Chapter 19:
Control of
Eukaryotic Genes
AP Biology
2007-2008
The BIG Questions…


How are genes turned on & off
in eukaryotes?
How do cells with the same genes differentiate to
perform completely different, specialized
functions?
 Differential gene expressions
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1. DNA packing
How do you fit all
that DNA into
nucleus?

DNA coiling &
folding





double helix
nucleosomes
chromatin fiber
looped
domains
chromosome
from DNA double helix to
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condensed
Nucleosomes

8 histone
molecules
“Beads on a string”
1st level of DNA packing
 histone proteins




8 protein molecules
positively charged amino acids
bind tightly to negatively charged DNA
ps://www.youtube.com/watch?v=gbSIBhFwQ4s&list=PLAD3D
E96CA98E831E&index=3
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DNA
packing movie
DNA packing as gene control

Degree of packing of DNA regulates transcription

tightly wrapped around histones


no transcription
genes turned off
 Heterochromatin (Interphase)
darker DNA (H) = tightly packed
 euchromatin
lighter DNA (E) = loosely packed
H
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E
Points of control

The control of gene
expression can occur at any
step in the pathway from
gene to functional protein
1. packing/unpacking DNA
2. Transcription (most common)
3. mRNA processing
4. mRNA transport
5. translation
6. protein processing
7. protein degradation
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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
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Amino acids (N-terminus)
available
for chemical
modification
(a) Histone tails protrude outward from a nucleosome
Histone acetylation

Acetylation of histones unwinds DNA

loosely wrapped around histones



attachment of acetyl groups (–COCH3) to postive
charged lysines


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enables transcription
genes turned on
Neutralized (+) charged tails no longer bind to
neighboring nucleosomes
transcription factors have easier access to genes
Acetylated histones
Unacetylated histones
(b) Acetylation of histone tails promotes loose
chromatin structure that permits transcription
DNA methylation

Methylation of DNA blocks transcription factors


no transcription
 genes turned off
attachment of methyl groups (–CH3) to cytosine


C = cytosine
nearly permanent inactivation of genes


ex. inactivated mammalian X chromosome = Barr body
Ex. Epigenetic inheritance
 Inheritance of traits by mechanisms not involving the nucleotide
sequence
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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
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2. Transcription initiation

Noncoding control regions on DNA



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promoter
 nearby control sequence on DNA
 binding of RNA polymerase & transcription factors
proximal control elements
 UTR located close to the promoter
enhancer
 distant control
sequences on DNA
 binding of activator
proteins
 “enhanced” rate (high level)
of transcription
Organization of a Typical Eukaryotic
Gene
Enhancer
(distal control elements)
Poly-A signal
sequence
Proximal
control elements
Exon
Intron
Exon
Intron
Termination
region
Exon
DNA
Downstream
Upstream
Promoter
Chromatin changes
Transcription
Exon
Primary RNA
transcript 5
(pre-mRNA)
Intron
Exon
Intron RNA
RNA processing
mRNA
G
P
5
Figure 19.5
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Cleared 3 end
of primary
transport
Coding segment
Translation
Protein processing
and degradation
Exon
RNA processing:
Cap and tail added;
introns excised and
exons spliced together
Transcription
mRNA
degradation
Intron
Poly-A
signal
P
P
Cap
5 UTR
(untranslated
region)
Start
codon
Stop
codon
Poly-A
3 UTR
(untranslated tail
region)
Model for Enhancer action

Enhancer DNA sequences


Activator proteins


distant control sequences
bind to enhancer sequence &
stimulates transcription
Silencer (repressor) proteins

bind to enhancer sequence &
block gene transcription
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Turning
on Gene movie
Transcription complex
Activator Proteins
• regulatory proteins bind to DNA at
Enhancer Sites
distant enhancer sites
• increase the rate of transcription
regulatory sites on DNA
distant from gene
Enhancer
Activator
Activator
Activator
Coactivator
A
E
F
B
TFIID
RNA polymerase II
H
Core promoter
and initiation complex
Initiation Complex at Promoter Site binding site of RNA polymerase
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Combinatorial Control of Gene
Activation
Enhancer
A particular
combination of
control elements

Albumin
gene
Control
elements
Crystallin
gene
Liver cell
nucleus
Will be able to
activate
transcription only
when the
appropriate
activator proteins
are present
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Promoter
Lens cell
nucleus
Available
activators
Available
activators
Albumin
gene not
expressed
Albumin
gene
expressed
Crystallin gene
not expressed
(a)
Liver cell
Crystallin gene
expressed
(b)
Lens cell
Coordinately Controlled Genes

