生物化学 （英文版）完整版

BiochemistryWhatisBiochemistryToexplain:

1.Structureandfunctionsofbiomolecules

2.Metabolism

(Chemicalreactions)

andregulation

3.GeneticinformationtransferandcontrolAtmolecularleveltoexplainthemechanismsoflivingprocesses

Biochemistrycontents

Proteins(1)NucleicAcids（2）Enzymes(3)

Metabolismofcarbohydrates,lipidsandaminoacids(49)

Geneticinformationtransferandcontrol（1317）Geneticinformationtransferandcontrol

contents

DNAbiosynthesis(replication)RNAbiosynthesis(transcription)Proteinbiosynthesis(translation)

RegulationofgeneexpressionGenerecombinationandengineeringMolecularbiologicaltechniquesBiochemistrycontents

Proteinstructureandfunction(1)NucleicAcids（2）Enzymes(3)

Metabolismofcarbohydrates,lipidsandaminoacids(49)

Geneticinformationtransferandcontrol（1317）

ChapterI

Proteins

Thecontents:1.Molecularconstitution(组成)ofproteins2.ProteinStructure(蛋白质的结构)3.Relationshipofstructureandfunction4.Propertiesofproteinsandpurification

(蛋白质的性质、纯化)5.Plasmaprotein（血浆蛋白质）Learningoutcomes*

Bytheendofthislecture,studentswilllearn:

Explainthemolecularcomponentsofproteinsandthechemicalbondslinkingaminoacidsintheproteins,thephysiochemicalpropertiesofaminoacids.Describetherelationshipbetweenthestructureandfunctionofproteins.ExplainthePropertiesofproteins.Section1

MOLECULARCOMPOSIONSOFPROTEIN

Section1

MOLECULARCOMPOSIONSOFPROTEINStructuralfunctionsDynamicfunctions1.1.Proteinsperformavarietyofdynamicandstructurefunctions

inmammalianorganisms（page1）Section1

MOLECULARCOMPOSIONSOFPROTEIN1.1.Proteinsperformavarietyofdynamicandstructurefunctions

inmammalianorganisms

Structuralfunctions:

providethematrixforboneandconnectivetissue,givingstructureandformtothehumanorganismMembraneproteinsjoinhandswiththefibrousproteinsofthecytoplasmandtheextracellularmatrixtokeepcellsandtissuesinshapeDynamicfunctions:

Catalysis,Transport,MetabolicControlandContractionForexample:EnzymeproteinscatalyzemetabolicreactionsDNA-bindingproteinsregulategeneexpressionHemoglobinandmyoglobintransportoxygeninbloodandinmuscle,respectivelyImmunoglobulinsandinterferonwithaprotectiverole,protectagainstbacterialorviralinfectionFibrinstopsthelossofbloodoninjurytothevascularsystemThesimplestproteinsconsistofasinglepolypeptidechainanunbranchedpolymer

ofthe

20aminoacids,

heldtogetherbypeptidebonds.

（肽键）Somepolypeptideslessthan100aminoacidsinlength,butothershavemorethan1000aminoacids

Someproteinsevenhaveanonpolypeptidegroupattachedtothem,eithercovalentlyornoncovalently.Thepolypeptidescomponentsoftheseproteinsiscalledtheapoprotein（脱辅基蛋白）,

andtheirnonpolypeptidecounterpart,theprostheticgroup（辅基）1.2Allα-aminoacidsinproteinsareL-steroisomers1.2.1AminoAcidsAreZwitterions（page2）Ofthetwoopticalisomers,onlytheL-aminoacidsoccurinproteins

D-AminoacidsarerareinnatureααLform

Dformorα

Typicalstructureofα-aminoacidsAminoacids:acarboxylgroupanaminogroupahydrogenatomavariablesidechainR(“residue”)boundtotheα–carbonThepKoftheα–carboxyl

is

alwaysclose

to2.0andthepKoftheα–amino

groupnear9or10Therefore,theprotonationstatevarieswithpH(protonconcentration[H+]),conclusionBelowthepKofthecarboxylgroup,theaminoacidispredominantly

acation(+)AbovethepKoftheaminogroup,

ananion(-)andbetweenthetwopKs,

azwitterion

(hermaphrodite):amoleculecarryingbothapositiveandanegativechargeTheisoelectricpoint(pI)isdefinedas

thepHvalueatwhichthenumberofpositivechargesequalsthenumberofnegativecharges.

