA molecule by the
homologous recombination
between the two or more linear
DNA fragments, one of which is
typically a vector carrying the
replicative sequences and a
selective marker. This technique
avoids the laborious and costly in
vitro purification and the ligation
of the DNA. The DNA repair
machinery can also close and ligate
the linear vector by mechanisms
other than the homologous
Glossary of Genetics
recombination, resulting in an
empty vector. The frequency of
these unwanted events can be
lowered by removing the 5’-
phosphate groups using the
phosphatase, which is the standard
method used for in vitro ligation.
However, the phosphatase
treatment is less effective for the
gap repair cloning than for in vitro
ligation, presumably due to the
ability of the S. Cerevisiae DNA
repair machinery to efficiently
repair the missing phosphate group
to allow the religation. We have
developed a more efficient method
to prevent the vector religation,
based on the treatment of the
vector fragment with the Taq DNA
polymerase and the dATP. This
procedure prevents the vector
recircularization almost
completely, facilitating the
screening for the true recombinant
clones.
• GENE CONVERSION - The
Gene conversion is the process by
which of the one DNA sequence
replaces a homologous sequence
such that the sequences become the
identical after the conversion
event. The Gene conversion can
be either the allelic, meaning that
the one allele of the same gene
replaces the another allele, or the
ectopic, meaning that one of the
paralogous DNA sequence
converts the another. The
Conversion of one allele to the
other is often due to the base
mismatch repair during the
© 2022 by JPS Scientific Publications, India
208
homologous recombination: if one
of the four chromatids during the
meiosis pairs up with the another
chromatid, as can occur because of
the sequence homology, DNA
strand transfer can occur followed
by the mismatch repair. This can
alter the sequence of one of the
chromosomes, so that it is identical
to the other. By one pathway, a
structure called as double Holliday
junction (DHJ) is formed, leading
to the exchange of the DNA
strands. By the other pathway,
referred to as the Synthesis
Dependent Strand Annealing
(SDSA), there is information
exchange but there no physical
exchange. The gene conversion
will occur during the SDSA if the
two DNA molecules are the
heterozygous at the site of the
recombinational repair. The Gene
conversion may also occur during
the recombinational repair
involving a DHJ, and this gene
conversion may be associated with
the physical recombination of the
DNA duplexes on the two sides of
the DHJ.
• GAL GENES - The GAL genes
provide a closely regulated system
in which to study the gene-specific
chromatin structure. The GAL
structural genes are inactive
without the galactose but are
highly transcribed in its presence,
the expression patterns of the
regulatory genes can account for
many of the features of the GAL
structural gene control. In the
Glossary of Genetics
inactive state, the GAL genes
demonstrate a characteristic
promoter chromosomal
organization; the major upstream
activation sequence (UASG)
elements which lie in the open,
hypersensitive regions, whereas the
TATA and the transcription start
sites are in the nucleosomes. This
organization helps implement gene
regulation in this state and may
benefit the organism. Induction of
tbe GAL expression triggers the
Gal4p-dependent upstream
nucleosome disruption. The
Disruption is transient and can
readily be reversed by a Gal80p-
dependent nucleosome deposition
process. Both are sensitive to the
metabolic state of the cell. The
Induction triggers the different
kinds of the nucleosome changes
on the coding sequences, perhaps
reflecting the differing roles of the
nucleosomes on coding versus the
promoter regions. The GAL gene
activation is a complex process
involving the multiple Gal4p
activities, numerous positive and
the negative cofactors, and the
histone tails. The DNA bending
and the chromosomal architecture
of the promoter regions may also
play a role in the GAL regulation
• GAL OPERON - The gal operon
is a prokaryotic operon, which
encodes the enzymes necessary for
the galactose metabolism. The
Repression of the gene expression
for this operon works via binding
of the repressor molecules to the
© 2022 by JPS Scientific Publications, India
209
two operators. These repressors
dimerize, creating a loop in the
DNA. The loop as well as the
hindrances from the external
operator prevent the RNA
polymerase from binding to the
promoter, and thus prevent the
transcription. Additionally, since
the metabolism of the galactose in
the cell is involved in both the
anabolic and the catabolic
pathways, a novel regulatory
system using the two promoters for
the differential repression has been
identified and characterized within
the context of the gal operon.
• GAGA FACTOR - The GAGA
factor (GAF) is one of the few
transcription factors that can
regulate the gene expression at the
multiple levels. It displays both the
activator/antirepressor and the
repressor activity, depending on its
target genomic location. The GAF-
mediated modulation of the
expression appears to be intimately
linked with the modifications of
the chromatin structure. The GAF
can associate with the highly
compacted heterochromatin,
contributing to the gene repression,
or participate in the nucleosome
remodeling to activate the specific
genes.
• GA1 GENE - The Glutaric
acidemia type 1 (GA1) is an
inherited disorder in which the
body is unable to completely break
down the amino acids lysine,
hydroxylysine and the tryptophan.
The excessive levels of their
Glossary of Genetics
intermediate breakdown products
(such as the glutaric acid, glutaryl-
CoA, 3-hydroxyglutaric acid,
glutaconic acid) can accumulate
and cause the damage to the brain
(and also to the other organs), but
particularly the basal ganglia,
which are the regions that help to
regulate the movement. The GA1
causes the secondary carnitine
deficiency, as the glutaric acid, like
other organic acids, is detoxified by
the carnitine. There can be an
occurenace of the mental
retardation.
• GAL 2 PROTEIN - The Galanin
receptor 2, (GAL2) is a G-protein
coupled receptor encoded by the
GALR2 gene. The Galanin is an
important neuromodulator present
in the brain, gastrointestinal
system, and in the
hypothalamopituitary axis. It is a
30-amino acid non-C-terminally
amidated peptide that potently
stimulates the growth hormone
secretion, inhibits the cardiac vagal
slowing of the heart rate, abolishes
sinus arrhythmia, and inhibits the
postprandial gastrointestinal
motility. The actions of the galanin
are mediated through the
jnteraction with the specific
membrane receptors that are
members of the 7-transmembrane
family of the G protein-coupled
receptors. The GALR2 interacts
with the N-terminal residues of the
galanin peptide. The primary
signaling mechanism for the
GALR2 is through the
© 2022 by JPS Scientific Publications, India
210
phospholipase C/protein kinase C
pathway (via Gq), in contrast to
the GALR1, which communicates
its intracellular signal by the
inhibition of the adenylyl cyclase
through the Gi. However, it has
been demonstrated that the
GALR2 couples efficiently to both
the Gq and the Gi proteins to
simultaneously activate the 2
independent signal transduction
pathways.
• GAL 80 - The Saccharomyces
cerevisiae Gal80 protein has the
two binding partners: the Gal4 and
the Gal3. In the absence of the
galactose, the Gal80 binds to and
inhibits the transcriptional
activation domain (AD) of the
GAL gene activator, Gal4 thus
preventing the GAL gene
expression. The Galactose triggers
an association between the Gal3
and the Gal80, relieving the Gal80
inhibition of the Gal4. The GAL80
mutants with the impaired capacity
of the Gal80 to bind to the Gal3 or
the Gal4AD. Most of the Gal80
variants selected for the impaired
binding to the Gal4AD retained
their capacity to bind to the Gal3
and to self-associate, whereas most
of those selected for the impaired
binding to the Gal3 lost their
ability to bind to the Gal4AD and
self-associate. Thus, some of the
Gal80 amino acids are
determinants for both the Gal80-
Gal3 association and the Gal80
self-association, and the Gal80 self-
Glossary of Genetics
association may be required for the
binding to the Gal4AD.
• G:C CONTENT - In the field of
molecular biology and the genetics,
the GC-content (or the guanine-
cytosine content) is the percentage
of the nitrogenous bases in a DNA
or the RNA molecule that are
either the guanine (G) or the
cytosine (C). This measure
indicates the proportion of the G
and C bases out of an implied four
total bases, also including the
adenine and the thymine in the
DNA and the adenine and uracil in
the RNA. In the polymerase chain
reaction (PCR) experiments, the
GC-content of the short
oligonucleotides known as the
primers is often used to predict
their annealing temperature to the
template DNA. A higher GC-
content level indicates the
relatively higher melting
temperature. Many of the
sequencing technologies, such as
the Illumina sequencing, have
trouble reading the high-GC-
content sequences. The Bird
genomes are known to have many
such parts, causing the problem of
the "missing genes" expected to be
present from the evolution and the
phenotype but never sequenced
until the improved methods were
used.
• GCN4 - The Gcn4 is a
transcription factor and a “master
regulator” for the gene expression
which regulates the close to one
tenth of the yeast genome. In a
© 2022 by JPS Scientific Publications, India
211
study by the Razaghi et al, the
amino acid starvation activated the
transcription factor Gcn4p,
resulting in the transcriptional
induction of almost all the genes
involved in the amino acid
biosynthesis, including HIS4. Thus
involvement of the Gcn4 in the
regulation of both the histidinol
dehydrogenase HIS4 and the
interferon gamma hIFNγ was
hypothesised as a scenario
explaining the increased level of
the hIFNγ under the amino acid
starvation. The Gcn4 is a highly
conserved protein and its
mammalian homolog is known as
the activating transcription factor-4
(ATF4). The Overexpression of the
Gcn4 leads to the reduction in the
protein synthesis capacity which
contributes to the Gcn4-mediated
increase of the yeast lifespan. In
the budding yeast, deletion of the
Gcn4 prevents the HIS4 from
targeting to the nuclear periphery
upon the transcriptional activation,
indicating that the Gcn4 is
necessary for the regulation of the
gene positioning and the
transcription.
• GENE ENZYME
RELATIONSHIP - The Genes are
the regions of DNA that code for
the particular enzymes, proteins,
etc. It is at the level of the gene
transcription followed by the
translation in the ribosome in
which we get the expressed
proteins. Thus, the relationship
between the genes and the
Glossary of Genetics
enzymes is that genes code for the
enzymes.
• GENE FOR GENE
RELATIONSHIP - The gene-for-
gene relationship was discovered
by the Harold Henry Flor who was
working with the rust (Melampsora
lini) of the flax (Linum
usitatissimum). Flor showed that
the inheritance of the both
resistance in the host and the
parasite ability to cause the disease
is controlled by the pairs of the
matching genes. One is a plant
gene called as the resistance (R)
gene. The other is a parasite gene
called as the avirulence (Avr) gene.
The Plants producing a specific R
gene product are resistant towards
a pathogen that produces the
corresponding Avr gene product.
The Gene-for-gene relationships
are a widespread and very
important aspect of the plant
disease resistance. Another
example can be seen with the
Lactuca serriola versus the Bremia
lactucae. The Clayton Oscar
Person was the first scientist to
study the plant pathosystem ratios
rather than the genetics ratios in
the host-parasite systems. In doing
so, he discovered the differential
interaction that is common to all
the gene-for-gene relationships and
that is now known as the Person
differential interaction.
• GENERALIZED
TRANSDUCTION - The
generalized transduction occurs
© 2022 by JPS Scientific Publications, India
212
when the random pieces of the
bacterial DNA are packaged into a
phage. It happens when a phage is
in the lytic stage, at the moment
that the viral DNA is packaged
into the phage heads. If the virus
replicates using the 'headful
packaging', it attempts to fill the
head with the genetic material. If
the viral genome results in the
spare capacity, viral packaging
mechanisms may incorporate the
bacterial genetic material into the
new virion. Alternatively, the
generalized transduction may
occur via the recombination. The
Generalized transduction is a rare
event and occurs on the order of
the 1 phage in 11,000. The new
virus capsule that contains the part
bacterial DNA then infects the
another bacterial cell. When the
bacterial DNA packaged into the
virus, the virus us inserted into the
recipient cell three things can
happen to it, the DNA is recycled
for spare parts. If the DNA was
originally a plasmid, it will re-
circularize inside the new cell and
become a new plasmid again. If the
new DNA matches with the
homologous region of the recipient
cell's chromosome, it will then
exchange the DNA material
similar to the actions in the
bacterial recombination.
• GENE REGULATION IN
DEVELOPMENT AND
EVOLUTION - Over the time
during the evolution, most of the
genes will move around the
Glossary of Genetics
relative to the position of the other
genes. However, it is thought that
the genes that remain adjacent to
the each other are somehow
dependent on the each other and
share the coordinated
transcriptional regulation and the
gene expression. For example, the
expression of one of the genes
might depend on the cis-regulatory
sequence near the neighbouring
gene. Indeed, the previous research
has shown that the linked gene
pairs that also share the common
cis-regulatory elements remain
linked through the evolution. The
linked gene pairs in the
Amphimedon, they found that
many did contain these predicted
distal elements, supporting the
results that these elements are
indeed the functional. These
findings indicate that such
regulatory elements are shared
with all the animals, but are absent
in the related single-cell species.
• GENETIC CODE - The genetic
code is the set of the rules used by
the living cells to translate the
information encoded within the
genetic material (DNA or the RNA
sequences of the nucleotide triplets,
or the codons) into the proteins.
The Translation is accomplished
by the ribosome, which links the
proteinogenic amino acids in an
order specified by the messenger
RNA (mRNA), using the transfer
RNA (tRNA) molecules to carry
the amino acids and to read the
mRNA three nucleotides at a time.
© 2022 by JPS Scientific Publications, India
213
The genetic code is highly similar
among all the organisms and can
be expressed in a simple table with
the 64 entries. The codons specify
which amino acid will be added
next during the protein synthesis.
With some of the exceptions, a
three-nucleotide codon in a nucleic
acid sequence specifies a single
amino acid. The vast majority of
the genes are encoded with a single
scheme. That scheme is often
referred to as the canonical or the
standard genetic code, or simply
the genetic code, though the
variant codes (such as in the
mitochondria) exist.
• GENOME EDITING - The
Genome editing, or the genome
engineering, or the gene editing, is
a type of the genetic engineering in
which the DNA is inserted,
deleted, modified or replaced in the
genome of a living organism.
Unlike the early genetic
engineering techniques that
randomly inserts the genetic
material into a host genome,
genome editing targets the
insertions to the site specific
locations. A common form of the
Genome editing relies on the
concept of the DNA double
stranded break (DSB) repair
mechanics. There are two major
pathways that repair the DSB; non-
homologous end joining (NHEJ)
and the homology directed repair
(HDR). The NHEJ uses a variety
of the enzymes to directly join the
DNA ends while the more accurate
Glossary of Genetics
HDR uses a homologous sequence
as a template for the regeneration
of the missing DNA sequences at
the break point. This can be
exploited by creating the vector
with the desired genetic elements
within the sequence that is
homologous to the flanking
sequences of the DSB. This will
result in the desired change being
inserted at the site of the DSB.
While the HDR based gene editing
is similar to the homologous
recombination based on the gene
targeting, the rate of recombination
is increased by at least three orders
of the magnitude.
• GSC - The GSC is termed as the
Goosecoid Homeobox. This gene
encodes a member of the bicoid
subfamily of the paired (PRD)
homeobox family of the proteins.
The encoded protein acts as a
transcription factor and alos may
be autoregulatory. A similar
protein in the mice plays a role in
the craniofacial and the rib cage
development during the
embryogenesis.
• GINS - The GINS is a protein
complex essential to the DNA
replication process in the cells of
the eukaryotes. The complex
participates in the initiation and
the elongation stages of the
replication. The name GINS is an
acronym created from the first
letters of the Japanese numbers 5-
1-2-3 (go-ichi-ni-san) in a reference
to the 4 protein subunits of the
complex i.e Sld5, Psf1, Psf2, and
© 2022 by JPS Scientific Publications, India
214
the Psf3. A similar complex has
also been identified in the Archaea.
• GLI - The Gli proteins are
transcriptional effectors of the
Hedgehog (Hh) pathway in both
the normal development and the
cancer. The program of the
multisite phosphorylation that
regulates the conversion of the Gli
proteins into the transcriptional
activators. In the absence of the Hh
ligands, the Gli activity is
restrained by the direct
phosphorylation of the six
conserved serine residues by the
protein kinase A (PKA), a master
negative regulator of the Hh
pathway. The Activation of the
signaling leads to a global
remodeling of the Gli
phosphorylation landscape, the
PKA target sites then become
dephosphorylated, while a second
cluster of the sites undergoes the
phosphorylation. The pattern of
the Gli phosphorylation can
regulate the Gli transcriptional
activity in a graded fashion,
suggesting a phosphorylation-based
mechanism for how a gradient of
the Hh signaling in a
morphogenetic field can be
converted into a gradient of the
transcriptional activity.
• GSC - TheHomeobox protein
goosecoid (GSC) is a homeobox
protein that is encoded in the
humans by the GSC gene. Like
other oomeobox proteins, the
goosecoid functions as a
transcription factor involved in the
Glossary of Genetics
morphogenesis. In the Xenopus,
the GSC is thought to play a
crucial role in the phenomenon of
the Spemann-Mangold organizer.
Through lineage tracing and the
timelapse microscopy, the effects
of the GSC on the neighboring cell
fates could be observed. In an
experiment that injected cells with
the GSC and observed the effects
of the uninjected cells, GSC
recruited the neighboring
uninjected cells in the dorsal
blastopore lip of the Xenopus
gastrula to form the twinned dorsal
axis, suggesting that the goosecoid
protein plays a role in the
regulation and in the migration of
the cells during the gastrulation.
• GEM - The GTP-binding protein
GEM is a protein that in the
humans is encoded by the GEM
gene. The protein encoded by this
gene belongs to the RAD/GEM
family of the GTP-binding
proteins. It is associated with the
inner face of the plasma membrane
and could play a role as a
regulatory protein in the receptor-
mediated signal transduction. The
Alternative splicing occurs at this
locus and the two transcript
variants encoding the same protein
have been identified.
• GAMMARETROVIRUS - The
Gammaretrovirus is a part of the
retroviridae family. The
Gammaretroviruses are considered
zoonotic viruses because they are
found in many of the different
mammalian species, such as the
© 2022 by JPS Scientific Publications, India
215
mice, cats, pigs, primates, cows,
and the birds. However, the bats
are the primary reservoir for many
of the gammaretroviruses. The
Bats can have a prolonged
exposure to a variety of the
pathogens without showing any of
the warning signs, which leads to
the debated belief that bats have
the ability to develop the immunity
to the viruses that may harm the
other species.
• GLUTAMINYL CYCLASE -
The Pyroglutamate (pE)
modification, catalyzed mainly by
the glutaminyl cyclase (QC), is
prevalent throughout the nature
and is particularly important in the
mammals including humans for
the maturation of the hormones,
peptides, and the proteins. In the
humans, the upregulation of QC is
involved in the multiple diseases
and the conditions including the
Alzheimer’s disease, Huntington’s
disease, melanomas, thyroid
carcinomas, accelerated
atherosclerosis, septic arthritics,
etc. This upregulation catalyzes the
generation of the modified
mediators such as the pE-amyloid
beta (Aß) and the pE-chemokine
ligand 2 (CCL2) peptides. Not
surprisingly, the QC has emerged
as a reasonable target for the
development of the therapeutics to
combat these diseases and the
conditions. In this manuscript the
deleterious effects of the
upregulated QC resulting in the
disease manifestation are reviewed,
Glossary of Genetics 216

along with the progress on the cytosolic-nuclear glycosylation.

development of the QC inhibitors. The glycoproteins of the cytosol
• GLUTAMINYL PEPTIDE and the nucleus can be modified
CYCLOTRANSFERASE - In the through the reversible addition of a
field of enzymology, a glutaminyl- single GlcNAc residue that is
peptide cyclotransferase is an considered reciprocal to the
enzyme that catalyzes the chemical phosphorylation and the functions
reaction. This enzyme belongs to of these are likely to be an
the family of the transferases, additional regulatory mechanism
specifically the that controls the phosphorylation-
aminoacyltransferases. The based signalling. In contrast, the
systematic name of this enzyme classical secretory glycosylation
class is the L-glutaminyl-peptide can be structurally essential. For
gamma-glutamyltransferase example, the inhibition of the
(cyclizing). Other names in the asparagine-linked, i.e. N-linked,
common use include the glycosylation can prevent the
glutaminyl-tRNA cyclotransferase, proper glycoprotein folding and the
glutaminyl cyclase, and the full inhibition can be toxic to an
glutaminyl-transfer ribonucleate individual cell. In contrast, the
cyclotransferase. perturbation of the glycan
• GLYCOPROTEINS - The processing, which occurs in both
Glycoproteins are the proteins the endoplasmic reticulum and the
which contain the oligosaccharide Golgi apparatus, is dispensable for
chains (glycans) covalently the isolated cells, but can lead to
attached to the amino acid side- the human disease (congenital
chains. The carbohydrate is disorders of glycosylation) and can
attached to the protein in a also be lethal in the animal models
cotranslational or the • GLYCINE - The Glycine is an
posttranslational modification. amino acid that has a single
This process is known as the hydrogen atom as its side chain. It
glycosylation. The secreted is the simplest stable amino acid
extracellular proteins are often (carbamic acid is unstable), with
glycosylated. The Glycoproteins the chemical formula as
are also often consider as the NH2‐CH2‐COOH. The glycine is
important integral membrane one of the proteinogenic amino
proteins, where they play a role in acids. It is encoded by all the
the cell–cell interactions. It is codons starting with the GG
important to distinguish the (GGU, GGC, GGA, GGG). The
endoplasmic reticulum-based glycine is integral to the formation
glycosylation of the secretory of the alpha-helices in the
system from the reversible secondary protein structure due to

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
its compact form. For the same
reason, it is the most abundant
amino acid in the collagen triple-
helices. The Glycine is also an
inhibitory neurotransmitter – endoplasmic reticulum undergo the
interference with its release within
the spinal cord (such as during a
Clostridium tetani infection) can
cause the spastic paralysis due to
the uninhibited muscle contraction.
The Glycine is an intermediate in
the synthesis of a variety of the
chemical products. It is used in the
manufacture of the herbicides
glyphosate, iprodione, glyphosine,
imiprothrin, and the eglinazine. It
is used as an intermediate of the
medicine such as the
thiamphenicol.
• GLYCOSYLATION - The
Glycosylation is the reaction in
which a carbohydrate (or the
'glycan'), i.e. a glycosyl donor, is
attached to a hydroxyl or the other
functional group of the another
molecule (a glycosyl acceptor) in
order to form a glycoconjugate. In
the biology, the glycosylation
usually refers to an enzyme-
catalysed reaction, whereas the
glycation (also 'non-enzymatic
glycation' and 'non-enzymatic
glycosylation') may refer to a non-
enzymatic reaction (though in the
practice, the 'glycation' often refers
more specifically to the Maillard-
type reactions). The Glycosylation
is a form of the co-translational
and post-translational
modification. The Glycans serve a
variety of the structural and the
© 2022 by JPS Scientific Publications, India
217
functional roles in the membrane
and the secreted proteins. The
majority of the proteins
synthesized in the rough
glycosylation. The Glycosylation is
also present in the cytoplasm and
in the nucleus as the O-GlcNAc
modification.
• GLYCATION - The Glycation
(sometimes also called as the non-
enzymatic glycosylation) is the
covalent attachment of a sugar to a
protein or the lipid. The tpical
sugars that participate in the
glycation are the glucose, fructose,
and their derivatives. The
Glycation is the non-enzymatic
process responsible for many (e.g.
micro and macrovascular)
complications in the diabetes
mellitus and is implicated in some
of the diseases and in the aging.
The Glycation end products are
believed to play a causative role in
the vascular complications of the
diabetes mellitus. In contrast with
the glycation, glycosylation is the
enzyme-mediated ATP-dependent
attachment of the sugars to protein
or the lipid. The glycosylation
occurs at the defined sites on the
target molecule. It is a common
form of the post-translational
modification of the proteins and is
required for the functioning of the
mature protein.
• GLYOXAL - The Glyoxal is an
organic compound with the
chemical formula OCHCHO. It is
the smallest dialdehyde (a
Glossary of Genetics
compound with the two aldehyde
groups). It is a crystalline solid,
white at the low temperatures and
the yellow near the melting point
(15 °C). The liquid is yellow, and
the vapor is the green. The pure
glyoxal is not commonly
encountered because the glyoxal is
usually handled as a 40% aqueous
solution (density near 1.24 g/mL).
It forms a series ofthe the hydrates,
including the oligomers. For many
purposes, these hydrated oligomers
behave equivalently to the glyoxal.
The Glyoxal is produced
industrially as a precursor to the
many of the products. The Glyoxal
is a valuable building block in the
organic synthesis, especially in the
synthesis of the heterocycles such
as the imidazoles. A convenient
form of the reagent for use in the
laboratory is its bis(hemiacetal)
with the ethylene glycol, 1,4-
dioxane-2,3-diol. This compound
is commercially available. The
Glyoxal solutions can also be used
as a fixative for the histology, that
is, a method of preserving the cells
for examining them under a
microscope.
• GFP - The green fluorescent
protein (GFP) is a protein that
exhibits the bright green
fluorescence when exposed to the
light in the blue to the ultraviolet
range. The label GFP traditionally
refers to the protein first isolated
from the jellyfish Aequorea
victoria and is sometimes called as
the avGFP. However, the GFPs
© 2022 by JPS Scientific Publications, India
218
have been found in the other
organisms including the corals, sea
anemones, zoanithids, copepods
and the lancelets. The Green
fluorescent protein may be used as
the reporter gene. For example, the
GFP can be used as a reporter for
the environmental toxicity levels.
This protein has been shown to be
an effective way to measure the
toxicity levels of the various
chemicals including the ethanol, p-
formaldehyde, phenol, triclosan,
and the paraben. The GFP is great
as a reporter protein because it has
no effect on the host when
introduced to the host's cellular
environment. Due to this ability,
no external visualization stain,
ATP, or the cofactors are needed.
• GRE FACTOR - The Gre factors
reactivate the stalled elongation
complexes by enhancing the
intrinsic transcript cleavage activity
of the RNA polymerase. The
Mycobacterium tuberculosis Gre
factor is essential for the survival.
Apart from their role in the
transcription regulation, the Gre
factors have also been implicated
in the stress response. A recent
study has shown the role of the
E.coli GreA as a cellular
chaperone, which inhibits the
aggregation of the substrate
proteins under the heat stress
condition. Moreover it was shown
that the GreA enables the E.coli to
survive the heat shock. The
moonlighting chaperone activity
and its plausible mechanism is also
Glossary of Genetics
found in the Mycobacterium
smegmatis Gre (MsGre) factor.
The MsGre prevents heat-induced
aggregation of the substrate protein
also protects the enzymatic
activity. Interestingly the Gre
factor exists as a dimer in the
solution and does not undergo the
heat induced oligomerization.
From the 8-anilino-1-naphthalene
sulfonate (ANS) binding studies
the MsGre was shown to expose
the hydrophobic surface upon the
heat stress that would allow the
binding to unfolded or partially
folded substrate protein.
• GENETICALLY MODIFIED
MICE - The genetically modified
mouse or the genetically
engineered mouse model (GEMM)
is a mouse (Mus musculus) that
has had its genome altered through
the use of the genetic engineering
techniques. The Genetically
modified mice are commonly used
for the research or as the animal
models of the human diseases, and
are also used for the research on
the genes. Together with the
patient-derived xenografts (PDXs),
the GEMMs are the most common
in vivo models in the cancer
research. Both the approaches are
considered complementary and
may be used to recapitulate the
different aspects of the disease. The
GEMMs are also of the great
interest for the drug development,
as they facilitate the target
validation and the study of the
© 2022 by JPS Scientific Publications, India
219
response, resistance, toxicity and
the pharmacodynamics.
• GENOMIC IMPRINTING - The
Genomic imprinting is an
epigenetic phenomenon that causes
genes to be expressed or not,
depending on the whether they are
inherited from the mother or the
father. The Genes can also be
partially imprinted. The Partial
imprinting occurs when the alleles
from both the parents are
differently expressed rather than
the complete expression and the
complete suppression of one
parent's allele. The Forms of the
genomic imprinting have been
demonstrated in the fungi, plants
and the animals. In 2014, there
were about 150 imprinted genes
known in the mice and about half
that in the humans. As of 2019,
around 260 imprinted genes have
been reported in the mice and 228
in the humans. The Genomic
imprinting is an inheritance
process independent of the classical
Mendelian inheritance. It is an
epigenetic process that involves the
DNA methylation and the histone
methylation without altering the
genetic sequence. These epigenetic
marks are established ("imprinted")
in the germline (sperm or egg cells)
of the parents and are maintained
through the mitotic cell divisions in
the somatic cells of an organism.
• GLD 2 - The GLD-2 (which
stands for the Germ Line
Development 2) is a cytoplasmic
poly(A) polymerase (cytoPAPs)
Glossary of Genetics
which adds the successive AMP
monomers to the 3’ end of the
specific RNAs, forming a poly(A)
tail, which is a process known as
the polyadenylation. The GLD-2
primarily stabilizes the mRNAs
that are translationally repressed as
well as it strongly promotes the
bulk polyadenylation. Surprisingly,
those functions seem to have a very
little impact on the dynamizing
efficient target mRNA translation,
as it is an efficient Poly(A)
Polymerase which helps
developing the polyadenylation
activity. This activity is stimulated
by its interaction with a putative
RNA-binding protein. The GLD-2,
as a poly(A) polymerase (PAP)
acts aa a incorporating ATP at the
3' end of the mRNAs in a template-
independent manner. The GLD-2
protein together with 136 proteins
more, is involved in the molecular
process of the hematopoietic
progenitor cell differentiation, in
the human proteome. This is the
process in which the precursor cell
type acquires the specialized
features of a hematopoietic
progenitor cell, a kind of the cells
types including the myeloid
progenitor cells and the lymphoid
progenitor cells.
• GROUP 1 INTRONS - The
Group I introns are the large self-
splicing ribozymes. They catalyze
their own excision from the
mRNA, tRNA and the rRNA
precursors in a wide range of the
© 2022 by JPS Scientific Publications, India
220
organisms. The core secondary
structure consists of the nine paired
regions (P1-P9). These fold to
essentially the two domains – the
P4-P6 domain (formed from the
stacking of the P5, P4, P6 and the
P6a helices) and the P3-P9 domain
(formed from the P8, P3, P7 and
the P9 helices). The secondary
structure mark-up for this family
represents only this conserved core.
The Group I introns often have
long open reading frames inserted
in the loop regions. The Group I
introns are distributed in the
bacteria, lower eukaryotes and the
higher plants. However, their
occurrence in the bacteria seems to
be more sporadic than in the lower
eukaryotes, and they have become
prevalent in the higher plants. The
genes that group I introns interrupt
differ significantly: They interrupt
the rRNA, mRNA and the tRNA
genes in the bacterial genomes, as
well as in the mitochondrial and in
the chloroplast genomes of the
lower eukaryotes, but only invade
the rRNA genes in the nuclear
genome of the lower In the higher
plants, these introns seem to be
restricted to a few tRNA and the
mRNA genes of the chloroplasts
and the mitochondria. The group I
introns are also found inserted into
the genes of a wide variety of the
bacteriophages of the Gram-
positive bacteria. However, their
distribution in the phage of the
Gram-negative bacteria is mainly
Glossary of Genetics
limited to the T4, T-even and the
T7-like bacteriophages.
• GROUP 2 INTRONS - The
Group II introns are a large class of
the self-catalytic ribozymes and the
mobile genetic elements found
within the genes of all thr three
domains of the life. The Ribozyme
activity (e.g. , self-splicing) can
occur under the high-salt
conditions in vitro. However, the
assistance from the proteins is
required for the in vivo splicing. In
contrast to the group I introns, the
intron excision occurs in the
absence of the GTP and involves
the formation of a lariat, with an
A-residue branchpoint strongly
resembling that found in the lariats
formed during the splicing of the
nuclear pre-mRNA. It is
hypothesized that the pre-mRNA
splicing may have evolved from the
group II introns, due to the similar
catalytic mechanism as well as the
structural similarity of the Group II
Domain V substructure to the
U6/U2 extended snRNA. Finally,
their ability to site-specifically
insert into the DNA sites has been
exploited as a tool for the
biotechnology. For example, the
group II introns can be modified to
make the site-specific genome
insertions and deliver the cargo
DNA such as the reporter genes or
the lox sites.
• GTPASE - The GTPases are a
large family of the hydrolase
enzymes that bind to the
nucleotide guanosine triphosphate
© 2022 by JPS Scientific Publications, India
221
(GTP) and hydrolyze it to
guanosine diphosphate (GDP).
The GTP binding and the
hydrolysis takes place in the highly
conserved P-loop "G domain", a
protein domain common to the
many of theGTPases. The
GTPases function as a molecular
switches or the timer in many of
the fundamental cellular processes,
such as transport of the vesicles
within the cell, and the vesicle-
mediated secretion and uptake,
through the GTPase control of the
vesicle coat assembly. The
GTPases are active when bound to
the GTP and inactive when bound
to the GDP. In the generalized
receptor-transducer-effector
signaling model of the Martin
Rodbell, the signaling GTPases act
as transducers to regulate the
activity of the effector proteins.
This inactive-active switch is due
to the conformational changes in
the protein distinguishing these
two forms, particularly of the
"switch" regions that in the active
state are able to make the protein-
protein contacts with the partner
proteins that alter the function of
these effectors.
• GEFS - The Guanine nucleotide
exchange factors (GEFs) are the
proteins or the protein domains
that activate the monomeric
GTPases by stimulating the release
of the guanosine diphosphate
(GDP) to allow the binding of the
guanosine triphosphate (GTP). A
variety of the unrelated structural
Glossary of Genetics
domains have been shown to
exhibit the guanine nucleotide
exchange activity. Some of the
GEFs can activate the multiple
GTPases while the others are
specific to a single GTPase. The
Guanine nucleotide exchange
factors (GEFs) are the proteins or
the protein domains involved in
the activation of the small
GTPases. The Small GTPases act
as molecular switches in the
intracellular signaling pathways
and have many downstream
targets. The most well-known
GTPases comprise the Ras
superfamily and are involved in the
essential cell processes such as the
cell differentiation and the
proliferation, cytoskeletal
organization, vesicle trafficking,
and the nuclear transport. The
GTPases are active when bound to
the GTP and inactive when bound
to the GDP, allowing their activity
to be regulated by the GEFs and
the opposing GTPase activating
proteins (GAPs).
• GUANYLYL TRANSFERASES
- The guanylyl transferases are the
enzymes that transfer a guanosine
mono phosphate group, usually
from the GTP to the another
molecule, releasing the
pyrophosphate. Many of the
eukaryotic guanylyl transferases
are capping enzymes that catalyze
the formation of the 5' cap in the
co-transcriptional modification of
the messenger RNA. Because the 5'
end of the RNA molecule ends in a
© 2022 by JPS Scientific Publications, India
222
phosphate group, the bond formed
between the RNA and the GTP
molecule is an unusual 5'-5'
triphosphate linkage, instead of the
3'-5' linkages between the other
nucleotides that form the RNA
strand. In the capping enzymes, a
highly conserved lysine residue
serves as the catalytic residue that
forms a covalent enzyme-GMP
complex. The transfer RNA
(tRNA) for the histidine is unique
among the eukaryotic tRNAs in
requiring the addition of the
guanine nucleotide before being
aminoacylated by the synthetase
known as the histidine tRNA
synthetase. The yeast guanylyl
transferase specific to the tRNAHis
is unique in being the only known
non-tRNA synthetase enzyme that
specifically recognizes the tRNA
anticodon. The guanylyl
transferases also exist for
transferring the guanosine
nucleotides to the sugar molecules,
such as the mannose and the
fructose.
• GUIDE RNA - A guide RNA
(gRNA) is a piece of the RNA that
functions as a guide for the RNA-
or the DNA-targeting enzymes,
with which it forms the complexes.
Very often these enzymes will
delete, insert or otherwise alter the
targeted RNA or the DNA. They
occur naturally, serving the
important functions, but can also
be designed to be used for the
targeted editing, such as with the
CRISPR-Cas9 and the CRISPR-
Glossary of Genetics
Cas12. The targeting specificity of
the CRISPR-Cas9 is determined by
the 20-nt sequence at the 5' end of
the gRNA. The desired target
sequence must precede the
protospacer adjacent motif (PAM)
which is a short DNA sequence
usually around 2-6 base pairs in the
length that follows the DNA
region targeted for the cleavage by
the CRISPR system, such as the
CRISPR-Cas9. The PAM is
required for a Cas nuclease to cut
and is generally found in the 3-4
nucleotides downstream from the
cut site. After the base pairing of
the gRNA to the target, the Cas9
mediates a double-strand break
about the 3-nt upstream of the
PAM.
• GENE KNOCK-OUT - The Gene
knockout is a potent and the
irreversible means to inactivate a
gene. The Cre-LoxP system is one
of the possibility. The knockout
can be achieved using the
conventional homologous
recombination or with the
engineered endonucleases. A gene
knockout may also be obtained
using the NHEJ after a double
break of the DNA at the chosen
site using the engineered
endonucleases or the RGEN
system. The advantages of this
approach are its high efficiency and
the fact that the inactivation may
be achieved in of the one-cell
embryos.
• Gq ALPHA SUBUNIT - The Gq
protein alpha subunit is a family of
© 2022 by JPS Scientific Publications, India
223
the heterotrimeric G protein alpha
subunits. This family is also
commonly called as the Gq/11
(Gq/G11) family or the
Gq/11/14/15 family to include the
closely related family members.
The G alpha subunits may be
referred to as the Gq alpha, Gαq,
or the Gqα. The Gq proteins
couple to as the G protein-coupled
receptors to activate the beta-type
phospholipase C (PLC-β) enzymes.
The PLC-β in turn the hydrolyzes
phosphatidylinositol 4,5-
bisphosphate (PIP2) to the diacyl
glycerol (DAG) and the inositol
trisphosphate (IP3). The IP3 acts
as a second messenger to release
the stored calcium into the
cytoplasm, while the DAG acts as
a second messenger that activates
the protein kinase C (PKC). The
general function of the Gq is to
activate the intracellular signaling
pathways in response to activation
of the cell surface G protein-
coupled receptors (GPCRs). The
GPCRs function as part of a three-
component system of the receptor-
transducer-effector. The transducer
in this system is a heterotrimeric G
protein, composed of the three
subunits: a Gα protein such as the
Gαq, and a complex of the two
tightly linked proteins called as the
Gβ and the Gγ in a Gβγ complex.
When not stimulated by a receptor,
the Gα is bound to the guanosine
diphosphate (GDP) and to Gβγ to
form the inactive G protein trimer.
Glossary of Genetics 224

