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Regulation of Gene Regulation of Gene ExpressionExpressionChapter 18Chapter 18
Gene expression
Flow of genetic information Genotype to phenotype Genes to proteins Proteins not made at random Specific purposes Appropriate times
Control of gene expression
Selective expression of genes All genes are not expressed at the
same time Expressed at different times
Prokaryote regulation
Control of gene expression
Regulate at transcription Gene expression responds to Environmental conditions Type of nutrients Amounts of nutrients Rapid turn over of proteins
Fig. 18-2Fig. 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
Prokaryote
Anabolism: Building up of a substance Catabolism: Breaking apart a substance
Prokaryote
Operon Section of DNA Enzyme-coding genes Promoter Operator Sequence of nucleotides Overlaps promoter site Controls RNA polymerase access to the
promoter
Figure 18.3aFigure 18.3a
Promoter
DNA
trpR
Regulatory gene
RNApolymerasemRNA
5′
3′
ProteinInactiverepressor
mRNA 5′
(a) Tryptophan absent, repressor inactive, operon on
Promoter
trp operon
Genes of operon
trpE trpD trpC trpB trpA
Operator
Start codon Stop codon
Polypeptide subunits that make upenzymes for tryptophan synthesis
E D C B A
Prokaryote
Multiple genes are expressed in a single gene expression
trp operon– Trytophan– Synthesis
Lac operon– Lactose– Degradation
Prokaryote
trp Operon: Control system to make
tryptophan Several genes that make
tryptophan Regulatory region
Fig. 18-3aFig. 18-3a
Polypeptide subunits that make upenzymes for tryptophan synthesis
mRNA 5RNApolymerase
Promoter
trp operon
Genes of operon
OperatorStop codonStart codon
mRNA
trpA
5
trpE trpD trpC trpB
ABCDE
Prokaryote
⇧tryptophan present Bacteria will not make tryptophan Genes are not transcribed Enzymes will not be made Repression
Prokaryote
Repressors Proteins Bind regulatory sites (operator) Prevent RNA polymerase
attaching to promoter Prevent or decrease the initiation
of transcription
Prokaryote
Repressors Allosteric proteins Changes shape Active or inactive
Prokaryote
⇧tryptophan Tryptophan binds the trp repressor Repressor changes shape Active shape Repressor fits DNA better Stops transcription Tryptophan is a corepressor
Fig. 18-3b-2Fig. 18-3b-2
(b) Tryptophan present, repressor active, operon off
Tryptophan(corepressor)
No RNA made
Activerepressor
mRNA
Protein
DNA
Prokaryote
⇩tryptophan Nothing binds the repressor Inactive shape RNA polymerase can transcribe
Fig. 18-3aFig. 18-3a
Polypeptide subunits that make upenzymes for tryptophan synthesis
(a) Tryptophan absent, repressor inactive, operon on
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
Prokaryote
Lactose Sugar used for energy Enzymes needed to break it down Lactose present Enzymes are synthesized Induced
Prokaryote
lac Operon Promoter Operator Genes to code for enzymes Metabolize (break down) lactose
Prokaryote
Lactose is present Repressor released Genes expressed Lactose absent Repressor binds DNA Stops transcription
Prokaryote
Allolactose: Binds repressor Repressor releases from DNA Inducer Transcription begins Lactose levels fall Allolactose released from repressor Repressor binds DNA blocks transcription
Fig. 18-4b
(b) Lactose present, repressor inactive, operon on
mRNA
Protein
DNA
mRNA 5
Inactiverepressor
Allolactose(inducer)
5
3RNApolymerase
Permease Transacetylase
lac operon
-Galactosidase
lacYlacZ lacAlacI
Fig. 18-4aFig. 18-4a
(a) Lactose absent, repressor active, operon off
DNA
ProteinActiverepressor
RNApolymerase
Regulatorygene
Promoter
Operator
mRNA5
3
NoRNAmade
lacI lacZ
Prokaryote
Lactose & tryptophan metabolism Adjustment by bacteria Regulates protein synthesis Response to environment Negative control of genes Operons turned off by active repressors Tryptophan repressible operon Lactose inducible operon
Prokaryote
Prokaryote
Activators: Bind DNA Stimulate transcription Involved in glucose metabolism lac operon
Prokaryote
Activator: Catabolite activator protein (CAP) Stimulates transcription of operons Code for enzymes to metabolize sugars cAMP helps CAP cAMP binds CAP to activate it CAP binds to DNA (lac Operon)
Prokaryote
Glucose elevated cAMP low cAMP not available to bind CAP Does not stimulate transcription Bacteria use glucose Preferred sugar over others.
Prokaryote
lac operon Regulated by positive & negative
control Low lactose Repressor blocks transcription High lactose Allolactose binds repressor Transcription happens
Prokaryote
lac operon Glucose also present CAP unable to bind Transcription will proceed slowly Glucose absent CAP binds promoter Transcription goes quickly
Figure 18.5Figure 18.5Promoter
DNAOperator
PromoterDNA
CAP-binding site
cAMPActiveCAP
InactiveCAP
RNApolymerasebinds and transcribes
lac I
lac I
Allolactose
Inactive lacrepressor
(a) Lactose present, glucose scarce (cAMP level high):abundant lac mRNA synthesized
lacZ
lacZ
CAP-binding site RNApolymerase lesslikely to bind
Operator
InactiveCAP
Inactive lacrepressor
(b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized
Eukaryote gene expression
All cells in an organism have the same genes
Some genes turned on Others remain off Leads to development of
specialized cells Cellular differentiation
Eukaryote gene expression
Gene expression assists in regulating development
Homeostasis Changes in gene expression in
one cell helps entire organism
Control of gene expression
Chromosome structure Transcriptional control Posttranscriptional control
Fig. 18-6Fig. 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
Eukaryotes
1. DNA is organized into chromatin
2. Transcription occurs in nucleus 3. Each gene has its own
promoter
Chromatin structure
DNA is tightly packaged Heterochromatin: Tightly packed Euchromatin: Less tightly packed Influences gene expression Promoter location Modification of histones
Chromatin structure
Histone acetylation Acetyl groups (-COCH3) Attach to Lysines in histone tails Loosen packing Histone methylation Methyl groups (-CH3) Tightens packing
Fig. 18-7Fig. 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
Chromatin structure
Methylation of bases (cytosine) Represses transcription Embryo development
Eukaryotes
Epigenetic change: Chromatin modifications Change in gene expression Passed on to the next generation Not a DNA sequence change
Transcription control
RNA polymerase must bind DNA Proteins regulate by binding DNA RNA polymerase able to bind or
not Stimulates transcription or blocks
it
Fig. 18-8-3Fig. 18-8-3
Enhancer(distal control elements)
Proximalcontrol elements
Poly-A signalsequence
Terminationregion
DownstreamPromoter
UpstreamDNA
ExonExon ExonIntron Intron
Exon Exon ExonIntronIntron Cleaved 3 endof primarytranscript
Primary RNAtranscript
Poly-Asignal
Transcription
5
RNA processing
Intron RNA
Coding segment
mRNA
5 Cap 5 UTRStart
codonStop
codon 3 UTR Poly-Atail
3
Eukaryotes
Transcription RNA Polymerase Transcription factors (regulatory
proteins) General transcription factors
(initiation complex) Specific transcription factors
Eukaryotes
Initiation of transcription Activator proteins Activator binds the enhancers Enhancers (DNA sequences) Interacts with the transcription factors Binds to the promoter RNA polymerase binds and
transcription begins
Fig. 18-9-2Fig. 18-9-2
Enhancer TATAbox
PromoterActivators
DNAGene
Distal controlelement
Group ofmediator proteins
DNA-bendingprotein
Generaltranscriptionfactors
Fig. 18-9-3Fig. 18-9-3
Enhancer TATAbox
PromoterActivators
DNAGene
Distal controlelement
Group ofmediator proteins
DNA-bendingprotein
Generaltranscriptionfactors
RNApolymerase II
RNApolymerase II
Transcriptioninitiation complex RNA synthesis
Eukaryotes
Fig. 18-10Fig. 18-10
Controlelements
Enhancer
Availableactivators
Albumin gene
(b) Lens cell
Crystallin geneexpressed
Availableactivators
LENS CELLNUCLEUS
LIVER CELLNUCLEUS
Crystallin gene
Promoter
(a) Liver cell
Crystallin genenot expressed
Albumin geneexpressed
Albumin genenot expressed
Post transcriptional control
RNA processing Primary transcript: Exact copy of the entire gene RNA splicing Introns removed from the mRNA snRNP’s (small nuclear
ribonulceoproteins)
Post transcriptional control
Splicing plays a role in gene expression
Exons can be spliced together in different ways.
Leads to different polypeptides Originated from same gene
Post transcriptional control
Example in humans Calcitonin & CGRP Hormones released from different
organs Derived from the same transcript
Fig. 18-11Fig. 18-11
or
RNA splicing
mRNA
PrimaryRNAtranscript
Troponin T gene
Exons
DNA
Post transcriptional control
Post transcriptional control
Transport of transcript Passes through nuclear pores Active transport Cannot pass until all splicing is
done
Post transcriptional control
mRNA degradation Life span Some can last hours, a few weeks mRNA for hemoglobin survive
awhile
Post transcriptional control
Post transcriptional control
Translation of RNA Translation factors are necessary Regulate translation Translation repressor proteins Stop translation Bind transcript Prevents it from binding to the
ribosome
Post transcriptional control
Ferritin (iron storage) Aconitase: Translation repressor protein Binds ferritin mRNA Iron will bind to aconitase Aconitase releases the mRNA Ferritin production increases
Post transcriptional control
Post transcriptional control
Protein modification Phosphorylation Other alterations can affect the
activity of protein Insulin Starts out as a larger molecule Cut into more active sections
Post transcriptional control
Protein modification Degradation Protein is marked by small protein Protein complex then breaks down
proteins Proteasomes
Post transcriptional control
Post transcriptional control
Fig. 18-UN4Fig. 18-UN4
• Genes in highly compactedchromatin are generally nottranscribed.
Chromatin modification
• DNA methylation generallyreduces transcription.
• Histone acetylation seems toloosen chromatin structure,enhancing transcription.
Chromatin modification
Transcription
RNA processing
TranslationmRNAdegradation
Protein processingand degradation
mRNA degradation
• Each mRNA has acharacteristic life span,determined in part bysequences in the 5 and3 UTRs.
• Protein processing anddegradation by proteasomesare subject to regulation.
Protein processing and degradation
• Initiation of translation can be controlledvia regulation of initiation factors.
Translation
ormRNA
Primary RNAtranscript
• Alternative RNA splicing:
RNA processing
• Coordinate regulation:
Enhancer forliver-specific genes
Enhancer forlens-specific genes
Bending of the DNA enables activators tocontact proteins at the promoter, initiatingtranscription.
Transcription
• Regulation of transcription initiation:DNA control elements bind specifictranscription factors.
Post transcriptional control
Most gene regulation-transcription New discovery Small RNA’s 21-28 nucleotides long Play a role in gene expression New transcript before leaving the
nucleus
RNA interference RNA forming double stranded
loops from newly formed mRNA Loops are formed Halves have complementary
sequences Loops inhibit expression of genes Where double RNA came from
Post transcriptional control
Post transcriptional control
Dicer: Cuts double stranded RNA into
smaller RNA’s called microRNA (miRNA) Small interfering RNA (siRNA’s)
Fig. 18-13Fig. 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
Post transcriptional control
miRNA’s bind mRNA Prevents translation siRNA’s breaks apart mRNA before
it’s translated
Post transcriptional control
siRNAs play a role in heterochromatin formation
Block large regions of the chromosome
Small RNAs may also block transcription of specific genes
Fig. 18-UN5Fig. 18-UN5
Chromatin modification
RNA processing
TranslationmRNAdegradation
Protein processingand degradation
mRNA degradation
• miRNA or siRNA can target specific mRNAsfor destruction.
• miRNA or siRNA can block the translationof specific mRNAs.
Transcription
• Small RNAs can promote the formation ofheterochromatin in certain regions, blocking transcription.
Chromatin modification
Translation
Embryonic development
Zygote gives rise to many different cell types
Cells →tissues → organs → organ systems Gene expression Orchestrates developmental
programs of animals
Fig. 18-14aFig. 18-14a
(a) Fertilized eggs of a frog
Embryonic development
Zygote to adult results Cell division Cell differentiation: Cells become specialized in
structure & function Morphogenesis: “creation of from” Body arrangement
Fig. 47-6Fig. 47-6
(a) Fertilized egg (b) Four-cell stage (c) Early blastula (d) Later blastula
Fig. 47-1Fig. 47-1
1 mm
Fig. 46-17Fig. 46-17
(a) 5 weeks (b) 14 weeks (c) 20 weeks
Embryonic development
All cells same genome Differential gene expression Genes regulated differently in
each cell type
Fig. 18-10Fig. 18-10
Controlelements
Enhancer
Availableactivators
Albumin gene
(b) Lens cell
Crystallin geneexpressed
Availableactivators
LENS CELLNUCLEUS
LIVER CELLNUCLEUS
Crystallin gene
Promoter
(a) Liver cell
Crystallin genenot expressed
Albumin geneexpressed
Albumin genenot expressed
Embryonic development
Specific activators Materials in egg cytoplasm Not homogeneous Set up gene regulation Carried out as cells divide
Embryonic development
Cytoplasmic determinants Maternal substances in the egg Influence early development Zygote divides by mitosis Cells contain different
cytoplasmic determinants Leads to different gene
expression
Fig. 18-15aFig. 18-15a
(a) Cytoplasmic determinants in the egg
Two differentcytoplasmicdeterminants
Unfertilized egg cell
Sperm
Fertilization
Zygote
Mitoticcell division
Two-celledembryo
Nucleus
Embryonic development
Environment around cell influences development
Induction: Signals from nearby embryonic cells Cause transcriptional changes in
target cells Interactions between cells induce
differentiation of specialized cell types
Fig. 18-15bFig. 18-15b
(b) Induction by nearby cells
Signalmolecule(inducer)
Signaltransductionpathway
Early embryo(32 cells)
NUCLEUS
Signalreceptor
Embryonic development
Determination: Observable differentiation of a cell Commits a cell to its final fate Cell differentiation is marked by the
production of tissue-specific proteins Gives cell characteristic structure &
function
Embryonic development
Myoblasts: Produce muscle-specific proteins Form skeletal muscle cells MyoD One of several “master regulatory
genes” Produces proteins Commit cells to becoming skeletal
muscle
Embryonic development
MyoD protein Transcription factor Binds to enhancers of various
target genesCauses expression
Fig. 18-16-1Fig. 18-16-1
Embryonicprecursor cell
Nucleus
OFF
DNA
Master regulatory gene myoD Other muscle-specific genes
OFF
Fig. 18-16-2Fig. 18-16-2
Embryonicprecursor cell
Nucleus
OFF
DNA
Master regulatory gene myoD Other muscle-specific genes
OFF
OFFmRNA
MyoD protein(transcriptionfactor)
Myoblast(determined)
Fig. 18-16-3Fig. 18-16-3
Embryonicprecursor cell
Nucleus
OFF
DNA
Master regulatory gene myoD Other muscle-specific genes
OFF
OFFmRNA
MyoD protein(transcriptionfactor)
Myoblast(determined)
mRNA mRNA mRNA mRNA
Myosin, othermuscle proteins,and cell cycle–blocking proteinsPart of a muscle fiber
(fully differentiated cell)
MyoD Anothertranscriptionfactor
Embryonic development
Pattern formation: Development of spatial organization of
tissues & organs Begins with establishment of the major
axes Positional information: Molecular cues control pattern formation Tells a cell its location relative to the body
axes & neighboring cells
Figure 18.24Figure 18.24
G protein
Growth factor
Receptor Proteinkinases
Transcriptionfactor (activator)
NUCLEUS Protein thatstimulatesthe cell cycle
Transcriptionfactor (activator)
NUCLEUS
Overexpressionof protein
Ras
Ras
MUTATION
GTP
GTP
Ras protein activewith or withoutgrowth factor.
P P
P P
P P
1
3
2
5
4
6
Figure 18.25Figure 18.25
Protein kinases
DNA damagein genome
Active formof p53
Transcription
DNA damagein genome
UVlight
UVlight
Defective ormissingtranscriptionfactor.
Inhibitoryproteinabsent
Protein thatinhibits thecell cycleNUCLEUS
MUTATION
1 3 4
2
5
Fruit fly
Unfertilized egg contains cytoplasmic determinants
Determines the axes before fertilization
After fertilization, Embryo develops into a
segmented larva with three larval stages
Fig. 18-17aFig. 18-17a
ThoraxHead Abdomen
0.5 mm
Dorsal
Ventral
Right
Posterior
LeftAnteriorBODY
AXES
(a) Adult
Fig. 18-17bFig. 18-17bFollicle cell
Nucleus
Eggcell
Nurse cell
Egg celldeveloping withinovarian follicle
Unfertilized egg
Fertilized egg
Depletednurse cells
Eggshell
FertilizationLaying of egg
Bodysegments
Embryonicdevelopment
Hatching
0.1 mm
Segmentedembryo
Larval stage
(b) Development from egg to larva
1
2
3
4
5
Fruit fly
Homeotic genes: Control pattern formation in late
embryo,larva and adult
Fig. 18-18Fig. 18-18
Antenna
MutantWild type
Eye
Leg
Fruit fly
Maternal effect genes: Encode for cytoplasmic determinants Initially establish the axes of the body
of Drosophila Egg-polarity genes: Maternal effect genes Control orientation of the egg Consequently the fly
Fruit Fly
Bicoid gene Maternal effect gene Affects the front half of the body An embryo whose mother has a
mutant bicoid gene Lacks the front half of its body Duplicate posterior structures at
both ends
Fig. 18-19aFig. 18-19a
T1 T2T3
A1 A2 A3 A4 A5 A6A7
A8
A8A7 A6 A7
Tail
TailTail
Head
Wild-type larva
Mutant larva (bicoid)
EXPERIMENT
A8
