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Chapter 19
Eukaryotic Genomes:
Organization, Regulation, and
Evolution
Biology, Seventh Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Overview: How Eukaryotic Genomes Work and Evolve
• In eukaryotes, the DNA-protein complex, called
chromatin
– Is ordered into higher structural levels than the
DNA-protein complex in prokaryotes. How can this
structure be ordered in this intricate manner?
Figure 19.1
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• Both prokaryotes and eukaryotes
– Must alter their patterns of gene expression in
response to changes in environmental
conditions
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 19.1: Chromatin structure is based on
successive levels of DNA packing
• Eukaryotic DNA
– Is precisely combined with a large amount of protein
with the resulting chromatin undergoes striking
changes during the cell cycle
– When the cell prepare to mitosis, its chromatin coils
and folds to form the chromosomes
• Eukaryotic chromosomes
– Contain an enormous amount of DNA contain a single
linear DNA double helix that averages 200 million
base pairs in humans
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Nucleosomes, or “Beads on a String”
• Proteins called histones
– Are responsible for the first level of DNA
packing in chromatin
– Bind tightly to DNA because they have a high
proportion of positively charged a.a that binds
to the negatively charged DNA.
• The association of DNA and histones
– Seems to remain intact throughout the cell
cycle
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
In electron micrographs
– Unfolded chromatin has the appearance of beads on a
string
• Each “bead” is a nucleosome; The basic unit of DNA
packing
– Histones leave DNA only transiently during DNA replication
but stay with DNA during transcription.
2 nm
DNA double helix
Histones
Histone
tails
Histone H1
Linker DNA
(“string”)
Nucleosome
(“bad”)
(a) Nucleosomes (10-nm fiber)
Figure 19.2 a
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10 nm
Higher Levels of DNA Packing
• With the aid of the histone H1 (one of 5 histones involved
in the coiling process), the beaded string coils to from a
fiber roughly 30 nm in thickness known as the 30-nm
chromatin fiber.
30 nm
Figure 19.2 b
Nucleosome
(b) 30-nm fiber
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• The 30-nm fiber, in turn
– Forms looped domains, making up a 300-nm
fiber which are attached to a chromosome
scaffold (platform) made of non-histone
proteins.
Protein scaffold
Loops
300 nm
(c) Looped domains (300-nm fiber)
Figure 19.2 c
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Scaffold
• In a mitotic chromosome
– The looped domains themselves coil and fold
further compacting the chromatin forming the
characteristic metaphase chromosome
700 nm
1,400 nm
(d) Metaphase chromosome
Figure 19.2 d
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• In interphase
– Some portions of certain chromosomes exist in a
very condensed state that can be seen under
light microscope. This is called heterochromatin
and is distinguished from the less compact
chromatin that is called euchromatin.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 19.2: Gene expression can be regulated at
any stage, but the key step is transcription
• All organisms
– Must regulate which genes are expressed at any given
time. i.e not every gene will be active at all times.
• During development of a multicellular organism
– Its cells undergo a process of specialization in form
and function called cell differentiation. This results in
several cell types reaching up to 200 different cells
types in adult humans.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Differential Gene Expression
• Each cell of a multicellular eukaryote
– Expresses only a fraction of its genes (probably 20% )
at any given time.
• In each type of differentiated cell
– A unique subset of genes is expressed with the highly
differentiated cells such as muscle cells expressing a
lower number of genes at any given time.
– Differences between cell types are NOT due to
different genes but to different gene expression by
cells with the same genome.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The genome of eukaryotes may contain tens of thousands
of genes but only a small amount of DNA (1.5% in humans )
codes for proteins.
• What determine which genes to be expressed?
–
Environmental signals, certain genes turn on while others turn
off.
–
Cell differentiation during organism development.
• The enzymes that transcribe DNA must locate the target
genes at the right time. This task is like finding a needle in
haystack.