• GENE KNOCKDOWN - The

Gene knockdown is an
experimental technique by which
the expression of one or more of an
organism's genes is reduced. The
reduction can occur either through
the genetic modification or by the
treatment with a reagent such as a
short DNA or the RNA
oligonucleotide that has a sequence
complementary to the either gene
or an the mRNA transcript. So far,
the knockdown organisms with the
permanent alterations in their
DNA have been engineered chiefly
for the research purposes. Also
known as simply as the
knockdowns, these organisms are
most commonly used for the
reverse genetics, especially in the
species such as the mice or the rats
for which the transient knockdown
technologies cannot easily be
applied. There are several
companies that offer the
commercial services related to the
gene knockdown treatments.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
H crystallography and the protein
• HOMOLOGY MODELING -
The Homology modeling, which is
also known as the comparative
modeling of the protein, refers to
the constructing of an atomic-
resolution model of the "target"
protein from its amino acid
sequence and an experimental
three-dimensional structure of a
related homologous protein (the
"template"). The Homology
modeling relies on the
identification of one or more the
known protein structures likely to
resemble the structure of the query
sequence, and on the production of
the alignment that maps the
residues in the query sequence to
residues in the template sequence.
It has been seen that the protein
structures are more conserved than
the protein sequences amongst the
homologues, but sequences falling
below a 20% sequence identity can
have a very different structure. The
method of the homology modeling
is based on the observation that the
protein tertiary structure is better
conserved than the amino acid
sequence. Thus, even the proteins
that have diverged appreciably in
the sequence but still share the
detectable similarity will also share
the common structural properties,
particularly the overall fold.
Because it is difficult and the time-
consuming to obtain the
experimental structures from
© 2022 by JPS Scientific Publications, India
225
methods such as the X-ray
NMR for every protein of the
interest, homology modeling can
provide the useful structural
models for generating the
hypotheses about a protein's
function and directing the further
experimental
• HOTAIR - The HOTAIR (for the
HOX transcript antisense RNA) is
a human gene located between the
HOXC11 and the HOXC12 on the
chromosome 12. It is the first
example of an RNA expressed on
the one chromosome that has been
found to influence the transcription
of the HOXD cluster posterior
genes located on the chromosome
2. The sequence and the function
of the HOTAIR is different in the
human and in the mouse. The
sequence analysis of the HOTAIR
revealed that it exists in the
mammals, has poorly conserved
sequences and considerably
conserved the structures, and has
evolved faster than the nearby
HoxC genes. A subsequent study
identified the HOTAIR has 32
nucleotide long conserved
noncoding element (CNE) that has
a paralogous copy in the HOXD
cluster region (located between the
HOXD11 and the HOXD12),
suggesting that the HOTAIR
conserved sequences predates the
whole genome duplication events
at the root of the vertebrate.
• HOXB2 – The Homeobox protein
Hox-B2 is a protein that in the
Glossary of Genetics
humans is encoded by the HOXB2
gene. This gene is a member of the
Antp homeobox family and
encodes the nuclear protein with a
homeobox DNA-binding domain.
It is included in the cluster of the
homeobox B genes located on the
chromosome 17. The protein
which is encoded functions as a
sequence-specific transcription
factor that is involved in the
development. The increased
expression of this gene is
associated with the pancreatic
cancer.
• HOXB4 - The Homeobox protein
Hox-B4 is a protein that in the
humans is encoded by the HOXB4
gene. This gene is a member of the
Antp homeobox family and
encodes the nuclear protein with a
homeobox DNA-binding domain.
It is included in the cluster of the
homeobox B genes located on the
chromosome 17. The protein
which is encoded functions as a
sequence-specific transcription
factor that is involved in the
development. The intracellular or
the ectopic expression of this
protein expands the hematopoietic
stem and progenitor cells in vivo
and in vitro, making it a potential
candidate for the therapeutic stem
cell expansion.
• HOXB6 - The Homeobox protein
Hox-B6 is a protein that in the
humans is encoded by the HOXB6
gene. This gene is a member of the
Antp homeobox family and
encodes the protein with a
© 2022 by JPS Scientific Publications, India
226
homeobox DNA-binding domain.
It is included in a cluster of the
homeobox B genes located on the
chromosome 17. The protein
which is encoded functions as a
sequence-specific transcription
factor that is involved in the
development, including that of the
lung and the skin, and has been
localized to both the nucleus and
the cytoplasm. The Altered
expression of this gene or a change
in the subcellular localization of its
protein is associated with some of
the cases of the acute myeloid
leukemia and the colorectal cancer.
• HOXB7 - The Homeobox protein
Hox-B7 is a protein that in the
humans is encoded by the HOXB7
gene. This gene is a member of the
Antp homeobox family and
encodes the protein with a
homeobox DNA-binding domain.
It is included in the cluster of the
homeobox B genes located on
chromosome 17. The nuclear
protein which is encoded functions
as a sequence-specific transcription
factor that is involved in the cell
proliferation and the
differentiation. The increased
expression of this gene is
associated with some cases of the
melanoma and the ovarian
carcinoma.
• HOXB9 - The Homeobox protein
Hox-B9 is a protein that in the
humans is encoded by the HOXB9
gene. This gene is a member of the
Abd-B homeobox family and
encodes the protein with a
Glossary of Genetics
homeobox DNA-binding domain.
It is included in a cluster of the
homeobox B genes which is
located on the chromosome 17.
The nuclear protein which is
encoded functions as a sequence-
specific transcription factor that is
involved in the cell proliferation
and in the differentiation. The
increased expression of this gene is
associated with the some cases of
the leukemia, prostate cancer and
the lung cancer.
• HP1 PROTEIN - The family of
the heterochromatin protein 1
(HP1) ("Chromobox Homolog",
CBX) consists of the highly
conserved proteins, which have
important functions in the cell
nucleus. These functions include
the gene repression by the
heterochromatin formation,
transcriptional activation,
regulation of the binding of the
cohesion complexes to the
centromeres, sequestration of the
genes to the nuclear periphery,
transcriptional arrest, maintenance
of the heterochromatin integrity,
gene repression at the single
nucleosome level, gene repression
by the heterochromatization of the
euchromatin, and the DNA The
HP1 proteins are the fundamental
units of the heterochromatin
packaging that are enriched at the
centromeres and the telomeres of
nearly all the eukaryotic
chromosomes with the notable
exception of the budding yeast, in
which a yeast-specific silencing
© 2022 by JPS Scientific Publications, India
227
complex of the SIR (silent
information regulatory) proteins
serve a similar.
• HRP GENE - The hypersensitivity
and pathogenicity (hrp) genes
control the ability of the
phytopathogenic bacteria to cause
the disease and to elicit the
hypersensitive reactions on the
resistant plants. The Genetic and
the biochemical studies have
demonstrated that the Hrp proteins
are components of the Type III
secretion systems, regulatory
proteins, proteinaceous elicitors of
the hypersensitive reaction, and the
enzymes needed for the synthesis
of the periplasmic glucans.
Significantly, the Type III secretion
systems are involved with the
secretion of the pathogenicity
proteins in the bacterial pathogens
of animals. The transcriptional
activation of a number of the
bacterial avirulence (avr) genes is
controlled by the Hrp regulatory
proteins, and the recent
experimental evidence suggests
that the Avr proteins may be
transported by the Hrp secretion
systems. Thus, the hrp genes may
be one of the most important
groups of the genes found in the
phytopathogenic bacteria in
relationship to the pathogenicity
and the host range.
• HSP - The Hereditary spastic
paraplegias (HSPs) is the clinically
and genetically highly
heterogeneous. The key symptom
of the spastic paraparesis of the
Glossary of Genetics
lower limbs can be complicated by
a variety of the signs and
symptoms including the cognitive
impairment, optic atrophy,
cerebellar ataxia, peripheral nerve
involvement, or the seizures. At
least 48 loci have been identified,
termed as the SPG1–SPG48. Ten
genes for the autosomal dominant
HSP are currently known, the
SPG4 being by far the most
common subtype accounting for
around % of the cases. The SPG3
is especially common in the young-
onset cases. The Autosomal
recessive HSP seems to be even
more heterogeneous.
• HSP 70 - The 70 kilodalton heat
shock proteins (Hsp70s or
thecDnaK) are a family of the
conserved ubiquitously expressed
heat shock proteins. The Proteins
with the similar structure exist in
virtually all the living organisms.
The Intracellularly localized
Hsp70s are an important part of
the cell's machinery for the protein
folding, performing chaperoning
functions, and helping to protect
the cells from the adverse effects of
the physiological stresses.
Additionally, the membrane-bound
Hsp70s have been identified as a
potential target for the cancer
therapies and their extracellularly
localized counterparts have been
identified as having both the
membrane-bound and the
membrane-free structures. The
Hsp70 system interacts with the
extended peptide segments of the
© 2022 by JPS Scientific Publications, India
228
proteins as well as the partially
folded proteins to cause the
aggregation of the proteins in the
key pathways to downregulate the
activity. When not interacting with
a substrate peptide, the Hsp70 is
usually in an ATP bound state.
The Hsp70 by itself is
characterized by a very weak
ATPase activity, such that the
spontaneous hydrolysis will not
occur for many minutes.
• HSP 70 PROMOTER - The
HSP70 promoter contains at least
the two regulatory domains, a
distal domain responsive to the
heat shock or the heavy metals and
a proximal domain responsive to
the stimulation by the serum. The
activity of the HSP70 promoter can
be induced by the moderate
hyperthermia (39°C to 43°C),
reaching the expression levels
similar to the those of the CMV
promoter.
• HSPT5 - The human homolog of
the yeast elongation factor SPT5,
interacts directly with the capping
enzyme. The hSPT5 stimulated
capping enzyme guanylylation and
the mRNA capping by the
severalfold. Although the RNA 5′-
triphosphatase activity was
unaffected, the binding to this
domain in the full-length enzyme is
likely involved in the stimulation,
as the hSPT5 did not increase the
activity of the guanylyltransferase
fragment. Consistent with the
capping enzyme binding, the
TFIIH-phosphorylated CTD
Glossary of Genetics
stimulated guanylylation, and this
increase was not additive with the
hSPT5.
• H19 GENE - The H19 is a gene
for a long noncoding RNA, found
in the humans and elsewhere. The
H19 has a role in the negative
regulation (or the limiting) of the
body weight and in the cell
proliferation. This gene also has a
role in the formation of some of the
cancers and in the regulation of the
gene expression. The H19 gene is
expressed exclusively on one of the
parental allele in a phenomenon
known as the imprinting. The H19
is only transcribed from the
maternally inherited allele, the
paternal H19 allele is not
expressed. The H19 was first
named as the ASM (for the Adult
Skeletal Muscle) because of its
expression in the adult skeletal
muscle ("ASM") in the rats. The
H19 is also known as the BWS
because aberrant H19 expression
can be involved in the Beckwith-
Wiedemann Syndrome ("BWS"),
as well as the Silver-Russell
syndrome. The Epigenetics
deregulations at the H19 imprinted
gene in the sperm have been
observed associated with the male
infertility.
• HALDANE EFFECT - The
Haldane effect is a property of the
hemoglobin first described by the
John Scott Haldane, within which
the oxygenation of the blood in the
lungs displaces carbon dioxide
© 2022 by JPS Scientific Publications, India
229
from the hemoglobin, increasing
the removal of the carbon dioxide.
Consequently, the oxygenated
blood has a reduced affinity for the
carbon dioxide. Thus, the Haldane
effect describes the ability of the
hemoglobin to carry the increased
amounts of the carbon dioxide
(CO2) in the deoxygenated state as
opposed to the oxygenated state. A
high concentration of the CO2
facilitates dissociation of the
oxyhemoglobin.
• HAMMERHEAD RIBOSOME -
The hammerhead ribozyme is an
RNA motif that catalyzes the
reversible cleavage and the ligation
reactions at a specific site within an
RNA molecule. It is one of the
several catalytic RNAs (ribozymes)
known to occur in the nature. It
serves as a model system for the
research on the structure and the
properties of the RNA, and is used
for the targeted RNA cleavage
experiments, some with the
proposed therapeutic applications.
Named for the resemblance of the
early secondary structure diagrams
to a hammerhead shark. The
hammerhead ribozymes were
originally discovered in the two
classes of the plant virus-like
RNAs, satellite RNAs and the
viroids. They are also known in
some of the classes of the
retrotransposons, including the
retrozymes. The hammerhead
ribozyme motif has been
ubiquitously reported in the
lineages across the tree of the life.
Glossary of Genetics
The self-cleavage reactions, first
reported in the year 1986, are part
of a rolling circle replication
mechanism. The hammerhead
sequence is sufficient for the self-
cleavage and acts by forming a
conserved three-dimensional
tertiary structure.
• HATs - The Histone
acetyltransferases (HATs) are the
enzymes that acetylate conserved
the lysine amino acids on the
histone proteins by transferring an
acetyl group from the acetyl-CoA
to form ε-N-acetyllysine. The
DNA is wrapped around the
histones, and by transferring an
acetyl group to the histones, genes
can be turned on and off. In
general, the histone acetylation
increases the gene expression. In
general, the histone acetylation is
linked to the transcriptional
activation and associated with the
euchromatin. The
Euchromatin,which is less densely
compact, allows the transcription
factors to bind more easily to the
regulatory sites on the DNA,
causing the transcriptional
activation. When it was first
discovered, it was thought that the
acetylation of the lysine neutralizes
the positive charge normally
present, thus reducing the affinity
between the histone and the
negatively charged DNA, which
renders the DNA more accessible
to the transcription factors.
Research has emerged, since, to
show that the lysine acetylation
© 2022 by JPS Scientific Publications, India
230
and the other posttranslational
modifications of the histones
generate the binding sites for the
specific protein–protein interaction
domains, such as the acetyllysine-
binding bromodomain. The
Histone acetyltransferases can also
acetylate the non-histone proteins,
such as the nuclear receptors and
the other transcription factors to
facilitate the gene expression.
• HAT TRANSPOSONS - The hAT
transposons are a superfamily of
the DNA transposons, or the Class
II transposable elements, that are
common in the genomes of plants,
animals, and in the fungi. The hAT
transposon superfamily includes
the first transposon discovered, Ac
from the Zea mays (maize), first
reported by the Barbara
McClintock. McClintock was
awarded the Nobel Prize in the
Physiology or the Medicine in the
year 1983 for this discovery. The
family also includes a subgroup
which is known as the space
invaders or the SPIN elements,
which have very high copy
numbers in some of the genomes
and which are among the most
efficient known transposons.
Although no extant active example
is known, the laboratory-generated
consensus sequences of the active
SPIN elements are able to generate
the high copy numbers when
introduced to the cells from a wide
range of the species.
• HAYFLICK LIMIT - The
Hayflick limit, or the Hayflick
Glossary of Genetics
phenomenon, is the number of the
times a normal somatic,
differentiated human cell
population will divide before the
cell division stops. However, this
limit does not apply to the stem
cells. The concept of the Hayflick
limit was advanced by the
American anatomist Leonard
Hayflick in the year 1961, at the
Wistar Institute in Philadelphia,
Pennsylvania. The Hayflick
demonstrated that a normal human
fetal cell population will divide
between around 40 and 60 times in
the cell culture before entering a
senescence phase. This finding
refuted the contention by Alexis
Carrel that the normal cells are
immortal. Each time a cell
undergoes the mitosis, the
telomeres on the ends of the each
chromosome shorten slightly. The
Cell division will cease once
telomeres shorten to a critical
length. The Hayflick interpreted
his discovery to be aging at the
cellular level. The aging of the cell
populations appears to correlate
with the overall physical aging of
an organism.
• HCPRO - The HcPrRO is a
multifunction protein. The
proteasome is a multicatalytic
complex involved in the many
cellular processes in the
eukaryotes, such as the protein and
the RNA turnover, cell division,
signal transduction, transcription
and the translation. The
Intracellular pathogens are the
© 2022 by JPS Scientific Publications, India
231
targets of its enzymic activities,
and a number of the animal viruses
are known to interfere with these
activities. The first evidence that a
plant virus protein, the helper
component-proteinase (HcPro) of
the Lettuce mosaic virus (LMV;
genus Potyvirus), interferes with
the 20S proteasome ribonuclease is
reported here. The LMV infection
caused an aggregation of the 20S
proteasome to the high-molecular
mass structures in vivo, and
specific binding of the HcPro to the
proteasome was confirmed in vitro
using the two different approaches.
The HcPro inhibited the 20S
endonuclease activity in vitro,
while its proteolytic activities were
unchanged or slightly stimulated.
This ability of the HcPro, a
pathogenicity regulator of the
potyviruses, to interfere with some
of the catalytic functions of the 20S
proteasome suggests the existence
of a novel type of the defence and
the counter-defence interplay in the
course of the interaction between
the potyviruses and their hosts.
• HEAT SHOCK FACTOR - In the
field of the molecular biology, the
heat shock factors (HSF), are the
transcription factors that regulate
the expression of the heat shock
proteins. A typical example is the
heat shock factor of the Drosophila
melanogaster. The Heat shock
factors (HSF) are the
transcriptional activators of the
heat shock genes. These activators
bind specifically to the Heat Shock
Glossary of Genetics
sequence Elements (HSE)
throughout the genome, whose
consensus-sequence is a tandem
array of the three oppositely
oriented "AGAAN" motifs or a
degenerate version thereof. Under
the non-stressed conditions, the
Drosophila HSF is a nuclear-
localized unbound monomer,
whereas the heat shock activation
results in the trimerization and
binding to the HSE. The Heat
Shock sequence Element is highly
conserved from the yeast to the
humans. The Heat shock factor 1
(HSF-1) is the major regulator of
the heat shock protein transcription
in the eukaryotes. In the absence of
the cellular stress, the HSF-1 is
inhibited by the association with
the heat shock proteins and is
therefore not active. The Cellular
stresses, such as the increased
temperature, can cause the proteins
in the cell to misfold. The Heat
shock proteins bind to the
misfolded proteins and dissociate
from the HSF-1. This allows the
HSF1 to form the trimers and
translocate to the cell nucleus and
activate the transcription. Its
function is not only critical to
overcome the proteotoxic effects of
th3 thermal stress, but also needed
for proper animal the development
and the overall survival of the
cancer cells.
• HEMIMETHYLATION - The
Hemimethylation is a particular
kind of the methylation pattern. If
a CpG is methylated on the
© 2022 by JPS Scientific Publications, India
232
forward strand but not on the
reverse strand, it is defined as the
MU hemimethylation site. If a
CpG is methylated on the reverse
strand but not on the forward
strand, it is defined as the UM
hemimethylation site. If a CpG
exhibits no significant
hemimethylation, it is defined as
the NS site. If no data is available
to be analyzed at the CpG, that site
is defined as the NA site. The
Hemimethylation occurs not only
at the solitary CpG sites, but also
at the consecutive ones, known as
the hemimethylation clusters. Such
clusters can manifest in one of the
two distinct patterns: regular or the
polar. A regular cluster can be
observed when the sequential CpG
sites are methylated on the same
strand but the unmethylated on the
other. A polar or the polarity
cluster occurs when the
consecutive CpG sites are
methylated on the opposite
strands.
• HER 1 - The epidermal growth
factor receptor (EGFR; ErbB-1;
HER1 in the humans) is a
transmembrane protein that is a
receptor for the members of the
epidermal growth factor family
(EGF family) of the extracellular
protein ligands. The Epidermal
growth factor receptor (EGFR) is a
transmembrane protein that is
activated by the binding of its
specific ligands, including the
epidermal growth factor and the
transforming growth factor α
Glossary of Genetics
(TGFα). The ErbB2 has no known
direct activating ligand, and may
be in an activated state
constitutively or become the active
upon the heterodimerization with
the other family members such as
the EGFR. Upon the activation by
its growth factor ligands, the
EGFR undergoes a transition from
an inactive monomeric form to an
active homodimer. Although there
is some evidence that the
preformed inactive dimers may
also exist before the ligand binding.
In addition to the forming
homodimers after the ligand
binding, the EGFR may pair with
the another member of the ErbB
receptor family, such as the
ErbB2/Her2/neu, to create an
activated heterodimer. There is
also evidence to suggest that the
clusters of the activated EGFRs
form, although it remains unclear
whether this clustering is important
for the activation itself or occurs
subsequent to activation of the
individual dimers.
• HER 2 -The Receptor tyrosine-
protein kinase erbB-2, also known
as the CD340 (cluster of the
differentiation 340), proto-
oncogene Neu, Erbb2 (rodent), or
the ERBB2 (human), is a protein
that in the humans is encoded by
the ERBB2 gene. The ERBB is
abbreviated from the erythroblastic
oncogene B, a gene isolated from
the avian genome. It is also
frequently called as the HER2
(from the human epidermal growth
© 2022 by JPS Scientific Publications, India
233
factor receptor 2) or the
HER2/neu. The ErbB family
consists of the four plasma
membrane-bound receptor tyrosine
kinases. One of the which is erbB-
2, and the other members being
erbB-1, erbB-3 (neuregulin-binding
which lacks the kinase domain),
and the erbB-4. All the four
contain an extracellular ligand
binding domain, a transmembrane
domain, and an intracellular
domain that can interact with a
multitude of the signaling
molecules and exhibit both the
ligand-dependent and the ligand-
independent activity. Notably, no
ligands for the HER2 have yet been
identified. The HER2 can
heterodimerise with any of the
other three receptors and is
considered to be the preferred
dimerisation partner of the other
ErbB receptor. The Dimerisation
results in the autophosphorylation
of the tyrosine residues within the
cytoplasmic domain of the
receptors and initiates a variety of
the signaling pathways.
• HER 3 - The Receptor tyrosine-
protein kinase erbB-3, also known
as the HER3 (human epidermal
growth factor receptor 3), is a
membrane bound protein that in
the humans is encoded by the
ERBB3 gene. The ErbB3 has been
shown to bind the ligands
heregulin and the NRG-2. The
Ligand binding causes a change in
the conformation that allows for
the dimerization, phosphorylation,
Glossary of Genetics
and the activation of the signal
transduction. The ErbB3 can
heterodimerize with any of the
other three ErbB family members.
The theoretical ErbB3 homodimer
would be non-functional because
the kinase-impaired protein
requires the transphosphorylation
by its binding partner to be active.
Unlike the other ErbB receptor
tyrosine kinase family members
which are activated through the
autophosphorylation upon the
ligand binding, the ErbB3 was
found to be kinase impaired,
having only 1/1000 the
autophosphorylation activity of the
EGFR and no ability to
phosphorylate the other proteins.
Therefore, the ErbB3 must act as
an allosteric activator.
• HOMING ENDONUCLEASES -
The homing endonucleases are a
collection of the endonucleases
encoded either as the freestanding
genes within the introns, as fusions
with the host proteins, or as the
self-splicing inteins. They catalyze
the hydrolysis of the genomic
DNA within the cells that
synthesize them, but do so at very
few, or even singular, locations.
The Repair of the hydrolyzed
DNA by the host cell frequently
results in the gene encoding the
homing endonuclease having been
copied into the cleavage site, hence
the term 'homing' to describe the
movement of the these genes. The
Homing endonucleases can
thereby transmit their genes
© 2022 by JPS Scientific Publications, India
234
horizontally within a host
population, increasing their allele
frequency at the greater than the
Mendelian rates.
• HISTONE ACETYLATION
AND DEACETYLATION - The
Histone acetylation and
deacetylation are the processes by
which the lysine residues within
the N-terminal tail protruding from
the histone core of the nucleosome
are acetylated and deacetylated as
part of the gene regulation. The
Histone acetylation and
deacetylation are essential parts of
the gene regulation. These
reactions are typically catalysed by
the enzymes with the "histone
acetyltransferase" (HAT) or the
"histone deacetylase" (HDAC)
activity. The Acetylation is the
process where an acetyl functional
group is transferred from the one
molecule (in this case, the acetyl
coenzyme A) to the another. The
Deacetylation is simply the reverse
reaction where an acetyl group is
removed from the molecule. The
Acetylation removes the positive
charge on the histones, thereby
decreasing the interaction of the N
termini of the histones with the
negatively charged phosphate
groups of the DNA. As a
consequence, the condensed
chromatin is transformed into a
more relaxed structure that is
associated with the greater levels of
the gene transcription. This
relaxation can be reversed by the
Glossary of Genetics
deacetylation catalyzed by the
HDAC activity.
• HYPOGAMMAGLOBULINEN
MIA - The
Hypogammaglobulinemia is a
problem with the immune system
in which not enough of the gamma
globulins are produced in the
blood. This results in a lower
antibody count, which impairs the
immune system, increasing the risk
of the infection. The
Hypogammaglobulinemia may
result from a variety of the primary
genetic immune system defects,
such as the common variable
immunodeficiency, or it may be
caused by the secondary effects
such as the medication, blood
cancer, or the poor nutrition, or the
loss of the gamma globulins in the
urine, as in the nonselective
glomerular proteinuria. The
Patients with the
hypogammaglobulinemia have
reduced the immune function;
important considerations include
the avoiding use of the live
vaccines, and take precautionary
measures when traveling to the
regions with the endemic disease
or the poor sanitation such as
receiving the immunizations,
taking the antibiotics abroad,
drinking only safe or boiled water,
arranging appropriate medical
cover in advance of the travel, and
ensuring continuation of any of the
immunoglobulin infusions.
© 2022 by JPS Scientific Publications, India
235
• HAPPY MAPPING - In the field
of the genetics, HAPPY Mapping,
first proposed by the Paul H. Dear
and the Peter R. Cook in the year
1989, is a method used to study the
linkage between the two or the
more DNA sequences. According
to the Single Molecule Genomics
Group, it is "Mapping based on the
analysis of approximately HAPloid
DNA samples using the
PolYmerase chain reaction". In the
field of the genomics, HAPPY
mapping can be applied to assess
the synteny and orientation of the
DNA sequences across a particular
genome - the generation of a
"genomic" map. As with the
linkage mapping, the HAPPY
mapping relies on the differential
probability of the two or the more
DNA sequences being separated.
In the genetic mapping, the
probability of a recombination
event between the two genetic loci
on the same chromosome is
directly proportional to the
distance between them. HAPPY
mapping replaces the
recombination with the
fragmentation instead of relying on
the recombination to separate the
genetic loci, the entire genome is
fragmented, for example, by
radiation or the mechanical
shearing. If the DNA is broken on
a random basis, the longer the
distance between the two DNA
sequences, the higher the chances
of it to break between the two, and
the vice versa.
Glossary of Genetics
• HUMAN LEUCOCYTE
ANTIGEN - The human
leukocyte antigen (HLA) system or
the complex is a complex of the
genes on the chromosome 6 in the
humans which encode the cell-
surface proteins responsible for the
regulation of the immune system.
The HLA system is also known as
the human version of the major
histocompatibility complex (MHC)
found in many of the animals. The
Mutations in the HLA genes may
be linked to the autoimmune
disease such as the type I diabetes,
and the celiac disease. The HLA
gene complex resides on a 3 Mbp
stretch within the chromosome 6,
p-arm at the 21. The HLA genes
are the highly polymorphic, which
means that they have many
different alleles, allowing them to
fine-tune the adaptive immune
system. The proteins encoded by
the certain genes are also known as
the antigens, as a result of their
historic discovery as factors in the
organ transplants. The HLAs have
the other roles. They are important
in the disease defense. They are the
major cause of the organ transplant
rejections. They may protect
against or fail to protect against the
cancers. The HLA may also be
related to the people's perception of
the odor of the other people, and
may be involved in the mate
selection, as at least one study
found a lower-than-expected rate
of the HLA similarity between the
spouses in an isolated community.
© 2022 by JPS Scientific Publications, India
236
• HLA DR - The HLA-DR is an
MHC class II cell surface receptor
encoded by the human leukocyte
antigen complex on the
chromosome 6 region 6p21. The
complex of the HLA-DR (Human
Leukocyte Antigen – DR isotype )
and the peptide, generally between
the 9 and 30 amino acids in the
length, constitutes a ligand for the
T-cell receptor (TCR). The HLA
(human leukocyte antigens) were
originally defined as the cell
surface antigens that mediate the
graft-versus-host disease.
Identification of the these antigens
has led to the greater success and
the longevity in the organ
transplant. The HLA-DR is also
involved in the several
autoimmune conditions, disease
susceptibility and the disease
resistance. It is also closely linked
to the HLA-DQ and this linkage
often makes it difficult to resolve
the more causative factor in the
disease. The HLA-DR molecules
are upregulated in response to the
signalling. In the instance of an
infection, the peptide (such as the
staphylococcal enterotoxin I
peptide) is bound into a DR
molecule and the presented to a
few of a great many T-cell
receptors found on the T-helper
cells. These cells then bind to
antigens on the surface of the B-
cells stimulating the B-cell
proliferation.
Glossary of Genetics
• HLA DRB4 - The Major
histocompatibility complex, class
II, DR beta 4, also known as the
HLA-DRB4, is a human gene. The
protein which js encoded by this
gene belongs to the HLA class II of
the beta chain paralogues. The
class II molecule is a heterodimer
consisting of an alpha (DRA) and a
beta chain (DRB), both which are
anchored in the membrane. It
plays a central role in the immune
system by presenting the peptides
derived from the extracellular
proteins. The Class II molecules
are expressed in the antigen-
presenting cells (APC: B enzyme used in the molecular
lymphocytes, dendritic cells,
macrophages).
• HLA DRA - The HLA class II
histocompatibility antigen, DR
alpha chain is a protein that in the
humans is encoded by the HLA-
DRA gene. The HLA-DRA
encodes the alpha subunit of the
HLA-DR. Unlike the alpha chains
of the other Human MHC class II
molecules, the alpha subunit is
practically invariable. However it
can pair with, in any individual,
the beta chain from the 3 different
DR beta loci, DRB1, and the two
of the any DRB3, DRB4, or the
DRB5 alleles. Thus there is the
potential that any given individual
can form the 4 different HLA-DR
isoforms. The polypeptide subunit
which is encoded by this gene
belongs to the HLA class II alpha
chain paralogues. The class II
protein is a heterodimer consisting
© 2022 by JPS Scientific Publications, India
237
of an alpha (DRα) and a beta chain
(DRβ), both anchored in the
membrane. It plays a central role in
the immune system by presenting
the peptides derived from the
extracellular proteins. The Class II
molecules are expressed in the
antigen presenting cells (APC: B
lymphocytes, dendritic cells,
macrophages).
• HAR 3 - The HaeIII is one of the
many restriction enzymes
(endonucleases) a type of the
prokaryotic DNA that protects the
organisms from the unknown,
foreign DNA. It is a restriction
biology laboratories. It was the
third endonuclease that has been
isolated from the Haemophilus
aegyptius bacteria. The enzyme's
recognition site place where it cuts
the DNA molecules is the GGCC
nucleotide sequence which means
it cleaves the DNA at the site of 5′-
GG/CC-3. The recognition site is
usually around the 4-8 bps.This
enzyme's gene has been sequenced
and cloned. This is done to make
the DNA fragments in the blunt
ends. The HaeIII is not effective
for the single stranded DNA
cleavage. The enzyme cleaves the
DNA at the positions where the
GGCC sequence is found. The
cleavage occurs between the
second and the third nucleotides
(G and C). The resulting DNA
fragments are known as the
restriction fragments. The HaeIII
cuts both the strands of the DNA
Glossary of Genetics
in the same location, yielding the
restriction fragments with the blunt
ends. The heat denaturation occurs
at the 80°C after the 20 minutes.
• HER 4 - The Receptor tyrosine-
protein kinase erbB-4 is an enzyme
that in the humans is encoded by
the ERBB4 gene. The Alternatively
spliced variants that encode the
different protein isoforms have
been described, however, not all
variants have been fully
characterized. The Receptor
tyrosine-protein kinase erbB-4 is a
receptor tyrosine kinase that is a
member of the epidermal growth
factor receptor family. The ERBB4
is a single-pass type
transmembrane protein with the
multiple furin-like cysteine rich
domains, a tyrosine kinase
domain, a phosphotidylinositol-3
kinase binding site and a PDZ
domain binding motif. The protein
binds to and is activated by the
neuregulins-2, -3 and -4, heparin-
binding EGF-like growth factor
and the betacellulin. The Ligand
binding induces a variety of the
cellular responses including the
mitogenesis and the differentiation.
The Multiple proteolytic events
allow for the release of a
cytoplasmic fragment and an
extracellular fragment.
• HERMES TRANSPOSONS - The
Hermes are the hAT transposons
from the Musca domestica that are
very closely related to the hobo
transposons from the Drosophila
melanogaster and are useful as a
238
gene vectors in a wide variety of
the organisms including the
insects, planaria, and the yeast.
The hobo elements show the
distinct length variations in a
rapidly evolving region of the
transposase-coding region as a
result of the expansions and the
contractions of a simple repeat
sequence encoding 3 amino acids
threonine, proline, and the
glutamic acid (TPE). These
variations in the length may
influence the function of the
protein and the movement of the
hobo transposons in the natural
populations. Here, we determine
I the distribution of the Hermes in
the populations of the M.
domestica as well as whether the
Hermes transposase has undergone
the similar sequence expansions
and the contractions during its
evolution in this species. The
Hermes transposons were found in
all the M. domestica individuals
sampled from the 14 populations
collected from the 4 continents. All
the individuals with the Hermes
transposons had evidence for the
presence of the intact transposase
open reading frames, and the little
sequence variation was observed
among the Hermes elements. A
systematic analysis of the TPE-
homologous region of the Hermes
transposase-coding region revealed
no evidence for the length
variation. The simple sequence
repeat found in the hobo elements
is a feature of this transposon that
© 2022 by JPS Scientific Publications, India
Glossary of Genetics
evolved since the divergence of the
hobo and the Hermes.
• HETERODUPLEX - The
heteroduplex is a double-stranded
(duplex) molecule of the nucleic
acid originated through the genetic
recombination of the single
complementary strands derived
from the different sources, such as
from the different homologous
chromosomes or even from the
different organisms. One such
example is the heteroduplex DNA
strand formed in the hybridization
processes, usually for the
biochemistry-based phylogenetic
analyses. Another is the
heteroduplexes formed when the
non-natural analogs of the nucleic
acids are used to bind with the
nucleic acids; these heteroduplexes
result from performing the
antisense techniques using the
single-stranded peptide nucleic
acid, 2'-O-methyl
phosphorothioate or the
Morpholino oligos to bind with the
RNA. In the meiosis, the process
of crossing-over occurs between the
non-sister chromatids, which
results in the new allelic
combinations in the gametes. In
the crossing-over, a Spo11 enzyme
makes staggered nicks in a pair of
sister chromatid strands (in a tetrad
organization of prophase). The
Subsequent enzymes trim back the
5' ends of the strand and a protein
complex binds to the 3' single-
stranded ends. The Rad51 protein
is recruited and binds in a protein
© 2022 by JPS Scientific Publications, India
239
complex to search for a
complementary sequence
analogous to the double-strand-
break repair. The filament searches
for the homologous chromosome,
the strand invasion occurs where
the new chromosome forms a D-
loop over the bottom sister
chromatid, then the ends are
annealed. This process can yield
double Holliday junctions that
when cut in a transversal pattern
by the endonucleases form 2
heteroduplex strand products. The
Heteroduplex DNA is also a
source of the small RNAs
(smRNAs), causing the post-
transcriptional gene silencing.
• HNRNPS - The Heterogeneous
nuclear ribonucleoproteins
(hnRNPs) are the complexes of the
RNA and the protein present in the
cell nucleus during the gene
transcription and the subsequent
post-transcriptional modification of
the newly synthesized RNA (pre-
mRNA). The presence of the
proteins bound to the pre-mRNA
molecule serves as the signal that
the pre-mRNA is not yet fully
processed and therefore not ready
for the export to the cytoplasm.
Since most of the mature RNA is
exported from the nucleus
relatively quickly, most of the
RNA-binding protein in the
nucleus exist as the heterogeneous
ribonucleoprotein particles. After
the splicing has occurred, the
proteins remain bound to the
spliced introns and target them for
Glossary of Genetics
the degradation. The hnRNPs are
also integral to the 40s subunit of
the ribosome and therefore
important for the translation of the
mRNA in the cytoplasm.
However, the hnRNPs also have
their own nuclear localization
sequences (NLS) and are therefore
found mainly in the nucleus.
Though it is known that a few
hnRNPs shuttle between the
cytoplasm and the nucleus,
immunofluorescence microscopy
with the hnRNP-specific antibodies
shows the nucleoplasmic
localization of these proteins with
the little staining in the nucleolus
or the cytoplasm. This is likely
because of its major role in binding
to the newly transcribed RNAs.
High-resolution immunoelectron
microscopy has shown that the
hnRNPs localize predominantly to
the border regions of the
chromatin, where it has access to
these nascent RNAs.
• HEKOKINASE - The hexokinase
is an enzyme that phosphorylates
the hexoses (six-carbon sugars),
forming the hexose phosphate. In
most of the organisms, glucose is
the most important substrate for
the hexokinases, and the glucose-6-
phosphate is the most important
product. The Hexokinase possesses
the ability to transfer an inorganic
phosphate group from the ATP to
a substrate. The Genes that encode
the hexokinase have been
discovered in the every domain of
the life, and exist among a variety
© 2022 by JPS Scientific Publications, India
240
of the species that range from the
bacteria, yeast, and the plants to
the humans and the other
vertebrates. They are categorized
as the actin fold proteins, sharing a
common ATP binding site core
that is surrounded by the more
variable sequences which
determine the substrate affinities
and the other properties. Several
hexokinase isoforms or isozymes
that provide the different functions
can occur in a single species.
• HFQ - The Hfq protein (also
known as the HF-I protein)
encoded by the hfq gene was
discovered in the year 1968 as an
Escherichia coli host factor that
was essential for the replication of
the bacteriophage Qβ. It is now
clear that the Hfq is an abundant
bacterial RNA binding protein
which has many important
physiological roles that are usually
mediated by interacting with the
Hfq binding sRNA. The Hfq
mediates its pleiotropic effects
through the several mechanisms. It
interacts with the regulatory sRNA
and facilitates their antisense
interaction with their targets. It
also acts as independently to
modulate the mRNA decay
(directing the mRNA transcripts
for the degradation) and also acts
as a repressor of the mRNA
translation. The Genomic SELEX
has been used to show that the Hfq
binding RNAs are enriched in the
sequence motif 5'-AAYAAYAA-3'.
The Hfq was also found to act on
Glossary of Genetics
the ribosome biogenesis in the E.
coli, specifically on the 30S
subunit. The Hfq mutants
accumulate higher levels of the
immature small subunits and
decreased the translation accuracy.
This function on the bacterial
ribosome could also account for
the pleiotropic effect typical of the
Hfq deletion strains. The Electron
microscopy imaging reveals that,
in addition to the expected
localization of this protein in the
cytoplasmic regions and in the
nucleoid, an important fraction of
the Hfq is located in the close
proximity to the membrane.
• HFR – The high - frequency
recombination cell (Hfr cell) (also
called as an Hfr strain) is a
bacterium with the conjugative
plasmid (for example, the F-factor)
integrated into the its
chromosomal DNA. The
integration of the plasmid into the
cell's chromosome is through the
homologous recombination. A
conjugative plasmid capable of the
chromosome integration is also
called as an episome (a segment of
the DNA that can exist as a
plasmid or become integrated into
the chromosome). When the
conjugation occurs, the Hfr cells
are very efficient in delivering the
chromosomal genes of the cell into
the recipient F− cells, which lack
the episome. The Hfr strain was
first characterized by the Luca
Cavalli-Sforza. William Hayes also
© 2022 by JPS Scientific Publications, India
241
isolated the another Hfr strain
independently.
• HPLC - The High-performance
liquid chromatography (HPLC),
formerly referred to as the high-
pressure liquid chromatography, is
a technique in the analytical
chemistry used to separate,
identify, and quantify each of the
component in a mixture. It relies
on the pumps to pass a pressurized
liquid solvent containing the
sample mixture through a column
filled with a solid adsorbent
material. Each component in the
sample interacts slightly differently
with the adsorbent material,
causing the different flow rates for
the different components and then
leading to the separation of the
components as they flow out
through the column.
• HTPLC - The High-performance
thin-layer chromatography
(HPTLC) is an enhanced form of
the thin-layer chromatography
(TLC). A number of the
enhancements can be made to the
basic method of the thin-layer
chromatography to automate the
different steps, to increase the
resolution achieved, and to allow
the more accurate quantitative
measurements. The Automation is
useful to overcome the uncertainty
in the droplet size and the position
when the sample is applied to the
TLC plate by the hand. One
approach to automation has been
the use of the piezoelectric devices
and the inkjet printers for applying
Glossary of Genetics
the sample. The spot capacity
(analogous to peak capacity in
HPLC) can be increased by
developing the plate with the two
different solvents, using the two-
dimensional chromatography. The
procedure begins with the
development of the sample loaded
plate with the first solvent. After
removing it, the plate is rotated 90°
and developed with a second
solvent.
• HIND 3 - The HindIII
(pronounced "Hin D Three") is a
type II site-specific
deoxyribonuclease restriction
enzyme isolated from the
Haemophilus influenzae that
cleaves the DNA palindromic
sequence AAGCTT in the
presence of the cofactor Mg2+ via
the hydrolysis. HindIII as well as
the other type II restriction
endonucleases are very useful in
the modern science, particularly in
the DNA sequencing and
mapping. Unlike the type I
restriction enzymes, the type II
restriction endonucleases perform
very specific cleaving of the DNA.
The type I restriction enzymes
recognize the specific sequences,
but cleave the DNA randomly at
sites other than their recognition
site whereas the type II restriction
enzymes cleave only at their
specific recognition site. [6] Since
their discovery in the early 1970s,
type II restriction enzymes have
revolutionized the way scientists
work with the DNA, particularly
© 2022 by JPS Scientific Publications, India
242
in the genetic engineering and the
molecular biology.
• HIN RECOMBINASE - The Hin
recombinase is a 21kD protein
composed of the 198 amino acids
that is found in the bacteria
Salmonella. The Hin belongs to the
serine recombinase family (B2) of
the DNA invertases in which it
relies on the active site serine to
initiate the DNA cleavage and the
recombination. The related
protein, the gamma-delta resolvase
the shares high similarity to the
Hin, of which much structural
work has been done, including the
structures bound to the DNA and
reaction intermediates. The Hin
functions to invert a 900 base pair
(bp) DNA segment within the
salmonella genome that contains a
promoter for the downstream
flagellar genes, fljA and fljB. The
Inversion of the intervening DNA
alternates the direction of the
promoter and thereby alternates
expression of the flagellar genes.
This is the advantageous to the
bacterium as a means of escape
from the host immune response.
• HTS - The High-throughput
sequencing (HTS) is a newly
invented technology alternative to
the microarray. Although it is still
relatively more expensive than the
microarray, it has several
advantages even for the
measurements of the factors that
affect the regulation of the gene
expression. For example, the HTS
can be applied to the non-model
Glossary of Genetics
organism while the microarray is
restricted to the model organism to
which the microarray has already
been designed as mentioned above.
Although the RNA must be
converted to the DNA before the
HTS, since the HTS can directly
count the number of the
DNA/RNA fragments. The HTS
is believed to be also more
quantitative than the microarray. If
the HTS is binded to the ChIP
technology invented for the ChIP-
chip technology for the microarray.
The ChIP-seq technology can be
used to measure the histone
modification and the TFBS. If
HTS is combined with the bisulfite
treatments. The HTS can also be
used for the identification of the
DNA methylation. The
disadvantage of the short read
technology is that short read must
be mapped to the genome that is
not always available.
• HISTONE DEACETYALSE -
The Histone deacetylases are a
class of the enzymes that remove
the acetyl groups from the amino
acid known as the ε-N-acetyl lysine
amino acid on a histone, thereby
allowing the histones to wrap the
DNA more tightly. This is
important because the DNA is
wrapped around the histones, and
the DNA expression is regulated
by the acetylation and the de-
acetylation. Its action is opposite to
that of the histone
acetyltransferase. The HDAC
proteins are now also called as the
© 2022 by JPS Scientific Publications, India
243
lysine deacetylases (KDAC), to
describe their function rather than
their target, which also includes the
non-histone proteins. The Histone
acetylation plays an important role
in the regulation of the gene
expression. The Hyperacetylated
chromatin is transcriptionally
active, and hypoacetylated
chromatin is silent. A study on the
mice found that a specific subset of
the mouse genes (7%) was
deregulated in the absence of the
HDAC1. Their study also found a
regulatory crosstalk between the
HDAC1 and the HDAC2 and
suggest a novel function for the
HDAC1 as a transcriptional
coactivator. The HDAC1
expression was found to be
increased in the prefrontal cortex
of the schizophrenia subjects,
negatively correlating with the
expression of the GAD67 mRNA.
• HISTONE DEMETHYLASE -
The Histone demethylase proteins
have a variety of the domains that
serve the different functions. These
functions include the binding to the
histone (or sometimes the DNA on
the nucleosome), recognizing the
correct methylated amino acid
substrate and catalyzing the
reaction, and binding the cofactors.
The Cofactors include the alpha-
keto glutarate (JmjC-domain
containing demethylases),
CoREST (LSD), FAD, Fe (II) or
the NOG (N-oxalylglycine). There
are several families of the histone
demethylases, which act on the
Glossary of Genetics
different substrates and play a
different roles in the cellular
function. A very specific code has
been developed to indicate the
substrate for the histone
demethylase. The substrate is first
specified by the histone subunit i.e
H1, H2A, H2B, H3, H4 and then
the one of the letter designation
and number of the amino acid that
is methylated. Lastly, the level of
the methylation is sometimes noted
by the addition of the "me#", with
the numbers being 1, 2, and 3 for
the monomethylated,
dimethylated, and the
trimethylated substrates,
respectively. For example, the
H3K9me2 is achistone H3 with a
dimethylated lysine in the ninth
position.
• HISTONE FOLD - The histone
fold is a structurally conserved
motif found near the C-terminus in
the every core histone sequence in
a histone octamer responsible for
the binding of the histones into the
heterodimers. The histone fold
averages about 70 amino acids and
consists of the three alpha helices
connected by the two short and
unstructured loops. When not in
the presence of the DNA, the core
histones assemble into the head-to-
tail intermediates (H3 and H4 first
assemble into the heterodimers
then fuse two the heterodimers to
form a tetramer, while the H2A
and H2B form the heterodimers)
via the extensive hydrophobic
interactions between the each
© 2022 by JPS Scientific Publications, India
244
histone fold domain in a
"handshake motif". Also the
histone fold was first found in the
TATA box-binding protein-
associated factors, which is a main
component in the transcription.
• HISTONE
METHYLTRANSFERASES -
The Histone methyltransferases
(HMT) are the histone-modifying
enzymes that catalyze the transfer
of the one, two, or the three methyl
groups to the lysine and the
arginine residues of the histone
proteins. The attachment of the
methyl groups occurs
predominantly at the specific lysine
or the arginine residues on the
histones H3 and H4. The two
major types of the histone
methyltranferases exist, lysine-
specific (which can be the SET
(Su(var)3-9, Enhancer of Zeste,
Trithorax) domain containing or
the non-SET domain containing)
and the arginine-specific. In both
the types of the histone
methyltransferases, S-Adenosyl
methionine (SAM) serves as a
cofactor and the methyl donor
group. The genomic DNA of the
eukaryotes associates with the
histones to form the chromatin.
The level of the chromatin
compaction depends heavily on the
histone methylation and the other
post-translational modifications of
the histones. The Histone
methylation is a principal
epigenetic modification of the
chromatin that determines the gene
Glossary of Genetics
expression, genomic stability, stem
cell maturation, cell lineage
development, genetic imprinting,
DNA methylation, and the cell
mitosis.
• HISTONE METHYLATION -
The Histone methylation is a
process by which the methyl
groups are transferred to the amino
acids of the histone proteins that
make up the nucleosomes, which
the DNA double helix wraps
around to form the chromosomes.
The Methylation of the histones
can either increase or decrease the
transcription of the genes,
depending on the which amino
acids in the histones are
methylated, and how many methyl
groups are attached. The
Methylation events that weaken
the chemical attractions between
the histone tails and the DNA
increase the transcription because
they enable the DNA to uncoil
from the nucleosomes so that the
transcription factor proteins and
the RNA polymerase can access
the DNA. This process is critical
for the regulation of the gene
expression that allows the different
cells to express the different types
of genes.
• HISTONE DEACTYLATION -
The Histone deacetylation is
another mechanism of the
epigenetic control. The Histones
are the nuclear proteins that
package the DNA and allow the
ribosomal access to the DNA. The
Deacetylation of the histones is
© 2022 by JPS Scientific Publications, India
245
thus associated with the
compacting the DNA and tye
repressing transcription. In the
lung cancer cell lines, for example,
the deacetylation of the histone 3
correlated with the refractoriness to
the retinoic acid, a phenomenon
related to the RARbeta promoter
methylation in a subset of the cell
lines. 178 Inhibitors of the histone
deacetylases have already been
shown to decrease the level of a
series of the oncoproteins,179
suggesting a potential role as the
antitumor therapeutic agents.
• HIV - The human
immunodeficiency viruses (HIV)
are the two species of the
Lentivirus (a subgroup of the
retrovirus) that infect the humans.
Over time, they cause the acquired
immunodeficiency syndrome
(AIDS), a condition in which the
progressive failure of the immune
system allows the life-threatening
opportunistic infections and the
cancers to thrive. Without the
treatment, average survival time
after the infection with HIV is
estimated to be around 9 to 11
years, depending on the HIV
subtype. In most of the cases, the
HIV is a sexually transmitted
infection and occurs by the contact
with or transfer of the blood, pre-
ejaculate, semen, and the vaginal
fluids. The Non-sexual
transmission can occur from an
infected mother to her infant
during the pregnancy, during the
childbirth by exposure to her blood
Glossary of Genetics
or the vaginal fluid, and through
the breast milk. Within these
bodily fluids, the HIV is present as
both free virus particles and the
virus within the infected immune
cells. The Research has shown (for
both same-sex and opposite-sex
couples) that the HIV is
untransmittable through the
condomless sexual intercourse if
the HIV-positive partner has a
consistently undetectable viral
load.
• HMGA1 PROTEIN - The High-
mobility group protein HMG-
I/HMG-Y is a protein that in the
humans is encoded by the
HMGA1 gene. This gene encodes
a non-histone chromatin protein
involved in the many cellular
processes, including the tegulation
of the inducible gene transcription,
DNA replication, heterochromatin
organization, integration of the
retroviruses into the chromosomes,
and the metastatic progression of
the cancer cells. The HMGA1
proteins are quite very small (~10-
12 kDa) and the basic molecules,
and consist of the three AT-hooks
with the RGRP (Arg-Gly-Arg-Pro)
core motif, a novel cross-linking
domain located between the
second and the third AT-hook, and
a C-terminal acidic tail
characteristic for the HMG family
comprising the HMGA, HMGB
and the HMGN proteins. Recently
it has been shown that the
HMGA1 proteins, HMGA1a and
the HMGA1b, can cross-link the
© 2022 by JPS Scientific Publications, India
246
DNA fibers in vitro and can induce
the chromatin clustering in vivo
suggesting a structural role of the
HMGA1 proteins in the
heterochromatin organization.
• HMGA 2 PROTEIN - The High-
mobility group AT-hook 2, also
known as the HMGA2, is a protein
that, in the humans, is encoded by
the HMGA2 gene. This gene
encodes a type of protein that
belongs to the non-histone
chromosomal high-mobility group
(HMG) protein family. The HMG
proteins function as the
architectural factors and are
essential components of the
enhanceosome. This protein
contains the structural DNA-
binding domains and may act as a
transcriptional regulating factor.
The Identification of the deletion,
amplification, and the
rearrangement of this gene that are
associated with the lipomas
suggests a role in the adipogenesis
and the mesenchymal
differentiation. A gene knock-out
study of the mouse counterpart
demonstrated that this gene is
involved in the diet-induced
obesity. The Alternate
transcriptional splice variants,
encoding the different isoforms,
have also been characterized. The
expression of the HMGA2 in the
adult tissues is commonly
associated with both the malignant
and the benign tumor formation, as
well as the certain characteristic
cancer-promoting mutations.
Glossary of Genetics
• HMG PROTEINS - The High-
Mobility Group or the HMG is a
group of the chromosomal proteins
that are involved in the regulation
of the DNA-dependent processes
such as the transcription,
replication, recombination, and the
DNA repair. The HMG proteins
are thought to play a significant
role in the various human
disorders. The Disruptions and the
rearrangements in the genes coding
for some of the HMG proteins are
associated with some of the
common benign tumors. The
Antibodies to the HMG proteins
are found in the patients with the
autoimmune diseases. The SRY
gene on the Y Chromosome,
responsible for the male sexual
differentiation, contains an HMG-
Box domain. A member of the
HMG family of the proteins, the
HMGB1, has also been shown to
have an extracellular activity as a
chemokine, attracting the
neutrophils and the mononuclear
inflammatory cells to the infected
liver. The high-mobility group
protein such as the HMO1 alters
the DNA architecture by binding,
bending and the looping.
Furthermore, these HMG-box
DNA-binding proteins increase the
flexibility of the DNA upon the
binding.
• HMG BOX - In the field of the
molecular biology, the HMG-box
(high mobility group box) is a
© 2022 by JPS Scientific Publications, India
247
protein domain which is involved
in the DNA binding. The HMG-
box containing proteins only bind
the non-B-type DNA
conformations (kinked or
unwound) with very high affinity.
The HMG-box domains are found
in some of the high mobility group
proteins, which are involved in the
regulation of the DNA-dependent
processes such as the transcription,
replication, and the DNA repair,
all of which require changing the
conformation of the chromatin.
The single and the double box
HMG proteins alter the DNA
architecture by inducing the bends
upon the binding.
• HMGB 1 - The High mobility
group box 1 protein, which is also
known as the high-mobility group
protein 1 (HMG-1) and the
amphoterin is a protein that in the
humans is encoded by the HMGB1
gene. The HMGB1 is among the
most important chromatin
proteins. In the nucleus the
HMGB1 interacts with the
nucleosomes, transcription factors,
and the histones. This nuclear
protein organizes the DNA and
regulates the transcription. After
binding, the HMGB1 bends the
DNA, which facilitates the binding
of the other proteins. The HMGB1
supports the transcription of many
genes in interactions with many
transcription factors. It also
interacts with the nucleosomes to
loosen the packed DNA and
remodel the chromatin. Contact
Glossary of Genetics
with the core histones changes the
structure of the nucleosomes. The
presence of the HMGB1 in the
nucleus depends on the
posttranslational modifications.
When the protein is not acetylated,
it stays in the nucleus, but
hyperacetylation on the lysine
residues causes it to translocate
into the cytosol.
• HNRNPA1 - The Heterogeneous
nuclear ribonucleoprotein A1 is a
protein that in the humans is
encoded by the HNRNPA1 gene.
The Mutations in hnRNP A1 are
causative of the amyotrophic
lateral sclerosis and the syndrome
multisystem proteinopathy. This
gene belongs to the A/B subfamily
of the ubiquitously expressed
heterogeneous nuclear
ribonucleoproteins (hnRNPs). The
hnRNPs are the RNA binding
proteins and they complex with the
heterogeneous nuclear RNA
(hnRNA). These proteins are
associated with the pre-mRNAs in
the nucleus and appear to influence
the pre-mRNA processing and
other aspects of the mRNA
metabolism and the transport. The
hnRNP proteins have the distinct
nucleic acid binding properties.
The protein encoded by this gene
has two repeats of the quasi-RRM
domains that bind to the RNAs in
the N-terminal domain which are
pivotal for the RNA specificity and
the binding. The protein also has a
glycine rich arginine-glycine-
glycine (RGG) region called the
© 2022 by JPS Scientific Publications, India
248
RGG box which enables the
protein and the RNA binding.
• HUNTINGTON’S DISEASE -
The Huntington's disease (HD),
which is also known as the
Huntington's chorea, is a
neurodegenerative disease that is
mostly inherited. The earliest
symptoms are often the subtle
problems with the mood or the
mental abilities. A general lack of
the coordination and an unsteady
gait often follow. It is also a basal
ganglia disease causing a
hyperkinetic movement disorder
known as the chorea. As the
disease advances, the
uncoordinated, involuntary body
movements of the chorea become
more apparent. The Physical
abilities gradually worsen until the
coordinated movement becomes
difficult and the person is unable to
talk. The Mental abilities generally
decline into the dementia. The
specific symptoms vary somewhat
between the people. The
Symptoms usually begin between
the 30 and 50 years of the age but
can start at any age. About eight
percent of the cases start before the
age of the 20 years, and are known
as the juvenile HD, which typically
present with the slow movement
symptoms of the parkinson's
disease rather than those of the
chorea.
• HU PROTEIN - The HU is a
small (10 kDa) bacterial histone-
like protein that resembles the
eukaryotic Histone H2B. The HU
Glossary of Genetics
acts similarly to a histone by
inducing the negative supercoiling
into the circular DNA with the
assistance of the topoisomerase.
The protein has been implicated in
the DNA replication,
recombination, and in the repair.
With an α-helical hydrophobic core
and the two positively charged β-
ribbon arms, the HU binds non-
specifically to the dsDNA with the
low affinity but binds to the altered
DNA—such as the junctions,
nicks, gaps, forks, and the
overhangs with the high affinity.
The arms bind to the minor groove
of the DNA in the low affinity
states, in high affinity states, a
component of the α-helical core
interacts with the DNA as well.
However, this protein's function is
not solely confined to the DNA,
the HU also binds to the RNA and
the DNA-RNA hybrids with the
same affinity as the supercoiled
DNA.
• HNS PROTEIN - The H-NS is
about 15.6 kDa and assists in the
regulation of the bacterial
transcription in the bacteria by
repressing and activating the
certain genes. The H-NS binds to
the DNA with an intrinsic
curvature. In the E. coli, the H-NS
binds to a P1 promoter decreasing
the rRNA production during the
stationary and the slow growth
periods. The RNA polymerase and
the H-NS DNA binding protein
have the overlapping binding sites,
it is thought that the H-NS
© 2022 by JPS Scientific Publications, India
249
regulates rRNA production by
acting on the transcription
initiation site. It has been found
that the H-NS and the RNA
polymerase both bind to the P1
promoter and form a complex.
When the H-NS is bound with the
RNA Polymerase to the promoter
region, there are structural
differences in the DNA that are
accessible. It has also been found
that H-NS can affect translation as
well by binding to the mRNA and
causing its degradation.
• HYBRID DSYGENESIS - The
Hybrid dysgenesis is an epigenetic
phenomenon that has been linked
to the piRNAs in the Drosophila
melanogaster. It occurs when the
two fly lines are crossed that differ
in the TE families present in their
genome. Depending on the
direction of the cross, the resulting
offspring are sterile.The sterility is
caused by the presence of a specific
transposon family (e.g., P-element,
and the I-element) in one of the
lines and not the other. It was
originally observed when the wild-
caught male flies were crossed to
the female flies from the standard
laboratory strains, because the P-
element invaded wild strains after
the initial collection of the
laboratory strains.
• H BOND ACCEPOR AND
DONATER - The oxygen atom of
the hydroxy group is called as the
hydrogen bond donor, because it is
"donating" its hydrogen to the
nitrogen. The nitrogen atom is
Glossary of Genetics
called as the hydrogen bond
acceptor, because it is "accepting"
the hydrogen from the oxygen.
• HYPERCHROMICITY - The
Hyperchromicity is the increase of
the absorbance (optical density) of
a material. The most famous
example is the hyperchromicity of
the DNA that occurs when the
DNA duplex is denatured. When
the two single DNA strands are
being separated, either by the heat
or by the addition of denaturant or
by the increasing of the pH level,
the UV absorption is then
increased. The opposite, a decrease
of the absorbance is called as the
hypochromicity.
• HYPOXANTHINE - The
Hypoxanthine is a naturally
occurring purine derivative. It is
occasionally found as a constituent
of the nucleic acids, where it is
present in the anticodon of the
tRNA in the form of its nucleoside
inosine. It has a tautomer known
as the 6-hydroxypurine. The
Hypoxanthine is a necessary
additive in the certain cell,
bacteria, and the parasite cultures
as a substrate and nitrogen source.
For example, it is commonly a
required reagent in the malaria
parasite cultures, since the
Plasmodium falciparum requires a
source of the hypoxanthine for the
nucleic acid synthesis and the
energy metabolism. The
Hypoxanthine is also a hydrolysis of the PPi occurs after
spontaneous deamination product
of the adenine. Because of its
© 2022 by JPS Scientific Publications, India
250
resemblance to the guanine, the
spontaneous deamination of the
adenine can lead to an error in the
DNA transcription/replication, as
it base pairs with the cytosine. The
Hypoxanthine is removed from the
DNA by the base excision repair,
initiated by the N-methylpurine
glycosylase (MPG), which is also
known as the alkyl adenine
glycosylase (Aag).
• HOLLIDAY JUNCTION - The
Holliday junction is a branched
nucleic acid structure that contains
the four double-stranded arms
joined. These arms may adopt one
of the several conformations
depending on the buffer salt
concentrations and the sequence of
the nucleobases closest to the
junction. The Holliday junctions
are a key intermediate in many
types of the genetic recombination,
as well as in the double-strand
break repair. These junctions
usually have a very symmetrical
sequence and therefore they are
mobile, meaning that the four
individual arms may slide through
the junction in a very specific
pattern that are largely preserves
during the base pairing.
Additionally, the four-arm
junctions similar to the Holliday
junctions appear in some of the
functional RNA molecules.
HYDROLYSIS OF
PYROPHOSPHATE - The
the formation of the
phosphodiester bond and ensures
Glossary of Genetics
that the DNA synthesis reaction is
energetically favorable without the
need for the additional enzymes.
Also, we observe that the DNA
synthesis is a two Mg2+ ion
assisted stepwise associative as the
SN2 reaction. Overall, this study
provides the deep temporal insight
regarding the primary enzymatic
reaction responsible for the
genome duplication. The fact that
the DNA synthesis proceeds in
vitro in the absence of the
pyrophosphatases represents a
long-standing conundrum
regarding the thermodynamics of
the DNA synthesis reaction.
Using the time-resolved
crystallography, we show that
hydrolysis of the PPi is an intrinsic
and the very critical step of the
DNA synthesis reaction catalyzed
by the dPols.
• HUNCHBACK GENE - The
locus hunchback (hb) is a member
of the gap class of the segmentation
genes of the Drosophila. A number
of the X-ray-induced deletions
locate the hb locus at the
chromosomal site 85A3-B1, to the
right of the pink locus, which maps
in the same interval. A total of the
14 EMS and the 3 X-ray-induced
hb alleles have been studied very
intensively. The Homozygous
mutant embryos show the
deletions of the segments in the
two separate regions. In the six
strong alleles, the labium and all
the three thoracic segments are
deleted anteriorly while the
© 2022 by JPS Scientific Publications, India
251
posteriorly the 8th abdominal
segment and the adjacent parts of
the 7th abdominal segment are
lacking. The eight weak alleles
show the smaller deletions both in
the thoracic and in the posterior
abdominal region. In the weakest
allele only part of the mesothorax
is deleted. The three hb alleles
produce a homoeotic
transformation which is
superimposed on a strong or a
weak deletion phenotype, head or
the thoracic segments are then
transformed into the abdominal
segments, respectively. This
suggests that the hb might also be
involved in the regulation of the
genes in the Bithorax complex
(BX-C).
• HP1 - The Heterochromatin
Protein 1 (HP1) is a structural
component of the silent chromatin
at the telomeres and the
centromeres. The Euchromatic
genes repositioned near the
heterochromatin by the
chromosomal rearrangements are
typically silenced in an HP1-
dependent manner. Silencing is
thought to involve the spreading of
the heterochromatin proteins over
the rearranged genes. The HP1
associates with the centric
heterochromatin through an
interaction with the methylated
lysine 9 of the histone H3, a
modification generated by the
SU(VAR)3-9. The current model
for the spreading of the silent
chromatin involves the HP1-
Glossary of Genetics
dependent recruitment of the
SU(VAR)3-9, resulting in the
methylation of the adjacent
nucleosomes and the association of
the HP1 along the chromatin fiber.
• HSP70 - The 70 kilodalton heat
shock proteins (Hsp70s or the
DnaK) are a family of the
conserved ubiquitously expressed
heat shock proteins. Proteins with
the similar structure exist in
virtually in all the living organisms.
The Intracellularly localized
Hsp70s are an important part of
the cell’s machinery for the protein
folding, performing chaperoning
functions, and helping to protect
the cells from the adverse effects of
the physiological stresses.
Additionally, the membrane-bound
Hsp70s have been identified as a
potential target for the cancer
therapies and their extracellularly
localized counterparts have been
identified as having both the
membrane-bound and the
membrane-free structures. The
Hsp70 system interacts with the
extended peptide segments of the
proteins as well as the partially
folded proteins to cause the
aggregation of the proteins in the
key pathways to downregulate the
activity. When not interacting
with a substrate peptide, the Hsp70
is usually in an ATP bound state.
The Hsp70 by itself is
characterized by a very weak
ATPase activity, such that the
spontaneous hydrolysis will not
occur for the many minutes.
© 2022 by JPS Scientific Publications, India
252
• HYBRID DYSGENESIS - The
Hybrid dysgenesis is an epigenetic
phenomenon that has been linked
to the piRNAs in the Drosophila
melanogaster. It occurs when the
two fly lines are crossed that differ
in the TE families present in their
genome. Depending on the
direction of the cross, the resulting
offspring are the sterile. The
sterility is caused by the presence
of a specific transposon family
(e.g., P-element, and the I-element)
in one of the lines and not the
other. It was originally observed
when the wild-caught male flies
were crossed to the female flies
from the standard laboratory
strains, because the P-element
invaded wild strains after the initial
collection of the laboratory strains.
Interestingly, the dysgenesis is only
observed in one direction of the
cross, and this difference in the
reciprocal crosses suggested the
presence of a fertility factor in the
female parent. The Current
models ascribe the sterility to the
mobilization of the transposon in
the germline of the hybrids and a
failure to silence the novel TE
family.
• HYDROLYSIS - The Hydrolysis
is any chemical reaction in which a
molecule of the water breaks the
one or more chemical bonds. The
term is used broadly for the
substitution, elimination, and the
solvation reactions in which the
water is the nucleophile. The
Biological hydrolysis is the
Glossary of Genetics
cleavage of the biomolecules where
a water molecule is consumed to
effect the separation of a larger
molecule into the component parts.
When a carbohydrate is broken
into its component sugar molecules
by the hydrolysis (e.g., sucrose
being broken down into the
glucose and the fructose), this is
recognized as the saccharification.
The Hydrolysis reactions can be
the reverse of a condensation
reaction in which the two
molecules join into a larger one
and eject a water molecule. Thus
hydrolysis adds the water to break
down, whereas the condensation
builds up by removing the water.
• HOLOENZYME - The
Holoenzymes are the enzymes that
contain the metallic bindings
which are also known as the
metalloenzymes. The Transition
metals such as the copper, zinc,
iron, and the manganese are those
cofactors most frequently found
constituent in the metalloenzymes.
The Catalytic ions are often bound
to the active site of the
metalloenzyme with the covalent
bonds. However, the metallic ion
cofactors are rarely not necessary
for the catalytic function of the
metalloenzymes, such as in the
carbonic anhydrase that binds a
zinc ion solely for its structural
stability which does not impact its
activity.
© 2022 by JPS Scientific Publications, India
253
• HERSHEY CHASE
EXPERIMENT - The Hershey–
Chase experiments were a series of
the experiments conducted in the
year 1952 by the scientists such as
Alfred Hershey and the Martha
Chase that helped to confirm that
the DNA is the genetic material.
The Hershey and Chase inserted
the radioactive elements in the
bacteriophages by adding the
isotopes to separate the media
within which the bacteria were
allowed to grow for the 4 hours
before the bacteriophage
introduction. When the
bacteriophages infects the bacteria,
the progeny contained the
radioactive isotopes in their
respective structures. This
procedure was performed once for
the sulfur-labeled phages and once
for the phosphorus-labeled phages.
The labeled progeny were then
allowed to infect the unlabeled
bacteria. The phage coats remained
on the outside of the bacteria,
while the genetic material entered.
The Disruption of the phage from
the bacteria by the agitation in a
blender followed by the
centrifugation allowed for the
separation of the phage coats from
the bacteria. These bacteria were
lysed to release the phage progeny.
The progeny of the phages that
were labeled with the radioactive
phosphorus remained labeled,
whereas the progeny of the phages
labeled with the radioactive
sulphur were unlabeled. Thus, the
Glossary of Genetics
Hershey–Chase experiment helped
to confirm that the DNA, not the
protein, is the genetic material.
• HOMEOTIC GENES - In the
field of the evolutionary
developmental biology, the
homeotic genes are the genes
which regulate the development of
the anatomical structures in
various organisms such as the
echinoderms, insects, mammals,
and the plants. The Homeotic
genes often encode the
transcription factor proteins, and
these proteins affect the
development by regulating the
downstream gene networks
involved in the body patterning.
The Mutations in the homeotic
genes cause displaced body parts
(homeosis), such as the antennae
growing at the posterior of the fly
instead of at the head. The
mutations that lead to the
development of rye ectopic
structures are usually very lethal.
There are several subsets of the
homeotic genes. They include
many of the Hox and the ParaHox
genes that are important for the
segmentation. The Hox genes are
found in the bilateral animals,
including the Drosophila (in which
they were first discovered) and the
humans. The Hox genes are the
subset of the genes called as the
homeobox genes. The Hox genes
are often conserved across the
species, so some of the Hox genes
of Drosophila are homologous to
those in the humans. In general,
© 2022 by JPS Scientific Publications, India
254
the Hox genes play a role of the
regulating expression of the genes
as well as aiding in the
development and assignment of the
specific structures during the
embryonic growth.
• HUNCHBACK GENE - The
Hunchback is a bifunctional
transcription factor that can
activate and repress the gene
expression in the Drosophila
development. The study
investigated the regulatory DNA
sequence features that control the
Hunchback function by perturbing
enhancers for one of its target
genes, even-skipped (eve). While
the Hunchback directly represses
the eve stripe 3+7 enhancer, in the
eve stripe 2+7 enhancer,
Hunchback repression is prevented
by nearby sequences-this
phenomenon is called as the
counter-repression. The function
of the hunchback is the central to
the establishment of an anterior-
posterior gradient of the gene
activity in the transition from
unfertilized egg to the developing
zygote. As its name suggests, the
hunchback has a special role in the
development of the trunk (thorax)
of the fly. The Maternal HB
mRNA, is intitially distributed
evenly throughout the egg. Nanos,
whose mRNA is localized to the
posterior pole of the mature
oocyte, functions to inhibit the
Hunchback, the Nanos protein
inactivates the HB mRNA,
preventing its translation in the
Glossary of Genetics
posterior. Thus Nanos, through its
inhibition of the HB translation,
establishes a concentration
gradient of the maternally derived
the HB protein complementary to
the gradient of the Nanos protein.
• HOTSPOT OF MUTATIONS -
The Mutation frequencies vary
significantly along the nucleotide
sequences such that the mutations
often concentrate at the certain
positions called as the hotspots.
The Mutation hotspots in the
DNA reflect the intrinsic properties
of the mutation process, such as
the sequence specificity, that
manifests itself at the level of the
interaction between the mutagens,
DNA, and the action of the repair
and also the replication
machineries. The hotspots might
also reflect the structural and the
functional features of the respective
DNA sequences. When the
mutations in a gene are identified
using a particular experimental
system, resulting the hotspots
could reflect the properties of the
gene product and the mutant
selection scheme. Analysis of the
nucleotide sequence context of the
hotspots can provide the
information on the molecular
mechanisms of the mutagenesis.
However, the determinants of the
mutation frequency and specificity
are very complex in nature and
there are many more analytical
methods for their study. The
Mutations arise in the nucleic acids
as part of an important and the
© 2022 by JPS Scientific Publications, India
255
essential biological process which
results in generating the genetic
variation that is required for a
species to evolve. Thus, the
genomes are replicated at a level of
the fidelity that leads to a defined
rate of the spontaneous
mutagenesis.
• HIGHER ORDER STRUCTURE
- The Secondary, tertiary and the
quaternary structure is often
collectively termed as the higher
order structure (HOS) of a protein.
The HOS is responsible for the
correct folding and the three-
dimensional shape of a
biopharmaceutical. This can be
affected by the different
formulations, which in turn can
affect the protein activity. The
folding and the shape of the protein
impacts directly on the
functionality and efficiency of the
drug and this correlation is often
termed as the “structure function
relationship”. The Incorrect higher
order structure can also raise the
safety concerns. If the overall
folding and therefore the 3D shape
of a protein is wrong, the receptor
binding can be inhibited,
immunogenic epitopes can also be
exposed and the aggregation can
occur. It is therefore very crucial
to employ a thorough and
complete characterization of the
higher order structure of the
protein. The Biophysical
characterization methods should
be performed alongside the
functional analyses and also the
Glossary of Genetics
primary structure characterization
to completely allow a full
understanding of the overall
protein structure.
• HIGH PERFORMANCE
LIQUID
CHROMATOGRAPHY - The
High-performance liquid
chromatography (HPLC), formerly
referred to as the high-pressure
liquid chromatography, is a
technique in the analytical
chemistry which is used to
separate, identify, and quantify the
each component in a mixture. It
relies on the pumps to pass a
pressurized liquid solvent
containing the sample mixture
through a column filled with a
solid adsorbent material. Each of
the component in the sample
interacts slightly differently with
the adsorbent material, causing the
different flow rates for the different
components and leading to the
separation of the components as
they flow out of the column. The
HPLC has been used for the
manufacturing (e.g. during the
production process of the
pharmaceutical and the biological
products), legal (e.g. detecting the
performance enhancement drugs in
the urine), research (e.g. separating
the components of a complex
biological sample, or of the similar
synthetic chemicals from each
other), and medical (e.g. detecting
the vitamin D levels in the blood
serum) purposes. The HPLC relies
on the pumps to pass a pressurized
© 2022 by JPS Scientific Publications, India
256
liquid and a sample mixture
through a column filled with the
adsorbent, leading to the
separation of the sample
components.
• HETEROCHROMATIN - The
Heterochromatin is a tightly
packed form of the DNA or the
condensed DNA, which comes in
the multiple varieties. These
varieties lie on a continuum
between the two extremes of the
constitutive heterochromatin and
the facultative heterochromatin.
Both play a role in the expression
of the genes. Because it is tightly
packed, it was thought to be
inaccessible to the polymerases and
therefore not transcribed. The
Constitutive heterochromatin can
affect the genes near itself (e.g.
position-effect variegation). It is
usually repetitive and forms the
structural functions such as the
centromeres or the telomeres, in
addition to the acting as an
attractor for the other gene-
expression or the repression
signals. The Facultative
heterochromatin is the result of the
genes that are silenced through a
mechanism such as the histone
deacetylation or the Piwi-
interacting RNA (piRNA) through
the RNAi. It is not the repetitive
and shares the compact structure of
the constitutive heterochromatin.
However, under the specific
developmental or the
environmental signaling cues, it
can lose its condensed structure
Glossary of Genetics
and become the transcriptionally
active.
• HELIX-LOOP-HELIX - A helix–
loop–helix (HLH) is a protein
structural motif that characterizes
one of the largest families of the
dimerizing transcription factors.
The Helix-Loop-Helix are found in
the organisms such as the yeast to
the humans and function in the
critical developmental processes,
including the sex determination
and the development of the
nervous system and the muscles.
• HISTONE PROTEINS - The
Histones are the type of basic
proteins.The Histones contains
basic amino acids such as the
Lysine and the Arginine which are
found in the eukaryotic cells.
When the histone surrounds the
DNA it forms a structural structure
called as the Nucleosomes. The
Histone also provides the structural
support to the chromosome.
• HETERODIMERS - The
Heterodimers are the
transmembrane adhesion proteins
which are located at the the focal
adhesion sites which serves as
physical linkages between the
extracellular matrix and the
intracellular matrix. The
heterodimers appear to play a role
in the modulation of the analgesic
responses.
• HOMEODOMAI - The
homeodomain is a common DNA-
binding structural motif which is
mainly found in many of the
eukaryotic regulatory proteins.
© 2022 by JPS Scientific Publications, India
257
Homeodomain are the type of the
proteins which are involved in the
transcriptional control of many
developmentally important genes.
143 human loci have been linked
to the various genetic and the
genomic disorders.
• HIGH ENERGY SULPHUR
BOND - The High-energy sulfur
bond is an energy-rich sulfur
linkage, which is the most
important of the which occurs in
the acetyl-CoA molecule, the main
source of the energy in the fatty
acid biosynthesis. The Sulphur is
also an important element which is
present in all the biological
systems.
• HYDROPHOBIC SIDE CHAINS
- The Hydrophobic interactions are
the interactions which describe
relations the between the water and
the hydrophobes. The
Hydrophobic amino acids side
chains have little or no polarity in
their side chains. The lack of the
polarity means that they have no
way to interact with the highly
polar water molecules thereby
making them water fearing. The
nine amino acids that have the
hydrophobic side chains are the
glycine, alanine, phenylalanine,
valine, leucine, tryptophan,
isoleucine, proline and the
methionine.
• HYDROPHILIC SIDE CHAINS
- The Hydrophilic amino acids side
chains are a type of the side chains
with a polar nature. The name
“hydrophilic” derives because it
Glossary of Genetics
attracts the water. Due to the
hydrophilic properties of the side
chain, the polar amino acid
residues have a tendency to be on
the Outer surface of a protein.
Since the Acids have very stable
structure.
• HAND 1 - The Heart- and the
neural crest derivatives-expressed
protein 1 is a protein that in the
humans is encoded by the HAND1
gene. The protein encoded by this
gene belongs to the basic helix-
loop-helix family of the
transcription factors. This gene
product is one of the two closely
related family members, the
HAND proteins are expressed
within the developing ventricular
chambers, cardiac neural crest,
endocardium (HAND2 only) and
the epicardium (HAND2 only).
The HAND1 is expressed with the
myocardium of the primary heart
field and plays an essential role but
very poorly understood role in the
cardiac morphogenesis.
• HAND 2 - The Heart- and neural
crest derivatives-expressed protein
2 is a protein that in the humans is
encoded by the HAND2 gene. The
Hand2 also plays a critical role in
the establishment of a proper
implantation environment for the
pregnancy in the mice. The
induction of the Hand2 by
progesterone-dependent
mechanisms in the uterine stromal
tissue suppresses the fibroblast
growth factors (FGFs) that would
otherwise stimulate the estrogen
© 2022 by JPS Scientific Publications, India
258
producing pathways and the
impair embryo implantation. The
Hand2 plays a role in the lower
jaw formation and the tongue
morphogenesis in the mice by
suppressing the homeobox genes
Dlx5 and the Dlx6.
• HUMAN FOAMY VIRUS - The
Human foamy virus (HFV) is a
retrovirus and specifically belongs
to the genus Spumavirus. The
Foamy virus in the humans occurs
only as a result of the zoonotic
infection. The Persistence in the
absence of the disease, but in the
presence of the antibodies is a
defining characteristic of the FV
infection. The HFV has been
isolated from the patients with the
various neoplastic and
degenerative diseases such as the
myasthenia gravis, multiple
sclerosis, De Quervain's thyroiditis,
and the Graves’ disease but the
virus’ etiological role is still
unclear.
• HOMOLOGOUS
RECOMBINATION - The
Homologous recombination is a
type of genetic recombination in
which the genetic information is
exchanged between the two similar
or identical molecules of the
double-stranded or single-stranded
nucleic acids usually DNA as in
the cellular organisms but may be
also in the RNA in viruses. It is
widely used by the cells to
accurately repair the harmful
breaks that occur on the both
strands of the DNA, known as
Glossary of Genetics
double-strand breaks (DSB), in a
process called which is called as
the homologous recombinational
repair (HRR). Homologous
recombination also produces the
new combinations of the DNA
sequences during the meiosis, the
process by which the eukaryotes
make the gamete cells, like sperm
and egg cells in the animals. These
new combinations of the DNA
represent the genetic variation in
the offspring, which in turn enables
the populations to adapt during the
course of the evolution.
Homologous recombination is also
used in the horizontal gene transfer
to exchange the genetic material
between the different strains and
the species of the bacteria and
viruses. Although the homologous
recombination varies widely
among the different organisms and
the cell types, for the double-
stranded DNA (dsDNA) most of
the forms are involve the same
basic steps. After a double-strand
break occurs, the sections of the
DNA around the 5’ ends of the
break are cut away in a process
called resection. In the strand
invasion step that follows, an
overhanging 3’ end of the broken
DNA molecule then “invades” a
similar or the identical DNA
molecule that is not broken. After
the strand invasion, the further
sequence of the events may follow
either of the two main pathways in
the DSBR (double-strand break
repair) pathway or the SDSA
© 2022 by JPS Scientific Publications, India
259
(synthesis-dependent strand
annealing) pathway. The
Homologous recombination that
occurs during the DNA repair
tends to result in non-crossover
products, in effect restoring the
damaged DNA molecule as it
existed before the double-strand
break.
• HERSHEY CHASE
EXPERIMENT - The Hershey
and Chase were able to prove that
the DNA from the phage is
inserted into the bacteria shortly
after the virus attaches to its host.
Using a high-speed blender they
were also able to force the
bacteriophages from the bacterial
cells after the adsorption. The lack
of the 32P-labeled DNA remaining
in the solution after the
bacteriophages had been allowed
to adsorb to the bacteria showed
that the phage DNA was then
transferred into the bacterial cell.
The presence of almost all the
radioactive 35S in the solution
showed that the protein coat that
protects the DNA before the
adsorption stayed outside the cell.
Hershey and Chase concluded that
the DNA, not protein, was the
genetic material. They determined
that the protective protein coat was
able to formed around the
bacteriophage, but that the internal
DNA is what conferred its ability
to produce the progeny inside a
bacterium. They showed that, in
the growth, protein has no
particular function, while the DNA
Glossary of Genetics
has some function. They
determined this from the amount
of the radioactive material
remaining outside of the cell. Only
20% of the 32P remained outside
the cell, demonstrating that it was
all incorporated with the DNA in
the cell’s genetic material. All of
the 35S in the protein coats
remained outside the cell, showing
it was not incorporated into the
cell, and that the protein is not the
genetic material. Hershey and
Chase’s experiment concluded that
the little sulfur-containing material
entered into the bacterial cell.
However no specific conclusions
can be made regarding whether the
material that is sulfur-free enters
the bacterial cell after the phage
adsorption. Further research was
necessary to conclude that it was a
solely bacteriophages’ DNA that
entered the cell and not a
combination of protein and DNA
where the protein did not contain
any amount of the sulfur.
• HYDROLYTIC DAMAGE - The
Hydrolytic DNA damage involves
the deamination or the total
removal of the individual bases.
Loss of the DNA bases, known as
the AP (apurinic/apyrimidinic)
sites, can particularly be the
mutagenic and if left unrepaired
they can inhibit the transcription
process. The Hydrolytic damage
may result from the biochemical
reactions of the various metabolites
as well as the overabundance of the
reactive oxygen species.The
© 2022 by JPS Scientific Publications, India
260
Ultraviolet and the other types of
the radiation can damage the DNA
in the form of the DNA strand
breaks. This involves a cut in one
or both of the DNA strands, the
double-strand breaks are especially
very dangerous and can be
mutagenic, since they can
potentially affect the expression of
the multiple genes. The UV-
induced damage can also result in
the production of the pyrimidine
dimers, where the covalent cross-
links occur in the cytosine and in
the thymine residues. The most
common pyrimidine dimers are the
cyclobutane pyrimidine dimers
(CPD) and the pyrimidine (6-4)
pyrimidone photoproducts (6-4PP).
The CPD and the 6-4PP are the
most frequent DNA mutations
which are found in the p53 protein
in the skin cancers. The Pyrimidine
dimers can also disrupt the
polymerases and prevent the
proper replication of the DNA.
• HYDROGEN BONDING - The
hydrogen bonding is the bonding
between the complementary bases
that holds the two strands of the
DNA together. The Hydrogen
bonds are not the chemical bonds.
They can be very easily disrupted.
This permits the DNA strands to
separate for the transcription i.e
copying of the DNA to the RNA
and the replication i.e copying of
the DNA to DNA. The hydrogen
bonds are the reason for the
structure of the DNA and its
properties. When a DNA solution
Glossary of Genetics
is heated enough, the double-
strand of the DNA unwinds and
the hydrogen bonds that hold the
two strands together weaken and
finally breaks. The Hydrogen
bonds can be intermolecular which
is occurring between the separate
molecules or the intramolecular
which is occurring among parts of
the same molecule. The energy of
the hydrogen bond depends on the
factors such as the geometry, the
environment, and the nature of the
specific donor and the acceptor
atoms, and can vary between the 1
and 40 kcal/mol. This makes them
somewhat stronger than a van der
Waals interaction, and weaker
than the fully covalent or the ionic
bonds. This type of bond can occur
in the inorganic molecules such as
the water and in the organic
molecules like the DNA and the
proteins. Hydrogen bonds are
responsible for the holding of the
materials such as paper and the
felted wool together, and for
causing the separate sheets of the
paper to stick together after
becoming wet and subsequently
drying.
• HEXAMERIC HELICASE - The
Helicases are the motor proteins
that couple the hydrolysis of the
nucleoside triphosphate (NTPase)
to the nucleic acid unwinding. The
hexameric helicases have a
characteristic ring-shaped
structure, and all, except the
eukaryotic minichromosomal
maintenance (MCM) helicase, are
© 2022 by JPS Scientific Publications, India
261
the homohexamers. Most of the 12
known hexameric helicases play a
role in the DNA replication, the
recombination, and the
transcription. A human genetic
disorder, which is known as the
Bloom’s syndrome, is associated
with a defect in one member of the
class of the hexameric helicases.
Significant progress has been made
in the understanding of the
biochemical properties, structures,
and the interactions of these
helicases with the DNA and the
nucleotides. Cooperativity in the
nucleotide binding was observed in
many, and the sequential NTPase
catalysis has been observed in the
two proteins,the gp4 of the
bacteriophage T7 and the rho of
the Escherichia coli. The crystal
structures of the oligomeric T7 gp4
helicase and the hexamer of RepA
helicase show the structural
features that substantiate the
observed the cooperativity, and
both are consistent with the
nucleotide binding at the subunit
interface. The moodels are
presented that show how the
sequential NTP hydrolysis can lead
to the unidirectional and
processive translocation. The
Possible unwinding mechanisms
based on the DNA exclusion
model are proposed here, termed
as the wedge, torsional, and the
helix-destabilizing models.
Glossary of Genetics
I intergenic regions (but also the
• ISOFORMS - The Gene isoforms
are the mRNAs which are
produced from the same locus but
are different in their transcription
start sites, protein coding DNA
sequences and/or untranslated
regions, potentially altering gene
function. It provides a mechanism
to specialize the properties of a
gene or protein at one of the three
levels. Atleast 30 of the genes are
encoded as isoforms that varied
widely in the length and in the
number of the exons.
• INTERGENIC REGION - An
intergenic region is a stretch of the
DNA sequences located between
the genes. TheIntergenic regions
may contain thefunctional
elements and the junk DNA. The
Intergenic regions contain a
number of the functional DNA
sequences such as the promoters
and the regulatory elements and
the centromeres. They may also
contain the origins of the
replication, scaffold attachment
regions, transposons and the
viruses. The Non-functional DNA
elements such as the pseudogenes,
repetitive DNA, and the junk
DNA can also be found in the
intergenic regions although they
may also be located within the
genes in the introns. As all the
scientific knowledge is ultimately
tentative, and in principle subject
to the revision given the better
© 2022 by JPS Scientific Publications, India
262
evidence, it is possible some of the
intra-genic regions like the introns)
may hypothetically contain as yet
unidentified functional elements
such as the non-coding RNA genes
or the regulatory sequences. Such
discoveries occur from time to
time, but the amount of the
functional DNA discovered usually
constitute only a tiny fraction of
the overall amount of the
intergenic/intronic DNA.
• INBN1 - The Interferon beta is a
protein that in the humans is
encoded by the IFNB1 gene. The
natural and the recombinant
protein forms have the antiviral,
antibacterial, and the anticancer
properties. This gene encodes a
cytokine that belongs to the
interferon family of the signaling
proteins, which are released as part
of the innate immune response to
the pathogens. The protein
encoded by this gene belongs to the
type I class of the interferons,
which are important for the
defense against the viral infections.
In addition, the type I interferons
are involved in the cell
differentiation and in the anti-
tumor defenses. Following the
secretion in response to a
pathogen, the type I interferons
bind a homologous receptor
complex and induce the
transcription of the genes such as
those encoding inflammatory
cytokines and the chemokines.
Overactivation of type I interferon
Glossary of Genetics
secretion is linked to the
autoimmune diseases.
• IHF PROTEIN - The integration
host factor, IHF, is a nucleoid-
associated protein only found in
the gram negative bacteria. It is a
20 kDa heterodimer, composed of
the α and β subunits that bind to
the sequence 5' - mucous membranes. The IgA
WATCAANNNNTTR - 3' and
bends the DNA approximately
around 160 degrees. The β arms of
the IHF have Proline residues that
help to stabilize the DNA kinks.
These kinks can help the compact
DNA and allow for the
supercoiling. The mode of the
binding to the DNA depends on
the environmental factors, such as
the concentration of the ions
present. With a high concentration
of the KCl, there is weak DNA
bending. It has been found that
sharper the DNA bending occurs
when the concentration of the KCl
is less than the 100 mM, and the
IHF is not concentrated.
• INDEPENDENT
ASSORTMENT - The Principle of
the independent Assortment
describes how the different genes
independently separate from the
one another when the reproductive
cells develop. The Independent
assortment of the genes and their
corresponding traits was first
observed by the Gregor Mendel in
the year 1865 during his studies of
the genetics in the pea plants.
• IMMUNOGLOBULIN HEAVY
CONSTANT ALPHA 1 - The
© 2022 by JPS Scientific Publications, India
263
Immunoglobulin heavy constant
alpha 1 is a immunoglobulin gene
with the symbol IGHA1. It
encodes a constant (C) segment of
the Immunoglobulin A heavy
chain. The Immunoglobulin A is
an antibody that plays a critical
role in the immune function in the
shows the same typical structure of
the other antibody classes, with the
two heavy chains and the two light
chains, and the four distinct
domains: one variable region, and
the three variable regions. As a
major class of the immunoglobulin
in the body secretions, IgA plays a
role in defending against the
infection, as well as preventing the
access of the foreign antigens to the
immunologic system. The Ig alpha-
1 chain C region is contained on
the first of the constant regions of
the IgA, and is composed of an
amino acid sequence 353 residues
long. The secondary structure
contained within this region is
dominated by the beta strands,
which define the four antiparallel
beta sheets. These antiparallel beta-
sheets are then sandwiched to form
the two beta-sandwiches, a typical
tertiary structure of the
immunoglobulin fold class. The
two beta sheets that comprise the
each beta-sandwich are joined by
an alpha helix on one of the side.
• IMMUNOGLOBULIN C2 SET
DOMAIN - The basic structure of
the immunoglobulin (Ig) molecules
is a tetramer of the two light chains
Glossary of Genetics
and the two heavy chains linked by
the disulphide bonds. There are the
two types of the light chains: kappa
and the lambda, each composed of
a constant domain (CL) and a
variable domain (VL). There are
five types of the heavy chains:
alpha, delta, epsilon, gamma and
the mu, all consisting of a variable
domain (VH) and the three (in
alpha, delta and gamma) or the
four (in epsilon and mu) constant
domains (CH1 to CH4). The Ig
molecules are the highly modular
proteins, in which the variable and
constant domains have clear,
conserved sequence patterns. The
structural studies have shown that
the these domains share a common
core Greek-key beta-sandwich
structure, with the types differing
in the number of the strands in the
beta-sheets as well as in their
sequence patterns. The C2-set
domains, which are Ig-like
domains resembling the antibody
constant domain. The C2-set
domains are found primarily in the
mammalian T-cell surface antigens
CD2 (Cluster of the Differentiation
2), CD4 and CD80, as well as in
the vascular (VCAM) and the
intercellular (ICAM) cell adhesion
molecules.
• IMMUNOGLOBULIN V SET
DOMAIN - The V-set domains are
Ig-like domains resembling the
antibody variable domain. The V-
set domains are found in the
diverse protein families, including
the immunoglobulin light and the
© 2022 by JPS Scientific Publications, India
264
heavy chains; in several T-cell
receptors such as the CD2 (Cluster
of the Differentiation 2), CD4,
CD80, and CD86; in the myelin
membrane adhesion molecules; in
the junctional adhesion molecules
(JAM); in the tyrosine-protein
kinase receptors; and in the
programmed cell death protein 1
(PD1).
• IMMUNOGLOBULIN C1 SET
DOMAIN - The C1-set domains
are the classical Ig-like domains
resembling the antibody constant
domain. TheC1-set domains are
found almost exclusively in the
molecules involved in the immune
system, such as in the
immunoglobulin light and heavy
chains, in the major
histocompatibility complex (MHC)
class I and II complex molecules,
and in the various T-cell receptors.
• IMMOBILIZED METAL
AFFINITY
CHROMATOGRAPHY - The
Immobilized metal affinity
chromatography (IMAC) is the
most widely used method to purify
the proteins according to their
affinity to the specific metal ions,
which was first introduced by the
scientists named as the Porath
(1989). This involves the use of the
phosphate affinity metals which
are the chelated on the resin or the
beads and packed in a column. The
metal is attached to the resin
through a linker and the most
commonly used linker molecules
are the nitrilotriacetic acid and the
Glossary of Genetics
iminodiacetic acid. The Metals
such as the Fe2 + or the Ga3 + are
chelated on a matrix which is
made of the silica or the agarose to
hold the positively charged ions, to
which the negatively charged
phosphate ions interact. The
protein is incubated with the
matrix at the room temperature
and washed with the mixture of the
methanol and the water. The
Bound peptides are released with
the excess amount of the sodium
phosphate or the ammonium
phosphate.
• ICR - The imprinting control
region (ICR) located far upstream
of the H19 gene, in conjunction
with the enhancers, modulates the
transcription of the Igf2 and the
H19 genes in an allele-specific
manner. On the paternal
inheritance, the methylated ICR
silences the H19 gene and
indirectly facilitates the
transcription from the distant Igf2
promoter, whereas on the maternal
chromosome the unmethylated
ICR, together with the enhancers,
activates transcription of the H19
gene and thereby contributes to the
repression of the Igf2. This
repression of the maternal Igf2 has
recently been postulated to be due
to a chromatin boundary or the
insulator function of the
unmethylated ICR. Central to the
insulator model is the site-specific
binding of a ubiquitous nuclear
factor CTCF which exhibits the
remarkable flexibility in
© 2022 by JPS Scientific Publications, India
265
functioning as the transcriptional
activator or the silencer.
• IRES - An internal ribosome entry
site, abbreviated as the IRES, is an
RNA element that allows for the
translation initiation in a cap-
independent manner, as part of the
greater process of the protein
synthesis. In the eukaryotic
translation, the initiation typically
occurs at the 5' end of the mRNA
molecules, since the 5' cap
recognition is required for the
assembly of the initiation complex.
The location for the IRES elements
is often in the 5'UTR, but can also
occur elsewhere in the mRNAs.
The IRESs are often used by the
viruses as a means to ensure that
the viral translation is active when
host translation is inhibited. These
mechanisms of the host translation
inhibition are varied, and can be
initiated by the both virus and host,
depending on the type of the virus.
However, in the case of the most
picornaviruses, such as the
poliovirus, this is accomplished by
the viral proteolytic cleavage of the
eIF4G so that it cannot interact
with the 5'cap binding protein
eIF4E.
• INVERTED REPEATS - An
inverted repeat (or the IR) is a
single stranded sequence of the
nucleotides followed downstream
by its reverse complement. The
intervening sequence of the
nucleotides between the initial
sequence and the reverse
complement can be any length
Glossary of Genetics
including the zero. For example,
the 5'---TTACGnnnnnnCGTAA---
3' is an inverted repeat sequence.
When the intervening length is
zero, the composite sequence is a
palindromic sequence. Inverted
repeats have a number of
important biological functions.
They define the boundaries
in transposons and indicate regions
capable of self-complementary base
pairing (regions within a single
sequence which can base pair with
each other). These properties play
an important role in genome
instability[7] and contribute not
only to cellular
evolution and genetic
diversity[8] but also
to mutation and disease.[9] In order
to study these effects in detail, a
number of programs and databases
have been developed to assist in
discovery and annotation of the
inverted repeats in the various
genomes.
• INTEGRASE ENZYME - The
Retroviral integrase (IN) is an
enzyme produced by the retrovirus
(such as the HIV) that integrates or
forms the covalent links between
its genetic information into that of
the host cell it infects. The
Retroviral INs are not to be
confused with the phage integrases
(recombinases) used in the
biotechnology, such as the λ phage
integrase, as discussed in the site-
specific recombination. The main
function of the IN is to insert the
viral DNA into the host
© 2022 by JPS Scientific Publications, India
266
chromosomal DNA, an essential
step for the HIV replication. The
integration is a "point of no return"
for the cell, which becomes the
permanent carrier of the viral
genome i.e the provirus. The
Integration is in part responsible
for the persistence of the retroviral
infections. After the integration,
the viral gene expression and the
particle production may take place
immediately or at some point in
the future.
• IDEAOVIRUS - The Idaeovirus is
a genus of the positive-sense
ssRNA viruses that contains the
two species i.e the Raspberry bushy
dwarf virus (RBDV) and the Privet
idaeovirus. The RBDV has the two
host-dependent clades: one for the
raspberries; the other for the
grapevines. The infections are a
significant agricultural burden,
resulting in the decreased yield and
the quality of the crops. The
RBDV has a synergistic relation
with the Raspberry leaf mottle
virus, with the co-infection greatly
amplifying the concentration of the
virions in the infected plants. The
virus is transmitted via the
pollination with the RBDV-
infected pollen grains that first
infect the stigma before causing the
systemic infection. The RBDV is
non-enveloped with an isometric
protein coat about 33 nanometres
in the diameter. Inside the protein
coat is the viral genome, which is
bipartite, with the RNA strands
referred to as the RNA-1 and the
Glossary of Genetics
RNA-2. The RNA-1 is about 5,449
nucleotides in the length and
contains one open reading frame
(ORF) that encodes for a combined
protein that has the
methyltransferase, helicase, and an
RNA-dependent RNA polymerase
domains. The RNA-2 is 2,231
nucleotides in length and contains
the two ORFs, one at the 5' end
and the other at the 3' end.
• INTERACTOME - An
interactome is a complex
representation of the functional
interactions between thevmolecules
either within a cell or within the
organism as a whole. Often the
such interactomes reveal the
important interactions between the
molecules that at first would not
appear to be functionally related.
In this way, the functional
consequences of the genetic
mutation can be predicted without
the need for the lengthy
experimentation. An RPGR
interactome has also been
proposed. The RPGR is a
component of the centrioles, ciliary
axonemes, and the microtubular
transport complexes, although its
precise function is unknown. It
colocalizes with RPGRIP1 at the
axonemes of the connecting cilia in
the rod and the cone
photoreceptors503 by binding to
the RPGRIP1. This localization is
lost in the Rpgrip1 knockout (KO)
mice. The Rpgr KO mice develop a
slow retinal degeneration, with the
features resembling a cone–rod
© 2022 by JPS Scientific Publications, India
267
degeneration – cone
photoreceptors degenerate faster
than the rods and there is partial
mislocalization of the cone opsins.
Some of the residual RpgrORF15
expression has been reported in
this model. The RPGR has been
shown to co-immunoprecipitate in
the retinal extracts with a number
of the different axonemal, basal
body, and the microtubular
transport proteins.
• IGHV - The Ig heavy chain V-III
region VH26 is a protein that in the
humans is encoded by the IGHV@
gene. The IGHV is the
immunoglobulin heavy chain
variable region genes; in the B-cell
neoplasms like the chronic
lymphocytic leukemia, mutations
of the IGHV are associated with
the better responses to some of the
treatments and with the prolonged
survival.
• IPTG - The Isopropyl β-d-1-
thiogalactopyranoside (IPTG) is a
molecular biology reagent. This
compound is a molecular mimic of
the allolactose, a lactose metabolite
that triggers the transcription of the
lac operon, and it is therefore used
to induce the protein expression
where the gene is under the control
of the lac operator. The IPTG
binds to the lac repressor and
releases the tetrameric repressor
from the lac operator in an
allosteric manner, thereby allowing
the transcription of the genes in the
lac operon, such as the gene coding
for the beta-galactosidase, a
Glossary of Genetics
hydrolase enzyme that catalyzes
the hydrolysis of the β-galactosides
into the monosaccharides. But
unlike the allolactose, the sulfur (S)
atom creates a chemical bond
which is the non-hydrolyzable by
the cell, preventing the cell from
the metabolizing or degrading the
inducer. Therefore, its
concentration remains constant
during the experiment.
• ION EXCHANGE
CHROMATOGRAPHY - The
Ion chromatography (or the ion-
exchange chromatography)
separates the ions and the polar
molecules based on their affinity to
the ion exchanger. It works on
almost any kind of the charged
molecule—including the large
proteins, small nucleotides, and the
amino acids. However, ion
chromatography must be done in
the conditions that are one unit
away from the isoelectric point of a
protein. The Ion-exchange
chromatography separates the
molecules based on their respective
charged groups. The Ion-exchange
chromatography retains the analyte
molecules on the column based on
the coulombic (ionic) interactions.
The ion exchange chromatography
matrix consists of the positively
and the negatively charged ions.
Essentially, the molecules undergo
the electrostatic interactions with
the opposite charges on the
stationary phase matrix. The
stationary phase consists of an
immobile matrix that contains the
© 2022 by JPS Scientific Publications, India
268
charged ionizable functional
groups or the ligands. The
stationary phase surface displays
the ionic functional groups (R-X)
that interact with the analyte ions
of the opposite charge.
• IRE - In the field of the molecular
biology, the iron response element
or the iron-responsive element
(IRE) is a short conserved stem-
loop which is bound by the iron
response proteins (IRPs, also
named as the IRE-BP or the
IRBP). The IRE is found in the
UTRs (untranslated regions) of the
various mRNAs whose products
are involved in the iron
metabolism. For example, the
mRNA of the ferritin (an iron
storage protein) contains one IRE
in its 5' UTR. When the iron
concentration is low, the IRPs bind
the IRE in the ferritin mRNA and
cause the reduced translation rates.
In contrast, the binding to the
multiple IREs in the 3' UTR of the
transferrin receptor (involved in the
iron acquisition) leads to increased
the mRNA stability.
• ISOACCEPTING TRNAs - The
term “isoacceptor tRNA” is used
for the chemically different species
of the tRNA which are acylated by
the same amino acid. It is clear
that the degeneracy of the genetic
code requires the presence of the
isoacceptor tRNA’s. Analysis of
the tRNA by the counter current
distribution, MAK columns, BD-
cellulose columns and the 2
reversed phase chromatography
Glossary of Genetics
has shown, however, that the
number of the isoacceptor tRNA’s
is greater than would be predicted
from the genetic code. Isoacceptors
are tRNAs that have different
anticodons but still carry the same
amino acid. Mutations in the
anticodon site can generate new
isoacceptor tRNA families.
• ISOLEUCINE – The Isoleucine
(symbol Ile or the I) is an α-amino
acid that is used in the biosynthesis
of the proteins. It contains the α-
amino group (which is in the
protonated −NH+ 3 form under
biological conditions), an α-
carboxylic acid group (which is in
the deprotonated −COO− form
under the biological conditions),
and a hydrocarbon side chain with
a branch (a central carbon atom
bound to the three other carbon
atoms). It is classified as a non-
polar, uncharged (at physiological
pH), branched-chain, aliphatic
amino acid. It is essential in the
humans, meaning the body cannot
synthesize it, and must be ingested
in our diet. The Isoleucine is
synthesized from the pyruvate
employing the leucine biosynthesis
enzymes in the other organisms
such as the bacteria. It is encoded
by the codons such as the AUU,
AUC, and the AUA.
• ISOLEUCINE TRNA LIGASE -
In the field of enzymology, an
isoleucine—tRNA ligase is an
enzyme that catalyzes the chemical
reaction. This enzyme belongs to
the family of the ligases, to be
© 2022 by JPS Scientific Publications, India
269
specific those forming the carbon-
oxygen bonds in the aminoacyl-
tRNA and the related compounds.
The systematic name of this
enzyme class is the L-
isoleucine:tRNAIle ligase (AMP-
forming). Other names in common
use include the isoleucyl-tRNA
synthetase, isoleucyl-transfer
ribonucleate synthetase, isoleucyl-
transfer RNA synthetase,
isoleucine-transfer RNA ligase,
isoleucine-tRNA synthetase, and
the isoleucine translase. This
enzyme participates in the valine,
leucine and the isoleucine
biosynthesis and the aminoacyl-
trna biosynthesis.
• IF2 - The Initiation Factor 2 binds
to an initiator tRNA and controls
the entry of the tRNA onto the
ribosome. The IF2, bound to the
GTP, binds to the 30S P site. After
associating with the 30S subunit,
the fMet-tRNAf binds to the IF2
then the IF2 transfers the tRNA
into the partial P site. When the
50S subunit joins, it hydrolyzes the
GTP to the GDP and Pi, causing a
conformational change in the IF2
that causes the IF2 to release and
allow the 70S ribosome to form.
The Human mitochondria use a
nuclear-encoded homolog, MTIF2,
for the translation initiation
process.
• IF3 - In the field of the molecular
biology, the translation initiation
factor IF-3 (gene infC) is one of the
three factors required for the
initiation of the protein
Glossary of Genetics
biosynthesis in the bacteria. The
IF-3 is thought to function as a
fidelity factor during the assembly
of the complex which is known as
the ternary initiation complex
consists of the 30S ribosomal
subunit, the initiator tRNA and the
messenger RNA. The IF-3 is a
basic protein that binds to the 30S
ribosomal subunit. The homolog of
chloroplasts enhances the
poly(A,U,G)-dependent binding of
the initiator tRNA to the its
ribosomal 30s subunits. The IF1–
IF3 may also perform the ribosome
recycling.
• IGF2 - The Insulin-like growth
factor 2 (IGF-2) is one of the three
protein hormones that share the
structural similarity to the insulin.
It is a neutral peptide and a well-
characterized believed to be
secreted by the liver and to
circulate in the blood. It has
growth-regulating, insulin-like and
the mitogenic activities. The
growth factor has a major, but not
the absolute, dependence on the
somatotropin. It is believed to be a
major fetal growth factor in
contrast to the insulin-like growth
factor 1 (IGF-1), which is a major
growth factor in the adults. The
major role of the IGF-2 is as a
growth promoting hormone during
the gestation. The IGF-2 exerts its
effects by binding to the IGF-1
receptor and to the short isoform of
the insulin receptor (IR-A or exon
11-). The IGF-2 may also bind to
the IGF-2 receptor (also called as
© 2022 by JPS Scientific Publications, India
270
the cation-independent mannose 6-
phosphate receptor), which acts as
a signalling antagonist; that is to
prevent the IGF-2 responses.
• IGF1 - The Insulin-like growth
factor 1 (IGF-1), also called as the
somatomedin C, is a hormone
similar in the molecular structure
to the insulin which plays an
important role in the childhood
growth, and has anabolic effects in
the adults. The IGF-1 is a protein
that in humans is encoded by the
IGF1 gene. The IGF-1 consists of
around 70 amino acids in a single
chain with the three intramolecular
disulfide bridges. The IGF-1 has a
molecular weight of around 7,649
Daltons. In the dogs, an ancient
mutation in the IGF1 is the
primary cause of the toy
phenotype. The IGF-1 is produced
primarily by the liver. The
Production is stimulated by the
growth hormone (GH). Most of
the IGF-1 is bound to one of the 6
binding proteins (IGF-BP). The
IGFBP-1 is regulated by the
insulin. The IGF-1 is produced
throughout the life, the highest
rates of the IGF-1 production
occur during the pubertal growth
spurt. The lowest levels occur in
the infancy and in the old age. A
synthetic analog of the IGF-1,
mecasermin, is used in the children
for the treatment of the growth
failure.
• IHF - The Integration host factor
(IHF) is a small heterodimeric
protein that binds to the DNA and
Glossary of Genetics
induces a large bend (upto 180°),
which is critical for mediating the
long range interactions. The Major
processes such as the transcription,
replication, site-specific
recombination and the
transposition involve IHF,
although the exact role of tye
environmental conditions in
regulating its function is still
unclear. The IHF has been
implicated in the transcription
activation of the various aromatic
degradation genes such as the dmp
operon of the Pseudomonas sp.
strain CF600, the upper operon for
the xylene degradation in P. putida
mt-2, the phenylacetic acid
degradation in the E. coli and the
phenol degradation genes in the
Acinetobacter calcoaceticus
NCIB8250.
• IMAGINAL DISCS - The
imaginal disc is one of the parts of
a holometabolous insect larva that
will become a portion of the
outside of the adult insect during
the pupal transformation. The
Contained within the body of the
larva, there are pairs of the discs
that will form, for instance, the
wings or the legs or the antennae
or the other structures in the adult.
The role of the imaginal disc in the
insect development was first
elucidated by the Jan
Swammerdam. The study of the
imaginal discs in the fruit fly
Drosophila melanogaster led to the
discovery of the homeotic
mutations such as the
© 2022 by JPS Scientific Publications, India
271
antennapedia, where the
developmental fate of a disc could
sometimes change. It is of interest
to entomologists that the kinds of
the developmental switches that
occur are very specific (leg to
antenna, for instance). The Study
of this phenomenon led to the
discovery of the homeobox genes,
and started a revolution in the
understanding of the development
in the multi-celled animals.
• IMAC - The Immobilized metal
affinity chromatography (IMAC) is
a protein separation method based
on the interaction between the
proteins in the solution and in the
transition metal ions fixed to a
solid support. The specificity of the
separation is determined by the
occurrence and position of the
metal-coordinating residues on the
protein surface. The exposed
histidines and the cysteines, when
present, are the most important
metal-coordinating ligands at the
neutral pH. When such ligands are
in a sufficient number and are
accessible, the protein can be
efficiently purified from a complex
mixture. The proteins produced
through the recombinant DNA
technology can be engineered to
have high affinity for the metal ion
by adding a sequence of the poly-
histidines at the N-terminal
position, and thus can be easily
purified . The interactions of the
histidines with the metal ions are
sensitive to the variations of the
polypeptide chain conformation.
Glossary of Genetics
• IAC - The Immunoaffinity
chromatography (IAC) combines
the use of the LC with the specific
binding of the antibodies or the
related agents. The resulting
method can be used in the assays
for a particular target or for the
purification and the concentration
of the analytes prior to the further
examination by another technique.
The supports and the
immobilization methods used with
the antibodies in the IAC and the
selection of the application and the
elution conditions for the IAC are
also discussed. Several applications
of the IAC are considered,
including its use in the purification,
immunodepletion, direct sample
analysis, chromatographic
immunoassays and the combined
analysis methods. The Recent
developments include the use of
the IAC with the CE or the MS,
ultrafast immunoextraction
methods and the use of the
immunoaffinity columns in the
microanalytical systems.
• IMMUNOPRECIPITATION - others (products). In most of the
The Immunoprecipitation (IP) is
the technique of the precipitating a
protein antigen out of the solution
using an antibody that specifically
binds to that particular protein.
This process can be used to isolate
and concentrate a particular
protein from the sample containing
many of the thousands of different
types of proteins. The
immunoprecipitation requires that
the antibody be coupled to a solid
© 2022 by JPS Scientific Publications, India
272
substrate at some point in the
procedure. Immunoprecipitation is
one of the most widely used
methods for isolation of the
proteins and the other
biomolecules from the cell or the
tissue lysates for the purpose of the
subsequent detection by the
western blotting and the other
assay techniques. The principle of
thr immunoprecipitation relies on
the recognition of a target protein
antigen by a specific antibody. In
order for the antibody-protein
complex to precipitate out of
solution, it must be bound to a
solid-state material.
• INBORN ERRORS OF
METABOLISM - The Inborn
errors of metabolism form a large
class of the genetic diseases
involving the congenital disorders
of th3 enzyme activities. The
majority are due to the defects of
single genes that code for the
enzymes that facilitate the
conversion of the various
substances (substrates) into the
disorders, the problems arise due to
the accumulation of the substances
which are toxic or interfere with
the normal function, or due to the
effects of the reduced ability to
synthesize the essential
compounds. The inborn errors of
the metabolism are now often
referred to as the congenital
metabolic diseases or the inherited
metabolic disorders. To this
concept it's possible to include the
Glossary of Genetics
new term of the Enzymopathy.
This term was created following
the study of the Biodynamic
Enzymology, a science based on
the study of the enzymes and their
derivated products.
• IPS CELLS - The Induced
pluripotent stem cells (which is
also known as the iPS cells or the
iPSCs) are a type of the pluripotent
stem cell that can be generated
directly from a somatic cell. The
Pluripotent stem cells hold promise
in the field of the regenerative
medicine. Because they can
propagate indefinitely, as well as
give rise to the every other cell type
in the body (such as the neurons,
heart, pancreatic, and the liver
cells), they represent a single
source of the cells that could be
used to replace the those lost to
damage or the The most well-
known type of the pluripotent stem
cell is the embryonic stem cell.
However, since the generation of
the embryonic stem cells involves
the destruction (or at least the
manipulation) of the pre-
implantation stage embryo, there
has been much controversy
surrounding their use. The Patient-
matched embryonic stem cell lines
can now be derived using the
somatic cell nuclear transfer
(SCNT).
• INNER CELL MASS - In the
early embryogenesis of the
mammals, the inner cell mass
(ICM), (or the embryoblast),
(known as the pluriblast in the
© 2022 by JPS Scientific Publications, India
273
marsupials) is the mass of the cells
inside the primordial embryo that
will eventually give rise to the
definitive structures of the fetus.
This structure forms in the earliest
steps of the development, before
the implantation into the
endometrium of the uterus has
occurred. The ICM lies within the
blastocoele (more correctly termed
as the "blastocyst cavity", as it is
not strictly homologous to the
blastocoele of the anamniote
vertebrates) and is entirely
surrounded by the single layer of
the cells called as the trophoblast.
• INSERTION SEQUENCE - The
Insertion element (also known as
an IS, an insertion sequence
element, or the IS element) is a
short DNA sequence that acts as a
simple transposable element. The
Insertion sequences have the two
major characteristics: they are
small relative to the other
transposable elements (generally
around 700 to the 2500 bp in the
length) and only code for the
proteins implicated in the
transposition activity (they are thus
different from the other
transposons, which also carry the
accessory genes such as the
antibiotic resistance genes). These
proteins are usually known as the
transposase which catalyses the
enzymatic reaction allowing the IS
to move, and also one regulatory
protein which either stimulates or
inhibits the transposition activity.
The coding region in an insertion
Glossary of Genetics
sequence is usually flanked by the
inverted repeats. For example, the
well-known IS911 (1250 bp) is
flanked by the two 36bp inverted
repeat extremities and the coding
region has two genes partially
overlapping orfA and the orfAB,
coding the transposase (OrfAB)
and a regulatory protein (OrfA).
• INTERCALATING AGENTS -
The substance that inserts itself
into the DNA structure of a cell
and binds to the DNA. This causes
the DNA damage. In the cancer
treatment, the DNA intercalating
agents may kill the cancers cells by
damaging their DNA and stopping
them from the dividing process.
Intercalating agents are the
hydrophobic heterocyclic ring
molecules that resemble the ring
structure of the base pairs, and
include the ethidium bromide,
acridine orange, and the
actinomycin D. Insertion of these
agents distorts the DNA double
helix, thereby interfering with the
DNA replication, transcription,
and the repair.
• INTERACTOME - In the field of
the molecular biology, an
interactome is the whole set of the
molecular interactions in a
particular cell. The term
specifically refers to the physical
interactions among the molecules
(such as those among the proteins,
also known as the protein–protein
interactions, PPIs; or between the
small molecules and the proteins)
but can also describe the sets of the
© 2022 by JPS Scientific Publications, India
274
indirect interactions among the
genes (genetic interactions). In fact,
all the interactome types are
interconnected. For instance, the
protein interactomes contain many
enzymes which in turn form the
biochemical networks. Similarly,
the gene regulatory networks
overlap substantially with the
protein interaction networks and
the signaling networks.
• INTRAGENIC SUPPRESSION -
The Intragenic suppression results
from the suppressor mutations that
occur in the same gene as the
original mutation. In a classic
study, Francis Crick (et al.) used
the intragenic suppression to study
the fundamental nature of the
genetic code. The Researchers
showed that the mutations caused
by either a single base insertion (+)
or a single base deletion (-) could
be "suppressed" or restored by a
second mutation of the opposite
sign, as long as the two mutations
occurred in the same vicinity of the
gene. This led to the conclusion
that the genes needed to be read in
a specific "reading frame" and a
single base insertion or the deletion
would shift the reading frame
(frameshift mutation) in such a
way that the remaining DNA
would code for a different
polypeptide than the one intended.
Therefore, the researchers
concluded that the second
mutation of the opposite sign
suppresses the original mutation by
restoring the reading frame, as long
Glossary of Genetics
as the portion between the two
mutations is not critical for the
proteins function.
• known that, in the certain cases,
• INTERGENIC SUPPRESSION -
The Intergenic (also known as the
extragenic) suppression relieves the
effects of the mutation in one gene
by a mutation somewhere else
within the genome. The second
mutation is not on the same gene
as the original mutation. The
Intergenic suppression is useful for
identifying and studying the
interactions between the
molecules, such as the proteins.
For example, the mutation which
disrupts the complementary
interaction between the protein
molecules may be compensated for
by a second mutation elsewhere in
the genome that restores or
provides the suitable alternative
interaction between the those
molecules. Several proteins of the
biochemical, the signal
transduction, and the gene
expression pathways have been
identified using this approach.
Examples of such pathways
include the receptor-ligand
interactions as well as the
interaction of the components
involved in the DNA replication,
transcription, and in the
translation.
• IRESSs - The Internal ribosomal
entry sites (IRESs) are the regions
in the mRNAs that allow the
internal initiation of the
translation. Indeed, even though
© 2022 by JPS Scientific Publications, India
275
the vast majority of the cellular
mRNAs are translated by the cap-
dependent mechanisms, it is now
translation can also occur in the
cap-independent manner, thanks to
the specific mRNA sequences able
to recruit the 40S ribosomal
subunit in the vicinity of an AUG
starting The first IRES was
identified in the genome of the
poliovirus (PV) and the
encephalomyocarditis virus
(EMCV), and later in many of the
other viruses. During the infection,
the cap-dependent translation of
the cell is impaired, and the viral
RNAs use the internal initiation for
their gene expression. The Viral
IRESs are characterized by the
complex secondary and the tertiary
structures that allow them to
efficiently bind the 40S ribosomal
subunit. Moreover, they require
the little or the no binding to the
cellular eukaryotic initiation
factors. For example, in the
initiation promoted by the type 1
IRESs (such as the ones present in
the Poliovirus), the 43S ribosome is
recruited by an eIF4G/eIF4A
complex, whereas in the type 4
IRESs (e.g. , in the cricket paralysis
virus), no initiation factor is
needed to start the translation.
• ISE - The Exonic splicing
enhancers (ESEs) are the cis-acting
elements that activate the
definition of an otherwise weak
exon, promoting its inclusion into
the mature transcripts. Several
Glossary of Genetics
families of the ESEs have been
recognized, and the most common
are characterized by the purine-rich
sequences (consensus) and mediate
their action via the members of the
SR protein family. Although the
ESEs have been implicated in the
regulated splicing, they appear to
have a role in defining many of the
constitutive exons. The FGF-R2
IgIII alternative splicing unit does
not have the obvious ESEs .
• INTRINSIC AND EXTRINSIC
NOISE:-
• The Intrinsic noise is defined as the
stochasticity of the biochemical
interaction of the particles in the
gene expression process, while the
extrinsic noise is generated from
the other cellular processes or from
the environmental fluctuation.
• INTRINSIC TERMINATION -
The intrinsic, or the rho-
independent termination, is a
process in the prokaryotes to signal
the end of the transcription and
release of the newly constructed
RNA molecule. In the prokaryotes
such as the E. coli, transcription is
terminated either by a rho-
dependent process or the rho-
independent process. In the Rho-
dependent process, the rho-protein
locates and binds the signal
sequence in the mRNA and signals
for the cleavage. The Contrarily,
the intrinsic termination does not
require a special protein to signal
for the termination and is
controlled by the specific sequences
of the RNA. When the termination
© 2022 by JPS Scientific Publications, India
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process begins, the transcribed
mRNA forms a stable secondary
structure hairpin loop, also known
as the Stem-loop. This RNA
hairpin is followed by the multiple
uracil nucleotides. The bonds
between the uracil and the adenine
are very weak. A protein bound to
the RNA polymerase (nusA) binds
to the stem-loop structure tightly
enough to cause the polymerase to
temporarily stall. This pausing of
the polymerase coincides with the
transcription of the poly-uracil
sequence. The weak adenine-uracil
bonds lower the energy of the
destabilization for the RNA-DNA
duplex, allowing it to unwind and
dissociate from the RNA
polymerase. Overall, the modified
RNA structure is what terminates
the transcription.
• ION EXCHANGE
CHROMATOGRAPHY - The
Ion chromatography or the ion-
exchange chromatography
separates the ions and the polar
molecules based on their affinity to
the ion exchanger. It works on
almost any kind of the charged
molecule including the large
proteins, small nucleotides, and the
amino acids. However, the ion
chromatography must be done in
the conditions that are one unit
away from the isoelectric point of a
protein. One of the primary
advantages for the use of the ion
chromatography is only one
interaction involved during the
separation as opposed to the other
Glossary of Genetics
separation techniques. Therefore,
the ion chromatography may have
the higher matrix tolerance.
Another advantage of the ion
exchange is the predictability of the
elution patterns based on the
presence of the ionizable group.
However, there are also
disadvantages involved when
performing the ion-exchange
chromatography, such as the
constant evolution with the
technique which leads to the
inconsistency from the column to
column. A major limitation to this
purification technique is that it is
limited to the ionizable group.
• INTERGENIC SEQUENCES -
An intergenic region (IGR) is a
stretch of the DNA sequences
located between the genes. The
Intergenic regions may also
contain the functional elements
and the junk DNA. The intergenic
regions are the different from the
intragenic regions or the introns,
which are the short, non-coding
regions that are found within the
genes, especially within the genes
of the eukaryotic organisms.
According to the project which is
known as the ENCODE project’s
study of the human genome, due to
“both the expansion of the genic
regions by the discovery of the new
isoforms and the identification of
the novel intergenic transcripts,
there has been a marked increase
in the number of the intergenic
regions due to their fragmentation
and a decrease in their structure.
© 2022 by JPS Scientific Publications, India
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The Scientists have now artificially
synthesized proteins from
intergenic regions. The Intergenic
regions contain a number of the
functional DNA sequences such as
the promoters and the regulatory
elements and the centromeres.
They may also contain the origins
of the replication, scaffold
attachment regions, transposons
and the viruses. The Non-
functional DNA elements such as
the pseudogenes, repetitive DNA,
and the junk DNA can also be
found in the intergenic regions
although they may also be located
within the genes in the introns.
The Intergenic regions may
contain as yet the unidentified
functional elements such as the
non-coding RNA genes or the
regulatory sequences.
• INSERTION - In the field of the
genetics, an insertion which is also
called as an the insertion mutation
is the addition of the one or more
than one nucleotide base pairs into
a DNA sequence. This can often
happen in the microsatellite
regions due to the DNA
polymerase slipping. The
Insertions can be anywhere in the
size from one base pair incorrectly
inserted into a DNA sequence to a
section of the one chromosome
inserted into the another. The
mechanism of the smallest single
base insertion mutations is
somewhat believed to be the
through base-pair separation
between the template and the
Glossary of Genetics
primer strands followed by the
non-neighbor base stacking, which
can occur locally within the DNA
polymerase active site. On a
chromosome level, an insertion is
refers to the insertion of a larger
sequence into a chromosome. This
can happen due to the unequal
crossover during the meiosis. The
insertions can be particularly
hazardous if they occur in an exon,
the amino acid coding region of a
gene. A frameshift mutation, an
alteration in the normal reading
frame of a gene, results if the
number of the inserted nucleotides
is not divisible by the three, i.e. the
number of the nucleotides per
codon. The Frameshift mutations
will alter all the amino acids
encoded by the gene following the
mutation.
• INTRINSIC AND EXTRINSIC
NOISE - The Cellular noise is
often investigated in the framework
of the intrinsic and the extrinsic
noise. The intrinsic noise refers to
the variation in the identically-
regulated quantities within a single
cell, for example, the intra-cell
variation in the expression levels of
the two identically-controlled
genes. The Extrinsic noise refers to
the variation in the identically-
regulated quantities between the
different cells, for example, the
cell-to-cell variation in the
expression of a given gene. The
Intrinsic and the extrinsic noise
levels are often compared in the
dual reporter studies, in which the
© 2022 by JPS Scientific Publications, India
278
expression levels of the two
identically-regulated genes (often
fluorescent reporters like the GFP
and the YFP) are plotted for each
of the cell in a population. An issue
with the general depiction of the
extrinsic noise as a spread along
the main diagonal in the dual-
reporter studies is the assumption
that the extrinsic factors cause the
positive expression correlations
between the two reporters. In fact,
when the two reporters compete
for binding of a low-copy
regulator, the two reporters
become anomalously
anticorrelated, and the spread is
perpendicular to the main
diagonal. In fact, any deviation of
the dual-reporter scatter plot from
the circular symmetry indicates the
extrinsic noise. The information
theory offers a way to avoid this
anomaly.
• INVERSION - An inversion is the
chromosome rearrangement in
which a segment of a chromosome
is reversed in the end-to-end
direction. An inversion occurs
when a single chromosome
undergoes the breakage and the
rearrangement within itself. The
inversions are of the two types:
paracentric and the pericentric.
The Paracentric inversions do not
include the centromere, and both
breaks occur in one arm of the
chromosome. The pericentric
inversions include the centromere,
and there is a break point in each
of the arm. The Inversions usually
Glossary of Genetics 279

