2018生化1试题与知识总结

1、Biochemistry(1)RevieweredbyJerryfromchem-bioBiochemistry(1)RevieweredbyJerryfromchem-biofundamental（很多很简单的知识点没有纳入，主要整理了一些非常重要的、容易忘、容易错的知识点，后来者如果有心的话欢迎补充修改重新上传 eredbyJerryfromchem-biofundamentalBiochemistryExamNotablequestionMultiplechoiceSimpleanswerNotableChapterBiochemistryoftheanismandChapter2Hyd

2、rogenChapterAminoChemical Cofactor(metalionsanic ShotgunChapterPeptideSecondaryGlobularproteinvs.Fibrousprotein(onlyasinglesecondary Random CollagencollagentripleSilkQuaternaryCollagencollagentripleSilkQuaternary Chapter5:proteinMyoglobin(8nded-)ReasonswhymyoglobinisthebestsolutionforoxygenO2 H+CO2

3、2,3-BPGImmuneCellularimmuneHumoralimmuneChapter6:MichaelisLineweaverBurkThe KineticReasonsfor Twosubstrate -pongmechanism(doubleEnzyme Reversibleinhibitors(这个可以分为三类，不要与上面irreversibleinhibitor的搞混 tdeterminetheactivityof tdeterminetheactivityofanFeedback AllostericCovalentRegulatory Zymogenactivationb

4、yproteolyticChapter7:D-eractionwithPeptidoglycaninbacterialcellLPSSugar ChapterChemistryofnucleicStructureofDNAandSecondaryStructureofChapter10:General sas Fats(solid)&OilsWax(solid)ButbotonlyusedasChapter10:General sas Fats(solid)&OilsWax(solid)ButbotonlyusedasasstructuralEther ,sometimesbelongto)

5、)Gangliosidebloodtypeantigen注意分清楚ganglioside和 asfunctionalSignalingEicosanoids paracrineDruginhibitorofsynthesisofSteroidhormones messagesnCortisolandSex Brassinolide(BR)inJasmonateEnzyme Fatsoluble:VitaminA,D,E,Chapter11:Biologicalitionandarchitectureofegralprotein(firmlytedthroughcovalentbondsor i

6、candhydrogenbondsorsometimesanchored tedbutsometimes icandhydrogenbondsorsometimesanchored tedbutsometimes SoluteMembranePassiveGlucoseActive F-typeATPase reversible:ATPABCSecondaryactiveIonchannels(nottobeconfusedwithiontransporterand Chapter12:GeneralSignaltransductionGeneralAdaptorprotein egratio

7、nDovetoworkthroughthesameMultiplelevelsofmessenger:outsidetheSecondmessenger:hecIP3andAgonistandSignaltransductioninponentGatedionGprotein-coupledClassesofG Receptorenzymetyrosine(inplantsSer&Thr)ActivationofgeneActivationofReceptorenzymetyrosine(inplantsSer&Thr)ActivationofgeneActivationofglycogens

8、eby CrosstalkninsulinpathwayandReceptorswithrinsicenzyme(EPO,acytokine)&JAK SolubleNO-activatedguanylylcyclase(withhemeandGuanylinandendotoxinNuclearreceptors(steroidSH2andProtein ProteinkinaseProteinProtein BiochemistryExamSimpleanswerNotablequestionMultiplechoiceSimpleanswerKM isameasureoftheenzym

9、esbindingaffinityforbstrate,isthisementcorrect?No.Onlywhenk-1k2,NotablequestionMultiplechoiceSimpleanswerKM isameasureoftheenzymesbindingaffinityforbstrate,isthisementcorrect?No.Onlywhenk-1k2,KM=k-1/k1=KES,thenKM isameasureofthestrengthoftheES：MMequationWhatisthemolecularbasisforthe tether-linkedfat

10、tyacidsmaytoBecause ectricdensityandpolarityoftheetherHowisthelocationofphosphatidylinositolcriticaltoitsThe functions racellular Signaling, Exocytosis, s of Nucleation for supramolecular complex inside the leadtothelocationofthecytoplasmic(inner)sideofthecell357-e you had three polysaccharides, amy

11、lose, amylopection, and glycogen, each with the same number monosaccharide subunits. Which would be degraded the fastest, polysaccharidesallworkedatthesamet the enzymes acting to degrade What is the relationshipamong glycosaminoglycans, proteoglycans,fibrous egrins, proteins, theextracellularmatrix?

