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Chapter 16
Control of Gene Expression
16.1 Genes Controlled by Regulation of Transcription
• Critical for directing the development and maintaining homeostasis
• One way to control transcription is to regulate the initiation of transcription.
• Remember that RNA polymerase must have access to the DNA double helix and must be
able to bind to the gene’s promoter.
• Protein binding nucleotide sequences on the DNA regulate the initiation of transcription.
• Binding the protein to the regulatory sequence either blocks or stimulates transcription.
• The protein blocks transcription by getting in RNA polymerase’s way; it stimulates it by
facilitating it binding to the DNA.
• Control in Prokaryotes
1. Primary function of gene control is to adjust the cell’s activities to its
immediate environment.
2. Changes in gene expression alter which enzymes are present in the cell in
response to the quantity and type of available nutrients and the amount of O2
present. (changes are completely reversible)
16.1 cont’d
• Control in Eukaryotes
1. Primary function of gene control in a cell is not to respond to the cell’s
immediate environment, but rather to participate in regulating the body as a
whole.
Ex: right gene expressed in the right cell at the right time during development
16.3 Prokaryotic Regulation
• Control of transcription can be either positive or negative.
1. Positive control- increases the frequency of initiation.
2. Negative control- decrease the frequency of initiation.
• Both are mediated by regulatory proteins, but proteins have opposite effects.
• Repressors- proteins that bind to regulatory sites on DNA to prevent or decrease
the initiation of transcription.
• Operators- site on DNA that repressor can bind
• Activators- proteins that bind DNA to stimulate the initiation of transcription
(activators are the logically and physical opposite of repressors)
16.3 Prokaryotic Regulation
Best understood example of transcriptional control is the regulation of the
tryptophan producing genes (trp genes).
E. coli uses proteins encoded by a cluster of five genes to manufacture the amino
acid tryptophan.
1. All five genes are transcribed together as a unit called an operon. (produces a
single, long piece of DNA)
2. RNA polymerase binds to a promoter located at the beginning of the first
gene and proceeds down the DNA transcribing the genes one after the other.
3. When tryptophan is present in medium surrounding bacterium, the cell shuts
off transcription of trp gene by means of a repressor. (off switch)
16.3
http://highered.mcgrawhill.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/1
20080/bio26.swf::The%20Tryptophan%20Repressor
16.3 cont’d
• Activators are on switches.
• This regulatory protein helps hold RNA polymerase against the DNA promoter
site so transcription will begin. (comes in physical contact with RNA
polymerase)
By combining the on/off switch, bacteria can create sophisticated transcriptional
control systems.
• The lac operon is responsible for producing three proteins that import lactose
into the cell and break it down into glucose and galactose.
The lac (lactose) operon has two regulatory sites.
• One is the CAP (catabolite activator proteins) site; it lies adjacent to the
promoter. This ensures the lac operon is not transcribed when ample amounts
of glucose are present. It is the ON switch.
• When glucose is low, cAMP builds in the cell, will bind to the CAP and allow
it to change shape; CAP will now bind to DNA and activate the lac promoter.
16.3
• Repressor switch (OFF switch)
• Protein called the lac repressor can bind to the operator, but only when lactose
is absent. If operator is bound, promoter region is partially blocked-genes can
not be transcribed.
• This two switch control mechanism thus causes the cell to produce only what
the cell needs, when it needs it.
http://highered.mheducation.com/sites/0072556781/student_view0/chapter12/ani
mation_quiz_4.html
16.4 Eukaryotic Regulation
• Transcription factors must assemble on the promoter. These factors can be
general or specific
• General transcription factors- necessary to establish productive initiation; they
are required for transcription, but do not increase the rate.
• Specific transcription factors- act in tissue or time-dependent manner to
stimulate higher levels of transcription
• Assembly process begins 25 nucleotides upstream from the transcription start
site (TATA box)
16.4
• Enhancers- (binding sites for specific transcription factors) are distant sites
where one of two regulatory proteins bind. (could be thousands of nucleotides
away)
• This add a great deal of flexibility to the control process.
• This allows a large number of different regulatory sequences to be scattered
about DNA to influence a particular gene.
http://highered.mcgrawhill.com/sites/9834092339/student_view0/chapter16/transcription_complex_and_
enhancers.html
16.5 Eukaryotic Chromatin Structure
• Chromatin- the complex of DNA and proteins of which eukaryotic
chromosomes are composed.
• Chromatin at its lowest level is the organization of DNA and histone proteins
into nucleosomes; these may block the binding of RNA polymerase at the
promoter.
• The histone proteins can be modified to result in a greater condensation of
chromatin, making promoters even less accessible.
• Chromatin and histones can be altered to make DNA more accessible and thus
transcription easier.
16.5
• Chromatin- remodeling complexes can catalyze four different changes in
histone/DNA binging
1. Nucleosome sliding along DNA (changes position of nucleosome)
2. Create a remodeled state where DNA is more accessible
3. Removal of nucleosomes from DNA
4. Replacement of histones with variant histones
These function to make DNA more accessible to regulatory proteins that affect
gene expression.
16.6 Eukaryotic Posttranscriptional Regulation
Post-transcriptional Control in Eukaryotes
1. miRNA-micro-RNA-function via base-pairing with complementary sequences
within mRNA molecules. As a result, these mRNA molecules are silenced by
one or more of the following processes: 1) cleavage of the mRNA strand into
two pieces, 2) destabilization of the mRNA through shortening of its poly(A)
tail, and 3) less efficient translation of the mRNA into proteins by ribosomes.
2. Small interfering RNA (siRNA), sometimes known as short interfering RNA or
silencing RNA, is a class of double-stranded RNA molecules, 20-25 base pairs
in length. siRNA plays many roles, but it is most notable in the RNA
interference (RNAi) pathway, where it interferes with the expression of specific
genes with complementary nucleotide sequences. siRNA functions by causing
mRNA to be broken down after transcription, resulting in no translation.
16.6 cont’d
3. Processing of primary transcript (RNA splicing- introns out; exons spliced
together)
• Order of exons-determines proteins to be made
• Could get two or three proteins from one gene
• Ex: thyroid gland & hypothalamus
Thyroid gland- regulates metabolism by the production of hormones
Hypothalamus- releases hormones that in turn regulate the release of hormones
from other glands
Both produce two very different hormones (calcitonin & CGRP) with different
functions, but they are made using the same transcript.
16.4
4. Selecting which mRNAs are translated
• Translation repressor proteins shut down translation by binding to transcript.
5. Selectively degrading mRNA transcripts
• Enzymes can degrade transcripts in cytoplasm
• Removal of the poly A-tail from the 3/ end can destabilize mRNA
• Half lives of mRNA also play a role
http://highered.mcgrawhill.com/sites/9834092339/student_view0/chapter16/control_of_gene_expression_in_
eukaryotes.html
16.7 Protein Degradation
• Marking proteins for degradation- enzymes called proteases can degrade
proteins by breaking peptide bonds, converting a protein into its constituent
amino acids.
• Proteins to be degraded are marked by a ubiquitin molecule. Ubiquitin is a 76amino acid protein that can exist in isolation or in longer chains attached to
other proteins.
• Proteins become ubiquitinated for two reasons:
1. Proteins are improperly folded or are nonfunctional.
2. Proteins that are produced and degraded in a controlled fashion by the cell.
Ex: cyclin proteins that help drive the cell cycle.
• Organelle responsible for degrading these proteins is called proteasomes. (not
membrane bound)