Controlling Gene Expression

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Controlling Gene Expression

• Timothy G. Standish, Ph. D.

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All Genes Cant be Expressed At The Same Time

• Some genes are needed for the function of all
  cells all the time. These genes are called
  constitutive genes and are expressed by all
  cells.
• Other genes are only needed by certain cells or
  at specific times. The expression of these
  inducible genes is tightly controlled in most
  cells.
• For example, beta cells in the pancreas make the
  protein insulin by expressing the insulin gene.
  If neurons expressed insulin, problems would
  result.

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Operons Are Groups Of Genes Expressed By
Prokaryotes

• The genes grouped in an operon are all needed to
  complete a given task
• Each operon is controlled by a single control
  sequence in the DNA
• Because the genes are grouped together, they can
  be transcribed together then translated together

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The Lac Operon

• Genes in the lac operon allow E. coli bacteria
  to metabolize lactose
• Lactose is a sugar that E. coli is unlikely to
  encounter, so it would be wasteful to produce the
  proteins needed to metabolize it unless necessary
• Metabolizing lactose for energy only makes sense
  when two criteria are met
• Other more readily metabolized sugar (glucose) is
  unavailable
• Lactose is available

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The Lac Operon - Parts

• The lac operon is made up of a control region and
  four genes
• The four genes are
• LacZ - b-galactosidase - An enzyme that
  hydrolizes the bond between galactose and glucose
• LacY - Codes for a permease that lets lactose
  across the cell membrane
• LacA - Transacetylase - An enzyme whose function
  in lactose metabolism is uncertain
• Repressor - A protein that works with the control
  region to control expression of the operon

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The Lac Operon - Control

• The control region is made up of two parts
• Promoter
• These are specific DNA sequences to which RNA
  Polymerase binds so that transcription can occur
• The lac operon promoter also has a binding site
  for another protein called CAP
• Operator
• The binding site of the repressor protein
• The operator is located downstream (in the 3
  direction) from the promoter so that if repressor
  is bound RNA Polymerase cant transcribe

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The Lac OperonWhen Glucose Is Present But Not
Lactose
Come on, let me through
RNA Pol.
No way Jose!
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The Lac OperonWhen Glucose And Lactose Are
Present
Great, I can transcribe!
RNA Pol.
Lac
This lactose has bent me out of shape
Some transcription occurs, but at a slow rate
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The Lac OperonWhen Lactose Is Present But Not
Glucose
Bind to me Polymerase
Yipee!
RNA Pol.
Lac
This lactose has bent me out of shape
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The Lac OperonWhen Neither Lactose Nor Glucose
Is Present
Bind to me Polymerase
Come on, let me through!
RNA Pol.
STOP Right there Polymerase
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The Trp Operon

• Genes in the trp operon allow E. coli bacteria to
  make the amino acid tryptophan
• Enzymes encoded by genes in the trp operon are
  all involved in the biochemical pathway that
  converts the precursor chorismate to tryptophan.
• The trp operon is controlled in two ways
• Using a repressor that works in exactly the
  opposite way from the lac operon repressor
• Using a special attenuator sequence

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The TryptophanBiochemical Pathway
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The Trp OperonWhen Tryptophan Is Present
Foiled Again!
RNA Pol.
STOP Right there Polymerase
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Attenuation

• The trp operon is controlled both by a repressor
  and attenuation
• Attenuation is a mechanism that works only
  because of the way transcription and translation
  are coupled in prokaryotes
• Therefore, to understand attenuation, it is first
  necessary to understand transcription and
  translation in prokaryotes

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Transcription And Translation In Prokaryotes
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The Trp Leader and Attenuator
Met-Lys-Ala-Ile-Phe-Val
- AAGUUCACGUAAAAAGGGUAUCGACA-AUG-AAA-GCA-AUU-UUC-G
UA- Leu-Lys-Gly-Trp-Trp-Arg-Thr-Ser-STOP CUG-AAA-
GGU-UGG-UGG-CGC-ACU-UCC-UGA-AACGGGCAGUGUAUU CACC
AUGCGUAAAGCAAUCAGAUACCCAGCCCGCCUAAUGAGCGGGCUUUU
Met-Gln-Thr-Gln-Lys-Pro
UUUU-GAACAAAAUUAGAGAAUAACA-AUG-CAA-ACA-CAA-AAA-CCG

trpE . . . Terminator
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The mRNA Sequence Can Fold In Two Ways
Terminator hairpin
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The Attenuator When Starved For Tryptophan
RNA Pol.
Help, I need Tryptophan
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The Attenuator When Tryptophan Is Present
RNA Pol.
RNA Pol.
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Control Of Expression In Eukaryotes

• Some of the general methods used to control
  expression in prokaryotes are used in eukaryotes,
  but nothing resembling operons is known
• Eukaryotic genes are controlled individually and
  each gene has specific control sequences
  preceding the transcription start site
• In addition to controlling transcription, there
  are additional ways in which expression can be
  controlled in eukaryotes

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Eukaryotes Have Large Complex Genomes

• The human genome is about 3 x 109 base pairs or
  1 m of DNA
• Because humans are diploid, each nucleus contains
  6 3 x 109 base pairs or 2 m of DNA
• That is a lot to pack into a little nucleus!

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Eukaryotic DNA Must be Packaged

• Eukaryotic DNA exhibits many levels of packaging
• The fundamental unit is the nucleosome, DNA wound
  around histone proteins
• Nucleosomes arrange themselves together to form
  higher and higher levels of packaging.

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Highly Packaged DNA Cannot be Expressed

• The most highly packaged form of DNA is
  heterochromatin
• Heterochromatin cannot be transcribed, therefore
  expression of genes is prevented
• Chromosome puffs on some insect chomosomes
  illustrate where active gene expression is going
  on

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Only a Subset of Genes is Expressed at any Given
Time

• It takes lots of energy to express genes
• Thus it would be wasteful to express all genes
  all the time
• By differential expression of genes, cells can
  respond to changes in the environment
• Differential expression allows cells to
  specialize in multicelled organisms.
• Differential expression also allows organisms to
  develop over time.

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Control of Gene Expression
Packaging
Transportation
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Logical Expression Control Points

• DNA packaging
• Transcription
• RNA processing
• mRNA export
• mRNA masking/unmasking and/or modification
• mRNA degradation
• Translation
• Protein modification
• Protein transport
• Protein degradation

The logical place to control expression is before
the gene is transcribed
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A Simple Eukaryotic Gene
Transcription Start Site
3 Untranslated Region
5 Untranslated Region
Introns
3
5
Int. 2
Int. 1
Exon 2
Exon 3
Exon 1
Terminator Sequence
Promoter/ Control Region
Exons
RNA Transcript
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Enhancers
Many bases
TF
TF
TF
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Eukaryotic mRNA
3 Untranslated Region
5 Untranslated Region
3
5
G
AAAAA
Exon 2
Exon 3
Exon 1
Protein Coding Region
3 Poly A Tail
5 Cap

• RNA processing achieves three things
• Removal of introns
• Addition of a 5 cap
• Addition of a 3 tail
• This signals the mRNA is ready to move out of the
  nucleus and may control its lifespan in the
  cytoplasm

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