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Control of
Gene
Expression
AP Chap 18
Prokaryotes and eukaryotes alter gene
expression in response to their changing
environment.
Clustering of genes producing mRNAs
for proteins (enzymes) in a pathway make
the control easier and more efficient.
Bacteria often respond to
environmental change by
regulating transcription
• Natural selection has favored
bacteria that produce only the
products needed by that cell.
We are
very
conservative!
How can cells regulate their
production of enzymes for
metabolic processes?
by feedback inhibition or
by gene regulation
Fig. 18-2
Precursor
Feedback
inhibition
trpE gene
Enzyme 1
trpD gene
Regulation
of gene
expression
Enzyme 2
trpC gene
trpB gene
Enzyme 3
trpA gene
Tryptophan
(a) Regulation of enzyme
activity
(b) Regulation of enzyme
production
• Gene expression in bacteria is
controlled by the operon model.
• The operon model works on a
feedback process.
• The operon model for gene
regulation was first described by
Jacob and Monod in 1961.
Jacob and Monod
OPERONS
• An operon is the entire stretch of
DNA that includes the promoter, the
operator, and the genes that they
control. The regulator may be located away
from the operon unit.
DNA
regulator promoter
operator genes
Remember: Clustering of genes for proteins (enzymes)
in a pathway make the control easier and more
efficient.
regulator
promoter
operator genes
STOP
RNA polymerase
binds here
Makes a
repressor
which binds
to operator
and stops/starts
transcription
GO
Induction System: inducible operon
think, induce……to turn on
• System initially off
• The system is off because an active
repressor is bound to the operator.
Fig. 18-4a
Regulatory
gene
Promoter
Operator
lacI
DNA
lacZ
No
RNA
made
3
mRNA
5
Protein
RNA
polymerase
Active
repressor
(a) Lactose absent, repressor active, operon off
• If the lacI gene is deleted, how will
transcription of the lac operon be
affected?
A)Transcription will always be turned off
B)Transcription will always be turned on.
C)No effect will be observed.
B
• The presence of an inducer (usually a
substrate that needs to be broken down)
turns it on.
• The inducer binds to the repressor and
makes it inactive so transcription can occur.
• The inducer acts as an allosteric effector
and changes the shape of the repressor.
• Ex- Lac (lactose) operon used to produce
enzymes to break down lactose (milk sugar).
• The inducer in the lac operon is lactose
(more specifically allolactose).
Fig. 18-4b
Lactose present, repressor inactive,
operon ON
lac operon
DNA
lacZ
lacY
-Galactosidase
Permease
lacI
3
mRNA
5
RNA
polymerase
mRNA 5
Protein
Allolactose
(inducer)
lacA
Inactive
repressor
(b) Lactose present, repressor inactive, operon on
VCAC: Molecular Processes: Lac Operon: First Look
http://highered.mheducation.com/sites/0072995246/st
udent_view0/chapter7/the_lac_operon.html
Transacetylase
• A mutation in the lacI gene leads to the
inability of the repressor to bind the inducer.
In the presence of lactose, how will this
mutation affect transcription of the lac
operon?
A) Transcription will always be turned off.
B) Transcription will always be turned on.
A, the repressor will always be active
and bound to the operator.
Repressible System
• System initially ON, transcription
ongoing and making a product
• Operator can be turned off by a
repressor which is made active by being
activated by a corepressor molecule
(usually the end product)
• The product acts as a corepressor
inhibiting further synthesis of enzymes
involved in the process.
• Ex – tryptophan operon –
trytophan (product) acts as a
corepressor inhibiting further
synthesis of enzymes involved in
the process
Fig. 18-3a
Tryptophan absent, repressor
inactive, operon ON
trp operon
Promoter
Promoter
Genes of operon
DNA
trpR
Regulatory
gene
mRNA
5
Protein
trpE
3
Operator
Start codon
mRNA 5
RNA
polymerase
Inactive
repressor
trpD
trpC
trpB
trpA
B
A
Stop codon
D
C
Polypeptide subunits that make up
enzymes for tryptophan synthesis
E
(a) Tryptophan absent, repressor inactive, operon on
Fig. 18-3b-1
Tryptophan present, repressor
active, operon OFF
DNA
No RNA made
mRNA
Active
repressor
Protein
(repressor)
Tryptophan
(corepressor)
(b) Tryptophan present, repressor active, operon off
http://highered.mheducation.com/sites/00729
95246/student_view0/chapter7/the_trp_opero
n.html
INDUCIBLE
REPRESSIBLE
OFF
turned on by
inducer (substrate)
used in catabolic
pathways
ON
turned off by
corepressor (product)
used in anabolic
pathways
Both use allosteric effectors and are
NEGATIVE CONTROL.
