Gene Expression...What’s that?
How do we regulate the
expression of our genes?
Involved in gene
expression
• DNA regulatory sequences
• Regulatory genes
• Small regulatory RNAs
Regulatory sequences
• Stretches of DNA that interact with regulatory
proteins to control transcription.
Regulatory genes
• A sequence of DNA encoding a regulatory
protein or RNA.
Gene Regulation among bacteria
• Bacteria cells are able
to express the genes
whose products are
needed by the cell.
– EX: need for
tryptophan.
• Have both positive &
negative control
mechanisms
-Expression
of specific genes can be turned “on”
by the presence of an inducer or can be inhibited
by the presence of a repressor.
-Inducers
& repressors are small molecules that
interact with regulatory proteins &/or regulatory
sequences.
Regulatory proteins inhibit gene expression by
binding to DNA and blocking transcription
(negative control).
Regulatory proteins stimulate gene expression by
binding DNA & stimulating transcription (positive
control) or binding to repressors to inactivate
repressor function.
Some genes are continuously expressed; they are
always turned “on” EX: ribosomal genes
Operons are one way in which
genes are regulated.
The switch is the operator (segment of DNA)
-it controls the access of RNA polymerase to the genes
- Regulatory proteins stimulate gene expression by binding to
DNA & stimulating transcription (positive control) or binding to
repressors to inactivate repressor function.
Operon= the operator, promoter, & genes they control –the entire
stretch of DNA required for enzyme production for the
tryptophan pathway.
Two types of Negative Gene
Regulation
• Repressible Operon: transcription is usually on
but can be inhibited (repressed) when a specific
small molecule binds to a regulatory protein.
– EX: tryptophan
• Inducible: usually off but can be stimulated
(induced) when a specific small molecule
interacts with a regulatory protein.
– EX: lac operon (lactose)
http://biology-animations.blogspot.com/2007/11/lac-operon-animation.html
Repressible Operon (trp)
Which do you think is more common
for inducible operons?- the gene in
its non-repressed state? Or in its
repressed state?
What about repressible operons?
Inducible operons are more commonly
found in the repressed state.
Repressible operons are more often
actively transcribing, thus are not
repressed
Which type of operon would be
used for anabolic reactions
(making new molecules)?
Repressible operons are only turned
off when there is an excess of gene
production
Which type of operon would be
used for catabolic reactions
(breaking down of molecules)?
Inducible operons are only turned on in
the presence of the a substance
produced by metabolism (metabolite)
in order to break nutrients down.
Positive Gene Regulation vs Negative
Gene Regulation
• Positive: When a regulatory protein interacts
directly with the genome to switch
transcription on.
• Negative: When the operons are switched
off by the active form of the repressor
protein
Positive Gene Regulation
When glucose is in short supply as an
energy source, E. coli will use lactose. E.
coli will then synthesize high quantities of
the enzymes to breakdown the lactose.
How does the cell sense a shortage of
glucose? cAMP accumulates when
glucose is scarce. cAMP binds with CAP
(the activator & regulatory protein) &
stimulates the transcription of a gene
cAMP binds to CAP & CAP
assumes its active shape. CAP
attaches at the upstream end of
the lac promoter which stimulates
gene expression. =positive
If the amount of glucose
increases the cAMP
concentration falls &
therefore CAP detaches
from the operon.
The lac operon is under
negative regulation by
the lac repressor &
positive regulation by
CAP.
Can you hypothesize some other ways
that might increase or completely shut
down the transcription of a gene?
EX: activators that help the RNA polymerase have
greater affinity with the promoter region.
What differences in gene
regulation might we see in the
eukaryotic genes?
Identical twins share the same DNA but are
they exactly identical?
How might they be different?
WHY????
Consider the cells that are in the tissue of your big toe.
Which genes are
those cells going to
need to use?
How much DNA will be
present in a given cell that
won’t be used at any point
except when the cell
replicates?
95-97% of the genome of any given cell goes untranscribed
When a cell receives a signal to transcribe specific genes, what
facilitates its search for the genes?
DNA is organized very precisely on a scaffolding of proteins that
attach to nuclear lamina & cytoskeleton, thus every part of every
strand is in a known location.
Each “bead” is a
nucleosome.
-the basic unit
of DNA packing
The looped domains coil
& fold forming the
characteristic metaphase
chromosome
Gene expression in eukaryotes is controlled by a variety of mechanisms
that range from those that prevent transcription to those that prevent
expression after the protein has been produced.
5 kinds of
general
mechanisms
that can be
used.
Transcriptional - These mechanisms prevent transcription.
Posttranscriptional - These mechanisms control or regulate mRNA after
it has been produced.
Translational - These mechanisms prevent translation. They often involve
protein factors needed for translation.
Posttranslational - These mechanisms act after the protein has been produced.
