Regulation of Gene Expression

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Regulation of Gene Expression
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Chapter 11 Regulation of Gene Expression

• Key Concepts
• 11.1 Several Strategies Are Used to Regulate Gene
  Expression
• 11.2 Many Prokaryotic Genes Are Regulated in
  Operons
• 11.3 Eukaryotic Genes Are Regulated by
  Transcription Factors and DNA Changes
• 11.4 Eukaryotic Gene Expression Can Be Regulated
  after Transcription

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Chapter 11 Opening Question

• How does CREB regulate the expression of many
  genes?

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Concept 11.1 Several Strategies Are Used to
Regulate Gene Expression

• Gene expression is tightly regulated.
• Gene expression may be modified to counteract
  environmental changes, or gene expression may
  change to alter function in the cell.
• Constitutive proteins are actively expressed all
  the time.
• Inducible genes are expressed only when their
  proteins are needed by the cell.

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Figure 11.1 Potential Points for the Regulation
of Gene Expression
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Concept 11.1 Several Strategies Are Used to
Regulate Gene Expression

• Genes can be regulated at the level of
  transcription.
• Gene expression begins at the promoter where
  transcription is initiated.
• In selective gene transcription a decision is
  made about which genes to activate.
• Two types of regulatory proteinsalso called
  transcription factorscontrol whether a gene is
  active.

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Concept 11.1 Several Strategies Are Used to
Regulate Gene Expression

• These proteins bind to specific DNA sequences
  near the promoter
• Negative regulationa repressor protein prevents
  transcription
• Positive regulationan activator protein binds to
  stimulate transcription

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Figure 11.2 Positive and Negative Regulation
(Part 1)
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Figure 11.2 Positive and Negative Regulation
(Part 2)
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Concept 11.1 Several Strategies Are Used to
Regulate Gene Expression

• Acellular viruses use gene regulation to take
  over host cells.
• A phage injects a host cell with nucleic acid
  that takes over synthesis.
• New viral particles (virions) appear rapidly and
  are soon released from the lysed cell.
• This lytic cycle is a typical viral reproductive
  cyclein a lysogenic phase, the viral genome is
  incorporated into the host genome and is
  replicated too.

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Concept 11.1 Several Strategies Are Used to
Regulate Gene Expression

• A bacteriophage may contain DNA or RNA and may
  not have a lysogenic phase.
• The lytic cycle has two stages
• Early stagepromoter in the viral genome binds
  host RNA polymerase and adjacent viral genes are
  transcribed
• Early genes shut down transcription of host
  genes, and stimulate viral replication and
  transcription of viral late genes.
• Host genes are shut down by a posttranscriptional
  mechanism.
• Viral nucleases digest the hosts chromosome for
  synthesis in new viral particles.

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Concept 11.1 Several Strategies Are Used to
Regulate Gene Expression

• Late stageviral late genes are transcribed
• They encode the viral capsid proteins and enzymes
  to lyse the host cell and release new virions.
• The whole process from binding and infection to
  release of new particles takes about 30 minutes.

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Figure 11.3 A Gene Regulation Strategy for Viral
Reproduction
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Concept 11.1 Several Strategies Are Used to
Regulate Gene Expression

• Human immunodeficiency virus (HIV) is a
  retrovirus with single-stranded RNA.
• HIV is enclosed in a membrane from the previous
  host cellit fuses with the new host cells
  membrane.
• After infection, RNA-directed DNA synthesis is
  catalyzed by reverse transcriptase.
• Two strands of DNA are synthesized and reside in
  the hosts chromosome as a provirus.

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Figure 11.4 The Reproductive Cycle of HIV
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Concept 11.1 Several Strategies Are Used to
Regulate Gene Expression

• Host cells have systems to repress the invading
  viral genes.
• One system uses transcription terminator
  proteins that interfere with RNA polymerase.
• HIV counteracts this negative regulation with Tat
  (Transactivator of transcription), which allows
  RNA polymerase to transcribe the viral genome.

