notes: ch 18 part 1 regulation of gene expression ... of gene expression: gene expression in both...
TRANSCRIPT
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NOTES: CH 18 – part 1
Regulation of Gene Expression:
Prokaryotes vs. Eukaryotes
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Regulation of Gene Expression:
● Both prokaryotes & eukaryotes must alter
their patterns of gene expression in
response to changes in environmental
conditions;
● Multicellular eukaryotes must also develop
and maintain multiple cell types
-each cell type contains the same genome
but expresses a different subset of
genes…how is this accomplished??
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Regulation of Gene Expression:
● Gene expression in both eukaryotes &
prokaryotes is often regulated at the stage
of TRANSCRIPTION (DNA mRNA)
● we now know that RNA molecules play
many roles in regulating gene expression
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18.1: BACTERIA
● bacterial cells that can conserve resources
and energy have a selective advantage
over cells that are unable to do so…
● thus, natural selection has favored
bacteria that express ONLY the genes
whose products are needed by the cell at
any given moment…
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Rapid reproduction, mutation, and genetic
recombination contribute to the genetic
diversity of bacteria
● Bacteria allow researchers to
investigate molecular genetics
in the simplest true organisms
● The well-studied intestinal
bacterium Escherichia coli
(E. coli) is “the laboratory rat
of molecular biology”
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The Bacterial Genome and Its
Replication:
● The bacterial chromosome is usually a
circular DNA molecule with few associated
proteins
● Many bacteria also have PLASMIDS,
smaller circular DNA molecules that can
replicate independently of the chromosome
● Bacterial cells divide by BINARY FISSION,
which is preceded by replication of the
chromosome
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Origin of
replication
Replication fork
Termination
of replication
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Mutation and Genetic
Recombination as Sources of
Genetic Variation
● Since bacteria can
reproduce rapidly, new
mutations quickly increase
genetic diversity
● More genetic diversity arises
by recombination of DNA
from two different bacterial
cells
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Individual bacteria respond to
environmental change by regulating
their gene expression
● A bacterium can tune its metabolism to the changing environment and food sources
● This metabolic control occurs on two levels:
1) Adjusting activity of metabolic enzymes
2) Regulating genes that encode metabolic
enzymes
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Regulation of enzyme
activity
Regulation of enzyme
production
Enzyme 1
Regulation
of gene
expression
Enzyme 2
Enzyme 3
Enzyme 4
Enzyme 5
Gene 2
Gene 1
Gene 3
Gene 4
Gene 5
Tryptophan
Precursor
Feedback
inhibition
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EXAMPLE:
● consider an individual E. coli cell living in
the constantly-changing environment of a
human colon…it depends on the eating
habits of its host!!
● if, for example, the environment is lacking
in the amino acid tryptophan, which it
needs to survive, the cell responds by
activating a metabolic pathway that makes
tryptophan from another compound…
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EXAMPLE:
● later, if the human host eats a tryptophan-
rich meal, the bacterial cell stops
producing tryptophan, thus saving itself
from wasting resources to produce a
substance that is readily available from its
surroundings…
● this is one example of how bacteria
respond and fine-tune their metabolism to
a changing environment!
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Regulation of enzyme
activity
Regulation of enzyme
production
Enzyme 1
Regulation
of gene
expression
Enzyme 2
Enzyme 3
Enzyme 4
Enzyme 5
Gene 2
Gene 1
Gene 3
Gene 4
Gene 5
Tryptophan
Precursor
Feedback
inhibition
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Individual bacteria respond to
environmental change by regulating
their gene expression
● A bacterium can tune its metabolism to the changing environment and food sources
● This metabolic control occurs on two levels:
1) Adjusting activity of metabolic enzymes
(Allosteric regulation; short-term feedback
inhibition)
2) Regulating genes that encode metabolic
enzymes (occurs at the level of
transcription!...how?...OPERONS!!)