Gene expression can be regulated at any
stage, but the key step is transcription
• All organisms
– Must regulate which genes are expressed at any
given time
• During development of a multicellular
organism
– Its cells undergo a process of specialization in
form and function called cell differentiation
ON/OFF SWITCHES
Complete loss of
genes or
chromosomes that
occurs in amphibians
after each phase of
metamorphosis
VOLUME CONTROLS
Enhancers that bind
~1000 base pairs
upstream of a promoter
can help RNA Polymerase
find & bind to the
promoter more often so
that more transcriptions
are made for say, insulin
Why is it an evolutionary advantage to be
able to turn some genes off temporarily or
permanently?
Having genes that are always turned on when the
gene product is not needed would be wasteful &
use up the resources within a cell.
Why are “volume controls” an advantage?
Some gene products are in very high demand & need to have
a greater number of transcriptions made so that the cell can
function efficiently.
Signal
NUCLEUS
Chromatin
Chromatin modification:
DNA unpacking involving
histone acetylation and
DNA demethlation
DNA
Gene available
for transcription
Many key stages of
gene expression can
be regulated in
eukaryotic cells
Gene
Transcription
RNA
Exon
Primary transcript
Intron
RNA processing
Tail
Cap
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypetide
Cleavage
Chemical modification
Transport to cellular
destination
Active protein
Degradation of protein
Degraded protein
Regulation of
Chromatin Structure
&
Histone Modifications
Can affect the
configuration of
chromatin and thus gene
expression
DNA Methylation
The addition of methyl groups to certain bases
(usually cytosine) in DNA is associated with
reduced transcription in some species.
Genes that are not being expressed have a
tendency to be heavily methylated
Removal of the extra methyl groups can turn on
certain genes.
Experiments have shown that deficient DNA methylation due to lack of a methylating
enzyme leads to abnormal embryotic development. In these cases, DNA methylation is
essential for the long-term inactivation of certain genes.
Epigenetic Inheritance
Chromatin modifications don’t necessarily involve a
change in DNA and yet they may be passed on from
parent to offspring
The inheritance of traits transmitted by mechanisms not
directly involving the nucleotide sequence is called:
Epigenetic Inheritance
Let’s read an article 
Combinatorial Control of Gene Activation
• In Eukaryotes, the
control of
transcription depends
largely on the binding
of activators to DNA
control elements.
– Will be able to
activate transcription
only when the
appropriate activator
proteins are present
Enhancer
Albumin
gene
Control
elements
Crystallin
gene
Liver cell
nucleus
Available
activators
Lens cell
nucleus
Available
activators
Albumin
gene not
expressed
Albumin
gene
expressed
Crystallin gene
not expressed
Figure 19.7a, b
Promoter
(a) Liver cell
Crystallin gene
expressed
(b) Lens cell
upstream
The rate of gene expression can
be increased or decreased by the
binding of specific transcription
factors, either activators or
repressors to the control
elements of the enhancers.
The combination of
transcription factors binding
to the regulatory regions at
any one time determines how
much, if any, of the gene
product will be produced.
What determines
how much of a gene
product will be
produced?
The combination of
transcription factors
binding to the
regulatory regions at
any one time
determines how
much, if any, of the
gene product will be
produced.
Gene regulation accounts for some
of the phenotypic differences
between organisms with similar
genes.
Embryonic development
• A zygote going through cell division over and
over would just produce a ball of all the same
type of cells with the same genes.
• So…where does the differentiation come in?
– A sequential program of gene regulation placed in
the egg by the mom is carried out as cells divide.
How do they know this?
• In the 1950’s F.C.
Steward worked
with carrots
Conclusion: At least some differentiated
(somatic) cells in plants are totipotent,
able to reverse their differentiation and
then give rise to all the cell types in a
mature plant.
Using one or more somatic cells
from a multicellular organism to
make another genetically
identical individual is called:
CLONING
Nuclear Transplantation in Animals
• Not the same as
plants regarding
differentiated cells.
• Differentiated cells
in animals do not
develop into
multiple cell types.
Conclusion: The nucleus from a
differentiated frog cell can direct
development of a tadpole.
However, its ability to do so
decreases as the donor cell
becomes more differentiated,
presumably because of changes
in the nucleus.
Reproductive Cloning
of Mammals
• Clone mammals using
fully developed
differentiated cell.
– Would need to
“reprogram” to be
totipotent
Problems Associated with Animal
Cloning
• Only a small % of cloned embryos develop
normally.
• Many exhibit defects
– Prone to obesity, liver failure, premature death
• The donor nuclei is seen to have more methyl
groups on their DNA which will effect gene
expression compared to non-cloned embryos.
Stem Cells
• Cells that are
undifferentiated &
under the right
conditions is able to
differentiate.
• These cells are taken
during the blastula
stage (or blastocyst)
2 sources “tell” a cell which
genes to express
Cytoplasm of egg
Environment around a particular cell
• The egg’s cytoplasm contain cytoplasmic
determinants (influence development)
– Cytoplasm of the egg is distributed into other cells.
