Control of Gene Expression

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Control of Gene Expression

• Chapter 16

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replication (mutation!)
genes
DNA
Nucleic acids software
(nucleotides)
transcription
messages
RNA
(nucleotides)
nucleus
ribosome (cytoplasm)
translation
Protein
hardware
(amino acids)
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Fig. 16.1
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Helix-Turn-Helix Motif
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Homeodomain Motif
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Zinc Finger Motif
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Leucine Zipper Motif
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Data of Jacob and Monod, 1961
phenotype for
genotype
B-gal Permease
IPTG --IPTG
IPTG --IPTG
Lac
Lacc
Lac-
Lacc

Lac
lacI dominant in cis and trans
Lac

lacI-- dominant
Lac-

Lacc
lacOc dominant in cis
Lacc
/Lac
lacOc dominant in cis even in presence of lacI--

Lacc
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Data of Jacob and Monod, 1961
phenotype for
genotype
B-gal Permease
IPTG --IPTG
IPTG --IPTG
Lac
Lacc
Lac-
Lacc

Lac
lacI dominant in cis and trans
Lac

lacI-- dominant
Lac-

Lacc
lacOc dominant in cis
Lacc
/Lac
lacOc dominant in cis even in presence of lacI--

Lacc
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Data of Jacob and Monod, 1961
phenotype for
genotype
B-gal Permease
IPTG --IPTG
IPTG --IPTG
Lac
Lacc
Lac-
Lacc

Lac
lacI dominant in cis and trans
Lac

lacIS dominant
Lac-

Lacc
lacOc dominant in cis
Lacc
/Lac
lacOc dominant in cis even in presence of lacI--

Lacc
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Data of Jacob and Monod, 1961
phenotype for
genotype
B-gal Permease
IPTG --IPTG
IPTG --IPTG
Lac
Lacc
Lac-
Lacc

Lac
lacI dominant in cis and trans
Lac

lacIS dominant
Lac-

Lacc
lacOc dominant in cis
Lacc
/Lac
lacOc dominant in cis even in presence of lacI--

Lacc
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Data of Jacob and Monod, 1961
phenotype for
genotype
B-gal Permease
IPTG --IPTG
IPTG --IPTG
Lac
Lacc
Lac-
Lacc

Lac
lacI dominant in cis and trans
Lac

lacIS dominant
Lac-

Lacc
lacOc dominant in cis
Lacc
/Lac
lacOc dominant in cis even in presence of lacIS

Lacc
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Fig. 16.7
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From http//www.aw.com/mathews/ch26/c26lara.htm
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Attenuation of trp operon transcription
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Fig. 16.8
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Fig. 16.16
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Control of Gene Expression

• Controlling gene expression is often accomplished
  by controlling transcription initiation.
• Regulatory proteins bind to DNA to either block
  or stimulate transcription, depending on how they
  interact with RNA polymerase.

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Control of Gene Expression

• Prokaryotic organisms regulate gene expression in
  response to their environment.
• Eukaryotic cells regulate gene expression to
  maintain homeostasis in the organism.

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Regulatory Proteins

• Gene expression is often controlled by regulatory
  proteins binding to specific DNA sequences.
• regulatory proteins gain access to the bases of
  DNA at the major groove
• regulatory proteins possess DNA-binding motifs

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Regulatory Proteins

• DNA-binding motifs are regions of regulatory
  proteins which bind to DNA
• helix-turn-helix motif
• homeodomain motif
• zinc finger motif
• leucine zipper motif

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Prokaryotic Regulation

• Control of transcription initiation can be
• positive control increases transcription when
  activators bind DNA
• negative control reduces transcription when
  repressors bind to DNA regulatory regions called
  operators

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Prokaryotic Regulation

• Prokaryotic cells often respond to their
  environment by changes in gene expression.
• Genes involved in the same metabolic pathway are
  organized in operons.
• Some operons are induced when the metabolic
  pathway is needed.
• Some operons are repressed when the metabolic
  pathway is no longer needed.