12、ItmaybehelpfultodiagramthecellularlocationsofeachoftheseActineractwithfibrous FibrousDescribe the similarities and selectiven transporter-mediated ed and transport via an Similarities: both types of transport require a t spans the bilayer (probably several times) andDescribe the similarities and sel

13、ectiven transporter-mediated ed and transport via an Similarities: both types of transport require a t spans the bilayer (probably several times) and forms tprovidesapaththroughwhichaspecificsubstratecancrossthemembrane.ofsubstrateonlydownitsconcentration:Transportsaresaturable;therateoftransportrea

14、chesaVmaxathighsubstrateconcentrations.Ionarenot saturable.Whiletransportersspeeduptherateatwhichtheirspecificsubstrate cancrossthemembrane,theof flux through ion-selective channels can be orders of magnitude n for transporters. Transporters permanently “open” to their substrate,as longasthe concent

15、ration gradient exist. Ion channels are transient gates; they open or close in response to a specific signal. cytosol游离的都是可溶性的蛋白质。VitaminAntithrombinwithbloodclottingfactorXa,bindstoofcsynthesisaionchangesS198inchymotrypsinwithD,explainwhysacatalytic-specificityofionfromsmallersidegroupstolargerside

16、groupswillcausetheenzymetoselectivelycatalyzethereactionsmaller Notable Adrenal,adrenergic, Rectangularhyperbola Adrenal,adrenergic, Rectangularhyperbola Ether&esterChapterBiochemistryofthe celltransportAbout30elementsareessentialfor Stereoisomer:differentconfiguration,(notincludingconformation)incl

17、udinggeometricisomerandopticalisomersvs.Configurationvs.anismandAutotroph vs. heterotroph chemotrophvs.SolarenergyastheultimatesourceofallbiologicalConfigurationvs.anismandAutotroph vs. heterotroph chemotrophvs.Solarenergyastheultimatesourceofallbiological ( H等vs.endergonicanabolicH等complexbiomolecu

18、lesSpeedupreactionthroughtwoways:coupling,Chapter2HydrogenHdonorsandHreceptorsare bothelectronegative46kJ/molforbondswithneutralatoms,610kJ/molforbondswithonechargedHexagonalice:eachH2Oforms4HbondswithInwater:Covalentbonds:100Handersonbach Bufferingcapacity: Buffersystemsin he histidine,efficientbuf

19、feratneutralpH(sidechainpKR =ChapterAminoL-aminoacidsinproteininAromatic: notettheRgroup Polar, unchargedChapterAminoL-aminoacidsinproteininAromatic: notettheRgroup Polar, uncharged ryptophanisnotMostoftheabbreviationsarethe Glutamine, & AsparagineThererenoB,J,O,U,X,threelettersofthewordsofaminoacid

20、s.Apartfrom:Isoleucine,Attention:Glycine,Lysine(thedifference:G;Cor Chemical Note:carboxylgroupisoreninnincarboxylicacids-C缺电子whereasaminogroupisslightlylesspI:withoutionizablesidechainsvs.withionizableLeastEquilibriumofthereactionfavorshydrolysis,butpeptidebondsarestableN left, CConjugated Containc

21、hemicalgroupsnCofactor(metalionsanicCoenzyme Cellmembrane Cofactor(metalionsanicCoenzyme Cellmembrane Saltingout:(NH4)2SO4 (two Activityvs.Specific1U=1mol/min ,SDS1SDS:2aaOnlydependson Sangersmethod:FDNB(1-F-2,4-diN-bezene)&concentratedEdmandegradation:phenylisothiocyanate(PTH)&CF3COOH50ShotgunTryps