do not cause any of the known meteorite, which fell near

abnormalities in the carriers, as Murchison in Australia, in 1969,
long as the rearrangement is and meteorite NWA 801, which
balanced, with no extra or the was discovered in Morocco in
missing DNA. However, in the 2001, it reveals that they carry
individuals which are the small amount of ribose and trace
heterozygous for an inversion, amount of other sugars such as
there is an increased production of xylose and arabinose. Since ribose
the abnormal chromatids (this is an crucial part of RNA molecule
occurs when the crossing-over it is known to be that RNA has
occurs within the span of the been came from space.
inversion). This leads to lowered
the fertility, due to the production
of the unbalanced gametes. An
inversion does not involve a loss of
the genetic information, but simply
rearranges the linear gene
sequence. The Human families that
may be carriers of the inversions
may be offered genetic counseling
and the genetic testing.
• INITITAIORS PROTEINS - The
initiator proteins are the proteins
that recognize a specific DNA
sequence within the origin of the
replication process. The origin of
replication is the site where the
enzyme known as helicase attaches
to the template strand and starts to
unwind the DNA into two strands.
The activities that are provided by
the initiator proteins range from
the recognition of the ori site and
recruitment of the replication
factors, to the he melting of
double-stranded DNA and
replicative DNA-helicase activity.
• INCORPATION OF RNA IN
MURCHISON METEORITE - A
powder was collected from two
ancient meteorites: the Murchison

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
J •
• JACOB AND MONAD
EXPERIMENT - The Monod and
Jacob became the famous scientists
for their work on the E. Coli lac
operon, which encodes the proteins
necessary for the transport and the
breakdown of the sugar lactose
(lac). From their own work and the
work of others, they came up with
a model for how the levels of some
proteins in a cell are controlled in
the Manner. In their model, the
manufacture of the proteins, such
as the ones encoded within the lac
(lactose) operon, is prevented when
a repressor, encoded by a
regulatory gene, it binds to its
operator, a very important specific
site in the DNA sequence that is
close to the genes encoding into the
proteins. It is now known that a
repressor bound to an operator
physically blocks the RNA
polymerase from binding to the
promoter, the site where the
transcription of the adjacent genes
begins. The Study of the control of
expression of genes in the lac
operon provided the first example
of a system for the regulation of
transcription. Monod also
suggested that the existence of the
messenger RNA molecules that
link the information encoded in the
DNA and proteins. For these
contributions in the field of
genetics and in biology he is widely
© 2022 by JPS Scientific Publications, India
280
regarded as one of the founders of
the molecular biology.
JNK1 GENE - The Mitogen-
activated protein kinase 8 (which is
also known as the JNK1) is a
ubiquitous enzyme that in the
humans is encoded by the MAPK8
gene. The protein encoded by this
gene is a member of the MAP
kinase and the JNK family. The
MAP kinases act as an integration
point for the multiple biochemical
signals, and are involved in a wide
variety of the cellular processes
such as the proliferation,
differentiation, transcription
regulation and the development.
This kinase is activated by the
various cell stimuli, and the targets
specific transcription factors, and
thus mediates the immediate-early
gene expression in response to the
cell stimuli. The activation of this
kinase by the tumor-necrosis factor
alpha (TNF-alpha) is found to be
required for the TNF-alpha-
induced apoptosis. This kinase is
also involved in the UV radiation-
induced apoptosis, which is
thought to be related to the
cytochrome c-mediated cell death
pathway. The MAPK8 contains
the multiple amino acid sites that
are phosphorylated and also
ubiquitinated.
• JUNK DNA - The Junk DNA"
refers broadly to any of the DNA
sequence that does not play a
functional role in the development,
physiology, or some of the other
organism-level capacity. The term
Glossary of Genetics 281

"junk DNA" was used in the year

1960s, but it only became widely
known in tye year 1972 in a paper
by the scientist Susumu Ohno.
Ohno noted that the mutational
load from the deleterious
mutations placed an upper limit on
the number of the functional loci
that could be expected given a
typical mutation rate. He
hypothesized that the mammalian
genomes could not have more than
30,000 loci under selection before
the "cost" from the mutational load
would cause an inescapable decline
in the fitness, and eventually
extinction. The presence of the
junk DNA also explained the
observation that even the closely
related species can have widely
(orders-of-magnitude) different
genome sizes (C-value paradox).

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
K footnote in a 1934 Cytology book
• KINETIC PROOFREADING -
The Kinetic proofreading (or the
kinetic amplification) is a •
mechanism for the error correction
in the biochemical reactions,
proposed independently by the
John Hopfield (1974) and the
Jacques Ninio (1975). The kinetic
proofreading allows the enzymes
to discriminate between the two
possible reaction pathways leading
to the correct or the incorrect
products with an accuracy higher
than what one would predict based
on the difference in the activation
energy between the these two
pathways. The Increased
specificity is obtained by
introducing an irreversible step
exiting the pathway, with the
reaction intermediates leading to
the incorrect products more likely
to prematurely exit the pathway
than the reaction intermediates
leading to the correct product.
• KINETOCHORE - The
kinetochore is a disc-shaped
protein structure associated with
the duplicated chromatids in the
eukaryotic cells where the spindle
fibers attach during the cell
division to pull the sisters
chromatids apart. The kinetochore
assembles on the centromere and
links the chromosome to the
microtubule polymers from the
mitotic spindle during the mitosis
and the meiosis. The term
© 2022 by JPS Scientific Publications, India
282
kinetochore was first used in a
by the Lester W. Sharp and
commonly accepted in the year
1936.
KLUVYVEROMYCES LACTIS
- The Kluyveromyces lactis is a
Kluyveromyces yeast commonly
used for the genetic studies and the
industrial applications. Its name
comes from the ability to assimilate
the lactose and convert it into the
lactic acid. The K. lactis is a
heterothallic species with a
predominantly haplontic cycle, in
contrast to the S. cerevisiae in
which the predominantly
diplobiontic cycle is the pseudo-
heterothallic due to the mating-
type switching. This species has
roughly around 5,300 genes spread
out over the six nuclear
chromosomes and its
mitochondrial genome. The six
chromosomes are labeled as the A-
F.
• KNIRPS GENE - The knirps gene
appears to be spontaneously
activated. It is repressed by the
hunchback. The Hunchback
repression thus defines the anterior
boundary of the knirps gene. Due
to the more efficient inhibition of
the knirps gene by the hunchback,
knirps is expressed more posterially
in the embryo compared to the
Krüppel. The Tailless protein
inhibits the knirps gene expression
in the posterior part of the embryo,
allowing the knirps protein to be
expressed only in the central part
Glossary of Genetics
of the embryo (but more posterior
compared to the Krüppel). This is
due to the ability of the both
hunchback and the tailless to bind
to the enhancer regions of the
knirps.
• KNOTTED DNA - The Knotted
DNA was found first by the Liu et
al. in the year 1981, in a single-
stranded, circular, bacterial DNA,
though the double-stranded
circular DNA has been found to
also form the knots. In the year
1989, Sauvage and coworkers
reported the first synthetic knotted
molecule, a trefoil synthesized via
a double-helix complex with the
aid of the Cu+ ions.
• KOZAK SEQUENCE - The
Kozak consensus sequence (Kozak
consensus or the Kozak sequence)
is a nucleic acid motif that
functions as the protein translation
initiation site in most of the
eukaryotic mRNA transcripts.
Regarded as the optimum sequence
for initiating the translation in the
eukaryotes, the sequence is an
integral aspect of the protein
regulation and the overall cellular
health as well as having the
implications in the human disease.
It ensures that a protein is correctly
translated from the genetic
message, mediating ribosome
assembly and the translation
initiation. A wrong start site can
result in the non-functional
proteins. As it has become more
studied, the expansions of the
nucleotide sequence, bases of the
© 2022 by JPS Scientific Publications, India
283
importance, and the notable
exceptions have arisen.
• KRUPPEL GENE - The Krüppel
is a gap gene in the Drosophila
melanogaster, which is located on
the 2R chromosome, which
encodes a zinc finger C2H2
transcription factor. The Gap genes
work together to establish the
anterior-posterior segment
patterning of the insect through the
regulation of the transcription
factor encoding pair rule genes.
These genes in turn regulate the
segment polarity genes. The
Krüppel means "cripple" in the
german, named for the crippled
appearance of the mutant larvae,
who have failed to develop the
proper thoracic and the anterior
segments in the abdominal region.
The Mutants can also have the
abdominal mirror duplications.
• KU 70 - The Ku70 is a protein that
in the humans, is encoded by the
XRCC6 gene. The Ku70 make up
the Ku heterodimer, which binds
to the DNA double-strand break
ends and is required for the non-
homologous end joining (NHEJ)
pathway of the DNA repair. It is
also required for the V(D)J
recombination, which utilizes the
NHEJ pathway to promote the
antigen diversity in the
mammalian immune system. In
addition to its role in the NHEJ,
Ku is also required for the telomere
length maintenance and the
subtelomeric gene silencing. The
Ku was originally identified when
Glossary of Genetics
the patients with the systemic lupus
erythematosus were found to have
high levels of the autoantibodies to
the protein.
• KU 80 - The Ku80 is a protein
that, in the humans, is encoded by
the XRCC5 gene. Together, the
ku70 and Ku80 make up the Ku
heterodimer, which binds to the
DNA double-strand break ends
and is required for the non-
homologous end joining (NHEJ)
pathway of the DNA repair. It is
also required for the V(D)J
recombination, which utilizes the
NHEJ pathway to promote the
antigen diversity in the
mammalian immune system. The
protein expression level of the
Ku80 can be repressed by the
epigenetic hypermethylation of the
promoter region of the gene
XRCC5 which encodes the Ku80.
In a study of the 87 matched pairs
of the primary tumors of non-
small-cell lung carcinoma and the
nearby normal lung tissue, 25% of
the tumors had loss of the
heterozygosity at the XRCC5 locus
and a similar percentage of the
tumors had hypermethylation of
the promoter region of the The
Low protein expression of the
Ku80 was significantly associated
with the low mRNA expression
and with the XRCC5 promoter
hypermethylation but not with the
LOH of the gene.
• KINEMAGE - A kinemage (short
for the kinetic image) is an
interactive graphic scientific
© 2022 by JPS Scientific Publications, India
284
illustration. It often is used to
visualize the molecules, especially
proteins although it can also
represent the other types of the 3-
dimensional data (such as the
geometric figures, social networks,
or the tetrahedra of the RNA base
composition). The kinemage
system is designed to optimize ease
of the use, interactive performance,
and the perception and
communication of the detailed 3D
information. The kinemage
information is stored in a text file,
human- and machine-readable,
that describes the hierarchy of the
display objects and their properties,
and includes the optional
explanatory text. The kinemage
format is a defined chemical
MIME type of the 'chemical/x-
kinemage' with the file extension
'.kin'.
• KMT 2C - The Lysine N-
methyltransferase 2C (KMT2C)
also known as the
myeloid/lymphoid or thr mixed-
lineage leukemia protein 3 (MLL3)
is an enzyme that in the humans is
encoded by the KMT2C gene. This
gene is a member of the
myeloid/lymphoid or the mixed-
lineage leukemia (MLL) family
and encodes a nuclear protein with
an AT-hook DNA-binding
domain, a DHHC-type zinc finger,
six PHD-type zinc fingers, a SET
domain, a post-SET domain and a
RING-type zinc finger. This
protein is a member of the ASC-
2/NCOA6 complex (ASCOM),
Glossary of Genetics 285

which possesses the histone

methylation activity and is
involved in the transcriptional
coactivation. The Alternate
transcriptional splice variants,
encoding the different isoforms,
have been characterized.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
L the prophage. When the bacterium
• LYSOGENIC CYCLE - The
Lysogeny, or the lysogenic cycle, is
one of the two cycles of the viral
reproduction. Lysogeny is
characterized by the integration of
the bacterial affecting virus known
as bacteriophage. The
obacteriophage nucleic acid is
integrated into the host bacterium’s
genome or the formation of a
circular replicon in the bacterial
cytoplasm. In this condition the
bacterium continues to live and
reproduce normally in the
bacterium, while the bacteriophage
lies in a dormant state in the host
cell. The genetic material of the
bacteriophage, which is called a
prophage, can be transmitted to the
daughter cells at each subsequent
cell division process and later
events such as UV radiation or the
presence of certain chemicals and
can release it, causing the
proliferation of the new phages via
the lytic cycle. The Lysogenic
cycles can also occur in the
eukaryotes, although the method
of DNA incorporation is not fully
understood yet. For the instance
the AIDS viruses can either infect
the humans or some other primates
lytically, or lay the dormant
lysogenic as part of the infected
cells’ genome, keeping the ability
to return to the lysis at a later time.
In the lysogenic cycle, the phage
DNA first integrates into the
© 2022 by JPS Scientific Publications, India
286
bacterial chromosome to produce
reproduces, the prophage is also
copied and it is present in each of
the daughter cells. The daughter
cells can also continue to replicate
with the prophage present or the
prophage can exit the bacterial
chromosome to initiate the lytic
cycle. In the lysogenic cycle the
host DNA is not hydrolyzed but in
the lytic cycle the host DNA is
hydrolyzed in the lytic phase.
• LEAKY SCANNING - The
Leaky scanning is a mechanism
used during the initiation phase of
the eukaryotic translation that
enables the regulation of the gene
expression. During the initiation,
the small 40S ribosomal subunit (as
a 43S PIC) "scans" or moves in a 5'
--> 3' direction along the 5'UTR to
locate a start codon to commence
the elongation. Sometimes, the
scanning ribosome bypasses the
initial AUG start codon and begins
the translation at further
downstream AUG start codons.
The Translation in the eukaryotic
cells according to the most
scanning mechanisms occurs at the
AUG start codon proximal to the
5' end of the mRNA; however, the
scanning ribosome may encounter
an “unfavorable nucleotide
context” around the start codon
and continue scanning. There are
certain instances where the
initiation has been found to occur
upstream at a non-AUG codon.
The Eukaryotic genes containing
Glossary of Genetics
consistent G-C rich leader
sequences are frequently observed
performing this mechanism. It is
hypothesized that scanning is
slowed due to a secondary
structure which allows for the
binding of Met-tRNA with the
mismatch codon.
• LABELLING - In the field of the
genetic the labeling, once a gene of
the interest is identified, the
cDNAs coding for the FPs can be
inserted at any of the desired
location of the endogenous gene X
through the gene targeting. Since
the FP cDNA is embedded in the
native of the chromatin
environment with its regulatory
elements largely intact, the FP
expression often precisely and
reliably recapitulates the
expression of the gene X.
• LOOPING - The R-loop is a three-
stranded nucleic acid structure,
composed of a DNA:RNA hybrid
and the associated non-template
single-stranded DNA. The R-loops
may be formed in a variety of the
xircumstances, and may be
tolerated or cleared by the cellular
components. The term “R-loop”
was given to reflect the similarity
of these structures to the D-loops,
the “R” in this case represents the
involvement of the RNA moiety.
In the laboratory, the R-loops may
also be created by the hybridization
of the mature mRNA with the
double-stranded DNA under the
conditions favoring the formation
of a DNA-RNA hybrid; in this
© 2022 by JPS Scientific Publications, India
287
case, the intron regions (which
have been spliced out of the
mRNA) form the single-stranded
DNA loops, as they cannot
hybridize with the complementary
sequence in the mRNA.
• LYTIC CYCLE - The lytic cycke
is one of the two cycles of the viral
reproduction which also refers to
the bacterial viruses or
bacteriophages, the other being is
the lysogenic cycle. The lytic cycle
results in the destruction or
elimination of the infected cell and
its membrane. The Bacteriophages
that only use the lytic cycle are
called virulent phages in contrast to
the temperate phages. In the lytic
cycle, the viral DNA exists as a
separate free floating molecule
within the bacterial cell, and then
replicates separately from the host
bacterial DNA. However, in both
of the cases the virus/phage
replicates using the host DNA
machinery. The lytic cycle, which
is commonly referred to as the
“reproductive cycle” of the
bacterial effecting virus known as
bacteriophage, it is a six-stage
cycle. The six stages are 1)
Attachment, 2) Penetration, 3)
Transcription, 4) biosynthesis, 5)
Maturation, and 6) lysis.
• Attachment – In this phase the
phage attaches itself to the surface
of the host cell in order to inject its
DNA into the cell.
• Penetration – In this phase the
phage injects its DNA into the host
Glossary of Genetics
cell by penetrating through the cell
membrane.
• Transcription – In this phase the
host cell’s DNA is degraded and
the cell’s metabolism is directed to
initiate the phage biosynthesis.
• Biosynthesis – In this phase the
phage DNA replicates inside the
cell, synthesizing the new phage
DNA and proteins
• Maturation – In this phase the
replicated material assembles into
fully formed viral phages each
made up of a head, a tail and tail
fibers.
• Lysis – In this phase the newly
formed phages are released from
the infected cell which is itself
destroyed in the process to seek out
new host cells to infect.
• LEUCINE ZIPPER MOTIF - A
leucine zipper is a 3 dimensional
Motif Structure which is present in
Proteins. This are mainly present
in eukaryotic cells.Leucine zipper
domains are made up of two
motifs: a basic region that
recognizes a specific DNA
sequence and a series of leucines
spaced 7 residues apart along an α-
helix that mediate dimerization.
• LAC OPERON CONTROL - Lac
operon is an operon which is
needed for the of transport of
lactose in Escherichia coli. It uses a
two-part control mechanism to
ensure that the cell expends energy
producing the enzymes encoded by
the lac operon only when it is
necessary. It exhibits both positive
and negative control.
© 2022 by JPS Scientific Publications, India
288
• LYMPHOID ENHANCER
FACTOR - The Lymphoid
enhancer-binding factor 1 (LEF1)
is a protein that in the humans is
encoded by the LEF1 gene. The
Lymphoid enhancer-binding
factor-1 (LEF1) is a 48-kD nuclear
protein that is expressed in the pre-
B and in the T cells. It binds to a
functionally important site in the
T-cell receptor-alpha (TCRA)
enhancer and confers the maximal
enhancer activity. The LEF1
belongs to a family of the
regulatory proteins that share the
homology with the high mobility
group protein-1 (HMG1). The
LEF1 is highly overexpressed and
associated with the disease
progression and rye poor prognosis
in the B-cell chronic lymphocytic
leukemia and the other kinds of the
malignancies like the colorectal
cancer. It is also a promising
potential drug target.
• LAC OPERON - The lactose
operon (lac operon) is an operon
required for the transport and the
metabolism of the lactose in the E.
coli and many of the other enteric
bacteria. Although the glucose is
the preferred carbon source for
most of the bacteria, the lac operon
allows for the effective digestion of
the lactose when glucose is not
available through the activity of the
beta-galactosidase. The Gene
regulation of the lac operon was
the first genetic regulatory
mechanism to be understood
clearly, so it has become a
Glossary of Genetics
foremost example of the
prokaryotic gene regulation. It is
often discussed in the introductory
molecular and in the cellular
biology classes for this reason. This
lactose metabolism system was
used by the François Jacob and
Jacques Monod to determine how
a biological cell knows which of
the enzyme to synthesize. Their
work on the lac operon won them
the Nobel Prize in the field of
Physiology in the year 1965. The
bacterial operons are polycistronic
transcripts that are able to produce
the multiple proteins from one
mRNA transcript. In this case,
when the lactose is required as a
sugar source for the bacterium, the
three genes of the lac operon can
be expressed and their subsequent
proteins translated: lacZ, lacY, and
lacA. The gene product of the lacZ
is β-galactosidase which cleaves the
lactose, a disaccharide, into the
glucose and the galactose. The
lacY encodes the Beta-galactoside
permease, a membrane protein
which becomes embedded in the
cytoplasmic membrane to enable
the cellular transport of lactose into
the cell. Finally, the lacA encodes
the Galactoside acetyltransferase.
• LINEAR CHROMOSOME - The
linear chromosome is a opposite
chromosome which is in linear in
the shape, and contains the
terminal ends. In most of the
eukaryotic cells, the DNA is
arranged in the multiple linear
chromosomes. In contrast, rye
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289
most prokaryotic cells generally
contain a singular circular
chromosome. However, the linear
chromosomes are not limited to
the eukaryotic organisms, some of
the prokaryotic organisms have
linear chromosomes as well, such
as the Borrelia burgdorferi. In fact,
the experiments in which the
circular chromosomes of the
prokaryotic organisms have been
linearized have demonstrated that
some of the prokaryotes can
maintain viability even with the
linear chromosomes. In general,
the factors which led to the
evolution of the linear
chromosomes in the eukaryotes are
not well understood. One potential
selective pressure in the favour of
the linear chromosomes relates to
the size of an organism’s genome,
the linear chromosomes may make
transcription and replication of the
large genomes easier. In an
organism with a very large
genome, the circular chromosomes
could potentially cause problems
relating to the torsional strain.
• LAGGING AND LEADING
STRANDS - The lagging strand is
a single DNA strand that, during
the DNA replication, is replicated
in the 5′ – 3′ direction which is
direction to the
replication fork. The DNA is
added to the lagging strand in the
discontinuous chunks called as the
‘okazaki fragments’. The leading
strand is a single DNA strand that,
during the DNA replication, is
Glossary of Genetics
replicated in the 3’ – 5’ direction
which is same direction as the
replication fork. The DNA is
added to the leading strand
continuously, as the one
complementary base at a time.
• LINKING NUMBER - The
linking number is a very special
topological property of the DNA.
A linking number is a sum of the
twists and the writhes. The number
of the times one strand of the DNA
turned around the another strand is
called a twist while the inter-
coiling of the double helix is
termed as the writhe. In short, the
writhe is a number of a time DNA
double helix is crossed, coiled over
each other or the number of the
times one strand wraps around the
another strand. As per the Watson
and Cricks model, the eukaryotic
DNA is right-handed and the
negatively supercoiled. It is very
difficult to understand the DNA
topology in the two-dimensional
space because the topology is a
science that cannot be understood
without the three-dimensional
property. For the understanding of
the linking number, We can
assume that the winding of the
telephone wire model. The same
pattern DNA follows during the
packaging or the supercoiling.
• LEUKAEMIA - The Leukemia is
a group of the blood cancers that
usually begin in the bone marrow
and result in the high numbers of
the abnormal blood cells. These
blood cells are not fully developed
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290
and are called as the blasts or the
leukemia cells. The Symptoms
may include the bleeding and the
bruising, bone pain, fatigue, fever,
and an increased risk of the
infections. These symptoms occur
due to a lack of the normal blood
cells. The Diagnosis of the
leukemia is typically made by the
blood tests or the bone marrow
biopsy. The exact cause of the
leukemia is unknown.A
combination of the genetic factors
and the environmental factors are
believed to play a role. The Risk
factors include the smoking,
ionizing radiation, some
chemicals, prior chemotherapy,
and the Down syndrome. The
People with a family history of the
leukemia are also at a very higher
risk. There are four main types of
the leukemia—the acute
lymphoblastic leukemia (ALL),
The acute myeloid leukemia
(AML), the chronic lymphocytic
leukemia (CLL) and the chronic
myeloid leukemia (CML)—as well
as a number of less common types.
The Leukemias and the
lymphomas both belong to a
broader group of the tumors that
affect the blood, bone marrow, and
the lymphoid system, known as the
tumors of the hematopoietic and
the lymphoid tissues. The
Treatment may involve some of
the combination of the
chemotherapy, radiation therapy,
targeted therapy, and bone marrow
transplant, in addition to the
Glossary of Genetics
supportive care and palliative care
as needed.
• LAC SUPPRESSOR - The lac
repressor is a DNA-binding protein
that inhibits the expression of the
genes coding for the proteins
involved in the metabolism of the
lactose in the bacteria. These genes
are repressed when the lactose is
not available to the cell, ensuring
that the bacterium only invests the
energy in the production of the
machinery necessary for the uptake
and the utilization of the lactose
when the lactose is present. When
the lactose becomes available, it is
firstly converted into the
allolactose by the β-Galactosidase
(lacZ) in the bacteria. The DNA
binding ability of the lac repressor
bound with the allolactose is
inhibited due to the allosteric
regulation, thereby the genes
coding for the proteins involved in
the lactose uptake and the
utilization can be expressed.
• LCT GENE - The LCT (Lactase)
is a Protein Coding gene. The
protein encoded by this gene
belongs to the glycosyl hydrolase 1
family of the proteins. The
encoded preproprotein is a six helices into the C-terminal
proteolytically processed to
generate the mature enzyme. This
enzyme is integral to the plasma
membrane and has both the
phlorizin hydrolase activity and the
lactase activity. The Mutations in
this gene are associated with the
congenital lactase deficiency. The
Polymorphisms in this gene are
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291
associated with the lactase
persistence, in which the intestinal
lactase activity persists at the
childhood levels into the
adulthood. The Diseases
associated with the LCT include
the Lactase Deficiency, Congenital
and the Lactose Intolerance.
Among its related pathways are the
Galactose metabolism and the
Disease. The Gene Ontology (GO)
annotations related to this gene
include the hydrolase activity,
hydrolysing the O-glycosyl
compounds and the lactase
activity.
• LACTOSE PERMEASE - The
Lactose permease is a membrane
protein which is a member of the
major facilitator superfamily. The
Lactose permease can be classified
as a symporter, which uses the
proton gradient towards the cell to
the transport β-galactosides such as
the lactose in the same direction
into the cell. The protein has
around twelve transmembrane
alpha-helices and its molecular
weight is around 45,000 Daltons. It
exhibits the internal two-fold
symmetry, relating the N-terminal
helices. It is encoded by the lacY
gene in the lac operon. The sugar
lies in the hydrophilic core of the
protein which is accessible from
the periplasm. On the binding, a
large conformational change takes
place which makes the sugar
binding site accessible from the
cytoplasm.
Glossary of Genetics
• LARIATS - The Lariats are the
discarded byproducts of the RNA
splicing, the process by the which
genetic instructions for making the
proteins are assembled. A new
study has found that hundreds
more lariats than ever before,
yielding the new information about
how the splicing occurs and how it
can lead to the disease.
• LET 7 MIRNA - The Let-7
microRNA precursor was
identified from a study of the
developmental timing in the C.
elegans, and was later shown to be
part of a much larger class of the
non-coding RNAs termed as the
microRNAs. The miR-98
microRNA precursor from the
human is a let-7 family member.
The Let-7 miRNAs have now been
predicted or experimentally
confirmed in a wide range of the
species (MIPF0000002[3]). The
miRNAs are initially transcribed in
the long transcripts (up to the
several hundred nucleotides) called
as the primary miRNAs (pri-
miRNAs), which are processed in
the nucleus by the Drosha and
Pasha to the hairpin structures of
about 70 nucleotide. These
precursors (pre-miRNAs) are
exported to the cytoplasm by the
exportin5, where they are
subsequently processed by the
enzyme Dicer to a ~22 nucleotide
mature miRNA. The involvement
of the Dicer in the miRNA
processing demonstrates a They lack cell walls. The
© 2022 by JPS Scientific Publications, India
292
relationship with the phenomenon
of the RNA interference.
• LEX A - The Repressor LexA or
the LexA is a transcriptional
repressor that represses the SOS
response genes coding primarily for
the error-prone DNA polymerases,
DNA repair enzymes and the cell
division inhibitors. The LexA
forms de facto a two-component
regulatory system with the RecA,
which senses the DNA damage at
the stalled replication forks,
forming the monofilaments and
acquiring an active conformation
capable of the binding to the LexA
and causing the LexA to cleave
itself, in a process called as the The
Impaired LexA proteolysis has
been shown to interfere with the
ciprofloxacin resistance. This offers
potential for the combination
therapy that combines the
quinolones with the strategies
aimed at interfering with the action
of the LexA, either directly or via
the RecA. The LexA contains a
DNA binding domain. The winged
HTH motif of the LexA is a variant
form of the helix-turn-helix DNA
binding motif, and it is usually
located at the N-terminus of the
protein.
• L FORMS - The L-form bacteria,
which is also known as the L-phase
bacteria, the L-phase variants or
the cell wall-deficient (CWD)
bacteria, are the growth forms
derived from the different bacteria.
Peptidoglycan (murein) is absent.
Glossary of Genetics
The Two types of the L-forms are
distinguished as the unstable L-
forms, spheroplasts that are
capable of dividing, but can revert
to the original morphology, and
the stable L-forms, L-forms that are
unable to revert to the original
bacteria.
• LIGASE RIBOZYME - The RNA
Ligase ribozyme was the first of the
several types of the synthetic
ribozymes produced by in vitro
evolution and the selection
techniques. They are an important
class of the ribozymes because they
catalyze the assembly of the RNA
fragments into the phosphodiester
RNA polymers, a reaction required
of all the extant nucleic acid
polymerases and thought to be
required for any of the self-
replicating molecule. Ideas that the
origin of life may have involved the
first self-replicating molecules
being the ribozymes are called as
the RNA World hypotheses. The
Ligase ribozymes may have been
part of such a pre-biotic RNA
world.
• LIN 4 GENE - In the field of the
molecular biology, the lin-4 is a
microRNA (miRNA) that was
identified from a study of the
developmental timing in the
nematode Caenorhabditis elegans.
It was the first to be discovered of
the miRNAs, a class of the non-
coding RNAs involved in the gene
regulation. The miRNAs are
transcribed as ~70 nucleotide
precursors and subsequently
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293
processed by the Dicer enzyme to
give a 21 nucleotide product. The
extents of the hairpin precursors
are not generally known and are
estimated based on the hairpin
prediction. The products are
thought to have regulatory roles
through the complete or the partial
complementarity to the mRNA.
The lin-4 gene has been found to
lie within a 4.11kb intron of a
separate host gene.
• LINE - The Long interspersed
nuclear elements (LINEs) (which is
also known as the long interspersed
nucleotide elements or the long
interspersed elements are a group
of the non-LTR (long terminal
repeat) retrotransposons that are
widespread in the genome of the
many eukaryotes. They make up
around 21.1% of the human
genome. The LINEs make up a
family of the transposons, where
each LINE is about 7,000 base
pairs long. The LINEs are
transcribed into the mRNA and
translated into the protein that acts
as a reverse transcriptase. The
reverse transcriptase makes the
DNA copy of the LINE RNA that
can be integrated into the genome
at the new site. The only abundant
LINE in the humans is the LINE1.
The human genome contains an
estimated 100,000 truncated and
the 4,000 full-length LINE-1
elements. Due to the accumulation
of the random mutations, the
sequence of the many LINEs has
degenerated to the extent that they
Glossary of Genetics
are no longer transcribed or
translated. Comparisons of the
LINE DNA sequences can be used
to date the transposon insertion in
the genome.
• LISTERIA
MONOCYTOGENES - The
Listeria monocytogenes is the
species of the pathogenic bacteria
that causes the infection listeriosis.
It is a facultative anaerobic
bacterium, capable of surviving in
the presence or the absence of the
oxygen. It can grow and reproduce
inside the host's cells and is one of
the most virulent foodborne
pathogens. Around 20 to 30% of
the foodborne listeriosis infections
in the high-risk individuals may be
fatal. It is responsible for an
estimated 1,600 illnesses and the
260 deaths in the United States
annually, listeriosis ranks third in
the total number of the deaths
among the foodborne bacterial
pathogens, with the fatality rates
exceeding even the Salmonella spp.
and the Clostridium botulinum.
• LONG NON CODING RNA -
The Long non-coding RNAs (long
ncRNAs, lncRNA) are a type of
the RNA, generally defined as the
transcripts more than 200
nucleotides that are not translated
into the protein. This arbitrary
limit distinguishes the long
ncRNAs from the small non-
coding RNAs, such as the
microRNAs (miRNAs), small
interfering RNAs (siRNAs), Piwi-
interacting RNAs (piRNAs), small
© 2022 by JPS Scientific Publications, India
294
nucleolar RNAs (snoRNAs), and
the other short RNAs. The Long
intervening/intergenic noncoding
RNAs (lincRNAs) are the
sequences of the lncRNA which do
not overlap the protein-coding
genes. Despite the accumulating
evidence that the majority of the
long noncoding RNAs in the
mammals are likely to be
functional, only a relatively small
proportion has been demonstrated
to be biologically relevant. Some of
the lncRNAs have been
functionally annotated in the
LncRNAdb with the majority of
these being described in the
humans. The functions of the other
lncRNAs with the experimental
evidences have been community-
curated in the LncRNAWiki in
respect of the functional
mechanisms and the disease
associations, which can also be
accessed in the LncBook.
• LTR - A long terminal repeat
(LTR) is a pair of the identical
sequences of the DNA, several
hundred base pairs long, which
occur in the eukaryotic genomes
on either end of a series of the
genes or the pseudogenes that form
a retrotransposon or an
endogenous retrovirus or a
retroviral provirus. All the
retroviral genomes are flanked by
the LTRs, while there are some of
the retrotransposons without the
LTRs. Typically, an element
flanked by a pair of the LTRs will
encode a reverse transcriptase and
Glossary of Genetics
the integrase, allowing the element
to be copied and inserted at the
different location of the genome.
Copies of such an LTR-flanked
element can often be found
hundreds or thousands of the times
in a genome. The LTR
retrotransposons comprise about
8% of the human genome.
• LDL RECEPTOR - The low-
density lipoprotein receptor (LDL-
R) is a mosaic protein of the 839
amino acids (after removal of the
21-amino acid signal peptide) that
mediates the endocytosis of the
cholesterol-rich low-density
lipoprotein (LDL). It is a cell-
surface receptor that recognizes the
apolipoprotein B100 (ApoB100),
which is embedded in the outer
phospholipid layer of the LDL
particles. The receptor also
recognizes the apolipoprotein E
(ApoE) found in the chylomicron
remnants and a very low-density
lipoprotein (VLDL) remnants i.e.
intermediate-density lipoprotein
(IDL). In the humans, the LDL
receptor protein is encoded by the
LDLR gene on the chromosome
19. It belongs to the low density
lipoprotein receptor gene family. It
is most significantly expressed in
the bronchial epithelial cells and
the adrenal gland and in the cortex
tissue. The LDL receptor mediates
the endocytosis of the cholesterol-
rich LDL and thus maintains the
plasma level of the LDL. This
occurs in all the nucleated cells, but
mainly in the liver which removes
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~70% of the LDL from the
circulation. The LDL receptors are
clustered in the clathrin-coated
pits, and the coated pits pinch off
from the surface to the form coated
endocytic vesicles that carry LDL
into the cell.
• LUCIFERASE - The Luciferase is
a generic term for the class of the
oxidative enzymes that produce
the bioluminescence, and is usually
distinguished from a photoprotein.
The Luciferases are widely used in
the biotechnology, for the
bioluminescence imaging
microscopy and as the reporter
genes, for many of the same
applications as the fluorescent
proteins. However, unlike the
fluorescent proteins, luciferases do
not require an external light
source, but do require addition of
the luciferin, the consumable
substrate. In the luciferase reaction,
the light is emitted when the
luciferase acts on the appropriate
luciferin substrate. The Photon
emission can be detected by the
light sensitive apparatus such as a
luminometer or the modified
optical microscopes. This allows
the observation of the biological
processes. Since the light excitation
is not needed for the luciferase
bioluminescence, there is minimal
autofluorescence and therefore
virtually background-free
fluorescence. Therefore, as little as
0.02 pg can still be accurately
measured using the standard
scintillation counter.
Glossary of Genetics
• LEF 1 - The Lymphoid enhancer-
binding factor 1 (LEF1) is a protein
that in the humans is encoded by
the LEF1 gene. The Lymphoid
enhancer-binding factor-1 (LEF1)
is a 48-kD nuclear protein that is
expressed in the pre-B and in the T
cells. It binds to a functionally
important site in the T-cell
receptor-alpha (TCRA) enhancer
and confers the maximal enhancer
activity. The LEF1 belongs to a
family of the regulatory proteins
that share the homology with the
high mobility group protein-1
(HMG1). The LEF1 is the highly
overexpressed and associated with
the disease progression and the
poor prognosis in the B-cell
chronic lymphocytic leukemia and
the other kinds of the malignancies
like the colorectal cancer. It is also
a very promising potential drug
target.
• LATERAL TRANSDUCTION -
The Lateral transduction is the
process by which the very long
fragments of the bacterial DNA are
transferred to the another
bacterium. So far, this form of the
transduction has been only
described in the Staphylococcus
aureus, but it can transfer more
genes and at the higher frequencies
than generalized and specialized
transduction. In the lateral
transduction, the prophage starts
its replication in situ before the
excision in a process that leads to
the replication of the adjacent
bacterial DNA. After which, the
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packaging of the replicated phage
from its pac site (located around
the middle of the phage genome)
and the adjacent bacterial genes
occurs in situ, to 105% of a phage
genome size. The Successive
packaging after the initiation from
the original pac site leads to the
several kilobases of the bacterial
genes being packaged into the new
viral particles that are transferred
to the new bacterial strains. If the
transferred genetic material in
these transducing particles provides
the sufficient DNA for the
homologous recombination, the
genetic material will be inserted
into the recipient chromosome.
Because the multiple copies of the
phage genome are produced during
the in situ replication, some of
these replicated prophages excise
normally (instead of being
packaged in situ), producing the
normal infectious phages.
• LINKER DNA - The Linker DNA
is double-stranded DNA 38-53 bp
long in between the two
nucleosome cores that, in
association with the histone H1,
holds the cores together. The
Linker DNA is seen as the string in
the "beads and string model",
which is made by using an ionic
solution on the chromatin. The
Linker DNA connects to the
histone H1 and the histone H1 sits
on the nucleosome core. The
Nucleosome is technically the
consolidation of a nucleosome core
and one adjacent linker DNA,
Glossary of Genetics 297

however, the term nucleosome is The MS is not only sensitive, but

used freely for solely the core. The provides the selective detection,
Linker DNA may be degraded by relieving the need for the complete
the endonucleases. The linkers are chromatographic separation. The
the short double stranded DNA LC-MS is also appropriate for the
segments which are formed of the metabolomics because of its good
oligonucleotides. These contain the coverage of a wide range of the
target sites for the action of one or chemicals. This tandem technique
more restriction enzymes. The can be used to analyze the
linkers can be synthesized through biochemical, organic, and
chemically and can be ligated to inorganic compounds commonly
the blunt end of the foreign DNA found in the complex samples of
or the vector DNA. These are then the environmental and the
treated with the restriction biological origin. Therefore, the
endonuclease enzyme to produce LC-MS may be applied in a wide
the cohesive ends of the DNA range of the sector's including the
fragments. The commonly used biotechnology, environment
linkers are the EcoRI-linkers and monitoring, food processing, and
the sal-I linkers. the pharmaceutical, agrochemical,
• LC MS - The Liquid and the cosmetic industries. Since
chromatography–mass the early 2000s, LC-MS (or more
spectrometry (LC–MS) is an specifically the LC-MS-MS) has
analytical chemistry technique that also begun to be used in the clinical
combines the physical separation applications.
capabilities of the liquid
chromatography (or HPLC) with
the mass analysis capabilities of the
mass spectrometry (MS). The
Coupled chromatography - MS
systems are popular in the
chemical analysis because the
individual capabilities of the each
technique are enhanced
synergistically. While the liquid
chromatography separates the
mixtures with the multiple
components, mass spectrometry
provides a spectral information
that may help to identify or
confirm the suspected identity of
the each separated component.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
M expected to function as the DNA-
• MCM 2-7 COMPLEX - The
minichromosome maintenance
protein complex (MCM) is a DNA
helicase essential for the genomic
DNA replication. The Eukaryotic
MCM consists of the six gene
products, the Mcm2–7, which form
a heterohexamer. As a critical
protein for the cell division, the
MCM is also the target of the
various checkpoint pathways, such
as the S-phase entry and the S-
phase arrest checkpoints. Both the
loading and the activation of the
MCM helicase are strictly
regulated and are coupled to the
cell growth cycles. The
Deregulation of the MCM function
has been linked to the genomic
instability and a variety of the
carcinomas. The MCM2-7 is
required for both the DNA
replication initiation and the
elongation, its regulation at each of
the stage is a central feature of the
eukaryotic DNA replication.
During the G1 phase, the two
head-to-head Mcm2-7 rings serve
as the scaffold for the assembly of
the bidirectional replication
initiation complexes at the
replication origin. During the S
phase, the Mcm2-7 complex forms
the catalytic core of the Cdc45-
MCM-GINS helicase - the DNA
unwinding engine of the replisome.
• MACHO 1 - The macho-1 protein
has a zinc-finger domain and it
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298
accumulates in the nuclei, being
binding transcription factor. The
macho-1 is indeed a DNA-binding
transcriptional activator, and
directly or the indirectly regulates
the expression of the six
downstream genes. The Macho-1
was required and sufficient for the
expression of the muscle actin,
myosin, calcium transporter,
myogenic factor, Tbx6, and the
snail genes, whose expression is
initiated in the muscle blastomeres
at the cleavage stages in the normal
embryos. Furthermore, when the
macho-1 conjugated with a
transcription-repression domain of
the Drosophila engrailed (En(R))
was expressed in the embryos, it
repressed expression of these
downstream genes. In contrast, the
expression of the macho-1 fused
with a transcription-activation
domain of the VP16 caused ectopic
expression of these muscle genes in
the non-muscle blastomeres. The
PCR-assisted binding-site selection
and the gel-retardation assay
showed that the macho-1 protein
binds to the consensus target
sequence (TGGGTGGTC) for the
GLI/Zic-family proteins, and that
the three guanine residues with the
underlines are very crucial for the
specificity.
• MAGE - The multiplex automated
genome engineering (MAGE) is
used for the large-scale
programming and the evolution of
the cells. The MAGE
Glossary of Genetics
simultaneously targets many
locations on the chromosome for
the modification in a single cell or
across a population of the cells,
thus producing the combinatorial
genomic diversity. Because the
process is cyclical and scalable, it
needs a constructed prototype
devices that automate the MAGE
technology to facilitate the rapid
and the continuous generation of a
diverse set of the genetic changes
(mismatches, insertions, deletions).
The MAGE provides a highly
efficient, inexpensive and the
automated solution to
simultaneously modify many of the
genomic locations (for example,
the genes, regulatory regions)
across the different length scales,
from the nucleotide to the genome
level.
• MUTS 1 - The MutS is a mismatch
DNA repair protein, originally
described in the Escherichia coli.
The Homologues of the MutS have
been found in many species of the
including the eukaryotes (MSH 1,
2, 3, 4, 5, and 6 proteins), archaea
and the bacteria, and together these
proteins have been grouped into
the MutS family. Although many
of the these proteins have a very
similar activities to the E. coli
MutS, there is significant diversity
of the function among the MutS
family members. This diversity is
even seen within the species, where
many species encode the multiple
MutS homologues with the distinct
functions. The Inter-species
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homologues may have arisen
through the frequent ancient
horizontal gene transfer of the
MutS (and MutL) from the
bacteria to the archaea and the
eukaryotes via the endosymbiotic
ancestors of the mitochondria and
the chloroplasts.
• M CAPRICOLUM - The
Mycoplasma capricolum is a
species of the Mycoplasma
bacteria. It is primarily a pathogen
of the goats, but has also been
found in the sheep and the cows.
The species requires external
sources of the cholesterol to grow
or to survive (which usually comes
in the form of a natural fatty acid
auxotroph), but the uptaken fatty
acid is not used as a substrate for
the energy production but rather
for the phospholipid synthesis
instead.
• MADS BOX - The MADS box is
a type of the conserved sequence
motif. The genes which contain
this motif are called as the MADS-
box gene family. The MADS box
encodes the DNA-binding MADS
domain. The MADS domain binds
to the DNA sequences of the high
similarity to the motif
CC[A/T]6GG termed as the
CArG-box. The MADS-domain
proteins are generally the
transcription factors. The length of
the MADS-box reported by the
various researchers varies
somewhat, but typical lengths are
in the range of around 168 to the
180 base pairs, i.e. the encoded
Glossary of Genetics
MADS domain has a length of
around 56 to the 60 amino acids.
There is evidence that the MADS
domain evolved from a sequence
stretch of a type II topoisomerase
in a common ancestor of all the
extant eukaryotes. The MADS-box
genes have a variety of the
functions. In the animals, the
MADS-box genes are involved in
the muscle development and in the
cell proliferation and the
differentiation. The Functions in
the fungi range from the
pheromone response to the
arginine metabolism. In plants, the
MADS-box genes are involved in
the controlling all the major
aspects of the development,
including all the the male and the
female gametophyte development,
embryo and the seed development,
as well as the root, flower and the
fruit development.
• 6 MP - The 6-mercaptopurine (6-
MP) is the mainstay in the
pediatric acute lymphoblastic
leukemia (ALL) maintenance
treatment. The Variants in the
genes coding for the thiopurine S-
methyl transferase (TPMT) and the
inosine triphosphate
pyrophosphatase (ITPA) are
known to influence the 6-MP
metabolism.
• M GENITALIUM - The
Mycoplasma genitalium (MG,
commonly known as the Mgen) is
a sexually transmitted, small and
the pathogenic bacterium that lives
on the mucous epithelial cells of
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300
the urinary and the genital tracts in
the humans. The Medical reports
published in the year 2007 and in
the year 2015 state that Mgen is
becoming increasingly more
common. The Resistance to the
multiple antibiotics is becoming
more prevalent, including to the
azithromycin, which until recently
was the most reliable treatment.
The bacteria was first isolated from
the urogenital tract of the humans
in the year 1981, and was
eventually identified as a new
species of the Mycoplasma in the
year 1983. It can cause the negative
health effects in the men and in the
women. It also increases the risk
factor for the HIV spread with the
higher occurrences in those
previously treated with the
azithromycin antibiotics.
• MYOSIN - The Myosins are a
superfamily of the motor proteins
best known for their roles in
thevmuscle contraction and in a
wide range of the other motility
processes in the eukaryotes. They
are ATP-dependent and are
responsible for the actin-based
motility. Multiple myosin II
molecules generate the force in the
skeletal muscle through a power
stroke mechanism fuelled by the
energy released from the ATP
hydrolysis. The power stroke
occurs at the release of the
phosphate from the myosin
molecule after the ATP hydrolysis
while the myosin is tightly bound
to the actin. The effect of this
Glossary of Genetics
release is very important
conformational change in the
molecule that pulls against the
actin. The release of the ADP
molecule leads to the so-called
rigor state of the myosin. The
binding of a new ATP molecule
will release the myosin from the
actin. The ATP hydrolysis within
the myosin will cause it to bind to
the actin again to repeat the cycle.
The combined effect of the myriad
power strokes causes the muscle to
contract.
• MAPK 13 - The Mitogen-activated
protein kinase 13 (MAPK 13), also
known as the stress-activated
protein kinase 4 (SAPK4), is an
enzyme that in the humans is
encoded by the MAPK13 gene.
The protein encoded by this gene is
a member of the MAP kinase
family. The MAP kinases act as an
integration point for the multiple
biochemical signals, and are
involved in a wide variety of the
cellular processes such as the
proliferation, differentiation,
transcription regulation and the
development. This kinase is closely
related to the p38 MAP kinase,
both of which can be activated by
the proinflammatory cytokines and
the cellular stress. The MAP kinase
kinases 3, and 6 can phosphorylate
and activate this kinase. The
Transcription factor ATF2, and
microtubule dynamics regulator
stathmin have been shown to be
the substrates of this kinase.
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• MICROPROCESSOR
COMPLEX - The microprocessor
complex is a protein complex
involved in the early stages of the
processing microRNA (miRNA)
and the RNA interference (RNAi)
in the animal cells. The complex is
very minimally composed of the
ribonuclease enzyme known as the
Drosha and the dimeric RNA-
binding protein DGCR8 (also
known as the Pasha in the non-
human animals), and then cleaves
the primary miRNA substrates to
the pre-miRNA in the cell nucleus.
The Microprocessor is also the
smaller of the two multi-protein
complexes that contain the human
Drosha. The microprocessor
complex cleaves the primary
miRNA (pri-miRNA), typically at
least 1000 nucleotides long, into
the precursor miRNA (pre-
miRNA). Its two subunits have
been determined as necessary and
sufficient for the mediation of the
development of the miRNAs from
the pri-miRNAs. These molecules
of around 70 nucleotides contain a
stem-loop or the hairpin structure.
The Pri-miRNA substrates can be
derived either from the non-coding
RNA genes or from the introns. In
the latter case, there is evidence
that the microprocessor complex
interacts with the spliceosome and
that the pri-miRNA processing
occurs prior to the splicing.
• MIG 1- The Mig1p, is a zinc
finger DNA-binding protein, is the
main involved component that
Glossary of Genetics
mediates the glucose induced
repression of the sugars. The
inactivation of the MIG1 gene
derepresses the expression of the
invertase encoded by the SUC2 9.
This protein resembles the
mammalian Egr and the Wilms’
tumor proteins, the CreA repressor
in the Aspergillus nidulans and the
Migl repressor in the
Kluyveromyces lactis.
• MINOR SPLICESOME - The
minor spliceosome is a nonsynonymous substitution are
ribonucleoprotein complex that
catalyses the removal (splicing) of
an atypical class of the
spliceosomal introns (U12-type)
from the eukaryotic messenger
RNAs in the plants, insects,
vertebrates and in some of the
fungi (Rhizopus oryzae). This
process is called as the
noncanonical splicing, as opposed
to the U2-dependent canonical
splicing. The U12-type introns
represent less than 1% of all the
introns in the human cells.
However they are found in the
genes performing the essential
cellular functions. The location of
the spliceosomal activity for the
minor class spliceosome is
regarded by the most experts to be
in the nucleus. However, a single
paper has claimed that the minor
spliceosome is active in the cytosol
region. The data presented within
this paper are not fully accepted
within the field and directly
contradict the numerous other
papers
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302
• MISSENSE MUTATIONS - In
the field of the genetics, a missense
mutation is a point mutation in
which a single nucleotide changes
results in a codon that codes for the
different amino acid. It is a type of
the nonsynonymous substitution.
The Missense mutation refers to a
change in one of the amino acid in
a protein, arising from a point
mutation in the single nucleotide.
The two other types of the
the nonsense mutations, in which a
codon is changed to a premature
stop codon that results in the
truncation of the resulting protein,
and the nonstop mutations, in
which a stop codon erasement
results in a longer, nonfunctional
protein. The Missense mutations
can render the resulting protein
nonfunctional, and such mutations
are responsible for the human
diseases such as the Epidermolysis
bullosa, sickle-cell disease, and the
SOD1 mediated ALS. The LMNA
missense mutation introduced at
the LMNA gene position 1580 in
the DNA sequence (CGT) causing
the guanine to be replaced with the
thymine, yielding the CTT in the
DNA sequence. This results at the
protein level in the replacement of
the arginine by the leucine at the
position 527. This leads to the
destruction of the salt bridge and
the structure destabilization. At
phenotype level this manifests with
overlapping the mandibuloacral
Glossary of Genetics
dysplasia and the progeria
syndrome.
• MOLECULAR MIMICRY - The
Molecular mimicry is defined as
the theoretical possibility that
sequence the similarities between
the foreign and the self-peptides are
sufficient to result in the cross-
activation of the autoreactive T or
the B cells by the pathogen-derived
peptides. Despite the prevalence of
the several peptide sequences
which can be both the foreign and
the self in nature, a single antibody
or the TCR (T cell receptor) can be
activated by just a few crucial
residues which stresses the
importance of the structural
homology in the theory of the
molecular mimicry. Upon the
activation of the B or the T cells, it
is believed that these "peptide
mimic" specific T or the B cells can
cross-react with the self-epitopes,
thus leading to the tissue pathology
(autoimmunity). The Molecular
mimicry is a phenomenon that has
been just recently discovered as
one of the several ways in which
autoimmunity can be evoked. The
molecular mimicking event is
however, more than the
epiphenomenon despite its very
low statistical probability of the
occurring and these events have
serious implications in the onset of
the many human autoimmune
disorders.
• MRX COMPLEX - The MRX
complex is a heterotrimeric protein
complex consisting of the Mre11,
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303
Rad50, and the Xrs2. It is a type of
budding yeast homolog of the
mammalian Mre11-Rad50-Nbs1
(MRN) DNA damage repair
complex. The Cells are able to
accurately repair the DNA double-
strand breaks using a process called
as the homologous recombination.
By this process the DNA sequence
information that is lost because of
the breakage can be recovered from
a second homologous DNA
molecule. The Homologous
recombinational repair is
important for removing the DNA
damage both the during mitosis
and meiosis. The repair process
begins with the degradation of the
5’ end on the either side of the
double-strand break to yield the 3’
single-stranded DNA tails (a
process called as the end resection).
• MTOR PROTEIN - The
mammalian target of the
rapamycin (mTOR), also referred
to as the mechanistic target of the
rapamycin, and sometimes called
as the FK506-binding protein 12-
rapamycin-associated protein 1
(FRAP1), is a kinase that in the
humans is encoded by the MTOR
gene. The mTOR is a member of
the phosphatidylinositol 3-kinase-
related kinase family of the protein
kinases. The mTOR integrates the
input from the upstream pathways,
including the insulin growth factors
(such as the IGF-1 and IGF-2), and
the amino acids. The mTOR also
senses the cellular nutrient,
oxygen, and the energy levels. The
Glossary of Genetics
mTOR pathway is a central
regulator of the mammalian
metabolism and the physiology,
with important roles in the
function of the tissues including the
liver, muscle, white and the brown
adipose tissue, and the brain, and
is dysregulated in the human
diseases, such as the diabetes,
obesity, depression, and the certain
types of cancers. The rapamycin
inhibits the mTOR by associating
with its intracellular receptor
FKBP12. The FKBP12–rapamycin
complex binds directly to the
FKBP12-Rapamycin Binding
(FRB) domain of the mTOR,
inhibiting its activity.
• MUB PROTEIN - The MuB is an
ATP-dependent nonspecific DNA-
binding protein that regulates the
activity of the MuA transposase
and captures the target DNA for
the transposition. The Mechanistic
understanding of the MuB function
has previously been hindered by
the MuB's poor solubility. The
MuB is an ATPase associated with
the diverse cellular activities
(AAA+ ATPase) and forms the
ATP-dependent filaments with or
without the DNA. The helical
parameters of the MuB filament do
not match those of the coated
DNA. Despite this protein DNA
symmetry mismatch, the MuB
does not deform the DNA duplex.
These findings, together with the
influence of the MuB filament size
on the strand-transfer efficiency,
lead to a model in which the MuB-
© 2022 by JPS Scientific Publications, India
304
imposed symmetry transiently
deforms the DNA at the boundary
of the MuB filament and results in
a bent DNA favored by the MuA
for the transposition.
• MLV - The Murine leukemia
viruses (MLVs) are among the
simplest retroviruses. The
Prototypical gammaretroviruses
encode only the three polyproteins
that will be used in the assembly of
the progeny virus particles. These
are the Gag polyprotein, which is
the structural protein of a
retrovirus particle, the Pol protein,
comprising the three retroviral
enzymes protease, which catalyzes
the maturation of the particle,
reverse transcriptase, which copies
the viral RNA into DNA upon
infection of a new host cell, and
the integrase, which inserts the
DNA into the chromosomal DNA
of the host cell, and the Env
polyprotein, which induces the
fusion of the viral membrane with
that of the new host cell, initiating
infection. In general, a productive
MLV infection has no obvious
effect upon the host cells. Although
the gammaretroviral structure and
the replication follow the same
broad outlines as those of the other
retroviruses, we point out a
number of the significant
differences between the different
retroviral genera.
• MAPK PATHWAY - The
MAPK/ERK pathway (also
known as the Ras-Raf-MEK-ERK
pathway) is a chain of the proteins
Glossary of Genetics
in the cell that communicates a
available signal from the receptor
on the surface of the cell to the
DNA in the nucleus of the cell. In
many type of the cancers (e.g.
melanoma), a defect in the
MAP/ERK pathway leads to that
uncontrolled manner of growth.
Many compounds can inhibit the
steps in the MAP/ERK pathway,
and therefore are potential drugs
for treating the cancer e.g.,
Hodgkin disease. The first drug
licensed to act on this pathway is
the sorafenib which is a Raf kinase
inhibitor. The RAF-ERK pathway
is also involved in the
pathophysiology of the Noonan's
Syndrome, a polymalformative
disease, where thr Simvastatin was
proposed as a way to improve thr
CNS-cognitive symptoms of the
disorder.
• MAPK - A mitogen-activated
protein kinase (MAPK or the MAP
kinase) is a type of the protein
kinase that is specific to the amino
acids serine and the threonine (i.e.
a serine/threonine-specific protein
kinase). The MAPKs are involved
in directing the cellular responses
to a diverse array of the stimuli,
such as the mitogens, osmotic
stress, heat shock and the
proinflammatory cytokines. They
regulate the cell functions
including the proliferation, gene
expression, differentiation, mitosis,
cell survival, and the apoptosis.
The MAP kinases are found in the
eukaryotes only, but they are fairly
© 2022 by JPS Scientific Publications, India
305
diverse and encountered in all the
animals, fungi and in the plants,
and even in an array of the
unicellular eukaryotes. The
MAPKs belong to the the CMGC
(CDK/MAPK/GSK3/CLK)
kinase group. The closest relatives
of the MAPKs are the cyclin-
dependent kinases (CDKs).
• MAP3K - The Mitogen Activated
Protein (MAP) kinase kinase
kinase, MAPKKK (or MAP3K) is
a serine/threonine-specific protein
kinase which acts upon the MAP
kinase kinase. Subsequently, the
MAP kinase kinase activates the
MAP kinase. Several types of the
MAPKKK can exist but are mainly
characterized by the MAP kinases
they activate. The MAPKKKs are
stimulated by a large range of the
stimuli, primarily environmental
and the intracellular stressors. The
MAPKKK is responsible for the
various cell functions such as the
cell proliferation, cell
differentiation, and the apoptosis.
The duration and the intensity of
the signals determine which
pathway ensues. Additionally, the
use of the protein scaffolds helps to
place the MAPKKK in close
proximity with its substrate to
allow for a reaction. Lastly,
because the MAPKKK is involved
in a series of the several pathways,
it has been used as a therapeutic
target for the cancer, amyloidosis,
and the neurodegenerative
diseases. In the humans, there are
Glossary of Genetics
at least 19 genes which encode the
MAP kinase kinase kinases.
• MAP2K - The Mitogen-activated
protein kinase kinase (also known
as the MAP2K, MEK, MAPKK) is
a dual-specificity kinase enzyme
which phosphorylates the mitogen-
activated protein kinase (MAPK).
The MEK is a member of the
MAPK signaling cascade that is
activated in the melanoma. When
the MEK is inhibited, the cell
proliferation is blocked and the
apoptosis (controlled cell death) is
induced.
• MOI - In the field of the
microbiology, the multiplicity of
the infection or the MOI is the
ratio of the agents (e.g. the phage
or the more generally virus,
bacteria) to infection targets (e.g.
cell). For example, when referring
to a group of the cells inoculated
with the virus particles, the MOI is
the ratio of the number of the virus
particles to the number of the
target cells present in a defined
space. This application of the
Poisson's distribution was applied
and described by the Ellis and the
Delbrück. In fact, the infectivity of
the virus or the bacteria in question
will alter this relationship. One
way around this is to use a
functional definition of the
infectious particles rather than a
strict count, such as a plaque
forming unit for the viruses.
• MALT 1 - The Mucosa-associated
lymphoid tissue lymphoma
translocation protein 1 is a protein
© 2022 by JPS Scientific Publications, India
306
that in the humans is encoded by
the MALT1 gene. It's the type of
the human paracaspase. The
MALT1 has been shown to
interact with the BCL10, TRAF6
and the SQSTM1/p62. The
Genetic ablation of the paracaspase
gene in the mice and the
biochemical studies have shown
that the paracaspase is a crucial
protein for the T and the B
lymphocytes activation. It has an
very important role in the
activation of the transcription
factor NF-κB, in the production of
the interleukin-2 (IL-2) and in the
T and the B lymphocytes
proliferation. The Two
alternatively spliced transcript
variants encoding the different
isoforms have been described for
this gene.
• MUTUALLY EXCLUSIVE
SPLICING - It is a specific type of
the alternative splicing in which
only one of the exons in a cluster is
included in the functional
transcripts. It is a mechanism of
the functional gene and protein
diversification with the pivotal
roles in the organismal
development and diseases such as
the Timothy syndrome,
cardiomyopathy and cancer in the
humans.
• MUTAGENESIS - Mutagenesis is
a process by which the genetic
information of an organism is
changed by the production of a
mutation. It may be occur
spontaneously in nature, or as a
Glossary of Genetics
result of exposure to mutagens. It
can also be achieved through
experimentally using laboratory
procedures. A mutation is a
permanent and heritable change in
the genetic material, which can
result in altered protein function
and phenotypic changes.
Mutagenesis is a technique which
used for generating the mutations
that allows the functions of a genes
and gene products to be examined
in detail, producing the proteins
with improved characteristics or
novel functions, as well as mutant
strains with useful properties.
Examples of mutagens include the
radioactive substances such as x-
rays, ultraviolet radiation, and
certain chemicals.
• MS/MS - The tandem mass
spectrometry, which is also known
as the MS/MS or the MS2, is a
technique in the instrumental
analysis where the two or the more
mass analyzers are coupled
together using an additional
reaction step to increase their
abilities to analyse the chemical
samples. A common use of the
tandem MS is the analysis of the
biomolecules, such as the proteins
and the peptides. The molecules of
the given sample are first ionized
and then the first spectrometer
(designated MS1) separates these
ions by their mass-to-charge ratio
(often given as m/z or the m/Q).
The ions of a particular m/z-ratio
coming from the MS1 are selected
and then made to split into the
© 2022 by JPS Scientific Publications, India
307
smaller fragment ions, e.g. by the
collision-induced dissociation, ion-
molecule reaction, or the
photodissociation. These fragments
are then introduced into the second
mass spectrometer (MS2), which in
turn separates the fragments by
their m/z-ratio and finally detects
them. The fragmentation step
makes it possible to identify and
separate the ions that have very
similar m/z-ratios in the regular
mass spectrometers.
• MECP2 - The MECP2 (methyl
CpG binding protein 2) is a gene
that encodes the protein MECP2.
The MECP2 appears to be
essential for the normal function of
the nerve cells. The protein seems
to be particularly important for the
mature nerve cells, where it is
present in the high levels. The
MECP2 protein is most likely to be
involved in the turning off
("repressing" or "silencing") the
several other types of the genes.
This prevents the genes from
making the proteins when they are
not needed. The recent work has
shown that the MECP2 can also
activate the other genes. The
MECP2 gene is located on the long
(q) arm of the X chromosome in
the band 28 ("Xq28"), from the
base pair 152,808,110 to the base
pair 152,878,611. The MECP2
protein is found in all the cells in
the body, including the brain,
acting as a transcriptional repressor
and the activator, depending on the
context. However, the idea that the
Glossary of Genetics
MECP2 functions as an activator is
relatively new and remains very
controversial. In the brain, it is
found in the high concentrations in
the neurons and is associated with
the maturation of the central
nervous system (CNS) and in the
forming of the synaptic contacts.
• MEDIATORS - The Mediator is a
multiprotein complex that
functions as the transcriptional
coactivator in all the eukaryotes. It
was discovered in the year 1990 in
the lab of the Roger D. Kornberg,
recipient of the 2006 Nobel Prize
in the field of Chemistry. The
Mediator complexes interact with
the transcription factors and the
RNA polymerase II. The main
function of the mediator complexes
is to transmit the available signals
from the transcription factors to the
polymerase. During the period of
evolution, the mediator has
become very more complex.
During the evolution, the mediator
has become very more complex.
The yeast Saccharomyces
cerevisiae (a simple type of
eukaryote) is thought to have about
21 subunits in the core mediator
(exclusive of the CDK module),
while the mammals have up to 26.
• MEGANUCLEASES - The
Meganucleases are the
endodeoxyribonucleases
characterized by a large
recognition site (double-stranded
DNA sequences of the 12 to 40
base pairs); as a result this site
generally occurs only once in any
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308
of the given genome. For example,
the 18-base pair sequence which is
recognized by the I-SceI
meganuclease would require on an
average a genome twenty times the
size of the human genome to be
found once by chance (although
the sequences with a single
mismatch occur about the three
times per human-sized genome).
The Meganucleases are therefore
considered to be the most specific
naturally occurring restriction
enzymes. Among meganucleases,
the LAGLIDADG family of the
homing endonucleases has become
a valuable tool for the study of the
genomes and the genome
engineering over the past fifteen
years. The Meganucleases are the
"molecular DNA scissors" that can
be used to replace, eliminate or
modify the sequences in a highly
targeted way.
• MEOISIS 1 AND 2 - There are
two divisions in the meiosis
process, the first division is the
meiosis I: here the number of the
cells gets doubled but the number
of the chromosomes is not, i.e it
reamins same. This results in the
1/2 as many chromosomes per
cell. The second division is the
meiosis II: this division is like the
mitosis; the number of the
chromosomes still does not get
reduced.
• MEIOTIC RECOMBINATION -
The Meiotic recombination refers
to the reciprocal physical exchange
of the chromosomal DNA between
Glossary of Genetics
the parental chromosomes and
occurs at the meiosis during the
spermatogenesis and the oogenesis,
serving to ensure the proper
chromosome segregation. During
the four-strand stage of the meiosis,
the two duplex DNA molecules
(one from each of the parent) form
a hybrid, and then a single strand
of the one duplex is paired with its
complement from the other duplex.
The Single-stranded DNA is
exchanged between the
homologous chromosomes, and
the process involves the DNA
strand breakage and the resealing,
resulting in the precise
recombination and exchange of the
DNA sequences between the two
homologous chromosomes. This
process is highly efficient and does
not usually result in the mutations
at the sites of the recombination.
The Recombination thus shuffles
the genetic material between the
homologous chromosomes,
generating much of the genetic
diversity that characterizes the
differences between the
individuals, even within the same
family.
• MErR - The MerR family is a
group of the transcriptional
activators with the similar N-
terminal helix-turn-helix DNA
binding regions and the C-terminal
effector binding regions that are
specific to the effector recognised.
The signature of the family is the
amino acid similarity in the first
100 amino acids, including a helix-
© 2022 by JPS Scientific Publications, India
309
turn-helix motif followed by a
coiled-coil region. With the
increasing recognition of the
members of this class over the last
decade, particularly with the
advent of the rapid bacterial
genome sequencing, MerR-like
regulators have been found in a
wide range of the bacterial genera,
but not yet in the archaea or in the
eukaryotes. The Activation of the
transcription is through the
protein-dependent DNA distortion.
The majority of the regulators in
the family respond to the
environmental stimuli, such as the
oxidative stress, heavy metals or
the antibiotics. This subgroup
shows the sequence similarity in
the C-terminal effector binding
region as well as in the N-terminal
region. This subgroup of the MerR
family regulators includes the
MerR itself and may have evolved
to generate a variety of the specific
metal-responsive regulators by the
fine-tuning the sites of the metal
recognition.
• MerT - The MerT is a subclass of
the Mercury transporter
Superfamily. The MerT
homologues have been identified
in which the 3 TMS MerT is fused
to a MerP ''heavy metal associated''
(HMA) domain, possibly via a
linker region that includes the
fourth TMS. The HMA domains
of the 30 aas are found in the
MerP, copper chaperone proteins,
mercuric reductase, and at the N-
termini of both the copper and the
Glossary of Genetics
heavy metal P-type ATPases,
sometimes in the multiple copies.
• MerP - The MerP is a subclass of
the Mercury transporter
Superfamily. The MerP is a
periplasmic Hg2+-binding receptor
of about 70-80 amino acyl residues,
synthesized with a cleavable N-
terminal leader. It is homologous
to the N-terminal heavy metal
binding domains of the copper-and
the cadmium-transporting P-type
ATPases. The 3-D structure of the
MerP from Ralstonia
metallidurans has been solved to 2
Å resolution. It is about 91 amino
acyl residues (aas) long with its
leader sequence, is monomeric,
and binds a single Hg2+ ion. The
Hg2+ is bound to a sequence
GMTCXXC found in the
metallochaperones as well as the
metal-transporting ATPases. The
fold is βαββαβ, called the as the
''ferridoxin-like fold''.
• MerF - The MerF is a subclass of
the Mercury transporter
Superfamily. The MerF protein
encoded on the plasmid
pMER327/419 is an 81 residue
polypeptide with the two putative
TMSs. It catalyzes the uptake of
the Hg2+ in the preparation for the
reduction by the mercuric
reductase. The MerF gene is found
on the mercury resistant plasmids
from many of the gram-negative
bacteria, but the sequence of the
protein from these plasmids is the
same. Limited sequence similarity
is shown with the first two TMSs
© 2022 by JPS Scientific Publications, India
310
of the MerT and MerC. The MerF
has two vicinal pairs of the cysteine
residues which are involved in the
transport of the Hg(II) across the
membrane and are exposed to the
cytoplasm.
• MERCAPTOETHANOL - The 2-
Mercaptoethanol (also known as
the β-mercaptoethanol, BME,
2BME, 2-ME or the β-met) is the
chemical compound with the
formula HOCH2CH2SH. ME or
the βME, as it is commonly
abbreviated, is used to reduce the
disulfide bonds and can act as a
biological antioxidant by
scavenging the hydroxyl radicals
(amongst others). It is widely used
because the hydroxyl group confers
the solubility in the water and
lowers the volatility. Due to its
diminished vapor pressure, its
odor, while unpleasant, is less
objectionable than the related
thiols. Some of the proteins can be
denatured by the 2-
mercaptoethanol, which cleaves
the disulfide bonds that may form
between the thiol groups of the
cysteine residues.
• MRNA SURVEILLANCE - The
mRNA surveillance mechanisms
are the pathways utilized by the
organisms to ensure the fidelity
and quality of the messenger RNA
(mRNA) molecules. There are a
number of the surveillance
mechanisms present within the
cells. These mechanisms function
at various steps of the mRNA
biogenesis pathway to detect and
Glossary of Genetics
degrade the transcripts that have
not properly been processed. The
mRNA surveillance has been
documented in the bacteria and in
the yeast. In eukaryotes, these
mechanisms are known to function
in both the nucleus and in the
cytoplasm. The Fidelity checks of
the mRNA molecules in the
nucleus results in the degradation
of the improperly processed
transcripts before export into the
cytoplasm. The Transcripts are
subject to further surveillance once
in the cytoplasm. The Cytoplasmic
surveillance mechanisms assess the
mRNA transcripts for the absence
of or the presence of the premature
stop codons.
• METHYLCYTOSINE - The 5-
Methylcytosine is a methylated
form of the DNA base cytosine (C)
that regulates the gene
transcription and takes the several
other biological roles. When the
cytosine is methylated, the DNA
maintains the same sequence, but
the expression of the methylated
genes can be altered. The 5-
Methylcytosine is incorporated in
the nucleoside 5-methylcytidine. In
the 5-methylcytosine, a methyl
group is attached to the 5th atom
in the 6-atom ring, counting the
counterclockwise from the NH-
bonded nitrogen at the six o'clock
position. This methyl group
distinguishes the 5-methylcytosine
from the cytosine.
• 6-O-METHYLGUANINE - The
6-O-Methylguanine is a derivative
© 2022 by JPS Scientific Publications, India
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of the nucleobase guanine in which
a methyl group is attached to the
oxygen atom. It base-pairs to the
thymine rather than the cytosine,
causing a G:C to A:T transition in
the DNA. The Repair of the 6-O-
methylguanine in the DNA is
primarily carried out by the O-6-
methylguanine-DNA
methyltransferase (MGMT). The
Epigenetic reductions in the
MGMT expression are one of the
most frequent DNA repair defects,
associated with the carcinogenesis.
The 6-O-Methylguanine is formed
in the DNA by the alkylation of
the oxygen atom of the guanine,
most often by the N-nitroso
compounds (NOC) and sometimes
due to the methylation by other
compounds such as the
endogenous S-adenosyl
methionine. The NOC are
alkylating agents formed by the
reaction of the nitrite or the other
nitrogen oxides with the secondary
amines and the N-alkylamides,
yielding the N-alkylnitrosamines
and the N-alkylnitrosamides.
• METHYLTRANSFERASES -
The Methyltransferases are a large
group of the enzymes that all
methylate their substrates but can
be split into the several subclasses
based on their structural features.
The most common class of the
methyltransferases is the class I, all
of which contain a Rossmann fold
for the binding of the S-Adenosyl
methionine (SAM). The Class II
methyltransferases contain a SET
Glossary of Genetics
domain, which are exemplified by
the SET domain histone
methyltransferases, and the class
III methyltransferases, which are
the membrane associated. The
Methyltransferases can also be
grouped as the different types
utilizing the different substrates in
the methyl transfer reactions.
These types include the protein
methyltransferases, DNA/RNA
methyltransferases, natural product
methyltransferases, and the non-
SAM dependent
methyltransferases. The SAM is
the classical methyl donor for the
methyltransferases, however,
examples of the other methyl
donors are seen in nature. The
general mechanism for the methyl
transfer is a SN2-like nucleophilic
attack where the methionine sulfur
serves as the leaving group and the
methyl group which is attached to
it acts as the electrophile that
transfers the methyl group to the
substrate of the enzymes.
• MNASE-SEQ - The MNase-seq,
short for the micrococcal nuclease
digestion with the deep
sequencing, is a molecular
biological technique that was first
pioneered in the year 2006 to
measure the nucleosome
occupancy in the C. elegans
genome, and was subsequently
applied to the human genome in
the year 2008. However the
technique still relies on the use of
the non-specific endo-exonuclease
micrococcal nuclease, an enzyme
© 2022 by JPS Scientific Publications, India
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derived from the bacteria
Staphylococcus aureus, to bind and
cleave the protein-unbound regions
of the DNA on the chromatin. The
DNA bound to the histones or the
other chromatin-bound proteins
(e.g. transcription factors) can may
remain undigested. The uncut
DNA is then purified from the
proteins and sequenced through
the one or more of the various
Next-Generation sequencing
methods.
• MUB - The MuB is an ATP-
dependent nonspecific DNA-
binding protein that regulates the
activity of the MuA transposase
and captures the target DNA for
the transposition process.
Mechanistic understanding of the
MuB function has previously been
hindered by the MuB’s poor
solubility level. MuB is an AAA+
ATPase that upon ATP binding
assembles into the helical filaments
that coat the DNA. During the
immunity, where the MuB
filament stickiness could favor the
condensation of the DNA into a
compact state that occludes it from
the transposase. The target delivery
by the MuB occurs as a
consequence of the ability of MuB
to stimulate the MuA while
simultaneously tethering the MuA
to a selected target DNA.
• MULTIPLICITY OF
INFECTION - The MOI stands
for the Multiplicity of Infection
which refers to the number of the
viral particles per cell. To calculate,
Glossary of Genetics
take the number of the viral
particles used per well then divide
by the number of the cells that are
originally seeded in the well. This
equals the number of the MOI.
The multiplicity of the infection or
the MOI is the ratio of the agents
e.g. the phage or the more
generally the virus, and bacteria to
the infection targets (e.g. cell). For
example, when referring to a group
of the cells inoculated with the
virus particles, the multiplicity of
infection or MOI is the ratio of the
number of virus particles to the
number of the target cells present
in a defined space. The actual
number of the viruses or the
bacteria that will enter any of the
given cell is a stochastic process is
some cells may absorb more than
one infectious agent while others
may not absorb any of the
infectious agents. Before
determining the multiplicity of the
infection, it is absolutely very
necessary to have a well-isolated
agent, as crude agents may not be
able to produce reliable and
reproducible results. The
probability that a cell will absorb
the virus particles or the bacteria
when inoculated with an MOI can
be calculated for a given
population using the Poisson
distribution equation. This
application of Poisson’s
distribution was applied and
described by the Ellis and
Delbrück.
© 2022 by JPS Scientific Publications, India
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• miRNAs - The miRNAs are the
small non-coding RNAs, with an
average 22 nucleotides in the
length. Most of the miRNAs are
transcribed from the DNA
sequences into the primary
miRNAs as pri-miRNAs and
processed into the precursor
miRNAs as pre-miRNAs and the
mature miRNAs. In most of the
cases, the miRNAs interact with
the 3′ UTR of target mRNAs to
suppress the expression. However,
the interaction of the miRNAs
with the other regions, including
the 5′ UTR, coding sequence, and
the gene promoters, have also been
reported. Furthermore, the
miRNAs have been shown to
activate the gene expression under
the certain conditions. Recent
studies have suggested that the
miRNAs are shuttled between the
different subcellular compartments
to control the rate of the
translation, and even transcription.
The miRNAs are critical for the
normal animal development and
are involved in a variety of the
biological processes. Aberrant
expression of the miRNAs is
associated with many of the
human diseases. In the addition,
the miRNAs are secreted into the
extracellular fluids. The
Extracellular miRNAs have been
widely reported as the potential
biomarkers for a variety of the
diseases and they also serve as
signaling molecules to mediate the
cell-cell communications.
Glossary of Genetics
• MAF 1 - The Repressor of the
RNA polymerase III transcription
MAF1 homolog is a protein that in
the humans is encoded by the
MAF1 gene. This gene encodes a
protein that is homologous to the
Maf1, a Saccharomyces cerevisiae
protein which is highly conserved
in the eukaryotic cells. S.
cerevisiae. The Maf1 is a negative
effector of the RNA polymerase III
(Pol III). It responds to the changes
in the cellular environment and
represses the Pol III transcription.
Biochemical studies identified the
initiation factor TFIIIB as a target
for the Maf1-dependent repression.
• MEVALONATE PATHWAY -
The mevalonate pathway, which is
also known as the isoprenoid
pathway or the HMG-CoA
reductase pathway is an essential
metabolic pathway present in the
eukaryotes, archaea, and some of
the bacteria. The pathway
produces the two five-carbon
building blocks called as the
isopentenyl pyrophosphate (IPP)
and the dimethylallyl
pyrophosphate (DMAPP), which
are used to make the isoprenoids, a
diverse class of over 30,000
biomolecules such as the
cholesterol, vitamin K, coenzyme
Q10, and all the steroid hormones.
The mevalonate pathway begins
with the acetyl-CoA and ends with
the production of the IPP and
DMAPP. It is best known as the
target of the statins, a class of the
cholesterol lowering drugs. The
© 2022 by JPS Scientific Publications, India
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Statins inhibit the HMG-CoA
reductase within the mevalonate
pathway.
• MLH 1 - The DNA mismatch
repair protein Mlh1 or the MutL
protein homolog 1 is a protein that
in the humans is encoded by the
MLH1 gene located on the
chromosome 3. It is a gene
commonly associated with the
hereditary nonpolyposis colorectal
cancer. The Orthologs of the
human MLH1 have also been
studied in the other organisms
including the mouse and the
budding yeast Saccharomyces
cerevisiae. This gene was identified
as a locus frequently mutated in
the hereditary nonpolyposis colon
cancer. It is a human homolog of
the E. coli DNA mismatch repair
gene, mutL, which mediates the
protein-protein interactions during
the mismatch recognition, strand
discrimination, and the strand
removal.
• MLH 3 - The DNA mismatch
repair protein Mlh3 is a protein
that in the humans is encoded by
the MLH3 gene. This gene is a
member of the MutL-homolog
(MLH) family of the DNA
mismatch repair (MMR) genes.
The MLH genes are implicated in
maintaining the genomic integrity
during the DNA replication and
after the meiotic recombination.
The protein encoded by this gene
functions as a heterodimer with the
other family members. The
Somatic mutations in this gene
Glossary of Genetics 315

