an overview of biochemistry for biochem480 · an overview of biochemistry for biochem480 these are...

AnoverviewofbiochemistryforbioCHEM480 Thesearesomeofthemostimportanttopicsincoveredinanintroductiontomacromolecularbiochemistryinthiscourse:

• Acid-Basechemistry,theconceptofpKA,conjugateacid/basepairs,andtheuseof Henderson-HasselbalchequationV2(i.e.Voet,VoetandPrattChapter2)

• Principlesofbio-energetics;thelawsofthermodynamics,equilibria,kinetics, Enthalpy&entropyV1,V12

• Noncovalentinteractions(NCIs)andspecificintermolecularrecognition(SIR)V2• Functionalgroupsinorganiccompounds&theirmajorreactionsincludingredoxreactions• Aminoacids;classificationbytypesof“R”groupsV4 • Thepeptidebondandproteinstructures(primary,secondaryandtertiary)V4&5 • Collagenandelastin;structure/activity/biologicalfunctionrelationshipoffibrousproteinsV6 • Myoglobin&Hemoglobin;structure/activity/biologicalfunctionrelationshipofglobular

proteinsV7• Thestructure-activity-biologicalfunctionrelationshipofsaccharidesV8• Plasmamembranes;structure/activity/biologicalfunctionrelationshipoflipidsV9 • LipiddigestionandtransportbylipoproteinsandatherosclerosisV20• MembranetransportV10• Enzymes:activity,efficiency,specifityactive/binding/catalyticsites,V10 • Enzymekinetics;Michaelis-Menten,Lineweaver-Burkplots,andregulationV12 • Thestructure-activity-biologicalfunctionrelationshipofnucleicacidsV3• DNAsequencingandDNAengineeringV3

ForfuturereferenceThebioCHEM481course(‘IntermediaryMetabolism’)willconcentrateonbiochemistryasitrelatesto:

• BiochemicalsignalingV13• OverviewofmetabolismV14• Chemicalenergyproductionandconsumption;oxidativephosphorylationV14&18 • Metabolismofcarbohydrates:glycolysis,TCAcycle,gluconeogenesis,PPP,glycogenolyssisand

glyconeogenesisV15,16&17 • Metabolismoftriacylglycerols:degradationandsynthesisoffattyacidsV20 • Metabolismofaminoacids.V21

ThebioCHEM482coursewillconcentrateonbiochemistryasitrelatesto:

• Theintegrationofmetabolismbydifferentorgansandhormonestomaintainadynamicequilibriuminmammals.

• Themolecularprocessesofnucleotidemetabolismineukaryoticcells,particularly,mammaliantissues.

• Themolecularprocessesinphotosynthesisinplantandbacterialcells.

Preamble

PREAMBLE:TheVitalQuestions:

ForfuturereferenceThebioCHEM481course(‘IntermediaryMetabolism’)willconcentrateonbiochemistryasitrelatesto:

• BiochemicalsignalingV13• OverviewofmetabolismV14• Chemicalenergyproductionandconsumption;oxidativephosphorylationV14&18 • Metabolismofcarbohydrates:glycolysis,TCAcycle,gluconeogenesis,PPP,glycogenolyssisand

glyconeogenesisV15,16&17 • Metabolismoftriacylglycerols:degradationandsynthesisoffattyacidsV20 • Metabolismofaminoacids.V21

ThebioCHEM482coursewillconcentrateonbiochemistryasitrelatesto: • Theintegrationofmetabolismbydifferentorgansandhormonestomaintainadynamic

equilibriuminmammals. • Themolecularprocessesofnucleotidemetabolismineukaryoticcells,particularly,mammalian

tissues. • Themolecularprocessesinphotosynthesisinplantandbacterialcells. • Therelationshipbetweenbiochemicaleventsatthemolecularleveltophysiologicalprocessesin

wholeanimals. • Thecorrelationsofabnormalbiochemicalprocesseswithhumandiseasesandsyndromes. • Therelationshipbetweenbiochemicaleventsatthemolecularleveltophysiologicalprocessesin

wholeanimals.

• Thecorrelationsofabnormalbiochemicalprocesseswithhumandiseasesandsyndromes.

Whyislifethewayitis?Whatisthemeaningoflife?WhatisanswertotheUltimateQuestionofLife,TheUniverse,andEverything?[42?]Itstartshere……..

