CYTOGENETICS – Molecular Basis of Inheritance

BS Public Health 2B
Mylene C. Danao

amino acids. Proteins differ in the

OUTLINE
number, sequence, and kinds of amino
acids. Our bodies create some of these
Molecular Basis of Inheritance
amino acids, while others come directly
from food that we consume.
I. DNA: MOLECULE OF HEREDITY
II. THE CENTRAL DOGMA OF
MOLECULAR BIOLOGY NUCLEIC ACIDS
A. Genetic code • The largest molecules in people and
B. Protein Synthesis other organisms.
III. DNA REPLICATION • Like proteins, they consist of very long
A. The three models for DNA
chains of simpler units.
replication
IV. GENE EXPRESSION • There are two basic forms of nucleic
A. Transcription acids:
B. Translation o DNA (deoxyribonucleic acid)
C. Terminologies and RNA (ribonucleic acid).
V. SMALL RNA MOLECULES Both play critical roles in the
A. Types of RNA
production of proteins. Some
B. Non-coding RNAs
VI. EPIGENETICS kinds of RNA perform other
A. Epigenome critical functions in our cells not
B. Types of epigenetic changes related to protein synthesis.

CHROMOSOME
I. DNA: MOLECULE OF HEREDITY
• A chromosome consists mainly of a
single very long DNA molecule and
PROTEINS
proteins called histones that densely
• Proteins are large chain-like molecules
package the DNA. There are many small
that are twisted and folded back on
RNA molecules surrounding the DNA as
themselves in complex patterns.
well.
• They serve as structural material for the
• In a sense, a DNA molecule contains a
body, gas transporters in blood,
sequence of permanently stored
antibodies, neurotransmitters, and
blueprints or recipes that are used mostly
enzymes.
by our cells to assemble proteins out of
• Proteins acting as enzymes are
amino acids. In other words,
particularly important substances
chromosomes are packets of
because they trigger and control the
information encoded by DNA.
chemical reactions by which
carbohydrates, lipids, and other
DNA MOLECULE
substances are created.
• If all the DNA molecules in a single
• Our human bodies produce about 90,000
human cell were straightened out and
different kinds of proteins, all of which
arranged end to end, it would form a
consist of simpler units called amino
thread about 6 feet long but only a few
acids. Proteins in all organisms are
atoms across. If the DNA in all a normal
mostly composed of just 20 kinds of
adult human's cells were arranged in this