• When gene expression goes wrong, certain disease such as
cancer can arise.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Many key stages of gene expression
Signal
Stages in Gene Expression that can
be regulated in eukaryotic cells; The
colored boxes indicates these steps.
NUCLEUS
Chromatin
Chromatin modification:
DNA unpacking involving
histone acetylation and
DNA demethlation
DNA
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intron
RNA processing
Tail
Cap
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypetide
Cleavage
Chemical modification
Transport to cellular
destination
Active protein
Degradation of protein
Figure 19.3
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Degraded protein
Regulation of Chromatin Structure
• Genes within highly packed heterochromatin
– Are usually not expressed
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Histone Modification
• Chemical modification of histone tails
– Can affect the configuration of chromatin and
thus gene expression
Chromatin changes
Transcription
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Histone
tails
DNA
double helix
Figure 19.4a
Amino acids
available
for chemical
modification
(a) Histone tails protrude outward from a nucleosome
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Histone acetylation
• is the attachment of acetyl groups (--COCH3) to certain
amino acids of histone proteins.
– Seems to loosen chromatin structure and thereby lose
their grip on DNA thus enhance transcription
Unacetylated histones
Figure 19.4 b
Acetylated histones
(b) Acetylation of histone tails promotes loose chromatin structure
that permits transcription
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
DNA Methylation
• Addition of methyl groups (…CH3) to certain bases
in DNA
– Genes are usually more highly methylated when they
are not expressed.
– De-methylation to certain inactive genes turns them
on.
– In some species DNA methylation guarantees long
term inactivation of certain genes
– Once methylated, genes stay as such through
successive cell division. This property accounts for
genomic imprinting in mammals where methylation
permanently turns off either maternal or paternal allele
of a certain gene.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Epigenetic Inheritance
– Is the inheritance of traits transmitted by
mechanisms not directly involving the
nucleotide sequence.
– Chromatin modifying enzymes are integral part
of this process.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Regulation of Transcription Initiation
• Chromatin-modifying enzymes provide initial
control of gene expression
– By making a region of DNA either more or less
able to bind the transcription machinery.
– Once a gene is optimally modified for
expression, the initiation of transcription
process is the most important.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Organization of a Typical Eukaryotic Gene
• Associated with most eukaryotic genes are
multiple control elements which are;
– Segments of noncoding DNA that help regulate
transcription by binding certain proteins
Proximal
Enhancer
control
elements
(distal control elements)
Poly-A signal Termination
sequence
region
Exon
DNA
Upstream
Intron
Transcription
Primary RNA
transcript 5
(pre-mRNA)
Exon
Intron
Intron RNA
RNA processing
Intron Exon
Cleared 3 end
of primary
transport
Coding segment
Translation
Protein processing
and degradation
Exon
Poly-A
signal
RNA processing:
Cap and tail added;
introns excised and
exons spliced together
Transcription
Figure 19.5
Intron Exon
Downstream
Promoter
Chromatin changes
mRNA
degradation
Exon
mRNA
G
P
P
P
5 Cap 5 UTR
(untranslated
region)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Start
Stop
3 UTR Poly-A
codon codon (untranslated tail
region)
The Roles of Transcription Factors
• To initiate transcription
– Eukaryotic RNA polymerase requires the
assistance of proteins called transcription
factors. These factors are required for all types
of protein coding genes thus called general
transcription factors.
– One of these transcription factors recognize a
DNA sequence called the TATA box within the
promoter, while the others recognize other
proteins including the RNA polymerase.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Enhancers and Specific Transcription Factors
– The interaction of these transcription factors and
RNA polymerase II with a promoter usually
initiates transcription but inefficiently producing
few RNA transcripts.
– Control elements, proximal control elements
(near the promoter) greatly improve the
efficiency of promoters by binding additional
transcription factors.
– The more distant “ distal control elements” are
called the enhancers which might be thousands
of nucleotides away from the promoter or may
be located in an intron.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• An activator
– Is a protein that binds to an enhancer and
stimulates transcription of a gene
Distal control
element
Activators
Enhancer
1 Activator proteins bind
to distal control elements
grouped as an enhancer in
the DNA. This enhancer has
three binding sites.