• Depending on which portions of the zygotic cytoplasm a cell
received determines the cells fate because of the variants of
gene expression.
• The environment around the particular cell.
– Interactions between embryonic cells help induce
differentiation.
Once a cell has undergone determination it is irreversibly
committed to being that type of cell.
Determination at the molecular level is when
the cell is expressing tissue specific proteins.
Pattern Formation In Plants &
Animals
Development of a spatial organization
in which the tissues & organs of an
organism are all in their characteristic
places.
In Animals
• Occurs in embryo stage.
– Cytoplasmic determinants &
cell inductive signals provide
positional information
– Cell lineage
• genes affect formation
In Plants
• Mechanisms for plant development
– Cell lineage is less important
– Depend more on positional information
• Cell signaling & transcriptional regulation
• Formation In Flowers
– Environmental signals
• Day length & temperature
Plant Biotechnology
• Innovations in the use of plants for human usage.
• GMO’s (genetically modified organisms)
– DNA/genotype of an organism is artificially changed
• Use of GMO’s in agriculture and industry
– GMO corn is engineered to produce its own
insecticide by transferring the Bt (Bacillus
thuringiensis) crystal protein gene.
– GMO soy is engineered to resist being sprayed with
weed killers.
Why go GMO?
Let’s look at the GM corn:
• More food is grown
• Reduced the need to clear say
rainforests to grow crops
• Lowers cost of production
• Less pesticides/ fertilizers/
chemicals in general
Concerns over GMO’s
• Unknown risks to humans & the environment
– When drugs are tested & results show concerns it can be
stopped. Not so with crops.
– Risk of soil contamination over long term
• Possible human risks:
– Transfer allergens
• Effects on non-target organisms
– Ex: caterpillar died consuming laboratory milkweed because of
the pollen from the GM corn with bt gene
• Transgene Escape
– EX: GM crop for herbicide resistance & a wild relative have
genetic transfer
Besides GMO’s there’s….
Artificial Selection
Types of Genes Associated with
Cancer
Cancer results from genetic changes
that affect cell cycle control
What types of things influence
having cancer?
Mutations of genes associated with cell
growth such as: random mutation,
chemical carcinogens, X-rays, and some
viruses.
Types of Genes Associated with
Cancer
Oncogenes
Proto-oncogenes
Tumor-Suppressor Genes
Oncogenes & Proto-Oncogenes
Cancer causing genes
Genes that stimulate normal cell growth & division
• Converting Proto-Oncogenes into Oncogenes
Genetic changes that lead to an increase in
product or a change in activity of protein
Tumor-Suppressor Genes
• These genes encode proteins that prevent
uncontrolled cell growth.
– Repair damaged DNA
– Control the adhesion of cells to each other or to
the extracellular matrix
– Components of cell signaling pathways that inhibit
the cell cycle.
• A mutation happens here and cells will divide
uncontrollably = cancer.
Cell cycle – stimulating pathway
No growth factor
even needed with
this mutation 
Cell cycle – inhibiting pathway
This signal is started because of damaged DNA.
May be the result of exposure to UV light
p53 gene halts cell cycle
until DNA can be repaired
or activate genes that are
involved in DNA repair.
When DNA is irreparable the p53 gene activates the “suicide” genes
that cause cell death (apoptosis).
• Mutations that knock out the p53 gene or if the
p53 gene is defective or missing…
– Can lead to excessive cell growth and cancer
(c)
Effects of mutations. Increased cell
division, possibly leading to cancer, can
result if the cell cycle is overstimulated,
as in (a), or not inhibited when it
normally would be, as in (b).
EFFECTS OF MUTATIONS
Protein
overexpressed
Cell cycle
overstimulated
Figure 19.12c
Protein absent
Increased cell
division
Cell cycle not
inhibited
Multiple steps for the development of
cancer.
More than one somatic mutation is needed to produce
full-fledged cancer cells. (the older we get the more
likely we are to develop cancer)
At least: 1 active oncogene and mutation or loss of several tumor-suppressor
genes are recessive so both alleles must be “knocked out”
And finally…the telomerase gene is
usually activated in many tumors
Enzyme prevents DNA from shortening
and when activated removes a natural
limit on the number of times a cell can
divide
Genetic Predisposition & other
Factors Contributing to Cancer
Risk Factors
• Inheriting an oncogene puts you one step closer
to accumulating the mutations for cancer.
– Breast cancer: a person inheriting one mutant BRCA1
allele has a 60% probability of developing cancer
before the age of 50 compared to someone
homozygous for normal (2%).
• DNA breakage
– Minimize exposure to these agents:
• UV radiation, chemicals from cigarette smoke, X-rays
• Viruses
– Viral integration; can contribute oncogene, alter
tumor supressor genes, or convert proto-oncogenes
to oncogenes.
Genetic Basis of Development