Transcript Regulation of Gene Expression

Regulation
of
Gene Expression
Chapter 18
Regulation of Gene Expression
Overview of Gene Expression
 The
control of gene expression is vital to
the proper and efficient functioning of an
organism.
 Cells control metabolism by either
regulating enzyme activity –or- regulating
the expression of genes coding for
enzymes.
Figure 18.2
Prokaryotic Gene Regulation
Control of Gene Expression in Bacteria
 Bacteria
often respond to environmental
change by regulating transcription.
 In bacteria, genes are often clustered into
operons, with one promoter serving several
adjacent genes.
 An operator site on the DNA switches the
operon on or off, resulting in coordinate
regulation of the genes.
Prokaryotic Gene Regulation
Operons: The Basic Concept
 An
operon is essentially a set of genes and
the switches that control the expression of
those genes.
 An operon consists of:



operator
promotor
and genes that they control
 All
together, the operator, the promoter,
and the genes they control – the entire
stretch of DNA required for enzyme
production for the pathway – is called an
operon.
Prokaryotic Gene Regulation
The Operon Model
Prokaryotic Gene Regulation
Repressible & Inducible Operons



There are basically two types of operons found in
prokaryotes: repressible operons and inducible
operons.
Both the repressible and inducible operon are types of
NEGATIVE gene regulation because both are turned
OFF by the active form of the repressor protein.
In either type of operon, binding of a specific repressor
protein to the operator shuts off transcription.


Trp operon – repressible operon is always in the on position
until it is not needed and becomes repressed or switched
off.
Lac operon – inducible operon is always off until it is induced
to turn on.
Figure 18.3a – The trp Operon
http://bcs.whfreeman.com/thelifewire/content/chp13/1302002.html
Figure 18.3b – The trp Operon
http://highered.mcgraw-hill.com/olc/dl/120080/bio26.swf
Figure 18.4a – The lac Operon
http://www.sumanasinc.com/webcontent/animations/content/lacope
ron.html
Figure 18.4b – The lac Operon
http://highered.mcgrawhill.com/sites/dl/free/0072835125/126997/animation27.html
Prokaryotic Gene Regulation
Positive Gene Regulation
 When
glucose and lactose are both present in its
environment, E. coli prefer to use glucose.
 Only when lactose is present AND glucose is in
short supply does E. coli use lactose as an energy
source, and only then does it synthesize
appreciable quantities of the enzymes for lactose
breakdown.
 How does the E. coli cell sense the glucose
concentration and relay this information to its
genome?
 http://highered.mcgrawhill.com/olc/dl/120080/bio27.swf
Figure 18.5a – Positive Control
Figure 18.5b – Positive Control
Prokaryotic Gene Regulation
Factors Affecting Ability of Repressor to
Bind to Operator
•
Co-Repressor : Activates a Repressor
o
o
o
•
Seen in the trp Operon
Co-Repressor is tryptophan
Turns normally “on” Operon “off”
Inducer: Inactivates a Repressor, Induces the Gene
to be Transcribed
o
o
o
Seen in the lac Operon
Inducer is allolactose
Turns normally “off” Operon “on”
Prokaryotic Gene Regulation
Review: Structure/Function of Prokaryotic Chromosomes
1.
2.
3.
4.
5.
6.
7.
8.
□
shape (circular/nonlinear/loop)
less complex than eukaryotes (no histones/less
elaborate structure/folding)
size (smaller size/less genetic information/fewer genes)
replication method (single origin of replication/rolling
circle replication)
transcription/translation may be coupled
generally few or no introns (noncoding segments)
majority of genome expressed
operons are used for gene regulation and control
NOTE: plasmids – more common but not unique to
prokaryotes/not part of prokaryote chromosome
Chromosome Structure
The Structure of the Chromosome
 In
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 In
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Prokaryotes:
The bacterial chromosome is a double-stranded,
circular DNA molecule associated with a small
amount of protein
In a bacterium, the DNA is “supercoiled” and found
in a region of the cell called the nucleoid
Eukaryotes:
Eukaryotic chromosomes have linear DNA molecules
associated with a large amount of protein
Chromatin is a complex of DNA and protein, and is
found in the nucleus of eukaryotic cells
Histones are proteins that are responsible for the first
level of DNA packing in chromatin
Eukaryotic Chromosomes
Chromosome Structure of Eukaryotes
Eukaryotic chromosomes contain DNA wrapped around proteins called
histones. The strands of nucleosomes are tightly coiled and
supercoiled to form chromosomes.
Eukaryotic Chromosomes
Eukaryotic Gene Regulation
Control of Gene Expression in Eukaryotes
 Eukaryotic
gene expression can be
regulated at any stage.
 Because gene expression in eukaryotes
involves more steps, there are more places
where gene control can occur.
 Opportunities for the control of gene
expression in eukaryotes include:
1.
2.
3.
4.
5.
Chromatin Packing, modification
Assembling of Transcription Factors
RNA Processing
Regulation of mRNA degradation and Control
of Translation
Protein Processing and Degradation
Overview Figure 18.6

