分子生物学：Section A 细胞与大分子

Awonderfulmolecularworld!分子生物学重要单词

(1/5)molecularbiologystructurefunctioncentraldogmaDNAreplicationtranscriptiontranslationmechanismDNArecombinationevolution分子生物学结构功能中心法则DNA复制转录转译机理重组进化分子生物学重要单词(2/5)aminoacidproteinorganismcompositionconformationdynamicsaminogroupcarboxylgroupcarbonylgroupsidechain氨基酸蛋白质生物组成构象动力学氨基羧基羰基侧链分子生物学重要单词(3/5)hydrophobichydrophilicacidicbasicnegativechargepositivechargepeptidebondpartialdoublebondN-terminusC-terminus疏水的亲水的酸性的碱性的负电荷正电荷肽键部分双键氨基末端羧基末端分子生物学重要单词(4/5)freerotationpolymerproteinfoldingprimarystructuresecondarystructuretertiarystructurequaternarystructureα

helixβ

sheethydrogenbond自由旋转聚合物蛋白质折叠一级结构二级结构三级结构四级结构α螺旋β折叠氢键SectionA细胞与大分子原核细胞真核细胞ProteinDNARNAA1细胞分类ProkaryoticcellEukaryoticcell根据细胞类型划分有机体Prokaryotes（原核生物）(Simplestlivingcells)Eukaryotes（真核生物）Eubacteria（真细菌）Archaea（古细菌）Structuralfeatures1-10mm,nodistinctsubcellularorganelles,pili(纤毛),flagella(鞭毛)10-100mm,Organelles(细胞器)BiochemistryrRNAmoleculesaredifferentamongthesekingdoms(rRNAbasedphylogeny)Esterlinkage（酯键）Etherlinkage（醚键）Esterlinkage（酯键）Energyproduction,metabolismReplication,transcriptionandtranslationDifferentiationFormationofsporesEmbryoniccelldifferentiation重点PhylogenetictreedeterminedbyrRNAsequencecomparisons(rRNA序列比较得到的系统发育树）A1Cellularclassificationback典型原核细胞示意图(类核)(纤毛)(鞭毛)A1Cellularclassification(核糖体)Cellwall:topreventcelllysis细胞[菌]溶解

inenvironmentsoflowosmolarity低渗溶液Plasmamembrane:lipidbilayerandembedded植入的proteinsforsmallmoleculeexchangeGeneticmaterials:nucleiod(类核体singleandcircularchromosome),plasmid质粒Ribosmes:proteinsynthesismachineryPili纤毛:toallowthecelltoattachtoothercellsandsurfaceFlagella鞭毛:cellmovement典型真核细胞示意图A1CellularclassificationbackCytoskeletalFiber细胞骨架纤维：ControlstheshapeandmovementofthecellOrganizessomemetabolic

functionsDefinition:Thedaughtercellschangetheirpatternsofgeneexpressiontobecomefunctionallydifferentfromtheparentcellaftercelldivision.Themainmolecularreason:changeofthegenesbeingtranscribed,butnotthatoftheDNAcontent.Regulatedby

developmentalcontrolgenes,mutationsinthesegenesresultinabnormalbodyplans.A1CellularclassificationbackCellulardifferentiation(细胞分化)ForexampleSporeformation

芽孢形成amongprokaryotesandlowereukaryotesEmbryoniccelldifferentiate胚细胞分化intohighlyspecializedcellsamonghighereukaryotes.CrosswithCellBiologyCourseA2亚细胞器

Nucleus细胞核mitochondriaandchloroplasts,endoplasmicreticulum内质网,microbodies微体,organelleisolation细胞器的分离CrosswithCellBiology（核）DNAreplication

RNAtranscription&processing

Ribosomeassembly A2Subcellularorganelles（线粒体）Mainfunction:cellularrespiration/ATPproductionviaoxidativephosphorylationDNAreplication,RNAtranscription,proteinsynthesisNuclear-encodedMitochonrialproteins:synthesisandtransportationA2Subcellularorganelles（类囊体）（基粒）Photosynthesis,

thelight-dependentassimilationofCO2andH2OtoformcarbohydratesandO2

DNAreplication,RNAtranscription,proteinsynthesisAplantspecificorganelleA2Subcellularorganelles（叶绿体）Nuclear-encodedchloroplastproteins:synthesisandtransportationdrugoxidationanddetoxificatin(内质网)Proteinsynthesis蛋白质合成（酯类代谢）（药物的氧化和解毒）A2SubcellularorganellesMicrobodies(lysosomes,peroxisomesandglycoxysomes)（溶酶体，过氧化物酶体，乙醛酸循环体）Glyoxysomes（乙醛酸循环体）

