生物化學英文版課件：Chapter 8 Nucleotides and nucleic acids

Chapter8NucleotidesandnucleicacidsNucleicacidstructureNucleicacidchemistryOtherfunctionsofnucleotides2013-10-28

Proteins,carbohydrates,lipids,nucleicacidsarethefourcategoriesofmacromolecules,necessaryforlife.Nucleicacidsplayacriticalroleinthestorageandfunctionofgeneticinformationinalllivingorganisms.“Ageneticmaterialmustcarryouttwojobs:duplicateitselfandcontrolthedevelopmentoftherestofthecellinaspecificway.”-FrancisCrickOverviewSwissphysicianFriedrichMiescher

(1844-1895，細胞核化學的創(chuàng)始人，DNA發(fā)現(xiàn)者)during1869-1871FelixHopper-Seyler’slablocatedinTubingen’scastleThenucleinisolatedfromsalmonsperm(鮭魚精子)byF.MiescherDiscoveryofNuclein

(核素的發(fā)現(xiàn))FriedrichMiescher’sinterestingfindings:HumanGenet2008,122:565-581

Aim:determinethebiochemicalcompositionoflymphocytes(later,changedtoleukocytes);thenovelsubstancecouldbeprecipitatedbyacidifyingandre-dissolvedwithalkalinesolution;Thenucleiwasseparatedfromcytoplasm,thenewsubstancewereobtainedfromnuclei;Containedalargeportionofphosphorous;Resistanttoproteasedigestion

Conclusion:unlikeproteinsorlipids,itwascallednuclein((histone+DNA))

Speculate:storephosphorousoractasareservoirforothermoleculesderivedfromnuclei.

FriedrichMiescher’spaper(“Onthechemicalcompositionofpuscells”)(Medical-ChemicalInvestigation)Discoveryofa“TransformingPrinciple”FrederickGriffith,in1928

-Pneumonia(Diplococcus

pneumoniae,肺炎雙球菌)

infectsmice. -Micedeveloppneumoniaanddie.

Twotypesofbacteria:

-Sbacteriasmoothcoat–pneumonia，外包有莢膜，不能被白血球吞噬，具有強烈毒性

-Rbacteriaroughcoat-nopneumonia，外無莢膜，容易被白血球吞噬，沒有毒性

.

1881-1941

EnglisharmymedicalofficerGriffith’sTransformingExperiment

（Searchforgeneticmaterial）Searchforgeneticmaterial:

1928FrederickGriffith:transformingprincipleBacterialcoloniesRoughnonvirulent(strainR)InjectionResultsMousehealthySmoothvirulent(strainS)MousediesHeat-killedsmoothvirulent(strainS)LivestrainSbacteriainbloodsamplefromdeadmouseMousediesMousehealthy+Roughnonvirulent(strainR)Heat-killedsmoothvirulent(strainS)Griffith’sexperimentidentifyingthe“transformingprinciple”1877-1955OswaldAvery–Americanbacteriologist(TransformationwasdueexclusivelytoDNA)SR

DNAS1943,ProcessofeliminationwasappliedExtractstreatedwith:Proteases(todestroyprotein)

RNase(todestroyRNA)

DNase(todestroyDNA)Virulent,StrainSNonvirulent,StrainRHershey-Chase1952

(prove

thatDNAwasthehereditarymaterial)

Conclusion:TheactivecomponentofthebacteriophagethattransmitstheinfectivecharacteristicistheDNA.NucleicacidstructureNucleotidesNucleotide(核苷酸):(1)nitrogen-containingbase(2)apentose(3)aphosphateNucleoside(核苷)RNA:D-ribose

DNA:2’-deoxy-D-ribosePyrimidineandPurinebases嘧啶嘌呤胞嘧啶尿嘧啶胸腺嘧啶腺嘌呤鳥嘌呤Nomenclature核苷核苷酸腺嘌呤核苷腺嘌呤核苷酸ConformationsofriboseequilibriumRibofuranoseringscanexist4conformations1’2’3’4’5’

(A)(G)(C)(T)(U)BasesinDNA:AGCTBasesinRNA:AGCUDNARNAMinorpurineandpyrimidine

bases(nucleosides)SomeadenosinemonophosphateswereformedbyRNAhydrolysisAlteredorunusualbasesinDNAoftenhaverolesinregulatingorprotectingthegeneticinformation

DNAmethylationMinorbasesofmanytypesarefoundinRNA,especiallytRNARNAandDNAarechainsofeitherribonucleoside

monophosphatesordeoxyribonucleoside

monophosphatescovalentlyjoinedtogetherby

phosphodiesterlinkages(primarystructure).