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Prokaryotic Regulation

• The lac operon contains genes for the use of
  lactose as an energy source.
• Regulatory regions of the operon include the CAP
  binding site, promoter, and the operator.
• The coding region contains genes for 3 enzymes
• b-galactosidase, permease, and transacetylase

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Prokaryotic Regulation

• The lac operon is negatively regulated by a
  repressor protein
• lac repressor binds to the operator to block
  transcription
• in the presence of lactose, an inducer molecule
  binds to the repressor protein
• repressor can no longer bind to operator
• transcription proceeds

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Prokaryotic Regulation

• In the presence of both glucose and lactose,
  bacterial cells prefer to use glucose.
• Glucose prevents induction of the lac operon.
• binding of CAP cAMP complex to the CAP binding
  site is required for induction of the lac operon
• high glucose levels cause low cAMP levels
• high glucose ? low cAMP ? no induction

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Prokaryotic Regulation

• The trp operon encodes genes for the biosynthesis
  of tryptophan.
• The operon is not expressed when the cell
  contains sufficient amounts of tryptophan.
• The operon is expressed when levels of tryptophan
  are low.

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Prokaryotic Regulation

• The trp operon is negatively regulated by the trp
  repressor protein
• trp repressor binds to the operator to block
  transcription
• binding of repressor to the operator requires a
  corepressor which is tryptophan
• low levels of tryptophan prevent the repressor
  from binding to the operator

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Eukaryotic Regulation

• Controlling the expression of eukaryotic genes
  requires transcription factors.
• general transcription factors are required for
  transcription initiation
• required for proper binding of RNA polymerase to
  the DNA
• specific transcription factors increase
  transcription in certain cells or in response to
  signals

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Eukaryotic Transcription

• General transcription factors bind to the
  promoter region of the gene.
• RNA polymerase II then binds to the promoter to
  begin transcription at the start site (1).
• Enhancers are DNA sequences to which specific
  transcription factors (activators) bind to
  increase the rate of transcription.

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Eukaryotic Transcription

• Coactivators and mediators are also required for
  the function of transcription factors.
• coactivators and mediators bind to transcription
  factors and bind to other parts of the
  transcription apparatus

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Eukaryotic Chromosome Structure

• Eukaryotic DNA is packaged into chromatin.
• Chromatin structure is directly related to the
  control of gene expression.
• Chromatin structure begins with the organization
  of the DNA into nucleosomes.
• Nucleosomes may block RNA polymerase II from
  gaining access to promoters.

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Eukaryotic Chromosome Structure

• Methylation (the addition of CH3) of DNA or
  histone proteins is associated with the control
  of gene expression.
• Clusters of methylated cytosine nucleotides bind
  to a protein that prevents activators from
  binding to DNA.
• Methylated histone proteins are associated with
  inactive regions of chromatin.

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Posttranscriptional Regulation

• Control of gene expression usually involves the
  control of transcription initiation.
• But gene expression can be controlled after
  transcription, with mechanisms such as
• RNA interference
• alternative splicing
• RNA editing
• mRNA degradation

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Posttranscriptional Regulation

• RNA interference involves the use of small RNA
  molecules
• The enzyme Dicer chops double stranded RNA into
  small pieces of RNA
• micro-RNAs bind to complementary RNA to prevent
  translation
• small interfering RNAs degrade particular mRNAs
  before translation

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Posttranscriptional Regulation

• Introns are spliced out of pre-mRNAs to produce
  the mature mRNA that is translated.
• Alternative splicing recognizes different splice
  sites in different tissue types.
• The mature mRNAs in each tissue possess different
  exons, resulting in different polypeptide
  products from the same gene.

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Posttranscriptional Regulation

• RNA editing creates mature mRNA that are not
  truly encoded by the genome.
• For example
• apolipoprotein B exists in 2 isoforms
• one isoform is produced by editing the mRNA to
  create a stop codon
• this RNA editing is tissue-specific

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Posttranscriptional Regulation

• Mature mRNA molecules have various half-lives
  depending on the gene and the location (tissue)
  of expression.
• The amount of polypeptide produced from a
  particular gene can be influenced by the
  half-life of the mRNA molecules.

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Protein Degradation

• Proteins are produced and degraded continually in
  the cell.
• Proteins to be degraded are tagged with
  ubiquitin.
• Degradation of proteins marked with ubiquitin
  occurs at the proteasome.