Gene RegulationGene Regulation certain genes are transcribed all the certain genes are transcribed all the

time – time – constitutive genesconstitutive genes synthesis of some proteins is regulated synthesis of some proteins is regulated

and are produced only when needed and are produced only when needed under special conditionsunder special conditions

Gene Regulation in ProkaryotesGene Regulation in ProkaryotesBacteria often respond to environmental Bacteria often respond to environmental

change by regulating transcriptionchange by regulating transcriptionNatural selection has favored bacteria that Natural selection has favored bacteria that

produce only the products needed by that produce only the products needed by that cellcell

A cell can regulate the production of A cell can regulate the production of enzymes by feedback inhibition or by gene enzymes by feedback inhibition or by gene regulationregulation

Gene expression in bacteria is controlled Gene expression in bacteria is controlled by the operon modelby the operon model

Fig. 18-2

Regulationof geneexpression

trpE gene

trpD gene

trpC gene

trpB gene

trpA gene

(b) Regulation of enzyme production

(a) Regulation of enzyme activity

Enzyme 1

Enzyme 2

Enzyme 3

Tryptophan

Precursor

Feedbackinhibition

Operons: The Basic ConceptOperons: The Basic ConceptA cluster of functionally related genes can A cluster of functionally related genes can

be under coordinated controlbe under coordinated control by a single by a single on-off “switch”on-off “switch”

The regulatory “switch” is a segment of The regulatory “switch” is a segment of DNA called an DNA called an operator operator usually positioned usually positioned within the promoterwithin the promoter

An An operon operon is the entire stretch of DNA is the entire stretch of DNA that includes the operator, the promoter, that includes the operator, the promoter, and the genes that they controland the genes that they control

The operon can be switched off by a The operon can be switched off by a protein protein repressorrepressor

The repressor prevents gene transcription The repressor prevents gene transcription by binding to the operator and blocking by binding to the operator and blocking RNA polymeraseRNA polymerase

The repressor is the product of a separate The repressor is the product of a separate regulatory generegulatory gene

• The repressor can be in an active or The repressor can be in an active or inactive form, depending on the presence inactive form, depending on the presence of other moleculesof other molecules

• A A corepressorcorepressor is a molecule that is a molecule that cooperates with a repressor protein to cooperates with a repressor protein to switch an operon offswitch an operon off

• For example, For example, E. coli E. coli can synthesize the can synthesize the amino acid tryptophanamino acid tryptophan

• By default the By default the trp trp operon is on and the operon is on and the genes for tryptophan synthesis are genes for tryptophan synthesis are transcribedtranscribed

• When tryptophan is present, it binds to the When tryptophan is present, it binds to the trp trp repressor protein, which turns the repressor protein, which turns the operon off operon off

• The repressor is active only in the The repressor is active only in the presence of its corepressor tryptophan; presence of its corepressor tryptophan; thus the thus the trp trp operon is turned off operon is turned off (repressed) if tryptophan levels are high(repressed) if tryptophan levels are high

Fig. 18-3

Polypeptide subunits that make upenzymes for tryptophan synthesis

(b) Tryptophan present, repressor active, operon off

Tryptophan(corepressor)

(a) Tryptophan absent, repressor inactive, operon on

No RNA made

Activerepressor

mRNA

Protein

DNA

DNA

mRNA 5

Protein Inactiverepressor

RNApolymerase

Regulatorygene

Promoter Promoter

trp operon

Genes of operon

OperatorStop codonStart codon

mRNA

trpA

5

3

trpR trpE trpD trpC trpB

ABCDE

Repressible and Inducible Operons: Two Repressible and Inducible Operons: Two Types of Negative Gene RegulationTypes of Negative Gene Regulation

A repressible operon is one that is usually A repressible operon is one that is usually on; binding of a repressor to the operator on; binding of a repressor to the operator shuts off transcriptionshuts off transcription

The The trptrp operon is a repressible operon operon is a repressible operonAn inducible operon is one that is usually An inducible operon is one that is usually

off; a molecule called an inducer off; a molecule called an inducer inactivates the repressor and turns on inactivates the repressor and turns on transcriptiontranscription