Positive Gene Regulation
• Some operons are also subject to
positive control through a stimulatory
protein, such as catabolite activator
protein (CAP), an activator of
transcription
• When glucose (a preferred food source
of E. coli) is scarce, CAP is activated by
binding with cyclic AMP
• Activated CAP attaches to the promoter
of the lac operon and increases the
affinity of RNA polymerase, thus
accelerating transcription
Fig. 18-5
Promoter
Operator
DNA
lacI
lacZ
RNA
polymerase
binds and
transcribes
CAP-binding site
Active
CAP
cAMP
Inactive lac
repressor
Inactive
CAP
Allolactose
(a) Lactose present, glucose scarce (cAMP level
high): abundant lac mRNA synthesized
Promoter
DNA
lacI
CAP-binding site
Inactive
CAP
Operator
lacZ
RNA
polymerase less
likely to bind
Inactive lac
repressor
(b) Lactose present, glucose present (cAMP level
low): little lac mRNA synthesized
• When glucose levels increase, CAP
detaches from the lac operon, and
transcription returns to a normal rate
• CAP helps regulate other operons that
encode enzymes used in catabolic
pathways
The lac operon responds to lactose, while
sensing the levels of available glucose.
Lactose
Glucose
Lac mRNA
transcription
absent
high
“off”
present
low
“on”
What if lactose is high and glucose is
high, will lac mRNA transcription be off
or on?
Control of Gene Expression in
Eukaryotes
• In response to environmental signals
• More complicated than prokaryotes due to
specialized cells. No operons in eukaryotes.
• Essential for development and cell
specialization in multicellular organisms
• RNA is important in eukaryotic gene
expression.
• All cells contain the same DNA so
controlling gene expression is essential.
• Human cells only 20% genes expressed;
only 1.5% code for proteins!
• Commonly occurs at level of transcription;
hence,
gene expression = transcription of DNA
http://www.dnalc.org/resources/3d/09-how-much-dna-codes-for-protein.html
But, eukaryotic
gene
expression
< A>
can be regulated at any stage
Fig. 18-6
Signal
NUCLEUS
Chromatin
Chromatin modification
DNA
Gene available
for transcription
In the nucleus
Gene
Transcription
RNA
Exon
Primary transcript
Intron
RNA processing
Tail
Cap
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translatio
n
Polypeptide
Protein processing
Active protein
Degradation
of protein
Transport to cellular
destination
Cellular function
In the cytoplasm
Fig. 18-6a
Signal
NUCLEUS
Chromatin
Chromatin modification
DNA
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intron
RNA processing
Tail
Cap
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
Fig. 18-6b
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypeptide
Protein processing
Active protein
Degradation
of protein
Transport to cellular
destination
Cellular function
1) Chromatin Modification
• Heterochromatin – tightly wound DNA so
genes not expressed
• Euchromatin – DNA spread out, genes can
be expressed
Chemical modification:
• by histone acetylation which keeps
chromatin spread out and
• methylation (CH3) of DNA which keeps DNA
tightly packed and so inhibits transcription.
Fig. 18-7
http://www.d
nalc.org/reso
urces/3d/08how-dna-ispackagedadvanced.ht
ml
Histone
tails
DNA
double helix
Amino
acids
available
for chemical
modification
(a) Histone tails protrude outward from a
nucleosome
Unacetylated histones
Acetylated histones
(b) Acetylation of histone tails promotes loose
chromatin structure that permits transcription
Histone
acetylation
The effect of methylated DNA
Methylated
DNA
inhibits
transcription.
Epigenetic inheritance – not involve DNA
sequence but inherited defects in
chromatin modification enzymes
There may be more
to inheritance than
genes alone. New
clues reveal that a
second epigenetic
chemical code sits
on top of our regular
DNA and controls
how our genes are
expressed.
http://www.youtube.com/watch?v=OOiCu5kzGxg
NOVA | A Tale of Two Mice
Epigenetic effects in mice
• The mice were identical (so same genes).
Why are they different?
• What chemical modification occurred in the
“normal” mouse?