Longchainsofnucleotidesarecalled

polynucleotides;

Shortchainsofnucleotidesarecalled

oligonucleotides.PhosphodiesterlinkagesinthecovalentbackboneofDNAandRNA

Thephophodiesterlinkageshaveadirection(calledpolarity;theconventionis5'to3',fromlefttoright)

Thearrangement(ororder)of

specificnucleotidesalongthechainiscalledthesequencecontaininggeneticinformation.RNAishydrolyzedunderalkalinecondition,butDNAisnot.

Propertiesofnucleotidebases

weaklybasicandaromaticcompounds;

pyrimidinesareplanar,andpurinesareverynearlyplanar;existintwoormoretautomericformsdependingonpH;

hydrophobicstacking

（疏水堆疊）interactionwhichisimportantinstabilizingthethreedimensionalstructure;

hydrogen-bondingisthemostimportantmodeofinteractionbetweentwocomplementarystrandsofDNA.TautomericformsofUracil

(互變異構(gòu)式)pH=7內(nèi)酰胺內(nèi)酰胺亞胺內(nèi)酰胺雙亞胺Nucleicacidsarecharacterizedbyastrongabsorptionat260nmBasepairs:AtoT(orU)GtoCHydrophobicbasestackinginteractionsareimportantinstabilizationofnucleicacidstructuresHydrogen-bonding堿基堆積力是指在DNA雙螺旋結(jié)構(gòu)中，堿基對平面垂直于中心軸，層疊于雙螺旋的內(nèi)側(cè)，相鄰疏水性堿基在旋進中彼此堆積在一起相互吸引形成的作用力，在維持DNA雙螺旋結(jié)構(gòu)的穩(wěn)定性中發(fā)揮最重要的作用。

氫鍵（互補堿基）不是DNA雙螺旋結(jié)構(gòu)穩(wěn)定的主要作用力，因為氫鍵的能量很小。

磷酸基負電荷，與介質(zhì)中陽離子形成離子鍵，對DNA雙螺旋結(jié)構(gòu)也有一定的穩(wěn)定作用。穩(wěn)定DNA雙螺旋結(jié)構(gòu)的三種作用力Nucleicacidstructure(In1968,WatsonwroteTheDoubleHelix,oneoftheModernLibrary's100bestnon-fictionbooks)Establishmentofthestructurewasbasedon:i)DNAcomposition(polydeoxyribonucleotide);ii)X-raydiffractionofDNAfiber;iii)Chargaff’sdiscoveryJamesWatson(1928-)WatsonwenttouniversityinChicagoatage15,andteamedupwithCrickinCambridgeinlate1951.Aftersolvingthedoublehelix,hewentontoworkonvirusesandRNA.Healsohelpedlaunchthehumangenomeproject,andispresidentofColdSpringHarborLaboratoryinNewYork.FrancisCrick(1916-2004)

Cricktrainedandworkedasaphysicist,butswitchedtobiologyaftertheIIWorldWar.Afterco-discoveringthestructureofDNA,hewentontocrackthegeneticcodethattranslatesDNAintoprotein.CompetewithJamesWatsonFrancisCrickCambridgeUniversityRosalindFranklinMauriceWilkinsKing’sCollegeCaltechUniversityLinusPaulingTheprecipitatingeventsIn1953,triplexmodelwaspublishedin

PNAS

(Vol34:84-97)LinusPauling(1901-1994):titanoftwentieth-centurychemistryWatson&Crick’searlymodelofDNAshowedthatthestructure:However,Franklindisprovestheirmodel.

WasaTripleHelix

TheBaseswereontheoutside

Sugarphosphatebackbonewasontheinside1920–1958RosalindFranklin-EnglishChemistthemostbeautifulX-rayphotographs,crucialcontributionstothesolutionofthestructureofDNAin1952Thespotsformingacrossinthecenterdenoteahelicalstructure.Theheavybandsattheleftandrightarisefromtherecurringbases.X-raydiffractionofDNAIn1951,MauriceWilkinsgivesJamesWatsonRosalindFranklin’swork.Watson:“TheinstantIsawthepicturemymouthfellopenandmypulsebegantorace.”InTwoFormsofDNAweresolvedviaX-raydiffractionin1951byRosalindFranklin.A–DryFormB–WetFormTwoformsofDNAPhoto51Chargaff(ErwinChargaff:1905-1995)rules:

ThebasecompositionofDNAvariesfromspeciestoanother;DNAspecimensisolatedfromdifferenttissuesofthesamespecieshavethesamebasecomposition;InallcellularDNAs:quantitativerelationshipbetweenthebases(A=T;G=C)A+G=T+C=50%EvidenceofDNAStructure

UsingFranklinandWilkins’workthatDNAwasintheformofaDoubleHelix

Using

Chargaff’sRuletofigureouthowthe4BasesmatchupinpairsPhoto51Theyphysicallybuiltmodelsoutofwire,sheetmetal,nutsandboltstocomeupwiththestructureofDNAIthasnotescapedournotice…Ithasnotescapedournoticethatthespecificpairingwehavepostulatedsuggestsapossiblecopyingmechanismforthegeneticmaterial.Watson-CrickmodelforthestructureofDNA

Watson-CrickModel

ItconsistsoftwohelicalDNAchainswoundaroundthesameaxistoformaright-handeddoublehelix;Thehydrophilicbackbonesofalternatingdeoxyribose

andphosphategroupsareontheoutsideofthedoublehelix;Thepurineandpyrimidinebasesofbothstrandsarestackedinsidethedoublehelix;Hydrogen-bondedbasepairs:GC;A=T;TwocomplementaryDNAstrandsareantiparallel.Helixdiameteris2.0nanometers.Helixriseperbasepairis0.34nanometers.Helixpitch(distancealongtheaxisper360degreeturn)is3.4nanometers.Tenbasepairsperhelicalturn.(B-DNAhasanaverageof10.5

basepairsperhelicalturn.)ReplicationofDNAassuggestedbyWatsonandCrickWatson,Crick&WilkinswontheNobelPrizein1962

("fortheirdiscoveriesconcerningthemolecularstructureofnucleicacidsanditssignificanceforinformationtransferinlivingmaterial")RosalindFranklin,didbrilliantworkdevelopingthetechniquetophotographasinglestrandofDNA.Shereceivedlittlerecognitionforthisatthetimeanddiedtragicallyofcancerin1958.DNAoccurinthree-dimensionalforms

conformationofdeoxyribose;rotationaboutthebondsofthephosphodeoxyribosefreerotationabouttheC-1’-N-glycosylbondFreerotationabouttheC-1’-N-glycosylbond,resultingintwoconformations,synandanti

A,B,andZformsofDNA

(differentthreedimensionalforms)36basepairComparisonofA,B,andZformsofDNA(occurrenceisuncertain)RighthandhelixBformDNARighthandhelixAformDNA

majorgrooveisdeepminorgrooveisshallowerLefthandhelixZformDNAminorgrooveisnarrowanddeepBasepairsarerotatedinZ-DNA

Double-strandedRNAandDNA-RNAhybridduplexesessentiallyonlyexhibittheA-formsecondarystructure.NonaturallyoccurringlongDNAmoleculehasbeenshowntobeentirelyintheformofZ-DNA.

RegionsofnaturallyoccurringDNAcanformZ-DNA.

Regionsofalternatingpurine-pyrimidine(forexample,CGCG,etc.)aremorepronetoformZ-DNA.DNAcanassumeothersecondarystructurescalledA-DNAandZ-DNA

TheconformationofthebaserelativetothesugarisimportantforZ-DNA.BasesareONLYintheanti

conformationinA-DNAandB-DNA.Pyrimidinesusuallycannotadoptthesyn-conformation.InZ-DNAthealternatingCGCGhasalternatinganti-syn

conformations.FormationofaregionofZ-DNAinB-DNAunwindstheDNA(achangefromaright-handedhelixtoaleft-handedhelix).CertainDNAsequencesadoptunusualstructuresPalindromes:sequencesofdouble-strandednucleicacidswithtwofoldsymmetry.Minorrepeat:asymmetricsequencewithineachstrand..回文序列鏡像重復Hairpinsandcruciformsstructures

（十字形結(jié)構(gòu)）areformedbasedonpalindromicDNA(RNA)sequences發(fā)夾結(jié)構(gòu)HairpinsandcruciformsstructuresareformedbasedonpalindromicDNA(RNA)sequences十字形結(jié)構(gòu)DNAstructurescontainingthreeorfourDNAstrandstriplexDNAHoogsteenpairing:non-Watson-CrickparingN-7O6N6TriplehelixDNAGuanosine

tetraplex(Gtetraplex)QuadruplexDNA

（四股螺旋）PeptideNucleicAcid

(PNA)

PNAisanucleicacidanaloginwhichthesugarphosphatebackboneofDNAhasbeenreplacedbyasyntheticpeptidebackboneusuallyformedfromN-(2-amino-ethyl)-glycineunits,resultinginanachiralandunchargedmimic.

