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Chapter 19
The Organization and Control of Eukaryotic Genomes
Things to Know:
1. All those bold-faced words again
2. Figure 19.1: the basics of DNA structure
3. Spend some time thinking about these questions (and their
answers):
a) How does your genome get changed during your
lifetime (pg 359)
b) What controls the expression of eukaryotic genes (pgs
362 – 368) and how does this contrast with gene
regulation in prokaryotes?
c) Whazzzzzup with cancer at the molecular level?
Figure 19.0 Chromatin in a developing salamander ovum
White portion: part of the
chromatin of each sister
chromatid around which
the other chromatin is
arranged.
Red Loops are the actively
transcribed regions
Figure 19.1 Levels of chromatin packing
Figure 19.x1a Chromatin
Figure 19.x1b Chromatin, detail
Repetitive DNA and other noncoding sequences
Prokaryotic DNA
1. Codes for protein, rRNA and tRNA
2. The noncoding regions are regulatory regions such as the
promoters
3. The coding sequence goes from start to finish without
interruption
Repetitive DNA and other noncoding sequences
Eukaryotic DNA
1. 97% DOES NOT code for protein, rRNA and tRNA
2. Some regulatory sequences but most of the DNA is the
introns.
3. Also lots of repetitive DNA, which is noncoding and is
usually not within the genes.
Tandemly Repetitive DNA
Definition: a short sequence that is repeated in a series.
 Text’s example: GTTACGTTAC. . . Etc.
 you could have hundreds of repeats of the GTTAC
 these repeats are usually up to 10 bases long.
 this can be composed of specific bases to give this area a
different density so that you can cut the DNA, centrifuge it
and spin it out.
 originally known as satellite DNA because it was a
“separate” or satellite band from the other DNA that was
centrifuged.
Table 19.1 Types of Repetitive DNA
Tandemly Repetitive DNA
 minisatellite and microsatellite DNA refers to how big the
repeated segments are, 100 – 100,000 bps and 10 – 100
bps respectively.
 the microsatellite DNA can be used in DNA fingerprinting.
Tandemly Repetitive DNA
Genetic Disorders Caused by Tandem Repeats
 Fragile X: triplet (CGG) repeat about 100’s to 1000s of
times (normal is 30); causes different degrees of mental
retardation; the number of repeats increases each
generation; causes the tip of the X chromosome to hang
from the rest of the chromosome
 Huntington’s: CAG repeat; this repeat is translated
producing a protein containing lots of glutamines. The
more repeats, the more severe the disease.
Regular Satellite DNA is at the telomeres and centromeres and may
play a role in the basic structure of DNA.
Interspersed Repetitive DNA
Alu Inserts or elements
 These are repeats but they aren’t one right after another.
 We will find out about some of your Alu inserts in a lab
 Interspersed DNA makes up 20-40% of mammalian
genome
 An Alu insert is 300 bps long.
 An Alu insert may be transcribed but has no known
function yet.
Multigene Families
Multigene Family: a group of identical or very similar genes
 long repeating units since they are genes
 a part of the group may be close or far apart
 Example: genes for rRNA
 there are three of these genes each coding for a different
size rRNA.
 they are transcribed together but there are hundreds of
copies of this transcription unit throughout the
genome.
Figure 19.2 Part of a family of identical genes for ribosomal RNA
Multigene Families (cont’d)
Nonidentical Gene example: genes for hemoglobin
 there are different forms of the alpha genes and different
forms of the beta genes.
 the different versions are transcribed at different times so
they function at different times during mammalian
development.
 fetal Hb is different from adult Hb and has a higher affinity
for oxygen. This is due to the difference in the types of
alpha and beta strands.
Figure 19.3 The evolution of human -globin and -globin gene families
Multigene Families (cont’d)
How do you get a family of similar/identical genes from a single
gene?
 gene duplications occurring over and over again.
 Recombination can produce multiple copies
 Mutations can create different forms of the same gene and
the product still has a similar function.
Some of the mutations produce nonfunctioning products,
and these are called pseudogenes.
Gene Amplification, loss or rearrangement
can alter a cell’s genome
Important Concepts
1. These processes do not occur in gametes therefore are not
passed on to the offspring.
2. They do not contribute to evolution
3. They do occur in your somatic cells and therefore can
change your phenotype through alterations in gene
expression within cells and tissues.
Gene Amplification, (cont’d)
Gene Amplification and Selective Gene Loss
1. At a special stage of develop the number of copies of a
particular gene or gene family can change (increase).
a) This is gene amplification
b) Developing eggs of amphibians will produce bunches of
copies of the gene that makes rRNA so more ribosomes can
be made during early development and hence increase
protein production.
 These extra rRNA genes are then later broken down.
c) Cancer cells may also possess amplified genes that
increase resistance to a drug that is being administered.
Hence, treatment may be “incomplete.”
Gene Amplification, (cont’d)
Rearrangements in the Genome
1. Introduction