22、in: C-terminal K, R Chymotrypsin:C-terminalF,W,Y Pepsin: N-terminal L, F, W, Y or Chemicalsynthesis:fromCtoN!FmocandinsolublepolymerConsensusChapterPeptidetransconfiguration(withrespecttothetwo-C)Theplanarpeptidebond:partialond:C-nException:prolinecis-trans fullyextend:both常须注意特例：Proline很特殊! ionally

23、Globularproteinvs.Fibrousprotein(onlyasinglesecondaryphi:right(NtoC)handedhelixwith3.6residues(5.4angstrom)perhydrogenbond:carbonylRi pairwi helix former: Ala, Leu minoN+(maybemorenegativelychargedaa)Clargecoiledcoil: phi: 90180 -sheet:3.5foreachparallelbetasheetsvs.antiparallelbetasheets Beta sheet

24、 former: Gly, urns:4aa;Proition2(TypeI),Glyition3(TypeHydrogenbondwith1urns:4aa;Proition2(TypeI),Glyition3(TypeHydrogenbondwith1&Random Fibrousprotein(singletype2ndstructure)vs.Globularprotein(multithepatternofdisulfidebonds:tertiarystructurelongeractionnjustadjacent betabarrelissimultaneouslyamotif

25、andCalciumalpha helixtwo-chaincoiledcoil:*2to*2to*4ermediate Connectivee,no nded *3tonded Connectivee,no nded *3tonded Antiparallel beta sheet AlaandGlycloselypackS Extremelyerior2His:bindFe2+,Quaternaryheatand halsAllorNoneMolecular ronin:helpthosenon-spontaneousTwoenzymes:PDI(-S-S-),PPI(Procis-tra

26、nsPhe:A-helixtoAMolecular ronin:helpthosenon-spontaneousTwoenzymes:PDI(-S-S-),PPI(Procis-transPhe:A-helixtoAChapter5:proteintionconstantKa,tionconstantKd (P50 as),tionrateka,tionrate Boundfraction: 被bind了Induceditive&Myoglobin(8nded-)ReasonswhymyoglobinisthebestsolutionforoxygenO2 ispoorlysolubleina

27、queousProteinside-chainslackaffinityforSometransitionmetalsbindO2 wellbutwouldgeneratefreeradicalsiffreeinchashemeare more utFe2+infree hemecouldbeoxidizedtoFe3+iftwoanometallicmoleculesshareanoxygenprotoporphyrinIXwithferrousbindingO2:414nm;unbinding:429HisF8heme Fe2+O2 HisO2 P50:0.26kPa(Febondanda

28、lsohydrogenbondfromHisCO:1/20000,butonly200O2 P50:0.26kPa(FebondandalsohydrogenbondfromHisCO:1/20000,butonly200O2 ion,CO2 andH+CO2 Strongesteractionsoccurnthoseunlike:1and O2 Concerted()&SequentialAnemicindividualvs.COpoisonedindividual:binding（注意：CO实际上是增强了O2 的affinity 的H+ BohrCO2 directly(negativel

29、ychargedcarbamateformsadditionalionpairs)andindirectly(yield2,3-BPG NegativelychargedBPGbindsRe:BPGbindingpocket Fetalhemoglobin(22,HbF)vs.maternalhemoglobinImmuneCellular immune 注意：also Keyplayers:macrophages,killerTcells(Tc),andinflammatoryTcellsImmuneCellular immune 注意：also Keyplayers:macrophages

30、,killerTcells(Tc),andinflammatoryTcellsMacrophageisonekindofHumoralimmune tope,IgGmost ! ficationofSandwichficationof Chapter6:Globular protein or ribozyme Holoenzyme,apoenzyme,apoprotein【区分】Activesite&CatalyticEssence: specific binding to the transition se stronger compared to the ground selowerthe

