Transcript Gene Regulation Notes

Chapter 18
Regulation of Gene
Expression
Overview: Conducting the Genetic Orchestra
• Prokaryotes and eukaryotes alter gene
expression in response to their changing
environment
• Responding through conservation of energy
and resources favors these bacteria in terms of
natural selection
• In other words: Waste not . . . Want not!
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18.1: Bacteria respond to environmental change
• One method employed by bacteria we have
already discussed - feedback inhibition
• Feedback inhibition can control biosynthetic
pathways.
• The enzyme product inhibits the enzyme activity,
turning off production of the product
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18.1: Bacteria respond to environmental change by
regulation transcription
• A different method is to directly regulate
transcription.
• Prokaryotic DNA is often under “coordinate
control” – meaning multiple polypeptides are
made from the same stretch of DNA (makes it
easy to turn all the genes on or off).
• Gene regulation is how the switch is turned on
or off – in prokaryotes the regulatory parts are
called an operon.
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18.1: What is an operon?
• An operon consists of:
– Operator – a segment of DNA within the
promotor region that acts as the switch for
transcription
– Promotor – a segment of DNA where RNA
Polymerase II binds and starts transcription
– Genes – DNA that codes for polypeptides that
form enzymes or other cell products (trp
operon – codes for enzymes which make
tryptophan)
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18.1: The trp operon
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18.1: How to turn off the trp operon
• The operon can be switched off by a protein
repressor (ex. trpR repressor)
• The repressor prevents gene transcription by
binding to the operator and blocking RNA
polymerase
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18.1: Where do repressor proteins come from?
• The repressor is the product of a separate
regulatory gene on the DNA
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18.1: How is the repressor made active?
• The repressor is made active by binding with a
corepressor (in this case an actual tryptophan
molecule). Result = no RNA made.
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18.1: How is repressor made inactive?
• The repressor is inactive when no corepressor
(tryptophan) is available to bind with it. Result
= RNA is made.
• trp operon animation
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18.1: Follow up questions
1. In terms of the trp operon what would happen if
tryptophan were present at high levels in the cell?
2. Would the trpR be active or inactive?
3. What part of the operon is actually blocked by the
repressor?
4. What is the repressor actually blocking?
5. Where does the repressor protein actually come
from?
6. Why do cells seek to regulate gene expression?
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Fig. 18-3
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
E
trpD
trpB
trpA
B
A
Stop codon
D
C
Polypeptide subunits that make up
enzymes for tryptophan synthesis
(a) Tryptophan absent, repressor inactive, operon on
DNA
No RNA made
mRNA
Active
repressor
Protein
trpC
Tryptophan
(corepressor)
(b) Tryptophan present, repressor active, operon off
18.1 Repressible and Inducible Operons: Two
Types of Negative Gene Regulation
• Repressible operon - one that is usually on;
binding of a repressor to the operator shuts off
transcription (ex. trp operon)
• Inducible operon - one that is usually off; a
molecule called an inducer inactivates the
repressor and turns on transcription (ex. lac
operon)
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18.1 Repressible and Inducible Operons: Two
Types of Negative Gene Regulation
Inducible
Repressible
(Corepressor)
(Inducer)
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18.1 Lac operon - Inducible
• The lac operon contains genes that code for
enzymes used in the hydrolysis of lactose
• The lac repressor is active and keeps the lac
operon off (blocks RNA polymerase II)
• The inducer (lactose) inactivates the
repressor to turn the lac operon on – the
repressor leaves the operator
• lac operon animation
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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
Fig. 18-4b
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
Transacetylase
18.1 Inducible vs. Repressible Enzymes and
Negative Control of Genes
• Inducible enzymes usually function in catabolic
pathways; their synthesis is induced by a
chemical signal
• Repressible enzymes usually function in
anabolic pathways; their synthesis is repressed
by high levels of the end product
• Regulation of the trp and lac operons involves
negative control of genes because operons are
switched off by the active form of the repressor
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Positive Gene Regulation
• 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 (adenosine monophosphate)
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Positive Gene Regulation
• Activated CAP attaches to the promoter of the
lac operon and increases the affinity of RNA
polymerase, thus accelerating transcription
• CAP positive regulation animation
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Follow up questions
• What is the difference between repressible and
inducible enzymes?
