Amino acids

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  • 1.AminoAcidsAnas Bahnassi

2. WhatAreAminoAcids? Aminoacidsarebuildingblocksforproteins Theyhaveacentralcarbonandaminoand carboxylgroups 20differentaminoacids Samecorestructure,butdifferentsidegroup(R) TheCischiral(exceptglycine);proteinscontainonlyLisoforms. Aminoacidsareampholytes: pKa ofCOOHis~2 pKa ofNH2is~9 AtphysiologicalpHmostaminoacidsbehaveaszwitterion. 3. AminoAcidsClassification AminoacidscanbeclassifiedaccordingtoPOLARITY to: Hydrophobic/nonpolarRgroup:Glycine,alanine,valine,leucine,isoleucine,methionine,proline,phenylalanine,tryptophan PolarRgroup(netcharge0atpH7.4):Serine,threonine,cysteine,tyrosine,asparagine,glutamine,histidine PolarRgroup(ChargedionatpH7.4):aspartate,glutamate,lysine,arginine 4. NonPolarR Group O O CO-+H3NCH C O-CH3+H2N Proline alanineO OO +H3NCH CO- +H3N CH C O-+H3NCHC O- CH2 CH CH3CHCH3 CH CH3CH2CH3 CH3 CH3 valine leucineisoleucine 5. NonPolarR GroupO O +H3N CHC O-+H3NCHC O-CH2CH2CH2OS HN+H3N CHC O-CH3CH2 Methionine TryptophanPhenylalanine 6. O PolarR Group +H3N CHC O- OO +H3NCHCO- CH2 +H3N CHCO-CHOH CH2CH2C O CH3 threonine serineglutamineO NH2OH +H3NCH CO- CH2 O +H3NCHC O-O+H3NCHC O- CH2CH2SH Otyrosine OHC O +H3NCHCO-cysteineNH2Hasparagine Glycine 7. OOChargedR Groups+H3NCH CO- +H3N CHCO-CH2 CH2OCH2 CH2+H3N CH CO- lysine CH2 CH2CH2arginine CO CH2 NH O- O NH3+C NH2+aspartatic acid+H3NCHC O-NH2CH2CH2C O glutamicacidO- 8. AminoAcidsClassification AminoacidscanbeclassifiedaccordingtoRGroup to: Aliphatic:gly (G),ala (A),val (V),leu (L),ile (I) Aromatic:Trp (W),Phe (F),Tyr(Y),His(H), Sulphur :Met(M),Cys (C) Hydroxyl:Ser (S),Thr (T),Tyr(Y) Cyclic:pro(P) Carboxyl:asp(D),glu (E) Amine:lys (K),arg (R) Amide:asn (N),gln (Q) 9. AliphaticSideChainAminoAcidsO O +H3NCH C O- +H3N CHC O- HCH3glycine alanine O OO+H3NCH CO- +H3N CH C O-+H3NCHC O-CH2 CH CH3CHCH3CH CH3CH2CH3CH3 CH3 valineleucineisoleucine 10. HydroxyContainingAminoAcidsOO +H3N CHCO- +H3N CHC O-CH2CHOHOH CH3 serinethreonineSulfurContainingAminoAcids OO+H3N CHC O-+H3NCHC O- CH2CH2 CH2 SH S cysteinemethionine CH3 11. AcidicAminoAcidsOO +H3N CHC O-+H3N CH CO-CH2CH2C O CH2O-aspartaticacidCO glutamicacid O-AmidesofAcidicAminoAcidsO O +H3N CHCO- +H3NCHCO-CH2 CH2C O CH2C ONH2 asparagine NH2glutamine 12. BasicAminoAcids OO +H3N CH C O- +H3NCHCO-CH2 CH2CH2 CH2CH2 CH2CH2 NHNH3+C NH2+NH2 lysinearginine 13. BenzeneContainingAminoAcids O O +H3N CH C O-+H3NCHC O-CH2CH2 OH phenylalaninetyrosine 14. HeterocyclicAminoAcidsOOO+H3NCHC O- +H3NCHC O-CO-CH2CH2+H2N N NHHN Proline histidine tryptophan 15. LearnAminoAcidsStructures Thebestapproachistouselogicandnamerecognitionandtolookforsimilarities,notdifferencesinstructures. TheNameshouldtellyouthestructure. Structuresarebuiltononeanotherandinterrelate. Learningaminoacidspreparesyouforunderstandingproteinsstructure. 16. BASICS Letsstartwiththebasics.Allaminoacidshaveacommonstructuralunitthatisbuiltaroundthealphacarbon(click1).Letscallthisthecorestructure.Thefigureshowsthecorewithoneofthebondsonthecarbonunassigned.AgroupinthislocationisrepresentedbytheletterR(click1).COOH+H 3N CHRRRgroupsaretheonlyvariablegroupsinthestructure.ConsiderRtheonlyunknownandfocusonthisgrouptolearnthestructures.Hence,Rule(1)isaminoacidsarecomposedofacoregroupandanRgroup.Rule(2)istheRgroupgivesanaminoaciditsstructuralidentityand,lateraswewillsee,itsuniquebiochemicalproperties.Thus,ifyouinsistonusingflashcards,drawthemasshownabove(click1)withtheboxrepresentingthecore.Clicktogoon. 17. BuildinganRGroup YousawtheimportanceoftheRgroup.Now,youwillseehowRgroupsbuildandinterrelate.Fourthatillustratethispointareglycine,alanine,phenylalanineandtyrosine.TheRgroupsofeachwillbeshownbelow(click1).GlycineAlanine Phenylalanine Tyrosine H CH3CH2 CH2OH WithanH,glycineisthesimplestaminoacid,sonamedbecauseofitssugarytaste(click1). Alaninewithamethylgroupisthenextsimplest(click1).Theredcolorhelpsyouseehow eachRgroupstructurediffersfromthepreceding.Phenylalanineariseswhenaphenyl groupreplacesanHonalaninesmethylgroup(click1).TyrosineevolvesbyaddinganOH grouptotheparapositiononthephenylringofphenylalanine(click1).Clicktogoon. 