Forasimpleaminoacidsuchasalanine:pIis6.1ThepIoftheacidicaminoacidsishalfwaybetweenthepKvaluesofthetwoacidicgroups.（Asp2.95）ThepIofthebasicaminoacidsishalfwaybetweenthepKvaluesofthetwobasicgroups.

（Lys10.0）Molecularconstitution:

20L-α-aminoacids(氨基酸)---basicunitsofproteins(蛋白质的基本组成单位)AminoAcidsAreZwitterions：

isoelectricpoint(pI)1.2.2AminoAcidSideChainsFormManyNoncovalent（非共价键）Interactions（page3）The20aminoacidscanbeplacedinafewmajorgroupsThesmallaminoacidsglycineandalanineThebranched-chainaminoacidsvaline,leucine,andisoleucineThehydroxylaminoacidsserineandthreonineThesulfuraminoacidscysteineandmethionineThearomaticaminoacidsphenylalanine,tyrosine,andtryptophanTheacidicaminoacidsglutamateandaspartateThebasicaminoacidslysine,arginine,andhistidineafreakamongaminoacidsprolineThesmallaminoacids

HydrophobicThebranched-chainaminoacidsTheycaninteracthydrophobicallyinwatersolutionClassifiedaccordingtopolarity

ofRgroup:

Hydrophobic-waterfearing（疏水性）non-polarRgroup

Hydrophilic-waterloving（亲水性）polar,neutralchainsnegativelychargedpositivelychargedHydrophobicinteractions(expellingbywater,hydrophobic

attractions)

Interactions

betweenRgroupsofnon-polarAAs疏水作用疏水作用ThehydroxylaminoacidsThesulfuraminoacids

Cysteine半胱氨酸

+胱氨酸(Cystine)二硫键-HHDisulfidebondThearomaticaminoacidsTheyhavefunctionalgroupscapableofforminghydrogenbondsuchas–OH,-SHandamideHydrogenbonds氢键Theacidicaminoacids

&theirderivativesTheyhaveRgroupwithcarboxylgroupnegativelychargedatpH7.2ThebasicaminoacidsTheyhaveRgroupbearingapositivechargeatpH7.2AttractionbetweenoppositelychargedRgroupsofAAsIonicbonds(saltbonds)离子键（盐键）Iminoacid（亚氨基酸）1.3Peptidebondsanddisulfidebondsformtheprimarystructureofproteins1.3.1peptidebondsTheaminoacidsinthepolypeptidesareheldbypeptidebondsAdipeptideisformedbyareactionbetweentheα-carboxylandα-aminogroupsoftwoaminoacidspeptidebondoramidebond1.3.2Peptide肽Residue残基peptidechainAlinearsequenceofaminoacidsresidueslinkedtogetherbypeptidebondsDipeptideTripeptideOligopeptidesPolypeptidesPeptide肽

Dipeptide(二肽):twoAAresidues

Tripeptide(三肽):threeAAresidues

Oligopeptide(寡肽):fewerthan10AAresidues

Polypeptide(多肽):fewerthan50AAresiduesProtein(蛋白质):morethan50AAresidues

Eachpeptidehasanaminoterminus,conventionallywrittenontheleftside,andacarboxylterminus,

writtenontherightside

Peptidebondisnoionizable.Itcanformhydrogenbonds.Peptidesandproteinstendtobewatersoluble.1.3.3Disulfidebond

Disulfidebondsareformedbetweencysteineresiduesthathavebeenbroughtincloseapproximationduringthefoldingprocess.

Thedisulfidebondcanbeformedbetweentwocysteinesinthesamepolypeptide(intrachain)orindifferentpolypeptides(interchain).