2A DNA-bending protein
brings the bound activators
closer to the promoter.
Other transcription factors,
mediator proteins, and RNA
polymerase are nearby.
Promoter
TATA
box
Gene
General
transcription
factors
DNA-bending
protein
Group of
Mediator proteins
RNA
Polymerase II
Chromatin changes
3The activators bind to
certain general transcription
factors and mediator
proteins, helping them form
an active transcription
initiation complex on the promoter.
Transcription
RNA processing
mRNA
degradation
Figure 19.6
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Translation
Protein processing
and degradation
RNA
Polymerase II
Transcription
RNA synthesis
Initiation complex
• Some specific transcription factors function as
repressors
– To inhibit expression of a particular gene
• Some activators and repressors
– Act indirectly by influencing chromatin
structure
– A gene present in the region of chromatin with
high levels of histone acetylation is able to bind
to the transcription machinery while the one
with low levels can not bind.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
In yeast and some mammals some activator recruit
proteins that acetylate histones near the
promorter of a gene thus enhance transcription.
Repressors recruit proteins that deacetylate
histones leading to reduced transcription. This
phenomenon is called gene silencing.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Coordinately Controlled Genes
• Unlike the genes of a prokaryotic operon which are
regulated by one promoter
– Coordinately controlled eukaryotic genes each have
a promoter and control elements even if they are
located close to each other on the same chromosome.
• The same regulatory sequences
– Are common to all the genes of a group, enabling
recognition by the same specific transcription factors
– An example of such coordinate control is the activation
of a variety of genes by steroid home (sex hormones).
–
Genes with the same control elements are activated
by the same chemical signals.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Mechanisms of Post-Transcriptional Regulation
• The expression of a protein-coding gene is
ultimately measured in terms of amount of
functional protein the cell makes.
• In theory a gene expression may be blocked or
stimulated at any post-transcriptional step.
• A cell can therefore, use its regulatory
mechanisms that operate after the transcription to
fine tune gene expression in response to
environmental changes without altering its
transcription patterns.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
RNA Processing
• In alternative RNA splicing
– Different mRNA molecules are produced from the
same primary transcript, depending on which RNA
segments are treated as exons and which as
introns.
Chromatin changes
Transcription
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Exons
DNA
Primary
RNA
transcript
RNA splicing
Figure 19.8
mRNA
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
or
mRNA Degradation
• The life span of mRNA molecules in the cytoplasm
– Is an important factor in determining the protein
synthesis in a cell
– Prokaryotic mRNA have a very short life span i.e they
are degraded enzymatically after few minutes.
– In contrast eukaryotic mRNA life span is typically
hours, but could be days or even weeks such mRNA
for hemoglobin polypeptides
– It is believed that the removal of the 5’ cap provides a
site for the nuclease enzymes to chew up the mRNA.
– Nucleotide sequences that affect mRNA stability are
normally found in the trailer region (un-translated
region, UTR) at the 3’ end of the molecule.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Recent discoveries
• RNA interference by single-stranded microRNAs (miRNAs)
–
Can lead to degradation of an mRNA or block its translation
–
This happen due to a small interfering RNAs (siRNAs) which the
same size as miRNAs and does the same function
1
The microRNA (miRNA)
precursor folds
back on itself,
held together
by hydrogen
bonds.
2
An enzyme
called Dicer moves
along the doublestranded RNA,
cutting it into
shorter segments.
5
4
3
One strand of
each short doublestranded RNA is
degraded; the other
strand (miRNA) then
associates with a
complex of proteins.
The bound miRNA
can base pair with
any target mRNA
that contains the
complementary
sequence.
5
The miRNA-protein
complex prevents gene
expression either by
degrading the target
mRNA or by blocking
its translation.
