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Genetics
Wilfredo B. Barrera, Jr., LPT, M.Sc.
Department of Mathematics and Natural Sciences
Southern Luzon State University
REVIEWERS
Su Latt Phyu, Ph.D.
Department of Plant Breeding, Physiology and Ecology
Yezin Agricultural University
Sonali Bej, Ph.D. Jed Frank Marqueses, M.A.
Crop Improvement Division
Department of Mathematics and Natural Sciences
Indian Institute of Rice Research Southern Luzon State University
Module 2
Lesson 5: Replication and Transcription 1
The Structure of Nucleic Acid
The Structure of DNA
DNA as the Genetic Material
Level of Organization of DNA
Replication of the Genetic Material
RNA as the Genetic Material
Transcription: DNA to RNA
5 Replication &
organic base (Figure 5.1). In our example, the
phosphate residue is bonded to the carbon in
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Module 2 - Molecular Genetics Lesson 5 - Replication & Transcription
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Module 2 - Molecular Genetics Lesson 5 - Replication & Transcription
One end of the strand is terminated with a together by especially strong hydrogen
phosphate group that is attached to a 5’ bonding between specific pairs of nitrogenous
carbon; we call that end of the strand the 5’ bases, 10 base pairs per helix turn and
terminus. The other end of the strand is nitrogenous bases stacked with above the
terminated with a hydroxyl group (OH) that is other. Adenine (A) forms two hydrogen bonds
attached to a 5’ carbon; we call that end of with thymine (T) bonds while guanine (G)
the strand the 3’ terminus. bonds with cytosine (C) by three hydrogen
bonds. The reason for the strong hydrogen
The structure of DNA bonding between these organic base pairs is
that they have complementary shapes (Figure
Genetic information, the information used to
5.5). The hydrogen bonding between these
make the various proteins and thereby
pairs of organic bases is referred to as base
enabling life, is contained in the sequence of
pairing or complementary base pairing.
nucleotides in DNA. The sequence of
nucleotides in DNA is referred to as the
primary structure of DNA.
DNA is composed of a combination of
deoxyribonucleotides that contain adenine,
guanine, thymine, or cytosine nitrogenous
bases. Nucleotides are given a one-letter
abbreviation based on the first letter in the
name of their nitrogenous base. In order to
describe the primary structure of a DNA
strand, it is customary to list the one-letter
code abbreviation of nucleotides in the order
that the nucleotide residues appear in the
strand e.g. 5’TGCA3’.
X-ray diffraction studies by Rosalind
Franklin (1950–1953) showed that DNA has
3.4-angstrom periodicity; a characteristic of
the helical structure. It was proposed by
Watson and Crick in 1953 that DNA exists as a
double helix, which is made from two Figure 5.4 Double helical structure of the DNA and its
polynucleotide strands (Figure 5.4). The two complemenrary base pairing.
DNA strands of a DNA double helix have their
5’ terminuses and 3’ terminuses with opposite In a double helix DNA, base composition
orientations. We call this opposing orientation studies quantitatively demonstrated that the
of the DNA strands as an antiparallel amount of adenine is equal to the amount of
arrangement. The two DNA strands are held thymine. Similarly, the amount of guanine is
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Module 2 - Molecular Genetics Lesson 5 - Replication & Transcription
equal to the amount of cytosine. This known proteins have 20 different amino acids.
as Chargaff’s rule thus, the sum of purines (A + Recently, two additional amino acids such as
G) is equal to the sum of pyrimidines (C + T). selenocysteine and pyrrolysine were
However, the percentage of (G + C) is not discovered bringing the amino acids to 22.
necessarily equal to the percentage of (A + T). The major characteristics needed for a
molecule to serve as genetic material include
storage of tremendous genetic information,
accurate duplication and transfer of
information, stable (resistant to frequent
changes), capable of mutation, and dynamic
and flexible enough to respond to other
molecules or changing environment.
In eukaryotes, indirect and direct
evidence supports the concept that DNA is the
genetic material. There is a close correlation
between gametes and diploids in the amount
of DNA and the number of chromosome sets
while this is not observed in proteins.