5majortenetsofbiology/biochemistryCelltheory:Hooke,vanLeeuwenhoek,SchleidenandSchwannEvolution:Naturalselection:Darwin&WallaceDNAandinformationflow:TheCentralDogma:WatsonandCrick&(now)EpigeneticsEnergy:Transductionfromlightandchemicalstousefulenergy(ATP)MitchellRegulation…homeostasisandadaptingtochangesatthemolecular/cellularlevelsAGoldenRuleofBiochemistryLivingorganismsareremarkablysimilaratthemolecularlevel**despitetheobservedbiologicaldiversity.Innature,thereexistsabiochemicalunityofdiverselivingorganismsinthatthereisawiderangeofadaptationsaroundacommonchemicalframework(Canyounamesomecommoncompoundsfoundinalllivingspecies?).Thisembodiesjusttheuseofafewelementsi.e.mainlyNCHOPSthatexploitstheabilityofC(andNtoalesserextent)toformstrong(singleanddouble)covalentbondstobothtoitselfandtheseotherelements,especiallyHNOS(withlinear,cyclicandbranchedskeletons)togetherwithalimitednumberofmetalcations(Na,K,Ca,Mg,Mn,Fe,Co,Zn,etc.)toformneutral,cationicandanionicchemicalspecies.Theuniquefeatureofalllivingcellsisthewayinwhichsomanyreactionsthattakeplaceintheorganellesofcells(andcellsintissuesandtissuesinorgansandorgansinorganismsandorganismsinecosystems,etc)areorganizedtoserveasinglepurpose,"life"!**However,theresomesignificantdifferencesbetween'biologicaldomains',i.e.(1)theabilityofsomearcheatosurviveinzerooxygenandseeminglyhostileconditions,i.e.>80oC,highpressures,highsalt,etc),(2)theinventionofphotosynthesisbybacteria(andpassedontoplants),(3)thepossessionofcytoskeletonsbyeukaryaallowingforlargeandcomplexcellstructures.Theunderlyingcommonalityofbiochemicalprocessesarebrieflyreviewedinthefollowing12concepts. Beforeyouembarkasastudentinthisbiochemistrycourseyoushouldreadtheseconceptsforunderstanding.

1. Cells:theirroleandtheircontents. Thecellisthefundamentalunitoflife.Cells,whethertheybeunicellularormulti-cellularorganisms,mustoperateas"open"thermodynamicsystemsbyestablishingadynamicequilibriumwiththelocalmicroenvironment.Livingorganismscreateandmaintainacomplexsystemusingenergy(solarorchemical)extractedfromtheenvironmentandtheyhavetheabilitytodischargewastes.Themolecularorganisationofthecellinvolvesthe:genome,epigenome,transcriptome,proteome,&metabolme.Notallgenesareexpressedinthesamecellatthesametime!Consequentlytheremustbeelaboratecontroloftranscriptionbychemicalsignaling,receptors,feedbackmechanisms,transcriptionalfactorsetc.Furtherthereisaneedforposttranscriptionalandtranslationalchemical“processing”

Thereisnosuchitemasan‘averagecell’.Whatmakesthendifferent?

Allcellsarecomposedofamixtureof(a)smallchemicalspecies(organicandinorganic),(b)intermediate-sizedorganiccompounds,(c)macro-moleculesand(d)organellesinaclearhierarchy(seefigureonfollowingpage).

Intheintestines, digestiveenzymescatalysetheconversion(viahydrolysisreactions)ofproteinstoaminoacidsV21,complexcarbohydratesto(mainly)glucoseV15,fats/oilstofattyacidcarboxylates(RCO2

-)andglycerolV20asinthereverseofthearrowsinthediagramaboveforproteinspolysaccharidesandtriglycerides. Thebacterialcellsharboredwithinthehumangastrointestinaltract(GIT)outnumberthehost’scellsbyafactorof10andthegenesencodedbythebacteriaresidentwithintheGIToutnumbertheirhost’sgenesbymorethan100times.Thesehumandigestivetractassociatedmicrobesarereferredtoasthegutmicrobiome. Thegutmicrobiotainhumansevolvethroughoutlifeandappeartoplayapivotalroleinbothhealthanddisease.Inahealthystate,thegutmicrobiotahavemyriadpositivefunctions,includingenergyrecoveryfrommetabolismofnondigestiblecomponentsoffoods,protectionofahostfrompathogenicinvasion,andmodulationoftheimmunesystem.Further,lackofthemisanecdotallyassociatedwithanumberofdiseases,syndromesand‘functionalaberrations’.

