生物化學(xué) （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(組成)ofproteins2.ProteinStructure(蛋白質(zhì)的結(jié)構(gòu))3.Relationshipofstructureandfunction4.Propertiesofproteinsandpurification

(蛋白質(zhì)的性質(zhì)、純化)5.Plasmaprotein（血漿蛋白質(zhì)）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.

（肽鍵）Somepolypeptideslessthan100aminoacidsinlength,butothershavemorethan1000aminoacids

Someproteinsevenhaveanonpolypeptidegroupattachedtothem,eithercovalentlyornoncovalently.Thepolypeptidescomponentsoftheseproteinsiscalledtheapoprotein（脫輔基蛋白）,

andtheirnonpolypeptidecounterpart,theprostheticgroup（輔基）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(蛋白質(zhì)的基本組成單位)AminoAcidsAreZwitterions：

isoelectricpoint(pI)1.2.2AminoAcidSideChainsFormManyNoncovalent（非共價(jià)鍵）Interactions（page3）The20aminoacidscanbeplacedinafewmajorgroupsThesmallaminoacidsglycineandalanineThebranched-chainaminoacidsvaline,leucine,andisoleucineThehydroxylaminoacidsserineandthreonineThesulfuraminoacidscysteineandmethionineThearomaticaminoacidsphenylalanine,tyrosine,andtryptophanTheacidicaminoacidsglutamateandaspartateThebasicaminoacidslysine,arginine,andhistidineafreakamongaminoacidsprolineThesmallaminoacids

HydrophobicThebranched-chainaminoacidsTheycaninteracthydrophobicallyinwatersolutionClassifiedaccordingtopolarity

ofRgroup:

Hydrophobic-waterfearing（疏水性）non-polarRgroup

Hydrophilic-waterloving（親水性）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)二硫鍵-HHDisulfidebondThearomaticaminoacidsTheyhavefunctionalgroupscapableofforminghydrogenbondsuchas–OH,-SHandamideHydrogenbonds氫鍵Theacidicaminoacids

&theirderivativesTheyhaveRgroupwithcarboxylgroupnegativelychargedatpH7.2ThebasicaminoacidsTheyhaveRgroupbearingapositivechargeatpH7.2AttractionbetweenoppositelychargedRgroupsofAAsIonicbonds(saltbonds)離子鍵（鹽鍵）Iminoacid（亞氨基酸）1.3Peptidebondsanddisulfidebondsformtheprimarystructureofproteins1.3.1peptidebondsTheaminoacidsinthepolypeptidesareheldbypeptidebondsAdipeptideisformedbyareactionbetweentheα-carboxylandα-aminogroupsoftwoaminoacidspeptidebondoramidebond1.3.2Peptide肽Residue殘基peptidechainAlinearsequenceofaminoacidsresidueslinkedtogetherbypeptidebondsDipeptideTripeptideOligopeptidesPolypeptidesPeptide肽

Dipeptide(二肽):twoAAresidues

Tripeptide(三肽):threeAAresidues

Oligopeptide(寡肽):fewerthan10AAresidues

Polypeptide(多肽):fewerthan50AAresiduesProtein(蛋白質(zhì)):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一級(jí)結(jié)構(gòu)Secondarystructure二級(jí)結(jié)構(gòu)Tertiarystructure三級(jí)結(jié)構(gòu)Quaternarystructure四級(jí)結(jié)構(gòu)Spatialstructure(Three-dimensionalstructure)(Conformation)FromNtoCterminus,thelinearsequence(orarrangement)ofaminoacidsthatarecovalentlylinkedbypeptidebonds.Italsoincludesthelocationsof-S-S-bonds2.1TheSequenceofAminoAcidsIsthePrimaryStructureofaProtein

從N端至C端以肽鍵相連的氨基酸排列順序，包括二硫鍵的位置。Primary

StructureofproteinProinsulin(胰島素原)

Primarystructure

TheAAsequencefromNendtoCendinthepolypeptidechain(s)ofaproteinNumberingAAsequencefromNtoCend

