Gene Regulation

1
Gene Regulation

• Organisms have lots of genetic information, but
  they dont 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

2
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, dont 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.

3
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.

4
How is gene expression controlled?

• Transcription most common step in control.
• RNA processing only in eukaryotes.
• Alternate splicing changes type/amount of
  protein.
• Translation prokaryotes, stops transl. early.
• Stability of mRNA longer lived, more product.
• Post-translational change protein after its
  made. Process precursor or add PO4 group.
• DNA rearrangements. Genes change position
  relative to promoters, or exons shuffled.

5
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.

6
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/opero
n3.JPG
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Definitions concerning operon regulation

• Control can be Positive or Negative
• 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.

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Structure of an Operon

1. Regulatory protein gene need not be in the same
   area as the operon. Protein binds to DNA.
2. Promoter region site for RNA polymerase to bind,
   begin transcription.
3. Operator region site where regulatory protein
   binds.
4. Structural genes actual genes being regulated.

www.cat.cc.md.us
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Animations

• http//www.cat.cc.md.us/courses/bio141/lecguide/un
  it4/genetics/protsyn/regulation/ionoind.html
• http//www.cat.cc.md.us/courses/bio141/lecguide/un
  it4/genetics/protsyn/regulation/ioind.html
• Animation showing the effects of the lactose
  repressor on the lac operon.
• Cut and paste addresses into your browser will
  give you some idea of how repressor proteins
  interact with operator regions to control
  transcription.

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The Lactose Operon

• 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
12
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

• 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.
• Genes for transporting the sugar, breaking it
  down are produced.

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Repressible operons

• 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).

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Repression picture
Transcription by RNA polymerase prevented.
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Regulation can be fine tuned
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.
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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

• 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, doesnt 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.

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Cartoon of Positive Regulation
20
Attenuation fine tuning repression

• 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

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Mechanism of attenuation- tryp operon
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Mech. of attenuation -2
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Attenuation-3