Download Regulation of Gene Expression

Regulation of Gene
Expression
An In-depth Review of Chapter 18
“While all cells of an organism have
all genes in the genome, not all
genes are expressed in every cell.”
“Both unicellular organisms and
multicellular organisms must
continually turn genes on and off in
response to signals from their
external and internal environments”
Gene Expression:
A gene (a segment of DNA) is undergoing
transcription.
Transcription leads to translation, which leads to
proteins.
This takes energy!
Cells don’t want to waste energy if they don’t
have too! There is no need to make
‘photoreceptors’ if the cell is inside your big toe.
Gene Regulation
How do you regulate things in the body?
“On/Off” switches: chromatin remodeling,
operator
“Dimmer” switches: microRNA, RNAi
Feedback Mechanisms
POSITIVE
Final product of the
reaction
accelerates the
pathway
Ex. Childbirth/Labor
NEGATIVE
Final product of the
reaction
inhibits/stops the
pathway
Ex. Tryptophan
Synthesis in E. coli
Negative
feedback 
A
Enzyme 1
B
D
Excess D
blocks a step
D
Enzyme 2
D
C
Enzyme 3
D
(a) Negative feedback
W
Enzyme 4
Positive
feedback +
X
Enzyme 5
Excess Z
stimulates a
step
Z
Y
Z
Z
Enzyme 6
Z
(b) Positive feedback
Overview Gene Regulation
PROKARYOTE
Simpler
Regulate at the
level of
transcription
lac & trp operon
EUKARYOTE
Much, much, much
more complex.
Regulate at any
level really.
Differential gene
expression leads to
cell differentiation
Prokaryotes  E. coli
“Consider an individual E. coli cell living in the
erratic environment of the human colon,
dependent for its nutrients on the whimsical
eating habits of the host.”
“If the environment is lacking the amino acid
tryptophan (which the bacterium needs to
survive), the cell responds but activating a
biochemical pathway that creates it.”
“Later if the host eats a tryptophan-rich meal,
the bacterial cells stops producing it (saves
energy)”
Okay… so the E. coli can inhibit and
turn on gene expression… but how?
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
trp operon
Promoter
Genes of operon
trpE
Operator
Start codon
mRNA 5
E
trpD
trpC
trpB
trpA
B
A
Stop codon
D
C
Polypeptide subunits that make up
enzymes for tryptophan synthesis
 Promoter: region of DNA where RNA poly binds
 Operator: “on/off” switch, controls if RNA poly can bind or
not. NO RNA POLY. BINDING = NO TRANSCTIPTION
 Operon: Whole segment of DNA including the promoter,
operator, and the genes they control.
trp operon
Promoter
Promoter
DNA
trpR
Regulatory
gene
3
mRNA
Genes of operon
trpE trpD
Operator
Start codon
mRNA 5
5
E
Protein
D
Inactive
repressor
 Promoter: region of DNA where RNA poly binds.
 Regulatory Gene: genes that are located away from the
operon itself but control the transcription of specific genes.
 Repressor: protein that binds to the operator that turns off
(represses) transcription.
DNA
No RNA made
mRNA
Active
repressor
Protein
Tryptophan
(corepressor)
 Co-repressor: smaller molecule that activates the
repressor protein.
 Repressible operon: pathway that is normally “on” that
can be inhibited by a repressor.
 Inducible operon: pathway that is normally “off” that can
be turned “on” (induced).
trp operon
OVERVIEW
YES
TRYPTOPHAN
 If trp is available the cell
won’t waste energy
making it.
 Repressor protein
combines with the
available trp (corepressor) and bind to
the operator which stops
the transcription of the
enzymes that make
tryptophan.
 Negative Feedback
NO
TRYPTOPHAN
Operon is always “on”
The cell will continue to
make repressors but
without trp (corepressor) in the
environment, the
repressor is not active.
Cell makes enzymes
that make trp for the
cell.
Prokaryotes  E. coli
“Consider an individual E. coli cell living in the
erratic environment of the human colon,
dependent for its nutrients on the whimsical
eating habits of the host.”
“Lactose (milk sugar) is available in the colon if
the host drinks milk.”
“Bacteria break down lactose into two
monosaccharides by the enzyme
Bgalactosidase.”
“If lactose is increased in the E. coli’s
environment then the concentration of
Bgalactosidase increases rapidly.”
Regulatory
gene
Promoter
Operator
lacZ
lacI
DNA
No
RNA
made
3
mRNA
RNA
polymerase
5
Active
repressor
Protein
(a) Lactose absent, repressor active, operon off
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
Promoter
Regulatory
gene
Operator
lacI
DNA
lacZ
No
RNA
made
3
mRNA
5
Protein
RNA
polymerase
Active
repressor
NO LACTOSE IN ENVIRONMENT = repressor is
active = whole operon off = no enzymes created
(because none are needed)
lac operon
DNA
lacI
3
mRNA
5
lacY
-Galactosidase
Permease
lacA
RNA
polymerase
mRNA 5
Protein
Allolactose
(inducer)
lacZ
Transacetylase
Inactive
repressor
 Inducer: smaller molecule that binds to a repressor
making it inactive.
