Chapter 18: Regulation of Gene Expression
What we will cover:
1. How Proks regulate genes
based on environment
2. How Euks regulate gene
expression to maintain different
cell types
3. How gene regulation can
allow a single cell (zygote) to
become a fully functioning
organism of many cell types.
General Information:
Gene Expression – from genotype to phenotype (gene to protein)
Genes are turned “on” and “off” (transcribed or not transcribed)
First understanding of gene control came from E. coli which
changes activity based on environmental changes.
I. Gene Regulation in Prokaryotes (first seen in E.coli)
A. E.coli lives in an erratic environment in your intestines.
1. if deprived of amino acid tryptophan, it responds by activating
a metabolic pathway to make its own tryptophan
2. If you eat a tryptophan-rich meal (Thanksgiving) it stops
producing tryptophan thus saving resources.
3. Metabolic control occurs at two levels:
a. vary the # of specific enzymes made
b. adjust the activity of enzymes already present
B. Operons =
1. Only exist in prokaryotes
2. Expression of genes can be coordinated
3. Enable prokaryotes to thrive in changing environment
C. The basic parts of an operon (always on the AP Exam)
1. Promoter – where RNA polymerase attaches and initiates
transcription
2. Operator – segment of DNA positioned within the promoter or
between the promoter and coding genes. Acts as a “switch” by
determining whether RNA polymerase can attach to the promoter
or not.
3. Genes of the operon – have related functions (ex: all will be
involved in the synthesis of tryptophan)…benefit is they are
easily coordinated
4. Repressor – protein that binds to the operator blocking the
attachment of RNA polymerase to the promoter (no transcription)
the gene is “off.”
5. Regulatory gene – located outside the operon, codes for the
repressor…it is expressed continually
D. Three kinds of Operons (more details to follow)
1. Inducible Operon -- “repressor active alone”
Negative
a. inducer inactivates repressor
gene
b. lac operon
regulation
2. Repressible Operon -- “repressor inactive alone”
a. corepressor activates repressor
b. trp operon
3. Activators (type of positive gene regulation)
a. It is not enough for lactose to be present for bacteria to break
it down…glucose must also be in short supply. How does it
know?
b. cyclic AMP (cAMP) accumulates when glucose is absent.
c. when cAMP bind allosterically to cAMP regulatory protein
(CAP) it becomes active and binds next to the lac promoter.
This makes it easier for RNA polymerase to bond.
d. lac operon is under dual control (negative control by the lac
repressor and positive control by the CAP)
E. Inducible Operon (example: the lac operon in E. coli)
1. E. coli can use lactose to make energy. This operon codes for
3 enzymes that metabolize lactose.
2. Operator =
a. determines whether or not RNA polymerase can attach
b. When operon is turned “off” lactose is not present so a
repressor molecule binds to the operator.
c. When operon is turned “on” lactose is present in the cell’s
environment causing allolactoase (an isomer of lactose) to
bond to the allosteric site of the repressor. Therefore causing
the repressor to release from the operator.
Allolactose is an “inducer” – inactivates the repressor
3. Enzymes made from this type of regulation are called
“inducible enzymes”, because their synthesis is induced by a
chemical signal.
Arabinose Operon
• Works exactly the same way as the Lactose
Operon.
• Instead of digestive enzymes you make
GFP (green florescent protein)
• This is the operon used in the
Transformation lab (pGLO lab)
F. Repressible Operon – (example: the trp operon in E.coli)
1. E.coli makes tryptophan (when it is not in the environment) in
a series of steps, each catalyzed by a specific enzyme
2. The trp repressor is made in an inactive form with little affinity
for the trp operator.
a. if tryptophan binds to the repressor at the allosteric site, the
repressor is activated and can attach to the operator.
b. Tryptophan functions as a corepressor – a small molecule
that cooperates with a repressor protein to switch an operon
off.
3. If tryptophan levels drop, repressor is released and
transcription of the operon’s genes resumes.
