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Control of Gene
Expression
AP Chap 18
Overview: Conducting the Genetic Orchestra
• Prokaryotes and eukaryotes alter gene expression in response to their changing environment.
Bacteria often respond to environmental change by regulating transcription
• Natural selection has favored bacteria that produce only the products needed by that cell.
• A cell can regulate the production of enzymes by feedback inhibition or by gene regulation.
• Gene expression in bacteria is controlled by 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
• An operon is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control
regulator promoter operator genes
regulator promoter operator genes
Makes arepressorwhich bindsto operatorand stops/startstranscription
RNA polymerasebinds here
Induction System
• System initially off• The presence of an inducer (usually a
substrate that needs to be broken down) turns it on.
• The inducer binds to the repressor and makes it inactive so transcription can occur.
• The inducer acts as an allosteric effector and changes the shape of the repressor.
• Ex- Lac (lactose) operon
Fig. 18-4a
(a) Lactose absent, repressor active, operon off
DNA
ProteinActiverepressor
RNApolymerase
Regulatorygene
Promoter
Operator
mRNA5
3
NoRNAmade
lacI lacZ
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
Lactose present, repressor inactive, operon ON
Repressible System
• System initially ON, transcription ongoing and making a product
• Operator can be turned off by a repressor which is made active by being activated by a corepressor molecule (usually the end product)
• Ex – tryptophan operon – trytophan acts as a corepressor inhibitng further synthesis of enzymes involved in the process
Fig. 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
ABCD
E
Tryptophan absent, repressor inactive, operon ON
Fig. 18-3b-1
(b) Tryptophan present, repressor active, operon off
Tryptophan(corepressor)
No RNA made
Activerepressor
mRNA
Protein
DNA
Tryptophan present, repressor active, operon OFF
INDUCIBLE REPRESSABLE
OFF ON turned on by turned off by inducer corepressor used in catabolic used in anabolic pathways pathways
Both use allosteric effectors and are NEGATIVE CONTROL.
Positive Gene Regulation
• Some operons are also subject to positive control through a stimulatory protein, such as catabolite activator protein (CAP), an activator of transcription
• When glucose (a preferred food source of E. coli) is scarce, CAP is activated by binding with cyclic AMP
• Activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription
Fig. 18-5
(b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized
cAMP
DNA
Inactive lacrepressor
Allolactose
InactiveCAP
lacI
CAP-binding site
Promoter
ActiveCAP
Operator
lacZ
RNApolymerasebinds andtranscribes
Inactive lacrepressor
lacZ
OperatorPromoter
DNA
CAP-binding site
lacI
RNApolymerase lesslikely to bind
InactiveCAP
(a) Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized
• When glucose levels increase, CAP detaches from the lac operon, and transcription returns to a normal rate
• CAP helps regulate other operons that encode enzymes used in catabolic pathways
Control of Gene Expression in Eukaryotes
• In response to environmental signals
• Essential for development and cell specialization in multicellular organisms
• RNA is important in gene expression.
• All cells contain the same DNA so controlling gene expression is essential.
• Human cells only 20% genes expressed; only 1.5% code for proteins
• Commonly occurs at level of transcription; hence, gene expression = transcription of DNA
Eukaryotic gene expression can be regulated at any stage
< A>
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
Fig. 18-6a
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
CYTOPLASM
Transcription
Fig. 18-6b
mRNA in cytoplasm
Translation
CYTOPLASM
Degradationof mRNA
Protein processing
Polypeptide
Active protein
Cellular function
Transport to cellulardestination
Degradationof protein
1) State of chromatin (nucleosomes)
• Heterochromatin – genes not expressed due to tightly wound DNA
Chemical modification
- Histone acetylation – promotes transcription by inhibiting binding between nucleosomes so keeps DNA spread out; also may recruit transcription factors
- Methylation of DNA – inhibits transcription (indicated in inactive X)
Epigenetic inheritance – not involved DNA sequence but inherited defects in chromatin modification enzymes
There may be more to inheritance than genes alone. New clues reveal that a second epigenetic chemical code sits on top of our regular DNA and controls how our genes are expresse.
2) Transcription Level
• Remember, transcription factors bind to DNA promoters, then RNA polymerase binds to promoter region to form the Transcription Initiation Complex
Transcription Factors:General
Bind to RNA polymerase and each other to initiate transcription of all protein-coding genes
Low rate of transcription
Specific Transcription Factors
• (a) enhancers: proximal (close to promoters) and distal; specific for a gene
• (b) some are repressors and can block anywhere in the scheme and can also recruit proteins to affect chromatin structure
• (c) enhancers contain control elements (up to 10 different ones); the combination is specific for transcription factors. Also explains how genes in a related pathway are correlated (like flags on mailboxes to know which mail to pick up). The combination signals which genes are expressed.
