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Chapter14FromGene
toProteinChapter14FromGene
toProteMetabolismTeachesUsAboutGenesMetabolicdefectsstudyingmetabolicdiseasessuggestedthatgenesspecifiedproteinsalkaptonuria(blackurinefromalkaptona.k.a.homogentisicacid)PKU(phenylketonuria)eachdiseaseiscausedby
non-functionalenzymeABCDEGenes
create
phenotype…MetabolismTeachesUsAboutGe2Lecture-034---Protein-Sy教學(xué)講解課件31Gene–1EnzymeHypothesisBeadle&TatumComparedmutantsofbreadmold,NeurosporafunguscreatedmutationsbyX-raytreatmentsX-raysbreakDNAinactivateagenewildtypegrowson“minimal”mediasugars+requiredprecursornutrienttosynthesizeessentialaminoacidsmutantsrequireaddedaminoacidseachtypeofmutantlacksacertainenzymeneededtoproduceacertainaminoacidnon-functionalenzyme=brokengene1Gene–1EnzymeHypothesisBe4Beadle&Tatum1941|1958GeorgeBeadleEdwardTatumBeadle&Tatum1941|1958Geor5Beadle&Tatum’sNeurospora
ExperimentBeadle&Tatum’sNeurosporaEx6So…WhatisaGene?Onegene–oneenzymeallproteinsarecodedbygenesbutnotallproteinsareenzymesOnegene–oneproteineachproteinhasitsowngenebutmanyproteinsarecomposedofseveralpolypeptidesOnegene–onepolypeptidebutmanygenesonlycodeforRNAOnegene–oneproductbutmanygenescodefor
morethanoneproduct…Wheredoesthatleave
us?!So…WhatisaGene?Onegene–7DefiningaGene…“Definingageneisproblematicbecause…onegenecancodeforseveralproteinproducts,somegenescodeonlyforRNA,twogenescanoverlap,andtherearemanyothercomplications.”
–ElizabethPennisi,Science2003genepolypeptide1polypeptide2polypeptide3RNAgeneIt’shardtohuntforwabbits,ifyoudon’tknow
whatawabbit
lookslike.DefiningaGene…“Definingage8proteinRNAThe“CentralDogma”DNAtranscriptiontranslationreplicationHowdowemoveinformationfrom
DNAtoproteins?Forsimplicitysake,let’sgobackto
genesthatcode
forproteins…proteinRNAThe“CentralDogma”D9Fromnucleustocytoplasm…Wherearethegenes?genesareonchromosomesinnucleusWhereareproteinssynthesized?proteinsmadeincytoplasmbyribosomesHowdoestheinformationgetfromnucleustocytoplasm?messengerRNAnucleusFromnucleustocytoplasm…Wher10RNAribosesugarN-basesuracilinsteadofthymineU:AC:GsinglestrandedmRNA,rRNA,tRNA,
siRNA….RNADNAtranscriptionRNAribosesugarRNADNAtranscri11TranscriptionTranscribedDNAstrand=templatestranduntranscribedDNAstrand=codingstrandSynthesisofcomplementaryRNAstrandtranscriptionbubbleEnzymethatfacilitatesthebuildingofRNA:RNApolymeraseTranscriptionTranscribedDNAs12Roleofpromoter1.Wheretostartreading =startingpoint2.Whichstrandtoread =templatestrand3.DirectiononDNA =alwaysreads
DNA
3'5'TranscriptionInitiationRNApolymerasebindstopromotersequenceonDNARoleofpromoterTranscriptionI13TranscriptionElongationRNApolymeraseunwindsDNA