Forcesthatstabilizetheprimarystructuresarecovalentbonds—peptidebondsanddisulfidebonds(ifpresent).TheAAsequenceofaproteinisdeterminedbyitsgene.一級(jí)結(jié)構(gòu)是蛋白質(zhì)空間構(gòu)象和特異生物學(xué)功能的基礎(chǔ)。Spatialstructure(conformation)ofproteins2.2SecondStructureHasRegularlyRepetitiveFoldingPatternsofPolypeptidesThelocalizedfoldingsegmentsofthepolypeptidebackbone.Commonsecondarystructures:α-helix(α螺旋)β-pleatedsheet(β折疊)randomcoil(無(wú)規(guī)卷曲)β-turn(bend)(β轉(zhuǎn)角)Forces:

hydrogenbonds蛋白質(zhì)分子中某一段肽鏈的局部空間結(jié)構(gòu)，即該段肽鏈主鏈骨架原子的相對(duì)空間位置，并不涉及氨基酸殘基側(cè)鏈的構(gòu)象。主要化學(xué)鍵：氫鍵Backboneormain-chainSide-chain

COO-CH2

CH2NH3+CH2CH2CH2主鏈骨架PeptidebondsHavepartialdoublebondcharacterRestrictfreerotationaroundthepeptidebondsTwosinglebonds:Cα-CO,N-Cα(1)Peptideunit(plane)肽單元（平面）PeptidebondsTransconfiguration(構(gòu)型):--C=O(羰基氧)andN-H(氫)andtwoCαPeptideunit(plane)肽單元（平面）Anamideplaneconsistsofsixatoms,Cα1,C,O,N,H,Cα2onthesameplanePeptideunitdefinitionThepartialdouble-bondcharacterofthepeptidebondmakesCα1,C,O,N,H,Cα2sixatomscoplanar,Cα1andCα2aretranstoeachother,thissemi-rigidplanecomposedofthosesixatomsistermedaspeptideunit.參與肽鍵的6個(gè)原子—Cα1，C，O，N，H，Cα2位于同一平面，Cα1和Cα2在平面上所處的位置為反式（trans）構(gòu)型，此同一平面上的6個(gè)原子構(gòu)成肽單元。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折疊)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－轉(zhuǎn)角常發(fā)生于肽鏈進(jìn)行180°回折時(shí)的轉(zhuǎn)角上。*β一轉(zhuǎn)角通常由4個(gè)氨基酸殘基組成,其第一個(gè)殘基的羰基氧(O=C)與第四個(gè)殘基的氨基氫(H)可形成氫鍵。*β－轉(zhuǎn)角的第二個(gè)殘基常為脯氨酸,其他常見(jiàn)殘基有甘氨酸、天冬氨酸、天冬酰胺和色氨酸。(4)β-turnorβ-bend(β轉(zhuǎn)角)(5)Motif(5)Motif

Zincfingermotif

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

C端completethree-dimensionalstructureofonepolypeptidechain

肌紅蛋白

(Mb)

(1)Tertiarystructure

Noncovalentinteractions(非共價(jià)作用力)inspatialstructure

hydrogenbonds（氫鍵）hydrophobicinteractions（疏水作用）ionicbonds（離子鍵）Vanderwaalsforces（范德華力）Theseforcesoccur:withinproteinstructure,betweenproteinandsolvent(water)ForcesintheThetertiarystructureofsomeproteinscanbedividedintotwoormorerelativelyindependentcompactregionsthatmaybejoinedbyaflexiblesegmentofthechain,andhavespecialfunctions.Thesecompactunitscalleddomains.(2)Domain結(jié)構(gòu)域*Phosphoglyceratekinasehas2domainswitharelativelynarrowneckinbetween(2)Domain結(jié)構(gòu)域

Oneproteinmaycontainseveraldomains,eachofwhichmaybecomposedofseveralmotifs.