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Figure 11.5 Regulation of Transcription by HIV
(Part 1)
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Figure 11.5 Regulation of Transcription by HIV
(Part 2)
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Concept 11.2 Many Prokaryotic Genes Are
Regulated in Operons

• Prokaryotes conserve energy by making proteins
  only when needed.
• In a rapidly changing environment, the most
  efficient gene regulation is at the level of
  transcription.
• E. coli must adapt quickly to food supply
  changes. Glucose or lactose may be present.

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Concept 11.2 Many Prokaryotic Genes Are
Regulated in Operons

• Uptake and metabolism of lactose involve three
  proteins
• ?-galactoside permeasea carrier protein that
  moves sugar into the cell
• ?-galactosidasean enzyme that hydrolyses lactose
• ?-galactoside transacetylasetransfers acetyl
  groups to certain ?-galactosides
• If E. coli is grown with glucose but no lactose
  present, no enzymes for lactose conversion are
  produced.

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Concept 11.2 Many Prokaryotic Genes Are
Regulated in Operons

• If lactose is predominant and glucose is low, E.
  coli synthesizes all three enzymes.
• If lactose is removed, synthesis stops.
• A compound that induces protein synthesis is an
  inducer.
• Gene expression and regulating enzyme activity
  are two ways to regulate a metabolic pathway.

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Figure 11.6 Two Ways to Regulate a Metabolic
Pathway
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Concept 11.2 Many Prokaryotic Genes Are
Regulated in Operons

• Structural genes specify primary protein
  structurethe amino acid sequence.
• The three structural genes for lactose enzymes
  are adjacent on the chromosome, share a promoter,
  and are transcribed together.
• Their synthesis is all-or-none.

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Concept 11.2 Many Prokaryotic Genes Are
Regulated in Operons

• A gene cluster with a single promoter is an
  operonthe one that encodes for the lactose
  enzymes is the lac operon.
• An operator is a short stretch of DNA near the
  promoter that controls transcription of the
  structural genes.
• Inducible operonturned off unless needed
• Repressible operonturned on unless not needed

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Figure 11.7 The lac Operon of E. coli
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Concept 11.2 Many Prokaryotic Genes Are
Regulated in Operons

• The lac operon is only transcribed when a
  ?-galactoside predominates in the cell
• A repressor protein is normally bound to the
  operator, which blocks transcription.
• In the presence of a ?-galactoside, the repressor
  detaches and allows RNA polymerase to initiate
  transcription.
• The key to this regulatory system is the
  repressor protein.

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Figure 11.8 The lac Operon An Inducible System
(Part 1)
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Figure 11.8 The lac Operon An Inducible System
(Part 2)
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Concept 11.2 Many Prokaryotic Genes Are
Regulated in Operons

• A repressible operon is switched off when its
  repressor is bound to its operator.
• However, the repressor only binds in the presence
  of a co-repressor.
• The co-repressor causes the repressor to change
  shape in order to bind to the promoter and
  inhibit transcription.
• Tryptophan functions as its own co-repressor,
  binding to the repressor of the trp operon.

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Figure 11.9 The trp Operon A Repressible System
(Part 1)
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Figure 11.9 The trp Operon A Repressible System
(Part 2)
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Concept 11.2 Many Prokaryotic Genes Are
Regulated in Operons

• Difference in two types of operons
• In inducible systemsa metabolic substrate
  (inducer) interacts with a regulatory protein
  (repressor) the repressor cannot bind and allows
  transcription.
• In repressible systemsa metabolic product
  (co-repressor) binds to regulatory protein, which
  then binds to the operator and blocks
  transcription.