FuelMetabolism:

Asuccessfulorganismhastobeabletosynthesizecompoundsnotsuppliedbythedietinordertosurvive.Thisincludescompoundsofhighchemicalpotentialenergy(i.e.ATP)forbothgrowth,developmentandforprotectionofitsinternalenvironmentfromvariableexternalconditions(i.e.fromthewell-fedtostarvationstates,temperature,O2availability,xenobiotics,etc).

Fiveprocessesarerequired:

(1)conversionofnutrientsinthedietintouseablecompounds,

(2)oxidationofenergy-richmetabolites(seesection6page8)toATP

(3)storageandsubsequentmobilizationofnewenergy-richcompounds,

(4)biosynthesisofcrucialmetabolitesandnon-fuelmacromolecules(proteins,poly-nucleotides,somepolysaccharides,etc)

(5)detoxificationprocessesinwastedisposalpathways.

2.Macromolecules. Macromoleculesareubiquitousinalllivingspeciesandhavecomplexbutsomewhatflexiblestructures. Theystoreandexpressgeneticinformation,provideforcompartmentation,regulatemanyfunctions,andimportantly,allowforbiologicalspecificitybyspecificinter/intra-molecularrecognition(SIR).Macromoleculesfoldintocomplex3-Dstructures(‘conformations’)insuchawayastoenhancetheirstabilitybymaximizingintra-(i.e.internallywithinthemacromolecule)andinter-(betweenthemacromoleculeandthesolvent-usuallywaterexceptinmembranesandmicelles)molecularnon-covalentinteractions(‘NCI’).V2. Macromoleculesspontaneouslyfoldtoachievetheconformationofhighestthermodynamicstabilitythatisorisveryclosetotheconformationofthehighestbiologicalactivity.Itshouldbenotedthatthisfoldingisadynamicprocessandthesemacro-moleculescantakeupmorethanoneconformation,andthereisaconstantswitchingbetweentheconformations(inequilibria)dominatedbythedrivetothermodynamicstabilityunderpossiblyconstantlychangingmicro-environments(i.e.temperature,pH).

Thedrivingforcesfortheformationofthese3Dstructuresisconsideredtobepredominatelyentropicallydriven.Recallthatforanyspontaneousprocess(ΔGo=ΔHo-TΔSoV1),ΔGomustbe<0.[ChangeisconventionallyabbreviatedΔ]Considerthefoldingofaproteinfromtherandomorunfoldedconformationjustformedontheribosometoformingitsnativeorfoldedconformation.TheNCINETenthalpychangesis~0,butthespontaneityinvivorequiresNETΔSo>0.

Initially,watermoleculeshavetoform'cages'thatsurroundthenonpolarorhydrophobic‘R’groupsoftheaminoacidresiduesintherandomconformation.Asthemacromoleculefoldsthesenon-polar groupsonthepolypeptidechainformanon-polarcorethatstabilisesthemacromoleculebythe'expulsionorfreeingup'(tobulksolution)ofthesewatermolecules.TheeffectofthisistocauseextensivedisorderofthewatermoleculesandthusΔSoisNETpositiveandthusdrivestheNET

spontaneousfolding(withΔGo<0).V2

Someproteins(especiallymultisub-unitand/ormulti-domainproteins)areknowntouseotherproteins(disulfideisomerases)V4andchaperoninsV5)tocatalysetheseproteinfoldingprocesses.

Manyoftheseindividualmacro-moleculeswithspecificbiochemicalrolesthenspontaneouslyselfassembleinto"supra-molecularassemblies"(suchaschromosomes,ribosomes,multi-enzymecomplexes,membranes,seehierarchydiagramabove).

Thechemicalstructureandthemicroenvironmentofamacromoleculedeterminesitschemical(re)activitywhichinturndeterminesitsbiologicalfunction.Thisisknownasthe'structure/activity/biologicalfunction'(SAF)relationship[St->Act->Biol.Funct.]