PeptideNucleicacid(PNA)

Achiral,peptide-likebackbone

Backboneisuncharged

Highthermal

stability

High-specificityhybridizationwithDNA

ResistanttoenzymaticdegradationItcandisplaceDNAstrandofduplex

PyrimidinePNAstrandscanform2:1

triplexeswithssDNABiotechnologicalapplicationsRNABacterialmRNAMessengerRNAs(mRNAs)codeforpolypeptidechainsInbacteriaandarchaeaMonocistronic:asinglemRNAcodesforonlyonepolypeptidePolycistronic:asinglemRNAcodesfortwoormoredifferentpolypeptodes.單順反子多順反子Single-strandedRNA(right-handed)RNAtypes:mRNA(messengerRNA)

tRNA(transferRNA)

rRNA(ribosomalRNA)

miRNA(microRNAs)

siRNA(smallinterferingRNAs)

Base-stackinginteractionSecondarystructureofRNAsRNAbaseparingpattern:

GpairswithC,ApairswithUA-formright-handedhelix

(A-formispredominant)Base-pairedhelical(secondary)structuresinanRNAM1RNAcomponentofE.Coli

RNasePNon-Watson-CrickG=UbasepairThree-dimensionalstructureinRNATounderstandtherelationshipbetweenRNAstructureAnditsfunction!tRNAribozymeanintronDNAdenaturationandannealing

reversibleprocess

temperatureorextremepHaffectstheprocess

hydrogenbondsarebrokenEachDNAspecieshasaacharacteristicdenaturationtemperature(tm,meltingtemperature)TmdependsonpHandionicstrengthandthesizeandDNAbasecomposition.PartiallydenaturedDNAwasvisualizedbyElectronmicroscopy

Thearrowspointtosingle-strandedbubbleswhereDNAdenaturation

occurred.FormationofhybridduplexesofDNAIfthetwoDNAshavesignificantsequencesimilarity,theytendtoformduplexesorhybrids.Nonenzymaticreactionsofnucleotides

APsite(abasicsite脫堿基位點)N-

-glycosyl

bondAlterationinDNAstructureleadstomutation

Cytosinedeamination(uracil)occursinaboutoneper107

cytidineresiduesinoneday.DNAdepurinationoccursatahigherrateforpurine(oneper105

purines)thanforpyrimidines.RNAdepurinationismuchslowerandnotsignificant.

AbasicsitesarethemostfrequentlyoccurringcellularDNAdamage(generatedspontaneously).

Formationofpyrimidine

dimersinducedbyUVlightTwotypes:

Cyclobutanethyminedimer6-4Photoproductcyclobutane

thyminedimerChemicalagentsthatcauseDNAdamage(promotedeamination)Anexampleofguaninemethylation(methylguaninecannotbase-pairwithcytosine)dimethylsulfateDNAmethylation

DNAmethylationisabiochemicalprocessthatisimportantfornormaldevelopmentinhigherorganisms.Additionofamethylgrouptothe5positionofthecytosine

pyrimidineringorthenumber6nitrogenoftheadenine

purinering,iscatalyzedbymethylase.Thismodificationcanbeinheritedthroughcelldivision.Adenosineresidueswithinthesequence5’GATC3’aremethylated.Ineukaryoticcells,5%ofcytidineresiduesaremethylated,mostcommonat

CpGsequences.DNAmethylationatthe5positionofcytosinehasthespecificeffectofreducinggeneexpression(vertebrate).CommonInbacteriaCommonineukaryoteSaturday,December2,2023表觀遺傳學（Epigenetics）研究不涉及DNA序列改變的基因表達和調(diào)控的可遺傳變化的，或者說是研究從基因演繹為表型的過程和機制的一門新興的遺傳學分支。表觀遺傳就是不基于DNA差異的核酸遺傳。即細胞分裂過程中，DNA序列不變的前提下，全基因組的基因表達調(diào)控所決定的表型遺傳，涉及染色質(zhì)重編程、整體的基因表達調(diào)控（如隔離子，增強子，弱化子，DNA甲基化，組蛋白修飾等功能),及基因型對表型的決定作用。Saturday,December2,2023Saturday,December2,202383表觀遺傳學研究內(nèi)容表觀遺傳學的研究內(nèi)容：基因轉(zhuǎn)錄后的調(diào)控基因組中非編碼RNA微小RNA（miRNA）反義RNA