Proteinsandnucleicacids(lecture34):Weslowlymoveclosertothemoleculesthatmakeupacell.Everythinginbiologyisbasedoncarbonchemistry,becausecarboncanform4covalentbonds,andthereforecanformaninfinitevarietyofmolecules,coveredinorganicchemistry.ThedefaultmoleculehasonlyC-CandC-Hbonds,e.g.themoleculeoctane,whichyoucanfindingasoline.Wheneversomethingelseisattachedtocarbon,wecallitafunctionalgroup.Importantfunctionalgroupsare:Hydroxyl,Amino,andCarboxyl.Rstandsfortherestofthemolecule(canbeanything,butmuststartwithaC).Humansaremadeupofwater,largemolecules,ionsandsmallmolecules.Babieshavethehighestwatercontent,asyougetolderyoudryupmoreandmore.Weusuallycallproteins,nucleicacidsandcarbohydratesmacromolecules,becausetheycanformlargepolymers.Advantageofbiochemicalunity:wecanobtainenergyfromeatinganddigestingotherorganisms.Twoverycommonchemicalreactionsinmetabolism:Condensation:formationofapolymerlinkedbycovalentbonds,releasingonewatermoleculewitheachmonomeradded.Thisreactionisanabolic,requiresenergyinput.ExamplesareDNAreplication,proteinsynthesis,makingofstarch.Hydrolysis:Breakingofcovalentbondswiththehelpofwatertotransformapolymerintoitsconstituentmonomers.Thisreactioniscatabolic,releasesenergy.Example:digestionoffoodmoleculesforenergygeneration.Organismsconsistof100sofdifferentlipids,5nucleotidesformingRNAandDNA,1000sofdifferentsugars,and10000-30000differentproteinsfrombacteriatohumans(andreallymuchmoreifallmodificationsandisoformsarecounted).Proteins:Proteinsarethemachinesthatdoalloftheworkinacell:buildstructureslikehair,replicateDNA,catalyzemetabolicreactions,transportmaterialsinsidecellsandacrossthemembrane,etc.Proteinsaremadeofaminoacids,whichareionizedatneutralpH.Thereare20aminoacids,whichareclassifiedaccordingtothepropertiesoftheirsidechains:nonpolar,hydrophobicaminoacids;polaraminoacids;chargedaminoacids.Peptidebondformation(acondensationreaction)occursbetweenthecarboxylgroupofoneaminoacidandtheaminogroupofthenextaminoacidgeneratingapeptidebackboneconsistingofNCCNCCNCCNCCrepetitions(inthis

exampletherearefouraminoacidscovalentlybonded.Anaminoacidalwaysstartswithanaminogroup[N-terminus]andendswithacarboxylgroup[C-terminus]).Aminoacidsareabbreviatedwithathreelettercodeoraonelettercode:proline=Pro=PThenumberofaminoacidsusedandthesequenceinwhichtheyarearranged(covalentlybondedtoeachother)iscalledtheprimarystructure.Theprimarystructuredeterminesallthepropertiesoftheresultingprotein.Thereisanunimaginablylargeamountofpossibledifferentwaysaminoacidscanbearrangedinalargeprotein.Evenforasmall100aminoacidprotein,therearemorepossibilitiesthanatomsintheuniverse;enoughforbillionsofyearsoffurtherevolution!Asthepolypeptidebackboneconsistsofsinglecovalentbonds,itisprettyflexible(rotationaboutthesinglebondsispossible,fullrotationfortheC-Cbond,lesssofortheN-Cbond).Thisallowspolypeptidestofoldintoproteins.Thisoccursintwosteps.First,hydrogenbondsformwithinthepolypeptidebackbonebetweentheOofacarboxylgroupandtheHofanaminogroup.Thiscangiverisetoexactlytwosecondarystructuresthatformveryquicklyafterapolypeptidehasbeenmade:thealpha-helixandthebeta-pleatedsheet.Notethatthesehydrogenbondsdonotinvolvethesidechainsatall!Inthealpha-helix,hydrogenbondsforminthedirectionofthehelix,generatingastablerod-likestructure.Sidechainspointoutwards,awayfromthehelix.Inthebeta-pleatedsheet,hydrogenbondsformwithintheplaneofthesheet,generatingastablesheet.Sidechainspointawayfromtheplane,upordown.Therearenoobviousrules,whereyoullfindalphahelicesandbetasheetswithinaprotein.Proteinstructuredeterminationistheonlywaytoconfirmthepresenceorabsenceofsecondarystructureswithinaprotein.Importantformanystructuralproteinsisthecoiledcoil,whicharetwoalpha-heliceswrappedaroundeachother.Hydrophobicaminoacidsatevery4thpositiongeneratesabandofhydrophobicityrunningalongthelengthofthealpha-helixandslowlyrotatingaroundit.Hydrophobicinteractionthenensuresthattwosuchalpha-helicescometogetherjustatthatbandresultinginthecoiledcoil(exactlylikearopethatconsistsofintertwinedstrands).Thisstructureoccursinproteinsgivingstrengthtotendons,hair,feathersProlineisauniqueaminoacid,becausethesidechainiscovalentlybondedtoboththeCandtheNatomofthepeptidebackbone.ThisgeneratesakinkinthepeptidebecausetheringpreventsfreerotationoftheN-Cbond.Also,thebackbonehydrogenbondcannotform,becausethebackboneNlacksahydrogen.Thereforeformationofsecondarystructures(alphahelix,betapleatedsheet)isimpossible.Aprolineisoftenthelastaminoacidofanalphahelix.