Molecule serving as genetic material is
expected to absorb at a mutagenic
wavelength (260 nm). DNA absorbs UV at 260
nm while protein absorbs UV at 280 nm.
Recombinant technology provides direct
evidence that DNA is the genetic material.
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Module 2 - Molecular Genetics Lesson 5 - Replication & Transcription
In eukaryotic organisms such as plants, Depending on the cell life cycle, chromatin can
animals, and fungi, the DNA double helix coils undergo further coiling. For example, before a
into a more compact structure (Figure 5.7). cell divides chromatin is coiled into its tightest,
most compact shape, which is called a
chromosome.
the parent strands is used as a template for strands of the double helix are antiparallel and
the formation of a new daughter strand. DNA polymerase III only synthesizes 5ʹ to 3ʹ
Replication starts at the ORI site, proteins direction. As a result, one strand such as the
called helicases unwind and then open leading strand is continuously synthesized
sections of the double helices by disrupting while the other strand such as the lagging
the hydrogen bonds between base pairs thus strand is discontinuously synthesized.
creating a replication fork.
Figure 5.9 Overview of the DNA replication. Source: Klug et al. (2017).
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Module 2 - Molecular Genetics Lesson 5 - Replication & Transcription
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Module 2 - Molecular Genetics Lesson 5 - Replication & Transcription
helix of the gene. Next, RNA polymerase Eukaryotic mRNAs require processing
moves along one strand of the gene while or transcriptional modifications to produce
catalyzing the addition of free ribonucleotides mature mRNAs. This includes the addition of
that are complementary to the DNA template, 5' cap or capping, the addition of 3' tail or
to the 3’ end of a growing mRNA strand. tailing and excision of introns or splicing. The
When the RNA polymerase reaches a 5' cap protects the mRNA from nuclease
nucleotide sequence in the gene, called the attack and may be involved in transport of
termination site, the mRNA strand is released. transcript across the nucleus while the 3' poly-
In bacteria, termination transcribed into RNA A tail aids in the transport to cytoplasm.
causes newly formed transcript to fold back Basically, the mechanism of splicing involves
on itself e.g. hairpin. At times, termination the cutting of intron through its end by the
depends on the rho (ρ) termination factor. endonuclease.
free ribonucleotides
promoter
In bacteria during transcription, large The terminal ends of the adjacent exons
polycistronic mRNA is produced which joined by ligase to form the mature mRNA.
encodes more than one protein. Genes in This results in a mature mRNA smaller than
bacteria called cistrons. On the other hand, initial RNA. Alternative splicing produces
eukaryotes have monocistronic mRNAs. related protein from a single gene thus,
Transcription in eukaryotes differs from increasing the number of products derived
prokaryotic transcription in several ways. It from a single genome.
occurs within the nucleus unlike in
prokaryotes which happens in the cytoplasm.
After transcription, mRNA must leave the
nucleus for translation.
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Module 2 - Molecular Genetics Lesson 5 - Replication & Transcription
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Module 2 - Molecular Genetics Lesson 6 - Gene Expression
6 Gene
one-enzyme hypothesis which was changed to
one-gene: one-polypeptide chain hypothesis.
Expression Two factors modified the hypothesis because
(1) nearly all enzymes are proteins but not all
proteins are enzymes; and (2) proteins have a
In this lesson, you are going to learn about the subunit structure with two or more
chemical basis of heredity. At the end of the polypeptide chains. However, there should be
lesson you should be able to: a functional protein for a gene to be
1. Understand and explain the expressed, therefore, one-gene: one-
mechanism of translation. functional protein is more appropriate.
2. Explain what the genetic code is and In translation, the sequence of
identify its major characteristics. nucleotides in mRNA is converted (translated)
3. Use the genetic code table to predict to a sequence of amino acid residues in a
the sequence of amino acids in the polypeptide. The genetic code is based on
polypeptide that would be produced in three-nucleotide sequences called codons. A
translation. codon directs the addition of a specific amino
4. Define the term gene regulation and acid residue to a polypeptide that is being
compare and contrast the basic formed.