frequently occur in the tumors splicing results in the four

exhibiting the microsatellite transcript variants encoding the
instability, and the germline three different isoforms.
mutations have been linked to the • METHYLATION IN
hereditary nonpolyposis colorectal ARABIDOPSIS - The Arabidopsis
cancer type 7 (HNPCC7). genome contains methylation at
• MSH 4 - The MutS protein 24% of the CG sites, 6.7% of the
homolog 4 is a protein that in the CHG and the 1.7% of the CHH.
humans is encoded by the MSH4 Staining an Arabidopsis interphase
gene. The MSH4 hypomorphic nucleus with the DNA dye DAPI
(partially functional) mutant of the reveals the several bright spots
S. cerevisiae showed a 30% referred to as the chromocenters.
genome wide reduction in the The Immunostaining with a 5-
crossover numbers, and a large methylcytosine antibody results in
number of the meioses with the a strikingly similar distribution. On
non exchange chromosomes. each of the chromosome, the
Nevertheless this mutant gave rise chromocenters contain the
to the spore viability patterns repetitive DNA sequences
suggesting that segregation of the consisting of the 178 base pair
non-exchange chromosomes centromere tandem repeat
occurred efficiently. Thus, in the S. sequences flanked by the
cerevisiae, the proper segregation pericentromeric heterochromatin,
apparently does not entirely which is largely composed of the
depend on the crossovers between repetitive elements, including the
the homologous pairs. DNA transposons and the
• MSH 5 - The MutS protein retroelements. Each of the
homolog 5 is a protein that in the chromocenter encompasses the
humans is encoded by the MSH5 several megabases of the DNA. On
gene. This gene encodes a member the chromosomes 2 and 4 the
of the mutS family of the proteins additional chromocenters are
that are involved in the DNA formed from the nucleolar
mismatch repair or the meiotic organizing regions (NOR), which
recombination processes. This consist of arrays of the repeated
protein is similar to a 45S rDNA genes. It is clear that
Saccharomyces cerevisiae protein the preferred location for the DNA
that participates in the meiotic methylation is at the repetitive
segregation fidelity and the DNA sequences. This holds true
crossing-over. This protein forms outside of the chromocenters, as
the heterooligomers with the most of the euchromatic
another member of this family, the transposons are also highly
mutS homolog 4. The Alternative methylated, and within the

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
chromocenters, where the genes
surrounded by the methylated
transposons can themselves remain
free of the methylation.
• MRNA LOCALIZATION - The
Cytoplasmic mRNA localisation is
an essential part of the spatial
control of gene expression. The
Several putative functions for the
mRNA localization have been
proposed. They include the
efficient control of the local protein
synthesis and facilitation of the co-
translational complex assembly.
The Cytoplasmic messenger RNA
localization is a key post-
transcriptional mechanism of
establishing the spatially restricted
protein synthesis. The
characterization of the cis-acting
signals within the localized
mRNAs, and the identification of
the trans-acting factors that
recognize these signals, has opened
avenues towards identifying the
machinery and the mechanisms
involved in the mRNA transport
and in the localization. The
mRNA localization can be
achieved by the local transcript
protection, directed transport along
the cytoskeletal filaments and the
cytoplasmic streaming which is
also known as the facilitated
diffusion. A general model for the
localization by active transport
involves the mRNA recognition
(probably inside the nucleus),
association of a core
ribonucleoprotein (RNP) complex
with the cytoskeletal motor
© 2022 by JPS Scientific Publications, India
316
proteins and the tethering of the
delivered RNA at the destination
site. The mRNA localization
requires the specific cis-acting
signals (‘zi p codes’) that are
generally found in the 3′ UTR.
• MICROSATELLITE - A
microsatellite is a tract of the
repetitive DNA in which the
certain DNA motifs ranging in the
length from one to the six or the
more base pairs are repeated,
typically around 5–50 times. The
Microsatellites occur at thousands
of the locations within an
organism’s genome. They have a
higher mutation rate than the other
areas of the DNA leading to the
high genetic diversity. The
Microsatellites are often referred to
as short tandem repeats (STRs) by
the forensic geneticists and in the
fenetic genealogy, or as the simple
sequence repeats (SSRs) by the
plant geneticists. They are widely
used for the DNA profiling in the
cancer diagnosis, in kinship
analysis (especially paternity
testing) and in the forensic
identification. They are also used
in the genetic linkage analysis to
locate a gene or a mutation
responsible for a given trait or the
disease. The Microsatellites are
also used in the population
genetics to measure the levels of
the relatedness between subspecies,
groups and the individuals.
• MINISATELLITE - A
minisatellite is a tract of the
repetitive DNA in which the
Glossary of Genetics
certain DNA motifs ranging in the
length from around 10–60 base
pairs are typically repeated around
5-50 times. The Minisatellites
occur at more than 1,000 locations
in the human genome and they are
notable for their high mutation rate
and the high diversity in the
population. The Minisatellites are
prominent in the centromeres and
the telomeres of the chromosomes,
the latter protecting the
chromosomes from the damage.
The name “satellite” refers to the
early observation that the
centrifugation of the genomic
DNA in a test tube that separates a
prominent layer of the bulk DNA
from accompanying “satellite”
layers of the repetitive DNA. The
Minisatellites are small sequences
of the DNA that do not encode the
proteins but appear throughout the
genome hundreds of times, with
many repeated copies lying next to
the each other. The Minisatellites
have been implicated as the
regulators of the gene
[removed]e.g. at the levels of the
transcription, alternative splicing,
or imprint control). They are
generally the non-coding DNA but
sometimes are part of the possible
genes. The Minisatellites also
constitute the chromosomal
telomeres, which protect the ends
of a chromosome from
deterioration or from the fusion
with the neighbouring
chromosomes.
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• MAJOR AND MINOR
GROOVE - The major groove
occurs where the backbones are the
far apart from the each other
whereas the minor groove occurs
where they are very close together.
The grooves twist around the
molecule on the opposite sides.
The Certain proteins bind to the
DNA to alter its structure or to
regulate the transcription (copying
the DNA to the RNA) or the
replication (copying the DNA to
the DNA). It is easier for these
DNA binding proteins to interact
with the bases (the internal parts of
the DNA molecule) on the major
groove side because the backbones
are not in the same way.
• MOSAICS - The Mosaicism or the
genetic mosaicism is a condition in
the multicellular organisms in
which a single organism possesses
more than the one genetic line as
the result of rye genetic mutation.
This means that the various genetic
lines resulted from a single
fertilized egg. Genetic mosaics
may often be confused with the
chimerism, in which the two or
more genotypes arise in the one
individual similarly to the
mosaicism. In the chimerism,
though, the two genotypes arise
from the fusion of the more than
one fertilized zygote in the early
stages of the embryonic
development, rather than from a
mutation or the chromosome loss.
TheGenetic mosaicism can result
from the many different
Glossary of Genetics 318

mechanisms including the

chromosome nondisjunction,
anaphase lag, and the
endoreplication. The Anaphase
lagging is the most common way
by the which mosaicism arises in
the preimplantation embryo. The
Mosaicism can also result from a
mutation in the one cell during the
development, in which case the
mutation will be passed on only to
its daughter cells (and will be
present only in the certain adult
cells). The Somatic mosaicism is
not generally inheritable as it does
not generally affect the germ cells.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
N binding site of the NtrC is located
• NOTCH SIGNALLING - The
Notch signalling pathway is a
highly conserved cell signaling
system which is present in most of
the animals. The Mammals possess
the four different notch receptors,
referred to as the NOTCH1,
NOTCH2, NOTCH3, and the
NOTCH4. The notch receptor is a
type of protein which is also called
as the single-pass transmembrane
receptor protein. It is a hetero-
oligomer composed of a large
extracellular portion, which also
associates in a calcium-dependent,
non-covalent interaction with a
smaller piece of the notch protein
which is composed of a short
extracellular region, a single
transmembrane-pass, and also a
small intracellular region. The
Notch signaling promotes the
proliferative signaling during the
neurogenesis, and its activity is
inhibited by the Numb to promote
the neural differentiation. It also
plays a major role in the regulation
of the embryonic development.
The Notch signaling pathway is
also very important for the cell-cell
communication, which involves
the gene regulation mechanisms
that control the multiple cell
differentiation processes during the
embryonic and the adult life.
• NtrC - The NtrC is an activator
protein which enhances the
transcription process from the
© 2022 by JPS Scientific Publications, India
319
promoter of the glnA gene. The
in the kilobase pairs upstream of a
promoter that is recognized by the
RNA polymerase containing an
alternate σ factor, σ54. It functions
by enhancing the isomerization of
the closed to open complex of σ54-
RNA polymerase at the glnA
promoter. The NtrC acts as an
apoactivator which is
phosphorylated by a specific
protein called as the kinase, called
NtrB, to become an activator. The
enhancer-bound phosphorylated
NtrC physically contacts the
promoter-bound region called as
σ54-RNA polymerase by looping
out the intervening DNA
sequence. Such a loop-containing
DNA–multiprotein complex is also
called as the enhanceosome. In the
eukaryotic enhanceosomes, an
enhancer-bound activator often
needs an adapter protein or
proteins for making an indirect
contact with the RNA polymerase
assembled at the promoter.
• NON HOMOLOGOUS END
JOINING - The Non-homologous
end joining (NHEJ) is a pathway
that repairs the double-strand
breaks in the DNA. NHEJ is also
referred to as the “non-
homologous” because the break
ends are directly ligated without
the need for a homologous
template, in contrast to the
homology directed repair, which
requires a homologous sequence to
guide the repair. This term was
Glossary of Genetics
coined in the year 1996 by the
scientists named as the Moore J.K
and the James.E Haber. The
NHEJ is typically guided by a
short homologous DNA sequences
which is called as
microhomologies. These
microhomologies are often present
in the single-stranded overhangs on
the ends of double-strand breaks.
When the overhangs are perfectly
compatible, the NHEJ usually
repairs the break accurately. The
Imprecise repair leading to the loss
of the nucleotides can also occur,
but is much more common when
the overhangs are not that
compatible. The Inappropriate
NHEJ can also lead to the
translocations and the telomere
fusion, hallmarks of the tumor
cells. The NHEJ implementations
are understood to have been
existent throughout nearly the all
biological systems and it is the
predominant to the double-strand
break repair pathway in the
mammalian cells. In the budding
yeast (Saccharomyces cerevisiae),
however the homologous
recombination dominates when the
organism is grown under the
common laboratory conditions.
When the NHEJ pathway is
inactivated, the double-strand
breaks can be repaired by a more
error-prone pathway which is
called as the microhomology-
mediated end joining (MMEJ).
• NTRC - The NtrC (Nitrogen
regulatory protein C) is the name
© 2022 by JPS Scientific Publications, India
320
of the protein necessary for the
prokaryotic regulation
transcription factor sigma N (sigma
54) to form an open complex with
the RNA polymerase in order to
activate the glnA transcription.
The closed -> open conformational
change of the sigma N-RNA
polymerase complex around the
glutamine synthetase gene
promoter requires the ATP and
involves the formation of a loop
between the enhancer and the
promoter regions, which may be
facilitated by the DNA-bending
proteins (such as the IHF). The
NtrC proteins bind at the two sites
located at -160 and -80 upstream
from the point of the gene
transcription.
• NEGATIVE
AUTOREGULATION - The
Negative autoregulation is a
network of the motif in which a
transcription factor inhibits its own
expression. The Theoretical work
has shown that this type of the
regulation reduces the intrinsic
noise and quickens the response
time to the environmental
perturbations and the experiments
using artificial gene regulatory
circuits in the Coli. The Negative
autoregulation also speeds up the
response times of the transcription
networks. The Cells regulate the
gene expression using the networks
of the transcription interactions, it
is of the interest to discover the
principles that govern the
dynamical behavior of such
Glossary of Genetics
networks. An important
characteristic of these systems is
the rise-time and the delay from
the initiation of production until
the half maximal product
concentration is reached. The Non-
self-regulated units have a rise-time
of the one cell-cycle. The
demonstrated experimentally that
the negative autoregulation
feedback which is also termed as
the autogenous control reduces the
rise-time to about one fifth of a
cell-cycle. This agrees with an
analytical solution of a correlated to the abundance of the
mathematical model for the
negative autoregulation. This may
help in the understanding the
function of the negative
autoregulation, which appears in
over 40% of the known
transcription factors in the bacteria
E.coli. The negative autoregulation
also linearizes the dose response
and also suppress the heterogeneity
of the gene expression.
• NON SENSE CODON - In the
field of the molecular biology
specifically the protein biosynthesis
stop codon or the termination
codon is a codon i.e the nucleotide
triplet within the messenger RNA,
that signals the termination of the
translation process of the current
protein. Most of the codons in the
messenger RNA correspond to the
addition of an amino acid to a
growing polypeptide chain, which
may ultimately become a protein.
The stop codons signal the
termination of this process by
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321
binding the release factors, which
cause the ribosomal subunits to
disassociate, releasing the amino
acid chain. The Distribution of the
stop codons within the genome of
an organism is non-random and
can correlate with the GC-content.
For example, the E. Coli K-12
genome contains the 2705 TAA
(63%), 1257 TGA (29%), and the
326 TAG (8%) stop codons (GC
content 50.8%). Also the substrates
for the stop codons release factor 1
or the release factor 2 are strongly
stop codons. The Large scale study
of the bacteria with a broad range
of the GC-contents shows that
while the frequency of the
occurrence of the TAA is
negatively correlated to the GC-
content and the frequency of the
occurrence of the TGA is
positively correlated to the GC-
content, the frequency of the
occurrence of the TAG stop codon,
which is often the minimally used
the stop codon in a genome, is not
influenced by the GC-content. The
Recognition of stop codons in the
bacteria have been associated with
the so-called ‘tripeptide anticodon’,
which is a highly conserved amino
acid motif in the RF1 (PxT) and
the RF2 (SPF). Even though this
is supported by the structural
studies, it was shown that the
tripeptide anticodon hypothesis is
an oversimplification.
• NATURAL COMPETENCE - In
the field of microbiology, genetics,
Glossary of Genetics
cell biology, and the molecular
biology, competence is the ability
of a cell to alter its genetics by
taking up the extracellular
(“naked”) DNA from its
environment in the process which
is called as the transformation.
The Competence may be
differentiated between the natural
competence, a genetically specified
ability of the bacteria which is
thought to occur under the natural
conditions as well as in the
laboratory, and induced or the
artificial competence, which arises
when the cells in the laboratory
cultures are treated to make them
transiently permeable to the DNA.
The Competence allows for the
rapid adaptation and the DNA
repair of the cell. In almost all the
naturally competent bacteria
components of the extracellular
filaments called the type IV pili, a
type of the fimbria bind the
extracellular double stranded
DNA. The DNA is then
translocated across the membrane
or the membranes for the gram
negative bacteria, through the
multi-component protein
complexes driven by the
degradation of one strand of the
DNA. The Single stranded DNA
in the cell is bound by a well-
conserved protein, DprA, which
loads the DNA onto the RecA,
which mediates the homologous
recombination through the classic
DNA repair pathway.
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• NUCLEOSOMES ASSEMBLY -
During the S phase, the replicated
DNA must be assembled into the
nucleosomes using the both newly
synthesized and the parental
histones in a process tightly
coupled to the DNA replication.
This DNA replication-coupled
process is regulated by the
multitude of the histone
chaperones as well as the histone
modifying enzymes. The Two each
of the histones such as the H2A,
H2B, H3, and the H4 come
together to form a histone octamer,
which binds and wraps
approximately 1.7 turns of the
DNA, or about the 146 base pairs.
The Nucleosoe Assembly
Dynamics Involve the
Spontaneous Fluctuations in the
Handedness of the Tetrasomes.
• NONSENSE MUTATIONS - In
the field of the genetics, a nonsense
mutation is a point mutation in a
sequence of the DNA that results
in a premature stop codon, or a
nonsense codon in the transcribed
mRNA, and in a truncated,
incomplete, and usually as the
nonfunctional protein product. The
functional and the important effect
of a nonsense mutation depends on
the location of the stop codon
within the coding DNA. For
example, the effect of a nonsense
mutation depends on the proximity
of the nonsense mutation to the
original stop codon, and the degree
to which the functional
subdomains of the protein are
Glossary of Genetics
affected. As the nonsense
mutations leads to the premature
termination of the polypeptide
chains, hence it is also called as the
chain termination mutations. A
nonsense mutation differs from the
missense mutation, which is a
point mutation where a single
nucleotide is changed to cause the
substitution of a different amino
acid. A nonsense mutation also
differs from the nonstop mutation,
which is a point mutation that
removes the stop codon. Some
genetic disorders, such as the
thalassemia and the cystic fibrosis,
Duchenne Muscular Dystrophy
(DMD), Spinal Muscular Atrophy,
Cancers, Metabolic Diseases and
the Neurologic Disorders result
from the nonsense mutations.
• NEGATIVE SUPERCOILING -
The Negative supercoiling of DNA
is a process where the DNA strand
is under wound compared to the
relaxed state. This occurs when the
double helical conformation of the
DNA (left-handed) is twisted
lighter (under wound in a left-
handed mode) until the helical
structure becomes relaxed more
than the normal relaxed B form of
the DNA. It facilitates the DNA
replication and the transcription
through the topoisomerase
enzymes.
• NURSE CELLS - In the general
biology or the reproductive
physiology the term nurse cell is
defined as the cell which provides
the food, helps other cells and
© 2022 by JPS Scientific Publications, India
323
provides the stability to their
neighboring cells. The term nurse
cell is used in the several unrelated
ways in the different scientific
fields. The Nurse cells are the
specialized macrophages residing
in the bone marrow that assist in
the development of the red blood
cells. They absorb the nuclei of the
immature red blood cells and may
provide the growth factors to help
the red blood cells mature. In the
bone marrow, the immature red
blood cells (erythroblasts) can be
seen grouped in a cluster around
the nurse cell. The epithelial cell
found in the cortex of the thymus
is also called as a "nurse cell. These
cells produce the Thymic
hormones that cause the T
lymphocytes to mature and then
differentiate.
• NON STOP DECAY - The Non-
stop decay (NSD) is a cellular
mechanism of the mRNA
surveillance to detect the mRNA
molecules lacking a stop codon
and prevent these mRNAs from
the translation. The non-stop decay
pathway releases the ribosomes
that have reached the far 3' end of
an mRNA and guides the mRNA
to the exosome complex, or to the
RNase R in the bacteria for the
selective degradation. In contrast
to the Nonsense-mediated decay
(NMD), polypeptides do not
release from the ribosome, and
thus the NSD seems to involve the
mRNA decay factors distinct from
the NMD. The NSD pathway
Glossary of Genetics
discharges the ribosomes that have
stalled at the 3' end of the mRNA
and directs the mRNA to the
exosome complex in the
eukaryotes or the RNase R in the
bacteria. Once directed to their
appropriate sites, the transcripts are
then degraded. The NSD
mechanism requires the interaction
of the RNA exosome with the Ski
complex, a multi-protein structure
that includes the Ski2p helicase
and the Ski7p. The combination of
these proteins and the subsequent
complex formation activates the
degradation of the aberrant
mRNAs. The Ski7p is thought to
bind the ribosome stalled at the 3’
end of the mRNA poly(A) tail and
recruit the exosome to degrade the
aberrant mRNA. However in the
mammalian cells, the Ski7p is not
found, and even the presence of the
NSD mechanism itself has
remained relatively unclear.
• NONSENSE MEDIATED
DECAY - The Nonsense-mediated
mRNA decay (NMD) is a
surveillance pathway that exists in
all the eukaryotes. Its main
function is to reduce the errors in
the gene expression by eliminating
the mRNA transcripts that contain
the premature stop codons. The
Translation of these aberrant
mRNAs could, in some cases, lead
to the deleterious gain-of-function
or the dominant-negative activity
of the resulting proteins. The
NMD functions to regulate the
numerous biological functions in a
© 2022 by JPS Scientific Publications, India
324
diverse range of the cells, including
the synaptic plasticity of the
neurons which may shape the adult
behavior. Although the nonsense-
mediated mRNA decay reduces
the nonsense codons, mutations
can occur that lead to the various
health problems and diseases in the
humans. A dominant-negative or
the deleterious gain-of-function
mutation can occur if the
premature terminating (nonsense)
codons are translated. The NMD is
becoming increasingly evident in
the way it modifies the phenotypic
consequences because of the broad
way it controls the gene
expression.
• NGF - The Nerve growth factor
(NGF) is a neurotrophic factor and
the neuropeptide primarily
involved in the regulation of the
growth, maintenance,
proliferation, and the survival of
the certain target neurons. It is
perhaps the prototypical growth
factor, in that it was one of the first
to be described. Since it was first
isolated by Nobel Laureates Rita
Levi-Montalcini and Stanley
Cohen in the year 1956, numerous
biological processes involving the
NGF have been identified, two of
them being the survival of the
pancreatic beta cells and the
regulation of the immune system.
The NGF is involved primarily in
the growth, as well as the
maintenance, proliferation, and the
survival of the nerve cells
(neurons). In fact, the NGF is
Glossary of Genetics
critical for the survival and
maintenance of the sympathetic
and sensory neurons, as they
undergo apoptosis in its absence.
However, several recent studies
suggest that the NGF is also
involved in the pathways besides
those regulating the life cycle of the
neurons.
• NEUROTROPHIN 3 - The
Neurotrophin-3 is a protein that in
the humans is encoded by the
NTF3 gene. Although the vast
majority of the neurons in the
mammalian brain are formed
prenatally, parts of the adult brain
retain the ability to grow the new
neurons from the neural stem cells;
a process known as the
neurogenesis. Neurotrophins are
chemicals that help to stimulate
and control the neurogenesis. The
NT-3 is unique in the number of
the neurons it can potentially
stimulate, given its ability to
activate two of the receptor
tyrosine kinase neurotrophin
receptors (TrkC and TrkB). The
Mice born without the ability to
make the NT-3 have loss of the
proprioceptive and the subsets of
the mechanoreceptive sensory
neurons.
• NT4/5 - The Neurotrophin-4 (NT-
4), also known as the
neurotrophin-5 (NT-5), is a protein
that in the humans is encoded by
the NTF4 gene. It is a neurotrophic
factor that signals predominantly
through the TrkB receptor tyrosine
kinase.
© 2022 by JPS Scientific Publications, India
325
• NORTHERN BLOTTING - The
northern blot, or the RNA blot, is a
technique used in the molecular
biology research to study the gene
expression by detection of the
RNA (or the isolated mRNA) in a
sample. The Northern blotting
allows one to observe a particular
gene's expression pattern between
the tissues, organs, developmental
stages, environmental stress levels,
pathogen infection, and over the
course of the treatment. The
technique has been used to show
the overexpression of the
oncogenes and downregulation of
the tumor-suppressor genes in the
cancerous cells when compared to
the 'normal' tissue, as well as the
gene expression in the rejection of
the transplanted organs. If an
upregulated gene is observed by an
abundance of the mRNA on the
northern blot the sample can then
be sequenced to determine if the
gene is known to the researchers or
if it is a novel finding.
• NATURAL COMPETENCE - In
the field of the microbiology,
genetics, cell biology, and the
molecular biology, the competence
is the ability of a cell to alter its
genetics by taking up the
extracellular ("naked") DNA from
its environment in the process
called as the transformation. The
competence may be differentiated
between the natural competence, a
genetically specified ability of the
bacteria which is thought to occur
under the natural conditions as
Glossary of Genetics
well as in the laboratory, and
induced or the artificial
competence, which arises when the
cells in the laboratory cultures are
treated to make them transiently
permeable to the DNA. The
competence allows for the rapid
adaptation and the DNA repair of
the cell.
• NONSTOP MUTATIONS - A
nonstop mutation, which is also
called as a stop-loss variant, is a
point mutation that occurs within
the stop codon. The Nonstop
mutations cause the continued
translation of an mRNA strand
into what should be an
untranslated region. Most of the
polypeptides resulting from a gene
with a nonstop mutation lose their
function from their extreme length
and the impact on the normal
folding. The Nonstop mutations
differ from the nonsense mutations
in that they do not create a stop
codon but, instead, a delete one.
The Nonstop mutations also differ
from the missense mutations,
which are the point mutations
where a single nucleotide is
changed to cause the replacement
by a different amino acid. The
Nonstop mutations have been
linked with many of the inherited
diseases including the endocrine
disorders, eye disease, and
neurodevelopmental disorders.
• NULL MUTATIONS - A null
allele is a nonfunctional allele (a
variant of the gene) caused by the
genetic mutation. Such mutations
© 2022 by JPS Scientific Publications, India
326
can cause a complete lack of the
production of the associated gene
product or a product that does not
function properly in either of the
case, the allele may be considered
as the nonfunctional. A null allele
cannot be distinguished from the
deletion of the entire locus solely
from the phenotypic observation.
A mutant allele that produces the
no RNA transcript is called as an
RNA null, and one that produces
the no protein is called as a protein
null. A genetic null or the
amorphic allele has the same
phenotype when the homozygous
as when heterozygous with a
deficiency that disrupts the locus in
the question. A genetic null allele
may be both a protein null and an
RNA null, but may also express as
the normal levels of a gene product
that is nonfunctional due to the
mutation. The Null alleles can
have lethal effects depending on
the importance of the mutated
gene. For example, the mice
homozygous for a null allele for
the insulin die 48 to 72 hours after
the birth. The Null alleles can also
have the beneficial effects, such as
the elevated harvest index of the
semi-dwarf rice of the green
revolution caused by the null
alleles in the GA20ox-2.
• NANOG PROTEIN - The
Homeobox protein NANOG
(hNanog) is a transcriptional factor
that helps the embryonic stem cells
(ESCs) to maintain the
pluripotency by suppressing the
Glossary of Genetics
cell determination factors. The
hNanog is encoded in humans by
the NANOG gene. Several types of
the cancer are associated with the
NANOG. The NANOG is a
transcription factor in the
embryonic stem cells (ESCs) and is
thought to be a key factor in
maintaining the pluripotency. The
NANOG is thought to function in
the concert with the other factors
such as the POU5F1 (Oct-4) and
the SOX2 to establish the ESC
identity. These cells offer an
important area of the study
because of their ability to maintain
the pluripotency. In the other
words, these cells have the ability
to become virtually any cell of any
of the three germ layers
(endoderm, ectoderm, mesoderm).
• NEURAL TUBE
DEVELOPMENT - The neural
folds migrate toward the midline of
the embryo, eventually fusing to
form the neural tube beneath the
overlying ectoderm. The cells at
the dorsalmost portion of the
neural tube become the neural crest
cells. The Neurulation occurs in
somewhat the different ways in the
different regions of the body.
• NEUROTROPHIN MIMETICS -
Neurotrophin mimetics are the
small molecules or the peptide like
moleculess that can modulate the
action of the neurotrophin
receptor. One of the main causes of
the neurodegeneration involves
changes in the expression of the
neurotrophins (NTs) and/or their
© 2022 by JPS Scientific Publications, India
327
receptors (TrkA, TrkB, TrkC and
the p75NTR). Indeed, these
imbalances or the changes in their
activity, lead to the neuronal
damage resulting in the
neurological and the
neurodegenerative conditions. The
therapeutic properties of the
neurotrophins attracted the focus
of many researchers during the
years, but the poor
pharmacokinetic properties, such
as the reduced bioavailability and
the low metabolic stability, the
hyperalgesia, the inability to
penetrate the blood–brain barrier
and the short half-lives render the
large neurotrophin proteins not
suitable to be implemented as the
drugs. There are a number of
natural products with neurotrophic
activity, which results from several
mechanisms including enhancing
BDNF gene transcription,
upregulating the expression of
BDNF and TrkB, and extracellular
signal-regulated kinase (ERK) and
CREB signalling. There are a
number of the natural products
with the neurotrophic activity,
which results from the several
mechanisms including the
enhancing BDNF gene
transcription, upregulating the
expression of the BDNF and the
TrkB, and the extracellular signal-
regulated kinase (ERK) and the
CREB signalling.
• NON SENSE CODONS - One of
the mRNA sequences (UAA,
UAG, UGA) that signals the
Glossary of Genetics
termination of the translation. A
codon for which the no normal
tRNA molecule exists. The
presence of the nonsense codon
causes the termination of the
translation (ending polypeptide
chain synthesis). There are three
nonsense codons are called as the
amber(UAG) ochre(UAA) and the
opal (UGA).
• NOT 1 - The Not I belongs to the
class of the “rare-cutter” enzymes.
It is one of the two known
enzymes recognizing an octameric
sequence comprised the solely of
the G and the C residues. The Not
I cleaves the prokaryotic genomic
DNA to generate the fragments
between the 20 and the 1,000 kb
depending on the GC content.
• N PROTEIN - The nucleocapsid
(N) protein is a protein that
packages the positive-sense RNA
genome of the coronaviruses to
form the ribonucleoprotein
structures enclosed within the viral
capsid. The N protein is the most
highly expressed of the four major
coronavirus structural proteins. In
addition to its interactions with the
RNA, N forms protein-protein
interactions with the coronavirus
membrane protein (M) during the
process of the viral assembly. The
N also has additional functions in
the manipulating of the cell cycle
of the host cell. The N protein is
the highly immunogenic and the
antibodies to N are found in the
patients recovered from the SARS
and the Covid-19.
© 2022 by JPS Scientific Publications, India
328
• NUCLEAR PORE - A nuclear
pore is a part of the large complex
of the proteins, known as the
nuclear pore complex that spans
the nuclear envelope, which is the
double membrane surrounding the
eukaryotic cell nucleus. There are
approximately around 1,000
nuclear pore complexes (NPCs) in
the nuclear envelope of the
vertebrate cell, but this number
varies depending on the cell type
and the stage in the life cycle. nThe
human nuclear pore complex
(hNPC) is a 110 megadalton
(MDa) structure. The proteins that
make up the nuclear pore complex
are known as the nucleoporins;
each NPC contains at least 456
individual protein molecules and is
composed of the 34 distinct
nucleoporin proteins. About half of
the nucleoporins typically contain
the solenoid protein domains either
an alpha solenoid or a beta-
propeller fold, or in some of the
cases both as the separate
structural domains. The other half
show the structural characteristics
typical of the "natively unfolded"
or the intrinsically disordered
proteins, i.e. they are highly
flexible proteins that lack the
ordered tertiary structure. These
disordered proteins are the FG
nucleoporins, so called because
their amino-acid sequence contains
many of the phenylalanine glycine
repeats.
Glossary of Genetics
• NUCLEOSOMES
POSITIONING - The Genomic
nucleosome positioning is a non-
random, and represents a very
unique characteristic of a given cell
state and type. The Several
counteracting processes affect the
nucleosome positioning both at the
level of the genome (DNA
sequence) and at the epigenome
(beyond the DNA sequence). One
can distinguish the six major
determinants of the genomic
nucleosome positioning:-
1) The Intrinsic DNA sequence
affinity of the histone octamer
2) The Statistical positioning of
the nucleosomes by the
genomic boundaries. The
Chemical modifications of the
DNA or the histones
3) The Interaction of rye
nucleosomes with the linker
histones
4) The Binding of the
transcription factors and the
other chromatin proteins.
5) The ATP-dependent
nucleosome repositioning by
the chromatin remodellers.
• NUCLEOTIDE SEQUENCE -
Once the segment of the DNA has
been cloned, its nucleotide
sequence can be determined. The
nucleotide sequence is the most
fundamental level of the
knowledge of a gene or the
genome. It is the blueprint that
contains the instructions for the
building an organism, and no
© 2022 by JPS Scientific Publications, India
329
understanding of the genetic
function or the evolution could be
complete without obtaining this
information. The nucleotide
sequence of the template strand
determined the nucleic acid
sequence. The Two strands of the
DNA, each strand is a polymer of
the DNA nucleotides. A sugar, a
phosphate group, and one of the
four nitrogenous bases that hold
the two strands together.
• NESTED SETS MODEL - The
nested set model is a technique for
representing the nested sets (also
known as the trees or the
hierarchies) in the relational
databases. The nested set model is
to number the nodes according to a
tree traversal, which visits the each
node twice, assigning the numbers
in the order of visiting, and at the
both visits. This leaves rye two
numbers for the each node, which
are stored as the two attributes.
Querying becomes the inexpensive,
hierarchy membership can be
tested by comparing the these
numbers. Updating the requires
renumbering and is therefore very
expensive. The Refinements that
use the rational numbers instead of
the integers can avoid the
renumbering, and so are faster to
update, although very much more
complicated.
• NOISE IN GENE EXPRESSION
- The term “noise” in the gene
expression is used to refer to the
measured level of the variation in
the gene expression among the
Glossary of Genetics 330

cells, regardless of the source,

within a supposedly identical
population. The Genetically
identical cells and the organisms
exhibit remarkable diversity even
when they have identical histories
of the environmental exposure.
The Noise, or the variation, in the
process of the gene expression may
contribute to this phenotypic
variability. The Recent studies
suggest that the this noise has
various multiple sources, including
the stochastic or the inherently
random nature of the biochemical
reactions of the gene expression.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
•
O
• OCT 4 PROTEIN - The Oct-4
(octamer-binding transcription
factor 4), also known as the
POU5F1 (POU domain, class 5,
transcription factor 1), is a protein
that in the humans is encoded by
the POU5F1 gene. The Oct-4 is a
homeodomain transcription factor
of the POU family. It is critically
involved in the self-renewal of the
undifferentiated embryonic stem
cells. As such, it is frequently used
as a marker for the undifferentiated
cells. The Oct-4 expression must be
closely regulated, too much or too
little will cause the differentiation
of the cells. The OCT-4 consists of
an octamer motif, a particular
DNA sequence of the
AGTCAAAT that binds to their
target genes and activates or
deactivates the certain expressions.
These gene expressions then lead
to the phenotypic changes in the
stem cell differentiation during the
development of a mammalian
embryo. It plays a vital role in
determining the fates of both the
inner mass cells and the embryonic
stem cells and has the ability to
maintain the pluripotency
throughout embryonic
development. Recently, it has been
noted that the OCT-4 not only
maintains the pluripotency in the
embryonic cells but also has the
ability to regulate the cancer cell
proliferation.
© 2022 by JPS Scientific Publications, India
331
ONE GENE ONE HYPOTHESIS
- The one gene–one enzyme
speculation is the concept that
genes act via the manufacturing of
the enzymes, with every of the
gene accountable for generating a
unmarried enzyme that during flip
influences the unmarried step in a
metabolic pathway. The idea
changed into proposed via way of
means of the George Beadle and
Edward Tatum in an influential
1941 paper at the genetic
mutations withinside the mildew
Neurospora crassa, and finally
changed into dubbed the "one
gene–one enzyme speculation" via
way of means of their collaborator
Norman Horowitz. In the yr 2004,
Horowitz reminisced that "those
experiments based the technology
of what the Beadle and Tatum
known as because the 'biochemical
genetics.' In reality they proved to
be the hole gun in what have
become molecular genetics and all
of the traits which have observed
from that. The improvement of the
only gene–one enzyme speculation
is frequently taken into
consideration because the first full-
size bring about what got here to
be known as because the molecular
biology. Although it's been
extraordinarily influential, that the
speculation changed into
diagnosed quickly after its concept
to be as an oversimplification.
Even the following reformulation
of the "one gene–one polypeptide"
speculation is now taken into.
Glossary of Genetics
• ORC - In the molecular biology,
the origin recognition complex
(ORC) is a multi-subunit DNA
binding complex (6 subunits) that
binds in all the eukaryotes and the
archaea in an ATP-dependent
manner to the origins of the
replication. The subunits of this
complex are encoded by the
ORC1, ORC2, ORC3, ORC4,
ORC5 and the ORC6 genes. The
ORC is a central component for
the eukaryotic DNA replication,
and remains bound to the
chromatin at the replication origins
throughout the cell cycle. The
ORC directs the DNA replication
throughout the genome and is
required for its initiation. The ORC
and the Noc3p bound at the
replication origins serve as the
foundation for the assembly of the
pre-replication complex (pre-RC),
which includes the Cdc6, Tah11,
and the Mcm2-Mcm7 complex.
The Pre-RC assembly during G1 is
required for the replication
licensing of the chromosomes prior
to the DNA synthesis during S
phase. The Cell cycle-regulated
phosphorylation of the Orc2, Orc6,
Cdc6, and the MCM by the cyclin-
dependent protein kinase Cdc28
regulates initiation of the DNA
replication, including blocking
reinitiation in G2/M phase. The
ORC is present throughout the cell
cycle bound to the replication
origins, but is only active in the late
mitosis and the early G1.
• does not have this limitation,
© 2022 by JPS Scientific Publications, India
332
• ORF - In the molecular biology,
the open reading frames (ORFs)
are defined as the spans of the
DNA sequence between the start
and the stop codons. Usually, the
ORFs are considered within a
studied region of the prokaryotic
DNA sequence, where only one of
the six possible reading frames will
be "open". Such an ORF
maybcontain a start codon (usually
the AUG in terms of the RNA)
and by the definition cannot extend
beyond a stop codon (usually the
UAA, UAG UGA in the RNA).
That start codon indicates where
the translation may start. The
transcription termination site is
located after the ORF, which is
beyond the translation stop codon.
If the transcription were to cease
before the stop codon, an
incomplete protein would be made
during the translation.
• OLIGONUCLEOTIDES
SYNTHESIS - The
Oligonucleotide synthesis is the
chemical synthesis of the relatively
short fragments of the nucleic acids
with the defined chemical structure
(sequence). The technique is the
extremely useful in the current
laboratory practice because it
provides a rapid and inexpensive
access to the custom-made
oligonucleotides of the desired
sequence. Whereas the enzymes
synthesize DNA and the RNA
only in a 5' to 3' direction,
chemical oligonucleotide synthesis
Glossary of Genetics
although it is most often carried
out in the opposite, 3' to 5'
direction. Currently, the process is
implemented as the solid-phase
synthesis using the
phosphoramidite method and the
phosphoramidite building blocks
derived from the protected 2'-
deoxynucleosides (dA, dC, dG,
and T), ribonucleosides (A, C, G,
and U), or the chemically modified
nucleosides, e.g. LNA or the BNA.
• OSKAR MRNA - The Drosophila
oskar (osk) mRNA is unusual in
that it has both the coding and the
noncoding functions. As an
mRNA, the osk encodes a protein
required for the embryonic
patterning and for the germ cell
formation. The Independent of that
function, the absence of the osk
mRNA disrupts the formation of
the karyosome and blocks the
progression through the oogenesis.
This study shows that the loss of
the osk mRNA also affects the
distribution of the regulatory
proteins, relaxing their association
with the large RNPs within the
germline, and allowing them to
accumulate in the somatic follicle
cells. This and other noncoding
functions of the osk mRNA are
mediated by the multiple sequence
elements with the distinct roles.
One role, provided by the
numerous binding sites in the two
distinct regions of the osk 3’ UTR,
was to sequester the translational
regulator Bruno (Bru), which itself
controlled the translation of the osk
© 2022 by JPS Scientific Publications, India
333
mRNA. This defined a novel
regulatory circuit, with the Bru
restricting the activity of the osk,
and the osk in turn restricting the
activity of the Bru. Other
functional elements, which did not
bind to Bru and were positioned
close to the 3’ end of the RNA,
acted in the oocyte and were
essential. Despite the different roles
played by the different types of the
elements contributing to the RNA
function, mutation of the any led
to the accumulation of the
germline regulatory factors in the
follicle cells.
• OPERATORS - A genetic
operator is an operator which used
in the genetic algorithms to guide
the algorithm towards the solution
to a given problem. There are three
main types of the operators 1)
mutation, 2) crossover and 3)
selection, which very importantly
must work in the conjunction with
one another in order for the
algorithm to be successful. Genetic
operators are used to create and
maintain the genetic diversity i.e
mutation operator, combine
existing solutions which is also
known as the chromosomes into
new solutions i.e crossover and to
select between the solutions. In his
book discussing the use of genetic
programming for the optimization
of the complex problems, the
computer scientist John Koza has
also identified an ‘inversion’ or
‘permutation’ operator; however,
the effectiveness of this operator
Glossary of Genetics 334