Thusanychangesinstructure(chemicalorconformational:temporaryorpermanent)willcausechangesinactivityandfunction[ΔSt->ΔAct->ΔBF]Anexampleisaproteinbecoming'denatured'bychangesinpH;ΔpH->Δ[ConjugateBaseorCB]/[conjugateacidorCA]foreveryionisablegroup->ΔNCI->ΔStructure/conformation->ΔActivity->ΔBiolFunct).

Sicklecellanaemiarepresentsanotherexample:(V7)ThisdiseaseiscausedbyagenemutationthatleadstoachangeinaminoacidresidueonthesurfaceoftheβsubunitfromHbA(theβ6isaGlu)toHbS(β6isaVal).Thus,comparingHbAandHbS,therewillbeanalterationofthetypeofNCIsthatinwhichthese‘R’groupswillbeinvolved. ThisHbAGluwillbesolvatedbywaterwhereasinHbS,theValhasanon-polarhydrophobic‘R’group.To‘avoid’thisexposureoftheisopropylgroupinValtowater,HbSundercertainconditions,changesitsstructureandaggregatesintoinsolublefibrils. ThusachangeinstructurecauseschangesinNCIsthatcauseschangesinstructuresthatinturncausesachangeinbiologicalfunction(i.e.decreasedabilitytotransportoftransportofO2)

Otherexamplesinclude(1)cysticfibrosis(CF)usuallycausedbya3base/1aminoacidresiduedeletionintheCFTRproteinthatresultsinmisfoldingthanleadstoachangeinmembranepermeability,(V9)and(2)phenylketonuria(PKU)causedbymutationsinthePAHgeneandthusdiminishedenzymeactivitycauseabuildupofPhe(andsomeofitscatabolites)thathasadeleteriousphysiologicaleffect. (V21)

Mostmacromoleculesarechemicallyalteredorprocessedfromtheirinitialformationtothemature,activeconformation. Examplesinclude(i)modificationofaminoacidresiduesincollagenV5,(ii)additionofthehemeunittohemoglobin,myoglobin,andcytochromes,(iii)covalentmodificationbyphosphorylationinregulatoryenzymes,(iv)formationofglycoproteins,proteoglycansandglycolipidsV8(v)conversionoftheprimarytranscript(hnRNA)tothematuremRNAineukaryotesand,(vi)themethylationandacetylationofthebasesofDNAandthehistonesinthechromosomes(in‘epigenetics’).Mostprocessingrequiresspecificenzymesandrepresentsaformofregulationinvivo.

3.BiochemicalReactions. Thebiochemicalreactionsthattakeplacewithinthecellareasubsetofordinaryorganicreactions. Thesamerulesofelectronflow[relatedto(a)relativebondstrengths(b)bondbreaking&formation,(c)orbitalinteractionsofnucleophilicandelectrophilicatoms/sitesandthermodynamicstabilityofreactionintermediatesapplyinvivoasinvitroasdothelawsofthermodynamics!Biochemistry,asmostgeneralisedtextscurrentlypresentit,isacontinuationoforganicchemistrybutinaspecialmedium(water,pH7.4,ionicstrength~0.2M,37oC,etc).Thetypicalundergraduatebiochemistrycourseisinessenceanadvancedorganicchemistrycoursethatfeaturesthemoleculesandchemicalprocessesof'life'(seeearlier).Asyoustudyit,youwilldrawheavilyonwhatyoulearnedinorganicchemistry,aswellasgeneralchemistryI.e.bioenergetics).Examinationofapathway,i.e.glycolysis(V15),TCAcycle(V17),andFAcatabolism(V20)oftheproteins,fats/oilsand

carbohydrates,etcwillrevealtypesofreactionscoveredonorganicchemistry;i.e.dehydrationofalcohols,formationandhydrolysisofesters,amideandacetals,aldol/Claisen/mixedaldol-Claisencondensations,oxidationofalcoholsandaldehydes,etc.Onemajoromissionintheundergraduatecurriculumistheubiquitous(invivo)nucleophilicsubstitutionatP=OthatisusuallynotcoveredbutisanalogoustothesametypeofreactionatC=O(viaapentahedralratherthantetrahedralintermediate)requiringincomingnucleophilesandleavinggroupsusuallyphosphatesorthioethers).4. Metabolic Pathways. Biochemical reactions are organised in specific 'metabolic' pathways(glycolysis, gluconeogenesis, FA catabolism and synthesis, PPP (V15) amino acid and nucleosidecatabolism and synthesisV23, etc.Many intermediarymetabolites [‘IM’] (i.e. glucose-6’P, pyruvate,acetyl-CoA, succinate, asp(D), glu(E) etc.) servemore than one function, i.e. catabolised for energy(leadingtoATPformation)orusedas'building'blocksforthesynthesisoflargercompounds(requiringATP).FormoreclickontheselinksOverviewofCatabolismandATP/NADProles.