principles of gene regulation in The genetic code is degenerate—a
eukaryotes and prokaryotes. given amino acid can be specified by more
than one triplet codon. The start and stop
signals are triplets that initiate and terminate
Translation: protein synthesis translation. Once translation begins, codons
The information contained in the sequence of are read with no break i.e. commaless. Any
DNA nucleotides is used to generate proteins. single ribonucleotide within mRNA is part of
This process is central to the existence of all one triplet thus, nonoverlapping.
known life forms because proteins are critical Many amino acids are specified by
in directing and controlling cell growth and more than one codon. Figure 6.1 shows the
function, and in regulating the metabolism of codons that specify the 20 amino acids. Only
an organism. tryptophan and methionine are encoded by a
The process of making proteins from single codon. The genetic code shows order—
the information in DNA is called protein chemically similar amino acids share one or
synthesis or gene expression. The mRNA two middle bases in triplets encoding them.
produced in transcription contains the Wobble hypothesis states that codons that
information from a gene that is required to specify the same amino acid differ at third
produce a protein. Therefore, there is base position. Thus, the initial two
colinearity between the gene and the protein ribonucleotides of triplet codes are often
that will be produced. This led to one-gene: more critical than the third.
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Module 2 - Molecular Genetics Lesson 6 - Gene Expression
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Module 2 - Molecular Genetics Lesson 6 - Gene Expression
messenger RNA
(mRNA)
several cycles of
amino acid addition
(c)
Figure 6.2 Overview of translation (a) initiation; (b) elongation; and (c) termination.
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Module 2 - Molecular Genetics Lesson 6 - Gene Expression
lac operon
DNA
promoter (P site)
Figure 6.3 The lac operon showing the regulatory gene, promoter, operator and structural genes.
The lac operon consists of three The mRNAs from the lac operon genes are
protein-coding genes plus associated control translated to the three proteins: β-
regions that code for proteins involved in the galactosidase, β-galactoside permease, and β-
metabolism or transport of lactose. The three galactoside transacetylase. β-galactosidase is
genes of the lac operon are called lacZ, lacY, an enzyme involved in lactose metabolism. β-
and lacA. The lac operon is preceded by a lac galactoside permease is a transmembrane
regulator, lacI gene. The lacI gene produces an protein that transports lactose into cells. β-
active repressor protein that binds to a galactoside transacetylase is an enzyme
segment of DNA called an operator site. thought to be involved in the breakdown of
When the repressor protein is bound some nonlactose species that are transported
to the operator site, RNA polymerase is into cells by permease. The presence of
blocked from moving along the lac operon to lactose and the subsequent presence of
transcribe the three structural genes allolactose upregulate the genes of the lac
therefore, the operon is off (Figure 6.4a). In operon. Whenever lactose is no longer
the presence of glucose, lactose is not needed available, the concentration of allolactose will
as an energy source and almost zero lactose is decrease and then active regulator proteins
allowed into the bacterial cell, therefore it is become available again to downregulate the
not necessary for the genes of the lac operon lac operon.
to be expressed. Let us consider the scenario Another regulatory mechanism of the
in which lactose is present in the absence of lac operon is called the catabolite
glucose. Whenever lactose is present, some of repression—an example of positive regulation.
it is converted to a compound called RNA polymerase does not bind efficiently to
allolactose which binds to and thereby the promoter unless the catabolite activating
inactivate the repressor protein. The inactive protein (CAP) is present. CAP binds to the 5’
repressor protein cannot bind to the operator end of the promoter at the CAP binding site.
site thus, allowing RNA polymerase to move When the CAP is bound, the binding of RNA
along the lac operon and transcribe the lac polymerase is enhanced. The presence of
operon genes (Figure 6.4b). glucose determines whether cAMP levels are
high or low. If glucose is present, the cell does
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Module 2 - Molecular Genetics Lesson 6 - Gene Expression
not need to metabolize lactose for energy. operon, the operator and promoter are cis-
The presence of glucose results in low levels acting because they function just upstream of
of cAMP. Without cAMP, the transcription of the lac structural genes.
the lac operon is inefficient.
operator (O site)
(b)
RNA polymerase
Transcription
Translation
Figure 6.4 The lac operon: (a) no transcription of the structural genes; and (b) there is transcription of
structural genes.
