生物化学简介-课件

生物化学Biochemistry1ppt课件绪论大纲：课程主要内容及要求引子：生物化学的历史和发展趋势2ppt课件教材：《生物化学》，第三版，王镜岩等主编，

2002年，高教出版社参考书：1.Biochemistry,

JeremyM.Berg,JohnL.Tymoczko,LubertStryer5theditionW.H.FreemanandCompany2.Biochemistry,DonaldVoet,JudithG.Voet.3rdedition,2003,JohnWiley&Sons,Inc.NewYork.

3ppt课件生物化学（上）60学时其中上课时间：54学时4ppt课件第一章绪论(3学时)（周丛照）第二章蛋白质(15学时)（周丛照）§2.120种氨基酸的结构和性质（2学时）§2.2蛋白质中的二级结构（1学时）§2.3蛋白质的高级结构（3学时）§2.4血红蛋白和免疫球蛋白的结构与功能（3学时）§2.5维持蛋白质高级结构的作用力（1学时）§2.6蛋白质折叠和结构进化（2学时）§2.7蛋白质分离纯化（3学时）

第三章核酸（6学时)§3.1核酸和核苷酸的结构、性质和功能（3学时）§3.2核酸的研究方法（3学时）5ppt课件第四章糖（3学时）§4.1糖的生物学作用（1学时）§4.2单糖和多糖（1学时）§4.3糖蛋白（1学时）第五章脂类和生物膜（6学时）§5.1脂的分类和性质（3学时）§5.2生物膜（2学时）§5.3膜蛋白（1学时）6ppt课件第六章酶（15学时）§6.1酶的发展历史、作用特征及催化机理(3学时)§6.2酶的分类及酶功能的多样性（2学时）§6.3核酶（1学时）§6.4酶促反应动力学（3学时）§6.5酶的抑制作用（3学时）§6.6别构酶及其作用原理（3学时）

第七章维生素与激素（6学时）（周丛照）§7.1维生素与辅酶（3学时）§7.2激素及其作用原理（3学时）7ppt课件生物化学（下）40学时其中上课时间36学时8ppt课件第八章代谢总论（3学时）§8.1代谢及代谢途径的相关概念（1学时）§8.1生物能学（2学时）第九章生物膜和物质运输（3学时）§9.1物质跨膜运输的方式（0.5学时）§9.2小分子物质的运输（1学时）§9.3离子载体（1学时）§9.4生物大分子的跨膜运输（0.5学时）第十章糖酵解（6学时）§10.1糖酵解概述（1学时）§10.2糖酵解的第一阶段（2学时）§10.3糖酵解的第二阶段（2学时）§10.4糖酵解的调控（1学时）9ppt课件第十一章柠檬酸循环（3学时）§11.1柠檬酸循环的准备阶段（0.5学时）§11.2柠檬酸循环的反应机制（2学时）§11.3柠檬酸循环的调控（0.5学时）第十二章生物氧化（6学时）§12.1生物氧化基本概念和呼吸链（1.5学时）§12.2氧化还原电位和自由能变化（0.5学时）§12.2氧化磷酸化（4学时）第十三章光合作用（3学时）§13.1光合作用概况（1学时）§13.2光合磷酸化和CO2固定（2学时）10ppt课件第十四章糖原的分解和生物合成（3学时）§14.1糖原的降解和糖原的生物合成（2学时）§14.2糖原代谢的调控（1学时）第十五章脂肪酸代谢（3学时）第十六章氨基酸的分解代谢（3学时）第十七章核酸代谢（3学时）11ppt课件WhatisBiochemistry?

thestudyofthosemoleculesusedandmanufacturedbylivingthings.12ppt课件Threeaspectsofbiochemistry:

1)Biochemistryisconcernedwithstructuralchemistry.Itseekstodeterminethestructuresofmoleculesfoundinlivingsystemsinordertounderstandstructure-functionrelationships.StructuralBiology13ppt课件2)Biochemistryisconcernedwithchemicalchange,thisisreflectedinthestudyofmetabolicpathwaysMetabolism14ppt课件3)BiochemistryisconcernedwithinformationwhichhasaccumulatedthroughevolutionandispreservedinDNA(orsometimesRNA).MolecularBiologyTheCentralDogma15ppt课件BiochemistrythroughevolutionHowtobuildalifewithmolecules?OrTheMolecularDesignofLife