The The laclac operon is an inducible operon and operon is an inducible operon and contains genes that code for enzymes contains genes that code for enzymes used in the hydrolysis and metabolism of used in the hydrolysis and metabolism of lactoselactose

By itself, the By itself, the lac lac repressor is active and repressor is active and switches the switches the lac lac operon offoperon off

A molecule called an A molecule called an inducer inducer inactivates inactivates the repressor to turn the the repressor to turn the lac lac operon onoperon on

The Jacob-Monad ModelThe Jacob-Monad ModelThe Lac Operon (Inducible Operon):The Lac Operon (Inducible Operon):

Jacob and Monad demonstrated how genes Jacob and Monad demonstrated how genes that code for enzymes that metabolize lactose that code for enzymes that metabolize lactose are regulated are regulated

An An operonoperon consists of three elements: consists of three elements: the genes that it controlsthe genes that it controlsa promotor region where RNA polymerase first a promotor region where RNA polymerase first

bindsbindsan an operatoroperator region between the promotor and region between the promotor and

the first gene which acts as an “on-off switch”.the first gene which acts as an “on-off switch”.

Intestinal bacteria (Intestinal bacteria (E. coliE. coli) are able to ) are able to absorb the disaccharide, lactose, and break absorb the disaccharide, lactose, and break and break it down to glucose and galactose and break it down to glucose and galactose ((E. coliE. coli will only make these enzymes when will only make these enzymes when grown in the presence of lactose)grown in the presence of lactose)

Requires the production of 3 enzymes:Requires the production of 3 enzymes: - galactosidase – breaks down the lactose to - galactosidase – breaks down the lactose to

glucose and galactoseglucose and galactose galactose permease – needed to transport galactose permease – needed to transport

lactose efficiently across bacterial cell lactose efficiently across bacterial cell membranemembrane

galactoside transacetylase – function is not galactoside transacetylase – function is not clearclear

Production of these enzymes is controlled Production of these enzymes is controlled by three structural genes and some closely by three structural genes and some closely linked DNA sequences responsible for linked DNA sequences responsible for controlling the structural genes – entire controlling the structural genes – entire gene complex is called the gene complex is called the operonoperon

Structural genes of the lactose operon:Structural genes of the lactose operon: lacZ – codes for lacZ – codes for - galactosidase - galactosidase lacY – codes for galactose permeaselacY – codes for galactose permease lacA – codes for galactoside transacetylaselacA – codes for galactoside transacetylase

Next to the structural genes are 2 Next to the structural genes are 2 overlapping regulatory regions:overlapping regulatory regions:

promotorpromotor – region to which RNA polymerase – region to which RNA polymerase binds to initiate transcriptionbinds to initiate transcription

operatoroperator – region of DNA that acts as the – region of DNA that acts as the switch that controls mRNA synthesis; switch that controls mRNA synthesis; sequence of bases that overlaps part of the sequence of bases that overlaps part of the promotor regionpromotor region

when lactose is absent, a when lactose is absent, a repressor proteinrepressor protein (in (in this case the this case the lactose repressorlactose repressor) binds to the ) binds to the operator region – repressor protein is large operator region – repressor protein is large enough to cover part of the promotor sequence, enough to cover part of the promotor sequence, too, and blocks RNA polymerase from attaching too, and blocks RNA polymerase from attaching to promotor – transcription is blockedto promotor – transcription is blocked

when lactose is present, it acts as an when lactose is present, it acts as an inducerinducer and and “turns on” the transcription of the lactose operon“turns on” the transcription of the lactose operon

lactose binds to repressor protein, inactivates it, lactose binds to repressor protein, inactivates it, and unblocks the promotor region allowing RNA and unblocks the promotor region allowing RNA polymerase to attach and begin transcriptionpolymerase to attach and begin transcription

Inducible enzymes usually function in Inducible enzymes usually function in catabolic pathways; their synthesis is catabolic pathways; their synthesis is induced by a chemical signalinduced by a chemical signal

Repressible enzymes usually function in Repressible enzymes usually function in anabolic pathways; their synthesis is anabolic pathways; their synthesis is repressed by high levels of the end repressed by high levels of the end productproduct

