Regulation of Prokaryotic and Eukaryotic Gene Expression

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Regulation of Prokaryotic and Eukaryotic Gene
Expression
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• A bacterium can tune its metabolism to the
  changing environment and food sources
• This metabolic control occurs on two levels
• Adjusting activity of metabolic enzymes
• Regulating genes that encode metabolic enzymes

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LE 18-20
Regulation of enzyme production
Regulation of enzyme activity
Precursor
Feedback inhibition
Enzyme 1
Gene 1
Enzyme 2
Gene 2
Regulation of gene expression
Gene 3
Enzyme 3
Enzyme 4
Gene 4
Gene 5
Enzyme 5
Tryptophan
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Operons The Basic Concept

• In bacteria, genes are often clustered into
  operons, composed of
• An operator, an on-off switch
• A promoter
• Genes for metabolic enzymes

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LE 18-21a
trp operon
Promoter
Promoter
Genes of operon
DNA
trpE
trpC
trpB
trpA
trpR
trpD
Operator
Stop codon
RNA polymerase
Regulatory gene
Start codon
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mRNA 5
mRNA
5
D
B
E
C
A
Protein
Inactive repressor
Polypeptides that make up enzymes for tryptophan
synthesis
Tryptophan absent, repressor inactive, operon on
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LE 18-21b_1
DNA
mRNA
Protein
Active repressor
Tryptophan (corepressor)
Tryptophan present, repressor active, operon off
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LE 18-21b_2
DNA
No RNA made
mRNA
Protein
Active repressor
Tryptophan (corepressor)
Tryptophan present, repressor active, operon off
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Two Types of Negative Gene Regulation

• A repressible operon
• Is usually on
• binding of a repressor to the operator shuts off
  transcription
• The trp operon is a repressible operon
• An inducible operon
• Is one that is usually off
• a molecule called an inducer inactivates the
  repressor and turns on transcription
• the lac operon is an inducible operon, which
  contains genes coding for enzymes in hydrolysis
  and metabolism of lactose

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LE 18-22a
Promoter
Regulatory gene
Operator
lacl
lacZ
DNA
No RNA made
3
mRNA
RNA polymerase
5
Active repressor
Protein
Lactose absent, repressor active, operon off
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LE 18-22b
lac operon
DNA
lacl
lacZ
lacY
lacA
RNA polymerase
3
mRNA
mRNA 5
5
Permease
Transacetylase
?-Galactosidase
Protein
Inactive repressor
Allolactose (inducer)
Lactose present, repressor inactive, operon on
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• Inducible enzymes usually function in catabolic
  (breakdown) pathways
• Explain to a neighbor why this makes sense.
• Repressible enzymes usually function in anabolic
  (synthesis) pathways
• Explain to a neighbor why this makes sense.
• Regulation of the trp and lac operons involves
  negative control of genes because operons are
  switched off by the active form of the repressor

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Positive Gene Regulation

• Some operons are also subject to positive control
  through a stimulatory activator protein, such as
  catabolite activator protein (CAP)
• When glucose (a preferred food source of E. coli
  ) is scarce, the lac operon is activated by the
  binding of CAP
• When glucose levels increase, CAP detaches from
  the lac operon, turning it off

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LE 18-23a
Promoter
DNA
lacl
lacZ
RNA polymerase can bind and transcribe
Operator
CAP-binding site
Active CAP
cAMP
Inactive lac repressor
Inactive CAP
Lactose present, glucose scarce (cAMP level
high) abundant lac mRNA synthesized
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LE 18-23b
Promoter
DNA
lacl
lacZ
CAP-binding site
Operator
RNA polymerase cant bind
Inactive CAP
Inactive lac repressor
Lactose present, glucose present (cAMP level
low) little lac mRNA synthesized
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Summarize

• Explain to a neighbor why bacteria regulate gene
  expression
• Give an example of how bacteria regulate gene
  expression

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Eukaryotic Gene Regulation
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• Every cell in a multi-cellular eukaryote does not
  express all its genes, all the time (usually only
  3-5)
• Long-term control of gene expression in tissue
  differentiation
• How to prevent expression?
• Regulation at transcription
• Regulation after transcription

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Chromatin Regulation

• Chromatin remodeling allows transcription
• Chromatin DNA proteins
• Chromatin coiled around histones nucleosomes
• Allows DNA to be packed into nucleus, but also
  physically regulates expression by making regions
  available or not

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• Chromatin regulation can be small-scale (gene) or
  large scale (chromosome)
• Non-expressed heterochromatin (condensed)
• Expressed euchromatin (relaxed)

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Changes to Chromatin (DNA)

• Methylation
• Methylating (adding methyl groups) to DNA bases,
  keeping them tight and closed inaccessible
  to transcription.
• Histone Acetylation
• Acetylating histones (adding acetyl groups)
  promotes loose chromatin and permits transcription

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Transcription Regulation

• What we know from prokaryotes
• Several related genes can be transcribed together
  (ie. lac operon)
• Need RNA Polymerase to recognize a promoter
  region
• Why eukaryotes are different
• Genes are nearly always transcribed individually
• 3 RNA Polymerases occur, requiring multiple
  proteins to initiate transcription

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Transcription Regulation Cont

• Typical prokaryotic promoter
• recognition sequence TATA box -gt
• RNA Polymerase -gt transcription
• Typical eukaryotic promoter
• recognition sequence TATA box transcription
  factors -gt RNA Polymerase -gt transcription

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• RNA polymerase interacts w/promoter, regulator
  sequences, enhancer sequences to begin
  transcription
• Regulator proteins bind to regulator sequences to
  activate transcription
• Found prior to promoter
• Enhancer sequences bind activator proteins
• Typically far from the gene
• Silencer sequences stop transcription if they
  bind with repressor proteins

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Now, Can You

• Explain why gene expression control is necessary
  in a eukaryotic cell?
• Describe how expression is regulated in before
  during transcription?
• Tell me what differentiation is? Euchromatin? A
  silencer sequence?
• Explain how gene expression regulation is
  different in eukaryotes/prokaryotes?

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Post-Transcription Regulation

• Have mRNA variation
• Alternative splicing shuffling exons
• Allows various proteins to be produced in
  different tissues from the same gene
• Change the lifespan of mRNA
• Produce micro RNA that will damage mRNA,
  preventing translation
• Edit RNA change the polypeptide produced
• Insert or alter the genetic code

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Translation Regulation

• mRNA present in cytosol does not necessarily get
  translated into proteins
• Control the rate of translation to regulate gene
  expression
• How?
• Modify the 5 cap
• Feedback regulation (build up of products less
  translation)

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Translation Regulation Cont

• Modify the lifespan of proteins
• Attach ubiquitin target for breakdown via
  proteasome (woodchipper)

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So

• What are the ways that a cell can regulate gene
  expression AFTER transcription?
• How can the process of RNA splicing allow one
  pre-mRNA to produce 5 different proteins in 5
  different tissues?
• And

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• Can you accurately fill in this table?