生物化學(xué)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(xì)胞核化學(xué)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(qiáng)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(jìn)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(bǔ)堿基）不是DNA雙螺旋結(jié)構(gòu)穩(wěn)定的主要作用力，因?yàn)闅滏I的能量很小。

磷酸基負(fù)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(fù)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(diǎn))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(xué)（Epigenetics）研究不涉及DNA序列改變的基因表達(dá)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(jī)制的一門新興的遺傳學(xué)分支。表觀遺傳就是不基于DNA差異的核酸遺傳。即細(xì)胞分裂過程中，DNA序列不變的前提下，全基因組的基因表達(dá)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(dá)調(diào)控（如隔離子，增強(qiáng)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(xué)研究內(nèi)容表觀遺傳學(xué)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