4. Example of feedback inhibition…keeps the substrate at a
constant level.
?
A certain mutation in E. coli impairs the ability of the lac
operator to bind to the repressor. How would this affect
the cell?
II. Chromatin structure is based on levels of DNA packing
(pg.320…chapter 16)
Protein Scaffold
A. Nucleosomes
1."Beads on a String”.
2. DNA wound on a protein core.
3. Packaging for DNA.
4. Controls transcription.
B. 30-nm Chromatin Fibers
1. A cylinder of tightly coiled nucleosomes 30 - nm in
diameter.
C. Looped Domains
1. Loops of 30 - nm chromatin
D. Chromosomes
1. Large units of DNA.
2. Heterochromatin – region of highly condensed chromatin;
areas that are not transcribed.
3. Euchromatin – region of less condensed chromatin; areas of
active transcription.
Gene expression can occur at any step from gene to protein
 Potential control points where gene
expression can be turned on or off,
sped up or slowed down.
a. chromatin changes that unpack the DNA
b. transcription (most common)
c. RNA processing
d. translation
e. altering protein product
 Differential Gene Expression -- A typical
human cell expresses about 20% of its genes
at any given time (some fewer than that)
A. Regulation of Chromatin Structure
1. Packing of DNA prevents gene expression
a. RNA polymerase can not bond when DNA is packed
(heterochrome region)
b. Example: “X chromosome inactivation”
 One of the two X chromosomes in each cell is
inactivated at random
 A female that is heterozygous for genes on the X
chromosome, has cells that express different alleles.
2. Histone Modifications (Histone Acetylation/deacetylation)
a. attachment or removal of acetyl group (-COCH3) to or from
certain amino acids of histone proteins
b. acetylated histone of a nucleosome changes shape so their
grip on DNA is less tight. (transcription easier)
c. enzymes that do this are closely associated with
transcription factors (may be coupled reactions)
3. DNA methylation – attachment of methyl groups (-CH3) to DNA
bases (usually cytosine) after DNA is made.
a. genes not expressed – heavily methylated (removing them in
lab turns the genes on)
b. methylating enzymes act at DNA sites where one strand is
already methylated, thus correctly methylating the daughter
strand.
c. Accounts for Genomic Imprinting in mammals – permanently
regulating expression of either the maternal or paternal allele
of certain genes at the start of development.
4. Epigenetic Inheritance – inheritance of traits transmitted by
mechanisms not directly involving the nucleotide sequence
a. modifications to chromatin can be reversed.
B. Regulating Transcription Initiation
1. Regulatory proteins bind to DNA to turn transcription of genes
on or off
2. In contrast to operons, each Euk gene has its own promoter and
other control sequences.
3. The “default” state of most genes is off
a. exception, housekeeping genes…
b. therefore, activators are more important than repressors.
c. Activators = transcription factors that bind to “enhancer
region” of DNA
d. Enhancer Region = DNA sequence that recognizes certain
transcription factors that can stimulate transcription of genes
(usually 1000’s of nucleotides away)
4. Turning on a Euk gene involves regulatory proteins called
transcription factors plus RNA polymerase.
a. Activators bind to enhancer region of DNA
b. Enhancers are far away from gene it regulates
c. DNA then bends forming a complex with other transcription
factors and the gene’s promoter region.
d. Silencers =
5. Coordinating Euk gene expression
a. depends on association of specific enhancer or collection of
enhancers
•Only liver cells make
Albumin.
•Only Lens cells make
Crystallin.
•Both cells contain genes
to do both.
•The specific transciption
factors made in the cells
will determine which
genes are expressed.