Thereactiontakesplaceintheendoplasmicreticulum,wheresecretedproteinsandmembranceproteinsareprocessed.

OxidationoftwocysteinesSidechaininteractionsHelpmaintainspecificstructureDisulfidebondSection2

StructureofProteins

Primary

Secondary

Tertiary

QuaternaryFourlevelsofstructuralorganization:Primarystructure一级结构Secondarystructure二级结构Tertiarystructure三级结构Quaternarystructure四级结构Spatialstructure(Three-dimensionalstructure)(Conformation)FromNtoCterminus,thelinearsequence(orarrangement)ofaminoacidsthatarecovalentlylinkedbypeptidebonds.Italsoincludesthelocationsof-S-S-bonds2.1TheSequenceofAminoAcidsIsthePrimaryStructureofaProtein

从N端至C端以肽键相连的氨基酸排列顺序，包括二硫键的位置。Primary

StructureofproteinProinsulin(胰岛素原)

Primarystructure

TheAAsequencefromNendtoCendinthepolypeptidechain(s)ofaproteinNumberingAAsequencefromNtoCend

Forcesthatstabilizetheprimarystructuresarecovalentbonds—peptidebondsanddisulfidebonds(ifpresent).TheAAsequenceofaproteinisdeterminedbyitsgene.一级结构是蛋白质空间构象和特异生物学功能的基础。Spatialstructure(conformation)ofproteins2.2SecondStructureHasRegularlyRepetitiveFoldingPatternsofPolypeptidesThelocalizedfoldingsegmentsofthepolypeptidebackbone.Commonsecondarystructures:α-helix(α螺旋)β-pleatedsheet(β折叠)randomcoil(无规卷曲)β-turn(bend)(β转角)Forces:

hydrogenbonds蛋白质分子中某一段肽链的局部空间结构，即该段肽链主链骨架原子的相对空间位置，并不涉及氨基酸残基侧链的构象。主要化学键：氢键Backboneormain-chainSide-chain

COO-CH2

CH2NH3+CH2CH2CH2主链骨架PeptidebondsHavepartialdoublebondcharacterRestrictfreerotationaroundthepeptidebondsTwosinglebonds:Cα-CO,N-Cα(1)Peptideunit(plane)肽单元（平面）PeptidebondsTransconfiguration(构型):--C=O(羰基氧)andN-H(氢)andtwoCαPeptideunit(plane)肽单元（平面）Anamideplaneconsistsofsixatoms,Cα1,C,O,N,H,Cα2onthesameplanePeptideunitdefinitionThepartialdouble-bondcharacterofthepeptidebondmakesCα1,C,O,N,H,Cα2sixatomscoplanar,Cα1andCα2aretranstoeachother,thissemi-rigidplanecomposedofthosesixatomsistermedaspeptideunit.参与肽键的6个原子—Cα1，C，O，N，H，Cα2位于同一平面，Cα1和Cα2在平面上所处的位置为反式（trans）构型，此同一平面上的6个原子构成肽单元。CαisthejoiningpointfortwoplanesRotationofplanarpeptideunitispermittedabouttheN-CαandtheCα-CsinglebondsPeptideunit(plane)(2)α-helixright-handhelixleft-handhelixThebackboneofpolypeptideformsaright-handhelix3.6AAresiduesperturnPitch(螺距)is0.54nmAllRgroupspositionedoutsideofhelixHbondsrunnearlyparalleltotheaxisofthehelix(2)α-helix

Nend

Thestructureofα–helixisstabilizedbythehydrogenbondbetweenthehydrogenatomattachedtotheelectronegativenitrogenatomofapeptidelinkageandtheelectronegativecarbonyloxygenatomofthefourthaminoacidontheamino-terminalsideofthatpeptidebond.(3)β-pleatedsheet(β折叠)TheRgroupsofadjacentAAsprotrudeinoppositedirectionsfromthezigzagstructure(Rissmaller)AnothercommontypeofsecondarystructureThebackboneofpolypeptidechainisfullyextendedintoazigzagformOneβ-sheetcanbecomposedoftwoormorestrandsβ-strandscanassembleinparallelandantiparallelorientations(平行或反平行)StabilizedbyH-bondcross-linksbetweenadjacentchainsβ-pleatedsheetTheαHelixandβ-PleatedSheetAretheMostCommonSecondaryStructuresinProteinsThepolypeptidechainformsatightloop,whichcanmakethepolypeptidechainreverseitsdirectionand180-degreefoldback.InvolvingfourAAs,carbonyloxygenof

