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Chapter 19
• Eukaryotic Genomes
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Eukaryotes DNA-protein complex,  chromatin
– More complex structural levels than prokaryotes
Figure 19.1
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• Both prokaryotes and eukaryotes
– Must alter patterns of gene expression in
response to changes in environment
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• Chromatin structure based on successive
levels of DNA packing
• Eukaryotic DNA
– Combined w/ protein
• Eukaryotic chromosomes
– Contain an enormous amount of DNA relative
to their condensed length
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Nucleosomes, or “Beads on a String”
• Basic packing unit
• DNA wrapped around histone protein
2 nm
DNA double helix
Histones
Histone
tails
Histone H1
Nucleosome
(“string”)
(“bead”)
(a) Nucleosomes (10-nm fiber)
Linker DNA
Figure 19.2 a
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10 nm
• Next level of packing
– Forms 30-nm chromatin fiber
30 nm
Nucleosome
(b) 30-nm fiber
Figure 19.2 b
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• The 30-nm fiber, in turn
– Forms looped domains, making up a 300-nm
fiber
Protein scaffold
Loops
300 nm
(c) Looped domains (300-nm fiber)
Figure 19.2 c
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Scaffold
• Mitotic chromosome
– Looped domains coil and fold forming the
metaphase chromosome
700 nm
1,400 nm
(d) Metaphase chromosome
Figure 19.2 d
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• Interphase cells
– Most chromatin is highly extended
(euchromatin)
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• Gene expression can be regulated at any
stage, but the key step is transcription
• All organisms
– regulate which genes are expressed at any
given time
• During development of a multicellular organism
cell specialization in form and function (cell
differentiation)
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• Each cell of a multicellular eukaryote
– Expresses only a fraction of its genes
• In each type of differentiated cell
– Unique subset of genes is expressed
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Signal
NUCLEUS
Chromatin
• Many key stages of
Chromatin modification:
DNA unpacking involving
histone acetylation and
DNA demethlation
DNA
Gene available
gene expression
for
transcription
Gene
Transcription
RNA
(regulation)
Exon
Primary transcript
Intron
RNA processing
Tail
In eukaryotic cells
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
Degraded protein
Figure 19.3
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• Genes within highly packed heterochromatin
usually not expressed
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Histone acetylation
– Loosens chromatin structure  enhances
transcription
Unacetylated histones
Figure 19.4 b
Acetylated histones
(b) Acetylation of histone tails promotes loose chromatin structure that
permits transcription
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• Addition of methyl groups to DNA bases
– Associated w/ reduced transcription
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• Multiple control elements
– Noncoding DNA that regulate transcription
Enhancer
(distal control elements)
Proximal
control elements
Poly-A signal
sequence
Exon
Intron
Exon
Intron
Termination
region
Exon
DNA
Downstream
Upstream
Promoter
Chromatin changes
Transcription
Exon
Primary RNA
5
transcript
(pre-mRNA)
Intron
Intron RNA
RNA processing
mRNA
G
P
P
Cleared 3 end
of primary
transport
P
5 Cap
Figure 19.5
Exon
Coding segment
Translation
Protein processing
and degradation
Intron
RNA processing:
Cap and tail added;
introns excised and
exons spliced together
Transcription
mRNA
degradation
Exon
Poly-A
signal
5 UTR
(untranslated
region)
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Start
codon
Stop
codon
Poly-A
3 UTR
tail
(untranslated
region)
Alternate RNA Processing
• Different mRNA molecules produced from 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
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or
mRNA Degradation
• Life span of mRNA molecules in the cytoplasm
– Important in protein synthesis
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• RNA interference (RNAi) by single-stranded
microRNAs (miRNAs)
– degradation of mRNA or block its translation
1 The microRNA (miRNA)
precursor folds
back on itself,
held together
by hydrogen
bonds.
22 An enzyme
called Dicer moves
along the doublestranded RNA,
cutting it into
shorter segments.
3 One strand of
each short doublestranded RNA is
degraded; the other
strand (miRNA) then
associates with a
complex of proteins.
4 The bound
miRNA can base-pair
with any target
mRNA that contains
the complementary
sequence.
55 The miRNA-protein
complex prevents gene
expression either by
degrading the target
mRNA or by blocking
its translation.
Chromatin changes
Transcription
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Protein
complex
Dicer
Degradation of mRNA
OR
miRNA
Target mRNA
Figure 19.9
Hydrogen
bond
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Blockage of translation
• Proteasomes
– Giant protein complexes that degrade molecules
3 Enzymatic components of the
1 Multiple ubiquitin molChromatin changes
ecules are attached to a protein
by enzymes in the cytosol.
2 The ubiquitin-tagged protein
is recognized by a proteasome,
which unfolds the protein and
sequesters it within a central cavity.
proteasome cut the protein into
small peptides, which can be
further degraded by other
enzymes in the cytosol.
Transcription
RNA processing
mRNA
degradation
Proteasome
and ubiquitin
to be recycled
Ubiquitin
Translation
Proteasome
Protein processing
and degradation
Protein to
be degraded
Ubiquinated
protein
Protein entering a
proteasome
Figure 19.10
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Protein
fragments
(peptides)
• Cancer results from genetic changes that affect
cell cycle control
• The gene regulation systems that go wrong
during cancer are same systems found in
embryonic development
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• Oncogenes
– Cancer-causing genes
• Proto-oncogenes
– Normal genes that code for proteins that
stimulate normal cell growth and division
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• DNA changeproto-oncogene excessively active
 oncogeneexcessive cell division cancer
Proto-oncogene
DNA
Translocation or transposition:
gene moved to new locus,
under new controls
Gene amplification:
multiple copies of the gene
Oncogene
New
promoter
Normal growth-stimulating
protein in excess
Point mutation
within a control
element
Normal growth-stimulating
protein in excess
Figure 19.11
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Normal growth-stimulating
protein in excess
Point mutation
within the gene
Oncogene
Hyperactive or
degradationresistant protein
• Tumor-suppressor genes
– Code f/ proteins that inhibit abnormal cell
division
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• p53 gene encodes a tumor-suppressor protein
– (cell cycle–inhibiting proteins)
– ‘Guardian angel’ of the genome
(b) Cell cycle–inhibiting pathway. In this
pathway, 1 DNA damage is an intracellular
signal that is passed via 2 protein kinases
and leads to activation of 3 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.
2
Protein kinases
UV
light
3
1
DNA damage
in genome
Active
form
of p53
DNA
Protein that
inhibits
the cell cycle
Figure 19.12b
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MUTATION
Defective or
missing
transcription
factor, such as
p53, cannot
activate
transcription
• Mutations that knock out the p53 gene
 excessive cell growth and cancer
(c) Effects of mutations. 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
• Normal cells are converted to cancer cells
– By the accumulation of multiple mutations
affecting proto-oncogenes and tumorsuppressor genes
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• 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
3
Normal colon
epithelial cells
Small benign
growth (polyp)
Figure 19.13
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Larger benign
growth (adenoma)
Loss of
tumor-suppressor
gene p53
4
5 Additional
mutations
Malignant tumor
(carcinoma)
• Certain viruses
– Promote cancer by integration of viral DNA into
a cell’s genome
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• Inheritance of a mutant oncogene 
increased risk of developing cancer
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Noncoding DNA sequences
• Bulk of eukaryotic genomes
– In the past called “junk DNA”
• Evidence is accumulating
– noncoding DNA plays important roles in the
cell
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• Genomes of eukaryotes (v. prokaryotic)
– Larger
– Longer genes
– Much greater amount of noncoding DNA
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Most of the 98.5% that does not code for proteins
rRNAs, or tRNAs
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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Repetitive
DNA
unrelated to
transposable
elements
(about 15%)
Introns and
regulatory
sequences
(24%)
Unique
noncoding
DNA (15%)
Large-segment
duplications (5-6%)
Transposable Elements and Related Sequences
• Wandering DNA segments
– Barbara McClintock’s breeding experiments
with Indian corn
Figure 19.15
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Movement of Transposons and Retrotransposons
• Transposons: move by means of a DNA
intermediate
• Retrotransposons: move by means of an RNA
intermediate
Transposon
DNA of genome
Transposon
is copied
New copy of
transposon
Insertion
Mobile transposon
(a) Transposon movement (“copy-and-paste” mechanism)
Retrotransposon
New copy of
retrotransposon
DNA of genome
RNA
Reverse
transcriptase
Figure 19.16a, b
(b) Retrotransposon movement
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Insertion
• Multiple copies of transposable elements
– scattered throughout genome
• In humans and other primates
– are called Alu elements
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Other Repetitive DNA
• Simple sequence DNA
– Copies of tandemly repeated short sequences
– Common in centromeres and telomeres
(structural roles in chromosome)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Genes and Multigene Families
• Most eukaryotic genes
– present in one copy per haploid set of
chromosomes
• The rest of the genome
– Occurs in multigene families, collections of
identical or very similar genes
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• e.g. 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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