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 CYTOGENETICS – Molecular Basis of Inheritance
BS Public Health 2B
Mylene C. Danao
way, the thread could reach the moon
about 6,000 times.
• DNA molecules have the shape of a
double helix, which is like a twisted
ladder. The sides of the ladder are
composed of sugar and phosphate units,
while the rungs consist of complementary
pairs of four different chemical bases.
o The base guanine only bonds to
cytosine and adenine only bonds
to thymine.
• Each combined sugar, phosphate, and
base subunit is a nucleotide
II. THE CENTRAL DOGMA OF
MOLECULAR BIOLOGY
• The central dogma of biology describes
the flow of genetic information in cells,
sometimes called the central dogma of
genetics.
• It is an explanation of the flow of Genetic
information in a cell, including the
replication of the DNA, the transcription
of the RNA, and the translation of the
RNA to create the Proteins.
• It predicts that a particular sequence of
amino acids (a protein) cannot be used to
specify or even alter a particular
sequence of nucleotides (a gene).
• A genomic process refers to the
conversion of DNA information into a
functional product
PROTEIN SYNTHESIS
• The genetic code is central to two critical
functions within our cells.
o (1) They are the creation of
new proteins and (2) the
duplication of chromosomes
during cell division.
Creation of new proteins
• An assembly of existing amino acids in
their proper sequences for each type of
MOLECULAR BASIS OF INHERITANCE
protein. Subsequently, it is referred to as
protein synthesis rather than
production.
• In this process, the recipe for a needed
protein is first copied. Specifically, the
relevant DNA code sequence is
transcribed, or copied, to RNA. The
process begins by a section of a DNA
molecule unwinding and then unzipping
in response to several interacting
enzymes.
• Free nucleotides in the nucleus are
attracted to complimentary bases on the
exposed DNA strands (guanine to
cytosine and adenine to thymine). The
result of this sequential bonding of base
units is the formation of a messenger
RNA (mRNA) molecule that is a copy, or
transcription, of specific sections of the
nuclear DNA molecule corresponding to
a gene. Many identical copies are made,
one right after another. In the process of
mRNA formation, the non-coding
sections are removed, and the remaining
exons are spliced together.
• These new identical messenger RNA
molecules then leave the nucleus and go
out into the cytoplasm where the protein
they are coded for is synthesized or
assembled.
• Specifically, the messenger RNA
molecules migrate from the
chromosomes to the ribosomes, which
are small granule-like organelles in the
cytoplasm. Some ribosomes are on the
surface of long membrane networks
called endoplasmic reticula, while others
are free ribosomes. Assembly of
proteins takes place at the site of the
ribosomes.
• Protein synthesis begins as ribosomes
move along the messenger RNA strand
and attach transfer RNA (tRNA)
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 CYTOGENETICS – Molecular Basis of Inheritance
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anticodons (each with 3 bases) to triplets
of complementary bases on the mRNA.
Each transfer RNA attracts and brings a
specific amino acid along with it. As a
ribosome translates (or activates) the
messenger RNA code, a protein chain is
assembled, one amino acid at a time.
Each kind of amino acid has a particular
codon that specifies it.
o A codon is a sequence of three
nucleotide components
chemically bound together
(illustrated below).
• As mentioned earlier, every nucleotide
consists of a sugar, a phosphate, and a
base. Codons differ in terms of the
sequence of their three bases. For
example, the sequence CAG (cytosine-
adenine-guanine) is a code for the amino
acid glutamine. This genetic code
permits 64 different codons because
each of the 3 nucleotides can have 1 of
the 4 bases (4 X 4 X 4 = 64). Because
there are many fewer than 64 amino
acids, the code system has built in
redundancy--most amino acids can be
attracted by transfer RNA having several
different base triplet combinations. In
other words, some codons are
functionally equivalent. For instance,
asparagine is specified with the mRNA
codon sequence AAU (adenine-adenine-
uracil). However, AAC (adenine-
adenine-cytosine) also works.
MICRO RNA
• Recent research has shown that at least
200-255 of our genes code for microRNA
(miRNA) molecules instead. They are
small RNA molecules consisting of only
around 20-25 base units. They perform
important functions like enzymes in
MOLECULAR BASIS OF INHERITANCE
regulating chemical reactions in our cells,
especially in the embryonic stage at the
beginning of life. It is thought that at least
1/3 of human genes are controlled in
some way by micro-RNA molecules.
III. DNA REPLICATION
● DNA replication is the process by which
DNA makes a copy of itself during cell
division.
● The first step in DNA replication is to
‘unzip’ the double helix structure of the
DNA molecule. This is carried out by an
enzyme called helicase which breaks
the hydrogen bonds holding the
complementary bases of DNA together
(A with T, C with G). The separation of
the two single strands of DNA creates a
‘Y’ shape called a replication ‘fork’. The
two separated strands will act as
templates for making the new strands of
DNA.
● One of the strands is oriented in the 3’ to
5’ direction (towards the replication fork),
this is the leading strand. The other
strand is oriented in the 5’ to 3’ direction
(away from the replication fork), this is
the lagging strand. As a result of their
different orientations, the two strands are
replicated differently:
○ Leading Strand:
■ A short piece of RNA
called a primer
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(produced by an enzyme
called primase) comes
along and binds to the
end of the leading
strand. The primer acts
as the starting point for
DNA synthesis.
■ DNA polymerase binds
to the leading strand and
then ‘walks’ along it,
adding new
complementary
nucleotide bases (A, C,
G and T) to the strand of
DNA in the 5’ to 3’
direction.
■ This sort of replication is
called continuous.
○ Lagging strand:
■ Numerous RNA primers
are made by the primase
enzyme and bind at
various points along the