InordertoachievetheoptimaluseoftheATPsynthetisedbyanorganism,itiscrucialthatthefluxofchemicalsthroughthesepathwaysberegulatedtoprevent‘futilecycling’.Suchregulationisachievedbycontroloftheactivitiesofspecificenzymesbyallostericeffectors,covalentmodification,hormones,etc.(See#9belowformore.)Thediagrambelowillustratesbothsomeofthepathwaysand,importantly,theessentialinter-connectivityofthesepathways.

AmajorityofthecompoundsinlivingorganismscontainonlyC,HandO.ThenextmostcommoncombinationisCHOandN(aminoacids,proteins,nucleotides,etc).Onaverybasiclevel,‘CHO’endsupasCO2andwaterbutwithnitrogencontainingcompounds,organismsrequirespecialisedpathwaystoeliminateexcessnitrogenouscompounds.Inhumans,thisisaccomplishedmainlybytheformationandexcretionoftheverywater-solubleureaintheurineV21.Thisissynthetisedintheliverandeliminationviathekidneys.Anyammoniatransientlyformedbythedeaminationofaminoacidsetc istransportedfrommosttissuestotheliverwheretheNisincorporatedintoureabytheureacyclerequiringATP.TheureaandTCAcyclesarechemicallyinterconnected.

TransportofwaterinsolubleIMs:Therearealimitednumberofcompoundsoflowsolubilitiesinwater(i.eO2,cholesterols,TAG,FFA)sotheseneedspecifictransportpathwaystoensuretheappropriateconcentrationsofsuchcompoundsattheirspecificsitesofaction.5.Enzymes. Most,butnotall,reactionsinvivowouldeffectivelyNOTtakeplace(especiallyunderthespecialconditionsofmostcells)withoutthepresenceofspecificenzymes(V11). All(almost!)biochemicalreactionstakeplaceinactivesitesofenzymes:substratesbindcustomisedbindingsitesandthechemistry(bondbreakingandformation)ofthereactionsarecontrolledbythecatalyticsiteoftheenzyme.Thereiselectronic(byNCIs)andsteric(byspacerequirements)complementaritybetweenthesubstratesandthebindingsites.Thesubstrates"dock"ontothebindingsitesinspecificorientations(thiscontrolstheregiospecificityofreactions)insuchawaythattheflowofelectrons(see#3above)allowedinthe"catalyticsite"isinonlyonespecificdirection(thiscontrolsthestereospecificityofreactions).Thepresenceofenzymesisthekeytowhatreactionsactuallytakeplace(andatwhatrate)ataspecificbiologicalsitegiventhatthereusuallymanyhundredsofcompoundsavailableatanysuchsite.Specificinter-andintra-molecularrecognition[SIR]isoneofthecharacteristicsofbiochemistryandisespeciallyimportantinenzymespecificity.. Theratesofbiochemicalreactions(andthustherateofaccumulationofproducts)arecontrolledbytheconcentrationofenzymesintheir'active'conformation[Enz]active.[Enzyme]iscontrolled(ata'coarse'level)byboththerateofformationofthehnRNAfromthegeneandrateofprocessingofthehnRNAtomRNA(..andthislatterprocessishighlyregulatedbysmallRNAmolecules).Othertypesofenzymeactivity'fine'regulationareallosterismandhormone-controlledcovalentmodificationbyphosphorylation(requiring‘kinases’)anddephosphorylation(requiringphosphatases’).SeeVp617foranexampleTheseenzymescanberegulatedinwellorganisedin‘enzymecascades’(SeeVp424&535foranexample Fluxinbiochemicalpathwaysisregulatedbychangesintheactivitiesofspecificenzymes. Enzymaticactivityisregulatedbymultiplemechanismincluding(1)bindingviaNCIsofspecificintermediarymetabolites(allostericregulators),e.g.ATP,ADP,NAD+,NADH,NADP+,NADPHetc.usingnegativefeedbackandforwardactivation,(2)reversiblecovalentmodificationoftenbyphosphorylation/dephosphorylationofAAresiduessuchasTyr(Y)andSer(S)ontheproteininreactionsthatrequirespecificenzymesand(3)byhormonaldirectedactivation/deactivationofproteins)V12. Generally,entirebiochemicalpathwaysarecontrolledbytheregulationofoneortwospecificenzymes,PFK-1inglycolysis,ACCinfattyacidmetabolismandHMGCoAreductaseincholesterolsynthesis. Clicktheselinksforexamplesofregulationinthesespecificpathways:TCA&Glycolysis.

