Directionality (molecular biology) - Wikipedia

The mRNA is scanned by the ribosome from the 5′ end, where the start codon directs the incorporation of a methionine (bacteria, mitochondria, and plastids use N ... Directionality(molecularbiology) FromWikipedia,thefreeencyclopedia Jumptonavigation Jumptosearch End-to-endchemicalorientationofasinglestrandofnucleicacid Afuranose(sugar-ring)moleculewithcarbonatomslabeledusingstandardnotation.The5′isupstream;the3′isdownstream.DNAandRNAaresynthesizedinthe5′-to-3′direction. Directionality,inmolecularbiologyandbiochemistry,istheend-to-endchemicalorientationofasinglestrandofnucleicacid.InasinglestrandofDNAorRNA,thechemicalconventionofnamingcarbonatomsinthenucleotidepentose-sugar-ringmeansthattherewillbea5′ end(usuallypronounced"five-primeend"),whichfrequentlycontainsaphosphategroupattachedtothe5′carbonoftheribosering,anda3′ end(usuallypronounced"three-primeend"),whichtypicallyisunmodifiedfromtheribose-OHsubstituent.InaDNAdoublehelix,thestrandsruninoppositedirectionstopermitbasepairingbetweenthem,whichisessentialforreplicationortranscriptionoftheencodedinformation. Nucleicacidscanonlybesynthesizedinvivointhe5′-to-3′direction,asthepolymerasesthatassemblevarioustypesofnewstrandsgenerallyrelyontheenergyproducedbybreakingnucleosidetriphosphatebondstoattachnewnucleosidemonophosphatestothe3′-hydroxyl(−OH)group,viaaphosphodiesterbond.Therelativepositionsofstructuresalongstrandsofnucleicacid,includinggenesandvariousproteinbindingsites,areusuallynotedasbeingeitherupstream(towardsthe5′-end)ordownstream(towardsthe3′-end).(Seealsoupstreamanddownstream.) Directionalityisrelatedto,butdifferentfrom,sense.Transcriptionofsingle-strandedRNAfromadouble-strandedDNAtemplaterequirestheselectionofonestrandoftheDNAtemplateasthetemplatestrandthatdirectlyinteractswiththenascentRNAduetocomplementarysequence.Theotherstrandisnotcopieddirectly,butnecessarilyitssequencewillbesimilartothatoftheRNA.Transcriptioninitiationsitesgenerallyoccuronbothstrandsofanorganism'sDNA,andspecifythelocation,direction,andcircumstancesunderwhichtranscriptionwilloccur.Ifthetranscriptencodesoneor(rarely)moreproteins,translationofeachproteinbytheribosomewillproceedina5′-to-3′direction,andwillextendtheproteinfromitsNterminustowarditsCterminus.Forexample,inatypicalgeneastartcodon(5′-ATG-3′)isaDNAsequencewithinthesensestrand.Transcriptionbeginsatanupstreamsite(relativetothesensestrand),andasitproceedsthroughtheregionitcopiesthe3′-TAC-5′fromthetemplatestrandtoproduce5′-AUG-3′withinamessengerRNA(mRNA).ThemRNAisscannedbytheribosomefromthe5′end,wherethestartcodondirectstheincorporationofamethionine(bacteria,mitochondria,andplastidsuseN-formylmethionineinstead)attheNterminusoftheprotein.Byconvention,singlestrandsofDNAandRNAsequencesarewrittenina5′-to-3′directionexceptasneededtoillustratethepatternofbasepairing. Contents 15′-end 23′-end 3Seealso 4Furtherreading 5Externallinks 5′-end[edit] IntheDNAsegmentshown,the5′to3′directionsaredowntheleftstrandanduptherightstrand The5′-end(pronounced"fiveprimeend")designatestheendoftheDNAorRNAstrandthathasthefifthcarboninthesugar-ringofthedeoxyriboseorriboseatitsterminus.Aphosphategroupattachedtothe5′-endpermitsligationoftwonucleotides,i.e.,thecovalentbindingofa5′-phosphatetothe3′-hydroxylgroupofanothernucleotide,toformaphosphodiesterbond.Removalofthe5′-phosphatepreventsligation.Topreventunwantednucleicacidligation(e.g.self-ligationofaplasmidvectorinDNAcloning),molecularbiologistscommonlyremovethe5′-phosphatewithaphosphatase. The5′-endofnascentmessengerRNAisthesiteatwhichpost-transcriptionalcappingoccurs,aprocesswhichisvitaltoproducingmaturemessengerRNA.CappingincreasesthestabilityofthemessengerRNAwhileitundergoestranslation,providingresistancetothedegradativeeffectsofexonucleases.