Some genes can be shuffled around and have their
location (loci) changed.

This occurs in somatic cells ( not gametes)
2. Transposons and Retrotransposons

Definition: a transposon is simply a segment of DNA
that moves throughout the genome.

It moves into the middle of a coding region of a gene

It therefore interferes with normal gene transcription
Figure 19.4 The effect of a transposon on flower color
The lighter color of this morning glory
flower is due to the placement of a
genetic element, a transposon, into the
gene that codes for the purple flower
color. The production of the purple
color was altered.
Why wasn’t the entire flower
affected?
Gene Amplification, (cont’d)
2. Transposons and Retrotransposons (cont’d)

If the insertion into the gene occurs where transcription is
regulated, this could increase or decrease mRNA
production.

Sometimes the transposon carries a gene. If it inserts
downstream from the promoter, the transposon gene gets
transcribed, mRNA is made, new proteins, new
characteristics.
 Barbara McClintock demonstrated these kind of
mobile genetic elements with corn kernels that are
yellow, reddish, purple, etc.
Figure 19.x2 Transposons in corn
Figure 19.x3 Transposons in corn
Gene Amplification, (cont’d)
2. Transposons and Retrotransposons (cont’d)

To make it even more complicated. . .
Retrotransposons: these are pieces of DNA but they
were made from the mRNA of a transposon.
mRNA
DNA by reverse transcriptase

Alu inserts are retrotransposons (but no rev.
transcriptase)

The enzyme reverse transcriptase catalyzes the reaction
of mRNA to DNA and is part of the genetic code of the
retrotransposon.
Figure 19.5 Retrotransposon movement
Gene Amplification, (cont’d)
3. Immunoglobulin Genes
a) Some of the basics of the immune system
 Antibodies are also called immunoglobulins
 Antibodies are proteins
 Antibodies are made by special cells called B
lymphocytes or just “B cells”
 B cells are a type of white blood cell
 Each B cell can make a different type of antibody and
therefore attack a specific kind of antigen
 An antigen is a foreign “invader”: virus, bacteria,
fungi, protein.
Gene Amplification, (cont’d)
3. Immunoglobulin Genes
b) Antibody Structure
 Two chains held together by disulfide bonds
 Each chain has a constant region (C) or same series
of amino acids
 Then there is a variable (V) region that gives the
antibody its specificity to a particular antigen.
 It’s the variable region that recognizes the specific
antigen that is in your body.
Figure 43.15a,b The structure of a typical antibody molecule
Figure 43.15c Antibody molecule
Figure 43.14 Epitopes (antigenic determinants)
Gene Amplification, (cont’d)
3. Immunoglobulin Genes (cont’d)
c) How are these different antibodies made?
 One set of genes undergoes permanent rearrangement
of its DNA segments when cells differentiate when
you are a embryo.
 This places the antibody genes in different orders.
 As a cell becomes specialized (differentiates) the
antibody genes are moved around from different
DNA regions in the embryonic cell
Figure 19.6 DNA rearrangement in the maturation of an immunoglobulin (antibody) gene
1.
Undifferentiated cell
J is a junction region (?)
1.
Now the gene V3 has
been moved and genes V2
and J are next to an intron.
V2 is a variable region,
this is a sequence of
proteins that gives the Ab
its specificity so it can
bind to specific antigens.
3.
Processing and translation
occur and you have an
antibody with a specific
“end” or variable region
that recognizes V2 type of
antigens.
The Control of Gene Expression
Each cell of a multicellular eukaryote expresses only a small
fraction of its genes.

