Regulation of Gene Expression
Ch. 16.1-16.2;16.4-16.5
1 Embryo 200 Cell Types
• From a single embryo, 200
types of cells can be
produced (differentiation)
• Diversity comes from genes
being turned off
• Expression of the genes lead
to specialization of the cell
• Transcriptional regulation
controlling the expression of
genes
1) post-transcriptional
effect mRNA
2) Translational protein
translation
3) Post-translational life
span/activity of protein
Regulation in Prokaryotes
• Adjust biochemistry quickly
as environment changes
• Jacob and Monod
extensive studies into the
effects of lactose on
expression of lactase genes
• Operon regulatory
sequence in DNA for a
specific gene(s) + the genes
• Regulatory proteins bind
to operons to promote or
inhibit the transcription of
transcription unit (single
mRNA coded in the
operon)
Regulation of an Operon
• Operator section at
the start of the operon
• Activator protein
attaches to operator to
promote expression
• Repressor protein
attaches to operator to
inhibit expression
• Gene coding for
regulatory proteins
(activators/repressors)
are called regulatory
genes
• Non-regulating
proteins come from
structural genes
The lac Operon
• 3 genes:
1) lacZ codes for β-galactosidase;
breaks lactose into glucose +
glactose
2) lacY codes for permease;
actively transports lactose into
the cell
3) lacA codes for transacetylase;
We don’t know what it does
• Negatively regulated
– Regulator gene lacI codes for Lac
repressor
– Limits lac expression when lactose is
absent (normal)
– When lactose is added, it is made
into allolactose (inducer for lac
operon)
– Inhibits lac repressor by binding to it
Lac Operon Part II; Positive Regulation
• Lac operon is repressed in the
presence of lactose if glucose is
also added. Why?
– Glucose is a better source of
energy
– Converting lactose into usable
sugars (glucose) requires energy
• CAP (catabolite activator
protein) activator synthesized
in an inactive form; activated by
cAMP (produced when glucose
is absent)
– Active form binds to CAP site at
the lac operon promoter
allowing RNA Poly to attach
• If we add glucose, cAMP levels
drop so CAP is deactivated and
RNA Poly can bind to the DNA
trp Operon and Protein Synthesis
• Some proteins, like
tryptophan, must be
synthesized when not
present to be absorbed
• trp Operon codes
enzymes needed to make
tryptophan; regulated by
trpR (repressor) that is
normally inactive; trp
operon used to make
tryptophan
• When tryptophan levels are
high, the repressor is active
and trp operon is blocked
(repressible operon)
• Tryptophan is a
corepressor; activates
repressor
Regulation in Eukaryotes
• Eukaryotes do not have
operons; regulatory gene
are spread across the
genome (side effect of
variation)
• Eukaryotes use all forms
of gene regulation:
1) Transcriptional
Regulation
2) Post-transcriptional
regulation
3) Translational regulation
4) Post-translational
regulation
Transcriptional Regulation
• Promoter region of
DNA upstream (~25bp)
from the transcription
unit
– TATA Box 7-bp sequence
5’-TATAAAA-3’
• TFs (transcription factors)
recognize TATA and bind
to it; then RNA Poly II can
bind
• Further upstream are the
regulator sequences
(promoter proximal
elements) in the
promoter proximal region
• Regulatory proteins bind
here to enhance or
repress transcription
Activators and Transcription
• RNA Poly II + TFs
transcription initiation
complex; not that efficient
• Activators proteins that
help the complex attach and
start translation
• Activators can be specific
(one cell type for one gene)
or general (multiple genes in
all cell types) which are also
called Housekeeping genes
• Enhancer regions on the DNA
can increase transcription
rate by interacting with
activators (act as
coactivators) by bending DNA
into a loop
Motifs in DNA Binding Proteins
• Domains structures in a protein
made from the combination of
secondary folding options (helix,
sheet, coil)
– Ex. Helix-helix-coil-helix
• Motif specialized domains
conserved in different types of
proteins
• DNA interacting Motifs:
1) Helix-turn-helix DNA binding
region of protein
2) Zinc Finger finger shape with
zinc ion; bind to DNA grooves
3) Leucine zipper dimers held
together by hydrophobic regions;
bind to major groove of DNA
Combinational Gene Regulation
• Regulation of most genes in more
complex than just activation or
repression
• Genes can have multiple
activators and repressors
• These regulation points between
different genes overlap and
follow the stronger influence
• Gene A is regulated by enhancer
regions 1, 2 and 3; Gene B is
regulated by enhancer 2, 3, and 4
– Activators on 2 and 3 will produce
A and B proteins
– Repressors on 3, and 4 will limit B
protein a great deal and A proteins
a little bit
Coordinated Regulation
• Proteins can be
regulated in complex
organisms across many
types of tissues
through chemical
signals (hormones)
• Steroid Hormone
Response Element
region in gene that
hormone-receptor
complex binds to
– Allows regulation in
several cell types very
quickly
Methylation of DNA
• DNA methylation adding
methyl (-CH3) to cytosine bases
– Turn off gene (silencing) by
blocking access to promoter
region
• Epigenetics change in gene
expression but no change in the
DNA itself
• Hemoglobin turned off in all
other cell types this way
• Genomic Imprinting silencing
of one of two alleles during
development
– Methylated allele is not
expressed
Chromatin Structure
• Histones can block access
to DNA and thus regulate
it
• Chromatin remodeling
changing its structure
– Nucleosome remodeling
complex moves
histones along DNA or