THIS FIGURE IS
HIGHLIGHTING KEY STAGES
IN THE EXPRESSION OF A
PROTEIN-CODING GENE.

The expression of a given
gene will not necessarily
involve every stage
shown.

MAIN LESSON: each stage
is a potential control point
where gene expression
can be turned on or off,
sped up, or slowed down.
Eukaryotic Gene Regulation
Expression of Genes in Eukaryotes
 Eukaryotic
cells face the same challenges as
prokaryotic cells in expressing their genes, but with
two main differences:


 In
The much greater size of the typical eukaryotic
genome;
importance of cell specialization in multicellular
eukaryotes.
both prokaryotes and eukaryotes, DNA
associates with proteins to form chromatin, but in
the eukaryotic cell, the chromatin is ordered into
higher structural levels.
Eukaryotic Gene Regulation
Eukaryotic Chromosome
Structure
Chromatin structure is based on
successive levels of DNA packing.
Eukaryotic chromatin is composed
mostly of DNA and histone proteins
that bind to the DNA to form
nucleosomes, the most basic units of
DNA packing.
Additional folding leads ultimately to
highly compacted heterochromatin,
the form of chromatin in a metaphase
chromosome.
In interphase cells, most chromatin is in
a highly extended form, called
euchromatin.
Eukaryotic Gene Regulation
The Eukaryotic Genome
 In
prokaryotes, most of the DNA in a genome
codes for protein, with a small amount of
noncoding DNA that consists mainly of
regulatory sequences such as promoters.
 In eukaryotic genomes, most of the DNA (97% in
humans) does NOT encode protein or RNA.

This DNA includes introns and repetitive DNA:
 Repetitive
DNA are nucleotide sequences that are
present in many copies in a genome, usually not
within genes.
Eukaryotic Gene Regulation
Chromatin Modifications
 Chromatin
modifications affect the availability of
genes for transcription:
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The physical state of DNA in or near a gene is
important in helping control whether the gene is
available for transcription.
Genes of heterochromatin (highly condensed) are
usually not expressed because transcription
proteins cannot reach the DNA.
 DNA
methylation seems to diminish transcription
of that DNA.
 Histone acetylation seems to loosen nucleosome
structure and thereby enhance transcription.
Eukaryotic Gene Regulation
DNA Methylation