Chromatin changes
Transcription
RNA processing
Protein
complex
mRNA
degradation
Translation
Protein processing
and degradation
Dicer
Degradation of mRNA
OR
miRNA
Target mRNA
Figure 19.9
Hydrogen
bond
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Blockage of translation
Initiation of Translation
• The initiation of translation of selected mRNAs
– Can be blocked by regulatory proteins that bind to
specific sequences or structures of the mRNA. This
adds another opportunity for regulating gene expression
• Alternatively, translation of all the mRNAs in a cell
– May be regulated simultaneously. This global control
usually involves activation or inactivation of one or more
of the protein factors required to initiate translation.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Protein Processing and Degradation
• The final opportunities for controlling gene
expression occurs after translation
– Various types of protein processing, including cleavage
and the addition of chemical groups, or the length of
time each protein functions in the cell are subject to
control. Examples;
– Cleaving pro-insulin to form the active form, insulin.
– Addition of phosphate groups or sugars
– Cyclins which are proteins involved in regulating the
cell cylce must be short-lived if the cell to function
properly.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Proteasomes
– The protein molecules to be degraded must be bind to
another protein called ubiquitin before being degraded by
a giant protein complexes called proteasome.
1
3
2
Multiple ubiquitin molecules are attached to a protein
by enzymes in the cytosol.
Chromatin changes
The ubiquitin-tagged protein
is recognized by a proteasome,
which unfolds the protein and
sequesters it within a central cavity
Enzymatic components of the
proteasome cut the protein into
small peptides, which can be
further degraded by other
enzymes in the cytosol.
Transcription
RNA processing
mRNA
degradation
Translation
Proteasome
and ubiquitin
to be recycled
Ubiquitin
Proteasome
Protein processing
and degradation
Protein to
be degraded
Ubiquinated
protein
Protein entering a
proteasome
Figure 19.10
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Protein
fragments
(peptides)
• Concept 19.3: Cancer results from genetic
changes that affect cell cycle control
• The gene regulation systems that go wrong during
cancer turn out to be the very same systems that
play important roles in embryonic development
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Types of Genes Associated with Cancer
• The genes that normally regulate cell growth
and division during the cell cycle
– Include genes for growth factors, their
receptors, and the intracellular molecules of
signaling pathways.
• Its is believed that many causing-cancer mutations
results from environmental influences such as
chemical carcinogens, UV light, X-Ray or certain
viruses.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Examples of viruses that cause cancer are;
• EBV that cause infectious mononucleosis and is
associated with Burkitt’s lymphoma
• Papiloma virus associated with cervix cancer
• HTLV-1 virus associated with some adults
leukemia
All tumor viruses transform cells into cancer cells by
integrating their nucleic acids with host DNA.
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Oncogenes and Proto-Oncogenes
• Oncogenes
– Are cancer-causing genes
• Proto-oncogenes
– Are normal cellular genes that code for
proteins that stimulate normal cell growth and
division
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How a proto-oncogene become an
oncogene?
• An oncogene arises from a genetic change that
leads to an increase in either;
• the amount of the proto-oncogene’s protein
product
• or the intrinsic activity of each protein molecule.
• Now these genetic changes fall into three
catergories; (Figure 19-11).
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Gentic changes that change proto-onco to oncogene
• movement of DNA within the genome, where it
might land close to an especially active promoter
that increase transcription of the gene making it
an oncogene.
• amplification of proto-oncogene which increase
the number of copies of oncogene inside the cell
• point mutation in a proto-oncogene that change
the gene’s protein product to a more active or
more resistant to degradation than the normal
protein.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• A DNA change that makes a proto-oncogene
excessively active
– Converts it to an oncogene, which may promote
excessive cell division and cancer
Proto-oncogene
DNA
Translocation or transposition:
gene moved to new locus,
under new controls
Gene amplification:
multiple copies of the gene
New
promoter
Normal growth-stimulating
protein in excess
Point mutation
within a control
element
Oncogene
Normal growth-stimulating
protein in excess
Figure 19.11
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Point mutation
within the gene
Oncogene
Normal growth-stimulating Hyperactive or
degradationprotein in excess
resistant protein
Tumor-Suppressor Genes
• Tumor-suppressor genes
– Encode proteins that inhibit abnormal cell division.