DNA sequences can affect other In contrast, the lacI gene can act as trans
sequences either next to them on the same producing a diffusible repressor that can
chromosome e.g. at a cis-acting site, or at a travel to a sequence a great distance away.
relatively distant site or sites on different Several mutants were discovered and
chromosome (trans-acting site). In the lac developed in the laboratory to understand
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Module 2 - Molecular Genetics Lesson 6 - Gene Expression
how genes are regulated in the lac operon. In The repressor is by a regulatory gene, trpR
I- repressor mutants, the lacI gene does not and is inactive by default. Therefore, the five
produce a functional repressor protein and structural genes are transcribed. These
RNA polymerase is never inhibited therefore, structural genes codes for polypeptides
the lac operon is always transcribed. Similarly, subunits that make up enzymes for the
the operon is always on in I-d mutant repressor synthesis of tryptophan. When tryptophan is
gene because it cannot bind to the operator present, it binds to the trp repressor protein,
sequence. In Is super-repressed mutation, the which turns the operon off (Figure 6.6). The
mutant repressor gene cannot bind inducer. repressor is active only in the presence of its
Thus, the repressor protein binds very tightly corepressor tryptophan thus, the trp operon is
to the operator and does not bind to lactose. turned off (repressed) if tryptophan levels are
Therefore, the lac operon is always repressed, high.
even when lactose is present. For the
operator mutants Oc the gene to which it is promoter
attached is affected. The mutants are said to
act in cis or to be cis-dominant. The operator
X
DNA
is mutated so that the repressor can no longer
no mRNA
bind to it. Therefore, the structural genes are mRNA made
RNA polymerase
always transcribed. Conversely, in cis-acting Os blocked
mutants, the operator binds so tightly to the protein
repressor that it never gets released active
repressor
Therefore, the operon is always repressed.
tryptophan
An example of repressible operon is (corepressor)
the tryptophan (trp) operon. It is usually on
Figure 6.6 The tryptophan operon showing no
(Figure 6.5) and the binding of a repressor to transcription of the structural genes.
the operator shuts off transcription. Modified from Reece et al. (2011).
promoter
promoter
protein E D C B A
inactive repressor
Figure 6.5 The tryptophan operon showing the transcription of the structural genes. Modified from
Reece et al. (2011).
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Module 2 - Molecular Genetics Lesson 6 - Gene Expression
Mutant
Supplement Gene regulation in eukaryote
A B C
1 + + + Gene regulation in eukaryotes is mainly for
2 - + + the regulation of genetic program that
3 - - + underlies embryological development and
tissue differentiation and response to abiotic
Let us use the data in Table 6.1 to and biotic stress.
determine the biochemical pathway. The later Specific regulation of expression can
in the pathway a mutant is blocked, the fewer be facilitated by hormones or can be
nutritional supplements must be added to explained by the Davidson-Britten model. The
allow growth. In the data given, the nutritional model explains that the eukaryotic genome
supplements are listed in the order in which does not contain simple operons like
they appear in the pathway. Thus, initially, the prokaryotes. Instead, there is individual
pathway is: regulation of related genes in the
chromosomes since chromatin contains too
Compound A Compound B Compound C
few proteins to function as a repressor.
Another example of gene regulation in
Now, we need to use the mutants to
eukaryotes is by hormones e.g. steroid pass
help define the biochemical pathway. Mutant
freely through the cell membrane. The
1 will grow on all compounds. Therefore, the
hormone binds to receptors in the cytoplasm
defective enzyme in mutant 1 must act to
forming the hormone-receptor (H-R’) complex
convert a precursor molecule to compound A.
which can cross the nuclear membrane. This
Mutant 2 will on all compounds except
complex binds to a short stretch of DNA called
compound A. Thus, the defective enzyme
a response element (regulatory sequence)
must act on the conversion of compound A to
near a gene. The binding modifies the
compound B. Lastly, mutant 3 will grow only in
expression of the gene.