DNA methylation is the attachment of methyl groups
(-CH3) to DNA bases after DNA is synthesized.
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Methylation renders DNA inactive.
Inactive DNA, such as that of inactivated mammalian X
chromosomes (Barr bodies), is generally highly
methylated compared to DNA that is actively
transcribed.
Comparison of the same genes in different types of
tissues shows that the genes are usually more heavily
methylated in cells where they are not expressed.
In addition, de-methylating certain inactive genes
(removing their extra methyl groups) turns them on.
At least in some species, DNA methylation seems to
be essential for the long-term inactivation of genes
that occurs during cellular differentiation in the
embryo.
Eukaryotic Gene Regulation
Histone Acetylation
 Histone
acetylation is the attachment of acetyl
groups (-COOH3) to certain amino acids of
histone proteins; de-acetylation is the removal
of acetyl groups.
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When the histones of nucleosome are
acetylated, they change shape so that they grip
the DNA less tightly.
As a result, transcription proteins have easier
access to genes in the acetylated region.
Eukaryotic Gene Regulation
Transcription Initiation
 Transcription
is controlled by the presence or
absence of particular transcription factors,
which bind to the DNA and affect the rate of
transcription.
 Thus…transcription
initiation is controlled by proteins
that interact with DNA and with each other.
 Once
a gene is “unpacked”, the initiation of
transcription is the most important and
universally used control point in gene
expression.
Figure 18.8
Eukaryotic Gene and its Transcript
Assembling of Transcription Factors
1) Activator proteins bind to
enhancer sequences in the
DNA and help position the
initiation complex on the
promoter.
2) DNA bending brings the
bound activators closer to
the promoter. Other
transcription factors and
RNA polymerase are nearby.
3) Protein-binding domains
on the activators attach to
certain transcription factors
and help them form an active
transcription initiation
complex on the promoter.
http://highered.mcgrawhill.com/olc/dl/120080/bio28.
swf
Control elements are simply segments of noncoding DNA
that help regulate transcription of a gene by binding
proteins (transcription factors).
Eukaryotic Gene Regulation
Post-Transcriptional Factors
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Transcription alone DOES NOT constitute gene
expression!
Post-transcriptional mechanisms play supporting roles
in the control of gene expression:
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Alternative RNA splicing – where different mRNA
molecules are produced from the same primary
transcript, depending on which RNA segments are
treated as exons and which as introns.
Regulatory proteins specific to a cell type control intronexon choices by binding to regulatory sequences within
the primary transcript.
http://highered.mcgrawhill.com/olc/dl/120080/bio31.swf
Eukaryotic Gene Regulation
Alternative Splicing Offers New
Combinations of Exons = New Proteins
The RNA transcripts of some
genes can be spliced in more
than one way, generating
different mRNA molecules.
With alternative splicing, an
organism can get more than
one type of polypeptide from a
single gene.
Eukaryotic Gene Regulation
Further Control of Gene Expression
 After
RNA processing, other stages of gene
expression that the cell may regulate are mRNA
degradation, translation initiation, and protein
processing and degradation.
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The life span of mRNA molecules in the cytoplasm is
an important factor in determining the pattern of
protein synthesis in a cell.
Most translational control mechanisms block the
initiation stage of polypeptide synthesis, when
ribosomal subunits and the initiator tRNA attach to
an mRNA.
Eukaryotic Gene Regulation
Protein Processing and Degradation
 The
final opportunities for controlling gene
expression occur after translation:
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Protein processing – cleavage and the addition of
chemical groups required for function.
Transport of the polypeptide to targeted destinations
in the cell.
Cells can also limit the lifetimes of normal proteins by
selective degradation – chopped up by
proteasomes.
Overview Figure 18.6

THIS FIGURE IS
HIGHLIGHTING KEY STAGES
IN THE EXPRESSION OF A
PROTEIN-CODING GENE.

The expression of a given
gene will not necessarily
involve every stage
shown.

MAIN LESSON: each stage
is a potential control point
where gene expression
can be turned on or off,
sped up, or slowed down.
The Biology of Cancer
The Molecular Biology of Cancer
 Certain
genes normally regulate growth and
division – the cell cycle – and mutations that alter
those genes in somatic cells can lead to cancer.