16ppt课件胰岛素由A、B两个肽链组成。人胰岛素(InsulinHuman)A链有21个氨基酸，B链有30个氨基酸，共51个氨基酸组成。其中A7(Cys)-B7(Cys)、A20(Cys)-B19(Cys)四个半胱氨酸中的巯基形成两个二硫键，使A、B两链连接起来。此外A链中A6(Cys)与A11(Cys)之间也存在一个二硫键。人工合成胰岛素17ppt课件1958年，中国科学院在王应睐、曹天钦、邹承鲁、钮经义、沈昭文等先生的带领下，提出了“世界上第一次用人工方法合成的蛋白质在中华人民共和国实现”的宏伟目标。1959年初，人工合成胰岛素的工作全面展开。首先是由钮经义、沈昭文、龚岳亭几位研究人员组织有关人员解决了氨基酸的大量供应问题。

1965年，完成了结晶牛胰岛素的合成，它有着极为深远的意义。由于蛋白质和核酸两类生物高分子有生命现象中所起的主要作用，人工合成了第一个具有生物活力的蛋白质，便突破了一般有机化合物领域到信息量集中的生物高分子领域之间的界限，在人类认识生命现象的漫长过程中迈出了重要的一步。合成胰岛素工作的简报发表于1965年《中国科学》。18ppt课件Fourtransitionsthroughevolution:1,chemicals,micromolecules

2,macrobiomolecules3,energy4,stressresponse19ppt课件Theevolutionofliferequiredaseriesoftransitions,beginningwiththegenerationoforganicmoleculesthatcouldserveasthebuildingblocksforcomplexbiomolecules.20ppt课件Thenextmajortransitionintheevolutionoflifewastheformationofreplicatingmolecules.EvolutionRequires:Reproduction,Variation,SelectivePressure21ppt课件Variationwasintroducedbyanumberofmeans,fromsimplebasesubstitutionstotheduplicationofentiregenes.RNAappearstohavebeenanearlyreplicatingmolecule.Furthermore,someRNAmoleculespossesscatalyticactivity.However,therangeofreactionsthatRNAiscapableofcatalyzingislimited.Withtime,thecatalyticactivitywastransferredtoproteins,linearpolymersofthechemicallyversatileaminoacids.RNAdirectedthesynthesisoftheseproteinsandstilldoesinmodernorganismsthroughthedevelopmentofageneticcode,whichrelatesbasesequencetoaminoacidsequence.Eventually,RNAlostitsroleasthegenetothechemicallysimilarbutmorestablenucleicacidDNA.Inmodernorganisms,RNAstillservesasthelinkbetweenDNAandprotein.22ppt课件EnergyTransformationsAreNecessarytoSustainLivingSystemsATPservesasthecellularenergycurrencythatlinksenergy-yieldingreactionswithenergy-requiringreactions.ATPitselfisaproductoftheoxidationoffuelmolecules,suchasaminoacidsandsugars.Withtheevolutionofmembraneshydrophobicbarriersthatdelineatethebordersofcellsiongradientswererequiredtopreventosmoticcrises.ThesegradientswereformedattheexpenseofATPhydrolysis.Later,iongradientsgeneratedbylightortheoxidationoffuelmoleculeswereusedtosynthesizeATP.

23ppt课件CellsCanRespondtoChangesinTheirEnvironments

Thefinaltransitionwastheevolutionofsensingandsignalingmechanismsthatenabledacelltorespondtochangesinitsenvironment.Thesesignalingmechanismseventuallyledtocell-cellcommunication,whichallowedthedevelopmentofmore-complexorganisms.Therecordofmuchofwhathasoccurredsincetheformationofprimitiveorganismsiswritteninthegenomesofextantorganisms.(molecularevolution)24ppt课件HistoryofBiochemistry(upto1982)25ppt课件

1835JonsBerzelius

chemicalcatalysis,usesamylase(淀粉酶)asanexample.1859CharlesDarwinpublishes

OntheOriginofSpecies.LouisPasteur

fermationcatalyzedbyenzymes,"essence"ofyeast.1865GregorMendelpublisheshis

theoryofgenetics.1869FredrickMeischerdiscovers

DNAincellnuclei.EduardandHansBuchnerextractsmaterielfromyeast,conversionofglucosetoalcohol.26ppt课件