• What happened when mice were fed BPA?
• What happened when mice were feed
nutrients (soy) containing methylated
molecules?
How do environmental factors
affect gene expression?
• Mechanisms may involve DNA
methylation and histone acetylation
• Diet, chemicals, metals, and stress are
known to affect DNA methylation.
• Other enzymes have been identified for
demethylation, phosphorylation, and
many others.
• For example, methylation of cytosine(s) in
the promoter region could prevent the
binding of transcription factors or create
binding sites for complexes that deacetylate
neighboring histones that in turn compact
the chromatin, encouraging a gene to
become silent.
• A similar mechanism is now recognized in a
number of cancers. There is also indirect
evidence to suggest that methylation could
apply to a number of complex diseases,
including schizophrenia.
2) Transcription Level
• Regulation of transcription initiation:
DNA control elements (enhancers)
located away from the gene bind
specific transcription factors (tf’s) at
the gene.
• Bending of DNA is necessary to enable
activators in the enhancers to contact
tf’s at the promoter, initiating
transcription.
Fig. 18-9-1
Activators
Promoter
DNA
Enhancer
Distal control
element
TATA
box
Gene
Fig. 18-9-2
Promoter
Activators
DNA
Enhancer
Distal control
element
Gene
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
mediator proteins
Fig. 18-9-3
Promoter
Activators
DNA
Enhancer
Distal control
element
Gene
TATA
box
General
transcription
factors
DNA-bending
protein
Bending of DNA
enables activators
to contact proteins
at the promoter,
initiating
transcription.
Group of
mediator proteins
RNA
polymerase II
RNA
polymerase II
Transcription
initiation complex
RNA synthesis
Fig. 18-UN7
Specific enhancers control the
expression of genes.
Fig. 18-10
Enhancer Promoter
Control
elements
Albumin gene
Crystallin gene
LIVER CELL
NUCLEUS
Available
activators
LENS CELL
NUCLEUS
Available
activators
Albumin gene
not expressed
Albumin gene
expressed
Crystallin gene
not expressed
(a) Liver cell
Crystallin gene
expressed
(b) Lens cell
Post-transcriptional Control
•
•
•
•
RNA processing
Translation
mRNA degradation
Protein Processing and Degradation
RNA Processing
• Alternative RNA splicing – produce
different proteins
Fig. 18-11
Exons
DNA
Troponin T gene
Primary
RNA
transcript
RNA splicing
mRNA
or
mRNA Degradation
• mRNA can last a long time and be
subject to various intron splicing
• The mRNA life span is determined in
part by sequences in the leader and
trailer regions
Translation
• Initiation of translation can be
controlled via regulation of initiation
factors
Protein Processing and Degradation
• Alteration of polypeptide - can be cut,
groups (lipids, sugars) added, or
transported to target locations
• Selective degradation of proteins – the
protein ubiquitin is added to proteins for
degradation. Proteasomes (like garbage
disposals) recognize them and destroy
them.
Fig. 18-12
Ubiquitin
Proteasome
Protein to
be degraded
Ubiquitinated
protein
Proteasome
and ubiquitin
to be recycled
Protein entering a
proteasome
Protein
fragments
(peptides)
Remember
• Prokaryotic gene control: several
genes controlled by one promoter in
operon systems, mainly controlled at
transcription level.
• Eukaryotic gene control: one gene
controlled by one promoter, no
operators but have specific enhancers,
can be controlled at any level.
How important is RNA?
Noncoding RNA’s
play multiple roles in
controlling gene
expression.
RNAi’s
RNA Interference molecules
• They are noncoding RNAs that regulate
(interfere with) gene expression at
three points:
1. chromatin modification
2. block translation
3. mRNA degradation
•
epigenetics
Were used originally by cells to fiend
http://www.teachersdomain.org/asset/lsps0
off viruses
7_vid_rnai/
Types of RNAi’s
1. MicroRNAs (miRNA’s) – small singlestranded RNA’s that interfere with
mRNA and translation
An estimated 1/3 of human genes are
regulated by miRNAs.
2. Small interfering RNA’s (siRNA’s)
double-stranded RNA formed when
cells cut up intruding RNA. siRNA’s
are involved in formation of
heterochromatin as well as alter
translation.