arespecializedplantperoxisomeswhichcarryoutthereactionsofglyoxylatecycle（乙醛酸循环）.A2SubcellularorganellesOrganelleisolation:centrifugation(离心)DensitygradientcentrifugationRatezonal(velocity)centrifugation(速度区带离心)Equilibriumcentrifugation(等密度梯度离心)Differential(speed)centrifugation:A2Subcellularorganelles两者差异？例、蛋白质和核酸的分离和纯化A3生物大分子

Protein(SectionB)Nucleicacids(SectionC)Polysaccharides

LipidsComplexmacromoleculesMBcourse(X),

Biochemistry()

Immunology()A3MacromoleculesPolysaccharidesarepolymersofsimplesugarscovalentlylinkedbyglycosidicbonds(糖苷键).碘和淀粉的显色除吸附原因外，主要是由于生成包合物的缘故。什么是包合物呢?直链淀粉是由α-葡萄糖分子缩合而成螺旋状的长长的螺旋体，每个葡萄糖单元都仍有羟基暴露在螺旋外。碘分子跟这些羟基作用，使碘分子嵌入淀粉螺旋体的轴心部位，生成包合物。关于淀粉遇碘变蓝？包合物中，每个碘分子跟6个葡萄糖单元配合，淀粉链以直径1.3nm绕成螺旋状，碘分子处在螺旋的轴心部位。淀粉跟碘生成的包合物的颜色，跟淀粉的聚合度或相对分子质量有关。随分子质量的增加，包合物的颜色的变化由无色、橙色、淡红、紫色到蓝色。A3MacromoleculesLipids:individuallipidsarenotstrictlymacromolecules,largelipidmoleculesarebuiltupfromsmallmonomericunitsandinvolvedinmanymacromoleculeassemblyTriglycerides(甘油三酯)Complexmacromolecules(复杂大分子）Covalent(共价)ornoncovalentassociationsofmorethanonemajorclassesoflargebiomoleculeswhichgreatlyincreasesthefunctionalityorstructuralcapabilitiesofthecomplex.Nulceoprotein:nucleicacids+protein核蛋白

A3MacromoleculesGlycoprotein:糖蛋白carbohydrate+proteinLipoprotein:脂蛋白Lipid+proteinA4大分子的组装

Proteincomplexes(蛋白质复合体)Nucleoprotein(核蛋白)Membranes(膜)Noncovalentinteractions非共价相互作用proteincomplexes蛋白质复合体A4LargemacromolecularAssembliesNoncovalentinteraction被运送的货物绑在中央的头部区域，两条腿附着在微管上。在驱动蛋白的催化功能域发生的反应提供了双腿移动的能量。Crystalstructureof50SrRNAA4LargemacromolecularAssembliesNulceoprotein核蛋白(1)

associationsofnucleicacidsandproteinRibosome核糖体:ribosomalproteins＋rRNAsChromatin(染色质):Viruses:Telomerase

(端粒酶)

:RibonucleaseP：A4LargemacromolecularAssembliesdeoxyribonucleoproteinconsistingofDNA&histonestoformarepeatingunitcallednucleosomeproteincapsid衣壳+RNAorDNAreplicatingtheendsofeukaryoticchromosomes.RNAactsasthereplicationtemplate,andproteincatalyzes(催化)thereactiontRNAmaturation.Protein＋PRNANulceoprotein核蛋白(2)Plasmamembrane质膜Noncovalent非共价

interactionsTheforceofmacromoleculeassembly大分子组装的力A4LargemacromolecularAssembliesvanderWaalsforces:

noncovalentassociationsbetweenunchargedmolecules.