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Module 2 - Molecular Genetics Lesson 6 - Gene Expression
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Module 2 - Molecular Genetics Lesson 7 - Developmental Genetics
Developmental
regulation and cell differentiation which deals
7
with the coordinated expression of genes
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Module 2 - Molecular Genetics Lesson 7 - Developmental Genetics
of gene expression turns undifferentiated cells There are two different sets of genes
into differentiated cells and role of cell to cell that control the embryonic development of
communication in development. Drosophila such as maternal-effect genes and
zygotic genes. The mRNA and proteins
Embryonic development of D. produced by the maternal effect genes are
melanogaster deposited in the egg cytoplasm. The products
are distributed in gradient or concentrated in
The development of Drosophila has a ten-day
specific regions of the cell. Maternal effect
cycle and divided into five distinct phases
genes also encode transcription factors and
before the adult stage such as embryo, three
proteins that regulate gene expression by
larval stages, pupal stage, and adult stage.
activation or repression of the zygotic genome.
The early development of Drosophila
Gradients of maternal-effect gene products
starts when the egg is fertilized. After the
along the anterior-posterior axis of embryo
tenth division, the nuclei migrate to the
regulate expression of segmentation genes
periphery of the egg and the germ cells form.
(gap, pair-rule, and segment polarity genes)
Nuclei are enclosed in a membrane called
and homeotic selector (Hox) genes, which
blastoderm and segmentation pattern is
specify the fate of each segment.
established (Figure 7.1).
Figure 7.1 The early embryonic developmental stages of D. melanogaster. Source: Klug et al. (2017).
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Module 2 - Molecular Genetics Lesson 7 - Developmental Genetics
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Module 2 - Molecular Genetics Lesson 7 - Developmental Genetics
Gap (Krüppel)
Pair-rule (even-skipped)
Figure 7.3 Example of some mutants for the segmentation genes. Shown here are the effect of
mutation relative to the normal phenotype and the corresponding time of expression.
Source: Russell (2010).
Developmental programs in
plants and animals
The developmental patterns evolved
independently in plants and animals.
Multicellular development in animals and
plants follows a body plan or pattern. The
term pattern refers to the spatial arrangement
of different regions of the body. At the cellular
level, the body pattern is due to the
arrangement of cells and their specialization.
Plant pattern formation is studied
using a model organism Arabidopsis thaliana
while there are several model organisms to
study development in animals like D.
melanogaster, Danio rerio, and C. elegans. In
animals, development involves movement of
cells and tissues and the growth is limited to
Figure 7.4 The antennapedia and bithorax embryonic and juvenile periods. On the other
complexes in Drosophila and their hand, in plants, there is a presence of
corresponding genes and segment perpetual embryonic tissues called apical
position. Source: Klug et al. (2017).
meristems that are continuously growing.
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Module 2 - Molecular Genetics Lesson 7 - Developmental Genetics
Therefore, growth is not limited to embryonic Figure 7.6 shows the nuclear transplantation
and juvenile periods. The difference in experiment using two different types of
developmental programs among cells in animal cells from embryo and frog intestine.
multicellular organisms is due to different The cells from the frog embryo are less
patterns of gene expression and not from the differentiated while the intestinal cells are
differences in the genome of the cells. All cells fully differentiated. The nucleus from each
in an individual have the same genes (genomic type of cell was transplanted to enucleated
equivalence). In plants, differentiated somatic frog egg cell and observed if tadpoles will
cells can give rise to whole new plant (Figure develop. As expected, most tadpoles
7.5) while animal cells, will not always divide developed on the enucleated cell where the
in culture unless cell division is induced. In source of the nucleus is the frog embryo.
other words, many plant cells are totipotent In animals, specifically the bilaterians,
i.e. have the ability to differentiate into every researchers have discovered that
cell type and to produce an entire individual. development generally proceeds in four
Nuclear transplantation experiments overlapping stages such as (1) formation of
showed that animal cells if grown in culture, body axes - the first phase of pattern
do not have the capacity to develop into a development; (2) segmentation of the body -
whole new individual. However, once the body is subdivided into segments.
differentiated, it can be induced to
dedifferentiate into other types of cells.
Root of
carrot plant
Transverse
section of
root
“Embryoid”
(somatic embryo)
2-mg develops from
fragments cultured cells
Fragments cultured
in nutrient medium
Plantlets cultured on agar medium
and later transferred to soil
Figure 7.5 Tissue culture technology to show the genomic equivalence in plants. Any type of
plants can be grown to a whole new plant provided that suitable growing conditions
are provided. Source: Reece et al. (2011).