G A
Embryo Fetus



Adult
• 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 cell division
–  extra copies of all or part of a genome,
which may then diverge if one set accumulates
sequence changes
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• Unequal crossing over
–  one chromosome with a deletion and another
with a duplication
Transposable
element
Gene
Nonsister
chromatids
Crossover
Incorrect pairing
of two homologues
during meiosis
and
Figure 19.18
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• Genes for various globin proteins
– Evolved from one common ancestral globin gene,
which duplicated and diverged
Ancestral globin gene
Duplication of
ancestral gene
Mutation in
both copies
Transposition to
different chromosomes



Further duplications
and mutations


Figure 19.19


  2  2 1 
1
-Globin gene family
on chromosome 16
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


G

A

 -Globin gene family
on chromosome 11


• Similarity in the amino acid sequences of the
various globin proteins
– Supports this model of gene duplication and
mutation
Table 19.1
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• The copies of some duplicated genes
– Have diverged so much during evolutionary
time that the functions of their proteins are now
substantially different
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Rearrangements of Parts of Genes: Exon
Duplication and Exon Shuffling
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• Exon shuffling
– Mixing and matching of different exons either
within a gene or between two nonallelic genes
EGF
EGF
EGF
Epidermal growth
factor gene with multiple
EGF exons (green)
EGF
Exon
shuffling
F
F
F
Exon
duplication
F
Fibronectin gene with multiple
“finger” exons (orange)
F
EGF
K
K
Plasminogen gene with a
“kfingle” exon (blue)
Figure 19.20
Portions of ancestral genes
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Exon
shuffling
TPA gene as it exists today
K
How Transposable Elements Contribute to Genome Evolution
• Movement of transposable elements
– Can generates new sequence combinations
that are beneficial to the organism
• Some mechanisms
– Alter functions of genes or their patterns of
expression and regulation
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings