chem_482_annotations.ppt

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1、19-1,Chapter19,OverviewofNucleicAcidStructure,19-2,D-Riboseisa5carbonaldosugarwithOHatC2,A.Nucleosides:1.Sugarsfoundinnucleosides,The5-memberringisthefuranose,whereC1isahemiacetal,When1-OHisup,thestereochemistryiscalledbeta(b).,Thusthename,Indeoxyribose,the2positionhasHratherthanOH.,19-3,2.Basesfoun

2、dinnucleosides,Thebasesincludetwoclasses,thepyrimidineandpurines.,Thepyrimidinesarearomatic,six-membered,2-oxopyrimidines.,Uracil(RNA)andthymine(DNA)are4-oxo.,Cytosine(RNAandDNA)is4-amino.,Thepurinesarefused(6:5)aromaticringscontainingnitrogen.,19-4,3.Theglycosidicbondinnucleosides,Nucleosidesarenuc

3、leotideprecursors.,Inpurines,N9isconnectedtoC1ofthesugarcalledglycosidicbond.,Inpyrimidines,N1isconnectedtoC1ofthesugarcalledglycosidicbond.,Thetopareribonucleosides,withA,C,G,andU.,Nomenclature:Basehaspriority,sopositionsarenumbered1,2,3,etc.Sugarpositionsarenumbered1,2,3,etc.,Belowareallthedeoxyri

4、bonucleosides(Hand2),19-5,B.Nucleotides:1.Thephosphoesterbond,Innucleotides,thephosphoesterisatthe5-OH,TheesterisP(=O)O-RwhereRisthe5carbon.,RibonucleotideshaveanOHat2-carbon.,19-6,2.StandardAbbreviations,Nucleotidesarenamedafterthenucleoside.,Butabbreviationsaregivenrelativetothebase(A,G,C,U)and“MP

5、”formonophosphate.,Indeoxyribonucleotides,theabbreviationisprefacedby“d”for“deoxy”.,3.Lowenergyconformers,Sugaradoptsa“envelope”conformation(thatfoundinDNA).Forpyrimidines,theantinculeotideconformation(thatfoundinDNA)islargelyfavored.,NotetheenvelopeconformermaximizestheC8andC5distance.,Thesynconfor

6、merislessstablebecausethebulkofthebasestericallyconflictswiththesugar.,19-7,TheanticonformerofcourseisfoundindsDNA,19-8,4.ExamplesofHigherPhosphates,deoxyguanosinediphosphate(dGDP),deoxyguanosinetriphosphate(dGTP),Thehigherphosphatescontainthehighenergyphosphoanhydrideconnectingphosphates,Eachanhydr

7、ideisworth7.5kcal/molofenergy.,19-9,C.NucleicAcidsandthePhosphodiesterBond,Nucleicacidsarelinearpolymersofnucleotides.,ThephosphodiesterbondconnectsribonucleotidesinRNAanddeoxyribonucleotidesinDNA.,19-10,Twostrandsruninoppositedirections(calledantiparallel)Basesinoppositestrandspairbycomplementaryhy

8、drogenbonding,including:Adenine(A)-Thymine(T)Guanine(G)-Cytosine(C),D.Featuresofdoublestranded(ds)DNA,NaturalDNAisfunctionallydoublestranded.,Directionisrelativetothesugarbackbone,one5to3,thesecondis3to5.,Complementarityisbothafunctionalandstructuralimperative,A-Tarecomplementary,formingtwohydrogenb

9、ondsbetweenchains.,G-Carecomplementary,formingthreehydrogenbondsbetweenchains.,19-11,1.ChargoffsRule:%A=%Tand%G=%C,Chargofffoundtheinitialevidenceforcomplementarityinisolatingandweighingdeoxynucleotidebasesfromnaturalsources.,NotethatG-Careinequalmolaramount.,AndA-Tareinequalmolaramount,Thepurine/py

