Proteins: Characteristics and Properties of Amino Acids

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1 SBI4U:Biochemistry Macromolecules Eachaminoacidhasatleastoneamineandoneacidfunctionalgroupasthe nameimplies.thedifferentpropertiesresultfromvariationsinthestructuresof differentrgroups.thergroupisoftenreferredtoastheaminoacidsidechain. Aminoacidshavespecialcommonnames,however,athreeletterabbreviation forthenameisusedmostofthetime.asecondabbreviation,singleletter,is usedinlongproteinstructures.completetheactivityattheendofthisnoteto reviewthestructure,names,polarityandabbreviationsofthe20majoramino acids. Therearebasicallyfourdifferentclassesofaminoacidsdeterminedbydifferentsidechains: (1)non polarandneutral (3)acidicandpolar (2)polarandneutral (4)basicandpolar. PrinciplesofPolarity: Thegreatertheelectronegativedifferencebetweenatomsinabond,themorepolarthebond.Partialnegative chargesarefoundonthemostelectronegativeatoms,theothersarepartiallypositive. Non PolarSideChains: Sidechainswhichhavepurehydrocarbonalkylgroups(alkanebranches)oraromatic(benzenerings)arenonpolar.Examplesincludevaline,alanine,leucine,isoleucine,phenylalanine. Thenumberofalkylgroupsalsoinfluencesthepolarity.Themorealkylgroupspresent,themorenon polarthe aminoacidwillbe.thiseffectmakesvalinemorenon polarthanalanine;leucineismorenon polarthanvaline. PolarSideChains: Sidechainswhichhavevariousfunctionalgroupssuchasacids,amides,alcohols,andamineswillimparta morepolarcharactertotheaminoacid.therankingofpolaritywilldependontherelativerankingofpolarity forvariousfunctionalgroupsasdeterminedinfunctionalgroups.inaddition,thenumberofcarbon hydrogens inthealkaneoraromaticportionofthesidechainshouldbeconsideredalongwiththefunctionalgroup. Example:Asparticacidismorepolarthanserinebecauseanacidfunctionalgroupismorepolarthananalcohol group. Example:Serineismorepolarthanthreoninesincethreoninehasonemoremethylgroupthanserine.The methylgroupgivesalittlemorenon polarcharactertothreonine. Example:Serineismorepolarthantyrosine,sincetyrosinehasthehydrocarbonbenzenering. Acid BasePropertiesofAminoAcids: AcidicSideChains: Ifthesidechaincontainsanacidfunctionalgroup,thewholeaminoacidproducesanacidicsolution.Normally, anaminoacidproducesanearlyneutralsolutionsincetheacidgroupandthebasicamine groupontherootaminoacidneutralizeeachother.iftheaminoacidstructurecontainstwoacidgroupsand oneaminegroup,thereisanetacidproducingeffect.thetwoacidicaminoacidsareasparticandglutamic.

2 SBI4U:Biochemistry Macromolecules BasicSideChains: Ifthesidechaincontainsanaminefunctionalgroup,theaminoacidproducesabasicsolutionbecausethe extraaminegroupisnotneutralizedbytheacidgroup.aminoacidsthathavebasicsidechainsinclude:lysine, arginine,andhistidine. Aminoacidswithanamideonthesidechaindonotproducebasicsolutions(i.e.,asparagineandglutamine). NeutralSideChains: Sinceanaminoacidhasbothanamineandacidgroupwhichneutralizesitself,theaminoacidisneutralunless thereisanextraacidorbaseonthesidechain.ifneitherispresent,thenthewholeaminoacidisneutral. Aminoacidswithanamideonthesidechaindonotproducebasicsolutions(i.e.,asparagineandglutamine). Youneedtolookatthefunctionalgroupscarefullybecauseanamidestartsoutlookinglikeanamine,buthas thecarbondoublebondoxygen,whichchangestheproperty.amidesarenotbasic. Eventhoughtryptophanhasanaminegroupaspartofafive memberring,theelectronwithdrawingeffectsof thetworingsystemsdonotallownitrogentoactasabasebyattractinghydrogenions. LearningCheckQuestions: 1. CompletethepropertycolumnofTable1:Characteristicsofthe20MajorAminoAcidsonthe nextfewpagesbymatchingtheproperties(polarityandacid baseproperty)withthecorrect aminoacids.youwillneedtoanalyzether groupsidechainsinordertocorrectlycategorize theaminoacidsintothefourdifferentclassesofaminoacids.useyourknowledgeof electronegativityandtheinformationinthishandouttohelpyou. 2. Listallaminoacidswithnon polarsidechains.explainwhytheyarenon polar. 3. Rankthefollowingaccordingtoincreasingnon polarity:leu;phe;val;ala (i.e.,1=leastnon polar,4=mostnon polar).explain. 4. Listallaminoacidsbyabbreviationthatareconsideredsomewhatpolar.Explainwhytheyare somewhatpolar. 5. Rankthefollowingaminoacidsbyincreasingpolarity:ser;glu;asp;lys;ala;gln (i.e.,1=morenon polar).explainyourchoice. 6. Whichaminoacidismostinsolubleinwater:isoleucineoralanine?Explainwhy. 7. Whichaminoacidismostsolubleinwater:lysorser?Explainwhy. Checkanswershere

3 SBI4U:Biochemistry Macromolecules TABLE1:Characteristicsofthe20MajorAminoAcids AminoAcid Abbreviation Structure Property 1.Alanine Ala 2.Arginine Arg 3.Asparagine Asn 4.Aspartic Acid 5.Cysteine Asp Cys 6.Glutamic Acid Glu

4 SBI4U:Biochemistry Macromolecules AminoAcid Abbreviation Structure Property 7.Glutamine Gln 8.Glycine Gly 9.Histidine His 10.Isoleucine Ile 11.Leucine Leu 12.Lysine Lys

5 SBI4U:Biochemistry Macromolecules AminoAcid Abbreviation Structure Property 13. Methionine Met 14. Phenylalanine Phe 15.Proline Pro 16.Serine Ser 17.Threonine Thr 18. Tryptophan Trp

6 SBI4U:Biochemistry Macromolecules AminoAcid Abbreviation Structure Property 19.Tyrosine Tyr 20.Valine Val PropertyMatchingOptions(cutandpasteorcopyintotable) Acidic Polar Acidic Polar Basic Polar Basic Polar Basic Polar Neutral Non polar Neutral Non polar Neutral Non polar Neutral Non polar Neutral Non polar Neutral Non polar Neutral Non polar Neutral Non polar Neutral SlightlyPolar Neutral SlightlyPolar Neutral Polar Neutral Polar Neutral Polar Neutral Polar Neutral Polar

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