NOTES: CH 18 – part 1

Regulation of Gene Expression:

Prokaryotes vs. Eukaryotes
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??
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
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…
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”
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
Replication fork

Origin of
replication

Termination
of replication
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
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
Regulation of enzyme Regulation of enzyme
activity production
Precursor
Feedback
inhibition
Enzyme 1 Gene 1

Enzyme 2 Gene 2
Regulation
of gene
expression
Enzyme 3 Gene 3

Enzyme 4 Gene 4

Enzyme 5 Gene 5

Tryptophan
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…
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!
Regulation of enzyme Regulation of enzyme
activity production
Precursor
Feedback
inhibition
Enzyme 1 Gene 1

Enzyme 2 Gene 2
Regulation
of gene
expression
Enzyme 3 Gene 3

Enzyme 4 Gene 4

Enzyme 5 Gene 5

Tryptophan
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!!)
Regulation of enzyme Regulation of enzyme
activity production
Precursor
Feedback
inhibition
Enzyme 1 Gene 1

Enzyme 2 Gene 2
Regulation
of gene
expression
Enzyme 3 Gene 3

Enzyme 4 Gene 4

Enzyme 5 Gene 5

Tryptophan
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
trp operon

Promoter Promoter
Genes of operon
DNA trpR trpE trpD trpC trpB trpA
Operator
Regulatory RNA Start codon Stop codon
gene 3 polymerase
mRNA 5
mRNA
5
E D C B A

Protein Inactive Polypeptides that make up

repressor enzymes for tryptophan synthesis
Tryptophan absent, repressor inactive, operon on
DNA

mRNA

Protein Active
repressor

Tryptophan
(corepressor)
Tryptophan present, repressor active, operon off
DNA

No RNA made

mRNA

Protein Active
repressor

Tryptophan
(corepressor)
Tryptophan present, repressor active, operon off
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”)
Regulatory Promoter
gene

Operator

DNA lacl lacZ

No
RNA
made

3

mRNA RNA
5 polymerase

Active
Protein repressor

Lactose absent, repressor active, operon off

lac operon

DNA lacl lacZ lacY lacA

RNA
3 polymerase
mRNA mRNA 5
5

Protein -Galactosidase Permease Transacetylase

Inactive
Allolactose
repressor
(inducer)
Lactose present, repressor inactive, operon on
● 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
Positive Gene Regulation
● Some operons are also subject to positive
control 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
Promoter

DNA lacl lacZ

CAP-binding site RNA Operator

polymerase
Active can bind
cAMP CAP and transcribe

Inactive lac
Inactive
repressor
CAP
Lactose present, glucose scarce (cAMP level high): abundant lac
mRNA synthesized
Promoter

DNA lacl lacZ

CAP-binding site Operator

RNA
polymerase
can’t bind
Inactive
CAP Inactive lac
repressor

Lactose present, glucose present (cAMP level low): little lac

mRNA synthesized
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!

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)
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
1) regulation of
chromatin
structure
2) regulation of
transcription
initiation
3) post-
transcriptional
regulation
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!
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)
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!
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!
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
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
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!
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
A) RNA Processing
● we’ve already discussed: 5’ cap, 3’ poly-A
tail, and removal of introns (exons
remain)
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!!!
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!)
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
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!
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
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)
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
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…
LINK to RNA interference video!