*Hydrogenbonds(dipole-dipole):nucleicacids

*Hydrophobic疏水的interaction:proteins Charge-chargeinteractions(saltbridges):chargedmoleculesCharge-dipole偶极,dipole-dipole:eitherorbothofthe participantsisadipole.Dispersion色散力

interactions:non-poplarmolecule瞬时偶极(偶极)(unchargedmolecules)B蛋白质结构1.1ProteinComposition1.2ProteinConformations1.3ProteinStructureandFunction:AFewExamples1.4TheDynamicsofProteins1.5Experiments1.1蛋白质的组成1.2蛋白质的构象1.3蛋白质的结构与功能：几个例子1.4蛋白质动力学1.5实验研究Proteinsarevitaltolife对生命而言蛋白质至关重要Lifeismostdirectlytheworkofproteins.Proteinsalloworganismstogrowandreproduce.Theyprovideshape,strengthandmovement.Inthecell,proteinsareeverywhereanddoalmosteverything.生命几乎就是蛋白质的杰作。蛋白质让生物可以生长和繁殖。它们为生物提供了外形和力量，以及运动功能。在细胞中，蛋白质无处不在，行使着几乎任何功能。B2 Proteinstructure－SizesAfewthousandsDaltons(×103)tomorethan5millionDaltons(×106)Someproteinscontainboundnonproteinmaterials(prostheticgroups辅基orothermacromolecules),whichaccountsfortheincreasedsizesandfunctionalitiesoftheproteincomplexs.Globularproteins:enzymesComplementaryfitofasubstratemoleculetothecatalyticsite(groove-like)onanenzymemolecule.

B2 Proteinstructure－Shapeschymotrypsin(糜蛋白酶)Fibrousproteins:importantstructuralproteins(silkfibroin,keratininhairandwools)Keratin(角蛋白)Protofibril

(初原纤维)microfibril

(微管)1.1ProteinComposition/蛋白质的组成Sidechain—COOHH2N—H氨基羧基侧链三个基团总是相同，不同的氨基酸具有不同的侧链R基团。氨基酸A1

→Proteinsarecomposedof20kindsofaminoacids

蛋白质是由20种氨基酸组成的96231.“Acidic”aminoacids:containingadditionalcarboxyl羧基

groupswhichareusuallyionizedCanformsaltbridges,arehydrophilic(亲水)asparticacid(Asp,D，天冬氨酸)glutamicacid(Glu,E，谷氨酸)B1Aminoacids-charged2.“Basic”aminoacids:containingpositivelychargedgroupsLysine(Lys,K,赖氨酸)Theimidazolegroup(咪唑基)hasapKanearneutrality.Arginine(arg,R,精氨酸)deaguanidinogroup(胍基）Histidine(His,H，组氨酸)3.polaruncharged：Containgroupsthatformhydrogenbondswithwater,

hydrophilic亲水的Asparagine(Asn,N，天冬酰氨)Containhydroxyl羟基groups.Serine(Ser,S，丝氨酸)Threonine(Thr,T，苏氨酸)Glutamine(Gln,Q，谷氨酰氨)B1Aminoacids-polarunchargedCysteine(Cys,C，半胱氨酸)hasathiol(巯醇)group，whichisoftenoxidizestocystine胱氨酸x-S-S-xGlycine(Gly,G，甘氨酸)Proline(Pro,P，脯氨酸):iminoacid(亚氨基酸)Methionine(Met,M，甲硫氨酸):containsasulfuratom4.Aminoacids-nonpolaraliphatic脂肪族的(hydrophobic疏水)Alkyl(烷基)sidechainsAlanine(Ala,A，丙氨酸)Valine(Val,V，缬氨酸)Leucine(Leu,L，亮氨酸)Isoleucine(Ile,I，异亮氨酸)Phenylalanine(Phe,F，苯丙氨酸)Tyrosine(Tyr,Y，酪氨酸)Tryptophan(Trp,W，色氨酸)5.aromatic芳香族Aminoacids：AccountsformostofUVabsorbanceofproteinsat280nm，hydrophobic（疏水的)A2