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Concept 11.2 Many Prokaryotic Genes Are
Regulated in Operons

• Generally, inducible systems control catabolic
  pathwaysturned on when substrate is available
• Repressible systems control anabolic
  pathwaysturned on until product concentration
  becomes excessive

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Concept 11.2 Many Prokaryotic Genes Are
Regulated in Operons

• Sigma factorsother proteins that bind to RNA
  polymerase and direct it to specific promoters
• Global gene regulation Genes that encode
  proteins with related functions may have a
  different location but have the same promoter
  sequencethey are turned on at the same time.
• Sporulation occurs when nutrients are
  depletedgenes are expressed sequentially,
  directed by a sigma factor.

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Table 11.1 Transcription in Bacteria and
Eukaryotes
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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• Transcription factors act at eukaryotic
  promoters.
• Each promoter contains a core promoter sequence
  where RNA polymerase binds.
• TATA box is a common core promoter sequencerich
  in A-T base pairs.
• Only after general transcription factors bind to
  the core promoter, can RNA polymerase II bind and
  initiate transcription.

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Figure 11.10 The Initiation of Transcription in
Eukaryotes (Part 1)
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Figure 11.10 The Initiation of Transcription in
Eukaryotes (Part 2)
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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• Besides the promoter, other sequences bind
  regulatory proteins that interact with RNA
  polymerase and regulate transcription.
• Some are positive regulatorsactivators others
  are negativerepressors.
• DNA sequences that bind activators are enhancers,
  those that bind repressors are silencers.
• The combination of factors present determines the
  rate of transcription.

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In-Text Art, Ch. 11, p. 216
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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• Transcription factors recognize particular
  nucleotide sequences
• NFATs (nuclear factors of activated T cells) are
  transcription factors that control genes in the
  immune system.
• They bind to a recognition sequence near the
  genes promoters.
• The binding produces an induced fitthe protein
  changes conformation.

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Figure 11.11 A Transcription Factor Protein
Binds to DNA
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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• Gene expression can be coordinated, even if genes
  are far apart on different chromosomes.
• They must have regulatory sequences that bind the
  same transcription factors.
• Plants use this to respond to droughtthe
  scattered stress response genes each have a
  specific regulatory sequence, the dehydration
  response element.
• During drought, a transcription factor changes
  shape and binds to this element.

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Figure 11.12 Coordinating Gene Expression
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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• Gene transcription can also be regulated by
  reversible alterations to DNA or chromosomal
  proteins.
• Alterations can be passed on to daughter cells.
• These epigenetic changes are different from
  mutations, which are irreversible changes to the
  DNA sequence.

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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• Some cytosine residues in DNA are modified by
  adding a methyl group covalently to the 5'
  carbonforms 5'-methylcytosine
• DNA methyltransferase catalyzes the
  reactionusually in adjacent C and G residues.
• Regions rich in C and G are called CpG
  islandsoften in promoters

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Figure 11.13 DNA Methylation An Epigenetic
Change (Part 1)
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Figure 11.13 DNA Methylation An Epigenetic
Change (Part 2)
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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• This covalent change in DNA is heritable
• When DNA replicates, a maintenance methylase
  catalyzes formation of 5'-methylcytosine in the
  new strand.
• However, methylation pattern may be
  altereddemethylase can catalyze the removal of
  the methyl group.

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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• Effects of DNA methylation
• Methylated DNA binds proteins that are involved
  in repression of transcriptiongenes tend to be
  inactive (silenced).
• Patterns of DNA methylation may include large
  regions or whole chromosomes.

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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• Two kinds of chromatin are visible during
  interphase
• Euchromatindiffuse and light-staining contains
  DNA for mRNA transcription
• Heterochromatincondensed, dark-staining
  contains genes not transcribed

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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• A type of heterochromatin is the inactive X
  chromosome in mammals.
• Males (XY) and females (XX) contain different
  numbers of X-linked genes, yet for most genes
  transcription, rates are similar.
• Early in development, one of the X chromosomes is
  inactivatedthis Barr body is identifiable during
  interphase and can be seen in cells of human
  females.

