Gene RegulationGene Regulation

Chapter 14Chapter 14

Learning Objective 1Learning Objective 1

• Why do bacterial and eukaryotic cells have Why do bacterial and eukaryotic cells have different mechanisms of gene regulation?different mechanisms of gene regulation?

ProkaryotesProkaryotes

• Bacterial cellsBacterial cells• grow rapidlygrow rapidly• have a short life span have a short life span

• Transcriptional-level controlTranscriptional-level control• usually regulates gene expressionusually regulates gene expression

Eukaryotic CellsEukaryotic Cells

• Have long life spanHave long life span• respond to many different stimuli respond to many different stimuli

• One geneOne gene• may be regulated in different waysmay be regulated in different ways

• Transcriptional-level controlTranscriptional-level control • and control at and control at other levelsother levels of gene expression of gene expression

KEY CONCEPTSKEY CONCEPTS

• Cells can synthesize thousands of proteinsCells can synthesize thousands of proteins• but not all proteins are required in all cellsbut not all proteins are required in all cells

• Cells regulate which parts of the genome Cells regulate which parts of the genome will be expressed, and whenwill be expressed, and when

Learning Objective 2Learning Objective 2

• What is an What is an operonoperon??

• What are the functions of the What are the functions of the operatoroperator and and promoterpromoter regions? regions?

OperonOperon

• A gene complexA gene complex• structural genes with related functions structural genes with related functions • controlled by closely linked DNA sequences controlled by closely linked DNA sequences

• Regulated genes in bacteriaRegulated genes in bacteria• are organized into are organized into operonsoperons

PromoterPromoter RegionRegion

• Each operon has a Each operon has a promoterpromoter regionregion• upstream from protein-coding regionsupstream from protein-coding regions• where RNA polymerase binds to DNA before where RNA polymerase binds to DNA before

transcriptiontranscription

Operator (1)Operator (1)

• Regulatory switch for transcriptional-level Regulatory switch for transcriptional-level control of control of operonoperon

• Repressor proteinRepressor protein• binds to operator sequencebinds to operator sequence• prevents transcriptionprevents transcription

Operator (2)Operator (2)

• RNA polymeraseRNA polymerase• bound to promoterbound to promoter• is blocked from transcribing structural genesis blocked from transcribing structural genes

• If repressor is If repressor is notnot bound to operator bound to operator• transcription proceedstranscription proceeds

Learning Objective 3Learning Objective 3

• What is the difference between What is the difference between inducibleinducible, , repressiblerepressible, and , and constitutiveconstitutive genes? genes?

Inducible Genes (1)Inducible Genes (1)

• An An inducible operoninducible operon• such as such as lac lac operonoperon• is normally turned offis normally turned off

• Repressor proteinRepressor protein• is synthesized in active formis synthesized in active form• binds to operator binds to operator

Inducible Genes (2)Inducible Genes (2)

• If lactose is presentIf lactose is present• is converted to allolactose (is converted to allolactose (inducerinducer))• binds to repressor proteinbinds to repressor protein• changes repressor’s shape changes repressor’s shape

• Altered repressorAltered repressor• cannot bind to operatorcannot bind to operator• operon is transcribedoperon is transcribed

The The laclac Operon Operon

Fig. 14-2a, p. 307

lac operonRepressor

gene Promoter Operator lac Z lac Y lac A

DNA

Transcription Repressor protein

mRNA

Ribosome Translation

Fig. 14-2b, p. 307

Promoter Operator lac Z lac Y lac A

RNA polymerase

mRNA

Transcription

mRNA

TranslationInducer (allolactose)

Transacetylase

β-galactosidaseRepressor protein (inactive)

Enzymes for lactose metabolism

Lactose permease

lac operonRepressor

gene

Repressible Genes (1)Repressible Genes (1)

• A A repressible operon repressible operon ((trp trp operon)operon)• is normally turned onis normally turned on