has never been any conclusively

demonstrated and this operator is
very rarely discussed. The
Mutation or the mutation-like
operators are said to be very unary
operators, as they can only operate
on one chromosome at a time. In
this contrast, the crossover
operators are said to be the binary
operators, as they can operate on
the two chromosomes at a time,
combining the two existing
chromosomes into the one new
chromosome. The mutation
operator encourages the genetic
diversity amongst the solutions and
the attempts to prevent the genetic
algorithm converging to a local
minimum by stopping the solutions
to becoming too close to one
another. In the mutating the
current pool of the solutions, a
given solution may change entirely
from the previous solution. By
mutating the solutions, a genetic
algorithm can reach an improved
solution solely through the
mutation operator.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
P •
• PROTEIN RECOGNITION OF
DNA SEQUENCE - The
recognition of the specific DNA
sequences by the proteins is
thought to depend on the two types
of the mechanisms: one that
involves the formation of the
hydrogen bonds with tyrvspecific
bases, primarily in the major
groove, and one involving the
sequence-dependent deformations
of the DNA helix. By
comprehensively analyzing the
three dimensional structures of the
protein-DNA complexes, we show
that the binding of the arginines to
the narrow minor grooves is a
widely used mode for the protein-
DNA recognition. This readout
mechanism exploits the
phenomenon that the narrow
minor grooves strongly enhance
the negative electrostatic potential
of the DNA. The nucleosome core
particle offers a striking example of
this effect. The Minor groove
narrowing is often associated with
the presence of the A-tracts, AT-
rich sequences that exclude the
flexible TpA step. These findings
suggest that the ability to detect the
local variations in the DNA shape
and the electrostatic potential is a
general mechanism that enables
the proteins to use the information
in the minor groove, which
otherwise offers few opportunities
for the formation of the base-
© 2022 by JPS Scientific Publications, India
335
specific hydrogen bonds, to achieve
the DNA binding.
PYRIMIDINE DIMERS - The
Pyrimidine dimers are the
molecular lesions formed from the
thymine or the cytosine bases in
the DNA via photochemical
reactions, commonly associated
with the direct DNA damage. The
Ultraviolet light (UV; particularly
UVB) induces the formation of the
covalent linkages between the
consecutive bases along the
nucleotide chain in the vicinity of
their carbon–carbon double bonds.
The dimerization reaction can also
occur among the pyrimidine bases
in the dsRNA (double-stranded
RNA)—uracil or the cytosine. The
two common UV products are the
cyclobutane pyrimidine dimers
(CPDs) and the 6–4
photoproducts. It causes the
sunburn and it triggers the
production of the melanin. The
Pyrimidine dimers are the primary
cause of the melanomas in the
humans.
• PIC - The preinitiation complex
(abbreviated PIC) is a complex of
approximately around 100 proteins
that is necessary for the
transcription of the protein-coding
genes in the eukaryotes and in the
archaea. The preinitiation complex
positions RNA polymerase II at
the gene transcription start sites,
denatures the DNA, and positions
the DNA in the RNA polymerase
II active site for the transcription.
The minimal PIC includes the
Glossary of Genetics
RNA polymerase II and the six
general transcription factors:
TFIIA, TFIIB, TFIID, TFIIE,
TFIIF, and the TFIIH. The
Additional regulatory complexes
(such as the mediator coactivator
and the chromatin remodeling
complexes) may also be
components of the PIC.
• PS70 - The Ribosomal protein S6
kinase beta-1 (S6K1), also known
as the p70S6 kinase (p70S6K, p70-
S6K), is an enzyme (specifically, a
protein kinase) that in the humans
is encoded by the RPS6KB1 gene.
It is a serine/threonine kinase that
acts as a downstream of the PIP3
and phosphoinositide-dependent
kinase-1 in the PI3 kinase pathway.
As the name suggests, its target
substrate is the S6 ribosomal
protein. The Phosphorylation of
the S6 induces the protein
synthesis at the ribosome. This
gene encodes a member of the S6K
family of the serine/threonine
kinases, which phosphorylate the
several residues of the S6
ribosomal protein. The kinase
activity of this protein leads to an
increase in the protein synthesis
and the cell proliferation. The
Amplification of the region of the
DNA encoding this gene and
overexpression of this kinase are
seen in some of the breast cancer
cell lines. The alternate
translational start sites have been
described and alternate
transcriptional splice variants have
© 2022 by JPS Scientific Publications, India
336
been observed but have not been
thoroughly characterized.
• PAGE - The Polyacrylamide gel
electrophoresis (PAGE) is a
technique widely used in the field
of the biochemistry, forensic
chemistry, genetics, molecular
biology and the biotechnology to
separate the biological
macromolecules, usually the
proteins or the nucleic acids,
according to their electrophoretic
mobility. The Electrophoretic
mobility is a function of the length,
conformation and charge of the
molecule. The Polyacrylamide gel
electrophoresis is a powerful tool
used to analyze the RNA samples.
When the polyacrylamide gel is
denatured after the electrophoresis,
it provides information on the
sample composition of the RNA
species. The Hydration of the
acrylonitrile results in formation of
the acrylamide molecules
(C3H5NO) by the nitrile
hydratase. The Acrylamide
monomer is in a powder state
before the addition of water. The
acrylamide is toxic to the human
nervous system, therefore all the
safety measures must be followed
when working with it. The
acrylamide is soluble in the water
and upon addition of the free-
radical initiators it polymerizes
resulting in the formation of the
polyacrylamide. It is useful to
make the polyacrylamide gel via
acrylamide hydration because the
pore size can be regulated. The
Glossary of Genetics
Increased concentrations of the
acrylamide result in the decreased
pore size after the polymerization.
The Polyacrylamide gel with small
pores helps to examine the smaller
molecules better since the small
molecules can enter the pores and
travel through the gel while large
molecules get trapped at the pore
openings.
• POLYCISTRONIC MRNA - The
Polycistronic mRNA is a mRNA
that encodes the several types of
proteins and is characteristic of the
many bacterial and the chloroplast
mRNAs. The Polycistronic
mRNAs consist of a leader
sequence which precedes the first
gene. The gene is followed by an
intercistronic region and then the
another gene. A trailer sequence
follows the last gene in the mRNA.
The Examples of a polycistronic
transcripts are found in the
chloroplast. One region that
exhibits a group of the different
polycistronic messages from the
same region is the
psbb/psbH/petB/petD region.
• POLYCOMB GROUP
PROTEINS - The Polycomb
group (PcG) proteins are the
transcriptional repressors that
regulate the several crucial
developmental and the
physiological processes in the cell.
More recently, they have been
found to play an very important
roles in the human carcinogenesis
and the cancer development and in
the progression. The deregulation
© 2022 by JPS Scientific Publications, India
337
and the dysfunction of the PcG
proteins often lead to the blocking
or the inappropriate activation of
the developmental pathways,
enhancing cellular proliferation,
inhibiting apoptosis, and increasing
the cancer stem cell population.
The Genetic and the molecular
investigations of the PcG proteins
have long been focused on their
PcG functions. However, the PcG
proteins have recently been shown
to exert a non-polycomb functions,
contributing to the regulation of
the diverse cellular functions. The
PcG proteins regulate the
expression and function of the
several oncogenes and the tumor
suppressor genes in a PcG-
independent manner, and PcG
proteins are associated with the
survival of the patients with the
cancer.
• PRC 2 - The PRC2 (polycomb
repressive complex 2) is one of the
two classes of the polycomb-group
proteins or the (PcG). The other
component of this group of the
proteins is the PRC1 (Polycomb
Repressive Complex 1). This
complex has histone
methyltransferase activity and
primarily the methylates histone
H3 on the lysine 27 mark of the
transcriptionally silent chromatin.
The PRC2 is required for the initial
targeting of the genomic region
(PRC Response Elements or PRE)
to be silenced, while the PRC1 is
required for stabilizing this
silencing and underlies the cellular
Glossary of Genetics
memory of the silenced region after
the cellular differentiation. The
PRC1 also mono-ubiquitinates
histone H2A on the lysine 119
(H2AK119Ub1). These proteins
are required for the long term
epigenetic silencing of the
chromatin and have an important
role in the stem cell differentiation
and early embryonic development.
The PRC2 are present in most of
the multicellular organisms. The
PRC2 has a role in the X
chromosome inactivation, in
maintenance of the stem cell fate,
and in the imprinting. The
Aberrant expression of the PRC2
has been observed in the cancer.
Both loss and the gain-of-function
mutations in the PRC2
components have been identified in
the various human cancers,
suggesting complex roles of these
components in the malignancy.
• PLURIPOTENCY - It describes
the ability of a cell to develop into
the three primary germ cell layers
of the early embryo and therefore
into all cells of the adult body, but
not extra-embryonic tissues such as
the placenta. It is also described as
something that has no fixed
developmental potential.
Embryonic stem cells are
considered pluripotent cells.
• PROTEIN STRUCTURE
PREDICTION - Protein structure
prediction is the inference of the 3-
dimensional structure of a protein
from its amino acid sequence that
is the prediction of its secondary
© 2022 by JPS Scientific Publications, India
338
and tertiary structure from primary
structure. Structure prediction is
very much different from the
inverse problem of protein design.
The protein structure prediction is
so difficult because the polypeptide
chain is very flexible in nature with
the ability to rotate in multiple
ways at each amino acid which
means that the polypeptide chain is
able to fold into a staggering
number of different shapes.
• PEPTIDYL TRANSFERASES -
The peptidyl transferase is an
aminoacyltransferase as well as the
primary enzymatic function of the
ribosome, which forms peptide
bonds between the adjacent amino
acids using tRNAs during the
translation process of protein an
biosynthesis. This enzyme actively
catalyzes the reaction between the
amino group of the aminoacyl-
tRNA in the A site and the
carboxyl carbon of the peptidyl-
tRNA in the P site, forming a
peptide bond from an ester bond. It
is the primary enzymatic function
of the ribosome in prokaryotes.
The 23S rRNA nucleotides in the
peptidyl transferase center are
essential for tryptophanase operon
induction process.
• PEPTIDE DEFORMYLASE - In
the field of the enzymology, a
peptide deformylase is an enzyme
that catalyzes the chemical
reaction. This enzyme belongs to
the family of the hydrolases, those
acting on the carbon-nitrogen
bonds other than the peptide
Glossary of Genetics
bonds, specifically in the linear
amides. The systematic name of
this enzyme class is the formyl-L-
methionyl peptide
amidohydrolase. The PDF
catalyzes the removal of the N-
terminal formyl group from the
nascent polypeptides in the
bacteria to generate the mature free
N-terminal polypeptide and the
formate. To the date, several
bacterial PDFs have been
identified. Although the eukaryotes
do not use the formyl-methionine
in the protein translation, a human
homologue (HsPDF) has been
identified. This HsPDF contains a
mutation that renders this protein
much less active than its bacterial
counterpart, suggesting that the
human enzyme is an ‘evolutionary
remnant’ with no functional role.
Consequently, the PDF is an
excellent proposed drug target for
the development of the antibiotics.
The Mechanistically, EcPDF is the
most widely studied of these
enzymes.
• PLASMID CLONING - Plasmid
cloning is a technology which is
one of the most commonly used
techniques in the molecular
biology research. It plays a crucial
role in studying the structure,
function, and evolution of genes
while serving as an essential tool in
genetic, protein, and metabolic
engineering. However, the
traditional digestion-ligation
method is often limited, as both
vector and target fragments must
© 2022 by JPS Scientific Publications, India
339
have the compatible cleavage sites.
Moreover, the whole procedure
can be little bit a time-consuming
and labor-intensive procedure. In
a typical cloning experiment, a
target gene is inserted into the
circular piece of the DNA which is
called as plasmid. The plasmid is
then introduced into the bacteria
via a process called as
transformation, and the bacteria
carrying the plasmid are selected
using the antibiotics. The Most of
the general plasmids may be used
to clone the DNA insert of up to is
15 kb in size. One of the earliest
commonly used the cloning vectors
in the genetic engineering is the
pBR322 plasmid.
• PROMOTERS - A promoter is a
sequence of DNA to which the
proteins bind to initiate the
transcription process of a single
RNA transcript from the DNA
downstream of the promoter. The
RNA transcript may encode a
protein (mRNA), or can have a
function in and of itself, such as the
tRNA or the rRNA. The
Promoters are located near the
transcription start sites of the
genes, upstream on the DNA
(towards the 5' region of the sense
strand). The Promoters can be
about 100–1000 base pairs long,
the sequence of which is the highly
dependent on the gene and product
of the transcription, type or class of
the RNA polymerase recruited to
the site, and species of the
organism. The Promoters controls
Glossary of Genetics
the gene expression in the bacteria
and in the eukaryotes. The RNA
polymerase must attach to the
DNA near a gene for transcription
process to occur. The Promoter
DNA sequences provide an
enzyme for the binding site. The -
10 sequence is TATAAT and the -
35 sequences are conserved on the
average, but not in most of the
promoters. The Artificial
promoters with the conserved -10
and -35 elements transcribe the
information more slowly. All the
DNAs have the "Closely spaced
promoters" Divergent, tandem,
and the convergent orientations are
possible. The Two closely spaced
promoters will likely to interfere.
The Regulatory elements can be
several kilobases away from the
transcriptional start site in the gene
promoters which are known as
enhancers. In the eukaryotes, the
transcriptional complex can bend
the DNA, allowing the regulatory
sequences to be placed far from the
transcription site. The distal
promoter is the upstream of the
gene and can may contain the
additional regulatory elements
with a weaker influence. The RNA
polymerase II (RNAP II) bound to
the transcription start site promoter
can start the mRNA synthesis. The
CpG islands, a TATA box, and the
TFIIB recognition elements can be
found in the promoter DNA. The
Weingarten-Gabbay found these
elements have small effects on the
gene expression. A connector
© 2022 by JPS Scientific Publications, India
340
protein dimer e.g. CTCF or YY1
stabilizes the loop by anchoring
one member on the enhancer and
the other on the promoter. 47% of
the bidirectionally paired genes in
the Gene Ontology database
shared a functional category.
• POLYNUCLEOTIDE
PHOSPHORYLASE - The
Polynucleotide Phosphorylase
(PNPase) is a bifunctional enzyme
with a phosphorolytic 3' to 5'
exoribonuclease activity and a 3'-
terminal oligonucleotide
polymerase activity. bThat is, it
dismantles the RNA chain starting
at the 3' end and working toward
the 5' end. It also synthesizes the
long, highly heteropolymeric tails
in vivo. It accounts for all of the
observed residual polyadenylation
in the strains of the Escherichia
coli missing the normal
polyadenylation enzyme. It is
involved in the mRNA processing
and the degradation in the bacteria,
plants,[5] and in the humans. In
the humans, the enzyme is
encoded by the PNPT1 gene. In its
active form, the protein forms a
ring structure consisting of the
three PNPase molecules. Each of
the PNPase molecule consists of
the two RNase PH domains, an S1
RNA binding domain and a K-
homology domain. The protein is
present in the bacteria and in the
chloroplasts and mitochondria of
some eukaryotic cells. In the
eukaryotes and archaea, a
structurally and evolutionary
Glossary of Genetics
related complex exists, called as
the exosome complex. The same
abbreviation (PNPase) is also used
for the another, otherwise the
unrelated enzyme, Purine
nucleoside phosphorylase.
• POLYPRIMIDINE TRACT -
The polypyrimidine tract is a
region of the pre-messenger RNA
(mRNA) that promotes the
assembly of the spliceosome, the
protein complex specialized for
carrying out the RNA splicing
during the process of the post-
transcriptional modification. The
region is rich with the pyrimidine
nucleotides, especially the uracil,
and is usually around 15–20 base
pairs long, located about 5–40 base
pairs before the 3' end of the intron
to be spliced. A number of the
protein factors bind to or associate
with the polypyrimidine tract,
including the spliceosome
component U2AF and the
polypyrimidine tract-binding
protein (PTB), which plays a
regulatory role in the alternative
splicing. The PTB's primary
function is in exon silencing, by
which a particular exon region
normally spliced into the mature
mRNA is instead left out, resulting
in the expression of an isoform of
the protein for which the mRNA
codes. Because the PTB is
ubiquitously expressed in many of
the higher eukaryotes, it is thought
to suppress the inclusion of the
"weak" exons with the poorly
defined splice sites. However, the
© 2022 by JPS Scientific Publications, India
341
PTB binding is not sufficient to
suppress the "robust" exons
• POLYPYRIMIDINE TRACT
BINDING PROTEIN - The
Polypyrimidine tract-binding
protein, also known as the PTB or
the hnRNP I, is an RNA-binding
protein. The PTB functions mainly
as a splicing regulator, although it
is also involved in the alternative 3'
end processing, mRNA stability
and in the RNA localization. The
Two 2020 studies have shown that
the depleting PTB mRNA in
astrocytes can convert these
astrocytes to the functional
neurons. These studies also show
that such a treatment can be
applied to the substantia nigra of
the mice models of the Parkinson's
disease in order to convert the
astrocytes to the dopaminergic
neurons and as a consequence to
restore the motor function in the
these mice.
• POLYSOME PROFILING - The
Polysome profiling is a technique
in the molecular biology that is
used to study the association of the
mRNAs with the ribosomes. It is
important to note that this
technique is different from the
ribosome profiling. Both the
techniques have been reviewed and
both are used in the analysis of the
translatome, but the data they
generate are at a very different
levels of the specificity. When
employed by the experts, the
technique is remarkably
reproducible the 3 profiles in the
Glossary of Genetics
first image are from the 3 different
experiments. It is possible to use
this technique to study the overall
degree of the translation in the cells
but it can be used much more
specifically to study the individual
proteins and their mRNAs. As an
example shown in the lower
portion of the figure, a protein that
composes part of the small subunit
can first be detected in the 40S
fraction, then nearly disappears
from the 60S fraction, then
reappears in the 80S and in the
polysome fractions.
• POSITIONAL INFORMATION
- The concept of the positional
information proposes that the cells
acquire positional values as in a
coordinate system, which they
interpret by developing in a
particular ways to give rise to the
spatial patterns. Some of the best
evidence for the positional
information comes from the
regeneration experiments, and the
patterning of the leg and antenna
in the Drosophila, and the
vertebrate limb. The Central
problems are how positional
information is set up, how it is
recorded, and then how it is
interpreted by the cells. A number
of the models have been proposed
for the setting up of the positional
gradients, and most are based on
the diffusion of a morphogen and
its interactions with the
extracellular molecules, however,
diffusion may not be reliable
mechanism. There are also
© 2022 by JPS Scientific Publications, India
342
mechanisms based on the timing.
A key feature of positional
information being the basis for the
pattern formation is that there is no
prepattern in the embryo.
• POSITION WEIGHT MATRIX -
A position weight matrix (PWM),
also known as the position-specific
weight matrix (PSWM) or the
position-specific scoring matrix
(PSSM), is a commonly used
representation of the motifs
(patterns) in the biological
sequences. The PWMs are often
derived from a set of the aligned
sequences that are thought to be
functionally related and have
become an important part of the
many software tools for the
computational motif discovery.
There are various algorithms to
scan for the hits of the PWMs in
the sequences. One example is the
MATCH algorithm which has
been implemented in the
ModuleMaster. More sophisticated
algorithms for the fast database
searching with the nucleotide as
well as the amino acid
PWMs/PSSMs are implemented
in the possumsearch software.
• PHYSICAL MAPPING - The
Physical map is a technique used in
the molecular biology to find the
order and the physical distance
between the DNA base pairs by the
DNA markers. It is one of the gene
mapping techniques which can
determine the sequence of the
DNA base pairs with the high
accuracy. Genetic mapping,
Glossary of Genetics
another approach of the gene
mapping, can provide the markers
needed for the physical mapping.
However, as the former deduces
the relative gene position by
recombination frequencies, it is less
accurate than the latter. Physical
mapping uses the DNA fragments
and the DNA markers to assemble
the larger DNA pieces. With the
overlapping regions of the
fragments, researchers can deduce
the positions of the DNA bases.
There are different techniques to
visualize the gene location,
including the somatic cell
hybridization, radiation
hybridization and in situ
hybridization. The different
approaches to the physical
mapping are available for
analyzing the different sizes of the
genome and achieving the different
levels of accuracy. Low- and high-
resolution mapping are the two
classes for the various resolution of
the genome, particularly for the
investigation of the chromosomes.
The three basic varieties of the
physical mapping are the
fluorescent in situ hybridization
(FISH), restriction site mapping
and the sequencing by the clones.
• POTATO VIRUS Y - The Potato
virus Y (PVY) is a plant
pathogenic virus of the family
Potyviridae, and one of the most
important plant viruses affecting
the potato production. The PVY
infection of the potato plants
results in a variety of the symptoms
© 2022 by JPS Scientific Publications, India
343
depending on the viral strain. The
mildest of these symptoms is the
production loss, but the most
detrimental is the 'potato tuber
necrotic ringspot disease'
(PTNRD). The Necrotic ringspots
render the potatoes unmarketable
and can therefore result in a
significant loss of the income. The
PVY is transmissible by the aphid
vectors but may also remain
dormant in the seed potatoes. This
means that using the same line of
potato for the production of the
seed potatoes for the several
consecutive generations will lead to
a progressive increase in the viral
load and the subsequent loss of the
crop.
• POT 1 - The Protection of the
telomeres protein 1 is a protein that
in the humans is encoded by the
POT1 gene. This gene is a member
of the telombin family and encodes
a nuclear protein involved in the
telomere maintenance.
Specifically, this protein functions
as a member of a multi-protein
complex known as the shelterin,
that binds to the TTAGGG repeats
of the telomeres, regulating the
telomere length and protecting the
chromosome ends from the
illegitimate recombination,
catastrophic chromosome
instability, and the abnormal
chromosome segregation.
Alternatively the spliced transcript
variants have been described. The
absence of the POT1 in the mouse
embryonic fibroblasts and chicken
Glossary of Genetics
cells leads to a detrimental DNA
damage response on the telomeres
resulting in the telomere
dysfunction-induced foci (TIFs).
The POT1 is required for the
telomere protection because it
allows for the telomere inhibition
of the DNA damage response
factors. The protein also serves a
role in the regulation of the
telomerase activity on the
telomeres. In vitro experiments
utilizing the human POT1 have
shown that the reduction in the
POT1 levels result in the
elongation of the telomeres.
• PRFA - The PrfA, a transcription
factor structurally related to the
Crp/Fnr, activates Listeria
monocytogenes virulence genes
during the intracellular infection..
The in vitro transcriptional
properties of the recombinant PrfA
(I45S) and the PrfA (G145S) were
compared to those of the
PrfA(WT) at the two differentially
regulated PrfA-dependent
promoters, PplcA and the PactA.
The two PrfA mutations increased
the affinity for the target DNA to a
different extent, and the differences
in the DNA binding (PrfA (G145S)
> PrfA (I45S) >>> PrfA(WT))
correlated with the proportional
differences in the transcriptional
activity. The use of the PrfA
proteins revealed that the PplcA
had a greater affinity for, and was
more sensitive to the PrfA than the
PactA. RNA polymerase (RNAP)
initiated transcription
© 2022 by JPS Scientific Publications, India
344
independently of PrfA at the
PplcA, but not at the PactA,
consistent with the bandshift
experiments suggesting that the
PplcA has a greater affinity for the
RNAP than the PactA. Thus,
differences in the affinity for both
the PrfA and the RNAP appear to
determine the different expression
pattern of the PrfA-regulated
promoters.
• PEPTIDYL TRANSFERASE -
The peptidyl transferase is an
aminoacyltransferase as well as the
primary enzymatic function of the
ribosome, which forms the peptide
bonds between the adjacent amino
acids using the tRNAs during the
translation process of the protein
biosynthesis. The substrates for the
peptidyl transferase reaction are
the two tRNA molecules, one
bearing the growing peptide chain
and the other bearing the amino
acid that will be added to the
chain. The peptidyl chain and the
amino acids are attached to their
respective tRNAs via the ester
bonds to the O atom at the CCA-3'
ends of these tRNAs. The  Peptidyl
transferase is an enzyme that
catalyzes the addition of an amino
acid residue in order to grow the
polypeptide chain in the protein
synthesis. It is located in the large
ribosomal subunit, where it
catalyzes the peptide bond
formation. It is composed entirely
of the RNA. The alignment
between the CCA ends of the
ribosome-bound peptidyl tRNA
Glossary of Genetics
and aminoacyl tRNA in the
peptidyl transferase center
contribute to its ability to catalyze
the these reactions.
• PROBOSCIPEDIA - The
Proboscipedia (pb) is a protein
coding gene in the Drosophila
melanogaster, the fruit fly. This
hox gene participates in the
development of the labial and the
maxillary palps and the
mouthparts in the Drosophila fly.
The pb gene is known to regulate
the location of the antenna,
maxillary palp, tarsus and the
proboscis identities. The Mutated
versions of the pb gene result in the
prothoracic (anterior to thorax)
legs from the labial palps and the
maxillary palps that display the
malformation or the smaller size.
• PSEUDOGENE - The
Pseudogenes are the nonfunctional
segments of the DNA that
resemble the functional genes.
Most arise as the superfluous
copies of the functional genes,
either directly by the DNA
duplication or indirectly by the
reverse transcription of an mRNA
transcript. The Pseudogenes are
usually identified when the
genome sequence analysis finds the
gene-like sequences that lack the
regulatory sequences needed for
the transcription or the translation,
or whose coding sequences are
obviously defective due to the
frameshifts or the premature stop
codons. Most of the non-bacterial
genomes contain many
© 2022 by JPS Scientific Publications, India
345
pseudogenes, often as many as the
functional genes. This is not
surprising, since the various
biological processes are expected to
accidentally create the
pseudogenes, and there are no
specialized mechanisms to remove
them from the genomes.
Eventually the pseudogenes may
be deleted from their genomes by
the chance DNA replication or the
DNA repair errors, or they may
accumulate so many mutational
changes that they are no longer
recognizable as the former genes.
Analysis of these degeneration
events helps clarify the effects of
the non-selective processes in the
genomes.
• PROFLAVINE - The proflavine,
also called as the proflavin and the
diaminoacridine, is an acriflavine
derivative, a disinfectant
bacteriostatic against many of the
gram-positive bacteria. It has been
used in the form of the
dihydrochloride and as the
hemisulfate salts as a topical
antiseptic, and was formerly used
as a urinary antiseptic. The
Proflavine is also known to have a
mutagenic effect on the DNA by
intercalating between the nucleic
acid base pairs. It differs from most
of the other mutagenic components
by causing the basepair-deletions
or the basepair-insertions and not
substitutions. In the presence of the
light, proflavine can induce the
double-stranded breaks in the
DNA. The Proflavine absorbs
Glossary of Genetics
strongly in the blue region at the
445 nm (in water at pH 7) with the
molar extinction coefficient of c.
40,000.
• PROMOTER ESCAPE - The
Promoter escape is the process that
an initiated RNA polymerase
(RNAP) molecule undergoes to
achieve the initiation-elongation
transition. Having made this
transition, an RNAP molecule
would be relinquished from its
promoter hold to perform the
productive (full-length)
transcription. Prior to the
transition, this process is
accompanied by the abortive RNA
formation-the amount and pattern
of the which is controlled by the
promoter sequence information.
The Qualitative and the
quantitative analysis of the
abortive/productive transcription
from the several Escherichia coli
promoters and their sequence
variants led to the understanding
that a strong (RNAP-binding)
promoter is more likely to be rate
limited (during the transcription
initiation) at the escape step and
the produce abortive transcripts. Of
the two subelements in the
promoter, the PRR (which is the
core Promoter Recognition
Region) was found to set the
initiation frequency and the rate-
limiting step, while the ITS (which
is the Initial Transcribed Sequence
region) modulated the ratio of the
abortive versus productive
transcription.
© 2022 by JPS Scientific Publications, India
346
• PROTEIN FOLDING - The
Protein folding is the physical
process by which a protein chain is
translated to the it's native three-
dimensional structure, typically a
"folded" conformation by the
which the protein becomes
biologically functional. Via an
expeditious and the reproducible
process, a polypeptide folds into its
characteristic three-dimensional
structure from a random coil. Each
of the protein exists first as an
unfolded polypeptide or the
random coil after being translated
from a sequence of the mRNA to a
linear chain of the amino acids. At
this stage the polypeptide lacks any
stable (long-lasting) three-
dimensional structure (the left
hand side of the first figure). As the
polypeptide chain is being
synthesized by a ribosome, the
linear chain begins to fold into the
its three-dimensional structure. The
Folding of tye many of the proteins
begins even during the translation
of the polypeptide chain. The
Amino acids interact with each
other to produce a well-defined
three-dimensional structure, the
folded protein (the right hand side
of the figure), which is known as
the native state. The resulting
three-dimensional structure is
determined by the amino acid
sequence or the primary structure
(Anfinsen's dogma).
• PROTEIN PROTEIN
INTERACTIONS - The Protein–
protein interactions (PPIs) are
Glossary of Genetics
physical contacts of the high
specificity established between the
two or the more protein molecules
as a result of the biochemical
events steered by the interactions
that include the electrostatic forces,
hydrogen bonding and the
hydrophobic effect. Many are the
physical contacts with the
molecular associations between the
chains that occur in a cell or in a
living organism in a specific
biomolecular context. The PPIs
have been studied with many of
the methods and from the different
perspectives: biochemistry,
quantum chemistry, molecular
dynamics, signal transduction,
among others. All this information
enables the creation of the large
protein interaction networks
similar to the metabolic or the
genetic/epigenetic networks – that
empower the current knowledge on
the biochemical cascades and the
molecular etiology of the disease,
as well as the discovery of the
putative protein targets of the
therapeutic interests.
• PROPELLER TWIST - The
Propeller-Twist in the base-pairs
makes stacking into a dinucleotide
step more awkward than in the
plane base-pairs. In particular, it
provides a stereochemical
"locking" effect which can make
the steps with the highly Propeller-
Twisted base-pairs rigid. Although
the origins of the Propeller-Twist
are not yet clearly understood, this
result provides a key to
© 2022 by JPS Scientific Publications, India
347
understanding the flexibility of the
DNA in the bending around the
proteins.
• P53 GENE - The tumor protein
P53, also known as the p53,
cellular tumor antigen p53
(UniProt name), the Guardian of
the Genome, phosphoprotein p53,
tumor suppressor p53, antigen NY-
CO-13, or the transformation-
related protein 53 (TRP53), is any
isoform of the protein encoded by
the homologous genes in the
various organisms, such as the
TP53 (humans) and the Trp53
(mice). The p53 proteins (originally
thought to be, and often spoken of
as, a single protein) are crucial in
the vertebrates, where they prevent
the cancer formation. As such, the
p53 has been described as "the
guardian of the genome" because
of its role in the conserving
stability by preventing the genome
mutation. Hence the TP53 is
classified as a tumor suppressor
gene. The p53 plays a role in the
regulation or the progression
through the cell cycle, apoptosis,
and the genomic stability.
• P73 GENE - The p73 is a protein
which is related to the p53 tumor
protein. Because of its structural
resemblance to the p53, it has also
been considered a tumor
suppressor. It is involved in the cell
cycle regulation, and the induction
of the apoptosis. Like the p53, p73
is characterized by the presence of
the different isoforms of the
protein. This is explained by the
Glossary of Genetics
splice variants, and an alternative
promoter in the DNA sequence. It
is expressed as the distinct forms
differing at either at the C- or the
N-terminus. Currently, the six
different C-terminus splicing
variants have been found in the
normal cells. The p73 gene encodes
a protein with a significant
sequence homology and a sequences
functional similarity with the
tumor suppressor p53. The over-
expression of the p73 in cultured
cells promotes a growth arrest
and/or the apoptosis similarly to
the p53. The p73 gene has been
mapped to the chromosome region
(1p36. 2-3) a locus commonly
deleted in the various tumor
entities and the human cancers.
• PAIRED END TAGS - The
Paired-stop tags (PET) (from time
to time known as as the "Paired-
End diTags", or certainly the
"ditags") are the fast sequences on
the 5’ and 3' ends of a DNA
fragment which can
be specific sufficient that they
(theoretically)
exist collectively handiest as soon
as in a at the molecular level it was found
genome, consequently making
the series of the DNA
in among them to be had upon
thebsearch or upon
the similarly sequencing. The
Paired-stop tags (PET)
exist withinside the PET libraries
with the intervening DNA absent,
that is, a PET "represents" a
bigger fragment of the genomic or
© 2022 by JPS Scientific Publications, India
348
the cDNA via way of means
of such as a quick 5' linker series,
a quick 5' series tag,
a quick 3' series tag, and a quick 3'
linker series. It changed
into proven conceptually that
the thirteen base pairs
are enough to map the tags
uniquely. However, the longer
are extra realistic for
mapping the reads uniquely. The
endonucleases used to supply the
PETs provide longer tags, however
the sequences of the 50–100
• PAIR RULE GENE - A pair-rule
gene is a type of the gene involved
in the development of the
segmented embryos of the insects.
The Pair-rule genes are expressed
as a result of the differing
concentrations of the gap gene
proteins, which encode the
transcription factors controlling the
pair-rule gene expression. The
Pair-rule genes are defined by the
effect of a mutation in that the
gene, which causes the loss of the
normal development in the
alternating segments. Once the
pair-rule genes had been identified
that each of the gene is expressed
in the alternate parasegments
regions in the embryo that are
closely related to the segments, but
are slightly out of the register. Each
parasegment includes the posterior
part of the one (future) segment,
and an anterior part of the next
(more posterior) segment. The
bands of the expression of the pair-
Glossary of Genetics
rule genes correspond to the
regions missing in the mutant. The
expression of the pair-rule genes in
bands is dependent both upon the
direct regulation by the gap genes
and on the regulatory interactions
between the pair-rule genes
themselves.
• PROTOCELL - A protocell (or
the protobiont) is a self-organized,
endogenously ordered, spherical
collection of the lipids proposed as
a stepping-stone toward the origin
of the life. A central question in the
evolution is how the simple
protocells first arose and how they
could differ in the reproductive
output, thus enabling the
accumulation of the novel
biological emergences over the
time, i.e. biological evolution.
Although a functional protocell has
not yet been achieved in a
laboratory setting, the goal to
understand the process appears
well within the reach.
• PRNP - The PRNP (prion protein)
is the human gene encoding for the
major prion protein PrP (prion
protein, Pr for the prion, and P for
the protein), also known as the
CD230 (cluster of the
differentiation 230). The
Expression of the protein is most
predominant in the nervous system
but occurs in many of the other
tissues throughout the body. The
strong association to the
neurodegenerative diseases raises
many questions of the function of
PrP in the brain. A common
© 2022 by JPS Scientific Publications, India
349
approach is using the PrP-
knockout and the transgenic mice
to investigate the deficiencies and
the differences. The Initial attempts
produced the two strains of the
PrP-null mice that show no
physiological or the developmental
differences when subjected to an
array of the tests. However, more
recent strains have shown the
significant cognitive abnormalities.
The PrP is present in both the pre-
and the post-synaptic
compartments, with the greatest
concentration in the pre-synaptic
portion. Considering this and the
PrP's suite of the behavioral
influences, the neural cell functions
and the interactions are of the
particular interest. Based on the
copper ligand, one proposed
function casts PrP as a copper
buffer for the synaptic cleft.
• PRND - The Prion protein 2
(dublet), also known as the PRND,
or the Doppel protein, is a protein
which in the humans is encoded by
the PRND gene. This gene is
found on the chromosome 20,
approximately around 20 kbp
downstream of the gene which is
encoding the cellular prion protein,
to which it is biochemically and
structurally similar. The protein
encoded by this gene is a
membrane
glycosylphosphatidylinositol-
anchored glycoprotein that is
found predominantly in the testis.
The Mutations in this gene may
lead to the neurological disorders.
Glossary of Genetics
• PSEUDOKNOTS - A pseudoknot
is a nucleic acid secondary
structure containing at least the
two stem-loop structures in which
half of one stem is intercalated
between the two halves of the
another stem. The pseudoknot was
first recognized in the turnip
yellow mosaic virus in the year
1982. The Pseudoknots fold into
the knot-shaped three-dimensional
conformations but are not the true
topological knots. The Several
important biological processes rely
on the RNA molecules that form
the pseudoknots, which are often
RNAs with the extensive tertiary
structure. For example, the
pseudoknot region of the RNase P
is one of the most conserved
elements in all of the evolution.
The telomerase RNA component
contains a pseudoknot that is
critical for the activity, and the
several type ofv viruses use a
pseudoknot structure to form the
tRNA-like motif to infiltrate the
host cell. Many types of the
pseudoknots exist, differing by how
they cross and how many times
they cross. To reflect this
difference, the pseudoknots are
classed into the H-, K-, L-, M-
types, with each successive type
adding a layer of the step
intercalation.
• PSEUDOURIDINE - The
Pseudouridine is an isomer of the
nucleoside uridine in which the
uracil is attached via the carbon-
carbon instead of the nitrogen-
© 2022 by JPS Scientific Publications, India
350
carbon glycosidic bond. The
Pseudouridine is the most
abundant RNA modification in the
cellular RNA. After the
transcription and the following
synthesis, RNA can be modified
with over 100 chemically distinct
modifications. These can
potentially regulate the RNA
expression post-transcriptionally,
in addition to the four standard
nucleotides and play a variety of
the roles in the cell including the
translation, localization and the
stabilization of the RNA. The
Pseudouridine, being one of them,
is the C5-glycoside isomer of the
uridine that contains a C-C bond
between the C1 of the ribose sugar
and the C5 of the uracil, rather
than the usual C1-N1 bond found
in the uridine. The C-C bond gives
it more rotational freedom and
conformational flexibility. In
addition, the pseudouridine has an
extra hydrogen bond donor at the
N1 position. Also known as the 5-
ribosyluracil, the pseudouridine is
a ubiquitous yet enigmatic
constituent of the structural RNAs
(transfer, ribosomal, small nuclear
(snRNA) and small nucleolar).
Recently it has also been
discovered in the coding RNA.
Being the most abundant, it is
found in all the 3 phylogenetic
domains of the life and was the
first to be discovered. The
Pseudouridine accounts for 4% of
the nucleotides in the yeast tRNA.
This base modification is able to
Glossary of Genetics
stabilize the RNA and the improve
base-stacking by forming the
additional hydrogen bonds with
water through its extra imino
group.
• PSTL - The PstI is a type II
restriction endonuclease isolated
from the Gram negative species,
Providencia stuartii. The PstI
cleaves the DNA at the recognition
sequence 5′-CTGCA/G-3′
generating fragments with the 3′-
cohesive termini. This cleavage
yields the sticky ends 4 base pairs
long. The PstI is catalytically active
as a dimer. The two subunits are
related by a 2-fold symmetry axis
which in the complex with the
substrate coincides with the dyad
axis of the recognition sequence. It
has a molecular weight of the
69,500 and contains about 54
positive and 41 negatively charged
residues. The PstI preferentially
cleaves the purified pSM1 DNA
without being influenced by the
superhelicity of the substrate. Its
differential cleavage rates at
different restriction sites is due to
the five features of the duplex
structure. The proximity to the
ends in the linear DNA molecule,
variation in the DNA sequence
within the recognition sites for the
enzymes, short distance between
the regions of the unusual DNA
sequences and the recognition
sites, and lastly the special
structures such as the loops and
hairpins. The collective effect of
these five factors could affect the
© 2022 by JPS Scientific Publications, India
351
accessibility of the restriction
enzyme to its recognition sites.
• PTEN - The Phosphatase and the
tensin homolog (PTEN) is a
phosphatase in the humans and is
encoded by the PTEN gene. The
Mutations of this gene are a step in
the development of the many
cancers, specifically glioblastoma,
lung cancer, breast cancer, and the
prostate cancer. The genes
corresponding to the PTEN have
been identified in most of the
mammals for which the complete
genome data are available. The
PTEN protein acts as a
phosphatase to the
dephosphorylate
phosphatidylinositol (3,4,5)-
trisphosphate. The PTEN
specifically catalyses the
dephosphorylation of the 3`
phosphate of the inositol ring in
the PIP3, resulting in the
biphosphate product PIP2. This
dephosphorylation is very
important because it results in the
inhibition of the Akt signaling
pathway, which plays an important
role in the regulating of the cellular
behaviors such as tbe cell growth,
survival, and the migration. The
PTEN also has the weak protein
phosphatase activity, but this
activity is also crucial for its role as
a tumor suppressor. The PTEN's
protein phosphatase activity may
be involved in the regulation of the
cell cycle, preventing cells from the
growing and dividing too rapidly.
There have been numerous
Glossary of Genetics
reported protein substrates for the
PTEN, including IRS1 and
Dishevelled. The PTEN is one of
the targets for the drug candidates
such as the oncomiR, MIRN21.
• PULSE LABELLING - The Pulse
labeling tissue with the radioactive
amino acids offers the another way
to measure the elastin synthesis at
the protein level. Like the RNA
analysis, the pulse labeling is
restricted to providing a snapshot
of the elastin synthesis at the time
when the labeling is undertaken.
The procedure involves the
incubating viable tissue with the
radiolabeled glycine or the valine
(abundant amino acids in elastin),
and the “chasing” the label into the
insoluble elastin. Because the
cross-linked elastin once laid down
does not turn over at any
appreciable rate, measurement of
the accumulated radioactivity in
the purified insoluble elastin allows
for the estimation of the average
rate of the elastin production over
the time period of the labeling.
While relatively straightforward,
the procedure requires the viable
tissue, radioactive amino acids,
and the elastin purification after
the radiolabeling period.
• PUROMYCIN - The Puromycin
is an antibiotic protein synthesis
inhibitor which causes the
premature chain termination
during the translation. The
puromycin is an aminonucleoside
antibiotic, derived from the
Streptomyces alboniger bacterium,
© 2022 by JPS Scientific Publications, India
352
that causes the premature chain
termination during the translation
taking place in the ribosome. The
Part of the molecule resembles the
3' end of the aminoacylated tRNA.
It enters the A site and transfers to
the growing chain, causing the
formation of a puromycylated
nascent chain and the premature
chain release.The exact mechanism
of the action is unknown at this
time but the 3' position contains an
amide linkage instead of the
normal ester linkage of tRNA.
That makes the molecule much
more resistant to the hydrolysis
and stops the ribosome. The
Puromycin is selective for either
the prokaryotes or the eukaryotes.
The puromycin is critical in the
mRNA display. In this reaction, a
puromycin molecule is chemically
attached to the end of an mRNA
template, which is then translated
into the protein.
• PYRAZINAMIDE - The
Pyrazinamide is a medication used
to treat the tuberculosis. For the
active tuberculosis, it is often used
with the rifampicin, isoniazid, and
either thevstreptomycin or the
ethambutol. It is not generally
recommended for the treatment of
the latent tuberculosis. It is taken
by the mouth. The Pyrazinamide is
only used in the combination with
the other drugs such as the
isoniazid and rifampicin in the
treatment of the Mycobacterium
tuberculosis and as directly
observed therapy (DOT). It is
Glossary of Genetics
never used on its own. It has no
other indicated medical uses. In
particular, it is not used to treat the
other mycobacteria,
Mycobacterium bovis and the
Mycobacterium leprae are innately
resistant to the pyrazinamide. The
common side effects include the
nausea, loss of appetite, muscle
and joint pains, and the rash. More
serious side effects include the
gout, liver toxicity, and sensitivity
to the sunlight. It is not
recommended in those with the
significant liver disease or the
porphyria. It is unclear if the use
during pregnancy is safe but it is
likely okay during the
breastfeeding. The Pyrazinamide is
in the antimycobacterial class of
the medications.
• PYRUVATE KINASE - The
Pyruvate kinase is the enzyme
involved in the last step of the
glycolysis. It catalyzes the transfer
of a phosphate group from the
phosphoenolpyruvate (PEP) to the
adenosine diphosphate (ADP),
yielding one molecule of the
pyruvate and one molecule of the
ATP. The pyruvate kinase was
inappropriately named before it
was recognized that it did not
directly catalyze the
phosphorylation of the pyruvate,
which does not occur under the
physiological conditions. The
Pyruvate kinase is present in the
four distinct, tissue-specific
isozymes in the animals, each
consisting of the particular kinetic
© 2022 by JPS Scientific Publications, India
353
properties necessary to
accommodate the variations in the
metabolic requirements of the
diverse tissues. The Genetic defects
of this enzyme cause the disease
known as the pyruvate kinase
deficiency. In this condition, a lack
of the pyruvate kinase slows down
the process of the glycolysis. This
effect is especially devastating in
the cells that lack the
mitochondria, because these cells
must use the anaerobic glycolysis
as their sole source of the energy
because the TCA cycle is not
available. For example, the red
blood cells, which in a state of the
pyruvate kinase deficiency, rapidly
become deficient in the ATP and
can undergo the hemolysis.
Therefore, pyruvate kinase
deficiency can cause the chronic
nonspherocytic hemolytic anemia
(CNSHA).
• PAR - The Protease-activated
receptors (PAR) are a subfamily of
the related G protein-coupled
receptors that are activated by the
cleavage of part of their
extracellular domain. They are
highly expressed in the platelets,
and also on the endothelial cells,
myocytes and the neurons. The
cellular effects of the thrombin are
mediated by the protease-activated
receptors (PARs). The Thrombin
signalling in the platelets
contributes to the hemostasis and
the thrombosis. The Endothelial
PARs participate in the regulation
of the vascular tone and the
Glossary of Genetics
permeability while in vascular
smooth muscle they mediate the
contraction, proliferation, and the
hypertrophy. In the endothelial
cells PARs play a key role in thr
promotion vascular barrier
function as they provide a positive
signals for the endothelial adhesion
molecules, intercellular adhesion
molecule-1(ICAM-1), and E-
selectin). The PARs contribute to
the pro-inflammatory response.
For example the PAR4 induces
leukocyte migration and the PAR2
helps macrophages to produce the
cytokines such as the interleukin-8
(IL-8).
• PATCHED - The Patched (Ptc) is
a conserved 12-pass
transmembrane protein receptor
that plays an obligate negative
regulatory role in the Hedgehog
signaling pathway in the insects
and in the vertebrates. The Patched
is an essential gene in the
embryogenesis for the proper
segmentation in the fly embryo,
mutations in which may be
embryonic lethal. The Patched
functions as the receptor for the
Hedgehog protein and controls its
spatial distribution, in part via the
endocytosis of the bound
Hedgehog protein, which is then
targeted for the lysosomal
degradation. The Mutated patched
proteins have been implicated in a
number of the cancers including
the basal cell carcinoma,
medulloblastoma, and the
rhabdomyosarcoma. The
© 2022 by JPS Scientific Publications, India
354
Hereditary mutations in the human
patched homolog PTCH1 causes
the autosomal dominant Gorlin
syndrome, which consists of the
overgrowth and the hereditary
disposition to the cancer including
the basal cell carcinoma and
themedulloblastoma. Mice with
the mutations in the mouse
PTCH1 similarly develop the
medulloblastoma.
• PCNA - The Proliferating cell
nuclear antigen (PCNA) is a DNA
clamp that acts as a processivity
factor for the DNA polymerase δ
in the eukaryotic cells and is
essential for the replication. The
PCNA is a homotrimer and
achieves its processivity by
encircling the DNA, where it acts
as a scaffold to recruit the proteins
involved in the DNA replication,
DNA repair, chromatin
remodeling and the epigenetics.
Many of the proteins interact with
the PCNA via the two known
PCNA-interacting motifs PCNA-
interacting peptide (PIP) box and
the AlkB homologue 2 PCNA
interacting motif (APIM). The
Proteins binding to the PCNA via
the PIP-box are mainly involved in
the DNA replication whereas the
proteins binding to the PCNA via
APIM are mainly important in the
context of the genotoxic stress. The
protein encoded by this gene is
found in the nucleus and is a
cofactor of the DNA polymerase
delta. The encoded protein acts as
a homotrimer and helps to increase
Glossary of Genetics
the processivity of the leading
strand synthesis during the DNA
replication. In response to the
DNA damage, this protein is
ubiquitinated and is involved in the
RAD6-dependent DNA repair
pathway. Two transcript variants
encoding the same protein have
been found for the this gene. The
Pseudogenes of this gene have
been described on the chromosome
4 and on the X chromosome. The
PCNA is also found in the archaea,
as a processivity factor of the polD,
the single multi-functional DNA
polymerase in this domain of life.
• PEPTIDYL TRANSFERASE -
The peptidyl enzyme is an
associate degree
aminoacyltransferase additionally
because the primary accelerator
perform of the ribosome, that
forms the amide bonds between the
adjacent organic compounds
victimisation the ribonucleic acids
throughout the interpretation
method of the protein biosynthesis.
The substrates for the peptidyl
transferase reaction are the 2 tRNA
molecules, one bearing the growing
peptide chain and therefore the
different bearing the amino acid
that may be additional to the
chain. The peptidyl chain and the
amino acids are connected to their
various tRNAs via the organic
compound bonds to the O atom at
the CCA-3' ends of those tRNAs.
The Peptidyl transferase is
associate degree accelerator that
change states the addition of an
© 2022 by JPS Scientific Publications, India
355
organic compound residue so as to
grow the peptide chain within the
protein synthesis. it's set in the
massive ribosomal subunit,
wherever it catalyzes the bond
formation. it's composed entirely of
the RNA. The alignment between
the CCA ends of the ribosome-
bound peptidyl ribonucleic acid
and therefore the aminoacyl tRNA
in the peptidyl enzyme center
contribute to its ability to catalyze
these reactions. This reaction
happens via the nucleophilic
displacement.
• PROTEIN SYNTHESIS
INHIBITORS - A protein
synthesis inhibitor is a compound
that stops or slows the growth or
the proliferation of the cells by
disrupting the processes that lead
directly to the generation of the
new proteins. While a broad
interpretation of this definition
could be used to describe an nearly
any compound depending on the
concentration, in practice it usually
refers to the compounds that act at
the molecular level on the
translational machinery (either the
ribosome itself or the translation
factor), taking advantages of the
major differences between the
prokaryotic and the eukaryotic
ribosome In general, the protein
synthesis inhibitors work at the
different stages of the bacterial
mRNA translation into the
proteins, like the initiation,
elongation (including the
aminoacyl tRNA entry,
Glossary of Genetics
proofreading, peptidyl transfer, and
the bacterial translocation) and the
termination.
• PER 1 - The PER1 gene encodes
the period circadian protein
homolog 1 protein in the humans.
The PER1 protein is important to
the maintenance of the circadian
rhythms in the cells, and may also
play a role in the development of
the cancer. This gene is a member
of the period family of the genes. It
is expressed with a daily oscillating
circadian rhythm, or an oscillation
that cycles with a period of around
approximately 24 hours. The
PER1 is most notably expressed in
the region of the brain called as the
suprachiasmatic nucleus (SCN),
which is the primary circadian
pacemaker in the mammalian
brain. The PER1 is also expressed
throughout the mammalian
peripheral tissues. The Genes in
this family encode components of
the circadian rhythms of the
locomotor activity, metabolism,
and the behavior. The Circadian
expression of the PER1 in the
suprachiasmatic nucleus will free-
run in the constant darkness,
meaning that the 24-hour period of
the cycle will persist without the
aid of the external light cues. The
time of the gene expression is
sensitive to the light, as light
during a mammal's subjective night
results in a sudden increase in per
the expression and thus a shift in
the phase in the suprachiasmatic
nucleus.
© 2022 by JPS Scientific Publications, India
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• P75NTR RECEPTORS - The
Low affinity nerve growth factor
receptor commonly known as the
"p75", can signal for the apoptosis
or promote the neuronal survival.
Neurotrophins that interact with
the p75NTR include the NGF,
NT-3, BDNF, and the NT-4/5.
Neurotrophins activating p75NTR
may initiate the apoptosis (for
example, via the c-Jun N-terminal
kinases signaling), and this effect
can be counteracted by the anti-
apoptotic signaling by the TrkA.
The Neurotrophin binding to the
p75NTR can promote the neuronal
survival (for example, via the NF-
kB activation). Although the NGF
has been classically described as
promoting the neuron survival and
the differentiation, research
performed in the early 2000s
suggest that the NGF with its
prodomain attached (proNGF) can
elicit apoptosis of the cells that are
positive for the LNGFR and
negative for the TrkA.
• PERMISSIVE CELLS - A
permissive cell or the host is one
that allows a virus to circumvent
its defenses and then replicate.
Usually this occurs when the virus
has modulated one or the several
of the host cellular intrinsic
defenses and the host immune
system. The permissive state of the
host has now been determined to
be the primary factor in
determining whether a virus will
cause the pathological symptoms
in the host.
Glossary of Genetics
• PHD FINGER - The PHD finger
was discovered in the year 1993 as
a Cys4-His-Cys3 motif in the plant
homeodomain (hence PHD)
proteins HAT3.1 in the
Arabidopsis and in the maize
ZmHox1a. The PHD zinc finger
motif resembles the metal binding
RING domain (Cys3-His-Cys4)
and the FYVE domain. It occurs as
a single finger, but often in the
clusters of the two or the three, and
it also occurs together with the
other domains, such as the
chromodomain and the
bromodomain. The PHD fingers of
some of the proteins, including the
ING2, YNG1 and the NURF,
have been reported to bind to the
histone H3 tri-methylated on the
lysine 4 (H3K4me3), while the
other PHD fingers have tested
negative in the such assays. A
protein called as the KDM5C has a
PHD finger, which has been
reported to bind the histone H3 tri-
methylated lysine 9 (H3K9me3).
Based on these publications, the
binding to the tri-methylated
lysines on the histones may
therefore be a property widespread
among the PHD fingers. Domains
that bind to modified the histones,
are called as the epigenetic readers
as they specifically recognize the
modified version of the residue and
binds to it.
• PITC - The thermo Scientific
Pierce Phenylisothiocyanate
(PITC) is a high-purity reagent for
the pre-column quantitative
© 2022 by JPS Scientific Publications, India
357
derivatization of the amino acids
by the reverse-phase HPLC. The
Phenylisothiocyanate (PITC), also
known as Edman's Reagent,
enables the sequential degradation
of the amino acids in a polypeptide
chain, yielding the primary
structural information. The PITC
reacts readily with the amino acids
at the alkaline pH. The precolumn
derivatization results in the
phenylthiocarbamyl derivatives
(PTC-amino acids) that can be
separated and quantified using the
reverse-phase HPLC. This method
produces the stable products with
all the amino acids, including the
proline. The PITC is a volatile,
making it possible to remove th3
excess reagent in the vacuo,
thereby minimizing the possibility
of the reagent interference.
Detection of the picomole
quantities of the derivatives can be
achieved using a UV detector at
the 254nm. The PITC
derivatization followed by the
reverse-phase chromatography can
be used for the identification and
the quantitation of the methylated,
halogenated, phosphorylated and
the sulfonated amino acids.
• PHOSPHAMIDON - The
Phosphamidon is an
organophosphate insecticide first
reported in the year 1960. It acts as
a cholinesterase inhibitor. The
Phosphamidon is very highly toxic
to the mammals and is listed as the
WHO Hazard Class Ia. A
harvester developed the symptoms
Glossary of Genetics
of moderately severe poisoning
after working in a field that had
been sprayed with the chemical 2
weeks earlier. He collapsed and
exhibited a significant depression
of the serum cholinesterase, but
recovered completely within the 2
days after the successful treatment
with the atropine. The
International trade of the
phosphamidon is covered by the
Rotterdam Convention.
• PHOSPHOPROTEOME - The
Phosphoproteomics is a branch of
the proteomics that identifies,
catalogs, and characterizes the
proteins containing a phosphate
group as a posttranslational
modification. The Phosphorylation
is a key reversible modification that
regulates the protein function,
subcellular localization, complex
formation, degradation of proteins
and therefore the cell signaling
networks. With all of these
modification results, it is estimated
that between the 30%–65% of all
the proteins may be
phosphorylated, some of them
multiple times. Based on the
statistical estimates from many of
the datasets, 230,000, 156,000 and
40,000 phosphorylation sites
should exist in the human, mouse,
and the yeast, respectively.
• PROTEIN TYROSINE
PHOSPHATES - The Protein
tyrosine phosphatases (systematic
name as the protein-tyrosine-
phosphate phosphohydrolase) are a
group of the enzymes that remove
© 2022 by JPS Scientific Publications, India
358
the phosphate groups from the
phosphorylated tyrosine residues
on the proteins. The Protein
tyrosine (pTyr) phosphorylation is
a common post-translational
modification that can create the
novel recognition motifs for the
protein interactions and the cellular
localization, affect protein stability,
and regulate the enzyme activity.
As a consequence, maintaining an
appropriate level of the protein
tyrosine phosphorylation is
essential for many of the cellular
functions. The tyrosine-specific
protein phosphatases that catalyse
the removal of the a phosphate
group attached to a tyrosine
residue, using a cysteinyl-
phosphate enzyme intermediate.
These enzymes are a key
regulatory components in the
signal transduction pathways (such
as the MAP kinase pathway) and
the cell cycle control, and are
important in the control of the cell
growth, proliferation,
differentiation, transformation, and
the synaptic plasticity.
• PHOTOREACTIVATION - The
Photoreactivation is possibly the
simplest DNA repair mechanism
currently known. The Pyrimidine
dimers introduced into the DNA
by the UV irradiation can be
repaired by the action of a single
photoreactivating enzyme using
light in the range of around 310–
500 nm as an energy source. The
photoreactivation has a peculiar
phyletic distribution which has yet
Glossary of Genetics
to be satisfactorily explained. An
enzyme that can photoreactivate
UV-irradiated transforming the
DNA is detectable in the extracts
of most of the metazoan cells with
the exception of the placental
mammals. The Fish, amphibians,
and the reptiles all show the
photoreactivation. Among the
vertebrates, the marsupials have a
slowly acting photoreacti-vating
system. In the birds, only the
embryo and the adult brain show
the photoreactivation.
• PITX1 - The Paired-like
homeodomain 1 is a protein that in
the humans is encoded by the
PITX1 gene. This gene encodes a
member of the RIEG/PITX
homeobox family, which is in the
bicoid class of the homeodomain
proteins. The Members of this
family are involved in the organ
development and left-right
asymmetry. This protein acts as a
transcriptional regulator involved
in the basal and the hormone-
regulated activity of the prolactin.
The Mutations in this gene have
been associated with the autism,
club foot and the polydactyly in the
humans.
• piRNA - The Piwi-interacting
RNA (piRNA) is the largest class
of the small non-coding RNA
molecules expressed in the animal
cells. The piRNAs form the RNA-
protein complexes through the
interactions with the piwi-
subfamily Argonaute proteins.
These piRNA complexes are
© 2022 by JPS Scientific Publications, India
359
mostly involved in the epigenetic
and in the post-transcriptional
silencing of the transposable
elements and the other spurious or
the repeat-derived transcripts, but
can also be involved in the
regulation of the other genetic
elements in the germ line cells. The
piRNAs are mostly created from
the loci that function as the
transposon traps which provide a
kind of the RNA-mediated
adaptive immunity against the
transposon expansions and the
invasions. They are distinct from
the microRNA (miRNA) in the
size (26–31 nucleotides as opposed
to 21–24 nt), lack of the sequence
conservation, increased
complexity, and independence of
the Dicer for the biogenesis, at
least in the animals.
• PIWI - The Piwi (or PIWI) genes
were identified as the regulatory
proteins responsible for the stem
cell and the germ line cell
differentiation. The Piwi is an
abbreviation of the P-element
Induced WImpy testis in the
Drosophila. The Piwi proteins are
highly conserved RNA-binding
proteins and are present in both the
plants and in the animals. The Piwi
proteins belong to the
Argonaute/Piwi family and have
been classified as the nuclear
proteins. Studies on the Drosophila
have also indicated that the Piwi
proteins have no slicer activity
conferred by the presence of the
Piwi domain. In addition, the Piwi
Glossary of Genetics
associates with the
heterochromatin protein 1, an
epigenetic modifier, and the
piRNA-complementary sequences.
These are indications of the role
Piwi plays in the epigenetic
regulation. The Piwi proteins are
also thought to control the
biogenesis of the piRNA as many
as Piwi-like proteins contain the
slicer activity which would allow
the Piwi proteins to process the
precursor piRNA into the mature
piRNA.
• PLAQUE ASSAY - This assay is
based on a microbiological method
conducted in a plate. Specifically, a
confluent monolayer of the host
cells is infected with the virus at a
varying dilutions and covered with
a semisolid medium, such as the
agar, to prevent the virus infection
from spreading indiscriminately.
The Plaque formation can take
about 10–14 days, depending on
the virus being analyzed. The
Plaques are generally counted
manually and the results, in
combination with the dilution
factor used to prepare the plate,
can be used to calculate the
number of the pfu per sample unit
volume (pfu/mL). The Plaque
assay is limited to only a subset of
the animal viruses that can lead to
the cell lysis, forming plaques on
the monolayer of cells in a cell
culture plate. In fact, many of the
animal viruses do not form the
plaques on the monolayer, but
© 2022 by JPS Scientific Publications, India
360
nonetheless induce a discernible
CPE.8
• POLYNUCLEOTIDE
ADENYLTRANSFERASE - In
the field of enzymology, a
polynucleotide adenylyltransferase
is an enzyme that catalyzes the
chemical reaction. This enzyme is
responsible for the addition of the
3' polyadenine tail to a newly
synthesized pre-messenger RNA
(pre-mRNA) molecule during the
process of the gene transcription.
The protein is the final addition to
a large protein complex that also
contains the smaller assemblies
known as the cleavage and the
polyadenylation specificity factor
(CPSF) and the cleavage
stimulatory factor (CtSF) and its
binding is a necessary prerequisite
to the cleavage of the 3' end of the
pre-mRNA. After the cleavage of
the 3' signaling region that directs
the assembly of the complex,
polyadenylate polymerase (PAP)
adds the polyadenine tail to the
new 3' end. The PAP is
phosphorylated by the mitosis-
promoting factor, a key regulator
of the cell cycle. The high
phosphorylation levels decrease the
PAP activity.
• POLYCOMB PROTEIN EED -
The Polycomb protein EED is a
protein that in the humans is
encoded by the EED gene. The
Polycomb protein EED is a
member of the Polycomb-group
(PcG) family. The PcG family
members form the multimeric
Glossary of Genetics
protein complexes, which are
involved in maintaining the
transcriptional repressive state of
the genes over the successive cell
generations. This protein interacts
with the enhancer of the zeste 2,
the cytoplasmic tail of the integrin
β7, immunodeficiency virus type 1
(HIV-1) MA protein, and the
histone deacetylase proteins. This
protein mediates the repression of
the gene activity through the
histone deacetylation, and may act
as a specific regulator of the
integrin function. Two transcript
variants encoding the distinct
isoforms have been identified for
this gene. In the humans, a de-
novo mutation in the EED has
been reported in an individual
displaying symptoms similar to
those of the Weaver syndrome.
• PLOIDY - The Ploidy is the
number of the complete sets of the
chromosomes in a cell, and hence
the number of the possible alleles
for the autosomal and the
pseudoautosomal genes. Sets of the
chromosomes refer to the number
of the maternal and the paternal
chromosome copies, respectively,
in the each homologous
chromosome pair, which the
chromosomes naturally exist. The
Somatic cells, tissues, and the
individual organisms can be
described according to the number
of the sets of the chromosomes
present. There are many levels
which are as follows the “ploidy
level”, monoploid (1 set), diploid
© 2022 by JPS Scientific Publications, India
361
(2 sets), triploid (3 sets), tetraploid
(4 sets), pentaploid (5 sets),
hexaploid (6 sets), heptaploid[2] or
septaploid[3] (7 sets), etc. The
generic term of the polyploid is
often used to describe the cells with
three or more than three
chromosome sets.
• PROGRAMMED
REARRANGEMENT - The
Programmed gene rearrangements
are used in the nature to alter the
gene copy number i.e the gene
amplification and the deletion, to
create diversity by reassorting the
gene segments as in the formation
of the mammalian
immunoglobulin genes, or to
control the expression of a set of
the genes that code for the same
function such as the surface
antigens. The Two major
mechanisms for the expression
control are the DNA inversion and
the DNA transposition. In the
DNA inversion a DNA segment
flips around and is rejoined by the
site-specific recombination,
disconnecting or the connecting a
gene to the sequences required for
its expression. In the DNA
transposition a gene moves into an
expression site where it displaces
its predecessor by the gene
conversion. The Gene
rearrangements altering the gene
expression have mainly been found
in some of the unicellular
organisms. They allow a fraction of
the organisms to preadapt to the
sudden changes in the
Glossary of Genetics
environment, that is, to alter the
properties such as the surface
antigens in the absence of an
inducing stimulus. The antigenic
variation that helps the causative
agents of The African
trypanosomiasis, gonorrhea, and
the relapsing fever to elude the host
defense is controlled in this
arrangement.
• PRIMASE INTERACTION - The
interaction between the bacterial
replicative ring helicase which is
the DnaB and the primase which is
the DnaG is instrumental during
the priming and in the elongation
stages of the DNA replication.
Loading of the DnaB at the
bacterial replication origin (oriC)
and the subsequent recruitment of
the DnaG via a transient
interaction with the DnaB signify
the end of the initiation (priming)
and the onset of the elongation
stages of the DNA replication.
This interaction is needed
repeatedly to regulate the cyclic
synthesis of the Okazaki fragments
during rye lagging strand synthesis.
In the Escherichia coli, the DnaG
acts distributively by dissociating
and reassociating to synthesize
each primer for the Okazaki
fragment synthesis. Alternatively,
the DnaG may remain bound to
the newly synthesized primer and
the single-strand binding protein
(SSB) and it is subsequently is
competed off and released from the
DNA by the χ subunit of the DNA
polymerase holoenzyme III. In
© 2022 by JPS Scientific Publications, India
362
contrast to the weak and the
transient interaction in the E. Coli,
the Bacillus stearothermophilus
which s the DnaB-DnaG complex
is very stable, implying that the
two proteins remain permanently
associated and that DnaG does not
leave the replisome during the
lagging strand synthesis.
• PRIMER - The primer is a short
single-stranded nucleic acid used
by the all living organisms in the
initiation of the DNA synthesis.
The DNA polymerase (responsible
for the DNA replication) enzymes
are only capable of adding the
nucleotides to the 3’-end of an
existing nucleic acid, requiring a
primer be bound to the template
before the DNA polymerase can
begin the complementary strand.
The DNA polymerase adds the
nucleotides after binding to the
RNA primer and synthesizes the
whole strand. Later, the RNA
strands must be removed
accurately and replace them with
the DNA nucleotides forming a
gap region known as the nick that
is filled in using an enzyme called
as the ligase. The removal process
of the RNA primer requires the
several enzymes, such as the Lig1,
and the others that work in the
coordination with the DNA
polymerase, to ensure the removal
of the RNA nucleotides and the
addition of the DNA nucleotides.
The Living organisms use the
solely RNA primers, while
laboratory techniques in the
Glossary of Genetics
biochemistry and the molecular
biology that require in vitro DNA
synthesis (such as the DNA
sequencing and the polymerase
chain reaction) usually use the
DNA primers, since they are more
temperature stable. The Primers
can be designed in the laboratory
for the specific reactions such as
the polymerase chain reaction
(PCR). When designing the PCR
primers, there are specific measures
that must be taken into the
consideration, like the melting
temperature of the primers and the
annealing temperature of the
reaction itself.
• PAIR END TAGS - The Paired-
end tags (PET) (sometimes known
as the”Paired-End diTags”, or
simply as the “ditags”) are the
short sequences at the 5’ and 3’
ends of a DNA fragment which are
very unique enough that they
(theoretically) exist together only
once in a genome, therefore
making the sequence of the DNA
in between them available upon
the search (if full-genome sequence
data is available) or upon the
further sequencing (since the tag
sites are very unique enough to
serve as the primer annealing sites).
The Paired-end tags (PET) exist in
the PET libraries with the
intervening DNA absent, that is, a
PET “represents” a larger fragment
of the genomic or the cDNA by
consisting of a short 5’ linker
sequence, a short 5’ sequence tag, a
short 3’ sequence tag, and a short
© 2022 by JPS Scientific Publications, India
363
3’ linker sequence. It was shown
conceptually that the 13 base pairs
are sufficient to map the tags
uniquely. However, the longer
sequences are more practical for
mapping the reads uniquely. The
endonucleases which is used to
produce the PETs give longer tags
(18/20 base pairs and 25/27 base
pairs) but rye sequences of the 50–
100 base pairs would be optimal
for both the mapping and the cost
efficiency. After extracting the
PETs from many of the DNA
fragments, they are linked
(concatenated) together for the
efficient sequencing.
• PCR - The polymerase chain
reaction (PCR) is a method widely
used to rapidly make the millions
to the billions of copies (complete
or the partial) of a specific DNA
sample, allowing the scientists to
take a very small sample of the
DNA and amplify it (or a part of it)
to a large enough amount to study
in the detail. The PCR was
invented in the year 1983 by the
American biochemist Kary Mullis
at the Cetus Corporation; Mullis
and the biochemist Michael Smith,
who had developed the other
essential ways of manipulating the
DNA, were jointly awarded the
Nobel Prize in the field of
Chemistry in the year 1993. The
PCR is fundamental to many of the
procedures used in the genetic
testing and in the research,
including analysis of the ancient
samples of the DNA and the
Glossary of Genetics
identification of the infectious
agents. Using the PCR, copies of
the very small amounts of the
DNA sequences are exponentially
amplified in a series of cycles of the
temperature changes. The PCR is
now a common and often
indispensable technique used in the
medical laboratory research for a
broad variety of the applications
including the biomedical research
and the criminal forensics.
• PROTEIN GLUTAMINE
GLUTAMINASE - In the field of
enzymology, a protein-glutamine
glutaminase is an enzyme that
catalyzes the chemical reaction.
This enzyme belongs to the family
of the hydrolases, those acting on
the carbon-nitrogen bonds other
than the peptide bonds, specifically
in the linear amides. The
systematic name of this enzyme
class is the protein-L-glutamine
amidohydrolase. Other names in
the common use include the
peptidoglutaminase II, glutaminyl-
peptide glutaminase, destabilase,
and the peptidylglutaminase.
• PEPTIDYL GLUTAMINASE -
In the enzymology, a peptidyl-
glutaminase is an enzyme that
catalyzes the chemical reaction.
This enzyme belongs to the family
of the hydrolases, those acting on
the carbon-nitrogen bonds other
than the peptide bonds, specifically
in the linear amides. The
systematic name of this enzyme
class is the peptidyl-L-glutamine
© 2022 by JPS Scientific Publications, India
364
amidohydrolase. Other names in
common use include the
peptidoglutaminase I,
peptideglutaminase, and the
peptidoglutaminase.
• PROTEIN MACHINES - The
protein machines, acting as the
motors and pumps or performing
the operations with the other
biomolecules, such as the DNA,
underlie the basic functions of the
cell. Understanding of their
mechanisms is essential for the
molecular biology and for the
prospective biotechnology
applications. DNA
polymerases are the molecular
machines that govern genetic
replication. They are at the core of
any technologies that manipulate
and evolve DNA sequences. As a
result, DNA polymerases are
perhaps among the most-
engineered protein machines we
know of that are routinely used in
laboratories worldwide.
• PROCESSIVITY - In the fields of
molecular biology and the
biochemistry, the processivity is
the enzyme’s ability to catalyze or
increase its effectiveness of the the
“consecutive reactions without
releasing any of its substrate”. For
example, the processivity is the
average number of the nucleotides
added by a polymerase enzyme,
such as the DNA polymerase, per
association event with the template
strand. Because the binding of the
polymerase to the template is the
rate-limiting step in the DNA
Glossary of Genetics
synthesis, the overall rate of the
DNA replication during y S phase
of the cell cycle is dependent on the
processivity of the DNA
polymerases performing the
replication. The DNA clamp
proteins are the integral
components of the DNA
replication machinery and serve to
increase the processivity of their
associated polymerases. Some of
the polymerases add over about
50,000 nucleotides to a growing
DNA strand before dissociating it
from the template strand, giving a
replication rate of up to around
1,000 nucleotides per second.
• PROBE HYBRIDIZATION - In
the field of the molecular biology, a
hybridization probe (HP) is a
fragment of the DNA or the RNA
of usually 15–10000 nucleotide
long which can be radioactively or
fluorescently labeled. The HP can
be used to detect the presence of
the nucleotide sequences in the
analyzed RNA or the DNA that
are complementary to the sequence
in the probe. The labeled probe is
first denatured (by heating or under
the alkaline conditions such as
exposure to the sodium hydroxide)
into the single stranded DNA
(ssDNA) and then hybridized to
the target ssDNA (Southern
blotting) or the RNA (northern
blotting) immobilized on a the
membrane or in situ. The
Hybridization probes used in the
DNA microarrays refer to the
DNA covalently attached to an
© 2022 by JPS Scientific Publications, India
365
inert surface, such as the coated
glass slides or the gene chips, to
which a mobile cDNA target is
hybridized. Depending on the
types of method, the probe may be
synthesized using the
phosphoramidite method, or it can
be generated and labeled by the
PCR amplification or the cloning
(both are the older methods).
• PURINE NUCLEOSIDASE - In
the enzymology, a purine
nucleosidase is an enzyme that
catalyzes the chemical reaction.
This enzyme belongs to the family
of the hydrolases, specifically those
glycosylases that the hydrolyse N-
glycosyl compounds. The
systematic name of this enzyme
class is the purine-nucleoside
ribohydrolase. Other names in
common use include the
nucleosidase, purine beta-
ribosidase, purine nucleoside
hydrolase, purine ribonucleosidase,
ribonucleoside hydrolase,
nucleoside hydrolase, N-ribosyl
purine ribohydrolase, nucleosidase
g, N-D-ribosylpurine
ribohydrolase, inosine-adenosine-
guanosine preferring nucleoside
hydrolase, purine-specific
nucleoside N-ribohydrolase, IAG-
nucleoside hydrolase, and the
IAG-NH. This enzyme participates
in the purine metabolism and in
nicotinate and the
nicotinamide metabolism.
• POSITIVE SUPERCOILING -
The Positive supercoiling of the
DNA is a process where the DNA
Glossary of Genetics
strand is overwound compared to
the relaxed state. This occurs when
the double-helical conformation of
the DNA (right-handed) is twisted
tighter (over wound in a right-
handed mode) until the helical
structure becomes distorted and
develops into a level of the ‘knot.’
• PARACASPASE - The
Paracaspases are the members of
the C14 family of the cysteine
proteases. The Paracaspases are
the proteins related to the caspases
present in the animals and in the
slime mold, in contrast to the
metacaspases, which are present in
the plants, fungi, and the "protists".
The phylogenetic distribution is a
bit confusing, since the slime mold
diverged earlier than the
animal/fungal split. The
Paracaspase has been first
identified in a recurrent
t(11;18)(q21;q21) chromosomal
translocation associated with a
subset of the MALT lymphoma.
The Paracaspase in the animals has
mostly been studied in the humans
and in the mice, where it plays a
major role in the several pro-
inflammatory pathways in the
innate- and adaptive- immunity.
The distantly related zebrafish
PCASP3 show the conserved
MALT1-like activity in the NF-
kappaB activation and thr protease
substrate specificity, indicating that
the these functions were present in
the last common ancestor of the
three vertebrate paracaspase
paralogs.
© 2022 by JPS Scientific Publications, India
366
• POLYADENYLATION - The
Polyadenylation is the process of
the addition of a poly(A) tail to an
RNA transcript, typically a type of
messenger RNA (mRNA). The
poly(A) tail consists of the multiple
adenosine monophosphates; in the
other words, it is a stretch of the
RNA that has only adenine bases.
In the eukaryotes, polyadenylation
is part of the process that produces
the mature mRNA for the
translation. In many of the
bacteria, the poly(A) tail promotes
degradation of the mRNA. It
therefore, forms part of the larger
process of the gene expression. The
process of the polyadenylation
begins as the transcription of a
gene terminates. The 3′ segment of
the newly made pre-mRNA is first
cleaved off by a set of the proteins,
these proteins then synthesize the
poly(A) tail at the RNA's 3′ end.
The poly(A) tail is important for
the nuclear export, translation and
the stability of the mRNA. The tail
is shortened over the time, and
when it is short enough, the
mRNA is enzymatically degraded.
However, in a few cell types, the
mRNAs with the short poly(A)
tails are stored for the later
activation by the re-
polyadenylation in the cytosol. In
contrast, when the polyadenylation
occurs in the bacteria, it promotes
the RNA degradation. This is also
sometimes the case for the
eukaryotic non-coding RNAs.
Glossary of Genetics
• PHOTOREACTIVATION - The
Photoreactivation is possibly the
simplest DNA repair mechanism
currently which is known. Rye
Pyrimidine dimers introduced into
the DNA by the UV irradiation
can be repaired by the action of a
single photoreactivating enzyme
using the light in the range of the
310–500 nm as an energy source.
Although this repair process has
been very extensively reviewed
there have recently been a few
important additions to our
understanding, which will be given
most of the consideration here.
The Photoreactivation has a
peculiar phyletic distribution which
has yet to be satisfactorily
explained. An enzyme that can
photoreactivate UV-irradiated
transforming the DNA is
detectable in the extracts of the
most metazoan cells with the
exception of the placental
mammals. The Fish, amphibians,
and the reptiles all show the
photoreactivation. Among the
vertebrates, the marsupials have a
very slowly acting photoreacti-
vating system. In the birds, only
the embryo and the adult brain
show the photoreactivation.
• PROOFREADING – The term
proofreading is used in the field of
genetics to refer to the error-
correcting processes, first proposed
by the John Hopfield and the
Jacques Ninio, involved in the
DNA replication, immune system
specificity, enzyme-substrate
© 2022 by JPS Scientific Publications, India
367
recognition among many of the
other processes that require the
enhanced specificity. The
proofreading mechanisms of
Hopfield and Ninio are the non-
equilibrium active processes that
consume the ATP to enhance the
specificity of the various
biochemical reactions. In the
bacteria, all the three DNA
polymerases (I, II and III) have the
ability to proofread, using the 3’ →
5’ exonuclease activity. When an
incorrect base pair is recognized,
the DNA polymerase reverses its
direction by the one base pair of
the DNA and excises the
mismatched base. Following the
base excision, the polymerase can
re-insert the correct base and the
replication can continue. In the
eukaryotes, only the polymerases
that deal with the elongation (delta
and epsilon) have the proofreading
ability (3’ → 5’ exonuclease
activity). The Proofreading also
occurs in the mRNA translation
for the protein synthesis. In this
case, one mechanism is the release
of any incorrect aminoacyl-tRNA
before the peptide bond formation.
• PATCHED - The Patched (Ptc) is
a conserved 12-pass
transmembrane protein receptor
that plays an important obligate
negative regulatory role in the
Hedgehog signaling pathway in the
insects and in the vertebrates. The
Patched is an essential gene in the
embryogenesis for the proper
segmentation in the fly embryo
Glossary of Genetics
mutations in which may be
embryonic lethal. The Patched
functions as the receptor for the
Hedgehog protein and controls its
spatial distribution, in part via the
endocytosis of the bound
Hedgehog protein, which is then
targeted for the lysosomal
degradation. The Mutated patched
proteins have been implicated in a
number of the cancers including
the basal cell carcinoma,
medulloblastoma, and the
rhabdomyosarcoma. The
Hereditary mutations in the human
patched homolog PTCH1 cause
the autosomal dominant Gorlin
syndrome, which consists of the
overgrowth and the hereditary
disposition to the cancer including
the basal cell carcinoma and the
medulloblastoma. The Mice with
mutations in the mouse PTCH1
similarly develop the
medulloblastoma.
• POLYTENE CHROMOSOME -
The Polytene chromosomes are the
large chromosomes which have
thousands of the DNA strands.
They provide a high level of the
function in the certain tissues such
as the salivary glands of the insects.
The Polytene chromosomes were
first reported by the E.G.Balbiani
in the year 1881. The Polytene
chromosomes are found in the
dipteran flies, thhe best understood
are those of the Drosophila,
Chironomus and the
Rhynchosciara. They are present in
another group of the arthropods of
© 2022 by JPS Scientific Publications, India
368
the class Collembola, a protozoan
group Ciliophora, mammalian
trophoblasts and tyey antipodal,
and the suspensor cells in the
plants. In insects, they are
commonly found in the salivary
glands when the cells are not in the
dividing phase. The Polytene
chromosomes, at interphase, are
seen to have distinct thick and the
thin banding patterns. These
patterns were originally used to
help the map chromosomes,
identify the small chromosome
mutations, and in the taxonomic
identification. They are now used
to study the function of the genes
in the transcription.
• POINT MUTATIONS - The
point mutation is a genetic
mutation where a single nucleotide
base is changed, inserted or deleted
from a DNA or the RNA sequence
of an organism's genome. The
Point mutations have a variety of
the effects on the downstream
protein product consequences that
are very moderately predictable
which is based upon the specifics
of the mutation. These
consequences can range from the
no effect (e.g. synonymous
mutations) to the deleterious
effects (e.g. frameshift mutations),
with regard to the protein
production, composition, and the
function. The Point mutations
usually take place during the DNA
replication. The DNA replication
occurs when the one double-
stranded DNA molecule creates
Glossary of Genetics
the two single strands of the DNA,
each of which is a template for the
creation of the complementary
strand. A single point mutation can
change the whole DNA sequence.
Changing the one purine or the
pyrimidine may change the amino
acid that the nucleotides code for.
• PIE - The U1A polyadenylation
inhibition element (PIE) is an
RNA element which is responsible
for the regulation of the length of
the polyA tail of the U1A protein
pre-mRNA. The PIE is located in
the U1A mRNA 3' UTR. The PIE
adopts a U-shaped structure, with
the binding sites for a single U1A
protein at each of the bend and
when complexed with the two
proteins it blocks the activity of the
poly(A) polymerase (PAP), and
inhibits its activity.
• POSITIVE CONTROL
MUTANT - The “Positive
control” mutants of the cI protein
of the bacteriophage λ (λcI) bind to
the DNA but, unlike the wild-type
protein, it fail to activate the
transcription. According to the
original interpretation of Ptashne
and the co-workers, these mutants
bear the amino acid substitutions
that disrupt a stimulatory
interaction between the λcI bound
at the operator site OR2 and the
RNA polymerase bound at the
promoter PRM, an idea supported
by kinetic analysis in one of the
The Genetic analysis has suggested
that one of the residue in
particular, glutamate 34 (E34), is
© 2022 by JPS Scientific Publications, India
369
critical for the stimulatory effect of
the wild-type λcI. The OR3, is a
site that mediates the repression of
PRM. Under conditions where the
λ operator OR2 is fully occupied
and the operator OR3 is vacant,the
wild-type λcI activates the
transcription from the promoter
PRM whereas the mutant does not.
• POLYACRYLAMIDE GEL
ELECTROPHORESIS - The
Polyacrylamide gel electrophoresis
(PAGE) is a technique widely
which is widely used in the field of
biochemistry, forensic chemistry,
genetics, molecular biology and the
biotechnology to separate the
biological macromolecules, usually
proteins or the nucleic acids,
according to their electrophoretic
mobility. The Electrophoretic
mobility is a function of the length,
conformation and the charge of the
molecule. The polyacrylamide gel
electrophoresis is a powerful tool
which is widely used to analyze the
RNA samples. When
polyacrylamide gel is denatured
after the electrophoresis, it
provides the information on the
sample composition of the RNA
species. It possesses the several
electrophoretically desirable
features that make it a versatile
medium. It is a synthetic, thermo-
stable, transparent, strong,
chemically relatively inert gel, and
can be prepared with a wide range
of the average pore sizes. The pore
size of a gel and the reproducibility
in the gel pore size are determined
Glossary of Genetics 370

