• 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
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• 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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• 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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1. Transcription: most common step in control.
2. RNA processing: only in eukaryotes.
• Alternate splicing changes type/amount of protein.
3. Translation: prokaryotes, stops transl. early.
4. Stability of mRNA: longer lived, more product.
5. Posttranslational: change protein after it’s made. Process precursor or add PO
4 group.
6. DNA rearrangements. Genes change position relative to promoters, or exons shuffled.
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• 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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• 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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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.
7 http://omega.dawsoncollege.qc.ca/ray/genereg/operon3.JPG

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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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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• http://www.cat.cc.md.us/courses/bio141/lecguide/unit4/genetics/protsyn/regulation/ionoind.html
• http://www.cat.cc.md.us/courses/bio141/lecguide/unit4/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.

• 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.
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Green: repressor protein
Purple: RNA polymerase

• 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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• 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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• 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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Transcription by RNA polymerase prevented.

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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.

• 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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• Glucose is preferred nutrient source
– Other sugars (lactose, etc.) are not.
• Glucose inhibits activity of adenylate cyclase, the enzyme that makes cAMP from ATP.
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• 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.

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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

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