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Module 2 - Molecular Genetics Lesson 7 - Developmental Genetics
Fully differentiated
Less differentiated
(intestinal cell)
cell
Figure 7.6 Nuclear transplantation experiment to show the genomic equivalence in animals. Source:
Reece et al. (2011).
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Module 2 - Molecular Genetics Lesson 7 - Developmental Genetics
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Module 2 - Molecular Genetics Lesson 7 - Developmental Genetics
Unfertilized egg
backup, so any epigenetic change has a
greater impact on gene expression. Improper
Sperm Nucleus imprinting leads to developmental defects
such as cancer or syndromes e.g. Angelman
Fertilization Molecules of two syndrome (1 in 10,000) - abnormally silenced
different cytoplasmic gene on Chromosome 15 from the mother.
determinants
Other organisms like insects, mammals,
Zygote
(fertilized egg) flowering plants demonstrated imprinting. In
animals, the formation of hybrids with
Mitotic cell division
different appearance has been attributed to
genomic imprinting. For example, lions and
Two-celled embryo
tigers can produce hybrid offspring in captivity
and the offspring is different depending on
Figure 7.9 Cytolasmic determinants in egg. whether the tiger or the lion is the mother or
Source: Reece et al. (2011). father. A cross between male lion x female
tiger produces a liger (largest of big cats) while
As the zygote divides by mitosis, cells a cross between male tiger x female lion
contain different cytoplasmic determinants, produces a tigon (about the same size as
which lead to different gene expression. The parents). Another example is a cross between
other important source of developmental a horse x donkey which can produce either a
information is the environment around the mule or a hinny.
cell, especially signals from nearby embryonic
cells. In the process called induction, signal
molecules from embryonic cells cause Learning Check!
transcriptional changes in nearby target cells.
1. Genetic mechanisms underlying gene
Thus, interactions between cells induce
silencing involve DNA sequence alterations,
differentiation of specialized cell type.
while epigenetic mechanisms do not.
What are three epigenetic mechanisms
Genomic imprinting
that can lead to gene silencing? What
For most genes, we inherit two functional features do they share in common, and
copies each from the maternal and paternal how are they different?
origin. Imprinted genes are different—
depending on the gene, either the maternal 2. DNA, histones, promoter-binding proteins,
copy or paternal copy is epigenetically and enhancer-binding proteins are mixed
silenced which occurs during egg and sperm together in the following orders:
formation. a. afirst histones and DNA, then
The environment has a stronger effect promoter-binding proteins
on imprinted genes—only one active copy, no
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Module 2 - Molecular Genetics Lesson 7 - Developmental Genetics
b. first histones and promoter-binding the host, it will form eye, brain, and other
proteins, then DNA material characteristic of the head region.
c. first DNA and promoter-binding If the tissue is transplanted to other
proteins, then histones regions of the host, it will form organs and
d. first histones, promoter-binding tissues characteristic of those regions in
proteins, and enhancer-binding normal development. In contrast, in Figure
proteins, then DNA b, if tissue destined to be an eye is excised
from a neurula and transplanted into an
For each case, state whether transcription can
older embryo host to exactly the same
occur. Explain your answers.
places as used for the blastula or gastrula
3. There are several distinct genes that code transplants, in every case the transplanted
for - and -like globin polypeptides. These tissue differentiates into an eye. Explain
α-, β-, γ-, δ-, ε-, ζ–globin genes are these results.
transcriptionally active at specific stages of
development, resulting in the synthesis of
polypeptides that are assembled in
specific combinations to form different
types of hemoglobin. Fill in the following
table, indicating whether the globin gene
in question is sensitive (S) or resistant (R)
to DNase I digestion at each of the
developmental stages listed.
Tissue
Globin
Embryonic Fetal Adult bone
gene
yolk sac spleen marrow
α
β
γ
δ
ε
ζ
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Module 2 - Molecular Genetics Lesson 7 - Developmental Genetics
References
Brooker, Robert J. (2012). Genetics : Analysis
& Principles 4th edition. The McGraw-Hill
Companies, Inc.,
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