→Aminoacidsareconnectedbypeptidebonds氨基酸是由肽键连接在一起的Partialdoublebond/部分双键Partialdoublebond由于连接碳和氧的双键也在同一个碳和邻近的氮之间进行分配，电子密度的重新分布使得碳-氮键具有部分双键的特性。碳-氮键是肽键的核心成分，这种部分双键特性防止了肽键发生自由旋转。Rigidandflexiblebonds3Dstructure位于氨基酸里面的其它键是可以发生旋转的，因此氨基酸还是容易弯曲的。线性的蛋白质分子会发生弯曲、折叠和扭曲从而形成复杂的三维结构N-terminusandC-terminus/N-末端和C-末端在细胞中通常C-末端带有负电荷在细胞中通常N-末端带有正电荷1.2ProteinConformations/1.2蛋白质的构象1.2.1DescribingProteinStructure1.2.2ChemicalandPhysicalBasisforProteinFolding1.2.1描述蛋白质的结构1.2.2蛋白质折叠的化学和物理基础1.2.1DescribingProteinStructureβsheetαhelixPrimarystructureTertiarystructureSecondarystructureQuaternarystructurePrimarystructureSecondarystructure一级结构指多肽链中氨基酸的顺序二级结构指多肽中的区域通过折叠产生的最基本的结构形式。四级结构是由几条多肽链组成的蛋白质形状。三级结构是由不同二级结构组成的整条多肽链的更复杂的构象。αhelix/α螺旋Hydrogenbondα螺旋是多肽链的螺旋形弯曲弯曲中的一个N-H距离它3个氨基酸的羰基上的O发生相互作用，称为氢键。螺旋是靠链内氢键维持的。ProteinsmainlywithαhelicesHemoglobin/血红蛋白由两条α链和两条β链组成Keratin/角蛋白由处于α-螺旋或β-折叠构象的平行的多肽链组成βsheet/β折叠Hydrogenbondβ折叠相对扁平，氨基酸之间的结合与α螺旋相同。但发生相互作用的两个原子间的距离可以大大超过多肽链中的三个氨基酸，这种作用发生在多肽链中大致保持相互平行的不同区段之间。Parallelandantiparallelβsheets(b)Antiparallel(a)Parallel多肽链中一个区段自身往返折叠数次ProteinsmainlywithβsheetsFibroin丝心蛋白（β片层结构）Tertiarystructure/三级结构αhelixβsheetTurn多数蛋白质由α螺旋和β折叠两种结构混合而成，在一起以复杂的方式折叠产生更大的三级结构。Tertiarystructure

ofmyoglobin

肌红蛋白的三级结构Myoglobin:aproteinthatcarriesoxygeninmuscle.肌红蛋白：肌肉中运载氧的蛋白质。由一条肽链和一个血红素辅基组成的结合蛋白。三级结构，有8段α螺旋区。Quaternarystructure/四级结构Onesubunit每条多肽链都有各自的三级结构Quaternarystructureofimmunoglobulin

免疫球蛋白的四级结构LLHHOnesubunit由两条相同的轻链和两条相同的重链共四条肽链所组成ELISA酶联免疫吸附测定QuestionsQ1

→Whatforceshelptokeepthetertiarystructures?什么力帮助维持三级结构？Q2

→Whatfunctionsdoproteinshave?

蛋白质有哪些功能？Q3

→Areproteinstructuresfixed?

蛋白质结构是固定的吗？Q4

→Whatdeterminestheprotein’stertiarystructure?

什么决定了蛋白质的三级结构？Vocabulary(1/2)covalentbondhydrogenbondionicbondvanderWaalsforcehydrophobicinteractionsulfhydrylgroupdisulfidebondpartialpositivechargenon-polarmoleculecarbonicanhydrase共价键氢键离子键范德华力疏水相互作用巯基二硫键部分正电荷非极性分子碳酸酐酶Vocabulary(2/2)actinactinfilamentkinesininduced-fitmodellock-and-keymodelATPsynthetaseallostericregulationlacrepressorlactose肌动蛋白肌动蛋白丝驱动蛋白诱导-契合模型锁-钥模型ATP合成酶别构调节lac阻遏蛋白乳糖Q1

→Whatforceshelptokeepthetertiarystructures?什么力帮助维持三级结构？HydrogenbondsHexokinase/己糖激酶Physicalinteractionsinvolvedinproteinfolding1)Covalentbonding2)Hydrogenbonding3)Ionicbonding4)VanderWaalsforces5)Hydrophobicinteraction1.2.2ChemicalandPhysicalBasisfor

ProteinFolding1)Covalentbond/共价键SharedelectronsH－HH+1H+1+1+1Covalentbond:

Abondbetweentwoatomsinwhichelectronsareshared.共价键：两个原子共享电子形成的键。Covalentbondsinproteins

蛋白质中的共价键Covalentbond氨基酸的初级结构Disulfidebond/二硫键Covalentbond二硫键氢键发生在与有电负性的O或N原子连接的H原子上，O或N会改变H原子的电子密度，使H原子带部分正电荷。2)Hydrogenbond/氢键Hydrogenbond:

Relativelyweakinteratomicbondinvolvinghydrogenatomsthatarepartiallypositivelycharged.氢键：相对较弱的原子之间形成的键，由于氢原子上带有部分正电荷而引起。HydrogenbondPartialchargesvs.FullchargesClδ–δ+δ+Na部分电荷完全电荷Hydrogenbondsinproteins/蛋白质中的氢键Hydrogenbond氢键虽弱，但数量巨大，对蛋白质的折叠产生很大影响。3)Ionicbond/离子键Theionicbondofsodiumchloride,NaClNa+11Cl+17Ionicbonds:

Anattractionbetweentwoionsofoppositecharge.离子键：带相反电荷的两个离子之间的引力。Ionicbondsinproteins/蛋白质中的离子键GluLys4)VanderWaalsforces/范德华力Atom1Atom2vanderWaalsforceVanderWaalsforces:

Weakattractionscausedbyshiftsintheelectroncloudsaroundatoms.范德华力：由围绕原子的电子云发生变化产生的弱引力。(1837-1923)TheNetherlandsVanderWaalsforces

vs.

IonicbondAtom1Atom2VanderWaalsforcesTheatomitselfhasnegativeandpositivepartsTheinteractionis

transientIonicbondThewholeatomiseithernegativeorpositiveTheinteractionis

stableAtom1Atom2VanderWaalsforces

vs.

hydrogenbondAtom1Atom2VanderWaalsforcesTheatomitselfhasnegativeandpositivepartsTheinteractionis

transientHydrogenbondThewholeatomiseitherpartially

negativeor

positiveTheinteractionis

stableAtom1Atom2δ–δ+δ–δ+5)Hydrophobicinteraction/疏水相互作用Hydrophobicinteraction:

Interactionthatoccursbetweennon-polarmoleculesinthepresenceofwater.疏水相互作用：当非极性分子被置于水中发生的相互作用。?NonpolarmoleculesareforcedtogetherWatermoleculesgetcontactswitheachother.Hydrophobicinteractionsinproteins

蛋白质中的疏水相互作用非极性氨基酸被挤到了蛋白质的中心A1

→Fivetypesofforceshelptokeepthetertiarystructures五种力帮助维持三级结构CovalentbondvanderWaalsforceA2

→Proteinfunctionsaregreatlydiversified蛋白质功能极其多样Carbonicanhydrase–Catalysis（催化）Actin–Support（支撑）Kinesin–Movement（运动）------Whocangivemoreexamplesofdifferentproteinfunctions?Q

→Areproteinstructuresfixed?

蛋白质结构是固定的吗？1.4TheDynamicsofProteinsHexokinase/己糖激酶Glucose葡萄糖与该酶的结合会引起蛋白结构的变化，这样使葡萄糖分子接近ATP的末端磷酸基团。Induced-fitvs.lock-and-keymodels活性位点的结构不发生变化，这种催化机理称为锁-钥机理由于底物的结合引起较大结构变化从而促进催化作用的机理称诱导-契合机理酶-底物复合体Allostericregulation/别构调节指某些蛋白质的活性会因为结合到它的调控位点上的小分子而发生改变Theprimarystructuredeterminesprotein’stertiarystructure?

一级结构决定了蛋白质的三级结构TheAnfinsenExperiment/安芬森实验B2 Proteinstructure－motifs,DomainsandfamiliesStructuralmotifs（基序）:

GroupingsofsecondarystructuralelementsthatfrequentlyoccuringlobularproteinsOftenhavefunctionalsignificanceandrepresenttheessentialpartsofbindingorcatalyticsitesconservedamongaproteinfamilybabmotifDomains（结构域）:

structurallyindependentunitsofmanyproteins,connectedbysectionswithlimitedhigherorderstructurewithinthesamepolypeptide.TheycanalsohavespecificfunctionsuchassubstratebindingProteinfamilies（家族）:

structurallyandfunctionallyrelatedproteinsfromdifferentsourcesTheprimarystructuresofc-typecytochromesfromdifferentorganismsMotifB3 Proteinanalysis1.Purification:toobtainenoughpuresampleforstudy2.Sequencing:determinetheprimarystructureofapureproteinsample3.Massdetermination:determinethemolecularweight(MW)ofan interestedprotein.4.X-raycrystallographyandNMR:determinethetertiarystructureofagivensample.ProteinpurificationAnexperimentalsteptopurifytheinterestedproteinfromotherproteinsandnonproteinmoleculesexistinginthecellsAnessentialexperimentalstepwhenstudyanyindividualproteinTheprincipalpropertiesofproteinsusedforpurificationSize:gelfiltrationchromatography（层析）2.Charge:ion-exchangechromatography,isoelectricfocusingelectrophoresis3.Hydrophobicity:hydrophobicinteractionchromatography4.Affinity:affinity亲合