by the three factors, the total

amount of the acrylamide present.
The Pore size decreases with the
increasing %T; with cross-linking,
5%C gives the smallest pore size.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
Q R
• QUORUM SENSING - In the
field of biology, the quorum
sensing or the quorum signalling
(QS) is the ability to detect and
respond to the cell population
density by the gene regulation. As
one example, the QS enables
bacteria to restrict the expression of
the specific genes to the high cell
densities at which the resulting
phenotypes will be most beneficial.
Many species of the bacteria use
the quorum sensing to coordinate
the gene expression according to
the density of their local
population. In a similar fashion,
some social insects use the quorum
sensing to determine where to nest.
The Quorum sensing may also be
useful for the cancer cell
communications. In addition to its
function in the biological systems,
the quorum sensing has several
useful applications for computing
and robotics. In general, the
quorum sensing can function as a
decision-making process in any
decentralized system in which the
components have: (a) a means of
assessing the number of the other
components they interact with and
(b) a standard response once a
threshold number of the
components is detected.
© 2022 by JPS Scientific Publications, India
371
• RECRUITMENT OF
ELONGATION FACTORS - The
Translational elongation factors
are the proteins that play two
important roles during the
elongation cycle of the protein
biosynthesis on the ribosome. 1)
elongation factors are involved in
bringing The thevaminoacyl-
transfer RNA to the ribosome
during the protein synthesis. 2) an
elongation factor is involved in the
translocation, the step in the
elongation at which the peptidyl-
tRNA is moved from The one
ribosomal site to the another as the
messenger RNA moves through
the ribosome. Both the steps results
in the formation of the Guanosine
Triphosphate (GTP).
• RECRUITMENT OF
NUCLEOSOMES MODIFIERS -
The Nucleosomes Modifiers plays
an important role in the initiation
and the elongation process of the
Transcription. The Nucleosomes
Modifiers has allowed access to the
DNA to be regulated locally and
differentially as needed
Nucleosomes Modifiers involves
the changing histone DNA
interaction as a mean of disrupting,
assembling or moving the
Nucleosomes.
• RECRUITMENT OF
TRANSCRIPTIONAL
MACHINERY - The recruitment
model of a gene activation
Glossary of Genetics
stipulates that an activator works
by bringing the transcriptional
machinery to the DNA. The basal
promoter region of the DNA
associates with the general
transcription factors which recruits
and position of the RNA
polymerase for the transcription.
• RNA POLYMERASE
ACTIVATION ROLES IN
GENES - The Activation of the
RNA polymerase complex enables
the transcription initiation process.
The Acetyl Co-A an enzyme which
stimulates the RNA polymerase for
the transcription and promoter
binding. Multiple alternative
interactions between the activators
and the coactivators stimulate the
transcription process by the RNA
polymerase II. RNA polymerase is
an enzyme which is responsible for
copying the DNA sequences into
the RNA sequences during the
process of the transcription.
• RECOGNITION OF T-RNA -
The tRNA recognition has two
structural components. The
interaction between the acceptor
end and the active site domain is
class-specific and the binding mode
of the stem observed in the crystal
structures of the Glutamine-tRNA
and Aspergine-tRNA complexes
that can be generalized to their
respective classes. A tRNA
molecule has an “L” type structure
which is held together by the
hydrogen bonds between bases in
the different parts of the tRNA
sequence. One of the end of the
© 2022 by JPS Scientific Publications, India
372
tRNA binds to a specific amino
acid and the other end has an
anticodon that will bind to an
mRNA codon. When a tRNA
recognizes and it binds to its
corresponding codon in the
ribosome, the tRNA transfers the
appropriate amino acid to the end
of the growing amino acid chain.
The tRNAs and the ribosome
continue to decode the mRNA
molecule until it’s entire sequence
is translated into a protein.
• REVERSE GENETICS - The
Reverse genetics is a method that is
used to help to understand the
function of a gene by analyzing the
phenotypic effects of a specific
engineered gene sequences.
Reverse genetics usually proceeds
in the opposite direction of the so-
called forward genetic screens of
the classical genetics. It is an
experimental molecular genetics
technique that enables the
researchers to elucidate gene
function by examining changes to
the phenotypes (of cells or the
organisms) caused by genetically
engineering specific nucleic acid
sequences (within the DNA or the
RNA). It can be used to rapidly
engineer the viruses with the
desired mutations to study the
virus in vitro and in vivo. Viruses
can also be designed for live-
attenuated vaccine development
and can also be engineered with
the reporter genes to facilitate the
serodiagnosis, vaccine evaluation
and the antiviral screening. For eg.
Glossary of Genetics
The deletion of a gene by gene
targeting can be done in some of
the organisms, such as the yeast,
mice and the moss. Unique among
plants, in the Physcomitrella
patens, gene knockout via the
homologous recombination to
create the knockout moss is nearly
as efficient as in the yeast.
• REPETITIVE DNA - The
Repeated sequences are the
patterns of The nucleic acids that
occur in The multiple copies
throughout the genome. The
Repetitive DNA was first detected
because of its rapid re-association
kinetics mechanism. These
sequences generally do not code
for the Proteins. One class termed
as the highly repetitive DNA
consists of the short sequences
generally about 5-100 nucleotides
which are repeated thousands of
the times in a single stretch and
includes the satellite DNA. The
Generic repeated signals in the
DNA are necessary to format the
expression of a unique coding
sequence files and to organise an
additional functions essential for
the genome replication and
accurate transmission to the
progeny cells. This general type of
the DNA has been named as the
“selfish DNA” because it behaves
as if motivated by its own interests.
Number of the genetic diseases are
associated with the increase in the
repetitive DNA sequences. The
repeat sequence CpGpG is
associated with the fragile X
© 2022 by JPS Scientific Publications, India
373
syndrome other examples are
Huntington’s chorea, myotonic
dystrophy, and the spinobulbar
muscular dystrophy.
• RNA INTERFERENCE - The
RNA interference is a biological
process in which the RNA
molecules are involved in the
sequence-specific suppression of a
gene expression by a double-
stranded RNA, through the
translational or the transcriptional
repression process. It mediates
resistance to both the endogenous
parasitic and the exogenous
pathogenic nucleic acids, and
regulates the expression of the
protein-coding genes. The RNA
interference is an evolutionary
conserved mechanism triggered by
the double-stranded RNA that uses
the gene’s own DNA sequence to
turn it off. This process is known as
the gene silencing. It is thought to
serve as a cell’s natural defense
against the viruses, which attempt
to take over a cell’s protein-
production mechanism by inserting
their own genes into the host
DNA. Researchers have utilized
the RNAi pathway to explore the
effects of the systematically
silencing genes.
• REGULATION OF SEX
DETERMINATION - The Sex
determination is a process which is
essential for the sexual
reproduction to generate the next
generation by the formation of
functional male or the female
gametes. It is a complicated
Glossary of Genetics
process involving a large-scale
modifications in the gene
expression affecting virtually every
tissue in the body. Sex
determination is a developmental
process which allows the
differentiation of a bipotential
precursor in the two completely
different organs, the testis or the
ovary.
• RNA POLYMERASE - RNA
polymerase abbreviated as the
RNAP or the RNApol or more
specifically DNA-directed or the
dependent RNA polymerase, is an
enzyme that synthesizes the RNA
from a DNA template. RNA
polymerase is an essential to life,
and is also found in all the living
organisms and many of the viruses.
Depending on the organism, a
RNA polymerase can be a protein
complex i.e multi-subunit RNAP
or only consist of one subunit i.e
single-subunit RNAP, ssRNAP
each of the representing an
independent lineage. The former is
found in the bacteria, archaea, and
in the eukaryotes alike, sharing a
similar core structure and
mechanism. The latter is found in
the phages as well as the
eukaryotic chloroplasts and the
mitochondria, and is related to the
modern DNA polymerases.
Eukaryotic and the archaeal
RNAPs have more subunits than
the bacterial ones do, and are
controlled differently. Bacteria and
archaea only have one RNA
polymerase. Eukaryotes have
© 2022 by JPS Scientific Publications, India
374
multiple types of the nuclear
RNAP, each of these are
responsible for the synthesis of a
distinct subset of RNA. Using the
enzyme which is known as the
helicase, the RNAP locally opens
the double-stranded DNA so that
one of the strand of the exposed
nucleotides can be used as a
template for the synthesis of RNA,
a process called as the
transcription. A transcription factor
and its associated transcription
mediator complex must be
attached to the DNA binding site
which is called a promoter region
before RNAP can initiate the DNA
unwinding at that position. RNAP
not only initiates the RNA
transcription process it also guides
the nucleotides into the position,
facilitates the attachment and the
elongation, has intrinsic
proofreading and replacement
capabilities, and the termination
recognition capability. In the
eukaryotes, the RNAP can build
chains as long as 2.4 million
nucleotides. RNAP produces the
RNA that is functionally, either for
the protein coding, i.e. messenger
RNA (mRNA) or non-coding (so-
called “RNA genes”). At least four
functional types of the RNA genes
exist:
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
Micro RNA (miRNA)
Catalytic RNA (ribozyme)
• RIBOSWITCH - A riboswitch is a
machine which is a regulatory
Glossary of Genetics
segment of a messenger RNA
molecule that binds to a small
molecule, which results in a
change in production of the
proteins encoded by the mRNA.
Thus, an mRNA that contains a
riboswitch is directly involved in
the regulating its own activity, in
response to the concentrations of
its effector molecule. The discovery
that the modern organisms use the
RNA to bind small molecules, and
discriminate against the closely
related analogs, which are
expanded the known natural
capabilities of the RNA beyond its
ability to code for the proteins,
catalyze reactions, or to bind with
the other RNA or the protein
macromolecules. Riboswitches
could be a target for the novel
antibiotics. Indeed, some of the
antibiotics whose mechanism of
action was unknown for the
decades have been shown to
operate by targeting the
riboswitches. For example, when
the antibiotic pyrithiamine enters
the cell, it is metabolized into the
pyrithiamine pyrophosphate.
Pyrithiamine pyrophosphate has
been shown to bind and activate
the TPP riboswitch, causing the
cell to cease the synthesis and
import of the TPP. Because the
pyrithiamine pyrophosphate does
not substitute for TPP as a
coenzyme, thus the cell dies.
• RETROREGULATION - The
Retroregulation of the gene
expression was discovered in the
© 2022 by JPS Scientific Publications, India
375
int gene expression of the lambda
phage. The int gene encodes the
integrase that catalyzes the
integration and also excision of the
I DNA to or from the Escherichia
coli chromosome. It can also
transcribed from the PL promoter
of l in the lytic cycle. The P-
derived in the int transcript is,
however, very labile, and the level
of the integrase expression is very
low. The Point mutations in the
region 260 bp downstream of the
int gene are known to increase the
expression of the int gene. Because
these mutations are clustered in the
-2 region of the l, they are named
as the si- for something in -2. The
si- region does not encode a
protein, but its RNA transcript can
form an extended stem-loop
structure that provides a substrate
structure for the double-stranded
RNA-dependent ribonuclease,
which is known as RNase III.
Therefore, the wild-type sib RNA
is cleaved by the RNase III and it is
rapidly degraded by 3′-to-5′
exonuclease, such as the
polynucleotide phosphorylase
(PNPase). The sib mutations
destroy the RNase III recognition
structure and stabilize the int
mRNA, resulting in the increase in
the synthesis of the integrase,
hence this is referred to as the
retroregulation. In this case, the
retroregulation prevents l phage
from integrating into the bacterial
genome in the lytic cycle.
Although the little integrase
Glossary of Genetics
protein is synthesized from the PL
promoter after the phage infection,
the much integrase is expressed
after the induction of l prophage,
where the sib sequence is no longer
placed downstream of int because
of the l phage attachment site, attP,
truncates these two regions.
• RNA POLYMERASE 2 - The
RNA polymerase II (RNAP II and
Pol II) is a multiprotein complex
that transcribes the DNA into the
precursors of the messenger RNA
(mRNA) and most of the small
nuclear RNA (snRNA) and the
microRNA. It is one of the three
RNAP enzymes which is found in
the nucleus of the eukaryotic cells.
A 550 kDa complex of the 12
subunits, RNAP II is the most
studied type of the RNA
polymerase. A wide range of the
transcription factors are required
for it to bind to the upstream gene
promoters and begin the
transcription. The Oxidative DNA
damage may block the RNA
polymerase II transcription and
can cause the strand to breaks. An
RNA templated transcription-
associated recombination process
has been described that can protect
against the DNA damage. During
the G1/G0 stages of the cell cycle,
cells exhibit the assembly of the
homologous recombination factors
at the double-strand breaks within
the actively transcribed regions. It
appears that transcription is
coupled to repair of DNA double-
strand breaks by the RNA
© 2022 by JPS Scientific Publications, India
376
templated homologous
recombination. This repair process
efficiently and accurately rejoins
the double-strand breaks in the
genes being actively transcribed by
the RNA polymerase II.
• RETROVIRAL - A retrovirus is a
type of virus that inserts a copy of
the DNA of its RNA genome into
the DNA of the host cell that it
invades, thus changing the genome
of that cell. Once inside the host
cell’s cytoplasm, the virus uses its
own enzyme which is known as
the reverse transcriptase enzyme to
produce the DNA from its RNA
genome, the reverse of the usual
pattern, thus retro (backwards).
The new DNA is then
incorporated into the host cell
genome by an enzyme which is
known as the integrase enzyme, at
which point the retroviral DNA is
referred to as a provirus. The host
cell then treats the viral DNA as a
part of its own genome thus
transcribing and translating the
viral genes along with the cell’s
own genes, producing the proteins
required to assemble the new
copies of the virus. Many of the
retroviruses cause the serious
diseases in the humans, other
mammals, and the birds. The
Human retroviruses include the
HIV-1 and HIV-2, the cause of the
disease AIDS. Also, the human T-
lymphotropic virus (HTLV) causes
of the disease in the humans. The
murine leukemia viruses (MLVs)
cause the cancer in the mouse
Glossary of Genetics
hosts. The retroviruses are valuable
research tools in the field of the
molecular biology, and they have
been used successfully in the gene
delivery systems. Evidence from
endogenous retroviruses suggest
that the retroviruses have been
infecting the vertebrates for at least
450 million years.
• RETROTRANSPOSON - The
Retrotransposons which is also
called as the Class I transposable
elements or the transposons via the
RNA intermediates are a type of
the genetic component that copy
and paste themselves into the
different genomic locations
(transposon) by converting the
RNA back into the DNA through
the reverse transcription process
using an RNA transposition
intermediate. These
retrotransposons are regulated by a
family of the short non-coding
RNAs termed as the PIWI also
called as the P-element induced
wimpy testis interacting RNAs
(piRNAs). The piRNA is a
recently discovered class of the
ncRNAs, which are in the length
range of the 24-32 nucleotides.
Initially, the piRNAs were
described as repeat-associated
siRNAs (rasiRNAs) because of
their origin from the repetitive
elements such as the transposable
sequences of the genome.
However, later it was identified
that they acted via PIWI-protein.
In addition to having a role in the
suppression of the genomic
© 2022 by JPS Scientific Publications, India
377
transposons, various roles of the
piRNAs have been recently
reported like the regulation of the
3’ UTR of the protein-coding genes
via the RNAi, transgenerational
epigenetic inheritance to convey a
memory of the past transposon
activity, and the RNA-induced
epigenetic silencing.
• REVERSE TRANSCRIPTASE -
A reverse transcriptase (RT) is an
enzyme which is used to generate
the complementary DNA (cDNA)
from an RNA template, a process
which is termed as the reverse
transcription. The Reverse
transcriptases are used by the
viruses such as the HIV and the
hepatitis B to replicate their
genomes, by retrotransposon
mobile genetic elements to
proliferate within the host genome,
and by the eukaryotic cells to
extend the telomeres at the ends of
their linear chromosomes.
Contrary to a widely held belief,
the process does not violate the
flows of the genetic information as
described by the classical central
dogma, as transfers of information
from the RNA to DNA are
explicitly held possible. The
enzymes are encoded and used by
the viruses that use the reverse
transcription as a step in the
process of the replication. The
Reverse-transcribing RNA viruses,
such as the retroviruses, use the
enzyme to reverse-transcribe their
RNA genomes into the DNA,
which is then integrated into the
Glossary of Genetics
host genome and then replicated
along with it. The Reverse-
transcribing DNA viruses, such as
the hepadnaviruses, can allow the
RNA to serve as a template in
assembling and making the DNA
strands. The HIV infects humans
with the use of this enzyme.
Without the reverse transcriptase,
the viral genome would not be able
to incorporate into the host cell,
resulting in the failure to replicate.
• RECRUITMENT BY
ACTIVATORS - Many of the
transcriptional activators are
intrinsically unstructured yet
display the unique, defined
conformations when bound to the
target proteins. The Target-induced
folding provides a mechanism by
which the activators could form a
specific interactions with an array
of the structurally unrelated target
proteins. The Evidence for such a
binding mechanism has been
reported previously in the context
of the interaction between the
cancer-related c-Myc protein and
in the TATA-binding protein,
which can be modeled as a two-
step process in which a rapidly
forming, low affinity complex
slowly converts to a more stable
form, consistent with a coupled
binding and the folding reaction.
To test the generality of the target-
induced folding model, we
investigated the binding of the two
widely studied acidic activators,
the Gal4 and the VP16, to a set of
the target proteins, including the
© 2022 by JPS Scientific Publications, India
378
TATA-binding protein and the
Swi1 and the Snf5 subunits of the
Swi/Snf chromatin remodeling
complex. In all the cases, the
overall affinity increases with the
temperature and, in most of the
cases, with increased ionic
strength. These results are
consistent with a general
mechanism for the recruitment of
the transcriptional components to
promoters by naturally occurring
acidic activators, by which the
initial contact is mediated
predominantly through the
electrostatic interactions, whereas
the subsequent target-induced
folding of the activator results in a
stable complex.
• REPRESSOR - In the field of the
molecular genetics, a repressor is a
DNA- or the RNA-binding protein
that inhibits the expression of the
one or more genes by binding to
the operator or the associated
silencers. A DNA-binding
repressor blocks the attachment of
the RNA polymerase to the
promoter, thus preventing the
transcription of the genes into the
messenger RNA. An RNA-binding
repressor binds to the mRNA and
prevents the translation of the
mRNA into protein. This blocking
or reducing of the expression is
called as the repression. If an
inducer, a molecule that initiates
the gene expression, is present,
then it can interact with the
repressor protein and then detach it
from the operator. The RNA
Glossary of Genetics
polymerase then can transcribe the
message (expressing the gene). A
co-repressor is a molecule that can
bind to the repressor and make it
bind to the operator tightly, which
decreases the transcription. While
the repressors are more commonly
found in the prokaryotes, they are
rare in the eukaryotes.
Furthermore, most of the known
eukaryotic repressors are found in
the simple organisms (e.g. Yeast),
and act by the interacting directly
with the activators. This contrasts
prokaryotic repressors which can
also alter the DNA or the RNA
structure.
• RECURTIMENT OF RNA
POLYMERASE - The Nuclear
eukaryotic genomes are transcribed
by the three related RNA
polymerases (Pol), which
transcribe the distinct gene sets.
The specific Pol recruitment is
achieved through the selective core
promoter recognition by the basal
transcription factors (TFs). The
Transcription by an inappropriate
Pol appears to be very rare and to
generate mostly the unstable
products. A collection of the short
noncoding RNA genes for
example, the small nuclear RNA
(snRNA) or the 7SK RNA genes,
which play an essential roles in the
processes such as the maturation of
the RNA molecules or the control
of the Pol II transcription
elongation, possess highly similar
core promoters, and yet are
transcribed for some by the Pol II
© 2022 by JPS Scientific Publications, India
379
and for the others by the Pol III as
a result of the small promoter. It is
the mechanisms of the selective Pol
recruitment to the such type of the
promoters.
• RNA HELICASE - The RNA
helicases are the essential for most
of the processes of the RNA
metabolism such as the ribosome
biogenesis, pre-mRNA splicing,
and the translation initiation. They
also play an important role in the
sensing viral RNAs. The RNA
helicases are involved in the
mediation of the antiviral immune
response because they can identify
the foreign RNAs in the
vertebrates. About 80% of all the
viruses are the RNA viruses and
they contain their own RNA
helicases. The Defective RNA
helicases have been linked to the
cancers, infectious diseases and the
neuro-degenerative disorders.
Some of the neurological disorders
associated with the defective RNA
helicases are the amyotrophic
lateral sclerosis, spinal muscular
atrophy, spinocerebellar ataxia
type-2, Alzheimer disease, and the
lethal congenital contracture
syndrome. The RNA helicase
database is currently available
online that contains a
comprehensive list of the RNA
helicases with the information such
as the sequence, structure, and
biochemical and the cellular
functions.
Glossary of Genetics
• RECBCD HELICASE ENZYME
- The RecBCD which is also
known as the Exonuclease V,
Escherichia coli exonuclease V, E.
Coli exonuclease V, gene recBC
endoenzyme, RecBC
deoxyribonuclease, gene recBC
DNase, and the gene recBCD
enzymes is an enzyme of the E.
Coli bacterium that initiates the
recombinational repair from the
potentially lethal double strand
breaks in the DNA which may
result from the ionizing radiation,
replication errors, endonucleases,
oxidative damage, and a host of
the other factors. The RecBCD
enzyme is both a helicase that
unwinds, or separates the strands
of rye DNA, and a nuclease that
makes the single-stranded nicks in
the DNA. Both the RecD and the
RecB subunits are the helicases,
i.e., the energy-dependent
molecular motors that unwind the
DNA or the RNA in the case of
the other proteins. The RecB
subunit in addition has a nuclease
function. Finally, the RecBCD
enzyme (perhaps the RecC
subunit) recognizes a specific
sequence in the DNA, 5’-
GCTGGTGG-3’, known as the
Chi (sometimes designated with
the Greek letter χ).
• REC Q – The RecQ is a family of
the helicase enzymes initially
found in the Escherichia coli that
has been shown to be important in
the genome maintenance. They
function through catalyzing the
© 2022 by JPS Scientific Publications, India
380
reaction ATP + H2O → ADP + P
and thus driving the unwinding of
the paired DNA and translocating
in the 3’ to 5’ direction. These
enzymes can also drive the
reaction NTP + H2O → NDP + P
to drive the unwinding of either the
DNA or the RNA. In the
prokaryotes, the RecQ is necessary
for the plasmid recombination and
in the DNA repair from the UV-
light, free radicals, and the
alkylating agents. This protein can
also reverse the damage from the
replication errors. In the
eukaryotes, the replication does
not proceed normally in the
absence of the RecQ proteins,
which also function in the aging,
silencing, recombination and in the
DNA repair.
• REVERSE TRANSCRIPTASE -
The reverse transcriptase (RT) is an
enzyme used to generate the
complementary DNA (cDNA)
from an RNA template, a process
termed as the reverse transcription.
The Reverse transcriptases are used
by the viruses such as the HIV and
the hepatitis B to replicate their
genomes, by the retrotransposon
mobile genetic elements to
proliferate within the host genome,
and by the eukaryotic cells to
extend the telomeres at the ends of
their linear chromosomes.
Contrary to a widely held belief,
the process does not violate the
flows of the genetic information as
described by the classical central
dogma, as transfers of the
Glossary of Genetics
information from the RNA to the
DNA are explicitly held possible.
In the virus species with the reverse
transcriptase lacking the DNA-
dependent DNA polymerase
activity, creation of the double-
stranded DNA can possibly be
done by the host-encoded DNA
polymerase δ, mistaking the viral
DNA-RNA for a primer and
synthesizing a double-stranded
DNA by a similar mechanism as in
the primer removal, where the
newly synthesized DNA displaces
the original RNA The process of
the reverse transcription, which is
also called as the retrotranscription
or the retrotras, is extremely error-
prone, and it is during this step that
the mutations may occur. Such
mutations may cause the drug
resistance.
• RIBONUCLEOTIDES
TRIPHOSPHATE - The
Ribonucleotide reductase (RNR)
catalyzes the reductive synthesis of
the deoxyribonucleotides from
their corresponding
ribonucleotides. It provides the
precursors which is necessary for
the DNA synthesis. The RNRs are
separated into the three classes
based on their metallocofactor
usage. Class I RNRs, found in the
eukaryotes, bacteria, and in the
bacteriophage, use a diiron-tyrosyl
radical. The Class II RNRs, found
in the bacteria, bacteriophage,
algae and in the archaea, use the
coenzyme B12
(adenosylcobalamin, AdoCbl). The
© 2022 by JPS Scientific Publications, India
381
Class III RNRs, found in the strict
or the facultative anaerobic
bacteria, bacteriophage, and in the
archaea, use an FeS cluster and the
S-adenosylmethionine to generate
a glycyl radical. Many of the
organisms have more than one
class of the RNR present in their
genomes. All the three RNRs have
a ten-stranded α-β barrel domain
that is structurally similar to the
domain of the PFL (pyruvate
formate lyase). The class III
enzyme from the phage T4 consists
of the two subunits, this model
covers the larger subunit which
contains the active and the
allosteric sites.
• RECOMBINATION REPAIR -
The Recombination repair is a
mechanism for generating a
functional DNA molecule from the
two damaged molecules. It is an
essential repair process for dividing
the cells because a replication fork
may arrive at a damaged site, such
as a thymine dimer, before the
excision repair system has been
eliminated damage. When the pol
III reaches a thymine dimer, an
adenine is added to the growing
strand. However, the distortion of
the helix caused by the dimer
weakens the hydrogen bond and
activates the polymerase editing
function, and the adenine is
removed. The cycle begins again—
an adenine is added and then
removed—the net result of which
is that the replication fork fails to
Glossary of Genetics
the advance. A cell in which the
DNA synthesis is permanently
stalled cannot complete a round of
the replication and the does not
divide. However, in a way that is
not understood, after a pause of the
∼5 seconds per dimer, chain
growth begins again beyond the
thymine dimer block. The result of
this process is that the daughter
strands have a very large gaps, one
for the each unexcised thymine
dimer. The Viable daughter cells
cannot be produced by the
continued replication alone
because the strands having the
thymine dimer will continue to
turn out the defective daughter
strands and the first set of the
daughter strands would be
fragmented when the growing fork
enters a gap. However, by a
recombination mechanism called
as the sister-strand exchange the
proper double-stranded molecules
can be made.
• REASSOCIATION - The
Reassociation is the recombination
of the products of the dissociation.
It is very common in the molecular
microbiology. The term is most
commonly used in the DNA
amplification, the process by which
the DNA is copied in the lab. The
reassociation of the amylose
molecules in an aqueous system is
attributed to the gel formation.
This gel-forming process is known
as the retrogradation. The
reassociation kinetics reflect the
variety of the sequences that are
© 2022 by JPS Scientific Publications, India
382
present. The Reassociation kinetics
is a technique that measures the
rate of the reassociation. The
reassociation reaction can therefore
be used to quantify the represented
sequences. It’s believed that the
incomplete dissociated
fluorosilicate residues can
reassociate in the stomach and
during the food preparation to
produce the exposures to a variety
of the toxic forms, including the
silicon tetrafluoride—a known
hazardous substance. The
Hydrofluoric acid is highly
corrosive and can penetrate tissues
more rapidly than the other
• REPLICATIVE
TRANSPOSITION - The
Replicative transposition is a
mechanism of the transposition in
field of the molecular biology,
which was proposed by the james
A. Shapiro in the year 1979, in
which the transposable element is
duplicated during the reaction, so
that the transposing entity is a copy
of the original element. In this
mechanism, the donor and the
receptor DNA sequences form a
characteristic intermediate known
as the “theta” configuration, which
is sometimes called as the “Shapiro
intermediate”. The Replicative
transposition is very important
characteristic to the
retrotransposons and occurs from
the time to time in the class II
transposons.
• REPETITIVE DNA - The
Repeated sequences which is also
Glossary of Genetics
known as the repetitive elements,
repeating units or the repeats are
the patterns of the nucleic acids
(DNA or the RNA) that occur in
the multiple copies throughout the
genome. The Repetitive DNA was
first detected because of its rapid
re-association kinetics. In many of
the organisms, a significant
fraction of the genomic DNA is
highly repetitive, with over two-
thirds of the sequence consisting of
the repetitive elements in the
humans. The Repetitive elements
found in the genomes fall into the
different classes, depending on
their structure and/or the mode of
the multiplication. The disposition
of the repetitive elements consists
either in arrays of tandemly
repeated sequences, or in the
repeats dispersed throughout the
genome. The Debates regarding
the potential functions of these
elements have been long standing.
The Controversial references to the
‘junk’ or the ‘selfish’ DNA were
put forward early on, implying that
the repetitive DNA segments are
remainders from the past evolution
or the autonomous self-replicating
sequences hacking the cell
machinery to proliferate.
Originally discovered by the
Barbara McClintock, dispersed
repeats have been increasingly
recognized as a potential source of
the genetic variation and the
regulation.
• RUV C - The RuvC is the
resolvase, which cleaves the
© 2022 by JPS Scientific Publications, India
383
Holliday junction. The RuvC
proteins have been shown to form
the dimers in the solution and its
structure has been solved at 2.5A.
It is thought to bind either on the
open, the DNA exposed face of a
single RuvA tetramer, or to replace
one of the two tetramers. The
Binding is proposed to be mediated
by an unstructured loop on the
RuvC, which becomes structured
on the binding RuvA. RuvC can be
bound to the complex in either
orientation, therefore resolving the
Holliday junctions in either a
horizontal or the vertical manner.
• RUV A - The RuvA is a DNA-
binding protein that binds the
Holliday junctions with the very
high affinity. The structure of the
complex has been variously
elucidated through the X-ray
crystallography and the EM data,
and suggest that the complex
consists of either one or the two
RuvA tetramers, with charge lined
grooves through which the
incoming DNA is channelled. The
structure also showed the presence
of the so-called 'acidic pins' in the
centre of the tetramer, which serve
to separate the DNA duplexes. Its
crystal structure has been solved at
around 1.9A.
• RUV B - The RuvB is an ATPase
that is only active in the presence
of the DNA and compared to the
RuvA, RuvB has a low affinity for
the DNA. The RuvB proteins are
thought to form the hexameric
rings on the exit points of the very
Glossary of Genetics
newly formed DNA duplexes, and
it is proposed that they 'spool' the
emerging DNA through the RuvA
tetramer.
• REPLISOME - The replisome is a
complex molecular machine that
carries out the replication of the
DNA. The replisome first unwinds
the double stranded DNA into the
two single strands. For each of the
resulting single strands, a new
complementary sequence of the
DNA is synthesized. The Total
result is formation of the two new
double stranded DNA sequences
that are exact copies of the original
double stranded DNA sequence. In
terms of the structure, the
replisome is composed of the two
replicative polymerase complexes,
one of the which synthesizes the
leading strand, while the other
synthesizes the lagging strand. The
replisome is composed of a number
of the proteins including the
helicase, RFC, PCNA,
gyrase/topoisomerase, SSB/RPA,
primase, DNA polymerase III,
RNAse H, and the ligase.
• REPLICATION REGULATION
- The Eukaryotic DNA replication
is regulated to ensure that all the
chromosomes replicate once and
only once per cell cycle. The
Replication begins at many origins
scattered along the each
chromosome. Except for the
budding yeast, origins are not the
defined DNA sequences and
probably are inherited by the
epigenetic mechanisms. The
© 2022 by JPS Scientific Publications, India
384
initiation at the origins occurs
throughout the S phase according
to a temporal program that is
important in the regulating of the
gene expression during the
development. Most replication
proteins are conserved in evolution
in the eukaryotes and in the
archaea, but not in the bacteria.
However, the mechanism of the
initiation is conserved and consists
of the origin recognition, assembly
of the pre-replication (pre-RC)
initiative complexes, helicase
activation, and the replisome
loading. The Cell cycle regulation
by protein phosphorylation ensures
that the pre-RC assembly can only
occur in the G1 phase, whereas the
helicase activation and loading can
only occur in the S phase. The
checkpoint regulation maintains
the high fidelity by stabilizing the
replication forks and preventing the
cell cycle progression during the
replicating stress or the damage.
• RECQ HELICASES – The RecQ
helicase is a family of the helicase
enzymes initially found in the
Escherichia coli that has been
shown to be important in the
genome maintenance. They
function through catalyzing the
reaction ATP + H2O → ADP + P
and thus driving the unwinding of
the paired DNA and translocating
in the 3' to 5' direction. These
enzymes can also drive the
reaction NTP + H2O → NDP + P
to drive the unwinding of either the
DNA or the RNA. In the
Glossary of Genetics
prokaryotes RecQ is necessary for
the plasmid recombination and the
DNA repair from the UV-light,
free radicals, and the alkylating
agents. This protein can also
reverse the damage from the
replication errors. In the
eukaryotes, the replication does
not proceed normally in the
absence of the RecQ proteins,
which also function in the aging,
silencing, recombination and the
DNA repair.
• REGULATORY SEQUENCES -
The regulatory sequence is a
segment of the nucleic acid
molecule which is capable of
increasing or decreasing the
expression of the specific genes
within an organism. The
Regulation of the gene expression
is an essential feature of all the
living organisms and the viruses.
• REGULATORY SEQUENCES -
The regulatory sequence is a
segment of the nucleic acid
molecule which is capable of
increasing or decreasing the
expression of the specific genes
within an organism. The
Regulation of the gene expression
is an essential feature of all the
living organisms and the viruses. A
regulatory DNA sequence does not
regulate unless it is activated.
Different regulatory sequences are
activated and then implement their
regulation by different
mechanisms.
• RAD51 - The DNA repair protein
RAD51 homolog 1 is a protein
© 2022 by JPS Scientific Publications, India
385
encoded by the gene RAD51. The
enzyme encoded by this gene is a
member of the RAD51 protein
family which assists in the repair of
the DNA double strand breaks.
The RAD51 family members are
the homologous to the bacterial
RecA, Archaeal RadA and the
yeast Rad51. The protein is highly
conserved in most of the
eukaryotes, from the yeast to the
humans. In the humans, the
RAD51 is a 339-amino acid
protein that plays a major role in
the homologous recombination of
the DNA during the double strand
and break repair. In this process,
an ATP dependent DNA strand
exchange takes place in which a
template strand invades the base-
paired strands of the homologous
DNA molecules. The RAD51 is
involved in the search for the
homology and the strand pairing
stages of the process.
• RAGs - The recombination-
activating genes (RAGs) encode
parts of the protein complex that
plays an important roles in the
rearrangement and recombination
of the genes encoding
immunoglobulin and the T cell
receptor molecules. There are the
recombination-activating genes
such as the RAG1 and RAG2,
whose cellular expression is
restricted to the lymphocytes
during their developmental stages.
The enzymes encoded by the these
genes, RAG-1 and the RAG-2, are
essential to the generation of the
Glossary of Genetics
mature B cells and the T cells, the
two types of the lymphocyte that
are very crucial components of the
adaptive immune system. The
RAG proteins initiate the V(D)J
recombination, which is essential
for the maturation of the pre-B and
the pre-T cells. The Activated
mature B cells also possess the two
other remarkable, RAG-
independent phenomena of
manipulating their own DNA: so-
called as the class-switch
recombination (AKA isotype
switching) and the somatic
hypermutation (AKA affinity
maturation). The Current studies
have indicated that the RAG-1 and
the RAG-2 must work in a
synergistic manner to activate the
VDJ recombination.
• RESTRICTION
ENDONUCLEASES - A
restriction enzyme, restriction
endonuclease, or the restrictase is
an enzyme that cleaves the DNA
into the fragments at or near the
specific recognition sites within the
molecules known as the restriction
sites. The Restriction enzymes are
one class of the broader
endonuclease group of the
enzymes. The Restriction enzymes
are commonly classified into the
five types, which differ in their
structure and whether they cut
their DNA substrate at their
recognition site, or if the
recognition and the cleavage sites
are separate from the one another.
To cut the DNA, all the restriction
© 2022 by JPS Scientific Publications, India
386
enzymes make two incisions, once
through the each sugar-phosphate
backbone (i.e. each strand) of the
DNA double helix. These enzymes
are found in the bacteria and in the
archaea and provide a defense
mechanism against the invading
viruses. Inside a prokaryote, the
restriction enzymes selectively cut
up the goreign DNA in a process
called as the restriction digestion;
meanwhile the host DNA is
protected by a modification
enzyme (a methyltransferase) that
modifies the prokaryotic DNA and
blocks the cleavage. Together,
these two processes form the
restriction modification system.
• RBS - The ribosome binding site,
or the ribosomal binding site
(RBS), is a sequence of the
nucleotides upstream of the start
codon of an mRNA transcript that
is responsible for the recruitment of
the ribosome during the initiation
of the translation. Mostly, the RBS
refers to the bacterial sequences,
although the internal ribosome
entry sites (IRES) have been
described in the mRNAs of the
eukaryotic cells or the viruses that
infect the eukaryotes. The
Ribosome recruitment in the
eukaryotes is generally mediated
by the 5' cap present on the
eukaryotic mRNAs.
• RIBOSOMAL L28E PROTEIN
FAMILY - The Ribosomal L28e
protein family is a family of the
evolutionarily related proteins. The
Members include the 60S
Glossary of Genetics
ribosomal protein L28. The
Ribosomal protein L28e forms part
of the 60S ribosomal subunit. This
family is found in the eukaryotes.
In the rat there are 9 or 10 copies
of the L28 gene. The L28 protein
contains a possible internal
duplication of the residues.
• RAMCHANDRAN PLOT - In
the field of the biochemistry, a
Ramachandran plot (also known as
the Rama plot, a Ramachandran
diagram or a [φ,ψ] plot), originally
developed in the year 1963 by the
G. N. Ramachandran, C.
Ramakrishnan, and the V.
Sasisekharan, is a way to visualize
the energetically allowed regions
for the backbone dihedral angles ψ
against the φ of the amino acid
residues in the protein structure. A
Ramachandran plot can be used in
the two somewhat different ways.
One is to show in theory which
values, or the conformations, of the
ψ and φ angles are possible for an
amino-acid residue in a protein. A
second is to show the empirical
distribution of the datapoints
observed in a single structure in
usage for the structure validation,
or else in a database of the many
structures. Either case is usually
shown against the outlines for the
theoretically favored regions.
• RNA WORLD - The RNA world
is a hypothetical stage in the
evolutionary history of the life on
the Earth, in which the self-
replicating RNA molecules
proliferated before the evolution of
© 2022 by JPS Scientific Publications, India
387
the DNA and the proteins. The
term also refers to the hypothesis
that posits the existence of this
stage. Like the DNA, the RNA can
store and replicate the genetic
information like the protein
enzymes, the RNA enzymes
(ribozymes) can catalyze (start or
accelerate) chemical reactions that
are critical for the life. One of the
most critical components of the
cells, the ribosome, is composed
primarily of the RNA. The
Ribonucleotide moieties in many
coenzymes, such as the acetyl-
CoA, NADH, FADH, and the
F420, may be surviving remnants
of the covalently bound coenzymes
in an RNA world. Although the
RNA is fragile, some ancient
RNAs may have evolved the
ability to methylate the other
RNAs to protect them.
• RAD 51 - The DNA repair
protein RAD51 homolog 1 is a
protein encoded by the gene
RAD51. The enzyme encoded by
this gene is a member of the
RAD51 protein family which
assists in the repair of the DNA
double strand breaks. The RAD51
family members are homologous to
the bacterial RecA, Archaeal RadA
and the yeast Rad51. The protein is
highly conserved in most of the
eukaryotes, from the yeast to the
humans. In the humans, the
RAD51 is a 339-amino acid
protein that plays a major role in
the homologous recombination of
the DNA during the double strand
Glossary of Genetics
break repair. In this process, an
ATP dependent DNA strand
exchange takes place in which a
template strand invades the base-
paired strands of the homologous
DNA molecules. The RAD51 is
involved in the search for the
homology and the strand pairing
stages of the process. Unlike the
other proteins involved in the
DNA metabolism, the
RecA/Rad51 family forms a
helical nucleoprotein filament on
the DNA. This protein can interact
with the ssDNA-binding protein
RPA, BRCA2, PALB2 and the
RAD52.
• RAD 52 - The RAD52 homolog
(S. cerevisiae), also known as the
RAD52, is a protein which in the
humans is encoded by the RAD52
gene. The protein encoded by this
gene shares similarity with the
Saccharomyces cerevisiae Rad52, a
protein important for the DNA
double-strand break repair and the
homologous recombination. This
gene product was shown to bind
the single-stranded DNA ends, and
mediate the DNA-DNA
interaction necessary for the
annealing of the complementary
DNA strands. It was also found to
interact with the DNA
recombination protein RAD51,
which suggested its role in the
RAD51-related DNA
recombination and the repair.
• RAG 1 - The Recombination
activating gene 1 also known as the
RAG-1 is a protein that in the
© 2022 by JPS Scientific Publications, India
388
humans is encoded by the RAG1
gene. The protein encoded by this
gene is involved in the antibody
and the T-cell receptor V(D)J
recombination. The RAG-1 is
involved in the recognition of the
DNA substrate, but stable binding
and the cleavage activity also
requires the RAG-2. The RAG-1/2
complex recognizes the
recombination signal sequences
(RSSs) that flank the V, D and J
regions in the genes that encode
the heavy and the light chains of
the antibodies and components of
the T-cell receptors. The complex
binds to the RSSs and nicks the
DNA. This leads to the removal of
the intervening DNA and the
eventual ligation of the V, D and J
sequences. The Defects in this gene
can cause the several different
diseases.
• RAG 2 - The Recombination
activating gene 2 protein (also
known as the RAG-2) is a
lymphocyte-specific protein
encoded by the RAG2 gene on the
human chromosome 11. Together
with the RAG1 protein, the RAG2
forms a V(D)J recombinase, a
protein complex required for the
process of the V(D)J
recombination during which the
variable regions of the
immunoglobulin and the T cell
receptor genes are assembled in the
developing B and T lymphocytes.
Therefore, the RAG2 is essential
for the generation of the mature B
and the T lymphocytes. The RAG2
Glossary of Genetics
is one of the two core components
of the RAG complex. The RAG
complex is a multiprotein complex
that mediates the DNA cleavage
phase during the V(D)J
recombination. This complex can
make the double-strand breaks by
cleaving the DNA at the conserved
recombination signal sequences
(RSS). The mutations of the RAG2
gene can result in the severe
immune disorders such as the
SCID (Severe Combined
Immunodeficiency) or the Omenn
syndrome. The Omenn Syndrom is
caused by a hypomorphic mutation
of the RAG2 gene, which leads to
reduced but still present function of
the RAG complex. Although the
patients do not have any
circulating B cells, a small number
of the oligoclonal T cells is
developed.
• RAN - The Ran (RAs-related
Nuclear protein) also known as the
GTP-binding nuclear protein Ran
is a protein that in the humans is
encoded by the RAN gene. The
Ran is a small 25 kDa protein that
is involved in the transport into
and out of the cell nucleus during
the interphase and is also involved
in the mitosis. It is a member of the
Ras superfamily. The Ran exists in
the cell in the two nucleotide-
bound forms: the GDP-bound and
the GTP-bound. The RanGDP is
converted into the RanGTP
through the action of the RCC1,
the nucleotide exchange factor for
the Ran. The RCC1 is also known
© 2022 by JPS Scientific Publications, India
389
as the RanGEF (Ran Guanine
nucleotide Exchange Factor). The
Ran's intrinsic GTPase-activity is
activated through the interaction
with the Ran GTPase activating
protein (RanGAP), facilitated by
the complex formation with the
Ran-binding protein (RanBP). The
GTPase-activation leads to the
conversion of the RanGTP to the
EanGDP, thus closing the Ran
cycle. The Ran is a small G protein
that is essential for the
translocation of the RNA and the
proteins through the nuclear pore
complex. The Ran protein has also
been implicated in the control of
the DNA synthesis and the cell
cycle progression, as the mutations
in the Ran have been found to
disrupt the DNA synthesis.
• RAP 1 - The Rap1 (Ras-
proximate-1 or the Ras-related
protein 1) is a small GTPase,
which are the small cytosolic
proteins that act like the cellular
switches and are vital for the
effective signal transduction. There
are two isoforms of the Rap1
protein, each encoded by a
separate gene, the RAP1A and the
RAP1B. The Rap1 belongs to the
Ras-related protein family. The
GTPases are inactive when in their
GDP-bound form, and become
active when they bind to the GTP.
The GTPase activating proteins
(GAPs) and the guanine nucleotide
exchange factors (GEFs) regulate
the small GTPases, with the GAPs
promoting the GDP-bound
Glossary of Genetics
(inactive) form, and the GEFs
promoting the GTP-bound (active)
form. When bound to the GTP,
small GTPases regulate myriad
cellular processes. These proteins
are divided into the families
depending on their protein
structure, and the most well
studied is the Ras superfamily, of
which Rap1 is a member. Whereas
the Ras is known for its role in the
cell proliferation and survival. The
Rap1 is predominantly involved in
the cell adhesion and in the cell
junction formation. The Ras and
Rap are regulated by the different
sets of the guanine nucleotide
exchange factors and the GTPase-
activating proteins, thus providing
one level of the specificity.
• RDRP - The RNA-dependent
RNA polymerase (RdRp) or the
RNA replicase is an enzyme that
catalyzes the replication of the
RNA from an RNA template.
Specifically, it catalyzes the
synthesis of the new RNA strand
complementary to a given RNA
template. This is in contrast to the
typical DNA-dependent RNA
polymerases, which all organisms
use to catalyze the transcription of
the RNA from a DNA template.
The RdRp is an essential protein
encoded in the genomes of the
most RNA-containing viruses with
no DNA stage including the
SARS-CoV-2. Some of the
eukaryotes also contain the RdRps,
which are involved in the RNA
interference and differ structurally
© 2022 by JPS Scientific Publications, India
390
from the viral RdRps.The most
famous example of the RdRp is
that of the polio virus. The viral
genome is composed of the RNA,
which enters the cell through the
receptor-mediated endocytosis.
From there, the RNA is able to act
as a template for the
complementary RNA synthesis,
immediately. The complementary
strand is then, itself, able to act as a
template for the production of the
new viral genomes that are further
packaged and released from the
cell ready to infect the more host
cells.
• RHODOPSIN KINASE - The
Rhodopsin kinase is a
serine/threonine-specific protein
kinase which is involved in the
phototransduction process. The
Rhodopsin kinase is a member of
the family of the G protein-coupled
receptor kinases, and is officially
named ss the G protein-coupled
receptor kinase 1, or the GRK1.
The Rhodopsin kinase is found
primarily in the mammalian retinal
rod cells, where it phosphorylates
the light-activated rhodopsin, a
member of the family of the G
protein-coupled receptors that
recognizes the light.
Phosphorylated, light-activated
rhodopsin binds to the protein
arrestin to terminate the light-
activated signaling cascade. The
Mutations in the rhodopsin kinase
are associated with a form of the
night blindness called as the
Oguchi disease.
Glossary of Genetics
• RECOVERIN - The Recoverin
(abbreviated Recov) is a 23
kilodalton (kDa) neuronal calcium-
binding protein that is primarily
detected in the photoreceptor cells
of the eye. It plays a key role in the
inhibition of the rhodopsin kinase,
a molecule which regulates the
phosphorylation of the rhodopsin.
A reduction in this inhibition helps
the regulate sensory adaptation in
the retina, since the light-
dependent channel closure in the
photoreceptors causes the calcium
levels to decrease, which relieves
the inhibition of the rhodopsin
kinase by the calcium-bound
recoverin, leading to a more rapid
inactivation of metarhodopsin II
(activated form of the rhodopsin).
The Recoverin is involved in the
recovery phase of the visual
excitation and in adaptation to the
background light. It controls the
life span of the photoexcited
rhodopsin by helping to inhibit the
rhodopsin kinase.
• RETINOBLASTOMA PROTEIN
- The retinoblastoma protein
(protein name abbreviated pRb;
gene name abbreviated Rb, RB or
RB1) is a tumor suppressor protein
that is dysfunctional in the several
major type of cancers. One
function of the pRb is to prevent
the excessive cell growth by
inhibiting the cell cycle progression
until a cell is ready to divide.
When the cell is ready to divide,
the pRb is phosphorylated,
inactivating it, and the cell cycle is
© 2022 by JPS Scientific Publications, India
391
allowed to progress. It is also a
recruiter of the several chromatin
remodeling enzymes such as the
methylases and the acetylases. The
pRb belongs to the pocket protein
family, whose members have a
pocket for the functional binding of
the other proteins. Should an
oncogenic protein, such as the
those produced by the cells infected
by the high-risk types of the human
papillomavirus, bind and inactivate
the pRb, this can lead to the
cancer. The RB gene may have
been responsible for the evolution
of the multicellularity in the several
lineages of the life including
animals.
• READING FRAMES - In the
sphere of molecular biology,
a analyzing body is a manner of
dividing the collection of the
nucleotides in a nucleic acid (DNA
or the RNA) molecule into a hard
and fast of the consecutive, non-
overlapping triplets. Where
the those triplets equate to the
amino acids or
the forestall alerts all through the
translation, they're known
as because the codons.
A unmarried strand of a nucleic
acid molecule has a phosphoryl
end, known as because the 5′-end,
and a hydroxyl or 3′-end.
These outline the 5′→3′ course.
There are 3 analyzing frames
that may be examine on
this 5′→3′ course, every starting fro
m a exceptional nucleotide in a
triplet. In the double stranded
Glossary of Genetics
nucleic acid, an
extra 3 analyzing frames can
be examine from the other,
complementary strand withinside
the 5′→3′ course alongside this
strand. As the 2 strands of a
double-stranded nucleic acid
molecule are antiparallel in nature,
the 5′→3′ direction on the second
strand corresponds to the 3′→5′
direction along the first strand.
• RELEASE FACTOR - A release
factor is a protein that allows for
the termination of the translation
by recognizing the termination
codon or the stop codon in an
mRNA sequence. They are named
so because they release the new
peptides from the ribosome. The
Crystal structures have been solved
for the bacterial 70S ribosome
bound to each of the three release
factors, revealing the details in the
codon recognition by the RF1/2
and the EF-G-like rotation of the
RF3. The Cryo-EM structures have
been obtained for the eukaryotic
mamallian 80S ribosome bound to
the eRF1 and/or the eRF3,
providing a view of the structural
rearrangements caused by the
factors. Fitting the EM images to
the previously known crystal
structures of the individual parts
provides the identification and a
more detailed view of the process.
In both the systems, the class II
(e)RF3 binds to the universal
GTPase site on the ribosome,
while the class I RFs occupy the A
site.
© 2022 by JPS Scientific Publications, India
392
• REPORTER GENE - In the field
of molecular biology, a reporter
gene (often simply reporter) is a
gene that researchers attach to a
regulatory sequence of the another
gene of the interest in the bacteria,
cell culture, animals or the plants.
Such genes are called as the
reporters because the
characteristics they confer on the
organisms expressing them are
easily identified and measured, or
because they are the selectable
markers. The Reporter genes are
often used as an indication of
whether a certain gene has been
taken up by or expressed in the cell
or the organism population. The
commonly used reporter genes that
induce the visually identifiable
characteristics usually involve the
fluorescent and the luminescent
proteins. Examples include the
gene that encodes the jellyfish
green fluorescent protein (GFP),
which causes the cells that express
it to glow green under the blue
light, the enzyme luciferase, which
catalyzes a reaction with the
luciferin to produce the light, and
the red fluorescent protein from the
gene dsred.
• REPLICATION BUBBLE - A
replication bubble is an unwound
and open region of a DNA helix
where the DNA replication occurs.
The enzyme Helicase unwinds
only a small section of the DNA at
a time in a place called as the
origin of the replication. In the
eukaryotes, there are several
Glossary of Genetics
origins of the replication on each of
the chromosome. The replication
bubble grows in the two directions
from its origin. There are the two
replication forks in a replication
bubble, which is where the parental
DNA double helix is split. The
Specialized proteins recognize the
origin, bind to this site, and open
up the DNA. As the DNA opens,
the two Y-shaped structures called
as the replication forks are formed,
together making up what's called
as a replication bubble. The
replication forks will move in the
opposite directions as the
replication proceeds.
• REPRESSILATOR - The
repressilator is a type of a genetic
regulatory network consisting of at
least one feedback loop with at
least three genes, each of them
expressing a protein that represses
the next gene in the loop. In the
biological research, the
repressilators have been used to
build the cellular models and to
understand the cell function. There
are both the artificial and the
naturally-occurring repressilators.
Recently, the naturally-occurring
repressilator clock gene circuit in
the Arabidopsis thaliana (A.
thaliana) and the mammalian
systems have been studied. The
Circadian circuits in plants feature
a transcriptional regulatory
feedback loop called as the
repressilator. In the core oscillator
loop (outlined in gray) in A.
thaliana, the light is first sensed by
© 2022 by JPS Scientific Publications, India
393
the two cryptochromes and the five
phytochromes. The two
transcription factors, Circadian
Clock Associated 1 (CCA1) and
the Late Elongated Hypocotyl
(LHY), repress genes associated
with the evening expression like
Timing of the CAB expression 1
(TOC1) and activate genes
associated with the morning
expression by binding to their
promoters. The TOC1, an evening
gene, positively regulates the
CCA1 and LHY via an unknown
mechanism. The Evening-phased
transcription factor CCA1 Hiking
Expedition (CHE) and the histone
demethylase jumonji C domain-
containing 5 (JMJD5) directly
repress the CCA1.
• RUNT DOMAIN - The Runt
domain is an evolutionary
conserved protein domain. The
AML1/RUNX1 gene is rearranged
by the translocation in the acute
myeloid leukemia. The gene is very
highly similar to the Drosophila
melanogaster segmentation gene
runt and to the mouse transcription
factor PEBP2 alpha subunit gene.
The region of the shared similarity,
known as the Runt domain, is
responsible for the DNA-binding
and the protein-protein interaction.
In addition to the highly conserved
Runt domain, the AML-1 gene
product carries the putative ATP-
binding site (GRSGRGKS), and
has a C-terminal region rich in the
proline and in the serine residues.
The protein (known as the acute
Glossary of Genetics
myeloid leukemia 1 protein,
oncogene AML-1, core-binding
factor (CBF), alpha-B subunit, etc.)
binds to the core site, 5'-pygpyggt-
3', of a number of the enhancers
and the promoters. The protein is a
heterodimer of the alpha- and the
beta-subunits. The alpha-subunit
binds the DNA as a monomer, and
appears to have a role in the
development of the normal
hematopoiesis. The CBF is a
nuclear protein expressed in the
numerous tissue types, except the
brain and the heart, the highest
levels have been found to occur in
the thymus, bone marrow and in
the peripheral blood. This domain
occurs towards the N-terminus of
the proteins in this entry.
• RESOLVASE - The term resolvase
is used to describe a related family
of the site-specific recombinases
that function to excise a segment of
the DNA contained between the
two recombination sites (called as
the res). The original resolvases
were encoded by the transposons
of the Tn3-family. These
transposons move by a replicative
pathway and, in the first step of the
transposition, form what is called
as abcointegrate. This is an
insertion into a target DNA of the
entire replicon that carries the
transposon with the one complete
copy of the transposon at each end
of the inserted DNA. The
transposon-encoded resolvase
protein excises the initial donor
replicon from the cointegrate,
© 2022 by JPS Scientific Publications, India
394
leaving behind one copy of the
transposon in the target site. The
Resolvases closely related to the
original Tn3 and γδ resolvase are
encoded by some of the other
transposons and serve the same
purpose, to resolve the cointegrate
transposition intermediates. The
Additional resolvases are not the
transposon-associated, but are
encoded by the bacterial plasmids.
The purpose of these is to maintain
the plasmids in a monomeric state.
Following the replication, two
monomeric copies of a plasmid
may recombine to form a single
dimer. If the plasmid remains as a
dimer at cell division, it will be
retained by the one daughter and
lost by the other. The plasmid
resolvases keep this from
happening by reducing the dimers
back to the two monomeric
precursors. This substantially
reduces the plasmid loss during the
vegetative growth.
• RETINITIS PIGMENTOSA -
The Retinitis pigmentosa (RP) is a
genetic disorder of the eyes that
causes the loss of the vision. The
Symptoms include the trouble
seeing at night and the decreasing
peripheral vision (side and upper or
lower visual field). As the
peripheral vision worsens, people
may experience the "tunnel
vision". The Complete blindness is
uncommon. The Onset of the
symptoms is generally gradual and
often begins in the childhood. The
Retinitis pigmentosa is generally
Glossary of Genetics
inherited from one or both the
parents or rarely it can be newly
evolved from a miscoding during
the DNA division. It is caused by
the genetic miscoding of the
proteins in one of more than 300
genes involved. The underlying
mechanism involves the
progressive loss of the rod
photoreceptor cells that line the
retina of the eyeball.[1] The rod
cells secrete a neuroprotective
substance known as Rod-derived
cone viability factor, RdCVF that
protects the cone cells from the
apoptosis (cell death). However,
when the rod cells die, this
substance is no longer provided.
The supportive testing may include
the electroretinogram (ERG),
visual field testing (VFT), ocular
coherence tomography (OCT) and
the DNA testing to determine the
gene responsible for a person's
particular type of RP.
• RETT SYNDROME - The Rett
syndrome (RTT) is a genetic
disorder that typically becomes
apparent after the 6–18 months of
the age in the females. The
symptoms include the impairments
in the language and in the
coordination and the repetitive
movements. Those affected often
have the slower growth, difficulty
walking, and a smaller head size.
The Complications of the Rett
syndrome can include the seizures,
scoliosis, and the sleeping
problems. The severity of the
condition is very variable. The Rett
© 2022 by JPS Scientific Publications, India
395
syndrome is due to a genetic
mutation in the MECP2 gene, on
the X chromosome. It almost
always occurs as a new mutation,
with less than one percent of the
cases being inherited from a
person's parents. It occurs almost
exclusively in the girls, boys who
have a similar mutation typically
die shortly after the birth. The
Diagnosis is based on the
symptoms and can be confirmed
with the genetic testing. There is
no known cure for the Rett
syndrome. The treatment is
directed at improving the
symptoms. The Anticonvulsants
may be used to help with the
seizures. The Special education,
physiotherapy, and braces may
also be useful. Many of those with
the condition live into the middle
age.
• REVERSE GYRASE - The
Reverse gyrases are the
topoisomerases that introduce the
positive supercoils into the DNA in
an ATP-dependent reaction. They
consist of a helicase domain and a
topoisomerase domain that closely
cooperate in the catalysis. The
mechanism of the functional
cooperation of these domains has
still remained elusive. The recent
studies have shown that the
helicase domain is a nucleotide-
regulated conformational switch
that alternates between an open
conformation with a low affinity
for the double-stranded DNA, and
a closed state with a high double-
Glossary of Genetics
stranded DNA affinity. The
conformational cycle leads to
thentransient separation of the
DNA duplexes by the helicase
domain. The Reverse gyrase-
specific insertions in the helicase
module are involved in binding to
the single-stranded DNA regions,
DNA unwinding and in the
supercoiling. The Biochemical and
the structural data suggest that the
DNA processing by the reverse
gyrase is not based on the
sequential action of the helicase
and the topoisomerase domains,
but rather the result of an intricate
cooperation of both the domains at
all stages of the reaction.
• REVERSE MUTATIONS - The
Reverse mutation, also called as
the reversion, denotes any
mutational process or the mutation
that restores the wild-type
phenotype to the cells already
carrying a phenotype-altering
forward mutation. The Forward
mutations confer a gene sequence
and the phenotype different from
that conferred by the wild-type
gene. True reversions restore the
wild-type gene sequence, whereas
thevpseudoreversions restore the
wild-type phenotype by a transcriptional units, to prevent
compensating gene sequence
change. The Pseudoreversions can
occur in the same gene as the
original forward mutation or in a
different gene or the sequence. The
Particular useful mutation assays
that employ reversion are
reviewed. The Stress-induced
© 2022 by JPS Scientific Publications, India
396
mutagenesis, the turning up of
mutation rate in response to the
cellular stress, often under the
control of the stress responses, has
been studied mostly using the
reversion assays. Th3 Reverse
mutations have been studied
preferentially by the geneticists
because, unlike most of the
forward mutations, many
reversions can be selected
genetically, making a very low-
frequency mutation events possible
to quantify and study. The Genetic
selection means the use of a
condition (e.g., growth medium,
temperature, or other) under which
the cells or the organisms
possessing the selected genotype
can grow, and those not possessing
the selected genotype cannot.
• RHO DEPENDENT
TERMINATORS - The Rho-
dependent transcription
terminators participate in the
sophisticated genetic regulatory
mechanisms, in both the bacteria
and the phages. They occur in the
regulatory regions preceding the
coding sequences of the genes and
within the coding sequences, as
well as at the end of the
readthrough transcription. Most of
the Rho-dependent terminators
have been found in the enteric
bacteria, but they also occur in the
Gram-positive bacteria and may be
widespread among the bacteria.
The Rho-dependent termination
requires both the cis-acting
Glossary of Genetics
elements, on the mRNA, and the
trans-acting factors. The only cis-
acting element common to the
Rho-dependent terminators is
richness in the rC residues. The
Additional sequence elements have
been observed at the different Rho
termination sites. The Rho is the
main factor required for the
termination; it is a ring-shaped
hexameric protein with the
ATPase and the helicase activities.
The NusG, NusA and the NusB
are the additional factors
participating in the termination
process. The Rho-dependent
termination occurs by the binding
of the Rho to the ribosome-free
mRNA, C-rich sites being good
candidates for the binding. The
Rho's ATPase is activated by the
Rho-mRNA binding, and provides
the energy for the Rho
translocation along the mRNA, the
translocation requires the sliding of
the message into the central hole of
the hexamer.
• RHO FACTOR - A ρ factor (Rho
factor) is a bacterial protein
involved in the termination of the
ranscription. The Rho factor binds
to the transcription terminator
pause site, an exposed region of the
single stranded RNA (a stretch of
about 72 nucleotides) after the
open reading frame at the C-
rich/G-poor sequences that lack
the obvious secondary structure.
The Rho's key function is its
helicase activity, for which the
energy is provided by an RNA-
© 2022 by JPS Scientific Publications, India
397
dependent ATP hydrolysis. The
initial binding site for the Rho is an
extended single-stranded region,
rich in the cytosine and poor in the
guanine, called as the rho
utilisation site (rut), in the RNA
being synthesised, upstream of the
actual terminator sequence. Several
of the rho binding sequences have
been discovered. The Rho binds to
the RNA and then uses its ATPase
activity to provide the energy to
translocate along the RNA until it
reaches the RNA–DNA helical
region, where it unwinds the
hybrid duplex structure. The RNA
polymerase pauses at the
termination sequence, which is
because there is a specific site
around 100 nt away from the Rho
binding site called as the Rho-
sensitive pause site.
• RHOMBOID PROTEASE - The
rhomboid proteases are a family of
the enzymes that exist in almost all
the species. They are proteases,
they cut the polypeptide chain of
the other proteins. This proteolytic
cleavage is irreversible in the cells,
and an important type of the
cellular regulation. Although the
proteases are one of the earliest
and the best studied class of the
enzyme, rhomboids belong to a
much more recently discovered
type, the intramembrane proteases.
What is unique about the
intramembrane proteases is that
their active sites are buried in the
lipid bilayer of the cell membranes,
and they cleave the other
Glossary of Genetics
transmembrane proteins within
their transmembrane domains.
About 30% of all the proteins have
the transmembrane domains, and
their regulated processing often has
major biological consequences.
Accordingly, the rhomboids
regulate many of the important
cellular processes, and may be
involved in a wide range of the
human diseases. The Rhomboids
were the first discovered as the
proteases that regulate the EGF
receptor signalling in the
Drosophila. By releasing the
extracellular domain of the growth
factor Spitz, from its
transmembrane precursor, the
rhomboid triggers signalling. Since
then, many of the other important
biological functions have been
proposed.
• RIBBON DIAGRAM - The
Ribbon diagrams, also known as
the Richardson diagrams, are the
3D schematic representations of
the protein structure and are one of
the most common methods of the
protein depiction used today. The
ribbon shows the overall path and
the organization of the protein
backbone in the 3D, and serves as
a visual framework on which to
hang the details of the full atomic
structure, such as the balls for the
oxygen atoms bound to the active
site of the nyoglobin in the
adjacent image. The Ribbon
diagrams are generated by
interpolating a smooth curve
through the polypeptide backbone.
© 2022 by JPS Scientific Publications, India
398
The α-helices are shown as the
coiled ribbons or the thick tubes, β-
strands as the arrows, and the non-
repetitive coils or the loops as lines
or the thin tubes. The direction of
the polypeptide chain is shown
locally by the arrows, and may be
indicated overall by a colour ramp
along the length of the ribbon. The
Ribbon diagrams are simple yet
powerful, expressing the visual
basics of a molecular structure.
This method has successfully
portrayed the overall organization
of the protein structures, reflecting
their three-dimensional nature and
allowing for the better
understanding of these complex
objects both by the expert
structural biologists and by the
other scientists, students, and the
general public.
• RBS - A ribosome binding site, or
the ribosomal binding site (RBS), is
a sequence of the nucleotides
upstream of the start codon of an
mRNA transcript that is
responsible for the recruitment of a
ribosome during the initiation of
the translation. Mostly, the RBS
refers to the bacterial sequences,
although the internal ribosome
entry sites (IRES) have been
described in the mRNAs of the
eukaryotic cells or the viruses that
infect the eukaryotes. The
Ribosome recruitment in the
eukaryotes is generally mediated
by the 5' cap present on the
eukaryotic mRNAs. The RBS in
the prokaryotes is a region
Glossary of Genetics
upstream of the start codon. This
region of the mRNA has the
consensus 5'-AGGAGG-3', also
called as the Shine-Dalgarno (SD)
sequence. The Ribosome
recruitment in the eukaryotes
happens when the eukaryote
initiation factors elF4F and the
poly(A)-binding protein (PABP)
recognize the 5' capped mRNA
and recruit the 43S ribosome
complex at that location.
• RRF - The Ribosome recycling
factor or the ribosome release
factor (RRF) is a protein found in
the bacterial cells as well as in the
eukaryotic organelles, specifically
in the mitochondria and
chloroplasts. It functions to recycle
the ribosomes after completion of
the protein synthesis (bacterial
translation). In the humans, the
mitochrondrial version is coded by
the MRRF gene. The RRF
accomplishes the recycling of the
ribosomes by splitting the
ribosomes into the subunits,
thereby releasing the bound
mRNA. This also requires the
participation of the EF-G (GFM2
in humans). Depending on the
tRNA, the IF1–IF3 may also
perform the recycling. In the
Bacteria (specifically Escherichia
coli), loss of the gene encoding
RRF is deleterious. This makes the
RRF a possible target for the new
antibacterial drugs. The yeast
mitochondrial RRF (mtRRF) is
encoded by a gene in the cell
nucleus. Loss of the function of
© 2022 by JPS Scientific Publications, India
399
this gene leads to the
mitochondrial genome instability
and the respiratory incompetence.
• RICIN - The Ricin is a lectin (a
carbohydrate-binding protein) and
a highly potent toxin produced in
the seeds of the castor oil plant,
Ricinus communis. The median
lethal dose of the ricin for the mice
is around 22 micrograms per
kilogram of the body weight via the
intraperitoneal injection. The Oral
exposure to ricin is far less toxic.
An estimated lethal oral dose in the
humans is approximately around 1
milligram per kilogram of the body
weight. The Ricin is classified as a
type 2 ribosome-inactivating
protein (RIP). Whereas the type 1
RIPs are composed of a single
protein chain that possesses the
catalytic activity, the type 2 RIPs,
also known as the holotoxins, are
composed of the two different
protein chains that form a
heterodimeric complex. The Type
2 RIPs consist of an A chain that is
functionally equivalent to a type 1
RIP, covalently connected by a
single disulfide bond to a B chain
that is catalytically inactive, but
serves to mediate transport of the
A-B protein complex from the cell
surface, via the vesicle carriers, to
the lumen of the endoplasmic
reticulum (ER). Both the type 1
and type 2 RIPs are functionally
active against the ribosomes in
vitro, however, only type 2 RIPs
display cytotoxicity due to the
lectin-like properties of the B chain.
Glossary of Genetics 400

• RISC - The RNA-induced similar fashion. dsRNA fragments

silencing complex, or the RISC, is are loaded into RISC with each
a multiprotein complex, strand having a different fate based
specifically a ribonucleoprotein, on the asymmetry rule
which functions in the gene phenomenon, the selection of one
silencing via a variety of the strand as the guide strand over the
pathways at the transcriptional and other based on thermodynamic
the translational levels. Using the stability.
single-stranded RNA (ssRNA) • RITS - The RNA-induced
fragments, such as the microRNA transcriptional silencing (RITS) is a
(miRNA), or the double-stranded form of the RNA interference by
small interfering RNA (siRNA), which the short RNA molecules
the complex functions as a key tool such as the small interfering RNA
in the gene regulation. The single (siRNA) trigger the
strand of the RNA acts as a downregulation of the transcription
template for the RISC to recognize of a particular gene or the genomic
the complementary messenger region. This is usually
RNA (mRNA) transcript. Once accomplished by the
found, one of the proteins in the posttranslational modification of
RISC, Argonaute, activates and the histone tails (e.g. the
cleaves the mRNA. This process is methylation of the lysine 9 of the
called as the RNA interference histone H3) which target the
(RNAi) and it is found in many of genomic region for the
the eukaryotes, it is a key process heterochromatin formation. The
in the defense against the viral protein complex that binds to the
infections, as it is triggered by the siRNAs and interacts with the
presence of the double-stranded methylated lysine 9 residue of
RNA (dsRNA). The RNase III histones H3 is the RITS complex.
Dicer is a critical member of the The maintenance of the
RISC that initiates the RNA heterochromatin regions by the
interference process by producing RITS complexes has been
the double-stranded siRNA or the described as a self-reinforcing
single-stranded miRNA. The feedback loop, in which the RITS
Enzymatic cleavage of dsRNA complexes stably bind the
within the cell produces the short methylated histones of a
siRNA fragments of the 21-23 heterochromatin region using the
nucleotides in length with a two- Chp1 protein and induce the co-
nucleotide 3' overhang. The Dicer transcriptional degradation of tye
also processes the pre-miRNA, any nascent messenger RNA
which forms a hairpin loop (mRNA) transcripts, which are
structure to mimic the dsRNA, in a then used as the RNA-dependent

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
RNA polymerase substrates to
replenish the complement of the
siRNA molecules to form the more
RITS complexes.
• RRM - The RNA recognition
motif, RNP-1 is a putative RNA-
binding domain of about 90 amino
acids that are known to bind the
single-stranded RNAs. It was
found in many of the eukaryotic
proteins. The RRM proteins have a
variety of the RNA binding
preferences and functions, and
include the heterogeneous nuclear
ribonucleoproteins (hnRNPs),
proteins implicated in the
regulation of the alternative
splicing, protein components of the
small nuclear ribonucleoproteins,
and the proteins that regulate the
RNA stability and the translation.
The RRM in the heterodimeric
splicing factor U2 snRNP auxiliary
factor appears to have the two
RRM-like domains with
specialised features for the protein
recognition. The motif also appears
in a few single stranded DNA
binding proteins. The typical RRM
consists of the four anti-parallel
beta-strands and the two alpha-
helices arranged in a beta-alpha-
beta-beta-alpha-beta fold with the
side chains that stack with the
RNA bases. A third helix is present
during the RNA binding in some
of the cases.
• RNASE H - The Ribonuclease H
(abbreviated as the RNase H or the
RNH) is a family of the non-
sequence-specific endonuclease
© 2022 by JPS Scientific Publications, India
401
enzymes that catalyze the cleavage
of the RNA in an RNA/DNA
substrate via a hydrolytic
mechanism. The Members of the
RNase H family can be found in
nearly all the organisms, from the
bacteria to the archaea to the
eukaryotes. The Ribonuclease H
enzymes cleave the phosphodiester
bonds of the RNA in a double-
stranded RNA:DNA hybrid,
leaving a 3' hydroxyl and a 5'
phosphate group on the either end
of the cut site with a two-metal-ion
catalysis mechanism, in which the
two divalent cations, such as the
Mg2+ and Mn2+, directly
participate in the catalytic function.
Depending on the differences in
their amino acid sequences, these
RNases H are classified into the
type 1 and the type 2 RNases H. In
many of the eukaryotes, including
the mammals, the RNase H1 genes
include a mitochondrial targeting
sequence, leading to the expression
of the isoforms with and without
the MTS present. In the knockout
mouse models, the RNase H1-null
mutants are lethal during the
embryogenesis due to the defects in
the replicating mitochondrial
DNA.
• RNASE H2 - In the prokaryotes,
the RNase H2 is enzymatically
active as a monomeric protein. In
the eukaryotes, it is an obligate
heterotrimer composed of a
catalytic subunit A and the
structural subunits B and C. While
the A subunit is closely
Glossary of Genetics
homologous to the prokaryotic
RNase H2, the B and C subunits
have no apparent homologs in the
prokaryotes and are poorly
conserved at the sequence level
even among the eukaryotes. The B
subunit mediates protein-protein
interactions between the H2
complex and the PCNA, which
localizes H2 to the replication foci.
Both the prokaryotic and the
eukaryotic H2 enzymes can cleave
the single ribonucleotides in a
strand. However, they have slightly
different cleavage patterns and
substrate preferences, prokaryotic
enzymes have lower processivity
and hydrolyze successive
ribonucleotides more efficiently
than the ribonucleotides with a 5'
deoxyribonucleotide, while the
eukaryotic enzymes are more
processive and hydrolyze both
types of the substrate with the
similar efficiency.
• RNASE 3 SUPERFAMILY - The
Ribonuclease III (RNase III or the
RNase C) is a type of ribonuclease
that recognizes the dsRNA and
cleaves it at specific targeted
locations to transform them into
the mature RNAs. nThese
enzymes are a group of the
endoribonucleases that are
characterized by their ribonuclease
domain, which is labelled the
RNase III domain. They are
ubiquitous compounds in the the
cell and play a major role in the
pathways such as the RNA
precursor synthesis, RNA
© 2022 by JPS Scientific Publications, India
402
Silencing, and the pnp
autoregulatory mechanism. The
RNase III superfamily is divided
into the four known classes: 1, 2, 3,
and 4. Each class is defined by its
domain structure.
• RNASE P :-
• The Ribonuclease P is a type of the
ribonuclease which cleaves the
RNA. The RNase P is unique from
the other RNases in that it is a
ribozyme a ribonucleic acid that
acts as a catalyst in the same way
that a protein-based enzyme
would. Its function is to cleave off
an extra, or the precursor,
sequence of the RNA on the tRNA
molecules. Further, the RNase P is
one of the two known multiple
turnover ribozymes in the nature.
It has been aslo shown that the
human nuclear RNase P is
required for the normal and the
efficient transcription of the
various small noncoding RNAs,
such as the tRNA, 5S rRNA, SRP
RNA and the U6 snRNA genes,
which are transcribed by the RNA
polymerase III, one of the three
major nuclear RNA polymerases in
the human
• RNA WORLD HYPOTHESIS -
The RNA world hypothesis
proposes that a world filled with
the RNA-based life predates the
current DNA-based lifeforms. The
RNA is also able to store the
information in a sequence
composed of the four recurring
nucleotides. The short sequences of
the RNA are able to be accurately
Glossary of Genetics
duplicated to form the identical
RNA molecules. The RNA is the
only molecule that is capable of
both the self-replication and the
catalytic functioning, but has since
been superseded. The Modern cells
use the RNA catalysts to remove
the introns from the mRNA and
help to synthesise the new RNA
molecules. In the ribosomes, the
rRNA functions as the catalytic
component and plays a pivotal role
in the peptide bond formation.
• RPA - The Replication protein A
(RPA) is the major protein that
binds to the single-stranded DNA
(ssDNA) in the eukaryotic cells. In
vitro, the RPA shows a much
higher affinity for the ssDNA than
the RNA or the double-stranded
DNA. The RPA is required in the
replication, recombination and in
the repair processes such as the
nucleotide excision repair and the
homologous recombination. It also
plays roles in responding to the
damaged DNA. During the DNA
replication, the RPA prevents the
single-stranded DNA (ssDNA)
from winding back on itself or
from forming the secondary
structures. It also helps protect the
ssDNA from being attacked by the
endonucleases. This keeps the
DNA unwound for the polymerase
to replicate it. The RPA also binds
to the ssDNA during the initial
phase of the homologous
recombination, an important
process in the DNA repair and
prophase I of the meiosis.
© 2022 by JPS Scientific Publications, India
403
• RPOS - The gene rpoS (RNA
polymerase, sigma S, also called as
the katF) encodes the sigma factor
sigma-38 (σ38, or the RpoS), a 37.8
kD protein in the Escherichia coli.
The Sigma factors are the proteins
that regulate the transcription in
the bacteria. The Sigma factors can
be activated in response to the
different environmental conditions.
The rpoS is transcribed in late
exponential phase, and the RpoS is
the primary regulator of the
stationary phase genes. The RpoS
is a central regulator of the general
stress response and operates in
both a retroactive and a proactive
manner: it not only allows the cell
to survive the environmental
challenges, but it also prepares the
cell for the subsequent stresses. The
transcriptional regulator CsgD is
central to the biofilm formation,
controlling the expression of the
curli structural and the export
proteins, and the diguanylate
cyclase, adrA, which indirectly
activates the cellulose production.
The rpoS gene is most likely
originated in the
gammaproteobacteria.
• RPSA - The RPSA gene provides
the instructions for making a
protein called as the ribosomal
protein SA, which is one of the
approximately 80 different
ribosomal proteins. These proteins
come together to form the
structures called as the ribosomes.
The Ribosomes process the cell's
genetic instructions to create the
Glossary of Genetics
proteins. The specific roles of each
of the ribosomal proteins within
the ribosome are not entirely still
yet understood. Some of the
ribosomal proteins are involved in
the assembly or the stability of the
ribosomes. Others help carry out
the ribosome's main function of the
building new proteins. The
research suggests that ribosomal
protein SA helps the ribosome
control the production of the
certain proteins, many of which are
likely important for the
development before birth.
• RIBOSOMAL PROTEIN SA -
The RPSA gene provides the
instructions for making a protein
called as the ribosomal protein SA,
which is one of the approximately
80 different ribosomal proteins.
These proteins come together to
form the structures called as the
ribosomes. The Ribosomes process
the cell's genetic instructions to
create the proteins. The specific
roles of each of the ribosomal
proteins within the ribosome are
not entirely still yet understood.
Some of the ribosomal proteins are
involved in the assembly or the
stability of the ribosomes. Others
help carry out the ribosome's main
function of the building new
proteins. Research suggests that
ribosomal protein SA helps the
ribosome control the production of
the certain proteins, many of which
are likely important for the
development before birth.
© 2022 by JPS Scientific Publications, India
404
• RUT SITE - The Rho utilisation
site, also known by the acronym
rut, is a sequence of the RNA in
bacteria upstream of the terminator
region which serves as a binding
site for the protein known as the
rho factor. This sequence is
necessary in the rho-dependent
termination of the DNA
transcription in the bacteria. The
common feature of the rut site is an
abundance of the cytosine and the
paucity of the guanine residues,
although the these sequences vary
widely in the different genes with
the little homology. A few
algorithms have been developed to
predict the such sites.
• RYBB RNA - The RybB is a small
non-coding RNA was identified in
a large scale screen of the
Escherichia coli. The function of
this short RNA has been studied
using a transcriptomic approach
and the kinetic analyses of the
target mRNA decay in vivo. The
RybB was identified as a factor that
selectively accelerates the decay of
the multiple major omp mRNAs
upon induction of the envelope
stress response. This RNA has
been shown to bind to the Hfq
protein.
• RBBP 5 - The Retinoblastoma-
binding protein 5 is a protein that
in the humans is encoded by the
RBBP5 gene. The protein encoded
by this gene is a ubiquitously
expressed nuclear protein and
belongs to a highly conserved
subfamily of the WD-repeat
Glossary of Genetics 405

proteins. It is found among the strand by the DNA polymerase

several proteins that bind directly function of the RT enzyme.
to the retinoblastoma protein,
which regulates the cell
proliferation. The encoded protein
interacts preferentially with the
underphosphorylated
retinoblastoma protein via the
E1A-binding pocket B.
• RETROVIRLA
RIB9ONUCLEASE H - The
retroviral ribonuclease H
(retroviral RNase H) is a type of
the catalytic domain of the
retroviral reverse transcriptase (RT)
enzyme. The RT enzyme is used to
generate the complementary DNA
(cDNA) from the retroviral RNA
genome. This process is called as
the reverse transcription. To
complete this complex process, the
retroviral RT enzymes need to
adopt a multifunctional type of the
nature. They therefore possess 3 of
the following biochemical
activities: RNA-dependent DNA
polymerase, ribonuclease H, and
the DNA-dependent DNA
polymerase activities. Like all the
RNase H enzymes, the retroviral
RNase H domain cleaves the
DNA/RNA duplexes and will not
degrade the DNA or the
unhybridized RNA. During the
reverse transcription of the viral
genomic RNA into the cDNA, an
RNA/DNA hybrid is created. The
RNA strand is then hydrolyzed by
the RNase H domain to enable the
synthesis of the second DNA