1914FritzLipmann,theroleofATPinenergymetabolism.1926JamesSumner,

crystallinejackbean(刀豆)urease,isaprotein.1926ThomasHuntMorganwrites

TheTheoryoftheGene.1934ArnoldBeckmandevelopes

thefirstpHmeter.1937HansKrebsdiscoversthecitricacidcycle(TCAcycle).1941GeorgeBeadle&EdwardTatum,theone-gene,one-enzymehypothesis.OswaldAvery,ColinMacLeod,andMaclynMcCarthy

DNAisthegeneticmaterial.27ppt课件

1950EdwinChargaff

A=T,G=C(Chargaff'srules).1952LinusPaulingandRobertCorey

α-helixandtheβ-pleatedsheet1953JamesWatsonandFrancesCrickthedoublehelixmodelofDNA.1953FredrickSangerthefirstaminoacidsequenceofaprotein(insulin).1956EarlSutherlandisolatescyclicAMP.1957MatthewMeselsonandFranklinStahl

semiconservativeDNAreplication.28ppt课件

1960JohnKendrewandMaxPertuzobtain

thefirst3-Dstructureofproteins

(hemoglobinandmyoglobin).1960JeraldHuritzandSamuelWeissdiscover

RNApolymerase.1961FrancoisJacobandJaquesMonodpropound

theoperonmodelofgenecontrol.1963Jean-PierrreChanguex,F.Jacob,andJ.Monod

Allostericmodelforinhibitionofenzymes1964Severalgroups

Acrylamidegelelectrophoresisofproteinsisdeveloped29ppt课件MarshalNirenberg,H.GobindKhorana,andSeveroOchoacompletetheelucidationofthegeneticcode1965DavidPhillips

3-Dmodeloffirstenzyme(lysozyme)1965RobertHolleydetermines

thestructureofatransfer-aaRNA.1965JeromeVinograddiscovers

superhelicaltwisting.1968MarkPtashneandWalterGilbertidentify

thefirstrepressorgenes1969Firstsynthesisofanenzyme(ribonuclease).30ppt课件

1970HamiltonSmithdiscovers

restrictionendonucleases.1970HowardTeminandDavidBaltimorediscover

reversetranscriptase.1973StanleyCohenandHerbertBoyerprepare

recombinantDNA.1974Sung-HouKim,etal.produce

thefirstX-raystructureoftransferRNA.1977CesarMilsteindiscovershowtoproduce

monoclonalantibodies.1977AllanMaxamandWalterGilbertdevelop

achemistryforsequencingDNA.1977FredrickSanger,S.NicklenandA.R.Coulsondevelop

achemistryforsequencingDNA.1977PhillipSharpandRichardRobertsdiscover

introns(interveningsequences).1982AmzelLM,McKinneyM,NarayananP,PedersenPL

Firstx-raystructureofamembraneprotein(9Å).31ppt课件1980sandearly1990sWonderfultimeforMolecularBiology32ppt课件HumanGenomeProject(1988-)CentralDogma(CrickF.1958)MolecularBiologyOmics:

MetabolomicsTranscriptomicsProteomics

StructuralGenomics

(1998-)

Genomics33ppt课件TheeraofOmics:(1998-2003orlater?)Omics=Oh!Mix!(millenniumchaos?)34ppt课件Whatis

StructuralGenomics?Itisanapproachaimingatsolving

3-Dstructures

oftheproteinsencodedbyan

entiregenome.

