Control of
Eukaryotic Genes
AP Biology
The BIG Questions…
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How are genes turned on & off in
eukaryotes?
How do cells with the same genes
differentiate to perform completely
different, specialized functions?
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Regulation of Gene Expression
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Gene
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Genome
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A complete set of genes of a given
species
Gene expression
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A DNA segment that contains all
the genetic information required to
encode RA and protein molecules
A process of gene transcription
and translation
Gene Regulation
A process of controlling
transcription and translation
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Types of Gene Expression
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Constitutive Expression
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Genes essential and necessary for life and are
continuously expressed. These are called
“housekeeping genes”
Induction and repression
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The expression levels of some genes fluctuate
in response to external signals
Evolution of gene regulation
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Prokaryotes
single-celled
 evolved to grow & divide rapidly
 must respond quickly to changes in
external environment

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exploit transient resources
Gene regulation

turn genes on & off rapidly

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flexibility & reversibility
adjust levels of enzymes
for synthesis & digestion
Outline
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Prokaryotic Regulation
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trp Operon
lac Operon
Eukaryotic Regulation
1. packing/unpacking DNA
5.
translation
2. Transcription
6.
protein processing
3. mRNA processing
7.
protein degradation
4. mRNA transport

Genetic Mutations

Cancer
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6
Prokaryotic Regulation
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Bacteria do not require the same
enzymes all the time
Enzymes are produced as needed
Francois Jacob and Jacques Monod
(1961) proposed the operon model to
explain regulation of gene expression
in prokaryotes
Operon is a group of structural and
regulatory genes that function as a
single unit
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Prokaryotic Regulation: The Operon Model
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Operon consist of three components
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Promoter
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Operator
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DNA sequence where RNA polymerase first attaches
to initiate transcription
Short segment of DNA
DNA sequence where active repressor binds
Short segment of DNA
Structural Genes/other regulatory sequences
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One to several genes coding for enzymes of a
metabolic pathway
Translated simultaneously as a block
Long segment of DNA
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Repressible Operons: The trp Operon
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The regulator codes for a repressor
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If tryptophan (an amino acid) is absent:
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Repressor is unable to attach to the operator
(expression is normally “on”)

RNA polymerase binds to the promoter

Enzymes for synthesis of tryptophan are produced
If tryptophan is present:

Combines with repressor as corepressor

Repressor becomes functional

Blocks synthesis of enzymes and tryptophan
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9
promoter
operator
regulator gene
structural genes
When the repressor
binds to the operator,
transcription is prevented.
active
repressor
regulator gene
promoter
operator
5
structural genes
inactive repressor
DNA
RNA polymerase
mRNA
enzymes
a. Tryptophan absent. Enzymes needed to synthesize tryptophan are produced.
RNA polymerase cannot bind to promoter.
DNA
active repressor
tryptophan
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inactive repressor
b. Tryptophan present. Presence of tryptophan prevents production of enzymes used to synthesize tryptophan.
3
Inducible Operons: The lac Operon

The regulator codes for a repressor (this is both a
repressible and inducible operon, so it exhibits
both positive and negative control)
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If lactose (a sugar that can be used for food) is
absent:
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Repressor attaches to the operator

Expression is normally “off”
If lactose is present:

It combines with repressor and renders it unable to bind
to operator

RNA polymerase binds to the promoter

The three enzymes necessary for lactose catabolism are
produced
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The lac Operon
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
RNA polymerase cannot bind to promoter.
regulator gene
promoter
structural genes
operator
DNA
active repressor
active repressor
a. Lactose absent. Enzymes needed to take up and use lactose are not produced.
RNA polymerase can bind to promoter.
DNA
inactive repressor
5
mRNA
active repressor
lactose
enzymes
b. Lactose present. Enzymes needed to take up and use lactose are produced only when lactose is present.
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12
3
Action of CAP
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
CAP binding site
promoter operator
DNA
RNA polymerase binds
fully with promoter.
cAMP
active CAP
inactive CAP
a. Lactose present, glucose absent (cAMP level high)
CAP binding site
promoter operator
DNA
RNA polymerase does
not bind fully with promoter.
inactive CAP
b. Lactose present, glucose present (cAMP level low)
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13
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Tryptophan Operon
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Attenuation of trp Operon
Lac Operon
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Evolution of gene regulation

Eukaryotes
multicellular
 evolved to maintain constant internal
conditions while facing changing
external conditions

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homeostasis
regulate body as a whole

growth & development
 long term processes

specialization
 turn on & off large number of genes

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must coordinate the body as a whole rather
than serve the needs of individual cells
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
3. mRNA processing
4. mRNA transport
5. translation
6. protein processing
7. protein degradation
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1. DNA packing
How do you fit all
that DNA into
nucleus?
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DNA coiling &
folding
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double helix
nucleosomes
chromatin fiber
looped
domains
chromosome
from DNA double helix to
AP Biology chromosome
condensed
Nucleosomes
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8 histone
molecules
“Beads on a string”
1st level of DNA packing
 histone proteins

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8 protein molecules
positively charged amino acids
bind tightly to negatively charged DNA
DNA packing as gene control
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Degree of packing of DNA regulates transcription
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tightly wrapped around histones
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no transcription
genes turned off
 heterochromatin
darker DNA (H) = tightly packed
 euchromatin
lighter DNA (E) = loosely packed
H
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E
DNA methylation
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Methylation of DNA blocks transcription factors
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no transcription
 genes turned off
attachment of methyl groups (–CH3) to cytosine