reshapes them to open a
region
• Adding Acetyl Groups
(CH3CO-) weakens the
interactions between the
histones and DNA
• Methylation of
Histones marks
histones wrapped with
deactivated DNA
Gene Regulation in Development
• Gene regulation is most
important during early
development; determine the
cell-types and physiology of
the organism
• Regulation sensitive to both
time (must all happen in the
right order and within a
certain window) and place
(location in embryo
determines location in body)
• Understanding comes from
our model organisms:
– Fruit fly, nematode worm,
zebrafish, and house mouse
From Zygote to Fetus
• After fertilization, a zygote
develops into a fetus through
several mechanisms
1) Mitosis need lots of cells
2) Movement of cells cells need
to form the right shape
3) Induction cell of a certain
type needs neighboring cells to
respond to get a result
4) Determination totipotent
cells becomes specific cell types
5) Differentiation cell types
become finalized so tissue and
systems can be made
Hold Up Mr. Nucleus…Cytoplasm has something
to say…
• Not all regulation of a zygote
comes from the nucleus
• Zygote’s cytoplasm is from the egg
used at fertilization
• Cytoplasmic determinants
– mRNA strands and proteins in
cytoplasm of egg also regulate the
zygote
– Not reproduced during cell divisions;
First divisions of zygote separate
determinants asymmetrically so
each daughter as an uncontrolled
amount
– Only really take effect during the
first few divisions but can last till
tissues form
– Inherited only on the maternal side
Induction
• Major step in the process
of determination
• Signal molecules from
very specific cells
(inducers) sent to
receptor cells
• Two methods:
1) Signal released and
travels short distances to
receptors
2) Cell-to-Cell contact
between proteins in the
membranes of inducers
and receptors
Differentiation
• Determination narrows
the type of cells possible
and differentiation limits
to one cell type
• Genes required for cell
type are left on while
other genes are “turned
off”
• Master regulatory genes
promote the
transcription of proteins
needed to specialize the
cell
– myoD master gene
regulates MyoD
transcription factors
which promotes skeletal
muscle proteins
Physical Position and Regulation
• Pattern formation
arrangement of organs
in the body
– Discovered studying
the effects of
mutations on the
embryogenesis of fruit
flies
– Particular genes
control the body plan
for all complex
organism
• Steps required:
1) Determine front, back,
head, and tail (ventral,
dorsal, anterior, and
posterior) of embryo
2) Divided zygote into
segments
3) Use segments to map
out body plan
Maternal-Effect Genes
• Expressed when egg
is produced by the
mother; mRNAs
made from the bicoid
gene
• Control the anteriorto-posterior polarity
of the egg (front to
back)
• Bicoid protein is
produced and the
highest conc. marks
the anterior (head)
and drops as move
along to the posterior
(butt) which has the
lowest conc.
Segmentation Genes
• 24 genes divide
embryo into regions
• 3 Types:
1) Gap Genes form
segments along A-P
axis; broad regions
2) Pair-rule Genes
divide broad regions
with units of two
segments each
3) Segment polarity
Genes sets the
boundaries for each
segment; each
segments needs an
A-P axis
Homeotic Genes
• Genes specify which
segment becomes
what; where are the
legs, eyes, wings, etc…
– Hox genes
– 8 Hox genes in fruit flies
– Actually occur in order
on chromosome (AP)
– Found in all animals and
is highly conserved
• Homeo-Box region in
all homeotic genes that
codes for its specific
homeodomain (TF for
its protein)
Genes and Cancer
• 2 types of Cancer
1) Familial Cancer inherited;
common with breast, colon, and
testicular cancers
2) Sporadic Cancer occur
randomly; more common form;
can happen from viruses altering
DNA
• All cancer is a multi-step process;
need several key mutations
• 3 Classes of Genes effect cancer
frequency:
1) Proto-oncogens
2) Tumor suppressor genes
3) microRNA genes
– (not covering this)
Proto-Oncogenes
• Genes that stimulate cell
division in regular healthy cells
• Code for growth factors, signal
receptors, transduction
components, and TFs
• When mutated, they can
become overactive oncogens
• Only one allele needs mutated
to take effect
– Mutation in the promoter
– Mutation in the transcription
unit
– Translocation moves gene to a
more active promoter or
enhancer
– Virus adds genes that activate or
enhance a gene
Tumor Suppressor Genes
• Code for proteins that inhibit
cell division
• Keep Proto-oncogenes
repressed
• TP53 codes for p53 that
inhibits CDKs used to pass the
G1/S checkpoint
• If mutated, p53 can’t inhibit
division
• p53 mutations are in 50% of
all cancers
• Both alleles must be inactive
for a tumor suppressor gene
to lose function
Homework
• Suggested Homework:
– Test Your Knowledge Ch.
16
• Actual Homework:
– Discuss the Concepts #1
– Interpret the Data Ch.
16
– Design the Experiment
Ch. 16
Assignments for Next Week
• PPT Presentations on Ch. 18:
– Groups of 3; 12-15 mins long
– Topics:
• DNA Cloning and Building DNA Libraries
• Gel Electrophoresis, Southern Blot, Northern Blot, and Western
Blot
• DNA Cloning and Bacteria Transformation for Protein Synthesis
• BLAST Program and How it is Used
• Papers on Ch. 19:
– 3 page paper discussing the following:
•
•
•
•
Darwin’s Journey
Data and Experiments by Darwin
World Reaction to Darwin’s Theories
Basic Principles of Evolution
– DO NOT answer these section by section. These are the BIG IDEAS
you paper must discuss. It should be a summary of Darwin’s life and
impact on Biology