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
S secretory pathway. These proteins
• SAGA - The SAGA transcription
co-activator plays an multiple roles
in regulating the transcription due
to the presence of the functionally
independent modules of the
subunits within the complex. It
also plays an role for the ubiquitin
protease activity of the SAGA in
regulating the tissue-specific gene
expression in the Drosophila. The
genes sensitive to the loss of the
ubiquitin protease activity of the
SAGA share the functional
characteristics that require the de-
ubiquitination of the ubH2B for the
full activation. The de-
ubiquitination of the ubH2B by the
SAGA destabilizes the promoter
nucleosomes, thus enhancing the
recruitment of the Pol II to weak
promoters. In addition, the SAGA-
mediated de-ubiquitination of the
ubH2B may facilitate the binding
of the factors that are important for
the transition of paused Pol II into
the transcription elongation.
• SIGNAL PEPTIDE - A signal
peptide (sometimes referred to as
the signal sequence, targeting
signal, localization signal,
localization sequence, transit
peptide, leader sequence or the
leader peptide) is a short peptide
(usually 16-30 amino acids long)
present at the N-terminus (or
occasionally nonclassically at the
C-terminus or internally) of the
most newly synthesized proteins
© 2022 by JPS Scientific Publications, India
406
that are destined toward the
include those that reside either
inside the certain organelles (the
endoplasmic reticulum, Golgi or
the endosomes), secreted from the
cell, or inserted into most of the
cellular membranes. Although
most of the type I membrane-
bound proteins have signal
peptides, the majority of the type II
and multi-spanning membrane-
bound proteins are targeted to the
secretory pathway by their first
transmembrane domain, which
biochemically resembles a signal
sequence except that it is not
cleaved. They are a kind of the
target peptide.
• SAM - The S-Adenosyl
methionine (SAM), also known
under the commercial names of the
SAMe, SAM-e, or the AdoMet, is
a common cosubstrate involved in
the methyl group transfers,
transsulfuration, and the
aminopropylation. Although the
these anabolic reactions occur
throughout the body, most of the
SAM is produced and consumed in
the liver. More than 40 methyl
transfers from the SAM are known,
to various substrates such as the
nucleic acids, proteins, lipids and
the secondary metabolites. It is
made from the adenosine
triphosphate (ATP) and
methionine by the methionine
adenosyltransferase. In the
bacteria, the SAM is bound by the
SAM riboswitch, which regulates
Glossary of Genetics
the genes involved in the
methionine or the cysteine
biosynthesis. In the eukaryotic
cells, the SAM serves as a regulator
of a variety of processes including
the DNA, tRNA, and the rRNA
methylation, immune response,
amino acid metabolism,
transsulfuration and many more.
In the plants, the SAM is crucial to
the biosynthesis of the ethylene, an
important plant hormone and the
signaling molecule.
• SANT DOMAIN - In the field of
the molecular biology, a SANT
domain is a protein domain that
allows the many of the chromatin
remodeling proteins to interact
with the histones. The name
SANT is an acronym standing for
the "Swi3, Ada2, N-Cor, and the
TFIIIB". It is part of the extended
SANT/Myb family.
• SAU3AI - The Sau3AI, an
unusually large type II restriction
enzyme with the sequence
homology to the mismatch repair
protein MutH, is a monomeric
enzyme as shown by the gel
filtration and the
ultracentrifugation. The Structural
similarities in the N- and C-
terminal halves of the protein
suggest that the Sau3AI is a
pseudo-dimer, i.e. a polypeptide
with the two similar domains.
Since the Sau3AI displays a
nonlinear dependence of the
cleavage activity on the enzyme
concentration and a strong
preference for the substrates with
© 2022 by JPS Scientific Publications, India
407
the two recognition sites over those
with only one, it is likely that the
functionally active form of the
Sau3AI is a dimer of a pseudo-
dimer. Indeed, the electron
microscopy studies demonstrate
that the two distant recognition
sites are brought together through
the DNA looping induced by the
simultaneous binding of the two
Sau3AI molecules to the DNA.
The dimeric form of the Sau3AI
supplies the two DNA-binding
sites, one that is associated with
the catalytic center and one that
serves as an effector site.
• SEX LETHAL GENE - The Sex-
lethal (Sxl) is a gene found in the
Dipteran insects, named for its
mutation phenotype in the
Drosophila melanogaster (P19339).
It is most closely related to the
ELAV/HUD subfamily of the
splicing factors. This protein
participates in the alternative
splicing of the transformer gene,
deciding the sex of the fly. It
induces the female-specific
alternative splicing of the
transformer (tra) pre-mRNA by
binding to the tra uridine-rich
polypyrimidine tract at the non-
sex-specific 3' splice site during the
sex-determination process. The
SXL binds also to its own pre-
mRNA and promotes the female-
specific alternative splicing. The
SXL contains an N-terminal
Gly/Asn-rich domain that may be
responsible for the protein-protein
interaction, and the tandem RNA
Glossary of Genetics
recognition motifs (RRMs) that
show the high preference to bind
the single-stranded, uridine-rich
target RNA transcripts.
• SF 2 SPLICING - The
Serine/arginine-rich splicing factor
1 (SRSF1) also known as the
alternative splicing factor 1
(ASF1), pre-mRNA-splicing factor
SF2 (SF2) or the ASF1/SF2 is a
protein that in the humans is
encoded by the SRSF1 gene. The
ASF/SF2 is an essential sequence
specific splicing factor involved in
the pre-mRNA splicing. The
SRSF1 is the gene that codes for
the ASF/SF2 and is found on the
chromosome 17. The resulting
splicing factor is a protein of
approximately around 33 kDa. The
ASF/SF2 is necessary for all
splicing reactions to occur, and
influences the splice site selection
in a concentration-dependent
manner, resulting in the alternative
splicing. In addition to being
involved in the splicing process, the
ASF/SF2 also mediates the post-
splicing activities, such as the
mRNA nuclear export and the
translation.
• SHH - The Sonic hedgehog
protein (SHH) is encoded for by
the SHH gene. The protein is
named after the character Sonic the
Hedgehog. The SHH controls the
organogenesis and the organization
of the central nervous system,
limbs, digits and many of the other
parts of the body. Of the hh
homologues, the SHH has been
© 2022 by JPS Scientific Publications, India
408
found to have the most critical
roles in the development, acting as
a morphogen involved in the
patterning of many of the systems
including the anterior pituitary,
pallium of the brain, spinal cord,
lungs, teeth and the thalamus by
the zona limitans In the
vertebrates, the development of the
limbs and the digits depends on the
secretion of the sonic hedgehog by
the zone of the polarizing activity,
located on the posterior side of the
embryonic limb bud. The
Mutations in the human sonic
hedgehog gene SHH cause the
holoprosencephaly type 3 HPE3,
as a result of the loss of the ventral
midline.
• SHINE DALGARNO
SEQUENCE - The Shine–
Dalgarno (SD) sequence is a
ribosomal binding site in the
bacterial and in the archaeal
messenger RNA, generally located
around the 8 bases upstream of the
start codon AUG. The RNA
sequence helps to recruit the
ribosome to the messenger RNA
(mRNA) to initiate the protein
synthesis by aligning the ribosome
with the start codon. Once it
recruited,the tRNA may add
amino acids in the sequence as
dictated by the codons, moving
downstream from the translational
start site. The Shine–Dalgarno
sequence is common in the
bacteria, but rarer in the archaea. It
is also present in some of the
chloroplast and in the
Glossary of Genetics
mitochondrial transcripts. The six-
base consensus sequence is the
AGGAGG; in Escherichia coli, for
example, the sequence is the
AGGAGGU, while the shorter
GAGG dominates in the E. coli
virus T4 early genes.
• SHRNA - A short hairpin RNA or
the small hairpin RNA
(shRNA/Hairpin Vector) is an
artificial RNA molecule with a
tight hairpin turn that can be used
to silence the target gene
expression via the RNA
interference (RNAi). The
Expression of the shRNA in the
cells is typically accomplished by
the delivery of the plasmids or
through the viral or the bacterial
vectors. The shRNA is an
advantageous mediator of the
RNAi in that it has a relatively low
rate of the degradation and the
turnover. However, it requires the
use of an expression vector, which
has the potential to cause the side
effects in the medicinal
applications. The Marina Biotech
developed CEQ508 which is used
to treat the Familial Adenomatous
Polyposis. The CEQ508 uses a
bacterial vector to deliver the
shRNA against the β-catenin.
• SIR PROTEINS - The Silent
Information Regulator (SIR)
proteins are involved in the
regulating of the gene expression.
The SIR proteins organize the
heterochromatin near the
telomeres, rDNA, and at silent loci
including the hidden mating type
© 2022 by JPS Scientific Publications, India
409
loci in the yeast. The SIR family of
the genes encodes the catalytic and
the non-catalytic proteins that are
involved in the de-acetylation of
the histone tails and the subsequent
condensation of the chromatin
around a SIR protein scaffold. The
Some SIR family members are
conserved from the yeast to the
humans. The SIR proteins are
conserved from the yeast to
humans, and lend their name to a
class of the mammalian histone
deacetylases. The Sirtuins have
been implicated in the myriad
human traits including the
Alzheimers and the diabetes, and
have been proposed to regulate of
the lifespan.
• SIN R - The SinR is a pleiotropic
DNA binding protein that is
essential for the late-growth
processes of the competence and
the motility in the Bacillus subtilis
and is also a repressor of the
others, e.g. the sporulation and the
subtilisin synthesis. In addition to
being an inhibitor of the
sporulation stage II gene
expression, is a repressor of the key
early sporulation gene spo0A. The
sporulation-specific rise in the
spo0A expression at the time zero
is absent in a SinR-overproducing
strain and is much higher than the
normal in strains with a disrupted
sinR gene. This effect is direct,
since the SinR binds specifically to
the spo0A in vitro, in a region
overlapping the -10 region of the
sporulation-specific Ps promoter
Glossary of Genetics
that is recognized by the E-sigma
H polymerase.
• 6S RNA - In the field of the
molecular biology the 6S RNA is a
non-coding RNA that was one of
the first to be identified and
sequenced. In the early 2000s
scientists found out the function of
the 6S RNA to be as a regulator of
the sigma 70-dependent gene
transcription. All the bacterial
RNA polymerases have a subunit
called a sigma factor. The sigma
factors are important because they
control how the DNA promoter
binding and the RNA transcription
start sites. The Sigma 70 was the
first one to be discovered in the
Escherichia coli. The function of
the 6S RNA is to regulate the
transcription for the E. coli cell
survival because it is essential in
the process. The 6S RNA
specifically associates with the
RNA polymerase holoenzyme
containing the sigma70 specificity
factor. This interaction represses
expression from the sigma70-
dependent promoters during the
stationary phase, which will lead to
activate the transcription from the
sigma 70 dependent promoters.
• SL 1 - The Selective factor 1 (also
known as the SL1) is a
transcription factor that binds to
the promoter of the genes and
recruits a preinitiation complex to
which the RNA polymerase I will
bind to and begin the transcription
of the ribosomal RNA (rRNA).
The SLI functions in assembling
© 2022 by JPS Scientific Publications, India
410
the transcription preinitiation
complex. It is also a major
determinant of the species-
specificity in the ribosomal RNA
gene transcription. The Research
suggests that the UBF and the SL1
act synergistically to stimulate the
transcription. Recent investigation
also suggests that the SL1 is a
target for the cancer therapy.
• SN RNP - The snRNPs
(pronounced "snurps"), or the
small nuclear ribonucleoproteins,
are the RNA-protein complexes
that combine with the unmodified
pre-mRNA and the various other
proteins to form a spliceosome, a
large RNA-protein molecular
complex upon which the splicing
of the pre-mRNA occurs. The
action of the snRNPs is essential to
the removal of the introns from the
pre-mRNA, a critical aspect of the
post-transcriptional modification of
the RNA, occurring only in the
nucleus of the eukaryotic cells.
Additionally, the U7 snRNP is not
involved in the splicing at all, as
the U7 snRNP is responsible for
the processing of the 3′ stem-loop
of the histone pre-mRNA. The two
essential components of the
snRNPs are the protein molecules
and the RNA. The RNA found
within the each snRNP particle is
known as the small nuclear RNA,
or the snRNA, and is usually about
150 nucleotides in the length.
• SMALL RNA - The Small RNA
are the polymeric RNA molecules
Glossary of Genetics
that are less than 200 nucleotides
in the length, and are usually non-
coding. The RNA silencing is often
a function of these molecules, with
the most common and the well-
studied example being the RNA
interference (RNAi), in which the
endogenously expressed
microRNA (miRNA) or the
exogenously derived small
interfering RNA (siRNA) induces
the degradation of the
complementary messenger RNA.
The Other classes of the small
RNA have been identified,
including the piwi-interacting
RNA (piRNA) and its subspecies
repeat associated small interfering
RNA (rasiRNA). The Small RNA
"is unable to induce the RNAi
alone, and to accomplish the task it
must form the core of the RNA
protein complex termed as the
RNA-induced silencing complex
(RISC), specifically with the
Argonaute protein". The Small
RNA have been detected or
sequenced using a range of the
techniques, including directly by
the MicroRNA sequencing on the
several sequencing platforms, or
indirectly through the genome
sequencing and analysis. The
Identification of the miRNAs has
been evaluated in detecting the
human disease, such as the breast
cancer.
• SMC PROTEINS - The SMC
complexes represent a large family
of the ATPases that participate in
many aspects of the higher-order
© 2022 by JPS Scientific Publications, India
411
chromosome organization and the
dynamics. The SMC stands for the
Structural Maintenance of the
Chromosomes. The SMC proteins
are conserved from the bacteria to
th3 humans. Most of the bacteria
have a single SMC protein in the
individual species that forms a
homodimer. In a subclass of the
Gram-negative bacteria including
the Escherichia coli, a distantly
related protein known as the MukB
plays an equivalent role. The
Eukaryotes have at least six SMC
proteins in individual organisms,
and they form three distinct
heterodimers with the specialized
functions. A pair of the SMC1 and
SMC3 constitutes the core subunits
of the cohesin complexes involved
in sister chromatid. A pair of the
SMC2 and the SMC4 acts as the
core of the condensin complexes
implicated in the chromosome
condensation. A dimer composed
of the SMC5 and the SMC6
functions as part of a yet-to-be-
named complex implicated in the
DNA repair and the checkpoint
responses.
• SVEDBERG – A Svedberg unit
or the svedberg (symbol S,
sometimes Sv) is a non-SI metric
unit for the sedimentation
coefficients. The Svedberg unit
offers a measure of a particle's size
indirectly based on its
sedimentation rate under the
acceleration (i.e. how fast a particle
of the given size and shape settles
to the bottom of a solution). The
Glossary of Genetics
svedberg is a measure of the time,
defined as exactly 10−13 seconds
(100 fs). For the biological
macromolecules and the cell
organelles like the ribosomes, the
sedimentation rate is typically
measured as the rate of travel in a
centrifuge tube subjected to the
high g-force. The svedberg (S) is
distinct from the SI unit sievert or
the non-SI unit sverdrup, which
also use the symbol Sv.
• SWI/SNF - In the filed of the
molecular biology, the SWI/SNF
(SWItch/Sucrose Non-
Fermentable), is a subfamily of the
ATP-dependent chromatin
remodeling complexes, which is
found in the eukaryotes. In the
other words, it is a group of the
proteins that associate to remodel
the way the DNA is packaged.
This complex is composed of the
several proteins products of the
SWI and the SNF gene, as well as
the other polypeptides. It possesses
a DNA-stimulated ATPase activity
that can destabilize the histone-
DNA interactions in the
reconstituted nucleosomes in an
ATP-dependent manner, though
the exact nature of this structural
change is still unknown. The
SWI/SNF subfamily provides an
crucial nucleosome rearrangement,
which is seen as the ejection
and/or the sliding. The movement
of the nucleosomes provides easier
access to the chromatin, allowing
the genes to be activated or
repressed.
© 2022 by JPS Scientific Publications, India
412
• SYNAPTONEMAL - The
synaptonemal complex (SC) is a
protein structure that forms
between the homologous
chromosomes (two pairs of the
sister chromatids) during the
meiosis and is thought to mediate
the synapsis and the recombination
during the meiosis I in the
eukaryotes. It is currently thought
that the SC functions primarily as a
scaffold to allow the interacting
chromatids to complete their
crossover activities. In the humans,
the three specific components of
the synaptonemal complex have
been characterized: SC protein-1
(SYCP1), SC protein-2 (SYCP2),
and the SC protein-3 (SYCP3).
The SYCP1 gene is on the
chromosome 1p13; the SYCP2
gene is on the chromosome
20q13.33; and the gene for the
SYCP3 is on the chromosome 12q.
The SCs can be seen with the light
microscope using the silver
staining or with the
immunofluorescence techniques
that label the proteins SYCP3 or
the SYCP2.
• SYNCTIUM - A syncytium or the
symplasm is a multinucleate cell
which can result from the multiple
cell fusions of the uninuclear cells
(i.e. cells with a single nucleus), in
contrast to a coenocyte, which can
result from the multiple nuclear
divisions without accompanying
the cytokinesis. The muscle cell
that makes up the animal skeletal
muscle is a classic example of a
Glossary of Genetics
syncytium cell. The term may also
refer to the cells interconnected by
the specialized membranes with
the gap junctions, as seen in the
heart muscle cells and in the
certain smooth muscle cells, which
are synchronized electrically in an
action potential. The field of the
embryogenesis uses the word
syncytium to refer to the
coenocytic blastoderm embryos of
the invertebrates, such as the
Drosophila melanogaster.
• SYNTHETIC BIOLOGY - The
Synthetic biology (SynBio) is a
multidisciplinary area of the
research that seeks to create the
new biological parts, devices, and
the systems, or to redesign the
systems that are already found in
the nature. It is a branch of the
science that encompasses a broad
range of the methodologies from
the various disciplines, such as the
biotechnology, biomaterials,
material science/engineering,
genetic engineering, molecular
biology, molecular engineering,
systems biology, membrane
science, biophysics, chemical and
biological engineering, electrical
and computer engineering, control
engineering and the evolutionary
Due to the more powerful genetic
engineering capabilities and the
decreased DNA synthesis and the
sequencing costs, the field of the
synthetic biology is rapidly
growing.
• SNAI 1 - The Zinc finger protein
SNAI1 (sometimes referred to as
© 2022 by JPS Scientific Publications, India
413
the Snail) is a protein that in the
humans is encoded by the SNAI1
gene. The Snail is a family of the
transcription factors that promote
the repression of the adhesion
molecule E-cadherin to regulate
the epithelial to mesenchymal
transition (EMT) during the
embryonic development. The
nuclear protein encoded by this
gene is structurally similar to the
Drosophila Snail protein, and is
also thought to be critical for the
mesoderm formation in the
developing embryo. At least the
two variants of a similar processed
pseudogene have been found on
the chromosome 2. The SNAI1
zinc-fingers (ZF) binds to the E-
box, an E-cadherin promoter
region, and represses the
expression of the adhesion
molecule, which induces the tightly
bound epithelial cells to break
loose from the each other and
migrate into the developing
embryo to become the
mesenchymal cells.
• SNAI 2 - The Zinc finger protein
SNAI2 is a transcription factor that
in the humans is encoded by the
SNAI2 gene. It promotes the
differentiation and migration of the
certain cells and has the roles in
initiating the gastrulation. This
gene encodes a member of the
Snail superfamily of the C2H2-type
zinc finger transcription factors.
The encoded protein acts as a
transcriptional repressor that binds
to the E-box motifs and is also
Glossary of Genetics
likely to repress the E-cadherin
transcription in the breast
carcinoma. This protein is involved
in the epithelial-mesenchymal
transitions and has antiapoptotic
activity. It regulates the
differentiation and migration of the
neural crest cells along with the
other genes (e.g. FOXD3, SOX9
and SOX10, BMPs) in the
embryonic life. The Mutations in
this gene may be associated with
the sporadic cases of the neural
tube defects. The SNAI2
downregulates the expression of
the E-cadherin in the premigratory
neural crest cells, thus the SNAI2
induces tightly bound epithelial
cells to break into a loose
mesenchymal phenotype, allowing
the gastrulation of the mesoderm
in the developing embryo.
• SOG GENE - The short
gastrulation (sog) gene is expressed
in the broad lateral stripes
comprising the neuroectoderm of
the Drosophila blastoderm
embryo. The sog encodes a
predicted secreted protein that
functions as nonautonomously to
antagonize the activity of the TGF-
beta-like Decapentaplegic (Dpp)
signaling pathway in the dorsal
region of the embryo. Recently, it
has been also shown that the sog
and the dpp are functionally
equivalent to their respective
Xenopus homologs chordin and
the BMP-4. The first direct
evidence that the sog plays a local
role in the lateral region of the
© 2022 by JPS Scientific Publications, India
414
blastoderm embryo to oppose the
Dpp activity in the neuroectoderm.
In the dorsal region, the Dpp
signaling both suppresses
neurogenesis and maintains the
expression of the genes that
promote the dorsal cell fates
(dorsalization).
• SOS RESPONSE - The SOS
response is a global response to the
DNA damage in which the cell
cycle is arrested and the DNA
repair and mutagenesis is induced.
The system involves the RecA
protein (Rad51 in the eukaryotes).
The RecA protein, stimulated by
the single-stranded DNA, is
involved in the inactivation of the
repressor (LexA) of the SOS
response genes thereby inducing
the response. It is an error-prone
repair system that contributes
significantly to the DNA changes
observed in a wide range of the
species. The Research has shown
that the SOS response system can
lead to the mutations which can
lead to the resistance to the
antibiotics. The increased rate of
the mutation during the SOS
response is caused by the three
low-fidelity DNA polymerases, Pol
II, Pol IV and Pol V. The
Researchers are now targeting
these proteins with the aim of
creating the drugs that prevent the
SOS repair.
• SOLENOID MODEL OF DNA -
The solenoid structure of the
chromatin is a model for the
structure of the 30 nm fibre. It is a
Glossary of Genetics
secondary chromatin structure
which helps to package the
eukaryotic DNA into the nucleus.
The solenoid structure's most
obvious function is to help to
package the DNA so that it is small
enough to fit into the nucleus. This
is a big task as the nucleus of a
mammalian cell has a diameter of
approximately around 6 µm, whilst
the DNA in one human cell would
stretch to just over around 2 metres
long if it were unwound. The
"beads on a string" structure can
compact the DNA to 7 times
smaller. The solenoid structure can
increase this to be around 40 times
smaller. When the DNA is
compacted into the solenoid
structure can still be
transcriptionally active in the
certain areas. It is the secondary
chromatin structure that is
important for this transcriptional
repression as in vivo active genes
are assembled in the large tertiary
chromatin structures.
• SOX 2 GENE - The SRY (sex
determining region Y)-box 2, also
known as the SOX2, is a
transcription factor that is essential
for maintaining the self-renewal, or
the pluripotency of the
undifferentiated embryonic stem
cells. The Sox2 has a critical role in
the maintenance of the embryonic
and in the neural stem cells. The
LIF (Leukemia inhibitory factor)
signaling, which maintains the
pluripotency in the mouse
embryonic stem cells, activates the
© 2022 by JPS Scientific Publications, India
415
Sox2 downstream of the JAK-
STAT signaling pathway and
subsequent activation of the Klf4.
The Oct-4, Sox2 and the Nanog
positively regulate the transcription
of all the pluripotency circuitry
proteins in the LIF pathway. The
Sox2 holds an great promise in the
research involving the induced
pluripotency, an emerging and
very promising field of the
regenerative medicine.
• SPACER DNA - The Spacer
DNA is a region of the non-coding
DNA between the genes. The
terms intergenic spacer (IGS) or
the non-transcribed spacer (NTS)
are used particularly for the spacer
DNA between the many tandemly
repeated copies of the ribosomal
RNA genes. In the bacteria, the
spacer DNA sequences are only a
few nucleotides long. In the
eukaryotes, they can be extensive
and include the repetitive DNA,
comprising the majority of the
DNA of the genome. In the
ribosomal DNA, there are spacers
within and between the gene
clusters, called as the internal
transcribed spacer (ITS) and the
external transcribed spacers (ETS),
respectively. In the animals, the
mitochondrial DNA genes
generally have very short spacers.
In the fungi, the mitochondrial
DNA spacers are common and
variable in the length, and they
may also be mobile.
• SMA - The Spinal muscular
atrophy (SMA) is a rare
Glossary of Genetics
neuromuscular disorder that results
in the loss of the motor neurons
and the progressive muscle
wasting. It is usually diagnosed in
the infancy or the early childhood
and if left untreated it is the most
common genetic cause of the
infant death. It may also appear
later in the life and then have a
milder course of the disease. The
common feature is the progressive
weakness of the voluntary muscles,
with arm, leg and the respiratory
muscles being affected first. The
Associated problems may include
the poor head control, difficulties
swallowing, scoliosis, and the joint
contractures. The Spinal muscular
atrophy is due to an abnormality
(mutation) in the SMN1 gene
which encodes the SMN, a protein
necessary for the survival of the
motor neurons. The Loss of these
neurons in the spinal cord prevents
the signalling between the brain
and the skeletal muscles. Another
gene, the SMN2, is considered a
disease modifying gene, since
usually the more the SMN2 copies,
the milder is the disease course.
The diagnosis of the SMA is based
on the symptoms and confirmed by
the genetic testing.
• SPO 11 - The Spo11 is a protein
that in the humans is encoded by
the SPO11 gene. The Spo11, in a
complex with the mTopVIB,
creates the double strand breaks to
initiate the meiotic recombination.
Its active site contains a tyrosine
which ligates and dissociates with
© 2022 by JPS Scientific Publications, India
416
the DNA to promote the break
formation. One Spo11 protein is
involved per strand of the DNA,
thus the two Spo11 proteins are
involved in each of the double
stranded break event. The SPO11
is considered to play a
predominant role in initiating the
meiotic recombination. However,
the recombination may also occur
by the alternative SPO11-
independent mechanisms that can
be studied experimentally using the
spo11 mutants.
• SUPTH16 - The FACT complex
subunit SPT16 is a protein that in
the humans is encoded by the
SUPT16H gene. The Transcription
of the protein-coding genes can be
reconstituted on the naked DNA
with only the general transcription
factors and the RNA polymerase
II. However, this minimal system
cannot transcribe the DNA
packaged into the chromatin,
indicating that the accessory
factors may facilitate the access to
the DNA. One such factor, the
FACT (facilitates chromatin
transcription), interacts specifically
with the histones H2A/H2B to
effect nucleosome disassembly and
the transcription elongation. The
FACT is composed of an 80 kDa
subunit and a 140 kDa subunit, the
latter of the which is the protein
encoded by this gene.
• SR PROTEIN - The SR proteins
are a conserved family of the
proteins involved in the RNA
splicing. The SR proteins are
Glossary of Genetics
named because they contain a
protein domain with the long
repeats of the serine and the
arginine amino acid residues,
whose standard abbreviations are
"S" and "R" respectively. The SR
proteins are around 200-600 amino
acids in the length and composed
of the two domains, the RNA
recognition motif (RRM) region
and the RS domain. The SR
proteins are more commonly found
in the nucleus than the cytoplasm,
but several SR proteins are known
to shuttle between the nucleus and
the cytoplasm. The SR proteins are
important in the constitutive and
the alternative pre-mRNA splicing,
mRNA export, genome
stabilization, nonsense-mediated
decay, and the translation. The SR
proteins alternatively splice the pre-
mRNA by preferentially selecting
the different splice sites on the pre-
mRNA strands to create the
multiple mRNA transcripts from
the one pre-mRNA transcript.
• SSRP 1 - The FACT complex
subunit SSRP1 also known as the
structure specific recognition
protein 1 is a protein that in the
humans is encoded by the SSRP1
gene. The protein which is encoded
by this gene is a subunit of a
heterodimer that, along with the
SUPT16H, forms the chromatin
transcriptional elongation factor
FACT. The FACT interacts
specifically with the histones
H2A/H2B to effect the
nucleosome disassembly and the
© 2022 by JPS Scientific Publications, India
417
transcription elongation. The
FACT and the cisplatin-damaged
DNA may be crucial to the
anticancer mechanism of the
cisplatin. This encoded protein
contains a high mobility group box
which most likely constitutes the
structure recognition element for
the cisplatin-modified DNA. This
protein also functions as the co-
activator of the transcriptional
activator known as the p63.
• STAT PROTEIN - The Members
of the signal transducer and
activator of the transcription
(STAT) protein family are
intracellular transcription factors
that mediate the many aspects of
the cellular immunity,
proliferation, apoptosis and the
differentiation. They are primarily
activated by the membrane
receptor-associated Janus kinases
(JAK). The Dysregulation of this
pathway is frequently observed in
the primary tumors and leads to
increased the angiogenesis which
enhances the survival of the tumors
and the immunosuppression. The
Gene knockout studies have
provided the evidence that the
STAT proteins are involved in the
development and the function of
the immune system and play a role
in maintaining the immune
tolerance and the tumor
surveillance. The STAT protein
can be dephosphorylated by the
nuclear phosphatases, which leads
to the inactivation of the STAT
and the subsequent transport out of
Glossary of Genetics
the nucleus by an exportin-
RanGTP complex.
• SDSA - The Synthesis-dependent
strand annealing (SDSA) is a
major mechanism of the
homology-directed repair of the
DNA double-strand breaks (DSBs).
Although many of the features of
the SDSA were first suggested in
1976, the double-Holliday junction
model proposed in the year 1983,
was favored by many of the
researchers. In 1994, studies of the
double-strand gap repair in the
Drosophila were found to be
incompatible with the double-
Holliday junction model, leading
researchers to propose a model
they called as the synthesis-
dependent strand annealing. The
Subsequent studies of the meiotic
recombination in the S. cerevisiae
found that the non-crossover
products appear earlier than the
double-Holliday junctions or the
crossover products, challenging the
previous notion that both the
crossover and the non-crossover
products are produced by the
double-Holliday junctions and
leading the authors to propose that
the non-crossover products are
generated through the SDSA.
• SDS PAGE - The SDS-PAGE
(sodium dodecyl sulfate–
polyacrylamide gel electrophoresis)
is a discontinuous electrophoretic
system developed by the Ulrich K.
Laemmli which is commonly used
as a method to separate the
proteins with the molecular masses
© 2022 by JPS Scientific Publications, India
418
between the 5 and 250 kDa. The
combined use of the sodium
dodecyl sulfate (SDS, also known
as the sodium lauryl sulfate) and
the polyacrylamide gel allows to
eliminate the influence of the
structure and the charge, and the
proteins are separated solely on the
basis of the differences in their
molecular weight. The SDS-PAGE
in combination with a protein stain
is widely used in the biochemistry
for the quick and exact separation
and subsequent analysis of the
proteins. It has comparatively low
instrument and reagent costs and is
an easy-to-use method. Because of
its low scalability, it is mostly used
for analytical purposes and less for
the preparative purposes, especially
when the larger amounts of a
protein are to be isolated.
• SELENOCYESTEINE - The
Selenocysteine is the 21st
proteinogenic amino acid. The
Selenoproteins contain the
selenocysteine residues. The
Selenocysteine is an analogue of
the more common cysteine with
the selenium in place of the sulfur.
The Selenocysteine is present in
the several enzymes (for example
the glutathione peroxidases,
tetraiodothyronine 5′ deiodinases,
thioredoxin reductases, formate
dehydrogenases, glycine
reductases, selenophosphate
synthetase 2, methionine-R-
sulfoxide reductase B1 (SEPX1),
and some of the hydrogenases). It
occurs in all three domains of the
Glossary of Genetics
life. It is specific use as a
radiolabeling, facilitation of phase
determination by the
multiwavelength anomalous
diffraction in the X-ray
crystallography of the proteins by
introducing the Sec alone, or the
Sec together with the
selenomethionine (SeMet), and
incorporation of the stable 77Se
isotope.
• SV40 T-ANTIGEN - The
polyomavirus simian virus 40
(SV40) is also known as an
oncogenic DNA virus which
induces primary brain and bone
cancers, malignant mesothelioma,
and lymphomas in laboratory
animals. The SV40 T-Antigen is
encoded by two large and small
tumour antigens which are the
major regulatory proteins. The
large T antigens is responsible for
both viral and cellular
transcriptional regulation, virion
assembly etc. SV40 transforms cells
that are nonpermissive for viral
productive infections.
• STEREOISOMERS OF
ALANINE - Alanine corresponds
to the L-stereoisomer or L-Ala. It is
the mirror image enantiomer of D-
stereoisomer, or D-Ala which is
rarely found in nature. Alanine has
a choral centre so it is considered
as optically active amino acid.
Alanine is the smallest chira amino
acid found in nature. It is has two
isomeric form and a racemic
mixture.
© 2022 by JPS Scientific Publications, India
419
• SELEX - The Systematic evolution
of the ligands by the exponential
enrichment (SELEX), also referred
to as in vitro selection or in vitro
evolution, is a combinatorial
chemistry technique in the
molecular biology for producing
the oligonucleotides of either the
single-stranded DNA or the RNA
that specifically bind to a target
ligand or the ligands. These single-
stranded DNA or the RNA are
commonly referred to as the
aptamers. Although the SELEX
has emerged as the most
commonly used name for the
procedure, some researchers have
referred to it as the SAAB (selected
and amplified binding site) and the
CASTing (cyclic amplification and
selection of targets). The SELEX
was first introduced in the year
1990. In 2015, a special issue was
published in the Journal of the
Molecular Evolution in the honor
of the quarter century of the
discovery of the SELEX.
• SLEEPING BEAUTY
TRANSPOSON SYSTEM - The
Sleeping Beauty transposon system
is a synthetic DNA transposon
designed to introduce the precisely
defined DNA sequences into the
chromosomes of the vertebrate
animals for the purposes of
introducing the new traits and to
discover the new genes and their
functions. It is a Tc1/mariner-type
system, with the transposase
resurrected from the multiple
inactive fish sequences. The SB
Glossary of Genetics
transposons have been developed
as the non-viral vectors for the
introduction of the genes into the
genomes of the vertebrate animals
and for the gene therapy. The
genetic cargo can be as an
expression cassette a transgene and
with the associated elements that
confer the transcriptional
regulation for the expression at a
desired level in the specific
tissue(s). An alternative use of the
SB transposons is to discover the
functions of the genes, especially
those that cause the cancer, by
delivering the DNA sequences that
maximally disrupt the expression
of the genes close to the insertion
site. This process is referred to as
the insertional mutagenesis or the
transposon mutagenesis. When a
gene is inactivated by the insertion
of a transposon (or other
mechanism), that gene is “knocked
out”. The Knockout mice and the
knockout rats have been made with
the SB system.
• SYNTENY - In the field of
genetics, the term synteny refers to
the two related concepts: In the
classical genetics, the synteny
describes the physical co-
localization of the genetic loci on
the same chromosome within an
individual or the species. In the
current biology, the synteny more
commonly refers to the colinearity,
i.e. conservation of the blocks of
order within the two sets of the
chromosomes that are being
compared with each other. These
© 2022 by JPS Scientific Publications, India
420
blocks are reffered to as the
synthetic blocks. The analysis of
the synteny in the gene order sense
has several applications in the
genomics. Synteny is widely used
in studying complex genomes as a
comparative genomics allows the
presence and posssibly function of
the genes in a simpler model
organism to infer those in a more
complex one.
• SEGMENTATION GENE - A
segmentation gene is a gene which
is involved in the early stages of the
pattern formation that define the
repeated units (metameres) in a
segmented organism, usually the
embryo. They are classified into
the 3 groups i.e the gap genes, pair-
rule genes, and the segment
polarity genes. The expression of
the gap genes result in the
formation of the gaps in the normal
pattern of the structure in the
embryo. The Expression of the
pair-rule genes subdivides the
embryo into a series of the stripes
and sets the boundaries of the
parasegments. The Segment
polarity genes define the anterior
and the posterior polarities within
each of the embryonic
parasegment.
• SEX DETERMINATION - The
sex-determination system is a
biological system that determines
the development of the sexual
characteristics in an organism.
Most of the organisms that create
their offspring using th sexual
reproduction have the two sexes.
Glossary of Genetics
In some of the species there are
hermaphrodites. There are also
some species that are only one sex
due to the parthenogenesis, the act
of a female reproducing without
any fertilization. In many of the
species, the sex determination is
genetic i.e the males and the
females have the different alleles or
even the different genes that
specify their sexual morphology. In
the animals this is often
accompanied by the chromosomal
differences, generally through the
combinations of the XY, ZW, XO,
ZO chromosomes, or the
haplodiploidy. The sexual
differentiation is generally
triggered by a main gene i.e a “sex
locus” with a multitude of the
other genes following in a domino
effect. In the other cases, sex of a
fetus is determined by the
environmental variables (such as
the temperature). The details of
some of the sex-determination
systems are not yet fully
understood. Such analysis of rye
biological systems could also signal
whether the fetus is hermaphrodite,
which includes the total or the
partial of both the male and the
female reproduction organs.
• SELF SPLICING - The Self-
splicing occurs for the rare introns
that form a ribozyme, performing
the functions of the spliceosome by
the RNA alone. There are three
kinds of the self-splicing introns,
Group I, Group II and the Group
III. The Group I and II introns
© 2022 by JPS Scientific Publications, India
421
perform the splicing similar to the
spliceosome without requiring any
of the protein. This similarity
suggests that the Group I and II
introns may be evolutionarily
related to the spliceosome. The
Self-splicing may also be very
ancient, and may have existed in
an RNA world present before the
protein.
• SOUTHERN BLOTTING - The
Southern blot is a method used in
the molecular biology for the
detection of a specific DNA
sequence in the DNA samples. The
southern blotting combines the
transfer of the electrophoresis-
separated DNA fragments to a
filter membrane and the
subsequent fragment detection by
the probe hybridization. The
Southern blotting transfer may be
used for the homology-based
cloning on the basis of the amino
acid sequence of the protein
product of the target gene. The
Oligonucleotides are designed so
that they are complementary to the
target sequence. The
oligonucleotides are chemically
synthesized, radiolabeled, and used
to screen a DNA library, or other
the collections of the cloned DNA
fragments. The Sequences that
hybridize with the hybridization
probe are further analysed, for
example, to obtain the full length
sequence of the targeted gene.
• 48S INITIATION COMPLEX -
The 48S initiation complex (48S
IC) formation is the first stage in
Glossary of Genetics
the eukaryotic translation process.
According to the canonical
mechanism, the 40S ribosomal
subunit binds to the 5'-end of the
messenger RNA (mRNA) and then
scans its 5'-untranslated region (5'-
UTR) to the initiation codon where
it forms the 48S initiation complex.
The Entire process is mediated by
the initiation factors. The eIF5 and
eIF5B together stimulate the 48S
IC formation influencing the
initiation codon selection during
the ribosomal scanning. The
Initiation on the non-optimal start
codons--following the structured 5'-
UTRs, in the bad AUG context,
within the few nucleotides from the
5'-end of the mRNA and the CUG
start codon--is the most affected.
The eIF5-induced hydrolysis of the
eIF2-bound GTP is essential for
the stimulation. The GTP
hydrolysis increases the probability
that scanning the ribosomal
complexes will recognize and
arrest the scanning at a non-
optimal initiation codon. Such 48S
ICs are less stable owing to the
dissociation of the eIF2*GDP from
initiator tRNA, and the eIF5B is
then required to stabilize the
initiator tRNA in the P site of the
40S subunit. Alternative model
that eIF5 and eIF5B cause the 43S
pre-initiation complex
rearrangement favoring the more
efficient initiation codon
recognition during the ribosomal
scanning is equally possible. The
Mutational analysis of the eIF1A
© 2022 by JPS Scientific Publications, India
422
and eIF5B revealed the distinct
functions of the eIF5B in 48S IC
formation and the subunit joining.
• 454 SEQUENCING - The 454
Sequencing used a large-scale
parallel pyrosequencing system
capable of the sequencing roughly
around 400-600 megabases of the
DNA per 10-hour run on the
Genome Sequencer FLX with the
GS FLX Titanium series reagents.
The system relied on the fixing
nebulized and adapter-ligated
DNA fragments to the small DNA-
capture beads in the water-in-oil
emulsion. The DNA fixed to these
beads was then amplified by the
PCR. Each DNA-bound bead was
placed into a~29 μm well on a
PicoTiterPlate, a fiber optic chip. A
mix of the enzymes such as the
DNA polymerase, ATP
sulfurylase, and the luciferase was
also packed into the well. The
PicoTiterPlate was then placed
into the GS FLX System for the
sequencing. 454 released the GS20
sequencing machine in the year
2005, the first next-generation
DNA sequencer on the market. In
the year 2008, 454 Sequencing
launched the GS FLX Titanium
series reagents for the use on the
Genome Sequencer FLX
instrument, with the ability to
sequence around 400-600 million
base pairs per run with around 400-
500 base pair read lengths. In the
late 2009, the 454 Life Sciences
introduced the GS Junior System,
Glossary of Genetics
a bench top version of the Genome
Sequencer FLX System.
• SIZE EXCLUSION
CHROMATOGRAPHY - The
Size-exclusion chromatography
(SEC), also known as the
molecular sieve chromatography,
is a chromatographic method in
which the molecules in solution are
separated by their size, and in
some of the cases molecular
weight. It is usually applied to the
large molecules or the
macromolecular complexes such as
the proteins and the industrial
polymers. Typically, when an
aqueous solution is used to
transport the sample through the
column, the technique is known as
the gel-filtration chromatography,
versus the name gel permeation
chromatography, which is used
when an organic solvent is used as
the mobile phase. The
chromatography column is packed
with the fine, porous beads which
are commonly composed of the
dextran, agarose, or the
polyacrylamide polymers. The
pore sizes of these beads are used
to estimate the dimensions of the
macromolecules. SEC is a widely
used polymer characterization
method because of its ability to
provide the good molar mass
distribution (Mw) results for the
polymers.
• SPECIALIZED
TRANSDUCTION - The
Specialized transduction is the
process by which a restricted set of
© 2022 by JPS Scientific Publications, India
423
the bacterial genes is transferred to
the another bacterium. The genes
that get transferred which is the
donor genes flank where the
prophage is located on the
chromosome. The specialized
transduction occurs when a
prophage excises imprecisely from
the chromosome so that the
bacterial genes lying adjacent to it
are included in the excised DNA.
The excised DNA is packaged into
a new virus particle, which is then
delivers the DNA to a new
bacterium. Here, the donor genes
can be inserted into the recipient
type of chromosome or can remain
in the cytoplasm, depending on the
nature of the bacteriophage. When
the partially encapsulated phage
material infects the another cell
and becomes a prophage, the
partially coded prophage DNA is
called as the "heterogenote". An
example of the specialized
transduction is the λ phage in
Escherichia coli.
• SUPPRESSOR MUTATIONS -
The suppressor mutation is a
second mutation that alleviates or
reverts the phenotypic effects of an
already existing mutation in a
process defined as the synthetic
rescue. The genetic suppression
therefore restores the phenotype
seen prior to the original
background mutation. The
Suppressor mutations are useful for
identifying the new genetic sites
which affect the biological process
of the interest. They also provide
Glossary of Genetics
tge evidence between the
functionally interacting molecules
and the intersecting biological
pathways.
• SHOTGUN SEQUENCING - In
the field of genetics, the shotgun
sequencing is a method used for
the sequencing random DNA
strands. It is named by the analogy
with the rapidly expanding, quasi-
random shot grouping of a
shotgun. The chain-termination
method of the DNA sequencing
("Sanger sequencing") can only be
used for the short DNA strands of
the 100 to 1000 base pairs. Due to
this size limit, the longer sequences
are subdivided into the smaller
fragments that can be sequenced
separately, and these separated
sequences are assembled to give
the overall sequence. In the
shotgun sequencing, the DNA is
broken up randomly into the
numerous small segments, which
are sequenced using the chain
termination method to obtain the
reads. The Multiple overlapping
reads for the target DNA are
obtained by performing the several
rounds of this fragmentation and
sequencing. The Computer
programs then use the overlapping
ends of the different reads to
assemble them into a continuous
sequence. The Shotgun sequencing
was one of the precursor
technologies that was responsible
for the enabling the whole genome
sequencing.
© 2022 by JPS Scientific Publications, India
424
• STRAND INVASION - The
process in which the nucleoprotein
complex which is composed of the
broken single-strand DNA and the
recombinase that searches and
identifies a region of the homology
in the intact duplex DNA. The
broken single-strand DNA
displaces the like strand and forms
the Watson-Crick base pairs with
its complement, forming a duplex
in the which each strand is from
one of the two recombining the
DNA molecules.
• SUPT5H - The transcription
elongation factor SPT5 is a protein
that in the humans is encoded by
the SUPT5H gene. Various Model
organisms have been used in the
study of the SUPT5H function. A
conditional knockout mouse line
called as the
Supt5tm2a(KOMP)Wtsi was
generated at the Wellcome Trust
Sanger Institute. The Male and the
female animals underwent a
standardized phenotypic screen to
determine the effects of the
deletion.
• SPLICING DEFECTS - The
Splicing defects are associated with
an increasing array of the disease
processes and are particularly well
represented in the inherited
endocrinopathies, such as the
congenital adrenal hyperplasia,
multiple endocrine neoplasia, and
the neurofibromatosis type 1. The
Mutations that directly affect the
splicing may be classified into
those that disrupt the splice sites
Glossary of Genetics
and those that change the non-
splice site sequences. In the former
class, the mutations at the 5′ splice
sites may cause the activation of
nearby cryptic 5′ splice sites or,
more commonly, the skipping of
the entire adjacent upstream exon.
In the latter class, the mutations of
the non-splice site sequences may
disrupt the regulatory elements for
the nearby splice sites, as
previously described for the
isolated GH deficiency. An
unusual endocrine splicing
mutation occurs in the GH
receptor gene, in which a deep
intronic point mutation directly
activates the pseudoexon, resulting
in an additional 36 amino acids
being included in the GH receptor,
which in turn leads to the GH
insensitivity (Laron's syndrome).
• SYNOPTEMAL COMPLEX -
The synaptonemal complex (SC) is
a protein structure that forms
between the homologous
chromosomes (the two pairs of the
sister chromatids) during the
meiosis and is thought to mediate
the synapsis and the recombination
during the meiosis I in the
eukaryotes. It is currently thought
that the SC functions primarily as a
scaffold to allow the interacting
chromatids to complete their
crossover activities. The
synaptonemal complex is a
tripartite structure consisting of the
two parallel lateral regions and a
central element. This “tripartite
structure” is seen during the
© 2022 by JPS Scientific Publications, India
425
pachytene stage of the first meiotic
prophase, both in the males and in
the females during the
gametogenesis. Previous to the
pachytene stage, during the
leptonema, the lateral elements
begin to form and they initiate and
complete their pairing during the
zygotene stage. After the
pachynema ends, the SC usually
becomes the disassembled and can
no longer be identified. In the
humans, the three specific
components of the synaptonemal
complex have been characterized
i.e SC protein-1 (SYCP1), SC
protein-2 (SYCP2), and the SC
protein-3 (SYCP3). The SYCP1
gene is on the chromosome 1p13,
the SYCP2 gene is on the
chromosome 20q13, and the gene
for the SYCP3 is on the
chromosome 12q.
• 80S INITIATION COMPLEX -
The translation initiation is a
complex process in which the
initiator tRNA, 40S, and 60S
ribosomal subunits are assembled
by the eukaryotic initiation factors
(eIFs) into an 80S ribosome at the
initiation codon of the mRNA.
The cap-binding complex eIF4F
and the factors eIF4A and eIF4B
are required for binding of 43S
complexes (comprising a 40S
subunit, eIF2/GTP/Met-tRNAi
and the eIF3) to the 5′ end of the
capped mRNA but are not
sufficient to promote the ribosomal
scanning to the initiation codon.
The eIF1A enhances the ability of
Glossary of Genetics
eIF1 to dissociate the aberrantly
assembled complexes from
mRNA, and these factors
synergistically mediate the 48S
complex assembly at the initiation
codon. Joining of the 48S
complexes to the 60S subunits to
form 80S ribosomes requires the
eIF5B, which has an essential
ribosome-dependent GTPase
activity and hydrolysis of the eIF2-
bound GTP induced by eIF5. The
Initiation on a few mRNAs is cap-
independent and occurs instead by
the internal ribosomal entry.
• 6S RNA - In the field of the
molecular biology the 6S RNA is a
non-coding RNA that was one of
the first to be identified and then
sequenced. In the early 2000s the
scientists found out the function of
the 6S RNA to be as a regulator of
the sigma 70-dependent gene
transcription. All the bacterial
RNA polymerases have a subunit
called as a sigma factor. The sigma
factors are important because they
control how the DNA promoter
binding and the RNA transcription
start sites. The sigma 70 was the
first one to be discovered in the
Escherichia coli. The function of
the 6S RNA is to regulate the
transcription for the E. coli cell
survival because it is essential in
the process. The 6S RNA
specifically associates with the
RNA polymerase holoenzyme
containing the sigma70 specificity
factor. This interaction represses
the expression from the sigma70-
© 2022 by JPS Scientific Publications, India
426
dependent promoters during the
stationary phase, Which will lead
to activate the transcription from
the sigma 70 dependent promoters.
Therefore, during the change in the
E. coli from the logarithmic growth
to the stationary phase, the 6S
RNA performs as a regulator of the
transcription. The 6S RNA
homologs have recently been
identified in most ofthe bacterial
genomes. The Polymerase
holoenzyme, which contains the
housekeeping sigma factor and it
can be expressed during the
different stages of the growth. In
many Pseudomonadota, the 6S
RNA may be processed from a
transcript encoding homologs of
the E. coli YgfA protein, which is a
putative methenyltetrahydrofolate
synthetase. The Diverged 6S
RNAs have been identified in the
additional bacterial lineages. The
purD RNA motif has been
experimentally shown to overlap
with the 6S RNA. One way to
examine if the activity of the 6S
RNA by doing a knockout of the6S
RNA.
• 23.5s RNA - The 23S rRNA is a
about 2904 nucleotide long (in the
E. coli) component of the large
subunit which is 50S of the
bacterial/archean ribosome and
makes up the center known as the
peptidyl transferase center (PTC).
The 23S rRNA is divided into the
six secondary structural domains
titled I-VI, with the corresponding
5S rRNA being considered as the
Glossary of Genetics
domain VII. The ribosomal
peptidyl transferase activity resides
in the domain V of this rRNA,
which is also the most common
binding site for the antibiotics that
inhibit the translation, making it a
target for the ribosomal
engineering. A well-known
member of this antibiotic class,
chloramphenicol, acts by inhibiting
the peptide bond formation, with
recent 3D-structural studies
showing that two different binding
sites depending on the species of
the ribosome. Numerous
mutations in the domains of the
23S rRNA with the Peptidyl
transferase activity have resulted in
the antibiotic resistance. The 23S
rRNA genes typically have higher
sequence variations, including the
insertions and/or deletions,
compared to the other rRNAs.
• S RNA - The bacterial small RNAs
(sRNA) are the small RNAs
produced by the bacteria; they are
about 50- to 500-nucleotide which
is non-coding RNA molecules,
highly structured and containing
the several stem-loops. The
Numerous sRNAs have been
identified using both the
computational analysis and the
laboratory-based techniques such
as the Northern blotting,
microarrays and the RNA-Seq in a
number of the bacterial species
including the Escherichia coli, the
model pathogen Salmonella, the
nitrogen-fixing
alphaproteobacterium
© 2022 by JPS Scientific Publications, India
427
Sinorhizobium meliloti, the marine
cyanobacteria, Francisella
tularensis (the causative agent of
the tularaemia), Streptococcus
pyogenes, the pathogen
Staphylococcus aureus, and the
plant pathogen which is
Xanthomonas oryzae pathovar
oryzae. The Bacterial sRNAs affect
how the genes are expressed within
the bacterial cells via the
interaction with the mRNA or the
protein, and thus can affect a
variety of the bacterial functions
like the metabolism, virulence,
environmental stress response, and
the structure. The Bacterial sRNAs
have a wide variety of the
regulatory mechanisms. Generally,
the sRNAs can bind to the protein
targets and modify the function of
the bound protein. Alternately, the
sRNAs may interact with the
mRNA targets and regulate the
gene expression by binding to the
complementary mRNA and
blocking the translation, or by
unmasking or blocking the
ribosome-binding site. sRNAs that
interact with mRNA can also be
categorized as cis- or trans-acting.
Cis-acting sRNAs interact with
genes encoded on the same genetic
locus as the sRNA. Some cis-acting
sRNAs act as riboswitches, which
have receptors for specific
environmental or metabolic signals
and activate or repress genes based
on these signals. Conversely, trans-
encoded sRNAs interact with
genes on separate loci.
Glossary of Genetics
• SUPERHELICAL DENSITY - It
is a quantitative measure of the
degree of the supercoiling of a
DNA molecule. The value, or ,
equals (L-Lo)/Lo, where the Lo is
the linking number of the relaxed
double-stranded DNA molecule
and L is the linking number for the
supercoiled DNA. A negative
value signifies a left-handed
supercoil.
• SPORULATION IN BACTERIA
- The Endospore formation i.e the
sporulation is the prime example of
a complex bacterial developmental
process. The Sporulating bacteria
undergo an intricate sequence of
the cell differentiation events
which leads to the formation of a
highly resistant dormant spore that
can germinate when the conditions
can improve. The Initiation and
the progression of the sporulation
is controlled by a complex network
of the protein-protein and the
protein-DNA interactions,
consisting of the regulatory
modules, signaling pathways, feed-
forward network motifs, and the
post-translational regulation. The
sporulation process has been
characterized in the sufficient
detail in the model organism
Bacillus subtilis to enable the
fundamental evolutionary analyses
from a functional perspective.
Similar to developmental processes
in the higher organisms, the
bacterial sporulation is governed
by a complex cascade of the
regulatory interactions that
© 2022 by JPS Scientific Publications, India
428
contains a strongly conserved
regulatory kernel. The
Transcriptional regulation in the
sporulation network is dominated
by the sigma factors – the subunit
of the bacterial RNA polymerase
holoenzyme which is responsible
for recognizing the promoter
regions on the DNA. The DNA
binding specificities of the different
sigma factors have been
determined experimentally and the
corresponding DNA binding sites
have been collected in the DBTBS,
the database of the transcriptional
regulation in the B. Subtilis.
• SANGER SEQUENCING - The
Sanger sequencing is a method of
the DNA sequencing that involves
the electrophoresis and is based on
the random incorporation of the
chain-terminating
dideoxynucleotides by the DNA
polymerase during in vitro DNA
replication. After first being
developed by the Frederick Sanger
and his colleagues in the year 1977,
it became the most widely used
sequencing method for
approximately 40 years. It was first
commercialized by the Applied
Biosystems in the year 1986. More
recently, the higher volume Sanger
sequencing has been replaced by
the next generation sequencing
methods, especially for the large-
scale, automated genome analyses.
However, the Sanger method
remains in wide use for the
smaller-scale projects and for the
validation of the deep sequencing
Glossary of Genetics
results. It still has the advantage
over the short-read sequencing
technologies in that it can produce
the DNA sequence reads of around
500 nucleotides and maintains a
very low error rate with the
accuracies around 99.99%. The
Sanger sequencing is still actively
being used in the efforts for the
public health initiatives such as the
sequencing the spike protein from
the SARS-CoV-2[2] as well as for
the surveillance of norovirus
outbreaks through the Center for
the Disease Control and the
Prevention's (CDC) CaliciNet
surveillance network.
• SELF REPLICATING
RIBOZYMES - The self-
replicating molecule directs the
covalent assembly of the
component molecules to form a
product that is of the identical
composition to the parent. When
the newly formed product also is
able to direct the assembly of the
product molecules, the self-
replicating system can be termed as
the autocatalytic. A self-replicating
system was developed which was
based on a ribozyme that catalyzes
the assembly of the additional
copies of itself through an RNA-
catalyzed RNA ligation reaction.
The R3C ligase ribozyme was
redesigned so that it would ligate
the two substrates to generate an
exact copy of itself, which then
would behave in a very similar
manner. This self-replicating
system depends on the catalytic
© 2022 by JPS Scientific Publications, India
429
nature of the RNA for the
generation of the copies. A linear
dependence was observed between
the initial rate of the formation of
the new copies and the starting
concentration of the ribozyme,
consistent with exponential
growth.
• SITE SPECIFIC
RECOMBINATION - The Site-
specific recombination, which is
also known as the conservative
site-specific recombination, is a
type of the genetic recombination
in which the DNA strand
exchange takes place between the
segments possessing at least a
certain degree of the sequence
homology. The Enzymes known
as the site-specific recombinases
(SSRs) perform the rearrangements
of the DNA segments by
recognizing and binding to the
short, specific DNA sequences
(sites), at which they cleave the
DNA backbone, exchange the two
DNA helices involved, and then
rejoin the DNA strands. In some
of the cases the presence of a
recombinase enzyme and the
recombination sites is sufficient for
the reaction to proceed, in other
systems a number of the accessory
proteins and/or accessory sites are
also required. Many of the
different genome modification
strategies, among these
recombinase-mediated cassette
exchange (RMCE), an advanced
approach for the targeted
introduction of transcription units
Glossary of Genetics
into the predetermined genomic
loci, rely on the SSRs.
• SS DNA BINDING PROTEIN -
The Single-strand DNA-binding
protein (SSB) is a protein found in
the Escherichia coli (E. Coli)
bacteria, that binds to the single-
stranded regions of the
deoxyribonucleic acid (DNA). The
Single-stranded DNA is produced
during all the aspects of rye DNA
metabolism i.e the replication,
recombination, and the repair. As
well as the stabilizing this single-
stranded DNA, SSB proteins bind
to the and modulate the function of
the numerous proteins involved in
all of the these processes. The
Active E. Coli SSB is composed of
the four identical 19 kDa subunits.
Binding of the single-stranded
DNA to the tetramer can occur in
the different “modes”, with the
SSB occupying different numbers
of the DNA bases depending on a
number of the factors, including
the salt concentration. For
example, the (SSB)65 binding
mode, in which approximately 65
nucleotides of the DNA wrap
around the SSB tetramer and
contact all four of its subunits, is
favoured at the high salt
concentrations in vitro. At the
lower salt concentrations, the
(SSB)35 binding mode, in which
about the 35 nucleotides bind to
the only two of the SSB subunits,
tends to form.
• SEQUENCE COVERAGE - The
Coverage (or the depth) in the
© 2022 by JPS Scientific Publications, India
430
DNA sequencing is the number of
the unique reads that include a
given nucleotide in the
reconstructed sequence. The Deep
sequencing refers to the general
concept of aiming for the high
number of the unique reads of the
each region of a sequence. Even
though the sequencing accuracy for
each of the individual nucleotide is
very high, the very large number of
the nucleotides in the genome
means that if an individual genome
is only sequenced once, there will
be a significant number of the
sequencing errors. Furthermore,
many of the positions in a genome
contain very rare single-nucleotide
polymorphisms (SNPs). Hence to
distinguish between the sequencing
errors and the true SNPs, it is
necessary to increase the
sequencing accuracy even further
by sequencing the individual
genomes a large number of the
times.
• SERINE RECOMBINASE - The
Serine recombinases are often
tightly controlled by the elaborate,
topologically-defined,
nucleoprotein complexes. The Hin
is a member of the DNA invertase
subclass of the serine recombinases
that are regulated by a remote
recombinational enhancer element
containing the two binding sites for
the protein Fis. The Two Hin
dimers bound to the specific
recombination sites associate with
the Fis-bound enhancer by the
DNA looping where they are
Glossary of Genetics
remodeled into a synaptic tetramer
competent for the DNA chemistry
and exchange. The serine
recombinase is the flexible beta-
hairpin arms of the Fis dimers
contact the DNA binding domain
of one subunit of each of the Hin
dimer. These contacts sandwich
the Hin dimers to promote the
remodeling into the tetramer. A
basic region on the Hin catalytic
domain then contacts the enhancer
DNA to complete the assembly of
the active Hin tetramer. The
enhancer generates the
recombination complex that
specifies the DNA inversion and
regulates the DNA exchange by
the mechanism known as the
subunit rotation mechanism.
• SYNERGISM - Synergism is a
process which occurs when the
contribution of two mutations to
the phenotype of a double mutant
exceeds the expectations from the
additive effects of the individual
mutations.
• STEREOISOMERS - unexplored design aspects of these
Stereochemistry is a form of
isomerism in which molecules
have the same molecular formula
and sequence of bonded atoms but
they differ in the 3-dimensional
orientations of their atoms in
space. The 3 types of
stereochemistry include meso
compounds, cis–trans isomers, E-Z
isomers, and non-enantiomeric
optical isomers. Another type of
Stereoisomers is called as
Diastereomers seldom which the
© 2022 by JPS Scientific Publications, India
431
have same physical properties.
Enantiomers an another type of
stereoisomers that are non-
superimposable mirror images.
Stereoisomers also occur as a result
of the different relative orientations
of distinct groups of molecules that
are connected to a central core. R-
Thalidomide and S-Thalidomide
are an example of stereoisomers.
• SYNTHETIC CIRCUITS AND
REGULATORY NOISE - The
Dynamic control of the enzyme
expression can be an effective
strategy to engineer the robust
metabolic pathways. It also allows
a synthetic pathway to self-regulate
in the response to changes in the
bioreactor conditions or the
metabolic state of the host. The
implementation of this regulatory
strategy requires the gene circuits
that couple the metabolic signals
with the genetic machinery, which
is also known to be noisy and one
of the main sources of the cell-to-
cell variability. One of the most
circuits is the propagation of
biochemical noise between the
enzyme expression and the
pathway activity. On the basis of
stochastic simulations and
analysis, it shows that depending
on the repression strength and
promoter strength, the
transcriptional repression of the
enzyme expression can amplify or
attenuate the noise in the number
of product molecules. The analytic
condition on the parameters that
Glossary of Genetics
lead to the attenuation of the
metabolic noise, suggesting that a
higher promoter sensitivity
enlarges the parameter design
space. In the theoretical case of a
switch-like promoter, it reveals that
the ability of the circuit to
attenuate the noise is subject to a
trade-off between the repression
strength and the promoter strength.
To the date, the pathway design
uses a combination of the
computer-aided optimization and
the trial-and-error experimentation.
This is the typically a lengthy
process aimed at ruling out the
designs in which the chosen
enzyme expression levels lead to
the lethal metabolic imbalances or
impractically low the yields.
• SLIDING DNA CLAMP - A
DNA clamp which is also known
as a sliding clamp, it is a type of
protein complex that serves as a
processivity-promoting factor in
DNA replication. As the critical
component of the DNA
polymerase III holoenzyme, the
clamp protein binds to the DNA
polymerase and prevents this
enzyme from dissociating from the
template DNA strand. The sliding
clamp is a ring-shaped protein that
encircles the duplex DNA, which
binds to the DNA polymerase and
tethers it to the DNA template,
preventing its dissociation and
providing high processivity.
Sliding clamps and the clamp
loaders were initially identified as
the DNA polymerase processivity
© 2022 by JPS Scientific Publications, India
432
factors. Sliding clamps are the ring-
shaped protein complexes that
encircle and slide along by the
duplex DNA, and clamp loaders
are enzymes that load these clamps
onto DNA. The proteins are found
in all the organisms and are called
proliferating cell nuclear antigen in
the eukaryotes and the β clamp in
the prokaryotes. Both the PCNA
and β form a ring around the
DNA, which is made up of the two
subunits of three domains each in β
but three subunits of two domains
each in PCNA.
• SUBTILIS BACTERIA - Bacillus
subtilis, also known as the hay
bacillus or grass bacillus, is a
Gram-positive, catalase-positive
bacterium, which is found in the
soil and in the gastrointestinal tract
of ruminants, humans and the
marine sponges. As a member of
the genus Bacillus, B. Subtilis is a
rod-shaped, and can form a tough,
protective endospore, allowing it to
tolerate the extreme environmental
conditions. B. Subtilis has
historically been classified as an
obligate aerobe, though the
evidence exists that it is a
facultative anaerobe. B. Subtilis is
considered the best studied Gram-
positive bacterium and a model
organism to study the bacterial
chromosome replication and cell
differentiation process It is one of
the bacterial champions in secreted
enzyme production and used on an
industrial scale by the
biotechnology companies. B.
Glossary of Genetics
Subtilis has been proven highly
amenable to the genetic
manipulation, and has become
widely adopted as a model
organism for the laboratory
studies, especially of the
sporulation, which is a simplified
example of cellular differentiation.
• SPOT INFECTION - A
bacteriophage is a type of virus that
infects the bacteria. In fact, the
word “bacteriophage” simply
means “bacteria eater,” because
the bacteriophages destroy their
host cells by engulfing their cell
wall. All the bacteriophages are
composed of a nucleic acid
molecule that is surrounded by a
protein structure. When the
bacteriophage infects a new
bacterium, it introduces the
original host bacterium’s DNA
into the new bacterium DNA. In
this way, the phages can introduce
a gene that is harmful to humans
e.g. an antibiotic resistance gene or
a toxin from one bacterium to the
another bacterium. The
bacteriophages can also interact
with the bacteria through the lytic
infection or the lysogenic infection,
both of the which can lead to the
lysis of the bacterial host cells,
significantly altering certain
bacterial populations and thereby
indirectly contributing to the shift
from health to disease in
mammals. A spot test is a quick
way to check whether a phage
sample is able to infect a bacterium
by placing a small drop or “spot”
© 2022 by JPS Scientific Publications, India
433
of phage onto a plate which is also
inoculated with the bacterium.
This test will determine if the
putative plaque will propagate the
phage.
• SPORULATION IN BACTERIA
- The Endospore formation also
known as sporulation is the prime
example of a complex bacterial
developmental process. The
Sporulating bacteria undergo an
intricate sequence of the cell
differentiation events leading to the
formation of a highly resistant
dormant spore that can germinate
when the conditions improve.
Initiation and the progression of
sporulation is controlled by a
complex network which is called as
protein-protein and protein-DNA
interactions, consisting of the
regulatory modules, signaling
pathways, feed-forward network
motifs, and the post-translational
regulation. The sporulation
process has been characterized in a
sufficient detail in the model
organism Bacillus subtilis to enable
the fundamental evolutionary
analyses from a functional
perspective. Similar to the
developmental processes in a
higher organisms, bacterial
sporulation is governed by a
complex cascade of the regulatory
interactions that contains a
strongly conserved regulatory
kernel. The Transcriptional
regulation in the sporulation
network is dominated by the sigma
factors i.e the subunit of the
Glossary of Genetics 434