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Figure 11.14 X Chromosome Inactivation
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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• Another mechanism for epigenetic regulation is
  chromatin remodeling, or the alteration of
  chromatin structure.
• Nucleosomes contain DNA and positively-charged
  histones in a tight complex, inaccessible to RNA
  polymerase.
• Histone acetyltransferases change the charge by
  adding acetyl groups to the amino acids on the
  histones tail.

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In-Text Art, Ch. 11, p. 219 (1)
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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• The change in charge opens up the nucleosomes as
  histone loses its affinity for DNA.
• More chromatin remodeling proteins bind and open
  the DNA for gene expression.
• Thus, histone acetyltransferases can activate
  transcription.

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Figure 11.15 Epigenetic Remodeling of Chromatin
for Transcription
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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• Histone deacetylase is another kind of chromatin
  remodeling protein.
• It can remove the acetyl groups from the
  histones, repressing transcription.

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Concept 11.3 Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes

• Environment plays an important role in
  epigenetic modifications.
• Even though they are reversible, some epigenetic
  changes can permanently alter gene expression
  patterns.
• If the cells form gametes, the epigenetic changes
  can be passed on to the next generation.
• Monozygotic twins show different DNA methylation
  patterns after living in different environments.

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Concept 11.4 Eukaryotic Gene Expression Can Be
Regulated after Transcription

• Eukaryotic gene expression can be regulated after
  the initial gene transcript is made.
• Different mRNAs can be made from the same gene by
  alternative splicing.
• As introns and exons are spliced out, new
  proteins are made.
• This may be a deliberate mechanism for generating
  proteins with different functions, from a single
  gene.

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Concept 11.4 Eukaryotic Gene Expression Can Be
Regulated after Transcription

• Examples of alternative splicing
• The HIV genome encodes nine proteins, but is
  transcribed as a single pre-mRNA.
• In Drosophila the Sxl gene with four exons is
  spliced differently to produce different
  combinations in males and females.

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Figure 11.16 Alternative Splicing Results in
Different Mature mRNAs and Proteins
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Concept 11.4 Eukaryotic Gene Expression Can Be
Regulated after Transcription

• MicroRNAs(miRNAs)small molecules of noncoding
  RNAare important regulators of gene expression.
• In C. elegans, lin-14 mutations cause the larvae
  to skip the first stagethus the normal role for
  lin-14 is to be involved in stage one of
  development.
• lin-4 mutations cause cells to repeat stage one
  eventsthus the normal role for lin-4 is to
  negatively regulate lin-14, so that cells can
  progress to the next stage of development.

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Concept 11.4 Eukaryotic Gene Expression Can Be
Regulated after Transcription

• lin-4 encodes not for a protein but for a 22-base
  miRNA that inhibits lin-14 expression
  posttranscriptionally by binding to its mRNA.
• Many miRNAs have been describedonce transcribed
  they are guided to a target mRNA to inhibit its
  translation and to degrade the mRNA.

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Figure 11.17 mRNA Degradation Caused by MicroRNAs
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Concept 11.4 Eukaryotic Gene Expression Can Be
Regulated after Transcription

• mRNA translation can be regulated.
• Protein and mRNA concentrations are not
  consistently relatedgoverned by factors acting
  after mRNA is made.
• Cells either block mRNA translation or alter how
  long new proteins persist in the cell.

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Concept 11.4 Eukaryotic Gene Expression Can Be
Regulated after Transcription

• Three ways to regulate mRNA translation
• Inhibition of translation with miRNAs
• Modification of the 5' cap end of mRNA can be
  modifiedif cap is unmodified mRNA is not
  translated.
• Repressor proteins can block translation
  directlytranslational repressors

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Figure 11.18 A Repressor of Translation
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Figure 11.19 A Proteasome Breaks Down Proteins
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Answer to Opening Question

• The CREB family of transcription factors can
  activate or repress gene expression by binding to
  the cAMP response element (CRE) sequence found in
  the promoter region of many genes.
• CREB binding is essential in many organs,
  including the brain, and has been linked to
  addiction and memory tasks as well as to
  metabolism.

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Figure 11.20 An Explanation for Alcoholism?