Continual turning on and off in response to signals from the
environment.

Cellular differentiation requires only certain genes to be
expressed

A typical human cell expresses only 3-5% of its genes at a
given time so something must be regulating this activity.

Control can occur anywhere from the unwinding of the
packed chromatin to translation.
The Control of Gene Expression (cont’d)
Chromatin modifications affect the availability of genes for
transcription
1. Introduction
a) The physical condition (state) of the DNA near the gene
of interest can control its availability for transcription
and thus expression.
i.
The highly condensed heterochromatin is usually not
expressed because the transcription factors can’t
reach those genes.
ii. If a gene is near a nucleosome is it more or less likely
to be transcribed? What about its proximity to the
chromosome scaffolding?
The Control of Gene Expression (cont’d)
Chromatin modifications affect the availability of genes for transcription
2. DNA Methylation
a) What is it?
b) Inactivated X chromosomes such as in Barr bodies are
highly methylated.
c) If you compare the same genes in different tissues, genes
that are being actively transcribed are not methylated.
d) Removing the methyl groups makes the genes active.
e) Methylation is involved in long-term inactivation of
genes during cellular differentiation of embryonic
development.
The Control of Gene Expression (cont’d)
Chromatin modifications affect the availability of genes for transcription
3. Histone Acetylation
a) What is it? The attachment of –COCH3 groups to certain
amino acids of the histones.
b) This acetylation causes the histones to change shape, not
bind to the DNA so tightly and therefore be more
available to transcription factors for transcription.
The Control of Gene Expression (cont’d)
Transcription initiation is controlled by proteins that interact
with DNA and with each other.
Transcription initiation is controlled by proteins that interact with
DNA and with each other.
1. Organization of a Typical Eukaryotic Gene
a) See next slide
b) Presence of introns
c) A transcription initiation complex forms at the promoter
which is upstream from the gene. RNA polymerase is a
part of this and it then begins transcription.
d) Editing, G’cap at the 5’ end and a poly A tail at the 3’
end.
e) Control elements are present: these bind transcription
factors.
Figure 19.8 A eukaryotic gene and its transcript
The Control of Gene Expression (cont’d)
Transcription initiation is controlled by proteins that interact
with DNA and with each other.
2. The Role of Transcription Factors
a) Ts factors recognize TATA boxes
b) These TATA boxes are within the promoter
c) Control Elements increase the efficiency of
transcription. What are control elements?
i.
Enhancers: may be far away from the promoter,
upstream or downstream or within an intron.
ii. DNA bending brings these distant areas with the
enhancers close to the promoter
iii. Interaction of these enhancers with Ts factors forms
the initiation complex on the promoter.
The Control of Gene Expression (cont’d)
Transcription initiation is controlled by proteins that interact
with DNA and with each other.
2. The Role of Transcription Factors
iv. Activator: a complex of Ts factor and enhancer
v. Repressors: this could be DNA methylation
d) Transcription factors. . .
i.
Possesses a DNA binding domain to which it binds
to the DNA
ii. It also possesses a site to bind to another Ts factor
Figure 19.9 A model for enhancer action
The Control of Gene Expression (cont’d)
Transcription initiation is controlled by proteins that interact
with DNA and with each other.
3. Coordinately Controlled Genes
a) This has to do with a bunch of genes that must be
coordinated together to be turned on or off.
i.
In prokaryotes: all related genes are located in an
operon, one right after another. They share the
same promoter.
ii. In eukaryotes, related genes can be scattered all
over the genome, different promoters.
b) There could be a main control element or a collection of
them that get bound by Ts factors at the same time and
thus all these related genes get transcribed
simultaneously.
i.
Steroids turn on different genes at the same time.
The Control of Gene Expression (cont’d)
Post-transcriptional mechanisms play supporting roles in the
control of gene expression.
Post-transcriptional mechanisms play supporting roles in the control
of gene expression
1. Introduction