lagging strand.
■ Chunks of DNA, called
Okazaki fragments, are
then added to the
lagging strand also in
the 5’ to 3’ direction.
■ This type of replication is
called discontinuous
as the Okazaki
fragments will need to
be joined up later.
• Once all of the bases are matched up (A
with T, C with G), an enzyme called
exonuclease strips away the primer(s).
The gaps where the primer(s) are then
filled by yet more complementary
nucleotides.
• The new strand is proofread to make
sure there are no mistakes in the new
DNA sequence.
• Finally, an enzyme called DNA ligase
seals up the sequence of DNA into two
continuous double strands.
• The result of DNA replication is two DNA
molecules consisting of one new and one
old chain of nucleotides. Therefore, DNA
replication is described as semi-
conservative, half of the chain is part
of the original DNA molecule, half is
brand new.
o Following replication, the new
DNA automatically winds up into
a double helix.
THE THREE MODELS FOR DNA
REPLICATION
• There were three models for how
organisms might replicate their DNA:
semi-conservative, conservative, and
dispersive.
i. Semi-conservative Replication
o In this model, the two strands of
DNA unwind from each other,
and each act as a template for
synthesis of a new,
complementary strand. This
results in two DNA molecules
with one original strand and one
new strand.
ii. Conservative Replication
o In this model, DNA replication
results in one molecule that
consists of both original DNA
strands (identical to the original
DNA molecule) and another
molecule that consists of two
new strands (with exactly the
same sequences as the original
molecule).
iii. Dispersive Replication
o In the dispersive model, DNA
replication results in two DNA
molecules that are mixtures, or
“hybrids,” of parental and
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 CYTOGENETICS – Molecular Basis of Inheritance
BS Public Health 2B
Mylene C. Danao
daughter DNA. In this model,
each individual strand is a
patchwork of original and new
DNA
IV. GENE EXPRESSION
● Gene expression is the process by which
the instructions in our DNA are converted
into a functional product, such as a
protein.
● Gene expression is a tightly regulated
process that allows a cell to respond to
its changing environment.
● It acts as both an on/off switch to control
when proteins are made and a volume
control that increases or decreases the
number of proteins made.
● There are two key steps involved in
making a protein, transcription, and
translation.
TRANSCRIPTION
● Transcription is when the DNA in a gene
is copied to produce an RNA transcript
called messenger RNA (mRNA).
● This is carried out by an enzyme called
RNA polymerase which uses available
bases from the nucleus of the cell to form
the mRNA.
○ RNA is a chemical similar in
structure and properties to DNA,
but it only has a single strand of
bases and instead of the base
thymine (T), RNA has a base
called uracil (U).
How Is Gene Expression Regulated?
● Introns
○ intervening sequences are
called introns, and they are
removed before the mature
mRNA leaves the nucleus.
● Exons
○ The remaining regions of the
transcript, which include the
protein-coding regions, are
called exons, and they are
spliced together to produce the
mature mRNA.
How Do Different Cells Express the Genes They
Need?
● Promoter sequence
○ Normally, transcription begins
when an RNA polymerase binds
to a so-called promoter
sequence on the DNA molecule.
○ This sequence is almost always
located just upstream from the
starting point for transcription
(the 5' end of the DNA), though it
can be located downstream of
the mRNA (3' end).
● Enhancer Sequences
○ also play an important part in
transcription by providing
binding sites for regulatory
proteins that affect RNA
polymerase activity. Binding of
regulatory proteins to an
enhancer sequence causes a
shift in chromatin structure that
either promotes or inhibits RNA
polymerase and transcription
factor binding. A more open
chromatin structure is
associated with active gene
transcription. In contrast, a more
compact chromatin structure is
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 CYTOGENETICS – Molecular Basis of Inheritance
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associated with transcriptional
inactivity.
TRANSLATION
● Translation occurs after the messenger
RNA (mRNA) has carried the transcribed
‘message’ from the DNA to protein-
making factories in the cell, called
ribosomes.
● The message carried by the mRNA is
read by a carrier molecule called
transfer RNA (tRNA).
● The mRNA reads three letters (a codon)
at a time. Each codon specifies a
particular amino acid. For example, the
three bases ‘GGU’ code for an amino
acid called glycine.
● As there are only 20 amino acids but 64
potential combinations of codons, more
than one codon can code for the same
amino acid. For example, the codons
‘GGU’ and ‘GGC’ both code for glycine.
● Each amino acid is attached specifically
to its own tRNA molecule. When the
mRNA sequence is read, each tRNA
molecule delivers its amino acid to the
ribosome and binds temporarily to the
corresponding codon on the mRNA
molecule. Once the tRNA is bound, it
releases its amino acid, and the adjacent
amino acids all join together into a long
chain called a polypeptide. This process
continues until a protein is formed.
● Proteins carry out most of the active
functions of a cell.
How Is Gene Expression Increased or Decreased
in Response to Environmental Change?
Two types of Protein
● Activator Proteins
○ bind to regulatory sites on DNA
nearby to promoter regions that
act as on/off switches. This
binding facilitates RNA
polymerase activity and
transcription of nearby genes.
● Repressor Proteins
○ bind to negative regulatory
proteins called repressors, which
in turn bind to regulatory sites in
the DNA that effectively block
RNA polymerase binding.
TERMINOLOGIES
i. 5′ Capping
o Capping describes the addition
of a methylated guanine cap to
the 5′ end of mRNA.
o Its presence is vital for the
recognition of the molecule by
ribosomes, and to protect the
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 CYTOGENETICS – Molecular Basis of Inheritance
BS Public Health 2B
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immature molecule from ▪ Small interfering RNA (siRNA)