10、rmidineratiois1.0independentG+Ccontent.,19-12,2.DoublestrandedDNA,Theleftstrandruns5to3(toptobottom).,Therightstrandisantiparallel,running3-5.,Theyellowlinesarehydrogenbondsbetweenthebases,threeforG-CandC-G,TwoforA-TandT-A.,ConvinceyourselfthatthepolaritiesareuniqueforG-C,A-T,C-G,andT-A,19-13,3.TheW

11、atson-Crickdoublehelix,StructureofB-DNASugarphosphatebackboneoutsideStackingcreatestwounequalgrooves(majorandminor),Theantiparallel,complementary,doublestrandedDNAfoldsintothedoublehelix.,Thesugar-phosphatebackboneformstheouterribbon.,Thebasepairsareplanar(maximizesH-bond),Andstackperpendiculartothe

12、ribbonaxis,Thebackbonewrapsaroundaverticalaxis.,Themajorgrooveiswideandopen.,Theminorgrooveisshallow.,19-14,(1)Hydrophobiceffects.Buryingpurineandpyrimidineringsinthedoublehelixinterior(2)Stackinginteractions.StackedbasepairsformvanderWaalscontacts(3)Hydrogenbonds.Hydrogenbondingbetweenbasepairs.(4)

13、Charge-chargeinteractions.Electrostaticrepulsionofnegativelychargedphosphategroupsisdecreasedbycations(e.g.Mg2+)andcationicproteins,4.Stabilizinginteractions,Thehydrophobiceffectisthereleaseoforderedwaterintobulksolution.,ItsthearomaticringsA-TandG-Cpairs,thatstack.,TheH-bondsofcourserequirecompleme

14、ntarity:A-TandG-C,Thephosphatesarespacedrelativetotheribbonmovementalongtheaxis.,19-15,5.MeltingDenaturation,AnnealingRenaturation,SeparationofthetwoDNAstrandsiscalledDenaturation.Thisprocessiscalledmeltingwhentemperatureisdenaturant,2.Therenaturationprocess,theassociationoftwocomplementarystrands,i

15、scalledannealing.,DenaturationistheseparationofstrandsindsDNA.,Thisseparationcanbeinducedbyheatandchaotropicagents.,Whenthedenaturantisremoved,thetwostrandswillannealtoreformdsDNA,19-16,6.PositiveandNegativeSupercoiling,Supercoilingallowsthereformationofthedoublehelixwhenover-orunder-wound.,Forexamp

16、le,cut,unwind,andligatecircularDNA.,Whenreleased,theDNAsupercoils,sounwoundregioncanreformthedoublehelix.,19-17,7.Topoisomerasehandlesupercoils,Cellscontaintopoisomerases(andgyrases)thataddorremovesupercoilsduringreplicationandtranscription.,TheproteingraspstheDNAonallsides.,Hereahelicalbundledomain

17、contactsDNA.,HereabetasheetdomaincontactsDNA.,Hereanalpha/betadomaincontactsDNA.,19-18,E.Chromosomepacking:1.Nucleosomes,EukaryoteDNAhasthecomplexityofbeinghighlypackedinacell.,CoresareformedbywrappingsupercoiledDNAaroundhistonecores,Thenucleosomesarelike“beadsonastring.”,19-19,2.NucleosomespackinSo

18、lenoids,Thenuclosomesfurthersupercoilandpackintosolenoids(cylinders).,Solenoidsundergotwoadditionalstagesofpackingandcondensationtogivechromatin.,19-20,RibosomalRNA(rRNA)-anintegralpartofribosomes,accountsfor80%ofRNAincellsTransferRNA(tRNA)-carryactivatedaminoacidstoribosomesforpolypeptidesynthesis(

19、smallmolecules73-95nucleotideslong)MessengerRNA(mRNA)-carrysequenceinformationtothetranslationcomplexSmallnuclearRNA(snRNA)-havecatalyticactivityorassociatewithproteinstoenhanceactivity,F.RNA:1.SingleStrandedRNAFunction,FunctionalRNAissinglestranded,butoftenformsinternal(intramolecular)doublehelical