• Protein products of tumor suppressor genes
could be;
– proteins normally repair damaged DNA
– some proteins control adhesion of cells to each other
or to an extracellular matrix
– other proteins are component of signaling pathways
that inhibit the cell cycle.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Interference with Normal Cell-Signaling Pathways
• Many proto-oncogenes and tumor suppressor
genes
– Encode components of growth-stimulating and
growth-inhibiting pathways, respectively.
• What protein products of cancer genes do or
fail to do?
– Let us look at products of two cancer genes;
the ras proto-ocogenes and p53 tumor
suppressor gene.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Mutations in these genes are very common in human
cancers; ras is mutated in about 30% of human cancers
while it is 50% for p53.
• Both proteins, ras and p53 are parts of the signal
transduction pathways that convey external signal to the
DNA in the nucleus. Figure 19-12 shows two possibilities of
an outcome when either gene goes wrong;
–
one an over expression of ras protein that ends in the
increase in the production of protein that stimulates cell
cycle and leads to cancer
–
An under expression of a protein that inhibits the cell cycle
as a result of mutation in the p53 gene and leads to cancer.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The p53 gene is names as it encodes for a protein of 53
kDa molecular weight. It is very important to the point that
its name is “the guardian angel of the genome”.
How does the p53 works in protecting the cells form cancer?
• A damage to the cell’s DNA leads to the expression of p53
• This in turn lead to the activation of a p21gene whose
product leads to halting the cell cycle thus allowing time for
the cell to repair its damaged DNA
• The protein p53 can turn on genes directly involved in DNA
repair
• When DNA damage is irreparable, p53 protein activates a
suicide genes whose protein products cause cell death in a
process called apoptosis
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Cell cycle stimulating pathway
• This pathway is triggered by a growth factor that binds
to its receptor in the plasma membrane.
• The signal is relayed to a G protein called Ras. Like all
G proteins, Ras is active when GTP is bound to it.
• Ras passes the signal to a series of protein kinases.
• The last kinase activates a transcription activator that
turns on one or more genes.
• For proteins that stimulate the cell cycle. If a mutation
makes Ras or any other pathway component
abnormally active, excessive cell division and cancer
may result. See next slide for explanation.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The Ras protein, encoded by the ras gene
– Is a G protein that relays a signal from a growth factor
receptor on the plasma membrane to a cascade of
protein kinases
1
Growth
factor
Mutation
Hyperactive
Ras protein
(product of
oncogene)
issues signals
on its own
3 protein
G
4
2
Receptor
Protein kinases
(phosphorylation
cascade)
Nucleus
5
Transcription
factor (activator)
Gene expression
Protein that
Stimulates
the cell cycle
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Cell cycle inhibiting pathway
• In this pathway, DNA damage is an intracellular signal that is
passed via protein kinases and leads to activation of p53.
• Activated p53 promotes transcription of the gene for a
• protein that inhibits the cell cycle.
• The resulting suppression of cell division ensures that the
damaged DNA is not replicated.
• Mutations causing deficiencies in any pathway component
can contribute to the development of cancer.
• See next slide for explanation.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The p53 gene encodes a tumor-suppressor protein
– That is a specific transcription factor that promotes the
synthesis of cell cycle–inhibiting proteins
2
Protein kinases
MUTATION
UV
light
3
1
DNA damage
in genome
Defective or missing
Transcription factor, such
as p53, cannot activate
transcription
Active
form
of p53
DNA
Protein that
inhibits
the cell cycle
Figure 19.12b
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• Mutations that knock out the p53 gene
– Can lead to excessive cell growth and cancer
Effects of mutations.