Unlike the genes of a prokaryotic operon


Coordinately controlled eukaryotic genes
each have a promoter and control elements
The same regulatory sequences

Are common to all the genes of a group,
enabling recognition by the same specific
transcription factors
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3. Post-transcriptional control

Alternative RNA splicing

Different mRNA molecules produced from
the same primary transcript
 Depends on which RNA segments are treated as
introns and exons
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4. Regulation of mRNA degradation

Life span of mRNA determines amount
of protein synthesis

mRNA can last from hours to weeks


Ex. Long lived hemoglobin & short lived
growth factor
Determined by sequences towards the 3’
end UTR
 Enzymatic shortening of poly A tail  removal of
5’ cap  nuclease degrades mRNA
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RNA
processing movie
RNA interference

Small interfering RNAs (siRNA)

short segments of RNA (21-28 bases)



bind to mRNA
create sections of double-stranded mRNA
“death” tag for mRNA
 triggers degradation of mRNA

cause gene “silencing”


post-transcriptional control
turns off gene = no protein produced
siRNA
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
RNA interference by single-stranded
microRNAs (miRNAs)

Can lead to degradation of an mRNA or
block its translation
1 The microRNA (miRNA)
precursor folds
back on itself,
held together
by hydrogen
bonds.
An enzyme
22
called Dicer moves
along the doublestranded RNA,
cutting it into
shorter segments.
One strand of
3
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
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Hydrogen
bond
Blockage of translation
RNA interference
1990s | 2006
“for their discovery of
RNA interference —
gene silencing by
double-stranded RNA”
Andrew
Fire
AP
Biology
Stanford
Craig Mello
U Mass
5. Control of translation

Block initiation of translation stage

regulatory proteins attach to 5' end of UTR
of mRNA


prevent attachment of ribosomal subunits &
initiator tRNA
block translation of mRNA to protein
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Control
of translation movie
6-7. Protein processing & degradation

Protein processing


folding, cleaving, adding sugar groups,
targeting for transport
Protein degradation
ubiquitin tagging
 proteasome degradation

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Protein
processing movie
1980s | 2004
Ubiquitin

“Death tag”
mark unwanted proteins with a label
 76 amino acid polypeptide, ubiquitin
 labeled proteins are broken down
rapidly in "waste disposers"


AP
proteasomes
Aaron Ciechanover
Biology Israel
Avram Hershko
Israel
Irwin Rose
UC Riverside
Proteasome

Protein-degrading “machine”
cell’s waste disposer
 breaks down any proteins
into 7-9 amino acid fragments


cellular recycling
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play
Nobel animation

Proteasomes

Are giant protein complexes that bind
protein molecules and degrade them
3 Enzymatic components of the
1
Chromatin changes
Multiple ubiquitin molecules are attached to a protein
by enzymes in the cytosol.
The ubiquitin-tagged protein
2
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
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Protein
fragments
(peptides)


Duplications, rearrangements, and
mutations of DNA contribute to genome
evolution
The basis of change at the genomic level is
mutation

Accidents in cell division

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Can lead to extra copies of all or part of a
genome, which may then diverge if one set
accumulates sequence changes
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
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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 duplicated and diverged
Ancestral globin gene
Duplication of
ancestral gene
Mutation in
both copies
Transposition to
different chromosomes
Further duplications
and mutations
2
1
2
-Globin gene family
on chromosome 16
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1
G A
-Globin gene family
on chromosome 11
Evolution of Genes with Related
Functions: The Human Globin Genes

Subsequent duplications of these genes
and random mutations

Gave rise to the present globin genes, all of
which code for oxygen-binding proteins
Ancestral globin gene
Duplication of
ancestral gene
Mutation in
both copies
Transposition to
different chromosomes
Further duplications
and mutations
2
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1
2
-Globin gene family
on chromosome 16
1
G A
-Globin gene family
on chromosome 11
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
▫ Ex: similar amino acid sequence in
lactalbumin and lysozyme enzyme
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Rearrangements of Parts of Genes:
Exon Duplication and Exon Shuffling

A particular exon within a gene

Could be duplicated on one chromosome
and deleted from the homologous
chromosome
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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
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 or
recombination between copies of the same
element


Occasionally generates new sequence
combinations that are beneficial to the
organism
Some mechanisms

Can alter the functions of genes or their
patterns of expression and regulation
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