Fig. 18-9-1
Enhancer TATAbox
PromoterActivators
DNAGene
Distal controlelement
Fig. 18-9-2
Enhancer TATAbox
PromoterActivators
DNAGene
Distal controlelement
Group ofmediator proteins
DNA-bendingprotein
Generaltranscriptionfactors
Fig. 18-9-3
Enhancer TATAbox
PromoterActivators
DNAGene
Distal controlelement
Group ofmediator proteins
DNA-bendingprotein
Generaltranscriptionfactors
RNApolymerase II
RNApolymerase II
Transcriptioninitiation complex RNA synthesis
Fig. 18-UN7
Fig. 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
3. Post-transcriptional Control
• Alternative RNA splicing (mRNA can last a long time and be subject to various intron splicing)
•The mRNA life span is determined in part by sequences in the leader and trailer regions
Fig. 18-11
or
RNA splicing
mRNA
PrimaryRNAtranscript
Troponin T gene
Exons
DNA
• Alteration of polypeptide - can be cut, groups added, or transported to target locations
• Selective degradation of proteins – the protein ubiquitin are added to proteins for degradation. Proteasomes recognize them and destroy them.
Fig. 18-12
Proteasomeand ubiquitinto be recycledProteasome
Proteinfragments(peptides)Protein entering a
proteasome
Ubiquitinatedprotein
Protein tobe degraded
Ubiquitin
Noncoding RNAs play multiple roles in controlling gene expression
• Only a small fraction of DNA codes for proteins, rRNA, and tRNA
• A significant amount of the genome may be transcribed into noncoding RNAs
• Noncoding RNAs regulate gene expression at two points: mRNA translation and chromatin configuration
Effects on mRNAs by MicroRNA’s
• MicroRNAs (miRNAs) are small single-stranded RNA molecules that can bind to mRNA
• These can degrade mRNA or block its translation
Hairpins?
• Long RNA precursors fold on themselves and look like hairpins. The hairpins are cut off and an enzyme called Dicer trims the ends. One strand becomes a microRNA (miRNA).
• These bind with proteins and block translation or degrades the mRNA.
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
• An estimated 1/3 of human genes are regulated by miRNAs
Small Interfering RNA’s
• The phenomenon of inhibition of gene expression by RNA molecules is called RNA interference (RNAi)
• Cells cut up the RNA into small interfering RNAs (siRNAs) that can inhibit expression like miRNA’s
• siRNAs and miRNAs are similar but form from different RNA precursors
CANCER AND GENE EXPRESSIONCancer results from genetic changes
that affect cell cycle control
• Cancer can be caused by mutations to genes that regulate cell growth and division
- mutagens are chemicals, X-rays, tumor viruses in animals
Fig. 18-21c
(c) Effects of mutations
EFFECTS OF MUTATIONS
Cell cycle notinhibited
Protein absent
Increased celldivision
Proteinoverexpressed
Cell cycleoverstimulated
Oncogenes and Proto-Oncogenes
• Oncogenes are cancer-causing genes• Proto-oncogenes are the
corresponding normal cellular genes that are responsible for normal cell growth and division
Conversion of a proto-oncogene to an oncogene can lead to abnormal
stimulation of the cell cycle
• Amplification of normal growth-stimulating gene
• Translocation of growth gene under control of a more active promoter
• Point mutation in control element or gene itself to make a hyperactive or degradation resistent growth protein.
Fig. 18-20
Normal growth-stimulatingprotein in excess
Newpromoter
DNA
Proto-oncogene
Gene amplification:Translocation ortransposition:
Normal growth-stimulatingprotein in excess
Normal growth-stimulatingprotein in excess
Hyperactive ordegradation-resistant protein
Point mutation:
Oncogene Oncogene
within a control element within the gene
Tumor-Suppressor Genes• help prevent uncontrolled cell growth
• Tumor-suppressor proteins
–Repair damaged DNA
–Control cell adhesion
–Inhibit the cell cycle
How do cancer genes work?
• 30% cancers – ras proto-oncogene gene is mutated
Ras gene codes for a protein that stimlates the production of a cell cycle stimulating protein; mutations cause a hyperactive protein
• 50% cancers – p53 gene mutated; codes for a transcription factor for growth-inhibiting proteins. These proteins bind to a p21 gene whose product binds to CDK’s and halt cell cycle. It can also activate DNA repair genes or “suicide genes” if DNA can’t be repaired.
Fig. 18-21b
MUTATIONProtein kinases
DNA
DNA damagein genome
Defective ormissingtranscriptionfactor, suchas p53, cannotactivatetranscription
Protein thatinhibitsthe cell cycle
Activeformof p53
UVlight
(b) Cell cycle–inhibiting pathway
2
3
1
p53 gene and DNA repair
P53 and suicide genes
Multistep Model of Cancer Development
• More than one somatic mutation is needed
• Both alleles must be defective
• In some, genes for telomerase becomes activated and cells divided continually
Breat cancer gene
Inherited Predisposition and Other Factors Contributing to Cancer
• Individuals can inherit oncogenes or mutant alleles of tumor-suppressor genes
• Inherited mutations in the tumor-suppressor gene adenomatous polyposis coli are common in individuals with colorectal cancer
• Mutations in the BRCA1 or BRCA2 gene are found in at least half of inherited breast cancers
• Even if you have cancer genes, it does not mean you will have cancer.
• Genes can be modified by siRNA’s, epigenesis, and the environment