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TheScopeof
Biochemistry
TheImportanceofWeak
Interactions
Introductionto
BiologicalEnergyFlow
OverviewofBiological
InformationFlow
ProteinStructure

Thenaturallyoccurringaminoacids
haveacommonstructure.Amino
acids,asthenameimplies,havetwo
functionalgroups,anaminogroup(
NH2)andacarboxylgroup(COOH).

PrimaryStructure

Thesegroupsarejoinedtoasingle
(aliphatic)carbon.Inorganic

SecondaryStructure
TertiaryStructure

chemistry,thecarbondirectly
attachedtoacarboxylgroupisthe
alpha()position,sotheaminoacids

Quaternary
Structures
LevelsofProtein
Structure

RelatedTopics:
BiochemistryII
Chemistry

AminoAcids

AminoAcids

OxygenBindingby
Myoglobinand
Hemoglobin
Enzymes
Organizationof
Metabolism
Glycolysis
TheTricarboxylicAcid
TCACycle
Oxidative
Phosphorylation
Carbohydrate
MetabolismII

inproteinsareallalphaaminoacids.
Thesidechainsthatdistinguishone
aminoacidfromanotherareattached
tothealphacarbon,sothestructures
areoftenwrittenasshowninFigure,whereRstandsforoneofthe20sidechains:

Figure1
Theaminoacidsfoundinproteinshaveacommonstereochemistry.Inthe
structureillustratedinFigure,theaminogroupisalwaystotheleftsideofthe
alphacarbon.Inorganicchemistry,thisstereochemistryisreferredtoasL(forlevo,
meaningleft).Thus,theaminoacidsfoundinproteinsareLalphaaminoacids.
(Biochemists,beingcreaturesofhabit,usuallydonotrefertoaminoacid
stereochemistryintheRandSnomenclature.)AfewDaminoacidsarefoundin
nature,althoughnotincellularproteins.(TheDcomesfromdextro,meaning
right.)Forexample,somepeptideantibiotics,suchasbacitracin,containDamino
acids.
Thecarboxyllandaminogroupsoftheaminoacidscanrespectivelydonateaproton
toandacceptaprotonfromwater.Thisexchangehappenssimultaneouslyin
solutionsothattheaminoacidsformdoublyionizedspecies,termedzwitterions
(fromGermanzwei,meaningtwo)insolution.Theformationofzwitterionscanbe
rationalizedfromtheprinciplesofacidbasechemistry.Thestrongestacidthatcan
existinwateristheconjugateacidofwater,thehydroniumion,H3O+ .Carboxyllic
acidsarestrongeracidsthanwater,sothecarboxylgroupofanaminoacid(pKa
near2)willdonateaprotontowater.Similarly,aminogroups(pKagreaterthan
9)arestrongerbasesthanwaterandwillacceptaprotonfromwater.Aminoacids
inwater,therefore,havethegeneralstructure:

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Aminoacidsidechains
Thesidechainsofaminoacidsgivethemtheirdifferentchemicalpropertiesand
allowproteinstohavesomanydifferentstructures.Howmanyproteinsare
possible?Proteinchainsgenerallyvaryinsizefrom100to1,000aminoacidsin
length.Eveniflimitedtothesmallestchainlength,therewouldbe20100,over10
130thatis,1with130zeroesafteritpossibleprimarystructures.(Again,

rememberthatthenumberofelementaryparticlesintheuniverseisestimatedto
be1080.)Obviously,notallthesepotentialproteinsexistinnature.Instead,the
primarystructuresofproteinsarerelatedtoeachother,andalmostallproteins
havehomologues,thatis,otherproteinssharingacommonancestor.
Whathomologuesarepossible?Ingeneral,homologousproteinssharesomeshort
aminoacidsequencesexactly.Inothercases,thedifferencesresultinthe
substitutionofoneaminoacidsidechainbyanotherchemicallysimilarone.Six
classesofaminoacidsidechainsexistwithinagroup,theaminoacidsidechains
arechemicallysimilar.Substitutionofoneaminoacidsidechainforanotherone
withinthesamegroupisknownasconservativesubstitution.Homologous
proteinsarerelatedbyconservativeaminoacidsubstitutions,asinFigure.
Althoughnonconservativesubstitutionsaretoleratedatsomepositionsinthe
primarysequenceofaprotein,thegeneralruleillustratedinFigureisfollowedwhen
evaluatingtherelationshipoftwoproteinprimarysequences.(Thedashesindicate
thatallthreeproteinshavethesameaminoacidatthatpositionthesearehighly
homologousproteins,indeed!)

Figure2

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Aliphaticaminoacids.Thesidechainsofglycine,alanine,valine,leucine,and
isoleucine,showninFigure,containsaturatedcarboncarbonandcarbonhydrogen
bondsonly.Thinkingofglycineascontainingasidechaincanbesomewhat
confusingbecausethefourthsubstituentonthecarbonisonlyasinglehydrogen
atom.Aloneamongthe20aminoacids,glycineisnotopticallyactivetheDandL
nomenclatureisirrelevant.Alaninehasamethylgroupforitssidechain,valinea3
carbonsidechain,whileleucineandisoleucinehave4carbonsidechains.