Regulation of the Regulation of the trptrp and and laclac operons operons involves negative control of genes involves negative control of genes because operons are switched off by the because operons are switched off by the active form of the repressoractive form of the repressor

Gene Regulation in EukaryotesGene Regulation in Eukaryotes most cells in a multicellular organism contain the most cells in a multicellular organism contain the

same DNA but they don’t all use the DNA all the same DNA but they don’t all use the DNA all the timetime

individual cells express only a small fraction of individual cells express only a small fraction of their genes – those genes that are appropriate to their genes – those genes that are appropriate to the function of that particular cell typethe function of that particular cell type

transcription of a cell’s DNA must be regulatedtranscription of a cell’s DNA must be regulated factors such pregnancy may affect gene factors such pregnancy may affect gene

expression (genes for milk production are not expression (genes for milk production are not used all the time)used all the time)

the environment may affect which genes are the environment may affect which genes are transcribed (length of day may increase a transcribed (length of day may increase a change in size of sex organs affecting the change in size of sex organs affecting the production of sex hormones in birds)production of sex hormones in birds)

Eukaryotic gene expression can be Eukaryotic gene expression can be regulated at any stageregulated at any stage

Gene expression is regulated at many Gene expression is regulated at many stagesstages

Fig. 18-6

DNA

Signal

Gene

NUCLEUS

Chromatin modification

Chromatin

Gene availablefor transcription

Exon

Intron

Tail

RNA

Cap

RNA processing

Primary transcript

mRNA in nucleus

Transport to cytoplasm

mRNA in cytoplasm

Translation

CYTOPLASM

Degradationof mRNA

Protein processing

Polypeptide

Active protein

Cellular function

Transport to cellulardestination

Degradationof protein

Transcription

Gene expression may be regulated by:Gene expression may be regulated by:1.1. Regulation of Chromatin StructureRegulation of Chromatin Structure

Genes within heterochromatin (chromatin that is very Genes within heterochromatin (chromatin that is very tightly packed) are usually not expressedtightly packed) are usually not expressed

Chemical modifications to histones and DNA of chromatin Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expressioninfluence both chromatin structure and gene expressionHistone modification:Histone modification:

Histone tails protrude outward from the nucleosomeHistone tails protrude outward from the nucleosomeHistone acetylationHistone acetylation – acetyl groups are added to – acetyl groups are added to

histone tails causing chromatin to loosen and histone tails causing chromatin to loosen and promote transcriptionpromote transcription

The addition of methyl groups (methylation) can The addition of methyl groups (methylation) can condense chromatin; the addition of phosphate condense chromatin; the addition of phosphate groups (phosphorylation) next to a methylated groups (phosphorylation) next to a methylated amino acid can loosen chromatinamino acid can loosen chromatin

Fig. 18-7

Histonetails

DNAdouble helix

(a) Histone tails protrude outward from a nucleosome

Acetylated histones

Aminoacidsavailablefor chemicalmodification

(b) Acetylation of histone tails promotes loose chromatin structure that permits transcription

Unacetylated histones

DNA MethylationDNA MethylationEnzymes may methylate certain bases in the Enzymes may methylate certain bases in the

DNA DNA DNA methylation is associated with reduced DNA methylation is associated with reduced

transcription in some species – ex. Barr transcription in some species – ex. Barr bodies in mammalsbodies in mammals

DNA methylation can cause long-term DNA methylation can cause long-term inactivation of genes in cellular differentiationinactivation of genes in cellular differentiation

In In genomic imprintinggenomic imprinting, methylation , methylation regulates expression of either the maternal or regulates expression of either the maternal or paternal alleles of certain genes at the start paternal alleles of certain genes at the start of developmentof development

Epigenetic InheritanceEpigenetic InheritanceAlthough the chromatin modifications Although the chromatin modifications

just discussed do not alter DNA just discussed do not alter DNA sequence, they may be passed to sequence, they may be passed to future generations of cellsfuture generations of cells

The inheritance of traits transmitted The inheritance of traits transmitted by mechanisms not directly involving by mechanisms not directly involving the nucleotide sequence is called the nucleotide sequence is called epigenetic inheritance epigenetic inheritance

2.2. Regulation of Transcription InitiationRegulation of Transcription Initiation Chromatin-modifying enzymes provide initial Chromatin-modifying enzymes provide initial

control of gene expression by making a region of control of gene expression by making a region of DNA either more or less able to bind the DNA either more or less able to bind the transcription machinerytranscription machinery

Transcription Factors play a roleTranscription Factors play a roleTo initiate transcription, eukaryotic RNA To initiate transcription, eukaryotic RNA

polymerase requires the assistance of proteins polymerase requires the assistance of proteins called transcription factorscalled transcription factors

General transcription factors are essential for General transcription factors are essential for the transcription of all protein-coding genesthe transcription of all protein-coding genes

In eukaryotes, high levels of transcription of In eukaryotes, high levels of transcription of particular genes depend on interactions of particular genes depend on interactions of specific transcription factorsspecific transcription factors

3.3. Post-Transcriptional RegulationPost-Transcriptional RegulationTranscription alone does not account for gene Transcription alone does not account for gene

expressionexpressionRegulatory mechanisms can operate at various Regulatory mechanisms can operate at various

stages after transcriptionstages after transcriptionSuch mechanisms allow a cell to fine-tune gene Such mechanisms allow a cell to fine-tune gene

expression rapidly in response to environmental expression rapidly in response to environmental changeschanges

RNA processing:RNA processing:In In alternative RNA splicingalternative RNA splicing, different mRNA , different mRNA

molecules are produced from the same molecules are produced from the same primary transcript, depending on which RNA primary transcript, depending on which RNA segments are treated as exons and which as segments are treated as exons and which as intronsintrons

Fig. 18-11

or

RNA splicing

mRNA

PrimaryRNAtranscript

Troponin T gene

Exons

DNA

mRNA Degradation:mRNA Degradation:The life span of mRNA molecules in the cytoplasm is The life span of mRNA molecules in the cytoplasm is

a key to determining protein synthesisa key to determining protein synthesisEukaryotic mRNA is more long lived than prokaryotic Eukaryotic mRNA is more long lived than prokaryotic

mRNAmRNAThe mRNA life span is determined in part by The mRNA life span is determined in part by

sequences in the leader and trailer regionssequences in the leader and trailer regions Initiation of TranslationInitiation of Translation

The initiation of translation of selected The initiation of translation of selected mRNAs can be blocked by regulatory proteins that mRNAs can be blocked by regulatory proteins that bind to sequences or structures of the mRNAbind to sequences or structures of the mRNA

Alternatively, translation of all mRNAs Alternatively, translation of all mRNAs in a cell may be regulated simultaneouslyin a cell may be regulated simultaneously

For example, translation initiation factors are For example, translation initiation factors are simultaneously activated in an egg following simultaneously activated in an egg following fertilizationfertilization

Protein Processing and DegradationProtein Processing and DegradationAfter translation, various types of After translation, various types of

protein processing, including cleavage protein processing, including cleavage and the addition of chemical groups, and the addition of chemical groups, are subject to controlare subject to control

The length of time each protein functions in a cell can be regulated

Proteasomes Proteasomes are giant protein are giant protein complexes that bind protein complexes that bind protein molecules and degrade themmolecules and degrade them

Noncoding RNAs play multiple roles in Noncoding RNAs play multiple roles in controlling gene expressioncontrolling gene expression

Only a small fraction of DNA codes for Only a small fraction of DNA codes for proteins, rRNA, and tRNA (only about proteins, rRNA, and tRNA (only about 1.5% of human genome codes for 1.5% of human genome codes for proteins)proteins)

A significant amount of the genome may A significant amount of the genome may be transcribed into noncoding RNAsbe transcribed into noncoding RNAs

Noncoding RNAs regulate gene Noncoding RNAs regulate gene expression at two points: mRNA expression at two points: mRNA translation and chromatin configurationtranslation and chromatin configuration

Effects on mRNAs by MicroRNAs and Effects on mRNAs by MicroRNAs and Small Interfering RNAsSmall Interfering RNAs

MicroRNAs MicroRNAs ((miRNAsmiRNAs) are small single-) are small single-stranded RNA molecules that can bind to stranded RNA molecules that can bind to mRNAmRNA

These can degrade mRNA or block its These can degrade mRNA or block its translationtranslation

Fig. 18-13

miRNA-proteincomplex(a) Primary miRNA transcript

Translation blocked

Hydrogenbond

(b) Generation and function of miRNAs

Hairpin miRNA

miRNA

Dicer

3

mRNA degraded

5

A program of differential gene expression leads to A program of differential gene expression leads to the different cell types in a multicellular organismthe different cell types in a multicellular organism

During embryonic development, a fertilized egg During embryonic development, a fertilized egg gives rise to many different cell typesgives rise to many different cell types

Cell types are organized successively into Cell types are organized successively into tissues, organs, organ systems, and the whole tissues, organs, organ systems, and the whole organismorganism

Gene expression orchestrates the Gene expression orchestrates the developmental programs of animalsdevelopmental programs of animals

A Genetic Program for Embryonic A Genetic Program for Embryonic DevelopmentDevelopment

The transformation from zygote to adult The transformation from zygote to adult results from three processes: cell division, results from three processes: cell division, cell differentiation, and morphogenesiscell differentiation, and morphogenesis

Cell differentiation Cell differentiation is the process by is the process by which cells become specialized in which cells become specialized in structure and functionstructure and function

The physical processes that give an The physical processes that give an organism its shape constitute organism its shape constitute morphogenesismorphogenesis

Differential gene expression results from Differential gene expression results from genes being regulated differently in each genes being regulated differently in each cell typecell type

Materials in the egg can set up gene Materials in the egg can set up gene regulation that is carried out as cells divideregulation that is carried out as cells divide

Cytoplasmic Determinants and Cytoplasmic Determinants and Inductive SignalsInductive Signals

An egg’s cytoplasm contains RNA, An egg’s cytoplasm contains RNA, proteins, and other substances that are proteins, and other substances that are distributed unevenly in the unfertilized eggdistributed unevenly in the unfertilized egg

Cytoplasmic determinants Cytoplasmic determinants are maternal are maternal substances in the egg that influence early substances in the egg that influence early developmentdevelopment

As the zygote divides by mitosis, cells As the zygote divides by mitosis, cells contain different cytoplasmic determinants, contain different cytoplasmic determinants, which lead to different gene expressionwhich lead to different gene expression

Fig. 18-15a

(a) Cytoplasmic determinants in the egg

Two differentcytoplasmicdeterminants

Unfertilized egg cell

Sperm

Fertilization

Zygote

Mitoticcell division

Two-celledembryo

Nucleus

The other important source of The other important source of developmental information is the developmental information is the environment around the cell, especially environment around the cell, especially signals from nearby embryonic cellssignals from nearby embryonic cells

In the process called In the process called inductioninduction, signal , signal molecules from embryonic cells cause molecules from embryonic cells cause transcriptional changes in nearby target transcriptional changes in nearby target cellscells

Thus, interactions between cells induce Thus, interactions between cells induce differentiation of specialized cell typesdifferentiation of specialized cell types

Fig. 18-15b

(b) Induction by nearby cells

Signalmolecule(inducer)

Signaltransductionpathway

Early embryo(32 cells)

NUCLEUS

Signalreceptor

Sequential Regulation of Gene Expression Sequential Regulation of Gene Expression During Cellular DifferentiationDuring Cellular Differentiation

Determination Determination commits a cell to its final fatecommits a cell to its final fate Determination precedes differentiationDetermination precedes differentiation Cell differentiation is marked by the production Cell differentiation is marked by the production

of tissue-specific proteinsof tissue-specific proteins On the molecular level, different sets of genes On the molecular level, different sets of genes

are sequentially expressed in a regulated are sequentially expressed in a regulated manner as new cells arisemanner as new cells arise

Cells become specialists for making their tissue-Cells become specialists for making their tissue-specific proteinsspecific proteins