a) Proteins need to be functional to represent gene
expression
b) RNA processing does not always occur the same way
with the same pre-mRNA transcript.
i.
Alternative RNA-splicing: this means that different
RNA molecules are produced from the same premRNA transcript by changing which segments are
treated as exons and which as introns.
Figure 19.11 Alternative RNA splicing
The Control of Gene Expression (cont’d)
Post-transcriptional mechanisms play supporting roles in the
control of gene expression.
2. Regulation of mRNA Degradation
a) Prokaryotic mRNA is degraded quickly (few minutes).
This affords the bacterium a quick adaptation to
environmental changes.
b) Eukaryotic mRNA lasts hours, days, weeks
c) Degradation begins with the shortening of the poly A tail
and then the G’cap.
d) Nucleases, enzymes that eat up nucleic acids, then digest
the mRNA.
The Control of Gene Expression (cont’d)
Post-transcriptional mechanisms play supporting roles in the
control of gene expression.
3. Control of Translation
a) Stop the beginning so ribosomes can’t bind to the mRNA.
This can be blocked by regulatory proteins that bind to
the 5’ end of the mRNA
i.
These can be temporary blocks so the mRNA is
simply “stored” for later such as in an ovum that
stores bunches of mRNA waiting for fertilization and
then BAM they all become active.
The Control of Gene Expression (cont’d)
Post-transcriptional mechanisms play supporting roles in the
control of gene expression.
3. Control of Translation (cont’d)
b) Global control of translation: all mRNA’s are kept
“silent”
i.
Hemoglobin is made of a Heme or iron containing
group and polypeptides. If the Heme group is in short
supply, the translation of all Hb polypeptides are
turned off.
ii. Egg Cells: mRNA’s are in waiting for fertilization
iii. Plants and algae: mRNA’s are stored during periods
of darkness and then the light triggers translation.
The Control of Gene Expression (cont’d)
Post-transcriptional mechanisms play supporting roles in the
control of gene expression.
4. Protein Processing and Degradation
a) Modifications to the translated proteins can be
inactivated
i.
Sugars are not added so proteins never make it to the
cell’s surface.
ii. Cystic Fibrosis: a chloride ion channel protein never
makes it to the cell membrane and is eventually
degraded.
5. Proteasomes: degrade “tagged for destruction” proteins.
The tag is a molecule called ubiquitin.
Figure 19.12 Degradation of a protein by a proteasome
Figure 19-12x Proteasomes
Figure 19.7 Opportunities for the control of gene expression in eukaryotic cells
Molecular Biology of Cancer
Cancer results from genetic changes that affect the cell cycle
1.
Many genes regulate the cell cycle so any mutation in these genes may
cause cells to lose the control of cell division resulting in cancerous
growth.
2.
Oncogenes: cancer causing genes first found in retroviruses
3.
Proto-oncogene: normal gene found in humans and other animals that
coded for proteins regulating cell growth and division that can become an
oncogene.
Molecular Biology of Cancer
Cancer results from genetic changes that affect the cell cycle
4.
How does a proto-oncogene that is functioning normally and in a
healthy fashion become an oncogene? What are the genetic changes?
a) A gene can move to a new location and become under the control
of a new promoter that is more active and thus more of the gene’s
product is produced which stimulates the cell cycle.
b) A gene can be duplicated (amplified) in a cell and therefore there
are bunches of copies of this gene in a cell and they are all being
transcribed, making their gene product that affects the cell cycle.
c)
Point mutations can occur in a gene and this mutation could alter
the protein product and this “abnormal” or unexpected gene
product affects the cell cycle putting the cell cycle regulation out
of control and thus a cell is now dividing bunches and bunches of
times (malignancy)
Molecular Biology of Cancer
Cancer results from genetic changes that affect the cell cycle
4.
How does a proto-oncogene that is functioning normally and in a
healthy fashion become an oncogene? What are the genetic changes?
i.
A mutation could affect a tumor suppressor gene. Normally
these genes produce proteins that prevent uncontrolled cell
division but if there is a mutation then this suppressor
product is not made and thus the cell can now divide out of
control.
a.
These tumor suppressor genes can normally:

Repair damaged DNA which if allowed to accumulate
can cause cancer.

Maintain the need for cells to adhere to other cells and
to the extra cellular matrix (something that cancer cells
do not need to do)

Act in cell-signaling pathways to keep cells from
dividing.
Figure 19.13 Genetic changes that can turn proto-ocogenes into oncogenes
Molecular Biology of Cancer
Oncogene proteins and faulty tumor-suppressor proteins interfere with normal
signaling pathways.
1.
ras Gene
a) This gene is mutated in about 30% of human cancers.
b) It is a component of a signal transduction pathway that affects the
DNA
c)
The product of the ras gene is the Ras protein and it is a G protein
which again is a protein, that requires GTP, and gets a signal from
a membrane bound receptor, a tyrosine-kinase receptor.
d) Normally, a growth factor is produced that stimulates the cell
cycle but an oncogene protein, a hyperactive version of the Ras
protein causes the stimulation of the tyrosine-kinase receptors
without the growth factor being around.
Figure 19.14 Signaling pathways that regulate cell growth (Layer 3)
Molecular Biology of Cancer
Oncogene proteins and faulty tumor-suppressor proteins interfere with normal
signaling pathways.
2.
p53 gene
a)
This gene gets activated when the cell’s DNA is damaged.
b)
The p53 gene makes a p53 protein which is a transcription factor
c)
This transcription factor can affect lots of different genes
i.
It can affect a gene called p21 that makes a protein that shuts
down the cell cycle so the DNA can be repaired.
ii.
It can turn on DNA repair genes
iii. It can stimulate “suicide genes” that produces a protein that
causes apoptosis.
Figure 19.14 Signaling pathways that regulate cell growth (Layer 3)
Figure 19.15 A multi-step model for the development of colorectal cancer
The accumulation of more than one mutation can cause cancer and thus the
older you are the more likely you will get cancer.
The tumor polyp genes may be benign initially and then become malignant
and more mutations then destroy the tumor-suppressor genes.
Molecular Biology of Cancer
Multiple mutations underlie the development of cancer
1.
2.
Many changes occur for a cell to become cancerous
a)
One active oncogene is usually present
b)
Mutation(s) in tumor-suppressor genes.
c)
Telomerase gene is activated so the cell keeps dividing
Some viruses can cause cancer.
a)
15% of world wide cancers are caused by viruses
b) Some forms of leukemia are caused by retroviruses (viruses that
contain RNA as their nucleic acid)
c)
Hepatitis viruses can cause liver cancer.
d) Wart viruses can cause cervical cancer
e)
This happens by the injected RNA representing an oncogene
f)
Viral DNA could also be injected and disrupt a tumor sup. gene.
Molecular Biology of Cancer
Multiple mutations underlie the development of cancer
3.
Breast Cancer
a)
BRCA1 and BRCA2 are two identified genes.
b) Strong genetic, inherited link.
c)
Mutations in either gene increase risk for breast and ovarian
cancer.
d) BRCA1 and 2 are tumor suppressor genes
e)
What their gene products due may still be unknown. They may
be DNA repair proteins.