Manyenzymes,especiallytransferases(V11),requirenon-protein‘co-factors’forfullbiologicalactivity. Theseco-factorscanbemetalions,coenzymes(derivedfromwatersolublevitamins(V14)heme,etc.Someareboundtotheenzymebynon-covalentinteractions(NCIs)andotherbycovalentbonds.6.RedoxReactions:DerivingEnergy. Thebasisofvirtuallyallenergytransductionprocessesinlivingcellsisthroughredoxreactions(i.e.electronflow)Oxidationreactions(involvingreleaseofelectrons)arenearlyalwaysexothermic/exogonicwhereasreductionreactions(involvingacceptanceofelectrons)arenearlyalwaysendothermic/endogonic.Thusfood(carbohydrates,fats/oilsandproteins)isdigestedintheintestinesbyhydrolysisreactionstoproducts(glucose,fattyacids,glycerolandaminoacids)thatcancrosstheepithelialcellsintothebloodstreamandaresubsequently(in

catabolicprocesses)oxidisedbyconvertinghighenergyC-HbondsintoC=Oinatwopartprocessinvolving(1)hydrideiontransferfrom'intermediarymetabolites'toNAD+andFAD(nature'stwooxidisingagents)and(2)recycling/oxidizingtheresultantNADH&FADH2backtoNAD+&FADbythereducingagentoxygen(usually)withtheconcomitantformationofATPfromADP&Piinthemitochondria.V14BiosynthesisisNETreductionandsorequiresareducingagent(NADPH)andanenergysource(ATP)

Linkedimagestoillustratethisredoxconcept:Glycolysis TCA Gly/TCA FAcatabolism FAmeta Lipid Fuelmeta ETS/NADH ETS/ATP ETS/detail7.SyntheticReactions:UsingEnergy. Manybiochemicalsyntheticreactionsrequireenergy:thisisusuallycarriedoutbychemicallyactivating(1)onesubstratebyreactionwithATP(oritsequivalent,UTP,GTP,CTP,etc)toformphosphateestersormixedcarboxylic/phosphoricanhydridesor(2)activatinganenzymebyphosphorylatingspecificfunctionalgroups(i.e.OHinaminoacidresidues).Thusistheexogonicityofonereaction(ATPtoADPorAMP)isusedto'drive'theendogonicityofanotherreactionsothattheNETΔGomustbe<0 Examples:ATPCoupledreactionsActivationofaminoacidfortransfertotRNA 8.Compartmentalization. Biochemicalreactionsarelocalisedintimeandspaceinacell.Compartmentationisakeytoacell'sorganisation.Thisseparationismaintainedbywaterinsolublelipidmembranes.However,theseorganisationalprocessesdecreaseentropyandthusrequireenergyforthesynthesisandsubsequentassemblyofthemembranesbuttheNETresultisΔGo<0solifeproceeds!9.Signaltransduction. Communicationbetweendifferenttissuesisrequiredinmulti-cellorganisms.Thisrequireshormones(thatcanbeproteins,peptides,steroidsandamines)tobereleasedbyonetissuetocauseoneormorebiochemicalchangesinanothertissue.Membrane-boundreceptorsinitiallybind(byspecificNCIs)thesechemicalmessengers(V13)andchangethe'biochemistry'(thepathways)insidethecell.