Fig. 18-13
Hairpin
miRNA
Hydrogen
bond
Dicer
miRNA
5 3
(a) Primary miRNA transcript
miRNAprotein
complex
Long RNA precursors fold
on themselves and look like
hairpins. The hairpins are
cut off and an enzyme
called dicer trims the ends.
One strand becomes a
microRNA (miRNA).
mRNA degraded
Translation blocked
(b) Generation and function of miRNAs
Small Interfering RNA’s (siRNAs)
• Small pieces of double-stranded RNA
formed when cells cut up intrudingRNA.
• siRNAs are involved in formation of
heterochromatin as well as alter
translation.
•Double stranded RNA
is introduced into a cell
and gets chopped up
by the enzyme dicer to
form siRNA.
•siRNA binds to its
corresponding mRNA
which is then cut
rendering it inactive.
• siRNAs and miRNAs are
similar but form from different
RNA precursors
• Both interfere with gene
expression
Practical use of RNAi’s
• RNA interference (RNAi), is being explored by
researchers as a therapeutic approach to treating a
host of diseases. A genetic malfunction is causing a
patient to lose her vision because of the overproduction of blood vessels in her eyes. To treat this
genetic malfunctioning, scientists attempt to
manipulate the mechanism so that genes that
normally trigger production of blood vessels instead
do the opposite.
http://www.teachersdomain.org/asset/lsps07_vid_rnaitherapy/
Cancer notes are NOT on the test!
CANCER AND GENE EXPRESSION
Cancer results from genetic changes
that affect cell cycle control
• Cancer can be caused by mutations to
genes that regulate cell growth and
division
- mutagens are chemicals, X-rays,
tumor viruses in animals
Fig. 18-21c
EFFECTS OF MUTATIONS
Protein
overexpressed
Cell cycle
overstimulated
(c) Effects of mutations
Protein absent
Increased cell
division
Cell cycle not
inhibited
Oncogenes and Proto-Oncogenes
• Oncogenes are cancer-causing genes
• Proto-oncogenes are the
corresponding normal cellular genes
that are responsible for normal cell
growth and division
Conversion of a proto-oncogene to an
oncogene can lead to abnormal
stimulation of the cell cycle
• Amplification of normal growthstimulating gene
• Translocation of growth gene under
control of a more active promoter
• Point mutation in control element or
gene itself to make a hyperactive or
degradation resistant growth protein.
Fig. 18-20
Proto-oncogene
DNA
Translocation or
transposition:
Point mutation:
Gene amplification:
within a control element
New
promoter
Normal growthstimulating
protein in excess
Oncogene
Normal growth-stimulating
protein in excess
Normal growthstimulating
protein in excess
within the gene
Oncogene
Hyperactive or
degradationresistant protein
Tumor-Suppressor Genes
• help prevent uncontrolled cell growth
• Tumor-suppressor proteins
–Repair damaged DNA
–Control cell adhesion
–Inhibit the cell cycle (ras and p53)
–Activate suicide genes in apoptosis
if DNA can’t be repaired (p53
protein)
How do cancer genes work?
• 30% cancers – ras proto-oncogene gene is
mutated
Ras gene codes for a protein that stimulates the
production of a cell cycle protein
• 50% cancers – p53 gene mutated; codes for a
transcription factor for growth-inhibiting
proteins. These proteins bind to a p21 gene
whose product binds to CDK’s and halt cell
cycle. It can also activate DNA repair genes or
“suicide genes” if DNA can’t be repaired.
Fig. 18-21b
p53 gene and DNA repair
2 Protein kinases
MUTATION
3 Active
form
of p53
UV
light
1 DNA damage
in genome
DNA
Protein that
inhibits
the cell cycle
(b) Cell cycle–inhibiting pathway
Defective or
missing
transcription
factor, such
as p53, cannot
activate
transcription
P53 and suicide genes
Multistep Model of Cancer Development
• More than one somatic mutation is
needed
• Both alleles must be defective
• In some, genes for telomerase
becomes activated and cells divided
continually
Inherited Predisposition and Other Factors
Contributing to Cancer
• Individuals can inherit oncogenes or
mutant alleles of tumor-suppressor
genes
• Inherited mutations in the tumorsuppressor gene are common in
individuals with colorectal cancer
• Mutations in the BRCA1 or BRCA2
gene are found in at least half of
inherited breast cancers
• Even if you have
cancer genes, it does
not mean you will
have cancer.
• Genes can be
modified by siRNA’s,
epigenesis, and the
environment