KimSH.NatureStructuralBiology199835ppt课件OriginalgoalsofSG:1,toestablishacatalogue/libraryofallfoldscoveringtheentireproteinuniverse2,tohelptheannotationofsequencedgenomes36ppt课件InternationalStructuralGenomicsProjectsUSAandCanada:(1998-)9NIHStructuralGenomicsCentersEU:France(3centers:Paris-Sud,Marseille,Strasbourg)Germany(StructuralGenomicsFactory)UK(2centers)(SPINE:StructuralProteomicsinEurope,2001-)Asia:Japan(RIKEN…)China(Yun-YuSHI;ZiheRAO…)(2002-)Korea:Israel:WeizmannStructuralProteomicsCenter37ppt课件Flowchart:1,Targetsselection:Bioinformatics2,PCRandcloning:MolecularBiology3,Proteinproduction:Biochemistry4,Datacollection(X-raydiffraction/NMR)5,Structuredetermination:StructuralBiology6,Functioninterpretation:GeneralBiology38ppt课件Corecharacteristics:Highthroughput(hundredstothousandssamples)Large-scale(milligramlevelofproteinsample)Multi-disciplineintegration(frommolecularbiologytostructuralbiology)39ppt课件highthroughput

parallelization(平行化)

miniaturization(微量化)

automation(自动化)40ppt课件cloningrobot:500-1000clones/3dayscrystallizationrobot:96x3drops/5minproteinsampleforcrystallizationtrialsinnanolitervolumes(<10nl)HansenCL.etal.PNAS;200241ppt课件TagSize(aa)ApplicationSequenceorGenBankaccessionno.His6--10affinityHHHHHH(HH)T711affinityASMTGGQQMGRS15affinityKETAAAKFERQHMDSArg1,5,6affinityRRRRR(R)CBP26affinityKRRWKKNFIAVSAANRFKKISSSGALFLAG4or8affinityDYKDorDYKDDDDKStrep8affinityWSHPQFEKNusA491SET,affinityAccessionno.AAN82367MBP396SET,affinityAccessionno.AAC43128GST220SET,affinityAccessionno.AAB59203ZZ116SET,affinityAccessionno.M74186TrxA109SETAccessionno.AAC40210Gb156SETAccessionno.1MPEADsbADsbC208236SETSETAccessionno.P24991Accessionno.P21892Differenttagswillmakethedifference

42ppt课件DifferentE.colistrains(DE3series)

BL21(DE3)BL21-pLysSBL21-codon-plusTunerRosettaRosetta-pLysSGoldStar43ppt课件Co-expressionwithchaperones(DnaK-DnaJ-GrpEand/orGroEL-GroES)

Mainlyworksforthosepartiallysolubletargets

Co-purificationofchaperoneswiththetargetprotein

Re-aggregation/precipitationafterremovalofchaperones44ppt课件Eukaryoticexpressionsystems(post-translationalmodifications)PichiapastorisSaccharomycescerevisiaeInsect

cells(Sf9、SF21)Mammaliancells(CHOetal.)Virus-mediatedQuantityandCost-effectivity45ppt课件DNAshufflingSaturationmutagenesisError-pronePCR…Toimprove:

thesolubility,activityand/orstabilityReetz,PNAS;2004invitro/directedevolution46ppt课件Proteinssamplesforcrystallizationtrials:1,pureandhomogenous2,stableinsolutionoflowsaltconcentration,properpHandreductant(BME,DTTorTCEP)3,athighconcentration(normally~10mg/ml)47ppt课件HangingdropSittingdrop48ppt课件49ppt课件ProteinsamplesforNMRdatacollection:1,doublelabelingwith13Cand15N2,nooligomerizationoraggregation3,stableforatleastoneweekatRTor4ºC4,highexpressionlevel(cost-effective)50ppt课件Optimizationofxtals:1,abouthalfofthextalswillnotdiffractat3Åorhigherresolution2,parameters:saltconcentration,buffersystem,pH,divalentortrivalentirons3,precipitants:PEGs,MPD,salt,alcohol,…4,ligandsorsubstrates/products/analogs5,proteinornucleicacidpartners51ppt课件Datacollection:X-raydiffraction:in-houseX-raygeneratorsynchrotronradiationacceleratorNMRspectrometry:500mHz,600mHz,800mHz900mHz52ppt课件in-houseX-raygeneratorDatacollection:synchrotronradiationaccelerator53ppt课件

Assignmentoffunctionbasedonstructuralsimilarity

Reciprocalstimulationandvalidation:biochemicalassaysversusstructureanalyses

Structure-directeddrugdesign

Functioninterpretationandapplication:54ppt课件

Assignmentoffunctionbasedonstructuralsimilarity3-DstructureDALIcomparisonCloseststructuresSimilarmolecularfunction?http://www.ebi.ac.uk/dali55ppt课件HolmL,KaariainenS,RosenstromP,SchenkelA.(2008)SearchingproteinstructuredatabaseswithDaliLitev.3.