31、activationenergy:GMThisalsogiveseractions with the transition e (not ground e!) e AcidbaseMetalioncatalysis CovalentcatalysisMichaelis= = ( = )S = ,2AcidbaseMetalioncatalysis CovalentcatalysisMichaelis= = ( = )S = ,2HighKm meanslowES = 2EtS = Earlystage(Pisnegligible)ofSteadye(notpre-steadye!): = Li

32、neweaverBurk 11Doublereciprocalplots:1/V0 vs.=+ bindtoES 1 & bindtoES 1 & bindtoEandES = tdeterminetheactivityofanFeedbackAllosteric itiveAllosteric Sigmoidcurve(donotfollowM-MOften:changeKm butdonotchangeVmax;lesscommon:changeVmax butdonotchangeCovalentRegulatorySequestrationZymogen activationbypro

33、teolyticChapter7:Dihydroxyacetonehasnochiralprojectionformula: RegulatorySequestrationZymogen activationbyproteolyticChapter7:Dihydroxyacetonehasnochiralprojectionformula: D-projectionOHhemostdistanttothecarbonylgroup)ontheL-form:-OHontheD-D-Hemiacetalandhemiketal(monosaccharides)thenacetalandketal(

34、disaccharidesorandstereoisomer(anomer!):6-Candacetal-COHdifferent:alpha;6-Candacetal-C-OHsame:beta Pyranose and furanoseChairforms:-CH2OHstretchingAldoseandTriose:smallestsugar(nottobeconfusedwithPentose:D-e,2-deoxy-D-eHexose:D-glucose(onlyDinvivo),D- uronicldehydeand still has one hemiacetalglucopy

35、ranose 的变构的（ still has one hemiacetalglucopyranose 的变构的（SucroseFru(21)Glc:consistsoftwoacetals! Lactose Gal(14)GlcO-glycosidicbonds:hydrolyzationbyacidbutnotbystarchandglycogen:compact;curvednlinearchains;tightlycoiledhelicalrachainhydrogencelluloseandchitin:linearstraight AmyloseAmylopectin (14) (a

36、t branched pos:16)branching:every2430 Only one reducing endExtensivelybranched:every812moreHydrogenbondbetntwoparallelHardexoskeletonsofarthropodsandcellwallsofmany Extracellularmatrix:ECMnthecell,viscosityandlubricationins,tensilestrengthinconnectiveOnlyexistinRepeatingdisaccharidealNAc)&uronicAtta

37、chingthemembraneproteinorsecretedp OnlyexistinRepeatingdisaccharidealNAc)&uronicAttachingthemembraneproteinorsecretedp ConnectiveBacteriacellOneormore sulfatedglycosaminoglycanandatypicaltetrasaccharidebridgetoprotein(GlcA-Gal-Gal-Xyl) the amino residue in protein is Ser. anderactionwithConformation

38、alactivationofantithrombin(AT)withNS,bindsbloodclottingfactorEnhancedprotein-eractionbytwo(ATandCoreceptorfor extracellular ligands:FGF(fibroblastgrowth factor)and itsreceptor Cell surface localization/concentration: negatively charged NS electrosicallyholdCanbedetectedbyYeast-two-hybridsystemLCIBiF

39、CFRET) Peptidoglycaninbacterial cellAntibioticslikepenicillinpreventpenta-glycinecrosslink Lysozyme hydrolyzes glycosidic bondAggregate: aggrecan core protein with chondroitin and keratan sulfate ( 与 -keratin 区分), both of which are eractsstronglywithcollageninextracellularmatrixofcartilage,contribut

40、ingtothedevelopmentandstrengthofthisconnectiveAntibody, milk proteins,lectin Carbohydratesmallerbutmorediverse!Twotypesofglycosidicbonds:O-linked(Ser)andN-linkedAntibody, milk proteins,lectin Carbohydratesmallerbutmorediverse!Twotypesofglycosidicbonds:O-linked(Ser)andN-linkedInfluencetheproteinProte

