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Colonie High AP Biology DeMarco/Goldberg
Chapter 16
Regulation of Gene
Expression
The BIG Questions…
How are genes turned on & off?
How do cells with the same genes
differentiate to perform completely different,
specialized functions in multicellular
eukaryotes?
Bacterial Metabolism
Bacteria need to respond quickly to
changes in their environment
ex. if have enough of a product,
need to stop production
why? waste of energy to produce more
how? stop production of synthesis enzymes
ex. if find new food/energy source,
need to utilize it quickly
why? metabolism, growth, reproduction
how? start production of digestive enzymes
Reminder: Regulation of Metabolism
Feedback inhibition
product acts
as an allosteric
inhibitor of
1st enzyme in
tryptophan
pathway
= inhibition-
Another Way to Regulate Metabolism
Gene regulation
block transcription of genes for all enzymes in tryptophan pathway saves energy by
not wasting it on unnecessary protein synthesis
= inhibition-
Gene Regulation in Bacteria
Control of gene expression enables
individual bacteria to adjust their
metabolism to environmental change
Cells vary amount of specific enzymes
by regulating gene transcription
turn genes on or turn genes off
ex. if you have enough tryptophan in your
cell then you don’t need to make enzymes
used to build tryptophan
waste of energy!
turn off genes which codes for enzymes
Colonie High AP Biology DeMarco/Goldberg
Genes Grouped Together
Operon genes grouped together with related functions
ex. enzymes in a synthesis pathway
promoter = RNA polymerase binding site single promoter controls transcription of all
genes in operon
transcribed as 1 unit & a single mRNA is made
operator = DNA binding site of regulator protein
So how can genes be turned off?
First step in protein production?
transcription
stop RNA polymerase!
Repressor protein
binds to DNA near promoter region
blocking RNA polymerase
binds to operator site on DNA
blocks transcription
operatorpromoter
Repressor Protein Model
DNATATA
RNApolymerase
repressor
repressor repressor protein
Operon: The operator, promoter & genes they control
serve as a model for gene regulation
gene1 gene2 gene3 gene4RNA
polymerase
Repressor protein turns off gene by
blocking RNA polymerase binding site.operatorpromoter
Repressible Operon: Tryptophan
DNATATA
RNApolymerase
repressor
tryptophan (a corepressor)
repressor repressor protein
repressortryptophan – repressor protein
complex
Synthesis Pathway Model
When excess tryptophan is present,
binds to tryp repressor protein &
triggers repressor to bind to DNA.
(blocks [represses] transcription)
gene1 gene2 gene3 gene4RNA
polymerase
conformational change in
repressor protein!
Tryptophan Operon
What happens when tryptophan is present?
Don’t need to make tryptophan-building enzymes!
Tryptophan binds allosterically to regulatory protein.
operatorpromoter
Inducible Operon: Lactose
DNATATA
repressor repressor protein
repressorlactose – repressor protein
complex
lactose
repressor gene1 gene2 gene3 gene4
Digestive pathway model
When lactose is present, binds to
lac repressor protein & triggers
repressor to release DNA
(induces transcription)
RNApolymerase
conformational change in
repressor protein!
repressorRNA
polymerase
Colonie High AP Biology DeMarco/Goldberg
Lactose Operon
What happens when glucose is not available
and lactose is present?
Need to make lactose-digesting enzymes!
Lactose binds allosterically to regulatory protein.
Operon Summary
Repressible operon
usually functions in anabolic pathways
synthesizing end products
when end product is present in excess,
cell allocates resources to other uses
Inducible operon
usually functions in catabolic pathways
digesting nutrients to simpler molecules
produce enzymes only when nutrient is
available
cell avoids making proteins that have nothing
to do, cell allocates resources to other uses
Jacob & Monod: lac Operon
Francois Jacob & Jacques Monod
first to describe operon system
coined the phrase “operon”
1961 | 1965
Francois JacobJacques Monod
Transcription – Another Look…
The process of transcription includes
many points of control
when to start reading DNA
where to start reading DNA
where to stop reading DNA
editing the mRNA
protecting mRNA as it travels through
cell
Eukaryotic Transcription
Roger Kornberg
for his studies of the molecular basis of
eukaryotic transcription
1990s | 2006
Roger Kornberg
Transcription
Initiation complex
transcription factors
bind to promoter
region upstream of
gene
proteins which bind to
DNA & turn on or off
transcription
TATA box binding site
only then does RNA
polymerase bind to
DNA
Colonie High AP Biology DeMarco/Goldberg
RNA polymerase
molecules bound to
bacterial DNA
Transcription
Promoter sequences upstream of gene
Transcription Initiation
Control regions on DNA
promoter nearby control sequence on DNA
binding of RNA polymerase & transcription factors
“base” rate of transcription
enhancers distant control
sequences on DNA
binding of activator proteins
“enhanced” rate (high level) of transcription
Model for Enhancer Action
Enhancer DNA sequences
distant control sequences
Activator proteins
bind to enhancer sequence & stimulates transcription
Silencer proteins
bind to enhancer sequence & block gene transcription
Transcription in Eukaryotes
Prokaryote vs. Eukaryote Genome Prokaryotes
small size of genome
circular molecule of naked DNA DNA is readily available to RNA polymerase
control of transcription by regulatory proteins
operon system
most of DNA codes for protein or RNA no introns, small amount of non-coding DNA
regulatory sequences: promoters, operators
Prokaryote vs. Eukaryote Genome Eukaryotes
much greater size of genome
how does all that DNA fit into nucleus?