~20basepairsatatimereadsDNA3’5’buildsRNA5’3’(theenzymegovernsthesynthesis!)Noproofreading1error/105basesmanycopiesshortlifenotworthit!TranscriptionElongationNoproo14TranscriptionRNATranscriptionRNA15TranscriptionTerminationRNApolymerasestopsatterminationsequencemRNAleavesnucleusthroughporesRNAGC
hairpinturnTranscriptionTerminationRNAG16Prokaryotevs.EukaryoteGeneticsDifferencesbetweenprokaryotes&eukaryotestime&physicalseparationbetweenprocessesRNAprocessingProkaryotevs.EukaryoteGenet17TranscriptioninEukaryotesonly1prokaryoticenzyme3eukaryoticRNApolymeraseenzymesRNApolymeraseI
onlytranscribesrRNAgenesRNApolymeraseII
transcribesgenesintomRNARNApolymeraseIIIonlytranscribesrRNAgeneseachhasaspecificpromotersequenceitrecognizesTranscriptioninEukaryotesonl18AAAAA3'poly-AtailCH3mRNA5'5'cap3'GPPPEukaryoticPost-transcriptionalProcessingPrimarytranscript
eukaryoticmRNAneedsworkaftertranscriptionProtectmRNAfromRNA-aseenzymesincytoplasmadd5'GcapaddpolyAtailEditoutintronseukaryoticDNAexon=coding(expressed)sequenceintron=noncoding(inbetween)sequenceprimarymRNAtranscriptmaturemRNAtranscriptpre-mRNAsplicedmRNA50-250A’sAAAAA3'poly-AtailCH3mRNA5'5'19PrimaryTranscriptProcessingmRNAprotectingRNAfromRNaseincytoplasmadd5’capaddpolyAtailremoveintronsAUGUGAPrimaryTranscriptProcessingm20ProtectingRNA5’capaddedGtrinucleoside(G-P-P-P)protectsmRNAfromRNase(hydrolyticenzymes)3’poly-Atailadded50-250A’sprotectsmRNAfromRNase(hydrolyticenzymes)helpsexportofRNAfromnucleusUTRUTRProtectingRNA5’capaddedUTRU21Dicing&SplicingmRNAPre-mRNAmRNAeditoutintronsinterveningsequencessplicetogetherexonsexpressedsequencesInhighereukaryotes90%ormoreofgenecanbeintronnooneknowswhy…yetthere’saNobelprizewaiting…“AVERAGE”“gene”=8000bpre-mRNA=8000bmaturemRNA=1200bprotein=400aalotsa“JUNK”!Dicing&SplicingmRNAPre-mRNA22snRNPssmallnuclearRNARNA+proteinsSpliceosomeseveralsnRNPsrecognizesplicesitesequencecut&pasteRNAasribozymesomemRNAcanspliceitselfRNAasenzymeSplicingEnzymessnRNPsSplicingEnzymes23RibozymeSidneyAltmanThomasCech1982|1989YaleUofColoradoRNAasenzymeRibozymeSidneyAltmanThomasCe24SplicingDetailsNoroomformistakes!editing&splicingmustbeexactlyaccurateasinglebaseaddedorlostthrowsoffthereadingframeAUG|CGG|UCC|GAU|AAG|GGC|CAUAUGCGGCUAUGGGUCCGAUAAGGGCCAUAUGCGGUCCGAUAAGGGCCAUAUG|CGG|GUC|CGA|UAA|GGG|CCA|UAUGCGGCUAUGGGUCCGAUAAGGGCCAUAUGCGGGUCCGAUAAGGGCCAUMet|Arg|Ser|Asp
|Lys
|Gly
|His
Met
|Arg|Val
|Arg|STOP|SplicingDetailsNoroomformi25AlternativeSplicingAlternativemRNAsproducedfromsamegenewhenisanintronnotanintron…differentsegmentstreatedasexonsHardtodefine