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Regulation of enzyme
activity
Regulation of enzyme
production
Enzyme 1
Regulation
of gene
expression
Enzyme 2
Enzyme 3
Enzyme 4
Enzyme 5
Gene 2
Gene 1
Gene 3
Gene 4
Gene 5
Tryptophan
Precursor
Feedback
inhibition
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Operons: The Basic Concept● In bacteria, genes are often clustered into
operons, composed of:
– An OPERATOR, an “on-off” switch
– A PROMOTER
– GENES for metabolic enzymes
● An operon can be switched off by a protein
called a REPRESSOR
● A corepressor is a small molecule that
cooperates with a repressor to switch an
operon off
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Promoter Promoter
DNA trpR
Regulatory
gene
RNA
polymerase
mRNA
3
5
Protein Inactive
repressor
Tryptophan absent, repressor inactive, operon on
mRNA 5
trpE trpD trpC trpB trpA
Operator
Start codonStop codon
trp operon
Genes of operon
E
Polypeptides that make up
enzymes for tryptophan synthesis
D C B A
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DNA
Protein
Tryptophan
(corepressor)
Tryptophan present, repressor active, operon off
mRNA
Active
repressor
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DNA
Protein
Tryptophan
(corepressor)
Tryptophan present, repressor active, operon off
mRNA
Active
repressor
No RNA made
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Repressible and Inducible Operons:
Two Types of Negative Gene
Regulation
● A repressible operon is one that is usually on; binding of a REPRESSOR to the operator shuts off transcription
● The trp operon is a repressible operon
● An inducible operon is one that is usually off; a molecule called an INDUCER inactivates the repressor and turns on transcription
● The classic example of an inducible operon is the lac operon, which contains genes coding for enzymes used in hydrolysis and metabolism of lactose (disaccharide; “milk sugar”)
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DNA lacl
Regulatory
gene
mRNA
5
3
RNA
polymerase
Protein
Active
repressor
No
RNA
made
lacZ
Promoter
Operator
Lactose absent, repressor active, operon off
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DNA lacl
mRNA
5
3
lac operon
Lactose present, repressor inactive, operon on
lacZ lacY lacA
RNA
polymerase
mRNA 5
Protein
Allolactose
(inducer)
Inactive
repressor
-Galactosidase Permease Transacetylase
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● Inducible enzymes usually function in
catabolic pathways
● Repressible enzymes usually function in
anabolic pathways
● Regulation of both 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
● Some operons are also subject to positivecontrol through a stimulatory activator protein, such as catabolite activator protein (CAP)
● When glucose (a preferred food source of E. coli ) is scarce, the lac operon is activated by the binding of CAP (so the enzymes to break down lactose are produced)
● When glucose levels increase, CAP detaches from the lac operon, turning it off
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DNA
cAMP
lacl
CAP-binding site
Promoter
Active
CAP
Inactive
CAP
RNA
polymerase
can bind
and transcribe
Operator
lacZ
Inactive lac
repressor
Lactose present, glucose scarce (cAMP level high): abundant lac
mRNA synthesized
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DNA lacl
CAP-binding site
Promoter
RNA
polymerase
can’t bind
Operator
lacZ
Inactive lac
repressor
Inactive
CAP
Lactose present, glucose present (cAMP level low): little lac
mRNA synthesized
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18.2: Eukaryotic Gene Expression
● a typical human cell might express about 20% of its protein-coding genes at any given time;
● specialized cells (muscle, nerve cells) express an even smaller fraction;
● almost all cells contain an identical genome…however, the subset of genes expressed in each cell type is unique…
● DIFFERENTIAL GENE EXPRESSION!
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18.2: Eukaryotic Gene Expression
● when gene expression proceeds abnormally, serious imbalances and diseases, including cancer, can arise
● as in prokaryotes, much of the regulation of gene expression in eukaryotes occurs at the transcription stage…
● however, the greater complexity of eukaryotic cell structure & function provides opportunities for regulating gene expression at many additional stages (see fig. 18.6)
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18.2: Eukaryotic Gene
Expression
● eukaryotic gene expression is regulated at many stages:
1) regulation of chromatin structure
2) regulation of transcription initiation
3) post-transcriptional regulation
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1) regulation of chromatin structure
2) regulation of transcription initiation
3) post-transcriptional regulation
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1) regulation of chromatin
structure● recall that the DNA in eukaryotic cells is
packaged with proteins (HISTONES) into
an elaborate complex known as
CHROMATIN
● HOW the DNA is packed / coiled
regulates how it genes are expressed!