18. AcidicandAmideAminoAcidsTheacidicaminoacidshave()chargesintheirRgroup.Therearetwo,asparticacidandglutamicacid(click1).Notetheirsimilarity.GlutamicacidhasonemoreCH2 group(click1).NotethatbothhaveaCOO groupwhichgivesthenegativecharge.AsparticGlutamic AsparagineGlutamine acid Acid CH2 CH2CH2 CH2COO CH2COOC=O CH2COONH2C=O COOAspartateGlutamate NH2TheCOO canexchangeaprotonwiththesolventandhencebehaveasanacid.Thesuffixateisusedtodesignateanionizedacid(moreproperlycalledasalt).Hence,youwillseeasparticacidandglutamicacidreferredtoasaspartateandglutamate(click1).Byformingtheamidederivativesofaspartateandglutamateyougiverisetoasparagineandglutamine(click1).Notename andstructure similaritiesbetweentheopenandthecorrespondingamideaminoacids.Clicktogoon. 19. The(+)chargedaminoacidsarerepresentedbylysine,arginineandhistidine.Unfortunately,Rstructuresforbasicaminoacidshavelittleresemblancetooneanother.Buteachischaracterizedbya(+)NintheRgroup. LysineArginineHistidine CH2CH2 CH2 CH2CH2 CH2CH2HNNH+ CH2NH +HImidazole NH3+ 2N=CNH2 EpsilonaminoGuanidiniumItwillhelpyoutorememberthateach(+)Nispartofagroup.Forlysinethisgroupiscalledtheepsilonaminogroup(click1).Inarginineitstheguanidiniumgroupandforhistidineitstheimidazolegroup.Rememberthesegroupnamesandyouwillrememberthestructuresofthebasicaminoacids.Clicktogoon. 20. Serine,Threonine,CysteineandMethionineStartwithserine.SerinehasasimpleCH2OHforitRgroup(click1).Threonineisserinewithamethylgroup(click1).And,ifyoureplacetheOinserinewithanS,yougeneratecysteine(click1).Serine Threonine Cysteine MethionineCH2OH HCOH CH2SHCH2 CH3CH2SCH3 Methionineappearstocombinecysteinewiththreonine.Thenametellsyou methioninehasasulfur(thio)andamethylgroupinthestructure.Likethreonine methioninehasa2carbonchainattachedtothealphacarbon(click1).Thisis followedbysulfurandendswithamethylonthesulfur.Clicktogoon. 21. Valine,Leucine,Isoleucine These3branchedchainhydrophobicaminoacidshaveonlyCandHintheirRgroups.ValineiseasytorememberbecausethecarbonchainisarrangedastheletterV(click1).Leucineandisoleucinebothhavea4carbonRgroup.LeucineresemblesvalinebutwithaCH2 beforetheV(click1).IsoleucinessidechainresemblestheletterL,justtheoppositeofwhatyouwouldpredictfromthename(click1).Todistinguishthe3,focusonlyonthebranchedchainsintheRstructure.Valineandleucinehaveonlymethylgroups,whereasisoleucinesbranchesareonemethylandoneethylgroup(click1).Clicktogoon.LeucineIsoleucineValineC C C C C C CCEthylgroupC C C 22. TryptophanandProlineThelast2aminoacidtoconsideraretryptophan(pronouncedtriptoefane)andproline.Tryptophanisuniqueinhavinganindolering(click1).AttachthisringtothecoreviaaCH2groupandyoucompletethestructureoftryptophan(click1).Prolinealsohasaring,butthisringissaturated.Infactprolinesringlookslikehomeplateinbaseball(click1).Noteprolinedoesnothaveacorestructure.Thisisbecausethealphaaminogroupisincorporatedintothering. TryptophanProlineH2C CH2CH2 H H2CC NCOONHH Indole Thiscompletesalltheaminoacids.Reviewthislessonasmanytimesasnecessary.Usepaperandpenciltodrawoutthestructures.Soonyouwillhavemasteredaminoacidstructures.Clicktogoontoquiz. 23. TestYourKnowledge.Clicktoseetheanswer.Q:WhataminoacidhastheshortestcarbonchaininitsRgroup?A.Q:Whatstructuralfeatureiscommontoalanine,serineandcysteine?A:Q:WhichaminoacidhasthelongeststraightchainofcarbonsinitsRgroup? A:Q:WhatRgroupstructuralfeatureiscommontophenylalanine,tyrosine, tryptophan,andhistidine?A:Q:WhatstructuralfeatureiscommontoisoleucineandthreonineA: 24. PharmaceuticalBiotechnologyAnas Bahnassi PhD RPh abahnassi@gmail.comhttp://twitter.com/abahnassihttp://www.linkedin.com/in/abahnassihttp://www.udemy.com/Biotechnology http://www.slideshare.net/abahnassiattribution non-commercial share alike