agene!AlternativeSplicingAlternativ26DiscoveryofSplitGenes1977|1993RichardRobertsPhilipSharpNEBioLabsMITadenoviruscommoncoldDiscoveryofSplitGenes1977|27ssssssssssssssssssssssssssssssssssssStructureofAntibodieslightchainsantigen-bindingsiteheavychainsantigen-bindingsitelightchainlightchainheavychainsBcellmembranevariableregionantigen-bindingsiteYYYYYYYYYYYYYYYYYYYYYYYYYssssssssssssssssssssssssssssss28TranscriptionofgenemRNAchromosomeofundifferentiatedBcellBcellCCDJDNAofdifferentiatedBcellrearrangementofDNAVTranslationofmRNAHowdovertebratesproducemillionsofantibodyproteins,iftheyonlyhaveafewhundredgenescodingforthoseproteins?antibodyByDNArearrangement&somaticmutationvertebratescanproducemillionsof
B&Tcells
TranscriptionofgenemRNAchrom29AAAAAAAAGTP20-30b3'promotertranscriptionstoptranscriptionstartintronsTheTranscriptionalUnit(gene?)transcriptionalunitTACACTDNADNATATA5'RNApolymerasepre-mRNA5'3'translationstarttranslationstopmaturemRNA5'3'UTRUTRexonsenhancer1000+bAAAAAAAAGTP20-30b3'promotertra30Prokaryotevs.EukaryoteGeneticsProkaryotesDNAincytoplasmcircularchromosomenakedDNAnointronsEukaryotesDNAinnucleuslinearchromosomesDNAwoundonhistoneproteinsintronsvs.exonseukaryoticDNAexon=coding(expressed)sequenceintron=noncoding(inbetween)sequenceProkaryotevs.EukaryoteGenet31mRNAFromGenetoProteinDNAtranscriptionnucleuscytoplasmmRNAleavesnucleusthroughnuclearporesproteinssynthesizedbyribosomesusinginstructionsonmRNAaaaaaaaaaaaaaaaaribosomeproteintranslationmRNAFromGenetoProteinDNAtra32TranslationinProkaryotesTranscription&translationaresimultaneousinbacteriaDNAisin
cytoplasmnomRNA
editing
neededTranslationinProkaryotesTran33TACGCACATTTACGTACGCGGDNAAUGCGUGUAAAUGCAUGCGCCmRNAMet
Arg
Val
Asn
Ala
Cys
Alaprotein?Howcanyoucodefor20aminoacidswithonly4nucleotidebases(A,U,G,C)?HowDoesDNACodeforProteinsTACGCACATTTACGTACGCGGDNAAUGCGU34CrackingtheCodeNirenberg&Matthaeidetermined1stcodon–aminoacidmatchUUUcodedforphenylalaninecreatedartificialpoly(U)mRNAaddedmRNAtotesttubeof
ribosomes,tRNA&aminoacidsmRNAsynthesizedsingle
aminoacidpolypeptidechain1960|1968phe–phe–phe–phe–phe–pheCrackingtheCodeNirenberg&M35MarshallNirenbergHeinrichMatthaeiMarshallNirenbergHeinrichMat36TranslationCodonsblocksof3nucleotidesdecodedinto
thesequenceofaminoacidsTranslationCodons37mRNACodesforProteinsinTripletsmRNAAUGCGUGUAAAUGCAUGCGCCmRNAAUGCGUGUAAAUGCAUGCGCCTACGCACATTTACGTACGCGGDNAMetArgValAsnAlaCysAlaprotein?codonribosomemRNAcodesforproteinsintriplets…CODONS!mRNACodesforProteinsinTri38TheCode!ForALLlife!strongestsupportforacommonoriginforalllifeCodeisredundantseveralcodonsforeachaminoacidWhyisthisagoodthing?StartcodonAUGmethionineStopcodonsUGA,UAA,UAGTheCode!ForALLlife!Whyist395'3'3'5'TACGCACATTTACGTACGCGGDNAAUGCGUGUAAAUGCAUGCGCCmRNAanti-codoncodonUACMetGCAArgCAUValamino
acidtRNA3'5'HowareCodonsMatchedtoAminoAcids?5'3'3'5'TACGCACATTTACGTACGCGGD40proteintranscriptioncytoplasmnucleustranslationproteintranscriptioncytoplasmn41tRNAStructure“Cloverleaf”structureanticodonon“cloverleaf”endaminoacidattachedon3'endtRNAStructure“Cloverleaf”st42LoadingtRNAAminoacyltRNAsynthetaseenzymewhichbonds