thefirstAAishydrogenbondedtoN-HofthefourthAA.ThePro(2),Gly,Asp,AsnandTrpresiduesoftenoccurinβ–turns.*β－转角常发生于肽链进行180°回折时的转角上。*β一转角通常由4个氨基酸残基组成,其第一个残基的羰基氧(O=C)与第四个残基的氨基氢(H)可形成氢键。*β－转角的第二个残基常为脯氨酸,其他常见残基有甘氨酸、天冬氨酸、天冬酰胺和色氨酸。(4)β-turnorβ-bend(β转角)(5)Motif(5)Motif

Zincfingermotif

1helixand2antiparallelβ-pleatedsheetfingershapedBindwithZn2+oftenappearinDNAbindingdomain(5)Motif(模体)Simplearrangementsofseveralkindsofsecondarystructurethatoccurinproteinarecalledmotif(orsupersecondarystructure).Afunctionalstructureofproteinthatconsistsofonepeptidechain.2.3TertiarystructureThespatial,three-dimensionalarrangementofallatomsinapolypeptidechain,resultingfromtheinteractionsbetweentheRgroupsofproteinchains.(1)TertiarystructureN端

C端completethree-dimensionalstructureofonepolypeptidechain

肌红蛋白

(Mb)

(1)Tertiarystructure

Noncovalentinteractions(非共价作用力)inspatialstructure

hydrogenbonds（氢键）hydrophobicinteractions（疏水作用）ionicbonds（离子键）Vanderwaalsforces（范德华力）Theseforcesoccur:withinproteinstructure,betweenproteinandsolvent(water)ForcesintheThetertiarystructureofsomeproteinscanbedividedintotwoormorerelativelyindependentcompactregionsthatmaybejoinedbyaflexiblesegmentofthechain,andhavespecialfunctions.Thesecompactunitscalleddomains.(2)Domain结构域*Phosphoglyceratekinasehas2domainswitharelativelynarrowneckinbetween(2)Domain结构域

Oneproteinmaycontainseveraldomains,eachofwhichmaybecomposedofseveralmotifs.

domain>motif

Eachdomainisafunctionalunit,havingseparatefunctions.e.g.:Fattyacidsynthetasecontains7domains,eachhasanactivecenterandanenzymeactivity.DNAbindingprotein(transcriptionalfactor)containsatleast2domains

2.4Quaternarystructure四级结构(1)Someproteinscontaintwoormoreseparatepolypeptidechains,eachofwhichfoldedtoacompletetertiarystructureiscalledasubunit.2.4Quaternarystructure蛋白质分子中各亚基的空间排布及亚基接触部位的布局和相互作用，称为蛋白质的四级结构。含有四级结构的蛋白质,单独的亚基一般没有生物学功能,只有完整的四级结构寡聚体才有生物学功能。(2)Associationoftwoormoresubunitstoformafunctionalprotein(3)Subunitsmaybeidenticalornot:*homomultimeric:onekindofpolypeptidechain*heteromultimeric:severaldifferentkindsofpolypeptidechains(Homodimer&heterodimer)Thearrangementandinteractionofsubunitsinthespacehydrogenbonds(mainly)ionicbonds(mainly)VanderwaalshydrophobicforcesDisulfidebonds（二硫键）(ifpresent)ForcesinvolvedinquaternarystructureSection3Relationshipbetweenstructureandfunctionofprotein1.Primarystructureisthebasisofhighspatialstructureandfunctionofprotein(1).PrimarystructureisthebasisofspatialstructureofproteinAlloftheinformationnecessaryforpeptidechainfoldingintoitsnativestructureiscontainedintheAAsequenceofthepeptide.e.g.theexperimentofribonucleasedenaturation核糖核酸酶1peptidechain:124AAs4DisulfidebondsNativeribonuclease牛核糖核酸酶的一级结构二硫键denaturerenatureTheprimarystructureisthebasisofspatialstructureoftheproteinBut

mostproteinsneedmolecularchaperons（分子伴侣）tofacilitatethemtofoldintocorrectspatialstructure.