bacterial RNA polymerase

holoenzyme which is responsible
for recognizing the promoter
regions on the DNA.
• SINGLE STRAND DNA-
BINDING PROTEINS - The
Single-stranded binding proteins
(SSBs) are a class of the proteins
that have been identified in both
the viruses and the organisms from
the bacteria to the humans. The
mitochondria of the eukaryotic
cells contain their own single
stranded DNA binding protein.
The human mitochondrial SSB
(mtSSB) binds to the single-
stranded mitochondrial DNA as a
tetramer and has the sequence
similarity to the bacterial SSB. The
Human mtSSB is encoded by the
SSBP1 gene. In the yeast, it is
encoded by the gene known as the
RIM1 gene. Recently, it has also
been found that it, Helps to protect
the genome, Is the vital for the
stem cells and Is also involved with
maintaining telomere length.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
T recognized by the complex. The
• TRANSCRIPTOME
SEQUENCING - The Deep
sequencing of the transcriptomes,
also known as the RNA-Seq,
provides both the sequence and the
frequency of the RNA molecules
that are present at any particular
time in a specific cell type, tissue or
the organ. Counting the number of
the mRNAs that are encoded by
the individual genes provides an
indicator of the protein-coding
potential, a major contributor to
the phenotype. Improving methods
for the RNA sequencing is an
active area of the research both in
terms of the experimental and the
computational methods.
• TRXG - The Trithorax-group
proteins (TrxG) are
heterogeneous collection of the
proteins whose main action is to
maintain the gene expression. The
Trithorax-group proteins typically
function in the large complexes
formed with the other proteins.
The main function of the TrxG
proteins, along with the polycomb
group (PcG) proteins, is regulating
the gene expression. Whereas the
PcG proteins are typically
associated with the gene silencing,
TrxG proteins are most commonly
linked to the gene activation. The
trithorax complex activates the
gene transcription by inducing the
trimethylation of the lysine 4 of the
histone H3 (H3K4me3) at the
435
specific sites in the chromatin
TrxG proteins are also involved in
the other processes including such
as the apoptosis, cancer, and the
stress responses.
• T7 RNA POLYMERASES -
The T7 RNA Polymerase is an
RNA polymerase from the T7
bacteriophage that catalyzes the
formation of the RNA from the
DNA in the 5'→ 3' direction. The
T7 polymerase is extremely
promoter-specific and transcribes
only the DNA downstream of a T7
promoter. The T7 polymerase also
requires a double stranded DNA
template and the Mg2+ ion as
cofactor for the synthesis of the
RNA. It has a very low error rate.
T7 polymerase has a molecular
weight of around 99 kDa. The T7
a RNA polymerase is commonly
used to transcribe the DNA that
has been cloned into the vectors
that have two (different) phage
promoters in the opposite
orientation. The RNA can be
selectively synthesized from the
either strand of the insert DNA
with the different polymerases. The
enzyme is stimulated by the
spermidine and in vitro activity is
increased by the presence of carrier
proteins.
• TERT - The Telomerase reverse
transcriptase (abbreviated to the
TERT, or the hTERT in the
humans) is a catalytic subunit of
the enzyme telomerase, which
together with the telomerase RNA
© 2022 by JPS Scientific Publications, India
Glossary of Genetics
component (TERC), comprises the
most important unit of the
telomerase complex. The
Telomerases are part of a distinct
subgroup of the RNA-dependent
polymerases. The Telomerase
lengthens the telomeres in the
DNA strands, thereby allowing the
senescent cells that would
otherwise become the postmitotic
and undergo apoptosis to exceed
the Hayflick limit and become
potentially immortal, as is often the
case with the cancerous cells. To
be specific, the TERT is
responsible for catalyzing the
addition of the nucleotides in a
TTAGGG sequence to the ends of
a chromosome's telomeres. This
addition of the repetitive DNA
sequences prevents the degradation
of the chromosomal ends following
the multiple rounds of the
replication. The hTERT absence is
associated with the disorder known
as the Cri du chat. The enzyme is
consists of a protein component
with the reverse transcriptase
activity, encoded by this gene, and
an RNA component that serves as
a template for the telomere repeat.
Telomerase expression plays a role
in the cellular senescence, as it is
normally repressed in the postnatal
somatic cells, resulting in the
progressive shortening of the
telomeres.
• TRNA BINDING SITES -
The tRNA molecules bind to the
ribosome in a solvent-accessible
channel at the subunit interface.
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436
The Three binding sites for tRNA,
called as the aminoacyl site (A
site), peptidyl site (P site), and the
exit site (E site), have been
identified on both the large and the
small subunit. Each of the tRNA is
separated from its neighbor at the
elbow region (the site of ≈90°
bending) by around 25–45 Å. The
anticodon stem loops of the A- and
the P-site tRNA form the Watson–
Crick base pairs with the adjacent
mRNA codons on the 30S subunit,
whereas the 3′ CCA terminal
residues of the A- and P-site
tRNAs base-pair with the
conserved ribosomal RNA (rRNA)
loops within the 50S subunit
peptidyltransferase center, the site
of the peptide bond formation. The
Additional interactions with the
rRNA and the ribosomal proteins
position tRNA molecules on the
ribosome.
• TELEMORE HYPOTHESIS -
Telomere is said to be restrict the
lifespan of cells by counting the cell
number replication events or
triggering cell senescence. Cell
triggers senescene is caused by
sufficient telomere loss on one or
more chromosomes in normal
somatic cells. It is thought that as a
cell divides, the telomeres become
shorter and shorter each time until
they are gone.Individuals with
longer telomeres have been
reported to have a longer
subsequent lifespan.
Glossary of Genetics
• Ti PLASMID - Ti plasmid is a
Short tumour inducing plasmid. It
is an extra chromosomal DNA
which is commonly found in Plant
pathogen Agrobacterium
tumefaciens. It is used to carry
gene ka into plant cells. One of the
key feature is to drive the
production of opines which are
derivatives of various amino acids
or sugar phosphates, in host plant
cells.
• TROPONIN T GENE - Troponin
T is one of the three subunits that
form troponin which together with
tropomyosin is responsible for the
regulation of striated muscle
contraction. The troponin gene
provides instructions for making a
protein called cardiac troponin T,
which is found solely in the heart
(cardiac) muscle. TNNI3 is the
gene code for troponin T.
• T-RNA CHARGING - The tRNA
molecules become ‘charged’ or
aminoacylated in a two step
reactions in which an enzyme first
attaches the most of ATP molecule
to the amino acid to create a
temporary intermediate molecule.
In the second step the tRNA
molecule displaces it’s AMP from
the amino acid and joins with the
amino acid thus forming an amino
acid – tRNA complex. To function
as a substrate in a protein synthesis
the tRNA is charged with an
amino acid by its cognate
aminoacyl-tRNA synthetase. In
most of the cases aminoacyl-tRNA
synthetases are negatively charged
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437
as are the tRNA substrates. The
aminoacyl-tRNA synthetases is the
enzyme which is responsible for
charging the t-RNA molecules.
These enzymes charge each tRNA
molecules with the proper amino
acid thus allowing the each tRNA
to make the proper translation
from the genetic code of DNA into
the amino acid code of proteins.
• TFIIH - Transcription factor II
Human is an very important
protein complex, having roles in
the transcription of various protein-
coding genes and DNA nucleotide
excision repair pathways. TFIIH
first came to light in 1989 when the
general transcription factor-δ or
basic transcription factor 2 which
was characterized as an
indispensable transcription factor
in vitro. This factor was also
isolated from the yeast and finally
named as TFIIH in 1992. The
TFIIH is a general transcription
factor that acts to recruit the RNA
Polymerase II to the promoters of
genes. It functions as a helicase
that unwinds the DNA. It also
unwinds the DNA after a DNA
lesion has been recognized by
either the global genome repair
pathway or the transcription-
coupled repair pathway of NER.
The Purified TFIIH has role in
stopping the further RNA synthesis
by activatingtye enzyme known as
a-amanitin. The general functions
includes the Initiation transcription
of protein- coding gene and DNA
nucleotide repairing.
Glossary of Genetics
• TRANSDUCTION -Transduction
is the process by which the foreign
DNA is introduced into a cell by a
virus or viral vector particles. An
example is the viral transfer of
DNA from one of the bacterium to
the another and hence an example
of horizontal gene transfer. The
Transduction process does not
require any physical contact
between the cell donating the DNA
and the cell receiving the DNA
which occurs in conjugation, and it
is DNase resistant transformation
is susceptible to DNase.
Transduction is a common tool
which is used by the molecular
biologists to the stably introduce
the foreign gene into the host cell’s
genome of both the bacterial and
mammalian cells. The
Generalized transduction process
occurs when the random pieces of
the bacterial DNA are packaged
into a phage. It happens when a
phage is in the lytic stage, at the
moment that the viral DNA is
packaged into the phage heads. If
the virus replicates using the
‘headful packaging’, it attempts to
fill the head with the genetic
material. If the viral genome results
in the spare capacity, viral
packaging mechanisms may
incorporate the bacterial genetic
material into the new virion.
Alternatively, the generalized
transduction may occur via
recombination. The Generalized
transduction is a rare event and
generally occurs on the order of 1
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438
phage in 11,000. The new virus
capsule that contains the part
bacterial DNA then infects another
bacterial cell.
• TRANSPOSON
MUTAGENESIS - The
Transposon mutagenesis
mechanism was first studied by the
American cytogenetics Barbara
McClintock in the mid-20th century
during her Nobel Prize-winning
work with the corn. The
Transposon mutagenesis, or the
transposition mutagenesis, is a
biological process that allows the
genes to be transferred to a host
organism’s chromosome, thereby
interrupting or modifying the
function of an extant gene on the
chromosome and causing the
mutation. The Transposon
mutagenesis is much more effective
than the chemical mutagenesis,
with a higher mutation frequency
and a lower chances of killing the
organism. The Other advantages
include the being able to induce the
single hit mutations, being able to
incorporate the selectable markers
in the strain construction, and
being able to recover the genes
after the mutagenesis. The
Disadvantages include the low
frequency of the transposition in
the living systems, and the
inaccuracy of most of the
transposition systems. In the case
of bacteria, the transposition
mutagenesis is usually
accomplished by the way of a
plasmid from the which a
Glossary of Genetics
transposon is extracted and then
inserted into the host chromosome.
This usually requires a set of
enzymes including transposase to
be translated. The transposase can
also be expressed either on a
separate plasmid, or on the
plasmid containing the gene to be
integrated. Alternatively, an
injection of the transposase mRNA
into the host cell can also induce
the translation and expression. The
Early transposon mutagenesis
experiments relied on the
bacteriophages and the conjugative
bacterial plasmids for the insertion
of sequences. These were very non-
specific, and made it difficult to
incorporate the specific genes. A
newer technique called as the
shuttle mutagenesis uses the
specific cloned genes from the host
species to incorporate the genetic
elements. Another effective
approach is to deliver the
transposons through the viral
capsids. This facilitates the
integration into the chromosome
and the long-term transgene
expression.
• TAUTOMERS - The Tautomers
are the structural isomers of the
chemical compounds that readily
interconvert. The chemical
reaction interconverting the two is
called as the tautomerization. This
conversion commonly results from
the relocation of a hydrogen atom
within the compound. The
phenomenon of tautomerization is
also called as tautomerism, also
© 2022 by JPS Scientific Publications, India
439
called as the desmotropism. The
Tautomerism is for example
relevant to the behavior of the
amino acids and the nucleic acids,
two of the fundamental building
blocks of the life.The Prototropy is
the most common form of the
tautomerism and refers to the
relocation of a hydrogen atom. The
prototropic tautomerism may be
considered as a subset of the acid-
base behavior. The Prototropic
tautomers are the sets of the
isomeric protonation states with
the same empirical formula and the
total charge. The Valence
tautomerism is a type of
tautomerism in which the single
and/or the double bonds are
rapidly formed and then ruptured,
without the migration of the atoms
or the groups. It is distinct from
the prototropic tautomerism, and
also involves the processes with the
rapid reorganisation of the bonding
electrons. A pair of the valence
tautomers with the formula
C6H6O are benzene oxide and
oxepin. Other examples of this
type of tautomerism can be found
in the bullvalene, and in the open
and closed forms of the certain
heterocycles, such as the organic
azides and the tetrazoles, or the
mesoionic münchnone and
acylamino ketene. The Valence
tautomerism requires a change in
the molecular geometry and should
not be confused with the canonical
resonance structures or the
mesomers.
Glossary of Genetics
• TYROSINE RECOMBINASE -
The Tyrosine-type site-specific
recombinases (T-SSRs) have
opened the new avenues for the
predictable modification of the
genomes as they enable the precise
genome editing in the heterologous
hosts. These enzymes are the
ubiquitous in the eubacteria,
prevalent in the archaea and the
temperate phages, present in the
certain yeast strains, but barely
found in the higher eukaryotes. As
tools they find the increasing use
for the generation and the
systematic modification of the
genomes in a plethora of the
organisms. If applied in the host
organisms, they enable the precise
DNA cleavage and the ligation
without the gain or the loss of the
nucleotides. The Criteria directing
the choice of the most appropriate
T-SSR system for the genetic
engineering include that, whenever
possible, the recombinase should
act as the independent of the
cofactors and that the target
sequences should be long enough
to be unique in a given genome.
There are many advancements in
the mechanistic understanding of
the simple T-SSRs and their
application in the developmental
and the synthetic biology, as well
as in the biomedical research.
• TBP - The TBP gene provides the
instructions for making a protein
which is called as the TATA box
binding protein. This protein is
active in the cells and in the tissues
© 2022 by JPS Scientific Publications, India
440
throughout the body, where it
plays an very essential role in
regulating the activity of most of
the genes. The TATA box binding
protein attaches (binds) to a
particular sequence of the DNA
which is known as the TATA box.
This sequence occurs in a
regulatory region of the DNA near
the beginning of the many genes.
Once the protein is attached to the
TATA box near a gene, it acts as a
landmark to indicate where the
other enzymes should start reading
the gene. The process of reading a
gene’s DNA and transferring the
information to a similar molecule
which is called as the mRNA is
known as the transcription. One of
the region of the TBP gene
contains a particular DNA
segment which is known as a
CAG/CAA trinucleotide repeat.
This segment is made up of a series
of the three DNA building blocks
(nucleotides) that appear multiple
times in a row. Normally, the
CAG/CAA segment is repeated
upto 25 to 42 times within the
gene. The TBP is a member of a
small gene family of the TBP-
related factors.The first TBP-
related factor (TRF/TRF1) was
identified in the fruit fly
Drosophila, but appears to be fly or
the insect-specific. Subsequently
the TBPL1/TRF2 was found in the
genomes of the many metazoans,
whereas the vertebrate genomes
encode a third vertebrate family
member, TBPL2/TRF3. In specific
Glossary of Genetics
the cell types or on the specific
promoters TBP can be replaced by
one of these TBP-related factors,
some of which thr interact with the
TATA box which is similarly to
the TBP.
• TRANS-SPLICING - The Trans-
splicing is a special form of the
RNA processing where the exons
from the two different primary
RNA transcripts are joined end to
end and they are ligated. It is
usually found in the eukaryotes
and mediated by the spliceosome,
although some of the bacteria and
the archaea also have the “half-
genes” for the tRNAs. Whereas the
“normal” (cis-)splicing processes a
single molecule, the trans-splicing
generates a single RNA transcript
from the multiple separate pre-
mRNAs. This phenomenon can be
exploited for the molecular therapy
to address the mutated gene
products. The Genic trans-splicing
allows the variability in theRNA
diversity and also increases the
proteome complexity.While some
of the fusion transcripts occur via a
trans-splicing in the normal human
cells, the trans-splicing can also be
the mechanism behind the certain
oncogenic fusion transcripts. The
Spliced leader (SL) trans-splicing is
used by a certain microorganisms,
notably protists of the
Kinetoplastae class to express the
genes. In these organisms, a
capped splice leader RNA is
transcribed, and then
simultaneously, genes are
© 2022 by JPS Scientific Publications, India
441
transcribed in the long
polycistrons. The capped splice
leader is trans-spliced onto each
gene to generate the monocistronic
capped and the polyadenylated
transcripts. These early-diverging
eukaryotes use very few introns,
and the spliceosome they possess
to show some unusual variations in
their structure assembly.
• TELEMORE BINDING
PROTEIN - The telomere-binding
proteins (also known as the TERF,
TRBF, TRF) function to bind the
telomeric DNA in the various
species. In particular, the telomere-
binding protein refers to the
TTAGGG repeat binding factor-1
(TERF1) and the TTAGGG repeat
binding factor-2 (TERF2). The
Telomere sequences in the humans
are composed of the TTAGGG
sequences which provide the
protection and replication of the
chromosome ends to prevent the
degradation. The Telomere-
binding proteins can generate a T-
loop to protect the chromosome
ends. The TRFs are double-
stranded proteins which are known
to induce the bending, looping,
and the pairing of the DNA which
aids in the formation of the T-
loops. They directly bind to the
TTAGGG repeat sequence in the
DNA. There are also the
subtelomeric regions present for
the regulation. However, in the
humans, there are six subunits
forming a complex known as the
shelterin.
Glossary of Genetics
• TELEMORE T LOOP - The
Telomere loops (t-loops) are
formed at the ends of the
chromosomes in the species
ranging from the humans to the
worms, plants, and with the
genetic manipulation, some yeast.
Recent in vitro studies
demonstrated that the transcription
of the telomeric DNA leads to the
highly efficient t-loop formation. It
was also shown that both the DNA
termini are inserted into the
preceding DNA to generate a
highly stable t-loop junction.
Furthermore, some of the
telomeric RNA remains present at
the junction, potentially acting as a
plug to further protect and stabilize
the t-loop.
• TELOMERES ACTIVITY - The
Telomerase is the enzyme which is
responsible for the maintenance of
the length of the telomeres by
addition of the guanine-rich
repetitive sequences. The
Telomerase activity is exhibited in
the gametes and in the stem and
tumor cells. In the human somatic
cells proliferation the potential is
strictly limited and the senescence
follows the approximately 50-70
cell divisions. In most of the tumor
cells, on the contrary, replication
potential is unlimited. The key role
in this process of the system of the
telomere length maintenance with
the involvement of the telomerase
is still poorly studied. The DNA
polymerase is not capable to
completely copy the DNA at the
© 2022 by JPS Scientific Publications, India
442
very ends of the chromosomes,
therefore, approximately 50
nucleotides are lost during the each
cell cycle, which results in the
gradual telomere length
shortening. Critically short
telomeres cause the senescence,
following crisis, and the cell death.
However, in the tumor cells the
system of the telomere length
maintenance is activated. Besides
the catalytic telomere elongation,
the independent telomerase
functions can be also involved in
the cell cycle regulation. Inhibition
of the telomerase catalytic function
and resulting of the cessation of the
telomere length maintenance will
help in the restriction of the tumor
cell replication potential. On the
other hand, the formation of the
temporarily active enzyme via its
intracellular activation or due to
the stimulation of the expression of
the telomerase components will
result in the telomerase activation
and the telomere elongation that
can be used for the correction of
the degenerative changes.
• TRANSPOSON - The
Transposable elements (TEs),
which is also known as the
“jumping genes,” are the DNA
sequences that move from one
location on the genome to the
another. These elements were first
identified more than 50 years ago
by the geneticist Barbara
McClintock of Cold Spring Harbor
Laboratory in the New York.
Biologists were initially skeptical of
Glossary of Genetics
the McClintock’s discovery. Over
the next several decades, however,
it became apparent that not only
do the TEs “jump,” but they are
also found in almost all the
organisms both prokaryotes and
eukaryotes and typically in large
numbers. For example, the TEs
make up approximately 50% of the
human genome and up to 90% of
the maize genome. The
Transposable elements make up a
large fraction of the genome and
are responsible for much of the
mass of the DNA in a eukaryotic
cell. Although the TEs are the
selfish genetic elements, many are
important in the genome function
and the evolution. The
Transposons are also very useful to
the researchers as a means to alter
the DNA inside a living organism.
There are at least two classes of the
TEs, Class I TEs or
retrotransposons generally function
via the reverse transcription, while
Class II TEs or the DNA
transposons encode the protein
transposase, which they require for
the insertion and the excision, and
some of these TEs also encode the
other proteins.
• TELOMERASE INHIBITORS -
The Telomerase inhibitors have
been developed for the treatment of
the cancer, although their effect on
the tissue aging is still unknown.
The Targeting telomerase activity
for the slowing aging is an active
domain, and many patents are
taken on the telomerase activators,
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some of them having the potential
anti-aging properties. That
telomerase residual activity is
present in a limited number of the
tissues, and the activation of the
telomerase occurs in the 90% of the
human tumors, may be a warning
about the safety of this approach.
It is an enzyme that rescues the
malignant cells from the
destruction by extending the
protective caps on the ends of the
chromosomes, kills the tumor cells
but also triggers the resistance
pathways that allow the cancer to
survive and to spread. Due to the
telomerase inhibition, activity, or
the expression, these drugs might
kill the tumor cells by allowing the
telomeres to shrink or by
provoking the apoptosis. First of
all, this process might have a
chance to be cell-specific without
any serious side effects.
• TY ELEMENTS - The Ty
elements belong to the
retrotransposons group. The
abbreviation “Ty” stands for the
“Transposons of the yeast”. The
Saccharomyces cerevisiae
retrotransposons and the retrovi-
ruses are often compared because
of the similarity between their life
cycles and their mechanism of
integrating the cDNA into the host
genomes. The Ty elements
generate the more copies of
themselves for inserting in the host-
cell genome. The Ty genome
contains two genes: TYA1 and
TYB1, which correspond to the
Glossary of Genetics
gag and the pol genes of the
retroviruses, respectively. As with
the certain retroviral pol genes, the
TYB1 expression requires the pro-
grammed ribosomal frameshifting.
The Ty mRNA is transcribed and
processed in the nucleus and then
transported to the cytoplasm,
where it is translated into the Gag
and the Gag-Pol proteins. The Ty
elements of the Saccharomyces
cere-visiae produce virus-like
particles (VLPs), which never leave
the cell. During the assembly
process, the Ty1 RNA is packed
within the VLPs and subsequently
reverse-transcribed into a full-
length cDNA. In the final step of
the transposition the cDNA is
integrated into a new site in the
host genome, and the cycle can
begin a new by transcribing the
newly transposed element.
• TN 10 - The Tn10 is a transposable
element, which is a sequence of the
DNA that is capable of mediating
its own movement from one
position in the DNA of the host
organism to the another. There are
a number of the different
transposition mechanisms in the
nature, but the Tn10 uses the non-
replicative cut-and-paste
mechanism. The transposase
protein recognizes the ends of the
element and cuts it from the
original locus. The protein-DNA
complex then diffuses away from
the donor site until the random
collisions brings it in contact with a
new target site, where it is
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444
integrated. To accomplish this
reaction the 50 kDa transposase
protein must break the four DNA
strands to free the transposon from
the donor site, and perform the two
strand exchange reactions to
integrate the element at the target
site. This leaves the two strands
unjoined at the target site, but the
host DNA repair proteins take care
of this. The target site selection is
essentially random, but there is a
preference for the sequence 5'-
GCTNAGC-3'. The 6-9 base pairs
that flank the sequence also
influence the selection of the
insertion site.
• TOPOLOGICAL PROPERTIES
- In the field of topology and the
related areas of the mathematics, a
topological property or the
topological invariant is a property
of a topological space that is
invariant under the
homeomorphisms. Alternatively, a
topological property is a proper
class of the topological spaces
which is closed under the
homeomorphisms. That is, a
property of the spaces is a
topological property if whenever a
space X possesses that property
every space homeomorphic to rye
X possesses that property.
Informally, a topological property
is a property of the space that can
be expressed using the open sets.A
common problem in the topology
is to decide whether the two
topological spaces are the
homeomorphic or not. To prove
Glossary of Genetics
that the two spaces are not the
homeomorphic, it is sufficient to
find a topological property which is
not shared by them.
• TWINKLE PROTEINS - The
Twinkle protein which is also
known as the twinkle mtDNA
helicase is a mitochondrial protein
that in the humans is encoded by
the TWNK gene (which is also
known as the C10orf2 or the
PEO1) located in the long arm of
the chromosome 10. The TWNK
gene makes the two types of the
proteins, Twinkle and the Twinky.
The proteins Twinkle and the
Twinky are both found in the
mitochondria. Each of the
mitochondrion contains a small
amount of the DNA which is
known as the mitochondrial DNA
(mtDNA). The Twinkle protein is
involved in the production of the
mtDNA by functioning as an
adenine nucleotide dependent
DNA helicase, an enzyme that
binds to the DNA and temporarily
unwinds the double helix of the
DNA molecule so that it can
replicate. They also serve as the
primases able to initiate the DNA
replication. They function as the
hexameric or as the heptameric
DNA helicases, which unwinds the
double-stranded DNA in the 5’ to
3’ direction in the short segments.
The proteins unwind the single-
stranded mitochondrial DNA
binding protein and the mtDNA
polymerase gamma. These
enzymes function similar to the T7
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445
phage helicase (gp4); however, the
Twinkle and/ or the Twinky are
capable of the both unwinding and
the recombining DNA making
them as the bifunctional helicases.
• TRK RECEPTORS - The Trk
receptors are a family of the
tyrosine kinases that regulates the
synaptic strength and the plasticity
in the mammalian nervous system.
The Trk receptors affect the
neuronal survival and the
differentiation through the several
signaling cascades. However, the
activation of these receptors also
has significant effects on the
functional properties of the
neurons. The common ligands of
the trk receptors are the
neurotrophins, a family of the
growth factors critical to the
functioning of the nervous system.
The binding of these molecules is
highly specific. Each type of the
neurotrophin has different binding
affinity toward its corresponding
Trk receptor. The activation of the
Trk receptors by the neurotrophin
binding may lead to activation of
the signal cascades resulting in the
promoting survival and the other
functional regulation of the cells.
• TRANSLESION - The
Translesion synthesis (TLS) is one
of the pathways to overcome the
stalled replication in which the
specific polymerases which is also
known as the TLS polymerase,
perform the bypass synthesis across
the DNA damage. The stalled
replication fork can be resolved by
Glossary of Genetics
a strand switch pathway involving
the DNA helicase Rad5. The
Disruption of both the AtPolζ and
the AtRAD5a shows the
synergistic or the additive effects in
the sensitivity to the DNA-
damaging agents.
• TROMBONE MODEL OF DNA
PROFILING - The “trombone”
model of the DNA replication
postulates that the lagging strand
forms a loop such that the leading-
and the lagging-strand replication
proteins contact one another. This
replication loop contains a nascent
Okazaki fragment and allows for
the coordination of the leading-
and the lagging-strand synthesis.
The bacteriophage T7 replisome
has been studied very extensively.
Thus, the macromolecular
complex of the T7 replication
proteins provides an excellent
model for the structural analysis of
a replisome. Notably, the human
mitochondrial and the T7
replication systems are very similar
in nature.
• TARGET SIZE DUPLICATION
- The target site duplication is the
identical sequences present on the
both end ends of the transposon,
originating due to the insertion of a
transposon.
• TC1 MARINER ELEMENT -
The Tc1/mariner is a class and
superfamily of the interspersed
repeats DNA (Class II)
transposons. The elements of this
class are found in all of the
animals,including the humans.
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446
They can also be found in the
protists and in the bacteria. The
class is named after its two best-
studied members, the Tc1
transposon of the Caenorhabditis
elegans and the mariner transposon
of the Drosophila. The transposon
is consists of a transposase gene,
flanked by the two terminal
inverted repeats (TIR). The Two
short tandem site duplications
(TSD) are present on the both sides
of the insert. The transposition
happens when the two
transposases recognize and bind to
the TIR sequences, join together
and then promote the DNA
double-strand cleavage. The DNA-
transposase complex then inserts
its DNA cargo at the specific DNA
motifs elsewhere in the genome,
creating the short TSDs upon the
integration. In the
IS630/Tc1/mariner system, the
motif used is a “TA” dinucleotide,
duplicated on the both ends after
the insertion.
• TAF’S - The TBP-associated
factors (TAF) are the proteins that
associate with the TATA-binding
protein in the transcription
initiation. It is a part of the
transcription initiation factor
TFIID multimeric protein
complex. It also makes up many of
the other factors, including the
SL1. They mediate the formation
of the transcription preinitiation
complex, a step preceding
transcription of the DNA to the
RNA by the RNA polymerase II.
Glossary of Genetics
The TFIID plays a central role in
mediating the promoter responses
to the various activators and the
repressors. It binds tightly to the
TAFII-250 and directly interacts
with the TAFII-40. The TFIID is
composed of the TATA binding
protein (TBP) and a number of the
TBP-associated factors (TAFS).
• T4 POLYNUCLEOTIDE
KINASE - The Thermo Scientific
T4 Polynucleotide Kinase (T4
PNK) catalyzes the transfer of the
gamma-phosphate from ATP to
the 5'-OH group of single- and the
double-stranded DNAs and the
RNAs, oligonucleotides, or the
nucleoside 3'-monophosphates
(forward reaction). The reaction is
the reversible. In the presence of
the ADP, T4 Polynucleotide
Kinase exhibits 5'-phosphatase
activity and catalyzes the exchange
of the phosphate groups between
the 5'-P-oligo-polynucleotides and
the ATP (exchange reaction). The
enzyme is also known as a 3'-
phosphatase.
• TILING ARRAYS - The Tiling
arrays are a subtype of the
microarray chips. Like the
traditional microarrays, they
function by hybridizing the labeled
DNA or the RNA target molecules
to probes fixed onto the solid
surface. The Tiling arrays differ
from the traditional microarrays in
the nature of the probes. Instead of
probing for the sequences of the
known or the predicted genes that
may be dispersed throughout the
© 2022 by JPS Scientific Publications, India
447
genome, tiling arrays probe
intensively for the sequences which
are known to exist in a contiguous
region. This is useful for
characterizing the regions that are
sequenced, but whose local
functions are largely unknown.
The Tiling arrays aid in the
transcriptome mapping as well as
in discovering the sites of the
DNA/protein interaction (ChIP-
chip, DamID), of the DNA
methylation (MeDIP-chip) and of
sensitivity to the DNase (DNase
Chip) and the array CGH. In
addition to the detecting previously
unidentified genes and the
regulatory sequences, improved
quantification of the transcription
products is possible. The Tiling
arrays are a useful tool in the
genome-wide association studies.
• TRIPLET REPEAT
EXPANSION - A trinucleotide
repeat expansion, also known as
the triplet repeat expansion, is the
DNA mutation responsible for
causing any type of the disorder
categorized as a trinucleotide
repeat disorder. These are labelled
in the dynamical genetics as the
dynamic mutations. The Triplet
expansion is caused by the slippage
during the DNA replication, also
known as the "copy choice" DNA
replication. Due to the repetitive
nature of the DNA sequence in
these regions, the 'loop out'
structures may form during the
DNA replication while
maintaining the complementary
Glossary of Genetics
base pairing between the parent
strand and the daughter strand
being synthesized. If the loop out
structure is formed from the
sequence on the daughter strand
this will result in an increase in the
number of the repeats. However, if
the loop out structure is formed on
the parent strand, a decrease in the
number of the repeats occurs. It
appears that the expansion of these
repeats is more common than the
reduction.
• TRP OPERON - The trp operon is
a collection of genes which can be
transcribed together, encoding the
enzymes that produce the amino
acid tryptophan in bacteria. The trp
operon changed into first
characterised in Escherichia coli,
and it has on the grounds that been
determined in lots of different
bacteria. The operon is regulated
so that, whilst tryptophan is gift
withinside the environment, the
genes for tryptophan synthesis are
repressed. The trp operon includes
5 structural genes: trpE, trpD,
trpC, trpB, and trpA, which encode
the enzymes had to synthesize
tryptophan. It additionally includes
a repressive regulator gene referred
to as trpR. When tryptophan is
gift, the trpR protein binds to the
operator, blocking off transcription
of the trp operon with the aid of
using RNA polymerase. This
operon is an instance of repressible
bad law of gene expression. The
repressor protein binds to the
operator withinside the presence of
© 2022 by JPS Scientific Publications, India
448
tryptophan (repressing
transcription) and is launched from
the operon whilst tryptophan is
absent (permitting transcription to
proceed). The trp operon moreover
makes use of the lac operon.
• TERNARY COMPLEX - A
ternary complex is a protein
complex containing the three
different molecules that are bound
together. In the structural biology,
the ternary complex can also be
used to describe a crystal
containing a protein with the two
small molecules bound, for
example the cofactor and substrate
or a complex formed between the
two proteins and a single substrate.
In the Immunology, the ternary
complex can refer to the MHC–
peptide–T-cell-receptor complex
formed when the T cells recognize
epitopes of an antigen. Some other
example can be taken like the
ternary complex while the
eukaryotic translation, in which
the ternary complex is composed
of the eIF-3 & eIF-2 + Ribosome
40s subunit+ tRNAi. A ternary
complex can be a complex formed
between the two substrate
molecules and an enzyme.
• TETRA LOOP - The tetraloops
are a type of the four-base hairpin
loop motifs in the RNA secondary
structure that cap many of the
double helices. There are many
variants of the tetraloop. The
published ones include the ANYA,
CUYG, GNRA, UNAC and the
UNCG. The three types of the
Glossary of Genetics
tetraloops are common in the
ribosomal RNA: GNRA, UNCG
and the CUUG, in which the N
could be either the uracil, adenine,
cytosine, or the guanine, and the R
is either the guanine or the
adenine. These three sequences
form the stable and conserved
tetraloops that play an important
role in the structural stability and
the biological function of the 16S
rRNA.
• TRANSCRIPTION FACTOR 2
A - The transcription factor TFIIA
is a nuclear protein which is
involved in the RNA polymerase
II-dependent transcription of the
DNA. The TFIIA is one of the
several general (basal) transcription
factors (GTFs) that are required for
all the transcription events that use
the RNA polymerase II. Other
GTFs include the TFIID, a
complex composed of the TATA
binding protein TBP and the TBP-
associated factors (TAFs), as well
as the factors TFIIB, TFIIE,
TFIIF, and the TFIIH. Together,
these factors are responsible for the
promoter recognition and the
formation of a transcription
preinitiation complex (PIC)
capable of the initiating the RNA
synthesis from a DNA template.
Interaction of TFIIA with TBP
facilitates formation of and
stabilizes the preinitiation
complex. The interaction of the
TFIIA with the TBP also results in
the exclusion of the negative
(repressive) factors that might
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449
otherwise bind to the TBP and
interfere with the PIC formation.
• TRANSCRIPTION FACTORS 2
B - The tanscription factor II D
(TFIID) is one of the several
general transcription factors that
make up the RNA polymerase II
preinitiation complex. The RNA
polymerase II holoenzyme is a
form of the eukaryotic RNA
polymerase II that is recruited to
the promoters of the protein-coding
genes in living cells. It consists of
the RNA polymerase II, a subset of
the general transcription factors,
and regulatory proteins known as
the SRB proteins. Before the start
of the transcription, the
transcription Factor II D (TFIID)
complex binds to the core
promoter DNA of the gene
through the specific recognition of
the promoter sequence motifs,
including the TATA box, Initiator,
Downstream Promoter, Motif Ten,
or the Downstream Regulatory
elements. It Coordinates the
activities of more than 70
polypeptides required for the
initiation of the transcription by the
RNA polymerase II. It also binds
to the core promoter to position the
polymerase properly.
• TRANSCRIPTION FACTORS 2
F - The transcription factor II F
(TFIIF) is one of the several
general transcription factors that
make up the RNA polymerase II
preinitiation complex. The TFIIF
binds to the RNA polymerase II
when the enzyme is already
Glossary of Genetics
unbound to any other transcription
factor, thus preventing it from
contacting the DNA outside the
promoter. Furthermore, the TFIIF
stabilizes the RNA polymerase II
while it's contacting the TBP and
the TFIIB.
• TRANSCRIPTION FACTORS 2
B - The transcription factor II B
(TFIIB) is a general transcription
factor that is involved in the
formation of the RNA polymerase
II preinitiation complex (PIC) and
aids in stimulating the transcription
initiation. The TFIIB is localised to
the nucleus and provides a
platform for the PIC formation by
binding and stabilising the DNA-
TBP (TATA-binding protein)
complex and by recruiting the
RNA polymerase II and the other
transcription factors. It is encoded
by the TFIIB gene, and is
homologous to the archaeal
transcription factor B and
analogous to the bacterial sigma
factors. The TFIIB is a single
33kDa polypeptide consisting of
the 316 amino acids. The TFIIB is
made up of four functional regions:
the C-terminal core domain, the B
linker, the B reader and the amino
terminal zinc ribbon.
• TRANSCRIPTION FACTORS 2
H - The transcription factor II
Human (transcription factor II H;
TFIIH) is an important protein
complex, having roles in the
transcription of the various protein-
coding genes and in the DNA
nucleotide excision repair (NER)
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450
pathways. The TFIIH first came to
light in the year 1989 when the
general transcription factor-δ or the
basic transcription factor 2 was
characterized as an indispensable
transcription factor in vitro. This
factor was also isolated from the
yeast and finally named as the
TFIIH in the year 1992. The
TFIIH is a general transcription
factor that acts to recruit the RNA
Pol II to the promoters of the
genes. It functions as a helicase
that unwinds the DNA. It also
unwinds the DNA after a DNA
lesion has been recognized by
either the global genome repair
(GGR) pathway or the
transcription-coupled repair (TCR)
pathway of NER.
• TRANSCRIPTION FACTORS 2
S - The transcription factor S-II
(TFIIS) induces the mRNA
cleavage by enhancing the intrinsic
nuclease activity of the RNA
polymerase (Pol) II, past template-
encoded pause sites. It is widely
distributed being found in the
mammals, Drosophila, yeast and
in the archaebacteria Sulfolobus
acidocaldarius. The S-II proteins
have a relatively conserved C-
terminal region but variable N-
terminal region, and some
members of this family are
expressed in a tissue-specific
manner.
• THIOGALACTOSIDE
TRANSACETYLASE - The
Galactoside acetyltransferase (also
known as the Galactoside O-
Glossary of Genetics
acetyltransferase, thiogalactoside
transacetylase, β-galactoside
transacetylase and the GAT) is an
enzyme that transfers an acetyl
group from the acetyl-CoA to the
β-galactosides, glucosides and the
lactosides. It is coded for by the
lacA gene of the lac operon in the
E. coli. The enzyme's role in the
classical E.coli lac operon still
remains unclear. However, the
enzyme's cellular role may be to
detoxify the non-metabolizable
pyranosides by acetylating them
and preventing their re entry into
the cell.
• THYMIDNE KINASE - The
thymidine kinase is an enzyme, a
phosphotransferase (a kinase), 2'-
deoxythymidine kinase, ATP-
thymidine 5'-phosphotransferase. It
can be found in most of the living
cells. It is present in the two forms
in the mammalian cells, TK1 and
TK2. The certain viruses also have
the genetic information for the
expression of the viral thymidine
kinases. The thymidine kinases
have a key function in the synthesis
of the DNA and therefore in the
cell division, as they are part of the
unique reaction chain to introduce
the thymidine into the DNA. The
thymidine is present in the body
fluids as a result of the degradation
of the DNA from the food and
from the dead cells. The thymidine
kinase is required for the action of
the many antiviral drugs. It is used
to select the hybridoma cell lines in
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451
the production of the monoclonal
antibodies.
• TIM BARREL - The TIM barrel
(triose-phosphate isomerase),
which is also known as an
alpha/beta barrel, is a conserved
protein fold consisting of the eight
alpha helices (α-helices) and the
eight parallel beta strands (β-
strands) that alternate along the
peptide backbone. The structure is
named after the triose-phosphate
isomerase, a conserved metabolic
enzyme. The TIM barrels are
ubiquitous, with approximately
10% of all the enzymes adopting
this fold. Further, the five of the
seven enzyme commission (EC)
enzyme classes include the TIM
barrel proteins. The TIM barrel
fold is most important
evolutionarily ancient, with many
of its members possessing very
little similarity today, instead
falling within the twilight zone of
the sequence similarity. The inner
beta barrel (β-barrel) is in many
cases stabilized by the intricate salt-
bridge networks. The Loops at the
C-terminal ends of the β-barrel are
responsible for the catalytic
activity, while the N-terminal end
loops are important for the stability
of the TIM-barrels.
• TITIN - The titin (also called
connectin) is a protein that in the
humans is encoded by the TTN
gene. The Titin is a giant protein,
greater than 1 µm in the length,
that functions as a molecular
spring that is responsible for the
Glossary of Genetics
passive elasticity of the muscle. It
comprises around 244 individually
folded protein domains connected
by the unstructured peptide
sequences. These domains unfold
when the protein is stretched and
refold when the tension is
removed. The Titin is important in
the contraction of the striated
muscle tissues. It connects the Z
line to the M line in the sarcomere.
The protein contributes to force the
transmission at the Z line and
resting tension in the I band region.
It limits the range of the motion of
the sarcomere in the tension, thus
contributing to the passive stiffness
of the muscle. The Variations in
the sequence of the titin between
the different types of the striated
muscle (cardiac or skeletal) have
been correlated with differences in
the mechanical properties of these
muscles.
• TM RNA - The transfer-messenger
RNA (abbreviated as the tmRNA,
also known as the 10Sa RNA and
by its genetic name SsrA) is a
bacterial RNA molecule with the
dual tRNA-like and the messenger
RNA-like properties. The tmRNA
forms a ribonucleoprotein complex
(tmRNP) together with the Small
Protein B (SmpB), Elongation
Factor Tu (EF-Tu), and the
ribosomal protein S1. In the trans-
translation, the tmRNA and its
associated proteins bind to the
bacterial ribosomes which have
stalled in the middle of the protein
biosynthesis, for example when
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452
reaching the end of a messenger
RNA which has lost its stop codon.
The tmRNA is remarkably very
versatile in nature. It recycles the
stalled ribosome, adds a
proteolysis-inducing tag to the
unfinished polypeptide, and
facilitates the degradation of the
aberrant messenger RNA. In the
majority of the bacteria these
functions are carried out by the
standard one-piece tmRNAs.
• TN 10 - The tn10 is a transposable
element, which is a sequence of the
DNA that is capable of mediating
its own movement from one
position in the DNA of the host
organism to the another. There are
a number of the different
transposition mechanisms in the
nature, but the Tn10 uses the non-
replicative cut-and-paste
mechanism. The transposase
protein recognizes the ends of the
element and cuts it from the
original locus. The protein-DNA
complex then diffuses away from
the donor site until the random
collisions brings it in contact with a
new target site, where it is
integrated. To accomplish this
reaction the 50 kDa transposase
protein must break the four DNA
strands to free the transposon from
the donor site, and perform the two
strand exchange reactions to
integrate the element at the target
site. This leaves the two strands
unjoined at the target site, but the
host DNA repair proteins take care
of this.
Glossary of Genetics
• TALEN - The transcription
activator-like effector nucleases
(TALEN) are the restriction
enzymes that can be engineered to
cut the specific sequences of the
DNA. They are made by the fusing
of a TAL effector DNA-binding
domain to a DNA cleavage
domain (a nuclease which cuts the
DNA strands). The transcription
activator-like effectors (TALEs)
can be engineered to bind to
practically any of the desired DNA
sequence, so when combined with
a nuclease, the DNA can be cut at
the specific locations. The
restriction enzymes can be
introduced into the cells, for use in
the gene editing or for the genome
editing in situ, a technique known
as the genome editing with
engineered nucleases. Alongside
the zinc finger nucleases and the
CRISPR/Cas9, TALEN is a
prominent tool in the field of the
genome editing.
• T DNA - The transfer DNA
(abbreviated T-DNA) is the
transferred DNA of the tumor-
inducing (Ti) plasmid of some of
the species of bacteria such as the
Agrobacterium tumefaciens and
the Agrobacterium rhizogenes
(actually an Ri plasmid). The T-
DNA is transferred from the
bacterium into the host plant's
nuclear DNA genome. The
capability of this specialized
tumor-inducing (Ti) plasmid is
attributed to the two essential
regions required for the DNA
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453
transfer to the host cell. The T-
DNA is bordered by the 25-base-
pair repeats on each end. The
transfer is initiated at the right
border and terminated at the left
border and requires the vir genes of
the Ti plasmid. The bacterial T-
DNA is about 24,000 base pairs
long and contains the plant-
expressed genes that code for the
enzymes synthesizing opines and
the phytohormones.
• T RNA - The Transfer RNA
(abbreviated as the tRNA and
formerly referred to as thevsRNA,
for the soluble RNA) is an adaptor
molecule composed of the RNA,
typically 76 to 90 nucleotides in the
length (in eukaryotes), that serves
as the physical link between the
mRNA and the amino acid
sequence of the proteins. Transfer
RNA (tRNA) does this by carrying
an amino acid to the protein
synthesizing machinery of a cell
called as the ribosome. The
Complementation of a 3-nucleotide
codon in a messenger RNA
(mRNA) by a 3-nucleotide
anticodon of the tRNA results in
the protein synthesis based on the
mRNA code. As such, the tRNAs
are a necessary component of the
translation, the biological synthesis
of the new proteins in accordance
with the genetic code.
• TRANSCRIPTION BUBBLE -
The transcription bubble is a
molecular structure formed during
the DNA transcription when a
limited portion of the DNA double
Glossary of Genetics
helix is unwound. The size of a
transcription bubble ranges from
the 12-14 base pairs. A associate with the TATA-binding
transcription bubble is formed
when the RNA polymerase
enzyme binds to a promoter and
causes the two DNA strands to
detach. It presents a region of the
unpaired DNA, where a short
stretch of the nucleotides are
exposed on the each strand of the
double helix.
• T7 DNA POLYMERASERASE -
The T7 DNA polymerase is an
enzyme used during the DNA
replication of the T7
bacteriophage. During this process,
the DNA polymerase “reads”
existing DNA strands and creates
the two new strands that match the
existing ones. The T7 DNA
polymerase requires a host factor
known as the E. coli thioredoxin,
in order to carry out its function.
This helps to stabilize the binding
of the necessary protein to the
primer-template to improve the
processivity by more than the 100-
fold, which is a feature unique to
this enzyme. It is a member of the
Family A DNA polymerases,
which include the E. coli DNA
polymerase I and the Taq DNA
polymerase. This polymerase has
various applications in the site-
directed the mutagenesis as well as
a high-fidelity enzyme suitable for
the PCR. It has also served as the
precursor to the Sequenase, an
engineered-enzyme optimized for
the DNA sequencing.
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• TAF - The TBP-associated factors
(TAF) are the proteins that
protein in th3 transcription
initiation. It is a part of the
transcription initiation factor
TFIID multimeric protein
complex. It also makes up many of
the other factors, including the
SL1. They mediate the formation
of the transcription preinitiation
complex, a step preceding
transcription of the DNA to the
RNA by the RNA polymerase II.
The TFIID plays a central role in
mediating the promoter responses
to the various activators and the
repressors. It binds tightly to the
TAFII-250 and directly interacts
with the TAFII-40. TFIID is
composed of the TATA binding
protein (TBP) and a number of the
TBP-associated factors (TAFS).
• TAT PROTEIN - In the field of
molecular biology, Tat is a protein
that is encoded for by the tat gene
in the HIV-1. The Tat is a
regulatory protein that drastically
enhances the efficiency of the viral
transcription. The Tat stands for
the "Trans-Activator of
Transcription". The protein
consists of around 86 and 101
amino acids depending on the
subtype. The Tat vastly increases
the level of the transcription of the
HIV dsDNA. Before the Tat is
present, a small number of the
RNA transcripts will be made,
which allow the Tat protein to be
produced. The Tat then binds to
Glossary of Genetics
the cellular factors and mediates
their phosphorylation, resulting in
the increased transcription of all
the HIV genes, providing a positive
feedback cycle. This in turn allows
the HIV to have an explosive
response once a threshold amount
of the Tat is produced, a useful tool
for defeating the body's response.
• T CELL RECEPTOR - The T-cell
receptor (TCR) is a protein
complex found on the surface of
the T cells, or the T lymphocytes,
that is responsible for recognizing
the fragments of the antigen as
peptides bound to the major
histocompatibility complex (MHC)
molecules. The binding between
the TCR and the antigen peptides
is of relatively low affinity and is
degenerate, that is, many of the
TCRs recognize the same antigen
peptide and many antigen peptides
are recognized by the same TCR.
The TCR is composed of the two
different protein chains (that is, it is
a heterodimer). In the humans, in
95% of the T cells the TCR consists
of an alpha (α) chain and a beta (β)
chain (encoded by the TRA and
the TRB, respectively), whereas in
the 5% of the T cells the TCR
consists of the gamma and the
delta (γ/δ) chains (encoded by the
TRG and TRD, respectively). This
ratio changes during the ontogeny
and in diseased states (such as the
leukemia). It also differs between
the species. Orthologues of the 4
loci have been mapped in various
species. Each of the locus can
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455
produce a variety of the
polypeptides with constant and the
variable regions.
• TWIST 1 - The Twist-related
protein 1 (TWIST1) also known as
the class A basic helix–loop–helix
protein 38 (bHLHa38) is a basic
helix-loop-helix transcription factor
that in the humans is encoded by
the TWIST1 gene. The Basic helix-
loop-helix (bHLH) transcription
factors have been implicated in the
cell lineage determination and in
the differentiation. The protein
encoded by this gene is a bHLH
transcription factor and shares
similarity with the another bHLH
transcription factor, Dermo1
(a.k.a. TWIST2). The strongest
expression of this mRNA is in
placental tissue, in the adults,
mesodermally derived tissues
express this mRNA preferentially.
The twist1 is thought to regulate
the osteogenic lineage.
• TWIST 2 - The Twist-related
protein 2 is a protein that in the
humans is encoded by the TWIST2
gene. The protein encoded by this
gene is a basic helix-loop-helix
(bHLH) transcription factor and
shares the similarity with the
another bHLH transcription factor,
TWIST1. The bHLH transcription
factors have been implicated in the
cell lineage determination and in
the differentiation. It is thought
that during the osteoblast
development, this protein may
inhibit the osteoblast maturation
and maintain cells in a
Glossary of Genetics
preosteoblast phenotype. The
Mutations in the TWIST2 gene
that alter the DNA-binding activity
through both the dominant-
negative and the gain-of-function
effects are associated with the
ablepharon macrostomia syndrome
and the Barber–Say syndrome.
• TRCF – The Mutation Frequency
Decline (mfd) is the gene which
encodes the protein Mfd (also
known as the Transcription Repair
Coupling Factor, TRCF). The Mfd
functions in the transcription-
coupled repair to remove a stalled
RNA polymerase that has
encountered the DNA damage and
is unable to continue the
translocating process. The Mfd
utilizes the ATP to translocate
along the DNA, most likely forcing
the RNA polymerase forward and
ultimately dissociating it from the
DNA template. The Mfd also
contains the binding domains
which recruit the UvrA and trigger
the associated nucleotide excision
repair pathway and was initially
discovered when its mutation led
to a decrease in the mutation rates
after the irradiation by the UV
light.
• T SIX - The Tsix is a non-coding
RNA gene that is antisense to the
Xist RNA. The Tsix binds Xist
during the X chromosome
inactivation. The name Tsix comes
from the reverse of the Xist, which
stands for the X-inactive specific
transcript. In the extra-embryonic
lineage in the mice and some of the
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456
other mammals, all the female
individuals have the two X
chromosomes. However, during
the embryonic development, an X
chromosome is deactivated, while
the other X chromosome is left
untouched, in a process called as
the imprinted X-inactivation. The
Xist inactivates an X chromosome
at random in female mice by
condensing the chromatin, via the
histone methylation among the
other mechanisms that are
currently being studied. This
inactivation happens at random in
each of the individual cell,
allowing for a different X
chromosome to be inactivated in
each cell. The Female mammals
are therefore called as the genetic
mosaics, for having the two
different X chromosomes
expressed throughout their body.
The Tsix binds complementary
Xist RNA and renders it non-
functional. After the binding it, the
Xist is made inactive through the
dicer.
• TRYPTOPHAN OPERON - The
trp operon is an operon-a group of
the genes that is used, or
transcribed, together—that codes
for the components for the
production of the tryptophan. The
trp operon is present in many of
the bacteria, but was first
characterized in the Escherichia
coli. The operon is regulated so
that, when tryptophan is present in
the environment, the genes for the
tryptophan synthesis are not
Glossary of Genetics 457

expressed. It was an important

experimental system for the
learning about the gene regulation,
and is commonly used to teach the
gene regulation. The trp operon
contains the five structural genes
i.e the trpE, trpD, trpC, trpB, and
trpA, which encode the enzymatic
parts of the pathway. It also
contains a repressive regulator gene
called as the trpR. trpR has a
promoter where the RNA
polymerase binds and synthesizes
the mRNA for a regulatory
protein. The protein that is
synthesized by the trpR then binds
to the operator which then causes
the transcription to be blocked. In
the trp operon, the tryptophan
binds to the repressor protein
effectively blocking the gene
transcription. In this situation, the
repression is that of the RNA
polymerase transcribing the genes
in the operon. Also unlike the lac
operon, the trp operon contains a
leader peptide and an attenuator
sequence which allows for the
graded regulation. It is an example
of the repressible negative
regulation of the gene expression.
Within the operon's regulatory
sequence, the operator is bound to
the repressor protein in the
presence of the tryptophan (thereby
preventing transcription) and is
liberated in the tryptophan's
absence (thereby allowing the
transcription).

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
U •
• ULTRA DEEP SEQUENCING -
The term "ultra-deep" can
sometimes also refer to as the
higher coverage (>100-fold), which
allows for the detection of the
sequence variants in the mixed
populations. In the extreme, the
error-corrected sequencing
approaches such as the Maximum-
Depth Sequencing can make it so
that coverage of a given region
approaches the throughput of a
sequencing machine, allowing the
coverages of around >10^8.
• U2AF2 - The Splicing factor
U2AF 65 kDa subunit is a protein
that in the humans is encoded by
the U2AF2 gene. In th3
eukaryotes, the introns in the
transcribed pre-mRNA first have to
be removed by the spliceosome in
the order to form a mature mRNA.
A spliceosome is assembled from
the small nuclear
ribonucleoproteins(snRNP) and
the small nuclear RNAs(snRNA).
And the splicing factor can be
divided into snRNP and the non
snRNP proteins. The U2 auxiliary
factor (U2AF), composed of a
large and a small subunit, is a non-
snRNP protein required for the
binding of the U2 snRNP to the
pre-mRNA branch site. This gene
encodes the U2AF large subunit,
which contains a sequence-specific
RNA-binding region with the 3
RNA recognition motifs and an
© 2022 by JPS Scientific Publications, India
458
Arg/Ser-rich domain necessary for
the splicing.
U5 SPLICESOMAL RNA - The
U5 snRNA is a small nuclear RNA
(snRNA) that participates in the
RNA splicing as a component of
the spliceosome. It forms the U5
snRNP (small nuclear
ribonucleoprotein) by associating
with the several proteins including
the Prp8 - the largest and most
conserved protein in the
spliceosome, the Brr2 - a helicase
required for the spliceosome
activation, Snu114, and the 7 Sm
proteins. The U5 snRNA forms a
coaxially-stacked series of the
helices that project into the active
site of the spliceosome. The Loop
1, which caps this series of the
helices, forms the 4-5 base pairs
with the 5'-exon during the two
chemical reactions of splicing. This
interaction appears to be especially
important during the step two of
the splicing, exon ligation.
• U6 SPLICESOMAL RNA - The
U6 snRNA is the non-coding small
nuclear RNA (snRNA) component
of the U6 snRNP (small nuclear
ribonucleoprotein), an RNA-
protein complex that combines
with the other snRNPs,
unmodified pre-mRNA, and the
various other proteins to assemble
a spliceosome, a large RNA-
protein molecular complex that
catalyzes the excision of the
introns from the pre-mRNA.
Splicing, or the removal of the
introns, is a major aspect of the
Glossary of Genetics
post-transcriptional modification
and takes place only in the nucleus
of the eukaryotes. The U6 snRNA
gene has been isolated in many of
the organisms, including the C.
elegans. Among them, the baker's
yeast (Saccharomyces cerevisiae) is
a commonly used model organism
in the study of the snRNAs.
• U11 SPLICESOMAL RNA - The
U11 snRNA (small nuclear
ribonucleic acid) is an important
non-coding RNA in the minor
spliceosome protein complex,
which activates the alternative
splicing mechanism. The minor
spliceosome is associated with the
similar protein components as the
major spliceosome. It uses the U11
snRNA to recognize the 5' splice
site (functionally equivalent to U1
snRNA) while the U12 snRNA
binds to the branchpoint to
recognize the 3' splice site
(functionally equivalent to the U2
snRNA). The U11 snRNA has a
stem-loop structure with a 5' end as
splice site sequence (5' ss) and
contains the four stem loops
structures (I-IV). A structural
comparison of the U11 snRNA
between the plants, vertebrates and
the insects shows that it is folded
into a structure with a four-way
junction at the 5' site and in a stem
loop structure at the 3' site.
• UBF - The UBF Recognizes the
ribosomal RNA gene promoter
and activates the transcription
mediated by the RNA polymerase
I through the cooperative
© 2022 by JPS Scientific Publications, India
459
interactions with the transcription
factor SL1/TIF-IB complex. It
binds specifically to the upstream
control element. Alternatively
spliced human isoforms have been
reported. Note:
• UCE - An ultra-conserved element
(UCE) is a region of the DNA that
is identical in at least two different
species. One of the first studies of
the UCEs showed that the certain
human DNA sequences of the
length 200 nucleotides or the
greater were entirely conserved
(identical nucleic acid sequence) in
the human, rats, and the mice.
Despite often being the noncoding
DNA, some ultra-conserved
elements have been found to be
transcriptionally active, giving the
non-coding RNA molecules. The
UCEs are often affected by the
copy number variation in the
cancer cells, much more than in
the healthy contexts, suggesting
that altering the copy number of
the ultraconserved elements may
be deleterious and associated with
the cancer. A study comparing the
ultra-conserved elements between
the humans and the Japanese
puffer fish Takifugu rubripes
proposed an importance in the
vertebrate development. Several
ultra-conserved elements are
located near the transcriptional
regulators or the developmental
genes. Other functions include the
enhancing and splicing regulation.
Double-knockouts of the UCEs
near the ARX gene in mice caused
Glossary of Genetics
a shrunken hippocampus in the
brain. The knockout effects are not
lethal in the laboratory mice, but
could be in the wild.
• UMU CHROMOTEST - For the
pharmacology and the genetics, the
Umu Chromotest, first developed
and published by the Oda is a
biological assay (bioassay) to assess
the genotoxic potential of the
chemical compounds. It is based
on the ability of the DNA-
damaging agents to induce the
expression of the umu operon. In
connection with the damage
inducible (din) genes recA, lexA
and umuD, the umuC gene is
essentially involved in the bacterial
mutagenesis through the SOS
response. The high correlation
between the Umu Chromotest and
the traditional Ames test for the
mutagenicity supports it as a
reasonable alternative for the early-
stage testing of the thousands of
the new pharmaceutical,
agricultural and the undustrial
chemicals synthesized every year.
Most of the large chemical
manufacturers have the ability to
screen 100 or more the synthetic
chemicals per year with the
traditional Ames test, which
requires the use of the several
Salmonella strains. The umu test,
using only a single Salmonella
strain, could potentially test a
greater range of the new chemicals
with the same resources. The
reduction in the material expense
and labor, as well as its robustness
© 2022 by JPS Scientific Publications, India
460
also position it as a suitable screen
for the complex environmental
samples.
• UKRF - The Upstream open
reading frames (uORFs) are the
major gene expression regulatory
elements. In many of the
eukaryotic mRNAs, one or more
the uORFs precede the initiation
codon of the main coding region.
Indeed, several studies have
revealed that almost half of the
human transcripts present uORFs.
Very interesting examples have
shown that the these uORFs can
impact the gene expression of the
downstream main ORF by
triggering the mRNA decay or by
regulating the translation. Also, the
evidence from the recent genetic
and the bioinformatic studies
implicates disturbed uORF-
mediated translational control in
the etiology of the many human
diseases, including the
malignancies, metabolic or the
disorders, and the inherited
syndromes.
• URACIL GLYCOL - The Uracil
glycol is a major oxidation product
of the cytosine in the DNA. It can
be readily bypassed by the E. coli
DNA polymerase I (unlike the
thymine glycol) and be a potent
premutagenic lesion.
• UORF - An upstream open
reading frame (uORF) is an open
reading frame (ORF) within the 5'
untranslated region (5'UTR) of an
mRNA. The uRFs can regulate
eukaryotic gene expression. The
Glossary of Genetics
Translation of the uORF typically
inhibits the downstream expression
of the primary ORF. However, in
some of the genes such as the yeast
GCN4, translation of specific
uORFs may increase the
translation of the main ORF. In
the bacteria, the uORFs are called
as the leader peptides and were
originally discovered on the basis
of their impact on the regulation of
the genes involved in the synthesis
or transport of the amino acids.
Approximately 50% of the human
genes contain the uORFs in their
5'UTR, and when present, these
cause reductions in the protein
expression. The Human peptides
derived from the translated uORFs
can be detected from the cellular
material with a mass spectrometer.
• UBX GENE - The Ultrabithorax
(Ubx) is a homeobox gene found in
the insects, and is used in the
regulation of th patterning in the
morphogenesis. There are many
possible products of this gene,
which function as the transcription
factors. The Ubx is used in the
specification of rye serially
homologous structures, and is used
at many levels of the
developmental hierarchies. In the
Drosophila melanogaster it is
expressed in the third thoracic (T3)
and in the first abdominal (A1)
segments and the represses wing
formation. The Ubx gene regulates
the decisions regarding the number
of wings and the legs the adult flies
will have. The developmental role
© 2022 by JPS Scientific Publications, India
461
of the Ubx gene is determined by
the splicing of its product, which
takes place after the translation of
the gene. The specific splice factors
of a particular cell allow the
specific regulation of the
developmental fate of that cell, by
making the different splice variants
of the transcription factors. In the
D. Melanogaster, at least six
different isoforms of the Ubx exist.
• UVR ABC - The UvrABC
endonuclease is a multienzyme
complex in bacteria which is
involved in the DNA repair by the
nucleotide excision repair, and it
is, therefore, sometimes called as
an excinuclease. This UvrABC
repair process, sometimes called as
the short-patch process, involves
the removal of the twelve
nucleotides where a genetic
mutation has been occurred
followed by a DNA polymerase,
replacing these aberrant
nucleotides with the correct
nucleotides and completing the
DNA repair. The subunits for this
enzyme are encoded in the uvrA,
uvrB, and in the uvrC genes. This
enzyme complex is also able to
repair many different types of the
damage, including the cyclobutyl
dimer formation.
Glossary of Genetics
V enzyme APOBEC (specifically
• VALYL TRNA SYNTHETASE -
The Valyl-tRNA synthetase
(ValRS), a large monomeric
enzyme in a free state, forms a
class-Ia subfamily, which
characteristically have an α-helix
bundle domain near the C-
terminus to recognize the tRNA
anticodon. The previous
mutagenesis studies on the
tRNAVal identified A35, C36,
nucleotide at the position 20, and
G45 as identity elements, with the
latter two being the minor
determinants. The 2. 9-Å
resolution crystal structure of the
Thermus thermophilus ValRS in a
complex with the tRNAVal and
the valyl-adenylate analogue
corroborates the biochemical work.
On the other hand, the C-terminal
coiled-coil domain of the ValRS
interacts with the electrostatically
with the adenosine at position at
20 and hydrophobically with the
G19•C56 tertiary base pair. The
interactions between the ValRS
and the variable pocket of the
tRNAVal induce a more open
conformation of the TΨC-loop/D-
loop core, which may account for
the previous results by the 19F and
the imino proton NMR of the
tRNAVal.
• VIF - Viral infectivity factor, or the
Vif, is an accessory protein found
in the HIV and the other
lentiviruses. Its role is to disrupt
© 2022 by JPS Scientific Publications, India
462
the antiviral activity of the human
APOBEC3G, "A3G" in short) by
targeting it for the ubiquitination
and the cellular degradation. The
APOBEC is a cytidine deaminase
enzyme that mutates the viral
nucleic acids. The vif is a 23-
kilodalton protein that is essential
for the viral replication. The Vif
inhibits the cellular protein,
APOBEC3G, from entering the
virion during the budding from a
host cell by targeting it for the
proteasomal degradation. The vif
binds to the A3G as well as the
cellular Cullin5 E3 Ubiquitin
Ligase (ELOB-ELOC-CUL5) and
a CBFB cofactor so that the ligase
can be hijacked to tag the A3G for
the degradation. The crystal
Structure of the HIV Vif BC-box in
the Complex with the Human
Elongin B and Elongin C was
solved in the 2008, and the
structure of the full Vif/E3
complex was solved in the 2014.
• VIGS - The Virus-induced gene
silencing (VIGS) is a technology
that exploits an RNA-mediated
antiviral defense mechanism. In
the plants infected with the
unmodified viruses the mechanism
is specifically targeted against the
viral genome. However, with virus
vectors carrying inserts derived
from the host genes the process can
be additionally targeted against the
corresponding mRNAs. The VIGS
has been used widely in the plants
for the analysis of the gene
Glossary of Genetics
function and has been adapted for
the high-throughput functional
genomics. Until now most
applications of the VIGS have been
in the Nicotiana benthamiana.
However, an new vector systems
and methods are being developed
that could be used in the other
plants, including the Arabidopsis.
• VIRULENCE FACTOR - The
Virulence factors (preferably
known as the pathogenicity factors
or the effectors in the plant science)
are the cellular structures,
molecules and the regulatory
systems that enable the microbial
pathogens (bacteria, viruses, fungi,
and protozoa) to achieve the
following, colonization of a niche
in the host (this includes the
movement towards and attachment
to the host cells), immunoevasion,
evasion of the host's immune
response, immunosuppression,
inhibition of the host's immune
response (this includes the
leukocidin-mediated cell death)
enntry into and exit out of the cells
(if the pathogen is an intracellular
one) obtain nutrition from the host.
• VISTA - The V-domain Ig
suppressor of the T cell activation
(VISTA) is a type I transmembrane
protein that functions as an
immune checkpoint which is
encoded by the C10orf54 gene.
The VISTA is approximately
50kDa and belongs to the
immunoglobulin superfamily and
has one IgV domain. The VISTA is
part of the B7 family, is primarily
© 2022 by JPS Scientific Publications, India
463
expressed in the white blood cells
and its transcription is partially
controlled by the p53. There is
evidence that the VISTA can act as
both a ligand and a receptor on the
T cells to inhibit the T cell effector
function and maintain the
peripheral tolerance.
• VULVA MUTATIONS - The C.
Elegans hermaphrodite vulva
develops during the postembryonic
i.e at the larval development from
ventral epidermal precursors, and
connects the developing uterus to
the external environment. In the
adult, the vulva is necessary for the
egg-laying and also for the
copulation with the males. The
Vulval development has attracted
the general interest for the three
main reasons. First, it serves as a
paradigm for the organogenesis. In
particular, the vulva development
represents a well-understood case
in which the invariant
development arises from the
multiple cell to cell interactions. It
is also a striking example of the
tissue remodeling i.e the formation
of a hole at a precise location in an
organism. Second, it has been
important for the genetic analyses
of the signaling and the signal
transduction by the epidermal
growth factor (EGF)-receptor
which is known as LET-23 and the
RAS LET-60, LIN-12 and the
WNT, as well as the functions of
the SynMuv and the mediator
proteins. Third, it has become a
paradigm also for examining the
Glossary of Genetics
interactions among the regulatory
pat.
• VDJ RECOMBINATION - The
V(D)J recombination is the
mechanism of the somatic
recombination that occurs only in
the developing lymphocytes during
the early stages of the T and the B
cell maturation. It results in the
highly diverse repertoire of the
antibodies/immunoglobulins and
the T cell receptors (TCRs) found
in the B cells and the T cells,
respectively. The process is a
defining feature of the adaptive
immune system. The V(D)J
recombination in the mammals
occurs in the primary lymphoid
organs (bone marrow for the B
cells and the thymus for T cells)
and in a nearly random fashion
rearranges variable (V), joining (J),
and in some of the cases, diversity
(D) gene segments. The process
ultimately results in the novel
amino acid sequences in the
antigen-binding regions of the
immunoglobulins and the TCRs
that allow for the recognition of the
antigens from nearly all the
pathogens including the bacteria,
viruses, parasites, and the worms
as well as the "altered self cells" as
seen in the cancer. The recognition
can also be allergic in the nature
(e.g. to pollen or other allergens) or
may match host tissues and lead to
the autoimmunity.
• VAR 1 PROTEIN - In the field of
the molecular biology, the VAR1
protein domain, otherwise known
© 2022 by JPS Scientific Publications, India
464
as the variant protein 1, is a
ribosomal protein that forms a part
of the small ribosomal subunit in
the yeast mitochondria. The
Mitochondria possess their own
ribosomes responsible for the
synthesis of a small number of the
proteins encoded by the
mitochondrial genome. The VAR1
is the only protein in the yeast
mitochondrial ribosome to be
encoded in the mitochondria - the
remaining approximately 80
ribosomal proteins are encoded in
the nucleus. The VAR1 along with
the 15S rRNA are necessary for the
formation of the mature 37S
subunits. It is thought that the Var1
plays a role in the early steps of the
small subunit assembly and is
required for the incorporation of at
least one ribosomal protein. It is
important for the mitochondrial
translational initiation, since it
requires the interaction between
the small ribosomal subunit and
the message-specific translation
factors.
• VIRAL PLAQUES - A viral
plaque is a visible structure formed
after the introducing a viral sample
to a cell culture grown on some of
the nutrient medium. The virus
will replicate and will also spread,
generating the regions of the cell
destruction which are known as
plaques. For example, the Vero cell
or the other tissue cultures may be
used to investigate an influenza
virus or the coronavirus, while
various bacterial cultures would be
Glossary of Genetics 465

able used for the bacteriophages.

Counting the number of plaques
can also be used as a method of the
process known as virus
quantification. These plaques can
sometimes be detected visually
using the colony counters, in much
the same way as the bacterial
colonies are counted. However,
they are not always visible to the
naked eye, and sometimes can only
be seen through a microscope, or
using the techniques such as
staining e.g. neutral red for the
eukaryotes or the giemsa for the
bacteria or the
immunofluorescence bacteria. The
Special computer systems have
also been designed with the ability
to scan the samples in the
batches.The chances of appearance
of the plaque depends on the host
strain, virus and the conditions that
it requires. The Highly virulent or
lytic strains create the plaques that
look very clear due to the total cell
destruction, while the strains that
only kill a fraction of their hosts
due to the partial resistance or
lysogeny, or can only reduce the
rate of the cell growth, and also
give turbid plaques. Some of the
partially lysogenic phages give the
bull’s-eye plaques with the spots or
rings of the growth in the middle of
clear regions of the complete lysis.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
W Harbor Laboratory, and headed up
• WATSON CRICK MODEL -
The Watson-Crick Model of DNA
which was invented in the year
1953. The model gives an basic
about the structure of the DNA.
The Deoxyribonucleic Acid
(DNA) is a double-stranded,
helical molecule. It consists of the
two sugar-phosphate backbones on
the outside, which is held together
by the hydrogen bonds between the
pairs of the nitrogenous bases on
the inside. The bases are of four
types i.e A, C, G, & T. The pairing
always occurs between the A & T,
and C & G. James Watson and
Francis Crick realized that these
pairing rules meant that the either
strand contained all the
information necessary to make a
new copy of the entire molecule,
and that the aperiodic order of
bases might provide a “genetic
code”. The Watson and Crick
shared the Nobel Prize in the year
1962 for their discovery, along with
the Maurice Wilkins, who also had
continued research to provide a
large body of the crystallographic
data supporting the model.
Working in the same lab, the
Rosalind Franklin had earlier
produced the first clear
crystallographic evidence for a
helical structure. Crick went on to
do fundamental work in the field of
molecular biology and the
neurobiology. Watson th n become
© 2022 by JPS Scientific Publications, India
466
the Director of the Cold Spring
the Human Genome Project in the
1990s.
• WESTERN BLOTTING - The
western blot which is sometimes
called as the protein
immunoblotting, or the western
blotting, is a widely used analytical
technique in the field of the
molecular biology and in the
immunogenetics to detect the
specific proteins in a sample of the
tissue homogenate or the extract.
The Western blot technique uses
the three elements to achieve its
task of separating a specific protein
from a complex: separation by size,
transfer of the protein to a solid
support, and marking the target
protein using a primary and the
secondary antibody to visualize. A
synthetic or the animal-derived
antibody which is known as the
primary antibody is also created
that recognizes and binds to a
specific target protein. The
electrophoresis membrane is
washed in a solution containing
the primary antibody, before the
excess antibody is washed off. A
secondary antibody is also added
to which recognizes and binds to
the primary antibody. The
secondary antibody is visualized
through the various methods such
as the staining,
immunofluorescence, and the
radioactivity, allowing the indirect
detection of the specific target
protein.
Glossary of Genetics 467

• WHITE MUTATIONS - The repeats. The Alternatively spliced

white, abbreviated w, was the first transcript variants encoding the
sex-linked mutation discovered, same protein have been identified.
found in the fruit fly Drosophila
melanogaster. The protein coded
by the white gene functions as an
ATP-binding cassette (ABC)
transporter. It carries the
precursors of the red and the
brown eye color pigments, guanine
and the tryptophan, into the
developing eyes during the
pupation. The White-eyed flies are
not blind instead they are easily
temporarily blinded by the bright
light at certain frequencies because
they lack the protection provided
by the red and the brown pigments.
The human version of the white is
the ABCG1, and is involved in
transporting the lipids and the
cholesterol into the cells.
• WDR 5 - The WD repeat-
containing protein 5 is a protein
that in the humans is encoded by
the WDR5 gene. This gene
encodes a member of the WD
repeat protein family. The WD
repeats are minimally conserved
regions of the approximately 40
amino acids typically bracketed by
the gly-his and trp-asp (GH-WD),
which may facilitate formation of
the heterotrimeric or the
multiprotein complexes. Members
of this family are involved in a
variety of the cellular processes,
including the cell cycle
progression, signal transduction,
apoptosis, and the gene regulation.
This protein contains the 7 WD

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
X the atomic and the molecular
• XER RECOMBINASE - The Xer
recombinases (Xer-cise) is shown
to be amenable for the genetic
manipulation and the construction
of the unmarked deletion mutants
in the Escherichia coli and in the
Bacillus subtilis. In this system,
the antibiotic resistance cassette,
flanked by the dif sites, is
intrinsically very unstable since the
endogenous recombinases XerC
and the XerD recognize and
resolve the dif sites that border the
cassette. This method, relying on
the endogenous recombinases,
does not require the introduction
and the subsequent removal of the
replicating plasmids carrying the
exogenous genes, making it
extremely simple and practical.
The E. Coli XerC and the XerD
recombinases are very essential for
the chromosome segregation
during the cell division, as their
role is to resolve the chromosome
dimers to the monomers
recognizing the 28-bp dif sequence
present at the replication terminus
region. The Xer site-specific
recombination system is very well
conserved in the prokaryotes with
the circular chromosomes, and the
homologues of the XerC and the
XerD have been identified among
the Gram-negative and in the
Gram-positive bacteria.
• X RAY CRYSTOLLAGRAPHY
- The x-ray crystallography is the
© 2022 by JPS Scientific Publications, India
468
experimental science determining
structure of a crystal, in which the
crystalline structure causes a beam
of the incident X-rays to diffract
into the many specific directions.
By measuring the angles and the
intensities of these diffracted
beams, a crystallographer can
produce a three-dimensional
picture of the density of the
electrons within the crystal. From
this the electron density, the mean
positions of the atoms in the crystal
can be determined, as well as their
chemical bonds, their
crystallographic disorder, and the
various other information.
• X INACTIVATION - The X-
inactivation (also called as the
Lyonization, after the English
geneticist Mary Lyon) is a process
by which one of the copies of the X
chromosome is inactivated in the
therian female mammals. The
inactive X chromosome is silenced
by being packaged into a
transcriptionally inactive structure
called as the heterochromatin. As
nearly all the female mammals
have the two X chromosomes, X-
inactivation prevents them from
having twice as many as the X
chromosome gene products as the
males, who only possess a single
copy of the X chromosome. The
choice of which X chromosome
will be inactivated in a particular
embryonic cell is random in the
placental mammals such as the
humans, but once the X
Glossary of Genetics
chromosome is inactivated it will
remain in the inactive phase
throughout the lifetime of the cell
and its descendants in the The
result is that the choice of the
inactivated X chromosome in all
the cells of the organism is a
random distribution, often with
about half of the cells having the
paternal X chromosome
inactivated and half with an
inactivated maternal X Xic – X-chromosome inactivation
chromosome, but commonly, the
X-inactivation is unevenly
distributed across the cell lines
within one of the organism.
• X GAL - The X-gal (also
abbreviated as the BCIG for 5-
bromo-4-chloro-3-indolyl-β-D-
galactopyranoside) is an organic
compound consisting of the
galactose linked to a substituted
indole. The compound was
synthesized by the Jerome Horwitz
and collaborators in the year 1964.
The formal chemical name is often
shortened to less accurate but also
less cumbersome phrases such as
the bromochloroindoxyl
galactoside. The X from the
indoxyl may be the source of the X
in the X-gal contraction. The X-gal
is often used in the molecular
biology to test for the presence of
an enzyme, β-galactosidase, in the
place of its usual target, a β-
galactoside. It is also used to detect
the activity of this enzyme in the
histochemistry and the
bacteriology. The X-gal is one of
the many indoxyl glycosides and
© 2022 by JPS Scientific Publications, India
469
esters that yield the insoluble blue
compounds similar to the indigo
dye as a result of the enzyme-
catalyzed hydrolysis.
• XIST - The Xist which is known
as the X-inactive specific transcript
is a non-coding RNA on the
chromosome X of the placental
mammals that can acts as a major
effector of the X-inactivation
process. It is a component of the
centre along with the two other
other RNA genes (Jpx and the Ftx)
and the two protein genes (Tsx and
the Cnbp2). The functional role of
the Xist transcript was definitively
demonstrated in the mouse female
ES cells using a novel antisense
technology, called as the peptide
nucleic acid (PNA) interference
mapping. In the reported
experiments, a single 19-bp
antisense cell-permeating PNA
targeted against a particular region
of the Xist RNA prevented the
formation of the Xi and inhibited
the cis-silencing of the X-linked
genes. The association of the Xi
with the macro-histone H2A is also
disturbed by the PNA interference
mapping.
• XPA - The DNA repair protein
complementing XP-A cells is a
protein that in the humans is
encoded by the XPA gene. The
nucleotide excision repair (NER) is
a major pathway for repairing a
variety of the bulky DNA damages
including the those introduced by
the UV irradiation. The XPA
Glossary of Genetics
protein appears to play a key role
in the NER at sites of damage as a
scaffold for the other repair
proteins in order to ensure that the
damages are appropriately excised.
Among the repair proteins with
which the XPA interacts is a
protein complex (including the
ERCC1 protein) that is capable of
incising the DNA at sites of the
damage. The Xpa mutant
individuals often show the severe
clinical symptoms of the
xeroderma pigmentosum, a repair cross-complementing protein
condition involving the extreme
sensitivity to the sunlight and a
high incidence of the skin cancer.
• XRCC4 - The DNA repair protein
XRCC4 also known as the X-ray
repair cross-complementing protein
4 or the XRCC4 is a protein that in
the humans is encoded by the
XRCC4 gene. In addition to the
humans, the XRCC4 protein is
also expressed in many of the other
metazoans, fungi and in the plants.
The X-ray repair cross-
complementing protein 4 is one of
th3 several core proteins involved
in the non-homologous end joining
(NHEJ) pathway to repair the
DNA double strand breaks (DSBs).
The human XRCC4 gene is
located on the chromosome 5,
specifically at the 5q14.2. This
gene contains eight exons and the
three mRNA transcript variants,
which encode the two different
protein isoforms. The XRCC4 is
the key protein that enables the
interaction of the LigIV to
© 2022 by JPS Scientific Publications, India
470
damaged the DNA and therefore
ligation of the ends, mutations in
the XRCC4 gene were found to
cause the embryonic lethality in the
mice and the developmental
inhibition and the
immunodeficiency in the humans.
Furthermore, certain mutations in
the XRCC4 gene are associated
with an increased risk of the
cancer.
• XRCC1 - The DNA repair protein
XRCC1, also known as the X-ray
1, is a protein that in the humans is
encoded by the XRCC1 gene. The
XRCC1 is involved in the DNA
repair, where it complexes with the
DNA ligase III. The XRCC1 is
involved in the efficient repair of
the DNA single-strand breaks
formed by exposure to the ionizing
radiation and the alkylating agents.
This protein interacts with the
DNA ligase III, polymerase beta
and the poly (ADP-ribose)
polymerase to participate in the
base excision repair pathway. It
may play a role in the DNA
processing during the meiogenesis,
i.e. during the induction of the
meiosis and recombination in the
germ cells. A rare microsatellite
polymorphism in this gene is
associated with the cancer in the
patients of the varying
radiosensitivity.
• XRCC2 - The DNA repair protein
XRCC2 is a protein that in the
humans is encoded by the XRCC2
gene. This gene encodes a member
Glossary of Genetics 471

of the RecA/Rad51-related type

protein family that participates in
the homologous recombination to
maintain the chromosome stability
and the repair DNA damage. This
gene is involved in the repair of the
DNA double-strand breaks by the
homologous recombination and it
functionally complements the
Chinese hamster irs1, a repair-
deficient mutant that exhibits
hypersensitivity to a number of the
different DNA-damaging agents.
• XRCC3 - The DNA repair protein
XRCC3 is a protein that in the
humans is encoded by the XRCC3
gene. This gene encodes a member
of the RecA/Rad51-related type
protein family that participates in
the homologous recombination to
maintain chromosome stability and
repair DNA damage. This gene
functionally complements the
Chinese hamster irs1SF, a type of
repair-deficient mutant that
exhibits the hypersensitivity to a
number of the different DNA-
damaging agents and is
chromosomally very unstable. A
rare microsatellite polymorphism
in this gene is associated with the
cancer in the patients of the
varying radiosensitivity.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
•
Y
• YELLOW LOCUS - The
molecular characteristics of the
yellow (y; 1-0.0) locus, which
determines the body coloration of
phenotypically wild-type and the
mutant alleles isolated from the
geographically distant populations
of the Drosophila melanogaster in
different years. According to the
Southern data, the restrictions map
of the yellow locus of all studied
strains differ from the each other as
well as from that of the Oregon
stock. The FISH analysis shows
that in the neighborhood of the
yellow locus in the X chromosome
neither P nor the hobo elements
are found in the y1-775 stock,
while only hobo is found there in
the y1-859 and the y1-866 stocks,
only P element in the y+sn849
stock, and both elements in the y1-
719 stock. Thus, all the studied
mutant variants of the yellow are
of independent origin. The Yellow
locus residing at the very end of the
X chromosome (region 1A5-8 of
cytologic map) carries significantly
more transposon than the
retrotransposon-induced
mutations, as compared to the
white locus (regions 3C2). It is
possible that the transposons are
more active than the
retrotransposons at the
chromosomal ends of the D.
Melanogaster.
© 2022 by JPS Scientific Publications, India
472
YEAST EXPRESSION
PLATFORM - The yeast
expression platform is a strain of
the yeast used to produce the large
amounts of the proteins, sugars or
the other compounds for the
research or the industrial uses.
While the yeast are often more
resource-intensive to maintain than
the bacteria, certain products can
only be produced by the eukaryotic
cells like the yeast, necessitating
use of a yeast expression platform.
The Yeast differ in the productivity
and with respect to their
capabilities to secrete, process and
modify the proteins. As such, the
different types of the yeast (i.e.
different expression platforms) are
better suited for the different
research and the industrial
applications. Since the onset of the
genetic engineering, a number of
the microorganisms have been
developed for the production of the
biological products. These products
are used in the medicine and
industry to create the
pharmaceuticals like the hepatitis B
vaccines or the insulin. Common
platforms for the development of
the medicine and other products
include the bacterium E. coli, and
the several yeasts and the
mammalian cells (including,
notably, the Chinese hamster ovary
cells). In general a microorganism
used as an expression platform has
to meet the several criteria such as,
it should be able grow rapidly in
the large containers, produce
Glossary of Genetics 473

proteins in an efficient way (i.e.

with the minimal resource input),
be safe and, in case of the
pharmaceuticals, it should produce
and modify the products to be as
ready for the human consumption
as possible.

© 2022 by JPS Scientific Publications, India

Glossary of Genetics
Z several different structural families.
• ZINC CONTAINING
DOMAINS - Zinc Finger
Domains are relatively small
protein motifs that contain
multiple finger like projection that
make tandem contacts with their
target molecules. This are most
commonly found in eukaryotic
cells, which employ the motif in
some of their most important
proteins (including TFIIIA, CTCF,
and ZiF268).
• ZINC FINGER PROTEIN - The
zinc finger is a small protein
structural motif that is
characterized by the coordination
of the one or the more zinc ions
(Zn2+) in order to stabilize the
fold. It was originally coined to
describe the finger-like appearance
of a hypothesized structure from
the African clawed frog (Xenopus
laevis) transcription factor IIIA.
However, it has been found to
encompass a wide variety of the
differing protein structures in the
eukaryotic cells.[1] Xenopus laevis
TFIIIA was originally
demonstrated to contain the zinc
and require the metal for function
in 1983, the first such reported zinc
requirement for a gene regulatory
protein followed soon thereafter by
the Krüppel factor in the
Drosophila. It often appears as a
metal-binding domain in the multi-
domain proteins. The Proteins that
contain the zinc fingers (zinc finger
© 2022 by JPS Scientific Publications, India
474
proteins) are classified into the
Unlike many other clearly defined
supersecondary structures such as
the Greek keys or β hairpins, there
are a number of types of the zinc
fingers, each with a unique three-
dimensional architecture. A
particular zinc finger protein’s class
is determined by this three-
dimensional structure, but it can
also be recognized based on the
primary structure of the protein or
the identity of the ligands
coordinating the zinc ion.
• Z DNA - The Z-DNA is one of the
many possible double helical
structures of the DNA. It is a left-
handed double helical structure in
which the helix winds to the left in
a pattern known as the zigzag
pattern, instead of to the right, like
the more common i.e the B-DNA
form. The Z-DNA is thought to be
one of the three biologically active
double-helical structures along
with the A-DNA and the B-DNA.
The Z-DNA is quite different from
the right-handed forms. In fact, the
Z-DNA is often compared against
the B-DNA in order to illustrate
the major differences. The Z-DNA
helix is the left-handed and has a
structure that repeats every other
base pair. The major and the minor
grooves, unlike the A- and the B-
DNA, show the little difference in
the width. The formation of this
structure is generally very
unfavourable, although the certain
conditions can promote it such as
Glossary of Genetics 475

the alternating purine–pyrimidine genomes of the many plants and

sequence (especially the animals including the arabidopsis,
poly(dGC)2), negative DNA tobacco, soybean, corn, Drosophila
supercoiling or the high salt and melanogaster, C. elegans,
some of the cations (all at the Platynereis dumerilii etc.
physiological temperature, 37 °C,
and the pH 7.3–7.4). The Z-DNA
can form a junction with the B-
DNA (called as the “B-to-Z
junction box”) in a structure which
involves the extrusion of the base
pair. The Z-DNA conformation
has been very difficult to study
because it does not exist as a stable
feature of the double helix. Instead,
it is a transient structure that is
occasionally induced by the
biological activity and then quickly
disappears.
• ZINC FINGER NUCLEASES -
The Zinc-finger nucleases (ZFNs)
are the artificial restriction
enzymes generated by the fusing a
zinc finger DNA-binding domain
to a DNA-cleavage domain. The
Zinc finger domains can be
engineered to target the specific
desired DNA sequences and this
enables the zinc-finger nucleases to
target a very unique sequences
within the complex genomes. By
taking the advantage of the
endogenous DNA repair
machinery, these reagents can be
used to precisely alter the genomes
of the higher organisms. Alongside
the CRISPR/Cas9 and the
TALEN, the ZFN is a prominent
tool in the field of the genome
editing. The Zinc finger nucleases
are useful to manipulate the

© 2022 by JPS Scientific Publications, India