aminoacidtotRNAendergonicreactionATPAMPenergystoredin
tRNA-aminoacidbondunstablesoitcanreleaseaminoacid
atribosomeLoadingtRNAAminoacyltRNAsy43RibosomesFacilitatecouplingof
tRNAanticodonto
mRNAcodonorganelleorenzyme?StructureribosomalRNA(rRNA)&proteins2subunitslargesmallRibosomesFacilitatecoupling44RibosomesPsite(peptidyl-tRNAsite)holdstRNAcarryinggrowingpolypeptidechainAsite(aminoacyl-tRNAsite)holdstRNAcarryingnextaminoacidtobeaddedtochainEsite(exitsite)emptytRNA
leavesribosome
fromexitsiteRibosomesPsite(peptidyl-tRN45BuildingaPolypeptideInitiationbringstogethermRNA,ribosomesubunits,
proteins&initiatortRNAElongationTerminationBuildingaPolypeptideInitiati46Elongation:GrowingaPolypeptideElongation:GrowingaPolypept47Termination:ReleasePolypeptideReleasefactor“releaseprotein”bondstoAsitebondswatermoleculetopolypeptidechainNowwhathappenstothepolypeptide?Termination:ReleasePolypepti48ProteinTargetingSignalpeptideaddresslabelDestinations:secretionnucleusmitochondriachloroplastscellmembranecytoplasmex.startofasecretorypathwayProteinTargetingSignalpepti49Canyoutelltheeukaryoticstory?DNApre-mRNAribosometRNAamino
acidspolypeptidematuremRNA5'cappolyAtaillargesubunitsmallsubunitaminoacyltRNA
synthetaseEPA5'3'RNApolymeraseexonintrontRNACanyoutelltheeukaryoticst50Puttingitall
together…Don’tforgettheYouTubevideos!Puttingitall
together…Don’t51Chapter14FromGene
toProteinChapter14FromGene
toProteMetabolismTeachesUsAboutGenesMetabolicdefectsstudyingmetabolicdiseasessuggestedthatgenesspecifiedproteinsalkaptonuria(blackurinefromalkaptona.k.a.homogentisicacid)PKU(phenylketonuria)eachdiseaseiscausedby
non-functionalenzymeABCDEGenes
create
phenotype…MetabolismTeachesUsAboutGe53Lecture-034---Protein-Sy教學(xué)講解課件541Gene–1EnzymeHypothesisBeadle&TatumComparedmutantsofbreadmold,NeurosporafunguscreatedmutationsbyX-raytreatmentsX-raysbreakDNAinactivateagenewildtypegrowson“minimal”mediasugars+requiredprecursornutrienttosynthesizeessentialaminoacidsmutantsrequireaddedaminoacidseachtypeofmutantlacksacertainenzymeneededtoproduceacertainaminoacidnon-functionalenzyme=brokengene1Gene–1EnzymeHypothesisBe55Beadle&Tatum1941|1958GeorgeBeadleEdwardTatumBeadle&Tatum1941|1958Geor56Beadle&Tatum’sNeurospora
ExperimentBeadle&Tatum’sNeurosporaEx57So…WhatisaGene?Onegene–oneenzymeallproteinsarecodedbygenesbutnotallproteinsareenzymesOnegene–oneproteineachproteinhasitsowngenebutmanyproteinsarecomposedofseveralpolypeptidesOnegene–onepolypeptidebutmanygenesonlycodeforRNAOnegene–oneproductbutmanygenescodefor
morethanoneproduct…Wheredoesthatleave
us?!So…WhatisaGene?Onegene–58DefiningaGene…“Definingageneisproblematicbecause…onegenecancodeforseveralproteinproducts,somegenescodeonlyforRNA,twogenescanoverlap,andtherearemanyothercomplications.”