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C = cytosine
nearly permanent inactivation of genes

ex. inactivated mammalian X , 2 chromosome = Barr body
HHMI X Inactivation
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X Chromosome Inactivation: Mozaicism
Histone acetylation
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Acetylation of histones unwinds DNA
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loosely wrapped around histones
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attachment of acetyl groups (–COCH3) to histones
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enables transcription
genes turned on
conformational change in histone proteins
transcription factors have easier access to genes
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2. Transcription initiation
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Control regions/regulatory sequences on DNA
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promoter
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nearby control sequence on DNA
binding of RNA polymerase & transcription factors
“base” rate of transcription
enhancer
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distant control
sequences on DNA
binding of activator
proteins
“enhanced” rate (high level)
of transcription
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Model for Enhancer action
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Enhancer DNA sequences
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Activator proteins
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distant control sequences
bind to enhancer sequence
& stimulates transcription
Silencer 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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3. Post-transcriptional control
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Alternative RNA splicing

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variable processing of exons “exon
shuffling” creates a family of proteins
4. Regulation of mRNA degradation

Life span of mRNA determines amount
of protein synthesis

mRNA can last from hours to weeks
AP Biology
RNA
processing movie
RNA interference
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Small interfering RNAs (siRNA)

short segments of RNA (21-28 bases)

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bind to mRNA
create sections of double-stranded mRNA
“death” tag for mRNA
 triggers degradation of mRNA

cause gene “silencing”
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post-transcriptional control
turns off gene = no protein produced
siRNA
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Action of siRNA
dicer
enzyme
mRNA for translation
siRNA
double-stranded
miRNA + siRNA
breakdown
enzyme
(RISC)
mRNA degraded
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functionally
turns gene off
5. Control of translation
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Block initiation of translation stage

regulatory proteins attach to 5' end of mRNA
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prevent attachment of ribosomal subunits &
initiator tRNA
block translation of mRNA to protein
AP Biology
Control
of translation movie
6-7. Protein processing & degradation
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Protein processing
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folding, cleaving, adding sugar groups,
targeting for transport
Protein degradation
ubiquitin tagging
 proteasome degradation

AP Biology
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


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cellular recycling
6
7
Gene Regulation
protein
processing &
degradation
1 & 2. transcription
- DNA packing
- transcription factors
5
4
initiation of
translation
mRNA
processing
3 & 4. post-transcription
- mRNA processing
- splicing
- 5’ cap & poly-A tail
- breakdown by siRNA
5. translation
- block start of
translation
1 2
initiation of
transcription
AP Biology mRNA splicing
3
6 & 7. post-translation
- protein processing
- protein degradation
4
mRNA
protection
Essential knowledge 3.B.1: Gene regulation
results in differential gene expression, leading to
cell specialization.
a. Both DNA regulatory sequences, regulatory genes, and
small regulatory RNAs are involved in gene expression.
1. Regulatory sequences are stretches of DNA that interact
with regulatory proteins to control transcription.
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
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Promoters
Terminators
Enhancers
2. A regulatory gene is a sequence of DNA encoding a
regulatory protein or RNA.
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Essential knowledge 3.B.1: Gene regulation
results in differential gene expression, leading to
cell specialization.
b. Both positive and negative control mechanisms regulate gene expression in
bacteria and viruses.
1. The expression of specific genes can be turned on by the presence of an inducer.
(Positive control: activator protein induces transcription. No repressor must be
overridden)
2. The expression of specific genes can be inhibited by the presence of a repressor.
(Negative control: repressor protein present which prevents transcription,
inducer (usually a small molecule) is needed to allow initiation of transcription)
3. Inducers and repressors are small molecules that interact with regulatory proteins
and/or regulatory sequences.
4. Regulatory proteins inhibit gene expression by binding to DNA and blocking
transcription (negative control).
5. Regulatory proteins stimulate gene expression by binding to DNA and stimulating
transcription (positive control) or binding to repressors to inactivate repressor
function.
6. Certain genes are continuously expressed; that is, they are always turned “on,”
e.g., the ribosomal genes.
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Essential knowledge 3.B.1: Gene regulation
results in differential gene expression, leading to
cell specialization.
c. In eukaryotes, gene expression is complex and control involves regulatory genes,
regulatory elements and transcription factors that act in concert.
1. Transcription factors bind to specific DNA sequences and/or other regulatory proteins.
2. Some of these transcription factors are activators (increase expression), while others are
repressors (decrease expression).
3. The combination of transcription factors binding to the regulatory regions at any one time
determines how much, if any, of the gene product will be produced.
d. Gene regulation accounts for some of the phenotypic differences between organisms with
similar genes.
LO 3.18 The student is able to describe the connection between the regulation of gene
expression and observed differences between different kinds of organisms.
LO 3.19 The student is able to describe the connection between the regulation of gene
expression and observed differences between individuals in a population.
LO 3.20 The student is able to explain how the regulation of gene expression is essential for
the processes and structures that support efficient cell function.
LO 3.21 The student can use representations to describe how gene regulation influences cell
products and function.
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Resources
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Master Genes Control Basic Body Plans
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Halting Hepatitis: Micro RNA as a Gene Regulator
Inherited Pollution: Environment Altering Expression
Micro RNA: Tiny Genes Big Role
Aging Secret
NOVA: Epigenetics
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Gene Regulation in Eukaryotes Website
Epigenetics Supplementary Materials
Medical Microbiology: Regulation of Gene Expression
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