DNA packaged in chromatin fibers
how to regulate access to DNA by RNA polymerase?
cell specialization
need to turn on & off large numbers of genes
most of DNA does not code for protein
97% “junk DNA” in humans; purpose?
Colonie High AP Biology DeMarco/Goldberg
Viral Gene Expressionbacteriophageinfluenza
A package of
genes in transit
from one host
cell to another
“A piece of bad news
wrapped in protein”
– Peter Medawar
Viral Diseases
Measles
Polio
Hepatitis
Chicken
pox
Smallpox
Eradicated in 1976
vaccinations ceased in 1980
at risk population?
Emerging Viruses Viruses that “jump” host
switch species
Ebola, SARS, bird flu, hantavirus
The Coming Plague by Laurie Garrett SARS
Ebola hantavirus
A Sense of Size
Comparing size
eukaryotic cell
bacterium
virus
What is a virus? Is it alive?
DNA or RNA enclosed in a protein coat
Viruses are not cells
Extremely tiny
need an electron microscope to see
smaller than ribosomes
~20–50 nm
1st discovered in plants (1800s)
tobacco mosaic virus
couldn’t filter out
couldn’t reproduce on media
like bacteria
Colonie High AP Biology DeMarco/Goldberg
Variation in Virusesplant virus pink eye
Parasites?
lack enzymes for metabolism
lack ribosomes for protein synthesis
need host “machinery”
Viral Genomes
Viral nucleic acids
DNA double-stranded
single-stranded
RNA double-stranded
single-stranded
Linear or circular smallest viruses
have only 4 genes, while largest have several hundred
Viral Protein Coat
Capsid
crystal-like
protein shell
1-2 types of
proteins
many copies of
same protein
Viral Envelope
Lipid bilayer membranes
cloaking viral capsid
envelopes are derived from
host cell membrane
glycoproteins on surface
HIV
Entry
virus DNA/RNA enters host cell
Assimilation
viral DNA/RNA takes over host
reprograms host cell to copy viral nucleic acid & build viral proteins
Self assembly
nucleic acid molecules & capsomeres then self-assemble into viral particles
exit cell
Generalized Viral Lifecycle Symptoms of Viral Infection
Link between infection & symptoms varies
kills cells by lysis
cause infected cell to produce toxins
fever, aches, bleeding…
viral components may be toxic
envelope proteins
Damage?
depends…
lung epithelium after the flu is repaired
nerve cell damage from polio is permanent
Colonie High AP Biology DeMarco/Goldberg
Viral Hosts
Host range
most types of virus can infect & parasitize
only a limited range of host cells
identify host cells via “lock & key” fit
between proteins on viral coat &
receptors on host cell surface
broad host range
rabies = can infect all mammals
narrow host range
human cold virus = only cells lining upper
respiratory tract of humans
HIV = binds only to specific white blood cells
Bacteriophages
Viruses that infect bacteria
ex. phages that infect E. coli
lambda (l) phage
20-sided capsid head
encloses DNA
protein tail attaches
phage to host & injects
phage DNA inside
Bacteriophage Lifecycles
Lytic
reproduce virus in
bacteria
release virus by
rupturing bacterial
host
Lysogenic
integrate viral DNA
into bacterial DNA
reproduce with
bacteria
Lytic Lifecycle of Phages
Lysogenic Lifecycle of Phages Defense Against Viruses
Bacteria have defenses against phages
bacterial mutants with receptors that
are no longer recognized by a phage
natural selection favors these mutants
bacteria produce restriction enzymes
recognize & cut up foreign DNA
It’s an escalating war!