–ElizabethPennisi,Science2003genepolypeptide1polypeptide2polypeptide3RNAgeneIt’shardtohuntforwabbits,ifyoudon’tknow
whatawabbit
lookslike.DefiningaGene…“Definingage59proteinRNAThe“CentralDogma”DNAtranscriptiontranslationreplicationHowdowemoveinformationfrom
DNAtoproteins?Forsimplicitysake,let’sgobackto
genesthatcode
forproteins…proteinRNAThe“CentralDogma”D60Fromnucleustocytoplasm…Wherearethegenes?genesareonchromosomesinnucleusWhereareproteinssynthesized?proteinsmadeincytoplasmbyribosomesHowdoestheinformationgetfromnucleustocytoplasm?messengerRNAnucleusFromnucleustocytoplasm…Wher61RNAribosesugarN-basesuracilinsteadofthymineU:AC:GsinglestrandedmRNA,rRNA,tRNA,
siRNA….RNADNAtranscriptionRNAribosesugarRNADNAtranscri62TranscriptionTranscribedDNAstrand=templatestranduntranscribedDNAstrand=codingstrandSynthesisofcomplementaryRNAstrandtranscriptionbubbleEnzymethatfacilitatesthebuildingofRNA:RNApolymeraseTranscriptionTranscribedDNAs63Roleofpromoter1.Wheretostartreading =startingpoint2.Whichstrandtoread =templatestrand3.DirectiononDNA =alwaysreads
DNA
3'5'TranscriptionInitiationRNApolymerasebindstopromotersequenceonDNARoleofpromoterTranscriptionI64TranscriptionElongationRNApolymeraseunwindsDNA
~20basepairsatatimereadsDNA3’5’buildsRNA5’3’(theenzymegovernsthesynthesis!)Noproofreading1error/105basesmanycopiesshortlifenotworthit!TranscriptionElongationNoproo65TranscriptionRNATranscriptionRNA66TranscriptionTerminationRNApolymerasestopsatterminationsequencemRNAleavesnucleusthroughporesRNAGC
hairpinturnTranscriptionTerminationRNAG67Prokaryotevs.EukaryoteGeneticsDifferencesbetweenprokaryotes&eukaryotestime&physicalseparationbetweenprocessesRNAprocessingProkaryotevs.EukaryoteGenet68TranscriptioninEukaryotesonly1prokaryoticenzyme3eukaryoticRNApolymeraseenzymesRNApolymeraseI
onlytranscribesrRNAgenesRNApolymeraseII
transcribesgenesintomRNARNApolymeraseIIIonlytranscribesrRNAgeneseachhasaspecificpromotersequenceitrecognizesTranscriptioninEukaryotesonl69AAAAA3'poly-AtailCH3mRNA5'5'cap3'GPPPEukaryoticPost-transcriptionalProcessingPrimarytranscript
eukaryoticmRNAneedsworkaftertranscriptionProtectmRNAfromRNA-aseenzymesincytoplasmadd5'GcapaddpolyAtailEditoutintronseukaryoticDNAexon=coding(expressed)sequenceintron=noncoding(inbetween)sequenceprimarymRNAtranscriptmaturemRNAtranscriptpre-mRNAsplicedmRNA50-250A’sAAAAA3'poly-AtailCH3mRNA5'5'70PrimaryTranscriptProcessingmRNAprotectingRNAfromRNaseincytoplasmadd5’capaddpolyAtailremoveintronsAUGUGAPrimaryTranscriptProcessingm71ProtectingRNA5’capaddedGtrinucleoside(G-P-P-P)protectsmRNAfromRNase(hydrolyticenzymes)3’poly-Atailadded50-250A’sprotectsmRNAfromRNase(hydrolyticenzymes)helpsexportofRNAfromnucleusUTRUTRProtectingRNA5’capaddedUTRU72Dicing&SplicingmRNAPre-mRNAmRNAeditoutintronsinterveningsequencessplicetogetherexonsexpressedsequencesInhighereukaryotes90%ormoreofgenecanbeintronnooneknowswhy…yetthere’saNobelprizewaiting…“AVERAGE”“gene”=8000bpre-mRNA=8000bmaturemRNA=1200bprotein=400aalotsa“JUNK”!Dicing&SplicingmRNAPre-mRNA73snRNPssmallnuclearRNARNA+proteinsSpliceosomeseveralsnRNPsrecognizesplicesitesequencecut&pasteRNAasribozymesomemRNAcanspliceitselfRNAasenzymeSplicingEnzymessnRNPsSplicingEnzymes74RibozymeSidneyAltmanThomasCech1982|1989YaleUofColoradoRNAasenzymeRibozymeSidneyAltmanThomasCe75SplicingDetailsNoroomformistakes!editing&splicingmustbeexactlyaccurateasinglebaseaddedorlostthrowsoffthereadingframeAUG|CGG|UCC|GAU|AAG|GGC|CAUAUGCGGCUAUGGGUCCGAUAAGGGCCAUAUGCGGUCCGAUAAGGGCCAUAUG|CGG|GUC|CGA|UAA|GGG|CCA|UAUGCGGCUAUGGGUCCGAUAAGGGCCAUAUGCGGGUCCGAUAAGGGCCAUMet|Arg|Ser|Asp