Summary:primarystructureisjustthesequenceofaminoacids,witheachaminoacidlinkedtothenextbypeptidebonds.Somestretchesofthispolypeptidefoldintoanalpha-helixorbeta-pleatedsheet(secondarystructure),orremainunfoldedatthisfirststageoffolding.Tertiarystructurefinishesthefoldingofapolypeptide,andismediatedbysidechaininteractions.Fourtypesofinteractioncontributetotertiarystructureformation:ionicbonds,hydrogenbonds,disulfidebonds,andhydrophobicinteractions,allofthemtypicallybetweenaminoacidsidechainsintheinterioroftheprotein.Curling/Uncurlingyourhair:reduce/breakdisulfidebondsinkeratin;thenshapehairasyouwish;finallyoxidize/reformdisulfidebondstokeephairinnewshape.Inthekeratinprotein,youfindcoiledcoilsformingthroughhydrophobicinteractionasdiscussedabove,andadditionally,youfinddisulfidebondsbetweenalpha-helicestoprovideadditionalstrength.Hydrophobicinteractionsarethemostimportantdeterminantofproteinfolding/tertiarystructure,becausestretchesofhydrophobicaminoacidsautomaticallyrearrangetowardstheinteriorofaprotein(awayfromwater),whereashydrophilicaminoacidsrearrangetobeontheoutsideinteractingwithwater.Important:primarystructure(peptidebondformation)requiresenergy,secondary/tertiaryfoldingreleasesenergy,i.e.occursautomaticallyQuaternarystructureindicatesseveralpolypeptidesinteractingtoformabiggerproteincomplex,e.g.hemoglobinconsistsoffourindividualpolypeptides,thecoiled-coilkeratinconsistsofthreealpha-helices.Manyproteins,however,consistofonlyonepolypeptide,thatis,theyarefullyfoldedaftertertiarystructureformation.Theimportanceoftheaminoacidsequence(primarystructure)forfoldingandfunctioncanbedemonstratedinmultipleways:First,asingleaminoacidmutationintheproteinhemoglobinchangestheshape(alsocalledconformation)ofhemoglobin,andthisresultsinashapechangeofredbloodcells(sickled),becauseredbloodcellscontainonlyhemoglobin.Second,atypicalproteinsufficientlydilutedinwaterysolutiondenaturesathightemperature(unfolds),butwillrenature(refold),whenthetemperatureislowered.Thisisevidencethattheprimarystructureissufficientforproteinfolding,orinotherwords,alltheinformationaboutproteinfoldingandfunctionisencodedbytheprimarystructure.

Proteinturnover:proteinshaveahalf-liferangingfromminutestoweeks(averageabout2days).Proteinturnoverisveryimportant,becauseproteinsoftengetdamaged:fever,pHchange(lemonjuiceinmilkchangestheprotonationstateofCOOHandNH3groups;milkproteinsprecipitate,samehappensincheeseproduction),otherchemicalchanges.Example:eggbecomeshardbyboilingbecauseproteinsdenature,andgetallentangledwhentheytrytorenature.Chaperoneshelpproteinstofoldproperlyaftersynthesisorafterstress-relatedunfolding.Nucleicacids:NucleotidesmakeRNAandDNA,andservefunctionsinsignalingandenergystorageasmonomers.Anucleotideismadeupofa5-carbonsugar,anitrogenousbaseandaphosphategroup.4nucleotidesinRNA:cytosine,uracil(pyrimidines);guanine,adenine(purines).InDNAuracilisreplacedbythymine.DNAlacksthehydroxylgroupatcarbon-2(deoxyribose).Nucleotidespolymerizeviaphosphodiesterlinkages(anothercondensationreaction),withthe3hydroxylgroupofthepolymerformingacovalentbondwiththe5phosphategroupoftheincomingnucleotide(5and3referstothepositionofthecarbonatom,wherethefunctionalgroupisattached).ThismeansthatalongRNA/DNAmoleculealwaysstartswitha5phosphategroupandendswitha3hydroxyl,wesay,polymerizationoccursin5to3direction.DNAismadeoftwoantiparallelstrandsheldtogetherbyhydrogenbondsbetweenthebases.Purinebasescanonlypairwithpyrimidinebases,andmorespecifically,guanine(G)withcytosine(C),andadenine(A)withthymine(T).G-Cformsthreehydrogenbonds,andisthereforemorestablethanA-T,whichformstwohydrogenbonds.DNAisadoublehelixwiththesugar-phosphatebackboneontheoutsideandthebasesontheinsidearrangedlikerungsonaladder.Thedouble-helicalstructureresultingfromtwostrandsbeingwoundaroundeachotherhasamajorgrooveandaminorgroove.Inthemajorgroove,thetwosugar-phosphatebackbonesaremorewidelyspacedallowingDNA-bindingproteinstorecognizethebasesintheinterior.Thisisveryimportantfortranscriptionfactors,restrictionenzymesetc,whichrecognizeauniqueDNAsequence.TheoverallDNAsequenceofagenomecarriesthegeneticinformation.BasepairingandthedoublehelicalstructuresmakesDNAmuchmorestablethanRNA.RNAcamefirstinevolution,becauseitcanstoreandexecuteinformation.RNAcanworklikeanenzymecatalyzingcertainreactions,becauseitcanfoldintocomplicated3Dstructuressimilartoproteins.Thefoldingoccursbecausenucleotidebaseswithinthesamemacromoleculepairviahydrogenbonds(in

contrasttoDNA,wherenucleotidebasesofdifferentmacromoleculespair).AparticularlyimportantRNAstructurefoundinmanymRNAsisthestem-loopstructure,whichcontributestotheregulationofmRNAfunction.