keyAAresidueschange(2).Primarystructurerelatedtofunctionmutationsinagene

mutantproteinsoftenresultinmoleculardiseases(分子病)Sickle-cellanemia镰刀型红细胞贫血这种由蛋白质分子发生变异所导致的疾病，称为“分子病”Crescent-shapederythrocytes(lackofblood)SpatialstructureisbasisofproteinfunctionBiologicalactivitywillbelostwhenspatialstructureisdestroyedMyoglobin(Mb)andhemoglobin(Hb)

areparadigms（范例）ofproteinstructureandfunction2.Spatialstructurerelatedtoproteinfunctionmyoglobin（Mb）andhemoglobin（Hb）

TypicalglobularproteinsBothareconjugatedwithheme(血红素)Similarfunction:O2bindingproteins(1).Subunitofhemoglobinandmyoglobinhavesimilarstructure(血红蛋白亚基与肌红蛋白结构相似)

Protein(solubilityandHemeandO2binding)Heme(bindingO2)Myoglobin(Mb)肌红蛋白Onepeptidewitheightrelativelystraightsegmentsofα-helix(A-H),tertiarystructure.HemegrouprestsinahydrophobicpocketHemoglobin(Hb)血红蛋白Hb：4subunits,α2β2(adult)，eachhastertiarystructureverysimilartothatofMb.FourhemegroupsQuaternarystructureHowisthesigmoidal（S形）curveofHbformed?Tensestate(Tstate):

8saltbonds4subunitstightlybound,affinityofeachsubunittoO2islowerHowistheS-shapecurveofHbformed?O2-Hbdiffersmarkedlyinitsquaternarystructurefromdeoxy-Hb.(别构效应)AllostericeffectHb

and

MbHb:4subunitsQuaternarystructureMb：onesubunitTertiarystructureHb:O2-transportproteinMb:O2-storageprotein

DifferentspatialstructureHb:positivecooperativityMb:nocooperativityDifferentpropertyofO2bindingDifferentfunctionSection4

Propertiesofproteins

蛋白质的理化性质Spatialstructureofproteinissensitivetodenaturingagents(highT,urea,strongacidsorbases,organicsolvents,detergents,heavymetalions)TheseagentsresultinunfoldinganddisorganizationofproteinspatialstructurewithoutchangeinAAssequencesofprimarystructure,andlossofbiologicalactivity.4.1Denaturationofprotein蛋白质变性在某些物理和化学因素(如加热，强酸，强碱，有机溶剂等)作用下，蛋白质的特定空间构象被破坏，也即有序的空间结构变成无序的空间结构，从而导致其理化性质改变和生物活性的丧失。蛋白质的变性(denaturation)变性的本质:破坏非共价键和二硫键，不改变蛋白质的一级结构(nopeptidebondbroken)。biologicalactivityispartiallyorcompletelylost,sensitivetoproteaseeffectphysicalandchemicalpropertieschangedusuallythesolubilityisreducedDenaturationandrenaturationMaybereversible(rarely)orirreversible复性Renaturationofprotein

(蛋白质复性)若蛋白质变性程度较轻，去除变性因素后，蛋白质仍可恢复或部分恢复其原有的构象和功能，称为复性。Aftersoftlydenaturation,removethedenaturationfactor,theconformationandactivityofdenaturedproteinarereturned.天然状态，有催化活性尿素、β-巯基乙醇去除尿素、β-巯基乙醇非折叠状态，无活性变性复性RenaturationdenaturationNH3+COOHNH3+COO-NH2COO-

+H++OH-

pI<pIpH=pIpH>pI4.2Thesolubilityofproteinsde