|Lys
|Gly
|His
Met
|Arg|Val
|Arg|STOP|SplicingDetailsNoroomformi76AlternativeSplicingAlternativemRNAsproducedfromsamegenewhenisanintronnotanintron…differentsegmentstreatedasexonsHardtodefine
agene!AlternativeSplicingAlternativ77DiscoveryofSplitGenes1977|1993RichardRobertsPhilipSharpNEBioLabsMITadenoviruscommoncoldDiscoveryofSplitGenes1977|78ssssssssssssssssssssssssssssssssssssStructureofAntibodieslightchainsantigen-bindingsiteheavychainsantigen-bindingsitelightchainlightchainheavychainsBcellmembranevariableregionantigen-bindingsiteYYYYYYYYYYYYYYYYYYYYYYYYYssssssssssssssssssssssssssssss79TranscriptionofgenemRNAchromosomeofundifferentiatedBcellBcellCCDJDNAofdifferentiatedBcellrearrangementofDNAVTranslationofmRNAHowdovertebratesproducemillionsofantibodyproteins,iftheyonlyhaveafewhundredgenescodingforthoseproteins?antibodyByDNArearrangement&somaticmutationvertebratescanproducemillionsof
B&Tcells
TranscriptionofgenemRNAchrom80AAAAAAAAGTP20-30b3'promotertranscriptionstoptranscriptionstartintronsTheTranscriptionalUnit(gene?)transcriptionalunitTACACTDNADNATATA5'RNApolymerasepre-mRNA5'3'translationstarttranslationstopmaturemRNA5'3'UTRUTRexonsenhancer1000+bAAAAAAAAGTP20-30b3'promotertra81Prokaryotevs.EukaryoteGeneticsProkaryotesDNAincytoplasmcircularchromosomenakedDNAnointronsEukaryotesDNAinnucleuslinearchromosomesDNAwoundonhistoneproteinsintronsvs.exonseukaryoticDNAexon=coding(expressed)sequenceintron=noncoding(inbetween)sequenceProkaryotevs.EukaryoteGenet82mRNAFromGenetoProteinDNAtranscriptionnucleuscytoplasmmRNAleavesnucleusthroughnuclearporesproteinssynthesizedbyribosomesusinginstructionsonmRNAaaaaaaaaaaaaaaaaribosomeproteintranslationmRNAFromGenetoProteinDNAtra83TranslationinProkaryotesTranscription&translationaresimultaneousinbacteriaDNAisin
cytoplasmnomRNA
editing
neededTranslationinProkaryotesTran84TACGCACATTTACGTACGCGGDNAAUGCGUGUAAAUGCAUGCGCCmRNAMet
Arg
Val
Asn
Ala
Cys
Alaprotein?Howcanyoucodefor20aminoacidswithonly4nucleotidebases(A,U,G,C)?HowDoesDNACodeforProteinsTACGCACATTTACGTACGCGGDNAAUGCGU85CrackingtheCodeNirenberg&Matthaeidetermined1stcodon–aminoacidmatchUUUcodedforphenylalaninecreatedartificialpoly(U)mRNAaddedmRNAtotesttubeof
ribosomes,tRNA&aminoacidsmRNAsynthesizedsingle
aminoacidpolypeptidechain1960|1968phe–phe–phe–phe–phe–pheCrackingtheCodeNirenberg&M86MarshallNirenbergHeinrichMatthaeiMarshallNirenbergHeinrichMat87TranslationCodonsblocksof3nucleotidesdecodedinto
thesequenceofaminoacidsTranslationCodons88mRNACodesforProteinsinTripletsmRNAAUGCGUGUAAAUGCAUGCGCCmRNAAUGCGUGUAAAUGCAUGCGCCTACGCACATTTACGTACGCGGDNAMetArgValAsnAlaCysAlaprotein?codonribosomemRNAcodesforproteinsintriplets…CODONS!mRNACodesforProteinsinTri89TheCode!ForALLlife
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