[1]Itconsistsofamethylatednucleotide(methylguanosine)attachedtothemessengerRNAinarare5′-to5′-triphosphatelinkage. The5′-flankingregionofageneoftendenotesaregionofDNAwhichisnottranscribedintoRNA.The5′-flankingregioncontainsthegenepromoter,andmayalsocontainenhancersorotherproteinbindingsites. The5′-untranslatedregion(5′-UTR)isaregionofagenewhichistranscribedintomRNA,andislocatedatthe5′-endofthemRNA.ThisregionofanmRNAmayormaynotbetranslated,butisusuallyinvolvedintheregulationoftranslation.The5′-untranslatedregionistheportionoftheDNAstartingfromthecapsiteandextendingtothebasejustbeforetheAUGtranslationinitiationcodonofthemaincodingsequence.Thisregionmayhavesequences,suchastheribosomebindingsiteandKozaksequence,whichdeterminethetranslationefficiencyofthemRNA,orwhichmayaffectthestabilityofthemRNA. 3′-end[edit] Phosphodiesterbonds(circled)betweennucleotides The3′-end(threeprimeend)ofastrandissonamedduetoitterminatingatthehydroxylgroupofthethirdcarboninthesugar-ring,andisknownasthetailend.The3′-hydroxylisnecessaryinthesynthesisofnewnucleicacidmoleculesasitisligated(joined)tothe5′-phosphateofaseparatenucleotide,allowingtheformationofstrandsoflinkednucleotides. Molecularbiologistscanusenucleotidesthatlacka3′-hydroxyl(dideoxyribonucleotides)tointerruptthereplicationofDNA.Thistechniqueisknownasthedideoxychain-terminationmethodortheSangermethod,andisusedtodeterminetheorderofnucleotidesinDNA. The3′-endofnascentmessengerRNAisthesiteofpost-transcriptionalpolyadenylation,whichattachesachainof50to250adenosineresiduestoproducematuremessengerRNA.ThischainhelpsindetermininghowlongthemessengerRNAlastsinthecell,influencinghowmuchproteinisproducedfromit. The3′-flankingregionisaregionofDNAthatisnotcopiedintothematuremRNA,butwhichispresentadjacentto3′-endofthegene.Itwasoriginallythoughtthatthe3′-flankingDNAwasnottranscribedatall,butitwasdiscoveredtobetranscribedintoRNAandquicklyremovedduringprocessingoftheprimarytranscripttoformthematuremRNA.The3′-flankingregionoftencontainssequencesthataffecttheformationofthe3′-endofthemessage.Itmayalsocontainenhancersorothersitestowhichproteinsmaybind. The3′-untranslatedregion(3′-UTR)isaregionoftheDNAwhichistranscribedintomRNAandbecomesthe3′-endofthemessage,butwhichdoesnotcontainproteincodingsequence.EverythingbetweenthestopcodonandthepolyAtailisconsideredtobe3′-untranslated.The3′-untranslatedregionmayaffectthetranslationefficiencyofthemRNAorthestabilityofthemRNA.Italsohassequenceswhicharerequiredfortheadditionofthepoly(A)tailtothemessage,includingthehexanucleotideAAUAAA. Seealso[edit] Sense(molecularbiology) Furtherreading[edit] HarveyLodish;ArnoldBerk;PaulMatsudaira;ChrisA.Kaiser(2004).MolecularCellBiology(5th ed.).NewYorkCity:W.H.FreemanandCompany.ISBN 978-0-7167-4366-8. ^GaoM,FritzDT,FordLP,WiluszJ(March2000)."Interactionbetweenapoly(A)-specificribonucleaseandthe5′capinfluencesmRNAdeadenylationratesinvitro".MolecularCell.5(3):479–488.doi:10.1016/S1097-2765(00)80442-6.PMC 2811581.PMID 10882133. 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