41、ctproteinfromattackingbyenzymes Increase the structural diversity LPSThedominantsurfacefeatureoftheoutermembraneofgram-negativehatcausesOutersurfaceoftheplasmaSuchasABOSugar StructureType of linkage (1 2, 1 3, 1 4, 1 6, 2 3, etc) Configuration ( and )Branchingorcell e hatbindstooligosaccharides,read

42、sugarediatedmovementofimmuneBacteriaediatedgastriculcerformation:lectinChapterhatbindstooligosaccharides,readsugarediatedmovementofimmuneBacteriaediatedgastriculcerformation:lectinChapter nucleosideadenosineguanosineosineuridinecytidinethymidineidinenucleosidebase的单词，有一个规律就是 nucleoside 的单词长度 相对应的 ba

43、se 的单词长度base:adenine,guanine,uracil,cytosine,thymine Pyrimidine1NtoPurine9NtoChemistryofnucleicHydrolysisofRNAunderalkalineconditions:thephosphatewillwithholdthe2,3-C3-monophosphaten5-C!Mixture of2-StructureofDNAand A,B(mostcommonnatureform,ndedhelix),Znded)formsofB:10.5bpper turn;asepair3.4 Hairpin

44、(onestrand,palindrome),cruciform(twostrands,TriplexDNA:H-DNA,Hoogsteenbasepair(polypurineorpolypyrimidine IncreaseofUVabsorptionItdependsonpH,ionicstrength,andsizeandbaseitionoftheStructureofernalIncreaseofUVabsorptionItdependsonpH,ionicstrength,andsizeandbaseitionoftheStructureofernal G=Ubasepairal

45、so be Depurination:not Methylation:inbacteria这个功能比较特殊andineukaryoticcellsCpGsequencesuppressChapter10:sGeneral ，length:numberofondsition Themostcommon:evennumbersofcarbon,unbranchedchain,1224carbons,ifondsthen9,12,15,naturally Neverconjugatedonds,alwaysusemethylgrouptoPhysicochemical MoreondsmoreRed

46、ucetheproportionofsaturatedfattyacids:lowertheriskofheartAbnormal accumulation of membrane accumulate,resultinginveryseriouss can cause diseases: If sugarAbnormal accumulation of membrane accumulate,resultinginveryseriouss can cause diseases: If sugar cannot be removed, the sasFats(solid)&Oils Advan

47、tagesofusingTAGasstoredfuels:twosOxidationlpy&FatsalsohavefunctionofWax(solid)ButbotonlyusedasLongchainfattyacidswithlongchainFunction（需要注意ChiefstoragefuelsforsomeProtectskinandhair(includingthefeathersofPreventswaterevaporationinProtectagainst asstructurals LecithinnottobeconfusedwithlectinXcholine

48、lecitho- 卵黄前缀Cephalin:X=serineorX=nolamineasstructurals LecithinnottobeconfusedwithlectinXcholinelecitho- 卵黄前缀Cephalin:X=serineorX=nolaminecepha- 头的前缀EtherPlasmalogen: with ether-linked alkene, more stable, exist in heart ti Pla et-activating es, halophilic bacteria, ciliated protists, s sMostabunda

49、ntmembranesinbiosphere(becausethethylakoidmembranesinplantshasalotofsSulfonatedglucoses(sometimesbelongto,sometimesbelongto)1Sphingosine+1fattyacid+1When X=H,then):phosphocholineorMyelin:membranetinsulatestheaxonsofsome(neutralOutersurfaceofcellCerebroside:X=ide:X=di-,tri-,or tetra-Gangliosidebloodt

50、ypeantigen!注意分清楚gangliosideX=oligosaccharidewithoneormoreresiduesofN-acetylneuraminicacid(sialicacid)attheExtremeLongchain(32C),branched,bothendsether-linkedwithalwayshydroxylCholesterol(-OHExtremeLongchain(32C),branched,bothendsether-linkedwithalwayshydroxylCholesterol(-OHpolarheadat3-C,steroidnucl