• Repressor proteinRepressor protein• is synthesized in inactive formis synthesized in inactive form• cannot bind to operatorcannot bind to operator

• A metabolite (metabolic end product)A metabolite (metabolic end product)• acts as acts as corepressorcorepressor

Repressible Genes (2)Repressible Genes (2)

• With high intracellular corepressor levelsWith high intracellular corepressor levels• corepressor molecule binds to repressorcorepressor molecule binds to repressor• changes repressor’s shapechanges repressor’s shape

• Altered repressor Altered repressor • binds to operatorbinds to operator• turns off transcription of operonturns off transcription of operon

The The trptrp OperonOperon

Fig. 14-4a, p. 310

trp operonRepressor

gene Promoter Operator trp E trp D trp C trp B trp A

DNARNA

polymeraseTranscription

mRNA

mRNA

TranslationRepressor protein (inactive)

Enzymes of the tryptophan biosynthetic pathway

Tryptophan(a) Intracellular tryptophan levels low.

Fig. 14-4b, p. 310

trp operonRepressor gene Promoter Operator trp E trp D trp C trp B trp A

DNAActive repressor – corepressor complex

mRNA

Inactive repressor protein

Tryptophan (corepressor)

(b) Intracellular tryptophan levels high.

Constitutive Genes (1)Constitutive Genes (1)

• Are neither inducible nor repressibleAre neither inducible nor repressible• active at all timesactive at all times

• Regulatory proteins Regulatory proteins • produced constitutively produced constitutively

• catabolite activator protein (CAP)catabolite activator protein (CAP)• repressor proteinsrepressor proteins

Constitutive Genes (2)Constitutive Genes (2)

• Regulatory proteinsRegulatory proteins• recognize and bind to specific base recognize and bind to specific base

sequences in DNAsequences in DNA

• Activity of constitutive genesActivity of constitutive genes• controlled by binding RNA polymerase to controlled by binding RNA polymerase to

promoter regionspromoter regions

Learning Objective 4Learning Objective 4

• What is the difference between What is the difference between positivepositive and and negative controlnegative control? ?

• How do both types of control operate in How do both types of control operate in regulating the regulating the lac lac operon?operon?

Negative ControlNegative Control

• Repressible and inducible operons are Repressible and inducible operons are under under negative controlnegative control

• When repressor protein binds to operatorWhen repressor protein binds to operator• transcription of operon is turned transcription of operon is turned offoff

Positive Control (1)Positive Control (1)

• Some inducible operons are under Some inducible operons are under positive positive controlcontrol

• Activator protein binds to DNAActivator protein binds to DNA• stimulates transcription of genestimulates transcription of gene

Positive Control (2)Positive Control (2)

• CAP activates CAP activates lac lac operonoperon• binds to promoter regionbinds to promoter region• stimulates transcription by tightly binding RNA stimulates transcription by tightly binding RNA

polymerasepolymerase

• To bind to To bind to lac lac operonoperon• CAP requires CAP requires cyclic AMP (cAMP)cyclic AMP (cAMP)

• cAMP levels increasecAMP levels increase• as glucose levels decreaseas glucose levels decrease

Positive ControlPositive Control

Fig. 14-5a, p. 311

Promoter

RNA polymerase – binding site

CAP- binding

siteRepressor

gene Operator lac Z lac Y lac A

DNA

mRNARNA polymerase

binds poorly

CAP (inactive)

Allolactose

Repressor protein (inactive)

(a) Lactose high, glucose high, cAMP low.

Fig. 14-5b, p. 311

Promoter

RNA polymerase – binding site

CAP- binding

siteRepressor

gene Operator lac Z lac Y lac A

DNARNA

polymerase binds efficiently

Transcription

mRNA

mRNACAP

Translation Galactoside transacetylase cAMP

Lactose permease

Allolactose

Repressor protein (inactive)

Enzymes for lactose metabolism

β -galactosidase

(b) Lactose high, glucose low, cAMP high.