•How do sets of
Activators come to be
present in different
cells? (answered on slide 29)
C. Post Transcriptional Regulation
1. RNA Processing -- “alternative splicing”
2. mRNA degradation
a. life span of mRNA varies
b. begins with shortening of poly A tail which triggers
enzymes to remove 5’ cap (regulated by nucleotide
sequences in the mRNA in “leader” portion of mRNA)
c. once cap is removed, nuclease enzymes rapidly breakdown
mRNA
d. miRNAs (microRNAs) – made from longer pieces of RNA
that folds on itself to make a double-stranded hairpin
structure. Enzyme called “dicer” cuts the strand into short
pieces. One of the two strands is broken down while the
other associates with a large protein to allow it to bind to
mRNA which degrades mRNA or blocks translation (this is
called RNA interference (RNAi) and is caused by “small
interfering RNAs (siRNAs)
3. Translation initiation
a. most control mechanisms block initiation
b. proteins with regulatory functions bind to specific sequences
within the leader region preventing ribosome attachment
c. control here can lead to “global” control (skip to picture)
Global Control in a Red Blood Cell
Global control is also important in
embryonic development. (eggs have
mRNA that are not translated until
after fertilization)
Global control in plants: store mRNA
in darkness…light triggers
reactivation of translation
D. Post-translation control (protein processing and degradation)
1. cutting Euk polypeptides into smaller, active final products
(example: insulin) (never cut)
2. some proteins require additions (can be blocked)
3. some proteins need to go to specific location of cell to
function…(never get there…example: cystic fibrosis)
4. Selective breakdown of proteins
a. to mark protein for destruction, cell attaches a small protein
called ubiquitin to the protein
b. Proteasomes = giant protein complexes that recognize
ubiquitin and degrade the tagged protein
IV. Noncoding RNAs (aka non-protein-coding RNAs) 2006 Nobel Prize
A. mRNA translation
1. microRNAs (miRNAs) bind to complementary sequences in
mRNA and degrades it or blocks translation.
2. estimated that 1/3 of our genes are regulated this way.
3. RNA interference (RNAi) – using synthetic double-stranded
RNA molecules that match the sequence of a particular gene
to trigger the breakdown of the gene’s mRNA
a. small interfering RNAs (siRNAs)
4. miRNA formed from a single hairpin in a precursor RNA
siRNA formed from longer double-stranded RNA molecules
5. Induction
B. Chromatin configuration
1. siRNAs play a role in forming heterochromatin
V. Genetic Control of Embryonic Development
A. Three processes:
1. Cell division
2. Cell differentiation
3. Morphogenesis
B. Revisit question from slide 22 (how do different sets of
activators come to be present in different cells)
1. Materials in the egg set up a sequential program of gene
regulation that occurs as cells divide…makes the cells become
different from each other in a coordinated fashion.
2. Two sources of information tell a cell which genes to express
at any given time during embryonic development, which leads
the cell to differentiate
a. egg’s cytoplasm
b. the environment around the cell
3. The egg’s cytoplasm
a. Contains RNA and proteins from the mother’s DNA
b. Things in the egg are distributed unevenly in the cytoplasm
-- “cytoplasmic determinants” -c. After the zygote divides, the combination of cytoplasmic
determinants in a cell helps determine the cell’s fate.
4. The environment around the cell
a. more important as the number of cells increases
b. Induction occurs –
5. Determination –the events that lead to the observable differentiation of a cell.
a. once a cell goes through determination, the embryonic cell is irreversibly
committed to its final fate.
b. This is “marked” by the expression of genes for tissue specific proteins
c. When the cell starts making mRNA’s for those proteins, it is considered
“differentiated”
C. Setting up the Body Plan (head vs. tail)
1. Pattern formation—
a. head, tail, back, front, right and left have to be determined
before organs can form
b. “positional information” is provided by cytoplasmic
determinants and inductive signals
c. cues tell cell its location relative to the “axes” which will in
turn, determine how it will respond to future signals
2. The fruit fly was extensively studied
Homeotic genes
Segmentation genes
Maternal effect gene (aka
“egg-polarity genes”)
EX: Bicoid gene
Morphogens