51、eus,andalkylsidechains)majorsterolinanimalBileacids:asfunctionalSignaling Eicosanoids paracrine (derivedfromarachidonicacid花生四烯酸Stimulatemusclecontraction,bloodflow,thewake-sleepcycle,andresponsivenesstohormonesignalsbyregulatingsynthesisof.Formationofbloodclotsandthereductionofbloodflowtothe siteof

52、aContractionofthemuscleliningtheairwaystog.roductionofleukotrienescausesasthmaticDruginhibitorofsynthesisofElevatedlevelofprostaglandinandthromboxanecancausepainandAspirin:inhibitionofprostaglandinH2SteroidhormonesmessagesDerivativesofsterolsbutlackthealkyn Cortisolandhecortexoftheadrenalgland,regul

53、ationofglucosemetabolismandsaltSexCortisolandhecortexoftheadrenalgland,regulationofglucosemetabolismandsaltSexBrassinolide(BR)inPromoteseedStimulatestemelongationandvascularEnhancepartitioningofphotoassimilatesfromsourcetoIncreasepollentubeAccelerateJasmonate CausepollenAccelerateEnzymePlant:isopren

54、eBirdfeathers:carotenoidVitamins(somearehormones,somegments,someareFatsoluble:VitaminA,D,E,SynthesizedbycondensationofmultipleisopreneVD:fromsterol,function:regulationofCaleadstodefectiveboneformationanddiseaseestineandCalevelsinkidneyandbone;DeficiencyofvitaminVA: from -carotene, two functions: hor

55、mone (deficiency leads to dryness of skin and eye, and mucous retardationofdevelopmentvisualpigment: 原理hVE(tocopherols):aromaticring+longisoprenoidchain(hydrogenated),function:cellmembrane,antioxidants(preventformationoflipofusin);Deficiency:fragileit, itionandarchitectureofMembrane enzymeAnotheregr

56、alprotein(firmlytedthroughcovalentbondsor itionandarchitectureofMembrane enzymeAnotheregralprotein(firmlytedthroughcovalentbondsorBacteriorhodopsin(-helix:20heTyrandTrphelpanchoringtheegralproteinwith-barrelstructure(-sheet79aaspanaAstransportersandionAsArecentraltooxidativephosphorylationandCell-ce

57、llandantigen-cellInvolvedinexocytosisandhitropic protein (sometimes ted but sometimes MembraneFluidmosaicTwoesofbilayer e(gel)vs.fluidMotionofsingle ,hop Solute3 Membrane Solute3 Membrane AsinglelongPassiveGlucoseInside:polarresidues;outside:non-MichaelisMentenActive ctivetransporter(3typesofATPases

58、andABCP-type Ca2+pump:phosphorylationfavorsthe conformationwithlowaffinitytoCa2+binding;Phosphorylationfavorsthe conformation with low affinity to Ca2+ binding. ( ): CatalyzetheuphilltransmembranepassageofprotonsdrivenbyATPhydrolysis. 4 H+ per ATP ABCCatalyzetheuphilltransmembranepassageofprotonsdri

59、venbyATPhydrolysis. 4 H+ per ATP ABCPumpoutof 2ATPs&2sSecondary active Lactosetransporter:rockingmotionsubstratebindingandprotonmovement Na+ - glucose symporter (driven by high extracellular Na+)Ionophores(suchasvalinomycin)andCN-candisruptsecondaryactive OligomericcomplexofseveralIonchannels(nottob

60、econfusedwith iontransporterandSinglelargepeptidewith4s(eachwith4-)Voltagesensor:has itively-chargedActivationgate:frompolarized(close)todepolarized(open) Inactivation gateTether:pulldown,inactivationgateopens;pullup,inactivationgatehe 5Afterbinding:s(eachwith4-)ion:hydrophobicHigh selectivity! （sta