Binding CAPBinding CAP

Fig. 14-6, p. 312

DNA

cAMP

CAP dimer

Learning Objective 5Learning Objective 5

• What are the types of What are the types of posttranscriptionalposttranscriptional control in bacteria?control in bacteria?

Posttranscriptional ControlsPosttranscriptional Controls in Bacteria in Bacteria

• Translational controlTranslational control• regulates translation rate of particular mRNAregulates translation rate of particular mRNA

• Posttranslational controlsPosttranslational controls• include include feedback inhibitionfeedback inhibition of key enzymes in of key enzymes in

metabolic pathwaysmetabolic pathways

KEY CONCEPTSKEY CONCEPTS

• Prokaryotes regulate gene expression in Prokaryotes regulate gene expression in response to environmental stimuliresponse to environmental stimuli

KEY CONCEPTSKEY CONCEPTS

• Gene regulation in prokaryotes occurs Gene regulation in prokaryotes occurs primarily at the transcription levelprimarily at the transcription level

Learning Objective 6Learning Objective 6

• Discuss the structure of a typical Discuss the structure of a typical eukaryotic gene and the DNA sequences eukaryotic gene and the DNA sequences involved in regulating that geneinvolved in regulating that gene

Eukaryotic GenesEukaryotic Genes

• Are Are notnot normally organized into operons normally organized into operons

• Regulation occurs at levels ofRegulation occurs at levels of• TranscriptionTranscription• mRNA processingmRNA processing• TranslationTranslation• Modifications of protein productModifications of protein product

TranscriptionTranscription

• RequiresRequires• Transcription initiation siteTranscription initiation site

•where transcription beginswhere transcription begins• PromoterPromoter

• to which RNA polymerase bindsto which RNA polymerase binds

• In multicellular eukaryotesIn multicellular eukaryotes• RNA polymerase binds to promoter (RNA polymerase binds to promoter (TATA TATA

box)box)

TranscriptionTranscription

Fig. 14-9a, p. 316

TATA box Transcription initiation

siteUPETATA A

pre-mRNA

A A

T T

(a) Eukaryotic promoter elements.

Fig. 14-9b, p. 316

TATA box Transcription initiation

siteUPE

pre-mRNA

TATA AA A

T T

(b) A weak eukaryotic promoter.

Fig. 14-9c, p. 316

TATA box Transcription initiation

siteUPE UPE UPE UPE

pre-mRNA

TATA AA A

T T

(c) A strong eukaryotic promoter.

Fig. 14-9d, p. 316

TATA box Transcription initiation

siteEnhancer UPE UPE

pre-mRNA

TATA AA A

T T

(d) A strong eukaryotic promoter plus an enhancer.

Regulated Eukaryotic GeneRegulated Eukaryotic Gene

• PromoterPromoter • RNA polymerase-binding siteRNA polymerase-binding site• short DNA sequences (short DNA sequences (upstream promoter upstream promoter

elements (UPEs)elements (UPEs) or or proximal control elementsproximal control elements))

• UPEsUPEs• number and types within promoter region number and types within promoter region

determine efficiency of promoterdetermine efficiency of promoter

Enhancers (1)Enhancers (1)

• Located far away from Located far away from promoterpromoter• control some eukaryotic genes control some eukaryotic genes

• Help form Help form active transcription initiation active transcription initiation complexcomplex

Enhancers (2)Enhancers (2)

• Specific Specific regulatory proteinsregulatory proteins• bind to bind to enhancerenhancer elements elements• activate transcription by interacting with activate transcription by interacting with

proteins bound to proteins bound to promoterspromoters

EnhancersEnhancers

Fig. 14-11a, p. 317

Enhancer Target proteins

RNA polymerase

TATA boxDNA

(a) Little or no transcription.