(c)
Increased cell division,
possibly leading to
cancer, can result if the
cell cycle is
overstimulated, as in (a),
or not inhibited when it
normally would be, as in
(b).
EFFECTS OF MUTATIONS
Protein
overexpressed
Cell cycle
overstimulated
Figure 19.12c
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Protein absent
Increased cell
division
Cell cycle not
inhibited
The Multistep Model of Cancer Development
• Normal cells are converted to cancer cells
– By the accumulation of multiple mutations
affecting proto-oncogenes and tumorsuppressor genes
• More than one somatic mutation is generally
needed to produce the entire changes
characteristic of cancer cell. That is why
cancers increase with increase age.
• Does this means that mutations accumulate
until they cause cancer?
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A study of colorectal cancer
• It affect 135,000 patients every year in US with
60,000 deaths each year.
• Like other cancers it develops gradually.
• The first sign is often a polyp which is small, benign
growth in the colon lining. Cells look normal
although they divide unusually frequently
• Tumor grows and may eventually become malignant
• Malignant tumor develops parallel by a graduate
accumulation of mutations that activate oncogenes
and knock out tumor suppressor genes.
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Colorectal cancer…. Cont.
• A bout a half dozen changes must occur at the DNA
level for a cell to become fully cancerous including;
• Appearance of at least one active oncogenes
• Mutation or loss of several tumor suppressor genes
• Since mutant tumor suppressor alleles are recessive,
mutation must knock out both alleles in a cell’s
genome to block tumor suppression
• The genes for tolemerase gets activated. This enzyme
prevent the erosion of the ends of the chromosomes
thus removing the natural limits on the number of
times the cell can divide.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• A multistep model for the development of
colorectal cancer
Colon
Loss of tumorsuppressor
Colon wall gene APC (or
other)
1
Activation of
ras oncogene
2
Loss of
tumorsuppressor
gene DCC
Loss of
tumor-suppressor
gene p53
4
3
Normal colon
epithelial cells
Small benign
growth (polyp)
Figure 19.13
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Additional
mutations
5
Larger benign
growth (adenoma)
Malignant tumor
(carcinoma)
Viruses and cancer
• Viruses seem to play a part of about 15% of
human cancer cases worldwide.
• Viruses contribute to cancer development by;
– Integrating their DNA into the host DNA thus
they might donate an oncogenes to the host
– They might insert a cellular gene that disrupts
a tumor suppressor gene or converts a protooncogene to an oncogene.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Inherited Predisposition to Cancer
•
That fact that multiple genetic changes are required to produce a
cancer help explain the predisposition to cancer that run in some
families. How does that happen?
•
Individuals who inherit a mutant oncogene or tumor-suppressor
allele Have an increased risk of developing certain types of
cancer
•
About 15% of colorectal cancers involve inhereted mutations that
affect a tumor-suppressor gene called adenomatous polyposis
coli (APC). This gene involves in cell migration and adhesion.
•
Breast cancer is another example where mutations of BRCA1 and
BRCA2 (tumor suppressor gene) are found in at least 50% if
inherited breast cancers.
•
A woman with inherited one mutant of BRCA1 allele has 60%
chance of developing breast cancer before age 50 compared with
only 2% probability for an individual homozygous for the normal
allele.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 19.4: Eukaryotic genomes can have
many noncoding DNA sequences in addition to
genes
• The bulk of most eukaryotic genomes
– Consists of noncoding DNA sequences, often
described in the past as “junk DNA”
• However, much evidence is accumulating
– That noncoding DNA plays important roles in
the cell.
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The Relationship Between Genomic Composition
and Organismal Complexity
• Compared with prokaryotic genomes, the
genomes of eukaryotes
– Generally are larger
– Have longer genes;
– Contain a much greater amount of noncoding
DNA both associated with genes and between
genes. This DNA includes the introns (noncoding DNA stritches that interrupt the coding
sequences) and repetitive DNA.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• In prokaryotes most of the DNA in the genome
account for proteins, tRNA or rRNA, with the
coding sequences proceed from the start to
finish without interruption.
