Download Gene Regulation

Gene Regulation
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• Organisms have lots of genetic information, but
they don’t necessarily want to use all of it (or
use it fully) at one particular time.
• Eukaryotes: Development, differentiation, and
homeostasis
– In going from zygote to fetus, e.g., many
genes are used that are then turned off.
– Liver cells, brain cells, use only certain genes
– Cells respond to internal, external signals
Gene regulation continued
• Prokaryotes: respond rapidly to environment
– Transcription and translation are expensive
• Each nucleotide = 2 ATP in transcription
• Several GTP/ATP per amino acid in translation
• If protein is not needed, don’t waste energy!
– Changes in food availability, environmental
conditions lead to differential gene expression
• Degradation genes turned on to use C source
• Bacteria respond to surfaces, new flagella etc.
• Quorum sensing: sufficient # of individuals turns
on genes.
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On/off, up/down, together
• Sometimes genes are off completely
and never transcribed again; some are just
turned up or down
– Eukaryotic genes typically turned up and down a
little compared to huge increases for prokaryotes.
• Genes that are “on” all the time = Constitutive
• Many genes can be regulated “coordinately”
– Eukaryotes: genes may be scattered about, turned
up or down by competing signals.
– Prokaryotes: genes often grouped in operons,
several genes transcribed together in 1 mRNA.
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How is gene expression controlled?
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1. Transcription: most common step in control.
2. RNA processing: only in eukaryotes.
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Alternate splicing changes type/amount of protein.
3. Translation: prokaryotes, stops transcrp. early.
4. Stability of mRNA: longer lived, more product.
5. Post-translational: change protein after it’s
made. Process precursor or add PO4 group.
6. DNA rearrangements. Genes change position
relative to promoters, or exons shuffled.
Gene regulation in Prokaryotes
• Bacteria were models for working out the basic
mechanisms, but eukaryotes are different.
• Some genes are constitutive, others go from
extremely low expression (“off”) to high
expression when “turned on”.
• Many genes are coordinately regulated.
– Operon: consecutive genes regulated, transcribed
together; polycistronic mRNA.
– Regulon: genes scattered, but regulated together.
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Rationale for Operon
• Many metabolic pathways
require several enzymes
working together.
• In bacteria, transcription of
a group of genes is turned
on simultaneously, a single
mRNA is made, so all the
enzymes needed can be
produced at once.
http://galactosaemia.com.hosting.domaindirect.com/images/metabolic-pathway.gif
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Proteins change shape
When a small molecule
binds to the protein, it
changes shape.
If this is a DNA-binding
protein, the new shape
may cause it to attach
better to the DNA, or
“fall off” the DNA.
http://omega.dawsoncollege.qc.ca/ray/genereg/operon3.JPG
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Definitions concerning operon regulation
• Control can be Positive or Negative
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– Positive control means a protein binds to the DNA
which increases transcription.
– Negative control means a protein binds to the DNA
which decreases transcription.
• Induction
– Process in which genes normally off get turned on.
– Usually associated with catabolic genes.
• Repression
– Genes normally on get turned off.
– Usually associated with anabolic genes.
Structure of an Operon
1. Structural genes: actual genes being regulated.
2. Promoter region: site for RNA polymerase to bind,
begin transcription.
3. Operator region: site where regulatory protein binds.
4. Regulatory protein gene: need not be in the same
area as the operon. Protein binds to DNA.
www.cat.cc.md.us
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Animations
• Look up Animations showing the effects of the
lactose repressor on the lac operon.
– As with translation, details will vary. For example,
the lactose repressor protein is a tetramer. How
many sites depict it this way?
– Be wary of oversimplification.
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The Lactose Operon
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• The model system for prokaryotic gene regulation,
worked out by Jacob and Monod, France, 1960.
• The setting: E. coli has the genes for using lactose
(milk sugar), but seldom sees it. Genes are OFF.
– Repressor protein (product of lac I gene) is bound
to the operator, preventing transcription by RNA
polymerase.
Green: repressor protein
Purple: RNA polymerase
Lactose operon-2
• When lactose does appear, E. coli wants to use it.
Lactose binds to repressor, causing shape change;
repressor falls off DNA, allows unhindered
transcription by RNA polymerase. Translation of
mRNA results in enzymes needed to use lactose.
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Lactose operon definitions
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• Control is Negative
– When repressor protein is bound to the DNA,
transcription is shut off.
• This operon is inducible
– Lactose is normally not available as a carbon
source; genes are “shut off”
– In bacteria, many similar operons exist for using
other organic molecules.
– Proteins for transporting the sugar, breaking it down
are produced.
Repressible operons
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• Operon codes for enzymes that make a needed amino
acid (for example); genes are “on”.
– Repressor protein is NOT attached to DNA
– Transcription of genes for enzymes needed to make
amino acid is occurring.
• The change: amino acid is now available in the
culture medium. Enzymes normally needed for making
it are no longer needed.
– Amino acid, now abundant in cell, binds to repressor protein
which changes shape, causing it to BIND to operator region
of DNA. Transcription is stopped.
• This is also Negative regulation (protein + DNA = off).
Repression picture
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Transcription by RNA
polymerase prevented.
Regulation can be fine tuned
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The more of the amino acid present in the cell, the more
repressor-amino acid complex is formed; the more likely
that transcription will be prevented.
Positive regulation
• Binding of a regulatory protein to the DNA
increases (turns on) transcription.
– More common in eukaryotes.
• Prokaryotic example: the CAP-cAMP system
– Catabolite-activating Protein
– cAMP: ATP derivative, acts as signal molecule
– When CAP binds to cAMP, creates a complex that
binds to DNA, turning ON transcription.
– Whether there is enough cAMP in the cell to
combine with CAP depends on glucose conc.
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Positive regulation-2
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• Glucose is preferred nutrient source
– Other sugars (lactose, etc.) are not.
• Glucose inhibits activity of adenylate cyclase,
the enzyme that makes cAMP from ATP.
• When glucose is high, cAMP is low, less cAMP
is available to bind to CAP.
– CAP is “free”, doesn’t bind to DNA, genes not on.
• When glucose is low, cAMP is high
– Lots of cAMP, so CAP-cAMP forms, genes on.
• Works in conjunction with induction.
Cartoon of Positive Regulation
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Attenuation: fine tuning repression
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• Attenuation occurs in prokaryotic repressible
operons. Happens when transcription is on.
• Regulation at the level of translation
• Several things important:
– Depends on base-pairing between complementary
sequences of mRNA
– Requires simultaneous transcription/translation
– Involves delays in progression of ribosomes on
mRNA
Mechanism of attenuation- tryp operon
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Mech. of attenuation -2
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Attenuation-3
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