Fig. 14-11b, p. 317

Enhancer

DNA TATA box Activator (transcription factor)

(b) High rate of transcription.

Learning Objective 7Learning Objective 7

• In what ways may eukaryotic DNA-binding In what ways may eukaryotic DNA-binding proteins bind to DNA?proteins bind to DNA?

Transcription FactorsTranscription Factors

• DNA-binding protein regulators control DNA-binding protein regulators control eukaryotic geneseukaryotic genes• some transcriptional activatorssome transcriptional activators• some transcriptional repressorssome transcriptional repressors

Transcription FactorsTranscription Factors

• Each has DNA-binding Each has DNA-binding domaindomain

• 3 types of regulatory proteins3 types of regulatory proteins• Helix-turn-helixHelix-turn-helix• Zinc fingersZinc fingers• Leucine zippersLeucine zippers

Helix-Turn-HelixHelix-Turn-Helix

• Inserts one helix into DNA Inserts one helix into DNA

Fig. 14-10a, p. 317

Turn

α -helix

DNA

(a) Helix-turn-helix.

Zinc FingersZinc Fingers

• Loops of amino acidsLoops of amino acids• held together by zinc ionsheld together by zinc ions• each loop has each loop has αα-helix that fits into DNA -helix that fits into DNA

Fig. 14-10b, p. 317

COO–

Finger 2Finger 3

Zinc ionFinger 1

NH3+

DNA

(b) Zinc fingers.

Leucine Zipper ProteinsLeucine Zipper Proteins

• Associate as dimers that insert into DNAAssociate as dimers that insert into DNA

Fig. 14-10c, p. 317

Leucine zipper region

DNA

(c) Leucine zipper.

Learning Objective 8Learning Objective 8

• How may a change in chromosome How may a change in chromosome structure affect the activity of a gene?structure affect the activity of a gene?

Gene Activity (1)Gene Activity (1)

• Changes in chromosome structureChanges in chromosome structure• inactivates genes inactivates genes

• HeterochromatinHeterochromatin• densely packed regions of chromosomesdensely packed regions of chromosomes• contain inactive genes contain inactive genes

Gene Activity (2)Gene Activity (2)

• Active genesActive genes• associated with loosely packed chromatin associated with loosely packed chromatin

structure (structure (euchromatineuchromatin))

• Cells change chromatin structureCells change chromatin structure• from from heterochromatinheterochromatin to to euchromatineuchromatin• by chemically modifying by chemically modifying histoneshistones (proteins (proteins

associated with DNA to form nucleosomes)associated with DNA to form nucleosomes)

Chromatin StructureChromatin Structure

Fig. 14-7, p. 314

Heterochromatin: genes silent Chromatin

decondensation

Nucleosome

Histones

DNA

Transcribed region

Euchromatin: genes active

Gene Activity (3)Gene Activity (3)

• Histone tailHistone tail• string of amino acids that extends from the string of amino acids that extends from the

DNA-wrapped nucleosome DNA-wrapped nucleosome

• Methyl groups, acetyl groups, sugars, and Methyl groups, acetyl groups, sugars, and proteinsproteins• may chemically attach to the may chemically attach to the histone tailhistone tail• may expose or hide genes (turn on or off)may expose or hide genes (turn on or off)

Gene Activity (4)Gene Activity (4)

• Epigenetic inheritanceEpigenetic inheritance• changes how a gene is expressed changes how a gene is expressed • important mechanism of gene regulationimportant mechanism of gene regulation

• DNA methylationDNA methylation • perpetuates gene inactivationperpetuates gene inactivation• patterns repeat in successive cell generationspatterns repeat in successive cell generations• mechanism for epigenetic inheritancemechanism for epigenetic inheritance

Gene AmplificationGene Amplification

• Some genesSome genes• products are required in large amountsproducts are required in large amounts• have multiple copies in the chromosomehave multiple copies in the chromosome

• Gene amplificationGene amplification• some cells selectively amplify genes by DNA some cells selectively amplify genes by DNA

replicationreplication

Gene AmplificationGene Amplification

Fig. 14-8, p. 315

Drosophila chorion gene

Gene amplification by repeated DNA replication of chorion gene region

Chorion gene in ovarian cell

Learning Objective 9Learning Objective 9

• How may a gene in a multicellular How may a gene in a multicellular organism produce different products in organism produce different products in different types of cells?different types of cells?

