chapter6structureofDNAandRNA

WelcometoMyMolecularBiologyLectureMolecularBiologyoftheGene,5/E---Watsonetal.(2004)PartI:ChemistryandGeneticsPartII:MaintenanceoftheGenomePartIII:ExpressionoftheGenomePartIV:RegulationPartV:MethodsPartII:MaintenanceoftheGenomeDedicatedtothestructureofDNAandtheprocessesthatpropagate(传递),maintain(保持)andalter(改变)itfromonecellgenerationtothenextMaintenanceoftheGenomeCh6:ThestructuresofDNAandRNACh7:Chromosomes,chromatinsandthenucleosomeCh8:ThereplicationofDNACh9:ThemutabilityandrepairofDNACh10:HomologousrecombinationatthemolecularlevelCh11:Site-specificrecombinationandtranspositionofDNAPROPAGATE&MAINTAINALTERCHAPTER6TheStructuresofDNAandRNAHowdothestructuresofDNAandRNAaccountfortheirfunctions?OUTLINE1.DNAStructure2.DNATopology3.RNAStructureDNASTRUCTUREStructure:twopolynucleotidechainsaretwistingaroundeachotherintheformofadoublehelix.SchematicmodelSpace-fillingmodelDNASTRUCTURE(1)DNAiscomposedofpolynucleotidechainsNucleoside&Nucleotide,thefundamentalbuildingblockofDNAglycosidicbondphosphoesterbondNucleoside3’5’AsymmetricDNApolarity:isdefinedbytheasymmetryofthenucleotidesandthewaytheyarejoined.Phosphodiesterlinkages:repeating,sugar-phosphatebackboneofthepolynucleotidechainBasesinDNApurinespyrimidinesAdenine(A)Guanine(G)Cytosine(C)Thymine(T)N9N1DNASTRUCTURE(2)Eachbaseshasitspreferredtautomericform(RelatedtoCh9)Thetwostrandsofthedoublehelixareheldtogetherbybasepairinginanantiparallelorientation,Whichisastereochemical(立体化学的)consequenceofthewaythatadenineandthymine,andguanineandcytosine,pairwitheachother.(Relatedtoreplicationandtranscription)DNASTRUCTURE(3)TheTwoChainsoftheDoubleHelixHaveComplementarySequencesExample:Ifsequence5’-ATGTC-3’ononechain,theoppositechainMUSThavethecomplementarysequence3’-TACAG-5’DNASTRUCTURE(4)Watson-CrickBasePairing(Relatedtoreplicationandtranscription)Thestrictnessoftherulesfor“Waston-Crick”pairingderivesfromthecomplementaritybothofshapeandofhydrogenbondingpropertiesbetweenadenineandthymineandbetweenguanineandcytosine.A:CincompatibilityHydrogenBondingIsImportantfortheSpecificityofBasePairingDNASTRUCTURE(5)ThehydrogenbondsbetweencomplementarybasesdeterminesthespecificityofbasepairingHydrogenbondingalsocontributetothethermodynamicstabilityofthehelix(?)Stackinginteractions(p-p)betweenbasessignificantlycontributetothestabilityofDNAdoublehelixH2Omoleculeslineduponthebasesaredisplacedbybase-baseinteractions,whichcreatesdisorder/hydrophobicityThedoublehelixhasMinorandMajorgrooves(What&Why)DNASTRUCTURE(5)(SeetheStructuralTutorialofthischapterfordetails)Itisasimpleconsequenceofthegeometryofthebasepair.TheMajorgrooveisrichinchemicalinformation(Whatarethebiologicalrelevance?)DNASTRUCTURE(6)Theedgesofeachbasepairareexposedinthemajorandminorgrooves,creatingapatternofhydrogenbonddonorsandacceptorsandofvanderWaalssurfacesthatidentifiesthebasepair.A:H-bondacceptorsD:H-bonddonorsH:non-polarhydrogensM:methylgroupsThedoublehelixexistsinmultipleconformations.DNASTRUCTURE(7)TheBform(10bp/turn),whichisobservedathighhumidity,mostcloselycorrespondstotheaveragestructureofDNAunderphysiologicalconditionsAform(11bp/turn),whichisobservedundertheconditionoflowhumidity,presentsincertainDNA/proteincomplexes.RNAdoublehelixadoptsasimilarconformation.DNAstrandscanseparate(denature)andreassociate(anneal)DNASTRUCTURE(8)Keytermstounderstand1.Denaturation(变性)2.Hybridization(杂交)3.Annealing/renature(复性)4.Absorbance(吸收度)5.Hyperchromicity(增色性)6.Tm(meltingpoint)(熔点)DNATOPOLOGYDNATOPOLOGY(1)Structure(1):Linkingnumberisaninvarianttopologicalpropertyofcovalentlyclosed,circularDNA(cccDNA)Linkingnumberisthenumberoftimesonestrandhavetobepassedthroughtheotherstrandinorderforthetwostrandstobeentirelyseparatedfromeachother.SpeciesofcccDNA1.Plasmidandcircularbacterialchromosomes2.LinearDNAmoleculesofeukaryoticchromosomesduetotheirextremelength,entrainmentinchromatinandinteractionwithothercellularcomponents(Ch7)Structure(2):LinkingnumberiscomposedofTwistandWritheThelinkingnumberisthesumofthetwistandthewrithe.Twististhenumberoftimesonestrandcompletelywrapsaroundtheotherstrand.WritheisthenumberoftimesthatthelongaxisofthedoublehelicalDNAcrossesoveritselfin3-Dspace.DNATOPOLOGY(2)LocaldisruptionofbasepairsFunction(1):DNAincellsisnegativelysupercoiled;nucleosomesintroducesnegativesupercoilingineukaryotesNegativesupercoilsserveasastoreoffreeenergythataidsinprocessesrequiringstrandseparation,suchasDNAreplicationandtranscription.StrandseparationcanbeaccomplishedmoreeasilyinnegativelysupercoiledDNAthaninrelaxedDNADNATOPOLOGY(3)Function(2):Topoisomerases(P115-119)1.Thebiologicalimportanceoftopoisomerase?2.Thefunctionaldifferenceofthetwotypesoftopoisomerases?3.TheworkingmechanismoftopoisomeraseDNATOPOLOGY(4)RNASTRUCTURERNASTRUCTURE(1)RNAcontainsriboseanduracilandisusuallysingle-strandedBiologicalrolesofRNA1.RNAisthegeneticmaterialofsomeviruses2.RNAfunctionsastheintermediate(mRNA)betweenthegeneandtheprotein-synthesizingmachinery.3.RNAfunctionsasanadaptor(tRNA)betweenthecodonsinthemRNAandaminoacids.4.RNAservesasaregulatorymolecule,whichthroughsequence