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1) regulation of chromatin
structure● examples of chromatin modifications:
A) Histone Modifications: chemical groups
(i.e. acetyl groups, methyl groups) can be
added to amino acids in the histone
structure to alter chromatin folding:
-make the chromatin fold “tighter” (harder
to transcribe) or “looser” (easier to
transcribe)
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1) regulation of chromatin
structure● examples of chromatin modifications:
B) DNA Methylation: enzymes add methyl
groups (CH3) to certain bases in DNA
(usually cytosine)…typically inactivates
these segments of DNA
-evidence: individual genes are more
heavily methylated in cells in which they
are NOT expressed…removal of these
methyl groups can turn some of these
genes on!
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1) regulation of chromatin
structure● examples of chromatin modifications:
C) Epigenetic Inheritance: inheritance of
traits transmitted by mechanisms not
directly involved with the DNA nucleotide
sequence (i.e. histone modifications &
DNA methylation!)…
-these are modifications that can typically
be reversed!
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2) regulation of transcription
initiation● most eukaryotic genes have multiple
control elements – segments of
noncoding DNA that serve as binding sites
for proteins known as TRANSCRIPTION
FACTORS, which in turn regulate
transcription
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2) regulation of transcription
initiation● as we saw in CH 11 (Cell Signaling),
signaling molecules (i.e. steroid or non-
steroid hormones) can cause the
activation of one or more transcription
factors, turning “on” the transcription of
one or more genes
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3) post-transcriptional
regulation● transcription alone does not constitute
gene expression…the expression of a
protein-coding gene is ultimately
measured by the amount of functional
protein it makes!
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3) post-transcriptional
regulation● much happens between the synthesis of
mRNA and the activity of the protein in the
cell:
A) RNA Processing
B) mRNA Degradation
C) Initiation of Translation
D) Protein Processing and Degradation
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A) RNA Processing
● we’ve already discussed: 5’ cap, 3’ poly-A
tail, and removal of introns (exons
remain)
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A) RNA Processing
● alternative RNA splicing: different mRNA
molecules can be made from the same
primary transcript! (depending on which
RNA segments are treated as exons &
which as introns)
-example: researchers have found 1
Drosophila gene with enough alternatively
spliced exons to produce 19,000
membrane proteins that have different
extracellular domains!!!
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B) mRNA Degradation
● the lifespan of mRNA molecules in the
cytoplasm is important in determining the
pattern of protein synthesis
● bacterial mRNA molecules are typically
degraded by enzymes within a few
minutes
● eukaryotic mRNAs are typically more
stable…can last for hours, days, weeks…
(i.e. mRNAs for hemoglobin
polypeptides are long-lived!)
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C) Initiation of Translation
● there are regulatory proteins that can bind
to specific sequences at the 5’ or 3’ end of
mRNA & prevent the attachment of
ribosomes
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D) Protein Processing and
Degradation● most polypeptides require some processing
before they are functional
-phosphate groups added / removed
-transported to target destination (i.e. cell
surface)
-proper folding or combining with other
polypeptides to form quaternary structure…
**regulation can occur at any of these steps!
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18.3: Noncoding RNAs play
multiple roles in controlling gene
expression● genome sequencing has shown that protein-
coding DNA only accounts for 1.5% of the human genome (& other eukaryotes)
● a small fraction of the non-protein coding DNA consists of genes for rRNAs and tRNAs
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18.3: Noncoding RNAs play multiple
roles in controlling gene expression
● until recently, researchers assumed that most of the remaining DNA was untranscribed…”junk” DNA
● however, new research suggests that a significant amount of the genome may be transcribed into non-protein-coding RNAs that are involved in regulation of gene expression!!
-noncoding RNAs (ncRNAs)
-microRNAs (miRNAs)
-RNA interference (RNAi)
-small interfering RNAs (siRNAs)
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microRNAs (miRNAs)
● small, single-stranded RNA molecules
● capable of binding to complementary
sequences in mRNA
● typically, a miRNA forms a complex with 1
or more proteins; this complex then binds
with a mRNA
● the result is the mRNA is either degraded
or translation of it is blocked
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RNA interference (RNAi)
● small interfering
RNAs (siRNAs),
similar to miRNAs,
can associate with
the same proteins
as miRNAs and
block expression of
a gene with the
same sequence as
the RNA…