10.GenometoProteomeandback!. Conventional version

Currentversion

GeneticinformationisstoredasDNA(usingmainlyonlyfourdifferentbases(A,G,C&T) andisusedtodirectthesynthesisofproteinsviaRNAintermediates(usingmainlyfourdifferentbases(A,G,C&U)invirtuallyallorganisms(exceptretroviruses).SeeCentralDogmasabove TheseconddiagramreflectsthecurrentideasdeducedfromrecentepigeneticstudiesthatsomesmallRNAsandproteinhistonesareinvolvedinthecontrolofgeneexpression.Thischangeseverything! Clearlyareal“paradigmshift”Eachgenus/speciesisdefinedbyadistinctsetofmacromoleculescodedfromthegenome.Thelastpartofthiscoursetherewillbecoverageofproteinsandnucleicacids.Itisassumedthatyouarefamiliarwiththefundamentalbuildingblocksofproteins,theaminoacids,andofDNA&RNA,thenucleotidebases(seebelow)alongwithageneralunderstandingofthestructureofDNAandRNA,andhowtheyareproducedand,inthecaseofDNA,replicated,andofthegeneticcode.

TheGeneticCodeV27, insidefrontorbackVVPcoverandnextpage

ThegeneticcodereferstothetripletsequenceofbasesinRNAthatrecognizethespecifictRNAcarryingaminoacidstobeincorporatedintoprotein.EachtripletonribonucleotidesiscalledacodonandspecifiesatRNAcorrespondingtooneofthe20aminoacids,oritencodesastopsignal.Athreebasecodeproduces64possibletripletcodons(43or4x4x4=64),andeachisusedforanaminoacidorastopcodon,sothegeneticcodeisdegenerate(thatis,someaminoacidsareencodedbymorethanonecodon).ThecodonsaretranslatedsequentiallyfromastartsiteonthemRNA,aninitiationcodon,whichisalmostalwaysAUG,whichencodesmethionine.ThestopcodonsareUGA,UAA,andUAG.Thegeneticcodeisnearlyuniversal,mitochondriaexcepted,butdifferentorganismsdouseparticularcodonspreferentiallytoinsertthesameaminoacid.

TheAminoAcidsV4&21

BycoverageofV4,youwillneedtobefamiliarwiththestructures(androlesinproteinsofAAresidues)ofalltheaminoacidsandtheirabbreviations(boththreeletterandoneletter).ThemostimportantaspectisknowingthefunctionalgroupsofeachAAandhowtheAAareclassifiedintousefulgroups NEUTRAL(polar/aliphaticnonpolar/aromaticnon-polar),IONIC(charged+/-),andwhethertheFGsarehydrophobicorhydrophilicorboth!).

ManipulationoftheHenderson-Hasselbalchequationisamustforthiscourse!

11. Biochemical Interconnectedness. Organelles, cellsandorganismsarechemicallydependentoneachother(‘synergy’).Ecologyfortheday!Tosurviveyouhavetobeahunter-gathererinthewilds,your garden or at the supermarket for nutrients. All terrestrial species rely on the physical andchemicaldecompositioninsoilofthewastes/deadofsomeorganismssothatthedecayproductsarethefuelforothers(Ncycleimage).Natureistheultimaterecycler! Manyenvironmentalproblemshavebeencausedbytheinductionand(over-)useofnon-biodegradablecompoundssuchasbiocidesincludingDDT-e.g.RachaelCarlson'sSilentSpring-,CFCs(stratosphericozonethinning),PCBs,syntheticpolymers-plastics,fibers,foams,paints,etc)inthelast150years.12.EvolutionaryInterconnectedness. Allsuccessfulorganismsmustbecapableofself-assembly,self-replication,catalysis,andallowforsomemutations. Thisisthebasisoftheevolutionarydevelopmentoflife. Biochemicalsystemshavebeenevolvingatleast~3.8billionyearsandalllivingsystemsarerelatedthroughacommonevolutionarypathway.Livingorganismsareremarkablysimilaratthemolecularleveldespitetheobservedbiologicaldiversity.Thus,innature,thereexistsabiochemicalunityofdiverselivingorganismsinthatthereisawiderangeofadaptationsaroundacommonchemicalframework.

Commonlyused480abbreviations:NCI=non-covalentinteractions,CA/CBconjugateacid/basepair,IM=intermediarymetabolite,Chol=cholesterol,CE=cholesterylesters,TAG=triacylglycerols,NG=energy,FA/FFA=freefattyacid/carboxylate,GLG-goodleavinggroup,Nu=nucleophile.Glc=glucose,(Glu=theAAglutamate),Gal=galactose,Fru=fructose,Man=Mannose.‡= transitionstate(ts)