domain>motif

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

2.4Quaternarystructure四級(jí)結(jié)構(gòu)(1)Someproteinscontaintwoormoreseparatepolypeptidechains,eachofwhichfoldedtoacompletetertiarystructureiscalledasubunit.2.4Quaternarystructure蛋白質(zhì)分子中各亞基的空間排布及亞基接觸部位的布局和相互作用，稱為蛋白質(zhì)的四級(jí)結(jié)構(gòu)。含有四級(jí)結(jié)構(gòu)的蛋白質(zhì),單獨(dú)的亞基一般沒(méi)有生物學(xué)功能,只有完整的四級(jí)結(jié)構(gòu)寡聚體才有生物學(xué)功能。(2)Associationoftwoormoresubunitstoformafunctionalprotein(3)Subunitsmaybeidenticalornot:*homomultimeric:onekindofpolypeptidechain*heteromultimeric:severaldifferentkindsofpolypeptidechains(Homodimer&heterodimer)Thearrangementandinteractionofsubunitsinthespacehydrogenbonds(mainly)ionicbonds(mainly)VanderwaalshydrophobicforcesDisulfidebonds（二硫鍵）(ifpresent)ForcesinvolvedinquaternarystructureSection3Relationshipbetweenstructureandfunctionofprotein1.Primarystructureisthebasisofhighspatialstructureandfunctionofprotein(1).PrimarystructureisthebasisofspatialstructureofproteinAlloftheinformationnecessaryforpeptidechainfoldingintoitsnativestructureiscontainedintheAAsequenceofthepeptide.e.g.theexperimentofribonucleasedenaturation核糖核酸酶1peptidechain:124AAs4DisulfidebondsNativeribonuclease牛核糖核酸酶的一級(jí)結(jié)構(gòu)二硫鍵denaturerenatureTheprimarystructureisthebasisofspatialstructureoftheproteinBut

mostproteinsneedmolecularchaperons（分子伴侶）tofacilitatethemtofoldintocorrectspatialstructure.

keyAAresidueschange(2).Primarystructurerelatedtofunctionmutationsinagene

mutantproteinsoftenresultinmoleculardiseases(分子病)Sickle-cellanemia鐮刀型紅細(xì)胞貧血這種由蛋白質(zhì)分子發(fā)生變異所導(dǎo)致的疾病，稱為“分子病”Crescent-shapederythrocytes(lackofblood)SpatialstructureisbasisofproteinfunctionBiologicalactivitywillbelostwhenspatialstructureisdestroyedMyoglobin(Mb)andhemoglobin(Hb)

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

TypicalglobularproteinsBothareconjugatedwithheme(血紅素)Similarfunction:O2bindingproteins(1).Subunitofhemoglobinandmyoglobinhavesimilarstructure(血紅蛋白亞基與肌紅蛋白結(jié)構(gòu)相似)

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

8saltbonds4subunitstightlybound,affinityofeachsubunittoO2islowerHowistheS-shapecurveofHbformed?O2-Hbdiffersmarkedlyinitsquaternarystructurefromdeoxy-Hb.(別構(gòu)效應(yīng))AllostericeffectHb

and

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

DifferentspatialstructureHb:positivecooperativityMb:nocooperativityDifferentpropertyofO2bindingDifferentfunctionSection4

Propertiesofproteins

蛋白質(zhì)的理化性質(zhì)Spatialstructureofproteinissensitivetodenaturingagents(highT,urea,strongacidsorbases,organicsolvents,detergents,heavymetalions)TheseagentsresultinunfoldinganddisorganizationofproteinspatialstructurewithoutchangeinAAssequencesofprimarystructure,andlossofbiologicalactivity.4.1Denaturationofprotein蛋白質(zhì)變性在某些物理和化學(xué)因素(如加熱，強(qiáng)酸，強(qiáng)堿，有機(jī)溶劑等)作用下，蛋白質(zhì)的特定空間構(gòu)象被破壞，也即有序的空間結(jié)構(gòu)變成無(wú)序的空間結(jié)構(gòu)，從而導(dǎo)致其理化性質(zhì)改變和生物活性的喪失。蛋白質(zhì)的變性(denaturation)變性的本質(zhì):破壞非共價(jià)鍵和二硫鍵，不改變蛋白質(zhì)的一級(jí)結(jié)構(gòu)(nopeptidebondbroken)。biologicalactivityispartiallyorcompletelylost,sensitivetoproteaseeffectphysicalandchemicalpropertieschangedusuallythesolubilityisreducedDenaturationandrenaturationMaybereversible(rarely)orirreversible復(fù)性Renaturationofprotein

(蛋白質(zhì)復(fù)性)若蛋白質(zhì)變性程度較輕，去除變性因素后，蛋白質(zhì)仍可恢復(fù)或部分恢復(fù)其原有的構(gòu)象和功能，稱為復(fù)性。Aftersoftlydenaturation,removethedenaturationfactor,theconformationandactivityofdenaturedproteinarereturned.天然狀態(tài)，有催化活性尿素、β-巰基乙醇去除尿素、β-巰基乙醇非折疊狀態(tài)，無(wú)活性變性復(fù)性RenaturationdenaturationNH3+COOHNH3+COO-NH2COO-

+H++OH-

pI<pIpH=pIpH>pI4.2Thesolubilityofproteinsde