degradation by RNAases. o silencing RNA and short
interfering RNA
ii. Polyadenylation ▪ MicroRNA (miRNA)
o Polyadenylation describes the o help control gene expression
addition of a poly(A) tail to the 3′ ▪ Piwi-interacting RNA (piRNA)
end of mRNA. The poly(A) tail o have a central role in animal
consists of multiple molecules of gametogenesis and fertility,
adenosine monophosphate. This silencing transposons, fighting
helps to stabilize RNA, which is viruses, and regulating
necessary as RNA is much more endogenous genes
unstable than DNA. ▪ Long non-coding RNA (lncRNA)
o play important roles in epigenetic
iii. Splicing regulation
o Splicing allows the genetic
sequence of a single pre-mRNA VI. EPIGENETICS
to code for many different • Epigenetics is the study of how your
proteins, conserving genetic behaviors and environment can cause
material. changes that affect the way your genes
o This process is sequence- work.
dependent and occurs within the • Unlike genetic changes, epigenetic
transcript. changes are reversible and do not
V. SMALL RNA MOLECULES change your DNA sequence, but they
can change how your body reads a DNA
• RNA was the first genetic material. sequence.
• Normally single-stranded • Epigenetic changes affect gene
• It contains uracil instead of thymine expression in different ways.

TYPES OF RNA EPIGENOME

1. mRNA (messenger RNA) acts as the • Whether a gene is copied for protein
template for transcription. synthesis and what the product of that
2. tRNA (transfer RNA) carries amino copy becomes is largely determined by
acids and reads the genetic code.
signals from proteins acting as markers
3. rRNA (ribosomal RNA) plays a
structural and catalytic role during and switches along the DNA double helix
translation. structure. This chemical signaling
system, referred to as the epigenome, is
NON-CODING RNA (ncRNA) very likely as important as the DNA itself
• RNA molecule that is not translated into in determining the phenotype of
a protein. individuals. It is becoming increasingly
clear that epigenetic signals can be
Regulatory ncRNA
▪ Small nuclear RNA (snRNA) altered by the environment. This partly
o components of the spliceosome explains why monozygotic twins
that catalyze the splicing of pre- progressively become different from one
mRNA another as they grow older despite the
▪ Small nucleolar RNA (snoRNA) fact that they are genetically identical.
o primarily guide chemical
• Epigenetic changes can be passed on to
modifications
future generations because epigenome

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 CYTOGENETICS – Molecular Basis of Inheritance
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Mylene C. Danao
proteins are inherited along with DNA in
chromosomes from parents.
• Unlike mutations in DNA sequences,
however, epigenetic alterations
potentially can be reversible. For
example, if a change in an epigenetic
protein causes a disease, it could be
possible to alter that protein and bring
about a cure.
o The effects of changes in an
individual's epigenome can be
far reaching. Not only can they
affect physical appearance and
health, but they can also alter
behavior. For instance, the
babies of rat mothers who are
unusually nurturing are likely to
have altered expressions of the
genes involved with stress
responses. These changes allow
them to handle stress better as
adults. It is thought that a similar
connection occurs in humans.
Likewise, some researchers
have suggested that children of
parents who were severely
undernourished at the time of
conception have a greater
chance of developing
Schizophrenia. The assumption
is that famine conditions resulted
in epigenome alterations
responsible for this severe
mental disorder in future
children.
• When sperm cells enter an egg at
conception, they bring along with them
substantial amounts of paternal RNA and
epigenetic proteins which apparently
play an important role in the development
of embryos.
TYPES OF EPIGENETIC CHANGES
DNA methylation
• DNA methylation works by adding a
chemical group to DNA. Typically, this
group is added to specific places on the
DNA, where it blocks the proteins that
attach to DNA to “read” the gene. This
chemical group can be removed through
a process called demethylation.
Typically, methylation turns genes
“off” and demethylation turns genes
“on.”
Histone Modification
• DNA wraps around proteins called
histones. When histones are tightly
packed together, proteins that ‘read’ the
gene cannot access the DNA as easily,
so the gene is turned “off.” When
histones are loosely packed, more DNA
is exposed or not wrapped around a
histone and can be accessed by proteins
that ‘read’ the gene, so the gene is turned
“on.” Chemical groups can be added or
removed from histones to make the
histones more tightly or loosely packed,
turning genes “off” or “on.”
Non-coding RNA
• DNA is used as instructions for making
coding and non-coding RNA. Coding
RNA is used to make proteins. Non-
coding RNA helps control gene
expression by attaching to coding RNA,
along with certain proteins, to break
down the coding RNA so that it cannot be
used to make proteins. Non-coding RNA
may also recruit proteins to modify
histones to turn genes “on” or “off.”
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