20、segments.,rRNAisthesiteofproteinsynthesis.,tRNAtransfersaminoacidsintranslation.,mRNAcodesforproteinsequence.,tRNAtransfersaminoacidsintranslation.,snRNAisinvolvedineukaryoticmRNAprocessing.,19-21,2.RNAstructureAhairpin,RNAissinglestranded,butitcanform3-Dstructures.,RNAissinglestranded,butitcanform3

21、-Dstructures.,Thisexampleisahairpincontainingacomplementariy,antiparalleldoublehelix.,Thehairpinisanintra-molecularassociation.,18-22,Chapter18,MetabolismofNucleotides,A.OverviewofNucleotideMetabolism,Dietarynucleicacidsareusedprimarilyasanenergysource,Nucleicacidsaresynthesizedalmostexclusivelyfrom

22、denovo(fromscratch)synthesis,Theabsenceofsalvagingcausesdisease,butitsfunctionisunknown,18-23,Mechanism,Fig27-3,B.PurineBiosynthesis:Step1:SugarActivationcatalyzedbyribose-5-phosphatepyrophosphatekinase(R5PPPkinase),PRPP,synthesizedfromR-5-P,isaprecursortoallribonucleotides,includingsalvage,via3path

23、ways.,18-24,Fig27-3,cont.,PropertiesofGln:PRPPamidotransferase,2.Catalyzesratedeterminingstep(RDS)forpurinebiosynthesis.,3.Negativeallostericeffectors:GMP,GDP,GTP,AMP,ADP,ATPbutnotthedeoxyforms(willdiscussinlaterslide).,Step2:AdditionofN9toC1ofSugar:Gln:PRPPamidotransferase,1.Mechanistically,thisisa

24、directdisplacementfollowedbyamidehydrolysis,TheaminogroupofPRbAcomesfromtheamideNofGln,andbecomesN9ofthepurinebase.,Inotherwords,PRbAiscommittedtopurinenucleotidebiosynthesis,18-25,NegativemeansthepresenceoftheseeffectorsreducesPRbAsynthesis,Fig27-3,cont.,3.PyrophosphataseandChemicalCoupling(Step1,F

25、ig18.5),Pyrophosphatasereleases-7.6kcal/molofchemicalenergyinhydrolyzingthephosphoanhydrideofppitotwoinorganicphosphates.,Hydrolysisofppibypyrophosphatasereleasesenergyandisirreversible,aprocessthatdrivesaPRPPPRbAtocompletioninonedirection.,18-26,But,ppiisaproduct,andcontainsonephosphoanhdrdideworth

26、-7.5kcal/mol,PRbAofcourseiscommittedtopurinenucleotidebiosynthesis,Chemically,theGlnamideisaweaknucleophile,Andamidebondsareverystable,SoPRbAisisanuphillclimbenergetically,Fig27-3,cont.,Metabolitesrequired:Glycine(N7,C4,C5)Glutamine(N3)Aspartate(N1)2N10-formyltetrahydrofolate(C2,C8)Carbondioxide(C6)

27、,4.Steps2to10:PRbAtoIMP(Figure18.5),Inosine5-phosphate(IMP),PRbA,1,2,3,4,5,6,BiosynthesisofthepurinenucleotidesrequiresR-5-P,Gly,CO2,Asp,thevitaminfolicacid,Gln,andenergy(8ATP).,Notethatthepurineisassembledontheribose5-phosphate.,18-27,IMP,witha6-oxopurine,isthefirstpurinenucleotidesynthesized.,Fig2

28、7-6,5.IMPisaBranchPointinPurineBiosynthesis(Fig18.7),Enzymes:a.IMPDehydrogenase(regulatory;inhibitedbyGMP)b.GMPsynthetase,Enzymes:c.adenolyosuccinatesynthetase(regulatory;inhibitedbyAMP)d.adenolyosuccinatelyase,AMPsynthesisrequiresaC6oxo/aminoexchangeandanelimination,Branchpointallowssynthesisofbothpurines,andbothbranchesarecontrolled,18-28,GMPfromIMPrequiresanoxidationandanoxo/aminoexchangeatC2,