Figure3

Aromaticaminoacids.Phenylalanine,tyrosine,andtryptophancontainring
systems.Inorderofincreasingcomplexity,phenylalaninehasabenzylgroup,while
tyrosineisphenylalaninewithanaddedhydroxylgroupinthetranspositionrelative
tothemethylgroup.Tryptophanhastworings,oneofwhichcontainsanitrogen
atom.ThenitrogenisnotionizableatbiologicallyrelevantpHvalues.
Ionizablebasicaminoacids.Histidine,lysine,andarginineeachhaveanitrogen
atomwhich,unlikethenitrogenoftryptophan,isionizedatthepHrangesfoundin
thecell.Histidinehasa5memberimidazolering.Oneofthetwonitrogenionshas
apKanear7.0.Thismeansthat,attheneutralpHvaluesfoundincells,abouthalf
ofthehistidinemoleculeswillhavetheirsidechainsprotonated(thatis,witha
positivecharge)andabouthalfwillhavetheirsidechainsunprotonatedand
uncharged.Histidineisoftenusedinenzymestobindandreleaseprotonsduring
theenzymaticreaction.
LysineandargininearealmostfullyionizedatthepHvaluesfoundinthecell.
Lysine'spKaisgreaterthan9therefore,itwillbe>99%protonatedinthecell.
Arginine'ssidechainisevenmorebasicitspKais>12.Therefore,theseamino
acidshaveanetpositivechargeinthecell.
Carboxyllatecontainingaminoacids.Asparticacidandasparaginehavefour
carbonsglutamicacidandglutaminehavefivecarbonsinall.Asparticacidhasa
carboxyllicacid,andasparginehasanamidesidechain.Similarly,glutamicacidhas

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AminoAcids
acarboxyllicacidsidegroup,andglutaminehasanamidegroup.ThepKasofthe
sidechaincarboxyllgroupsinaspartateandglutamatearenear4.0.Therefore,
thesesidechaingroupsarealmostfullyionizedintheneutralconditionsfoundin
cellsandarenegativelycharged.

Hydroxylandsulfurcontainingsidechains
Serineandcysteinecanbethoughtofasbeingrelatedtoalanine.Serineis
alaninewithahydroxyl(OH)groupandcysteineisalaninewithasulfhydryl(SH)
group.
Threoninehasfourcarbons,withahydroxylgrouponthebetacarbon.Thebeta
carbonisnexttotheonecontainingthealphacarbon(thealphacarbonhasthe
aminogrouponit).Thepresenceofthehydroxylgrouponthreoninemeansthat
thebetacarbonofthreonineisopticallyactive,inadditiontothealphacarbon.As
thenamesuggests,theOHgrouphastheDconfiguration,orthreotothealpha
carbon.(TheotherpossiblestereochemistryiserythrothinkoftheletterEto
rememberthisterm.ThearmsoftheEpointinthesamedirection.)
Methioninehasamethylgrouponitssulfur.Thebackboneofmethioninehasone
morecarbonthandoescysteine.(Cysteinewithanextracarbonistermed
homocysteinehomocysteineisanintermediateinthebiosynthesisof
methionine.)

Thecyclicaminoacid
Prolineistheoddoneoutamongtheaminoacids.Ithasfourcarbons,withthe
alphaaminogroupbondednotonlytothealphacarbonbutalsotothelastside
chaincarbon.Thecyclicsidechainmeansthatprolineisconformationallyrigid.That
is,thecarboncarbonbondsofprolinedonotrotateinsolution.Otheraminoacids
aremoreflexibleinsolution.
Peptidebond.Thepeptidebondjoinsthecarboxylandaminogroupsofamino
acids.Whenactivated,carboxyllicacidsandaminesformamides.Aminoacidsare
bifunctional,witheachaminoacidhavingbothaminoandcarboxylgroups.
Peptidesarecomposedofaminoacidsjoinedheadtotailwithamidebonds.
Peptidesareclassifiedaccordingtotheirchainlength.Oligopeptidesareshorter
thanpolypeptides,althoughnodefinedtransitionexistsbetweenthetwoforms.
Thejoiningofaminoacidstoformapeptidebondoccursformally(althoughthe
mechanismofitsformationismorecomplicated)inthefollowingway:

Notethattwoaminoacidscanformadipeptide(apeptidecomposedoftwounits)
ineitheroftwoways.Forexample,glycineandalaninecanformglycylalanine(gly
ala)oralanylglycine(alagly):

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Nomatterwhicharrangementoccurs,eachdipeptidewillhaveonefreeaminogroup
andonefreecarboxylgroup.Peptidesequencesarewritteninthedirectionfromthe
aminotothecarboxylend.
Peptidebondstructure.ThepeptidebondstructurefavorscoplanarN,C,andO
atoms.Althoughapeptidebondisformallyacarbonnitrogensinglebond,the
unpairedelectronsonthecarboxyloxygenandonthenitrogencanoverlapthrough
theirpiorbitalstomakethethreeatomsystempartiallydoublebondedin
character.Thepartiallydoublebondedsystemmakesithardertorotatethepeptide
bondinsolution.Asaresult,peptidebondscanexistinoneoftwoconformational
isomers,withthetwocarbonseithercisortranstoeachother.

Usually,thetransconformationisfavored.Prolineisanexceptionalcasebecauseits
peptidebonddoesnothaveahydrogen,makingthecisandtransisomersharderto
changeonefortheother:

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Prolineusuallyisfoundinthetransisomer,althoughconversion(isomerization)
betweenthecisandtransformscanbecatalyzedbyspecificenzymes.

Cliff'sNotes
Doyouknowofanywaytosimplifytheoverallsubjectofbiochemicalgenetics?
WhatdidMendeldiscoverabouthereditywhenhewasplayingaroundwithplants?
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