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Chapter 13.
GENE REGULATION:
THE CONTROL OF GENE EXPRESSION
Only certain portion of the genetic information is expressed in a cell.
Genes are regulated in several ways:
1. By controlling the amount of mRNA that is available
2. By controlling the rate of translation of the m RNA.
3. By controlling the activity of the protein product.
GENE REGULATION IN PROKARYOTES.
Some genes encode for proteins that are always needed. These genes are
constantly transcribed.
They are called constitutive genes. E.g. enzymes needed for glycolysis.
Most regulated genes in bacteria are organized into operons.
Operons permit coordinated control of functionally related genes.
An operon may encode for several proteins.
Each protein encoding sequence of an operon is called a structural gene.
Each operon has a single promoter region upstream from the protein coding
regions.
The promoter is the DNA sequence to which the RNA polymerases attach.
The operator is a sequence of bases that overlaps the promoter and serves as the
regulatory switch
responsible for transcriptional level control of the operon.
Repressor genes encode repressor proteins.
Repressor proteins bind specifically to the operator sequence and block
transcription by preventing RNA
polymerase from binding to the promoter.
Some repressor may always be “on” thus repressing the expression of a gene in a
cell.
1. An inducible operon is usually turned off.
An inducible gene is not transcribed unless a specific inducer inactivates its
repressor.
The inducer may bind to the allosteric site of the repressor protein causing it
to change shape. The altered
repressor cannot bind to the operator and the operon is free to transcribe.
2. A repressible operon is usually turned on.
They are turned off under special conditions, when a repressor-corepressor
complex is bound to the
DNA operator.
The repressor protein is synthesized in an inactive form that cannot bind to the
operator.
A metabolite, often an end product, acts as a corepressor that binds to the
allosteric site of the repressor
protein.
When the supply of the end product (corepressor) is low, all enzymes in the
pathway are actively
synthesized and the repressor cannot bind to the operator.
The metabolite (corepressor) and the protein (repressor) must come together to
repress the gene.
NEGATIVE REGULATORS
1. Inducible genes:

Repressor protein alone turns off regulated genes.

Repressor protein plus inducer inactivate the repressor and the gene continuous
to transcribe.
The inducer represses the repressor.
2. Repressible genes:

Repressor protein alone cannot turn off regulated genes.

Repressor protein and corepressor turn off the regulated gene.
POSITIVE REGUALTORS
Some inducible operons are under positive control.
Positive controls operate through an activator protein, catabolite gene
activator protein or CAP.
CAP increases the affinity of the promoter for RNA polymerases. It allows the
enzyme to recognize the
promoter efficiently and to bind tightly to the DNA.
The active form of CAP has cAMP bound to an allosteric site. cAMP is a
coactivator.

Activator protein (CAP) alone cannot stimulate transcription or regulated genes.

Activator protein and coactivator (CAP + cAMP) stimulate transcription of
regulated gene.
A regulon is a group of operons that are organized into a multigene system.
Regulons are controlled by a single regulatory protein.
Constitutive genes are constantly transcribed but not necessarily at the same
rate.
In general, constitutive genes that encode for enzymes required in large amount,
are transcribe more
rapidly.
The transcription rate of these genes is controlled by the promoter sequences.
POSTTRANSCRIPTIONAL REGULATION IN PROKARYOTES
There are regulatory mechanisms that operate after transcription.
Translational controls regulate the rate at which a particular mRNA molecule is
translated.



The life of bacterial mRNA is very short.
Some mRNA translate as much as 1000X faster than others do.
The difference in rate is related to the rate at which the mRNA is attached to
the ribosome.
Posttranlational controls act as switches that activate or inactivate one or
more existing enzymes.


The cell responds to changes in the concentration of certain molecules.
Feedback inhibition is a common method of controlling enzymatic activity.
GENE REGULATION IN EUKARYOTES
Most eukaryotic genes are not organized into operons.
Eukaryotic genes have specific regulatory sequences that are essential in the
control of transcription.

Temporal regulation: some genes seem to be inducible only at certain periods in
the life of the
organism.

Tissue-specific regulation: some genes are regulated by certain stimulus in one
type of tissue and by
a different stimulus in another tissue.
Regulation of eukaryotic genes can occur at the level of transcription, mRNA
processing, translation and
protein product.
TRANSCRIPTION REGULATION
Transcription in both eukaryotic and prokaryotic cells requires an initiation
site and a promoter to which
RNA polymerase binds.
In prokaryotes, the promoter has certain base sequences known as the Pribnow box
and the –35 box.

They are located 10 and 35 bases upstream from the transcription initiation
site.
In eukaryotes,

Transcription is controlled by upstream promoter elements (UPE), enhancers,
transcription initiation
sites , regulatory proteins and chromosomal organization.

The RNA polymerase binds to a sequence of bases known as the TATA box.
- The TATA box consists of about 30 base pairs upstream from the transcription
initiation site.

The promoter contains one or more sequences of 8 to base pairs upstream of the
RNA binding site,
called UPEs, upstream promoter elements.
- A gene having one UPE is generally weakly translated, whereas one containing
fire or six UPEs
is usually actively translated.

Enhancers are DNA sequences that increase the rate of transcription.
- An enhancer can regulate a gene thousands of base pairs away.
- They may be located upstream or downstream of the promoters they control.

Transcription factors are proteins that bind to the DNA and act as repressors or
activators.
- Transcription in eukaryotes requires multiple regulatory proteins that are
bound to different
parts of the promoter.
- These proteins have regions with characteristic tertiary structures called
domains.
- Each domain has a function.
- Regulatory proteins often function as dimers or groups of two.
- Dimers may consist of two identical polypeptides (homodimer) or two different
polypeptides
(heterodimer).
- In eukaryotes, multiple regulatory proteins bind to different parts of the
promoter.
- Addition of methyl groups to cytosines in the DNA strand allows certain
regulatory proteins to
bind to these regions and prevent transcription. This process probably
reinforces gene
deactivation rather than initiate repression.
A gene may be transcribed in more than one way, e.g. the gene may have two
initiation sites that encode
for a long and a short polypeptide.
CHROMOSOME STRUCTURE

The organization of a chromosome may affect the expression of some genes.
- Some genes exist in multiple copies because their products are needed in large
amounts.
- Genes that are needed by a special group of cells may be replicated in those
cells, this called gene
amplification.
- Genes can be inactivated by changes in chromosome structure; densely packed
regions are inactive
(heterochromatin) and active regions are more loosely packed (euchromatin).
DIFFERENTIAL PROCESSING THE mRNA
Prokaryotic mRNA is transcribed in a form that can be translated immediately.
Eukaryotic mRNA requires further modifications before it can be translated.
Multiple splicing patterns of exons can yield different proteins. The splicing
pattern depends on the
tissue.
Hormonal levels control the life of some mRNA.
Increasing the life of mRNA molecules allows more proteins to be formed.
MODIFICATION OF THE PROTEIN STRUCTURE
Regulating the activity of the gene product, a protein, can control the
expression of gene.

Proteolytic processing: the protein is synthesized as an inactive precursor,
which is converted to an
active form by removal of a portion of the polypeptide chain.

Selective degradation keeps the number of proteins constant within the cell.

Chemical modification, through the addition or removal of functional groups, can
reversibly alter the
activity of an enzyme.
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Gene Regulation Chapter 13 Biology, Copyright © 2005 Brooks/Cole — Thomson Learning
Control of Gene Expression
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