natural selection favors phage mutants
resistant to bacterial defenses
Colonie High AP Biology DeMarco/Goldberg
RNA Viruses
Retroviruses
have to copy viral RNA into host DNA enzyme = reverse transcriptase
RNA DNA mRNA
host’s RNA polymerase now transcribes viral DNA into viral mRNA mRNA codes for viral components
host’s ribosomes produce new viral proteins
proteinRNADNA
transcription translation
replication
Retroviruses
HIV
Human ImmunoDeficiency Virus
causes AIDS Acquired ImmunoDeficiency
Syndrome
opportunistic diseases
envelope with
glycoproteins
for binding to
specific WBC
capsid containing 2 RNA
strands & 2 copies of
reverse transcriptase
HIV Infection
HIV enters host cell
macrophage & CD4 WBCs
cell-surface receptor
reverse transcriptase
synthesizes double stranded
DNA from viral RNA
high mutation rate
Transcription produces
more copies of viral RNA
translated into viral proteins
proteins & vRNA self-
assemble into virus particles
released from cell by
“budding” or by lysis
HIV Treatments
inhibit vRNA replication
AZT thymine mimic
protease inhibitors
stops cleavage of polyprotein into capsid & enzyme proteins
Potential HIV treatments
Block receptors chemokines
bind to & block cell-surface receptors 11% of Caucasians have mutant receptor allele
Block vRNA replication CAF replication factor
HIV Treatments
inhibit vRNA replication
AZT thymine mimic
protease inhibitors
stops cleavage of polyprotein into capsid & enzyme proteins
Colonie High AP Biology DeMarco/Goldberg
Why turn genes on & off?
Specialization each cell of a multicellular eukaryote
expresses only a small fraction of its genes
Development different genes needed at different points
in life cycle of an organism afterwards need to be turned off permanently
Responding to organism’s needs homeostasis
cells of multicellular organisms must continually turn certain genes on & off in response to signals from their external & internal environment
Points of Control The control of gene expression
can occur at any step in the pathway from gene to functional protein
unpacking DNA
transcription
mRNA processing
mRNA transport out of nucleus
through cytoplasm
protection from degradation
translation
protein processing
protein degradation
DNA PackingHow do you fit all that DNA into the nucleus?
DNA coiling & folding double helix
nucleosomes
chromatin fiber
looped domains
chromosome
from DNA double
helix to condensed
chromosome
Nucleosomes
“Beads on a string”
1st level of DNA packing
histone proteins 8 protein molecules
many positively charged amino acids arginine & lysine
bind tightly to negatively charged DNA
8 histone
molecules
DNA Packing
Degree of packing of DNA regulates transcription
tightly packed = no transcription
= genes turned off
darker DNA (H) = tightly packed
lighter DNA (E) = loosely packed
Histone Acetylation
Acetylation of histones unwinds DNA
loosely packed = transcription
= genes turned on
attachment of acetyl groups (–COCH3) to histones
conformational change in histone proteins
transcription factors have easier access to genes
Colonie High AP Biology DeMarco/Goldberg
DNA Methylation
Methylation of DNA blocks transcription factors
no transcription = genes turned off
attachment of methyl groups (–CH3) to cytosine
C = cytosine
can be a permanent inactivation of genes
ex. inactivated mammalian X chromosome
X Chromosome Inactivation
Female mammals inherit two X
chromosomes
one X becomes inactivated during
embryonic development – EPIGENETICS!
condenses into compact object = Barr body
X-Inactivation & Tortoise Shell Cat
2 different cell lines in cat
Regulation of mRNA Degradation
Life span of mRNA determines pattern
of protein synthesis
mRNA can last from hours to weeks
RNA Interference
Small RNAs (miRNA, siRNA, RNAi)
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” even though post-transcriptional control,
still turns off a gene
siRNA
RNA Interference
Small RNAs
double-stranded RNA
sRNA + mRNA
mRNA
mRNA degraded
functionally turns
gene off!
1990s | 2006
Andrew Fire Craig Mello
Colonie High AP Biology DeMarco/Goldberg
Points of Control The control of gene expression
can occur at any step in the pathway from gene to functional protein
unpacking DNA
transcription
mRNA processing
mRNA transport out of nucleus
through cytoplasm
protection from degradation
translation
protein processing
protein degradation
Control of Translation
Block initiation stage
regulatory proteins attach to
5’ end of mRNA
prevent attachment of ribosomal subunits &
initiator tRNA
block translation of mRNA to protein
Protein Processing & Degradation
Protein processing
folding, cleaving, adding sugar groups, targeting for transport
Protein degradation
ubiquitin tagging
proteosome degradation
Aaron Ciechanover
Israel
Avram Hershko
Israel
Irwin Rose
UC Riverside
Ubiquitin
“Death tag”
mark unwanted proteins with a label
76 amino acid polypeptide, ubiquitin
labeled proteins are broken down
rapidly in "waste disposers"
proteasomes
1980s | 2004
Proteasome
Protein-degrading “machine”
cell’s waste disposer
can breakdown all proteins
into 7-9 amino acid fragments
transcription
1
mRNA
processing2mRNA transport
out of nucleus
3
translationmRNA
transport
in
cytoplasm
4
1. transcription
-DNA packing
-transcription factors
2. mRNA processing
-splicing
3. mRNA transport
out of nucleus
-breakdown by sRNA
4. mRNA transport
in cytoplasm
-protection by 3’ cap &
poly-A tail
5. translation
-factors which block
start of translation
6. post-translation
-protein processing
-protein degradation
-ubiquitin, proteasome
post-
translation
5
6