Differential mRNA ProcessingDifferential mRNA Processing

• Single gene produces different forms of Single gene produces different forms of protein in different tissuesprotein in different tissues• depending on how pre-mRNA is spliceddepending on how pre-mRNA is spliced

• Gene contains a segment that can be Gene contains a segment that can be either either intronintron or or exonexon• as intron, sequence is removedas intron, sequence is removed• as exon, sequence is retainedas exon, sequence is retained

Differential mRNA ProcessingDifferential mRNA Processing

Fig. 14-12, p. 318

Potential splice sites

Exon or intronExon Intron Exon

pre-mRNA

Differential mRNA processing

Exon Exon Exon Exon Exon

Functional mRNA in tissue A

Functional mRNA in tissue B

Learning Objective 10Learning Objective 10

• What types of regulatory controls operate What types of regulatory controls operate in eukaryotes after mature mRNA is in eukaryotes after mature mRNA is formed?formed?

mRNA StabilitymRNA Stability

• Certain regulatory mechanisms increase Certain regulatory mechanisms increase RNA stabilityRNA stability• allowing more protein synthesis before mRNA allowing more protein synthesis before mRNA

degradationdegradation

• Sometimes under hormonal controlSometimes under hormonal control

Posttranslational Control (1)Posttranslational Control (1)

• In eukaryotic gene expressionIn eukaryotic gene expression• feedback inhibitionfeedback inhibition• modification of modification of protein structureprotein structure

• Protein function changeProtein function change• by by kinaseskinases adding phosphate groups adding phosphate groups• by by phosphatasesphosphatases removing phosphates removing phosphates

Protein Degradation (1)Protein Degradation (1)

• Proteins targeted for destructionProteins targeted for destruction• covalently bonded to covalently bonded to ubiquitinubiquitin

• Protein tagged by ubiquitinProtein tagged by ubiquitin• degraded in a degraded in a proteasomeproteasome

Protein Degradation (2)Protein Degradation (2)

• ProteasomeProteasome• large macromolecular structurelarge macromolecular structure• recognizes ubiquitin tagsrecognizes ubiquitin tags

• ProteasesProteases• protein-degrading enzymesprotein-degrading enzymes• associated with proteasomesassociated with proteasomes• degrade protein into peptide fragmentsdegrade protein into peptide fragments

Protein Protein DegradationDegradation

Fig. 14-13, p. 318

Target protein

Ubiquitin 1 Ubiquitin molecules attach to protein tar- geted for degradation.

Ubiquitinylated protein

2 Protein enters proteasome.

Proteasome

3 Ubiquitins are released and available for reuse. Protein is degraded into peptide fragments.

Peptide fragments

Stepped Art

Fig. 14-13, p. 318

Target protein

Ubiquitin

3 Ubiquitins are released and available for reuse. Protein is degraded into peptide fragments.

Peptide fragments

2 Protein enters proteasome.

Proteasome

1 Ubiquitin molecules attach to protein tar- geted for degradation.

Ubiquitinylated protein

KEY CONCEPTSKEY CONCEPTS

• Gene regulation in eukaryotes occurs at Gene regulation in eukaryotes occurs at the levels of transcription, the levels of transcription, posttranscription, translation, and posttranscription, translation, and posttranslationposttranslation

Animation: Controls of Animation: Controls of Eukaryotic Gene ExpressionEukaryotic Gene Expression

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