Proto-Oncogenes are normal genes that code for
proteins which stimulate normal cell growth and
division.
Oncogenes – cancer causing genes; lead to
abnormal stimulation of cell cycle. Oncogenes arise
from genetic changes in proto-oncogenes:
1.
2.
3.
Amplification of proto-oncogenes
Point mutation in proto-oncogene
Movement of DNA within genome
The Biology of Cancer
Genetic Changes Can Turn Protooncogenes into Oncogenes
http://www.learner.org/courses/biology/units/cancer/images.html
The Biology of Cancer
Tumor-Suppressor Genes
 In
addition to mutations affecting growthstimulating proteins, changes in genes whose
normal products INHIBIT cell division also
contribute to cancer:

Such genes are called tumor-suppressor genes
because the proteins they encode normally
help prevent uncontrolled cell growth.
The Biology of Cancer
p53 Tumor Suppressor and ras Proto-Oncogenes
http://www.learner.org/courses/biology/units/cancer/images.html

Mutations in the p53 tumor-suppressor gene and the ras
proto-oncogene are very common in human cancers.
 Both are components of signal-transduction pathways
that convey external signal to the DNA in the cell’s
nucleus.

Product of ras gene is G Protein (relays a growth signal and
stimulates cell cycle).
 An oncogene protein that is a hyperactive version of this
protein in the pathway can increase cell division.

P53 protein – “guardian angel of the genome”
 DNA damage (UV, toxins) signals expression of p53 and
p53 protein acts as transcription factor for gene p21
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p21 halts cell cycle, allowing DNA repair
P53 also can cause ‘cell suicide’ if damage is too great
Many cancer patients p53 gene product does not
function properly!
RAS and P53 contribute to uninhibited cell stimulation and growth- Tumor Formation
Figure 18.21 Signaling pathways that regulate cell growth (Layer 2)
The Biology of Cancer
Figure 18.22 A multi-step model for the development of colorectal cancer
Review: Structure/Function of Eukaryotic Chromosomes

Chromatids
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Centromere
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noncoding/uncoiled/narrow/constricted region
joins/holds/attaches chromatids together
Nucelosome
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2/sister/pari/identical DNA/ genetic information
distribution of one copy to each new cell
histones/DNA wrapped arround special proteins
packaging compacting
Chromatin Form (heterochromatin/euchromatin)
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heterochromatin is condensed/supercoiled
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euchromatin is loosely coiled
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disc-shaped proteins
spindle attachment/alignment
Genes or DNA
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gene expression during interphase/replication occurs when loosely packed
Kinetochores
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proper distribution in cell division (not during replication)
brief DNA description
codes for proteins or for RNA
Telomeres
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tips, ends, noncoding repetitive sequences
protection against degradation/ aging, limits number of cell divisions
USEFUL ANIMATIONS
 http://highered.mcgraw-
hill.com/olc/dl/120080/bio31.swf
 http://highered.mcgrawhill.com/olc/dl/120077/bio25.swf
 http://highered.mcgrawhill.com/olc/dl/120080/bio28.swf
 http://highered.mcgrawhill.com/olc/dl/120082/bio34b.swf
 http://www.learner.org/courses/biology/units/ca
ncer/images.html
NEED TO KNOW
You should now be able to:
1.
2.
3.
Explain the concept of an operon
and the function of the operator,
repressor, and corepressor
Explain the adaptive advantage of
grouping bacterial genes into an
operon
Explain how repressible and inducible
operons differ and how those
differences reflect differences in the
pathways they control
NEED TO KNOW
4.
5.
6.
Explain how DNA methylation and
histone acetylation affect chromatin
structure and the regulation of
transcription
Define control elements and explain
how they influence transcription
Explain the role of promoters,
enhancers, activators, and repressors
in transcription control
NEED TO KNOW
7.
8.
9.
10.
Explain how eukaryotic genes can be
coordinately expressed
Describe the roles played by small
RNAs on gene expression
Explain why determination precedes
differentiation
Describe two sources of information
that instruct a cell to express genes
at the appropriate time
NEED TO KNOW
11.
12.
Explain how mutations in tumorsuppressor genes can contribute to
cancer
Describe the effects of mutations to
the p53 and ras genes