Bioinformatics24,2780-2781.

56ppt课件

Reciprocalstimulationandvalidation:biochemicalassaysvs.structureanalyses

AnexampleoflicTfromBacillussubstilis57ppt课件LicTmutant(active)H207D/H269DLicTwt(inactive)ComparisonoflicT-wtandlicTmutantGraille*andZhou*etal.JBC2005vanTilbeurghetal.EMBOJ.200158ppt课件Yangetal.EMBOJ.20021122mRNA1122mRNAPKD=10µMKD=1µMCATPRD2PRD1RATCATRNA59ppt课件

Structure-directeddrugdesign

AnexampleofThy1fromThermotogamaritima

Thy1:thymidylatesynthase-complementingprotein

presentinarchaea,prokaryotes,viruses

NOTineukaryotesLesley,SAetal.PNAS;200260ppt课件Thy1-FAD-dUMPThy1-dUMP-HEPES

61ppt课件谷胱甘肽硫转移酶（GST）Biochem.J.(2001)360,1±16Xenobiotics（异型生物质，芳香族化合物）GSH+XenobioticsGS-Xenobiotics毒性较强溶解度低体内富集毒性较弱溶解度高解毒排毒62ppt课件GST参与胞内氧化还原平衡维持，能防止芳香族有毒物质的体内富集，具有解毒功能。真核模式生物酿酒酵母中，有5个GST蛋白（Gtt1、Gtt2、Gto1、Gto2、Gto3），但是没有一个的三维结构被解析，并且与已报道的序列相比，相似度较低。真菌界中的GST蛋白家族分类很混乱，并且目前没有真菌的GST蛋白的三维结构被解析。我们希望通过对Gtt2的研究，阐述清楚生化功能和反应机制，并对真菌中GST的分类提供新的信息。Gtt2的研究意义63ppt课件Gtt2的晶体Apo-form2.2埃GTS-boundform磺化谷胱甘肽，2.2埃GSH-boundform谷胱甘肽，2.1埃64ppt课件Gtt2的结构溶液中为稳定二体，依靠静电和疏水作用力维持每个单体含有两个结构域，N端Trx-like和C端全螺旋结构域65ppt课件底物结合位点主要作用方式：氢键主要来源：N端结构域的残基66ppt课件经典的催化残基在Gtt2中缺失GSH的硫原子周围既没有酪氨酸，也没有丝氨酸，更没有半胱氨酸。67ppt课件经典的三种催化类型酪氨酸催化型丝氨酸催化型半胱氨酸催化型68ppt课件关键的催化残基：晶体结构的证据磺化谷胱甘肽谷胱甘肽Apo-formSer129和His133稳定的水分子很重要69ppt课件关键的催化残基：生化实验的证据突变了水分子游离活性下降70ppt课件还原经典的催化残基空间结构比对突变T24，G27偶然突变导致新的催化模式升高不变或下降71ppt课件从结构上分析分析G27的微环境推测：空间位阻生化实验验证72ppt课件生化试验验证GlyAlaSerCysPhe活性下降侧链体积增大73ppt课件GST家族的生物信息学分析74ppt课件首次定义了一支新的GST亚家族。该亚家族具有与经典模式（Tyr-，Ser-，Cys-type）不同的一种新的催化位点。Gtt2是首次报道的来源于真菌的GST蛋白结构，为目前混乱的真菌GST蛋白分类提供了新的思路。MaXXetal.EMBOReports200975ppt课件/pdb/home/home.do76ppt课件ProteinsNucleicAcidsProtein/NAComplexesOtherTotalX-ray48003116721961751383NMR698286914968006ElectronMicroscopybrid1511118Other114449131Total55285205724153359790Lastupdate:TuesdaySep01,2009

77ppt课件X-rayLastupdate:TuesdaySep01,2009

78ppt课件NMR79ppt课件ElectronMicroscopy80ppt课件GrowthOfUniqueFoldsPerYearAsDefinedBySCOP81ppt课件FutureorientationsofSG1,Reconstructi