• Now that the complete sequence of the
human genome is available we know what
makes up most of the 98.5% that does NOT
code for proteins, rRNAs, or tRNAs. Figure
19.14 shows this distribution.
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Types of DNA sequences in human genome
Exons (regions of genes coding
for protein, rRNA, tRNA) (1.5%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
Alu elements
(10%)
Figure 19.14
Simple sequence
DNA (3%)
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Introns and
regulatory
sequences
(24%)
Repetitive
DNA
unrelated to
transposable
elements
(about 15%)
Unique
noncoding
DNA (15%)
Large-segment
duplications (5-6%)
Transposable Elements and Related Sequences
• All organisms seem to have stretches of DNA that can
move from one location to another.
• The first evidence for these wandering DNA segments
– Came from geneticist Barbara McClintock’s breeding
experiments with Indian corn
Figure 19.15
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Movement of Transposons and Retrotransposons
• Eukaryotic transposable elements are of two types
– Transposons, which move within a genome by
means of a DNA intermediate and a copy and paste
or cut and paste mechanisms. Figure 19.16 a&b
– Retrotransposons, which move by means of an RNA
intermediate. Most of transposable elements in
eukaryotes are reterotransposons.
– These transposons encode for reverse transcriptase
(RT) enzyme. Thus RT can be present in cells not
infected with virus.
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Movement of eukaryotic transposable elements
Transposon
New copy of
transposon
DNA of genome
Transposon
is copied
Insertion
Mobile transposon
(a) Transposon movement (“copy-and-paste” mechanism)
Retrotransposon
New copy of
retrotransposon
DNA of genome
RNA
Reverse
transcriptase
(b) Retrotransposon movement
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Insertion
Figure 19.16a, b
Sequences Related to Transposable Elements
• Multiple copies of transposable elements and
sequences related to them
– Are scattered throughout the eukaryotic genome
and make about 25-50% of the human genome.
• In humans and other primates
– A large portion of transposable element–related
DNA consists of a family of similar sequences
called Alu elements (10% of the human genome).
– Alu elements are about 300 nucleotides long and
they do not code for any protein
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Other Repetitive DNA, Including Simple Sequence DNA
• Repetitive DNA that is not related to transposable
elements might have originated by mistake during
DNA replication and it accounts for 15% of human
genome of which 5% consist of very large segment
duplications.
• Simple sequence DNA
– Contains many copies of tandemly repeated short
sequences
– Is common in centromeres and telomeres, where
it probably plays structural roles in the
chromosome
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• The simple DNA sequences located at the
telomeres at the tip of the chromosome prevents
genes from being lost during replication.
• In mammals a considerable portion of the genome
is tandemly repetitive DNA, which are short
repetitive sequences in series such as;
• ….. GTTAC GTTAC GTTAC GTTAC GTTAC
GTTAC….
• The number of these repeated short series could
reach several hundred thousands and the
repeated units could be up to 10 base pairs.
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• The nucleotide composition of this DNA differs from
the rest of DNA to the point that it can be isolated by
differential ultracentrifugation.
• Repetitive DNA sequences originally isolated in this
way was called satellite DNA because it appears as
a satellite band in the centrifuge tube.
• The term satellite DNA is now used interchangeably
with the term simple sequence DNA.
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Genes and Multigene Families
• Most eukaryotic genes
– Are present in one copy per haploid set of
chromosomes
• The rest of the genome (particularly in humans)
– Occurs in multigene families, collections of
identical or very similar genes
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• Some multigene families
– Consist of identical DNA sequences, usually clustered
tandemly, such as those that code for RNA products
RNA transcripts
DNA
Non-transcribed
spacer
Transcription unit
DNA
18S
5.8S
28S
rRNA
Figure 19.17a Part
of the ribosomal
RNA gene family
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28S
18S
5.8S
• The classic examples of multigene families of
nonidentical genes
– Are two related families of genes that encode globins
-Globin
Heme
Hemoglobin
-Globin
-Globin gene family
-Globin gene family
Chromosome 16
Chromosome 11

Figure 19.17b The human
-globin and -globin
gene families
Embryo
  1 2 1 
2
Fetus
and adult
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
G A
Embryo
Fetus



Adult
• The previous figure shows that human hemoglobin
has two subunits located on different
chromosomes.
