Chapter1 Amino acids.ppt

Chapter1Aminoacids,Outline,StructureandclassificationofAAPropertiesandfunctionofAASeparationandpurificationofAA(self-study),Differentside-chain(Rgroup)Differentchemicalandphysicalproperties,Aminogroup,Carboxylicacidgroup,Aminoacidstructure,ProteinogenicAAorcanonicalAA.EncodedbygeneticcodesanddirectlyintroducedintoproteinduringtranslationDifferinsidechain(Rgroup)20commonlyfoundAllorganismshavesamesetof202rarelyfound(selenocysteineandpyrrolysine)Non-proteinogenicAAornon-canonicalAANeverdirectlyintroducedintoproteinsduringtranslationCanbenaturally-occurringorchemicalmodificationsofproteinogenicAA,ProteinogenicAA&non-protenogenicAA,AliphaticAromaticSulfurcontainingPolar/unchargedbasic/acidic,Hydrophobic:waterfearing.non-polarsidechains,Hydrophillic:waterloving.polar,neutralchains,negativelycharged,positivelycharged,AminoAcidClassification,6Non-polarAminoAcids,6Polar,UnchargedAminoAcids,3AromaticAminoAcids,6Polar,ChargedAminoAcids,21st&22ndAAs,DiagrammaticrepresentationofAAclassification,EssentialAminoAcids,All20commonaminoacidsarerequiredforproteinsynthesis,butthehumanbodyisabletosynthesizeonly12ofthem.Theother8(theessentialaminoacids)mustbeobtainedfromfood,whichincludethreonine,isoleucine,phenylalanine,methionine,tryptophan,valine,leucine,andlysine.Histidineandargininearecalledsemi-essentialaminoacidsbecausetheyarealsorequiredtobeobtainedfromfoodundersomeconditions.,Abbreviationsfor22aminoacids,Alanine-Ala-AArginine-Arg-RAsparagine-Asn-NAsparticAcid-Asp-DCysteine-Cys-CGlutamine-Gln-QGlutamicAcid-Glu-EGlycine-Gly-GHistidine-His-HIsoleucine-Ile-ILeucine-Leu-LLysine-Lys-K,Methionine-Met-MPhenylalanine-Phe-FProline-Pro-PSerine-Ser-SThreonine-Thr-TTryptophan-Trp-WTyrosine-Tyr-YValine-Val-VAsparagine/AsparticAcid-Asx-BGlutamine/GlutamicAcid-Glx-ZSelenocysteine-Sec-UPyrrolysine-Pyl-O,Propertiesof20CommonAminoAcids,AminoAcidsnotfoundinProteins,CapacitytopolymerizeChiralityNovelacid-basepropertiesVariedstructureandchemicalfunctionality,PropertiesofAminoAcids,AACondensationandPeptideBondFormation,APeptideBondisanamidebondlinkingtogetheraminoacidsformingpeptidesandproteins.,L-AminoAcids,SinceallaminoAcidsbutglycinearechiralmolecules,itspossibletohaveenantiomers.However,natureusesonlyoneenantiomer,theL-aminoacid.,L-glyceraldehyde,L-aminoacid,ZwitterionsandpI,AZwitterionisadipolarion.Sinceaminoacidscontainbothanacidandabase,aninternalacid-basereactionformsazwitterion.,Aminoacid,Zwitterion,Aminoacidsexistprimarilyaszwitterions.,Zwitterions,Aminoacidzwitterionsareamphoteric.Theycanreactaseitheracidsorbases.,Inacidsolution,Inbasesolution,zwitterion,protonated,zwitterion,deprotonated,IsoelectricPoints,TheisoelectricpointofanaminoacidoccursatthepHwheretheaminoacidexistsasthezwitterion.,deprotonatedbasesolutionhighpH,protonatedacidsolutionlowpH,zwitterionisoelectricpoint,pI(isoelectricpoint)=thepHatwhichthenumberofpositiveandnegativechargesonapopulationofmoleculesisequal(i.e.nonetcharge).,pK1carboxylicacid=2pK2aminogroup=10pI=(pK1+pK2)/2,TitrationCurveforAlanine,pK1carboxylicacid=2.2pK2Rgroup=4.3pK3aminogroup=9.7pI=(pK1+pK2)/2pI=(2.2+4.3)/2pI=3.25,TitrationCurveforGlutamicAcid,pK1carboxylicacid=2.2pK2aminogroup=9.0pK3Rgroup=10.5pI=(pK2+pK3)/2pI=(9+10.5)/2pI=9.75,TitrationCurveforLysine,NonetchargeMinimumsolubilityinwaterproteinwillprecipitateoutatitsisoelectricpointcanseparateaminoacidsandpeptidesbasedinelectrophoresis:+chargedaminoacidsmovetoelectrode-chargedaminoacidsmoveto+electrode0aminoacidsattheirisoelectricpointsdonotmove,IsoelectricPoints,ReactionwithHNO2ReactionwithDNFBandPITCReactionwithNinhydrin,ChemicalreactionsinvolvingAAs,ProcannotreactwithHNO2,ReactionwithHNO2andVanSlykeDetermination,ReactionwithDNFBandPITC,Usedtovisualizespotsorbandsofaminoacidsseparatedbychromatographyorelectrophoresis.DeeppurplecolorformedwithtracesofanyaminoacidexceptPro(yellow).,ReactionwithNinhydrin,Onlythreeaminoacids,Phe,Tyr,andTrp,absorblightinthenearUVrange(230nm-300nm).TheseaminoacidsdominatetheUVabsorptionspectraofproteins.Thewavelengthmaximafortyrosineandtryptophanarearound280nm.Incontrast,nucleicacidshaveabsorptionmaximumof260nm.ThusasimpleUVscancanallowonetodistinguishbetweenproteinandnucleicacids.,UV-absorbingPropertiesof3AromaticAAs,InsolutionitisthenatureoftheaminoacidR-groupsthatdictatestructure-functionrelationshipsofpeptidesandproteins.ThehydrophobicAAswillgenerallybeencounteredintheinteriorofproteinsshieldedfromdirectcontactwithwater.Conversely,thehydrophilicAAsaregenerallyfoundontheexteriorofproteinsaswellasintheactivecentersofenzymes.TheimidazoleringofhistidineallowsittoactaseitheraprotondonororacceptoratphysiologicalpH.Hence,itisfrequentlyfoundinthereactivecenterofenzymes.Theprimaryalcoholofserineandthreonineaswellasthethiol(-SH)ofcysteineallowtheseaminoacidstoactasnucleophilesduringenzymaticcatalysis.Additionally,thethiolofcysteineisabletoformadisulfidebondwithothercysteines:Cysteine-SH+HS-CysteineCysteine-S-S-CysteineDisulfidebondingbetweencysteinesindifferentpolypeptidechainsofoligomericproteinsplaysacrucialroleinorderingthestructureofcomplexproteins,e.g.theinsulinreceptor.,FunctionalSignificanceofAAR-Groups,Separatingaminoacidsinmixturesisusuallybasedonrelativedifferencesintheirphysicalandchemicaltraits.Theseareallmediatedbytheir“R”orfunctionalgroups.Thegeneralstrategyistoexploittheabilityofagivenaminoacidtopartitionbetweentwodifferentphases.Itcouldbetwoliquidphases,asolid-liquidphase,oragas-liquidphase.Inparticular,solid-liquidphasemethodsareroutinelyused,theprocedurebeingtermedchromatography.Typically,thefirststrategyistoexploitanychargedifferencesamongtheaminoacidsatagivenpH.Thisisdonebyion-exchangechromatography.,SeparationandAnalysisofAAMixtures,Electrophoresis,Amixtureofhistidine,serine,andglutamicacidcanbeseparatedbyelectrophoresisatpH=5.68.,-,+,negativelycharged(deprotonated)glutamicacid,serineatitsisoelectricpointatpH=5.68,positivelycharged(protonated)histidine,SeparationofAla,LysandAspbyElectrophoresis,Unfortunately,aminoacidsarenotcoloredasdescribedinthisoverhead.Therefore,whatmethodswouldyouusetofirstcheckifanaminoacidisindeedpresent?,AminoAcidSeparation,