• What is the difference between negative and
positive gene regulation?
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Concept 18.2: Eukaryotic gene expression can be
regulated at any stage
• Points at which gene expression can be
regulated: chromatin mod., transcription, RNA
processing, transport to cytoplasm, translation,
protein processing, transport to cell destination
• In multicellular organisms gene expression is
essential for cell specialization
• Although gene expression is regulated at many
stages, we will focus on eukaryotic gene
regulation at the stage of transcription.
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Differential Gene Expression
• Almost all the cells in an
organism are genetically
identical
• Differences between cell
types result from differential
gene expression, the
expression of different genes
by cells with the same
genome
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18.2 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 (particularly RNA
polymerase)
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18.2 Organization of a Typical Eukaryotic Gene
• Associated with most eukaryotic genes are
control elements, segments of noncoding DNA
that help regulate transcription by binding certain
proteins
• Control elements can be proximal (close) to the
gene, or distal (far from the gene, thousands of
bases away)
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18.2 Organization of a Typical Eukaryotic Gene
• Other parts of the gene include the promoter,
coding sequence (introns and exons), the poly A
signal sequence and the termination region
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18.2 The Roles of Transcription Factors
• Eukaryotic RNA polymerase requires the
assistance of proteins called transcription factors
• General transcription factors are essential for the
transcription of all protein-coding genes
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18.2 The Roles of Transcription Factors
• An activator is a protein that binds to an
enhancer (at the distal control element) and
stimulates transcription of a gene
• Bound activators interact with mediator
proteins and transcription factors at the
promoter
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Promoter
Activators
DNA
Enhancer
Distal control
element
Gene
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
mediator proteins
1. Enhancers are distal control
elements
2. Activators bind to enhancers
3. Activators on enhancer will
interact with transcription factors
and mediator proteins
Fig. 18-9-3
Promoter
Activators
DNA
Enhancer
Distal control
element
4. The activators are
brought into contact
with the proteins by a
DNA bending protein
5. The enhancer,
activator, transcription
factors, mediator
proteins, promoter
and polymerase all
form a transcription
initiation complex.
Gene
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
mediator proteins
RNA
polymerase II
RNA
polymerase II
Transcription
initiation complex
RNA synthesis
18.2 The Roles of Transcription Factors
• Some transcription
factors function as
repressors, inhibiting
expression of a
particular gene
• Some activators and
repressors act indirectly
by influencing chromatin
structure to promote or
silence transcription
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18.2 Mechanisms of Post-Transcriptional Regulation
• Transcription alone does not account for gene
expression
• Regulatory mechanisms can operate at various
stages after transcription to fine-tune gene
expression:
– Alternative RNA splicing
– mRNA degradation
– Initiation of translation
– Protein processing and degradation
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Concept 18.3: Noncoding RNAs play multiple roles
in controlling gene expression
• Only a small fraction of DNA codes for proteins,
rRNA, and tRNA
• A significant amount of the genome may be
transcribed into noncoding RNAs
• Noncoding RNAs regulate gene expression at two
points: mRNA translation and chromatin
configuration
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18.3 Effects on mRNAs by MicroRNAs and Small
Interfering RNAs
• MicroRNAs (miRNAs) are small singlestranded RNA molecules that can bind to
mRNA
• These miRNAs can degrade mRNA or block its
translation
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Fig. 18-13
Hairpin
miRNA
Hydrogen
bond
Dicer
miRNA
5 3
(a) Primary miRNA transcript
mRNA degraded
miRNAprotein
complex
Translation blocked
(b) Generation and function of miRNAs
18.3 RNA interference (RNAi) and Small
Interfering RNAs (siRNAs)
• The phenomenon of inhibition of gene
expression by RNA molecules is called RNA
interference (RNAi)
• RNAi is caused by small interfering RNAs
(siRNAs)
• siRNAs and miRNAs are similar but form from
different RNA precursors
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18.3 Chromatin Remodeling and Silencing of
Transcription by Small RNAs
• siRNAs play a role in heterochromatin formation
and can block large regions of the chromosome
• siRNAs that convert euchromatin to
heterochromatin block transcription of specific
genes
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18.1: The trp operon
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18.1: The trp operon – active repressor
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18.1: The lac operon – active repressor
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18.1: The lac operon – inactive repressor
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