LACTOSE PRESENT IN ENVIRONMENT = inducer
binds to repressor = repressor is inactivated =
operon stays on & enzymes are produced to break
down the lactose
lac operon
OVERVIEW
YES
LACTOSE
If lactose is available the
cell needs enzymes to
break it down.
Repressor protein
combines with the
available lactose
(inducer) which
inactivates the repressor.
This allows the cell to
make the enzyme.
NO
LACTOSE
Operon is normally
“off”
Repressor is active
because there is no
inducer to bind to it to
turn it off
no enzymes created
(because none are
needed)
Ok. Enough of the easy stuff.
Moving on to eukaryotes…
Differential Gene Expression
Many different cell types.
The differences in these cell types is not
because they have different DNA but rather
they are expressing different genes within
the same genome.
Prokaryotes regulate their genes by
controlling transcription… how do eukaryotes
regulate their genes?
Signal
All the boxes
in the picture
are areas
where
eukaryotes
can regulate
gene
expression.
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
mRNA in cytoplasm
Degradation
of mRNA
Translatio
n
Polypeptide
Protein processing
Complex.
Active protein
Degradation
of protein
Transport to cellular
destination
Cellular function
Signal
Chromatin (chromosome)
Modification:
NUCLEUS
Chromatin
Acetylation: loosen DNA structure
 makes it easier for transcription
to occur
Chromatin modification
DNA
Methylation: tightens DNA
structure  makes it harder for
transcription to occur
AKA:
Chromatin-modifying
enzymes provide initial
control of gene expression
by making DNA more or
less able to bind to
transcription machinery.
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intron
RNA processing
Tail
Cap
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
Signal
Transcription:
In order for transcription to
occur at all in eukaryotes,
enhancers and activators
interact with various
transcription factors to affect
gene expression.
NUCLEUS
Chromatin
Chromatin modification
DNA
Gene available
for transcription
Gene
Transcription
RNA
Primary transcript
AKA:
Complex folding and specific
binding occurs for every gene
that is transcribed.
Exon
Intron
RNA processing
Tail
Cap
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
Promoter
Activators
DNA
Enhancer
Distal control
element
Gene
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
mediator proteins
RNA
polymerase II
RNA
polymerase II
Transcription
initiation complex
RNA synthesis
Signal
RNA Processing:
Alternative RNA Splicing:
different mRNA molecules are
produced from the same
primary transcript.
NUCLEUS
Chromatin
Chromatin modification
DNA
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
mRNA Lifespan longer in
eukaryotes than prokaryotes.
Intron
RNA processing
Tail
Cap
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
Exons
DNA
Troponin T gene
Primary
RNA
transcript
RNA splicing
mRNA
or
Chromatin modification
Chromatin modification
• Small RNAs can promote the formation of
heterochromatin in certain regions, blocking
transcription.
Transcription
RNA processing
mRNA
degradation
Translation
• miRNA or siRNA can block the translation
of specific mRNAs.
Translation
Protein processing
and degradation
mRNA degradation
• miRNA or siRNA can target specific mRNAs
for destruction.
Noncoding
RNA’s Role
mRNA & proteins degrade over time
Much quicker in prokaryotes (which allows
them to adapt to new situations much more
rapidly than eukaryotes can)
Ubiquitin
Proteasome
Protein to
be degraded
Ubiquitinated
protein
Proteasome
and ubiquitin
to be recycled
Protein entering a
proteasome
Protein
fragments
(peptides)
Overview Gene Regulation
PROKARYOTE
Simpler
Regulate at the
level of
transcription
lac & trp operon
EUKARYOTE
Much, much, much
more complex.
Regulate at any level
really.
Differential gene
expression leads to
cell differentiation
Cell Differentiation
Cells express specific genes to become specialized in
structure and function
Embryology
Three main process that lead from a
fertilized egg to a fully developed organism.
1.) Cell Division
2.) Cell Differentiation (Specialize)
3.) Morphogenesis (form/distribution)
Cell Division
Cell Differentiation
From sperm and egg…
what tells each cell
which gene to express
at any given time in
development?
1.) Cytoplasmic
Determinants
2.) Inductions by nearby
cells
Morphogenesis
Spatial Organization
Homeotic genes (Hox genes)
Dorsal
Anterior
Left
Ventral
Right
Posterior
Mutated Hox Genes
Eye
Leg
Antenna
Wild type
Mutant
Mutated Hox Genes