• The different forms of each globin is expressed at
different stage of development.
• Example in humans embryonic and fetal forms of
HB have higher affinity to O2 than adult forms to
insure efficient transfer of O2 from mother to fetus.
• Also found in globin gene family clusters are
pseudogenes, which are non-functional sequences
similar to the functional ones.
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• Concept 19.5: Duplications, rearrangements,
and mutations of DNA contribute to genome
evolution
• The basis of change at the genomic level is
mutation which underlies much of genome
evolution.
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Duplication of Chromosome Sets
• Accidents in meiosis can result in one or more
extra sets of chromosomes (polyploidy).
• In such case one complete set of gene can provide
normal functions while the other can diverge by
accumulating mutations.
• This divergence might later lead to new phenotypes
if the organism survives.
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Duplication and Divergence of DNA Segments
• Unequal crossing over during prophase I of
meiosis
– Can result in one chromosome with a deletion and
another with a duplication of a particular gene
Transposable
element
Gene
Nonsister
chromatids
Crossover
Incorrect pairing
of two homologues
during meiosis
and
Figure 19.18
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Evolution of Genes with Related Functions: The
Human Globin Genes
• The genes encoding the various globin
proteins
– Evolved from one common ancestral globin
gene, which was duplicated and diverged
• Subsequent duplications of these genes and
random mutations
– Gave rise to the present globin genes, all of
which code for oxygen-binding proteins.
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Evolution of Genes with Related Functions: The
Human Globin Genes
Ancestral globin gene
Duplication of
ancestral gene
Mutation in
both copies


Transposition to
different chromosomes


Further duplications
and mutations


Figure 19.19

    
2
1
2
-Globin gene family
on chromosome 16
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

1 

G

A

 -Globin gene family
on chromosome 11


• The similarity in the amino acid sequences of the
various globin proteins
– Supports this model of gene duplication and
mutation
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Table 19.1
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Evolution of Genes with Novel Functions
• The copies of some duplicated genes
– Have diverged so much during evolutionary
time that the functions of their encoded
proteins are now substantially different
– Gene of lysozyme and α-lactoalbumin are
good examples as they have a similar a.a
seqeunce and 3-D structure yet completely
different function.
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Rearrangements of Parts of Genes: Exon
Duplication and Exon Shuffling
• The presence of introns in eukaryotic genes may
have promoted the development of new proteins
by facilitating duplication and rearrangement of
exons.
• A particular exon within a gene
– Could be duplicated on one chromosome and
deleted from the homologous chromosome
and this could happen due to unequal crossing
over.
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In exon shuffling
– Errors in meiotic recombination lead to the occasional
mixing and matching of different exons either within a
gene or between two nonallelic genes
EGF
EGF
EGF
EGF
Epidermal growth
factor gene with multiple
EGF exons (green)
Exon
shuffling
F
F
F
Fibronectin gene with multiple
“finger” exons (orange)
Exon
duplication
F
F
EGF
K
K
K
Plasminogen gene with a
“kfingle” exon (blue)
Portions of ancestral genes
Figure 19.20
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Exon
shuffling
TPA gene as it exists today
How Transposable Elements Contribute to Genome Evolution
• Movement of transposable elements or
recombination between copies of the same
element Can contribute to the evolution of the
genome in several ways;
• Promote recombination
• Disrupt cellular genes or control elements, thus
interfering with production of proteins.
• Carry entire genes or exons to new locations e.g
the presence of α and β-globin genes on two
different chromosomes.
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End of Chapter
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