NucleicAcids

1.Introduction
ThefirstisolationofwhatwenowrefertoasDNAwasaccomplishedbyJohannFriedrichMieschercirca1870.Hereportedfindingaweaklyacidic
substanceofunknownfunctioninthenucleiofhumanwhitebloodcells,andnamedthismaterial"nuclein".Afewyearslater,Miescherseparatednucleininto
proteinandnucleicacidcomponents.Inthe1920'snucleicacidswerefoundtobemajorcomponentsofchromosomes,smallgenecarryingbodiesinthe
nucleiofcomplexcells.Elementalanalysisofnucleicacidsshowedthepresenceofphosphorus,inadditiontotheusualC,H,N&O.Unlikeproteins,nucleic
acidscontainednosulfur.Completehydrolysisofchromosomalnucleicacidsgaveinorganicphosphate,2deoxyribose(apreviouslyunknownsugar)and
fourdifferentheterocyclicbases(showninthefollowingdiagram).Toreflecttheunusualsugarcomponent,chromosomalnucleicacidsarecalled
deoxyribonucleicacids,abbreviatedDNA.Analogousnucleicacidsinwhichthesugarcomponentisribosearetermedribonucleicacids,abbreviatedRNA.
Theacidiccharacterofthenucleicacidswasattributedtothephosphoricacidmoiety.

Thetwomonocyclicbasesshownhereareclassifiedaspyrimidines,andthetwobicyclicbasesarepurines.EachhasatleastoneNHsiteatwhichan
organicsubstituentmaybeattached.Theyareallpolyfunctionalbases,andmayexistintautomericforms.
BasecatalyzedhydrolysisofDNAgavefournucleosideproducts,whichprovedtobeNglycosidesof2'deoxyribosecombinedwiththeheterocyclic
amines.Structuresandnamesforthesenucleosideswillbedisplayedabovebyclickingontheheterocyclicbasediagram.Thebasecomponentsarecolored
green,andthesugarisblack.Asnotedinthe2'deoxycytidinestructureontheleft,thenumberingofthesugarcarbonsmakesuseofprimednumbersto
distinguishthemfromtheheterocyclicbasesites.ThecorrespondingNglycosidesofthecommonsugarribosearethebuildingblocksofRNA,andare
namedadenosine,cytidine,guanosineanduridine(athymidineanalogmissingthemethylgroup).
Fromthisevidence,nucleicacidsmaybeformulatedasalternatingcopolymersofphosphoricacid(P)andnucleosides(N),asshown:

~PNPN'PN''PN'''PN~
Atfirstthefournucleosides,distinguishedbyprimemarksinthiscrudeformula,wereassumedtobepresentinequalamounts,resultinginauniform
structure,suchasthatofstarch.However,acompoundofthiskind,presumablycommontoallorganisms,wasconsideredtoosimpletoholdthehereditary
informationknowntoresideinthechromosomes.Thisviewwaschallengedin1944,whenOswaldAveryandcolleaguesdemonstratedthatbacterialDNA
waslikelythegeneticagentthatcarriedinformationfromoneorganismtoanotherinaprocesscalled"transformation".Heconcludedthat"nucleicacidsmust
beregardedaspossessingbiologicalspecificity,thechemicalbasisofwhichisasyetundetermined."Despitethisfinding,manyscientistscontinuedto
believethatchromosomalproteins,whichdifferacrossspecies,betweenindividuals,andevenwithinagivenorganism,werethelocusofanorganism's
geneticinformation.
Itshouldbenotedthatsinglecelledorganismslikebacteriadonothaveawelldefinednucleus.Instead,theirsinglechromosomeisassociatedwithspecific
proteinsinaregioncalleda"nucleoid".Nevertheless,theDNAfrombacteriahasthesamecompositionandgeneralstructureasthatfrommulticellular
organisms,includinghumanbeings.
ViewsabouttheroleofDNAininheritancechangedinthelate1940'sandearly1950's.ByconductingacarefulanalysisofDNAfrommanysources,Erwin
Chargafffounditscompositiontobespeciesspecific.Inaddition,hefoundthattheamountofadenine(A)alwaysequaledtheamountofthymine(T),andthe
amountofguanine(G)alwaysequaledtheamountofcytosine(C),regardlessoftheDNAsource.Assetforthinthefollowingtable,theratioof(A+T)to
(C+G)variedfrom2.70to0.35.Thelasttwoorganismsarebacteria.

NucleosideBaseDistributioninDNA
BaseComposition(mole%)

BaseRatios

A/T

G/C

Human

30.9

19.9

29.4

19.8

1.05

1.00

1.52

Chicken

28.8

20.5

29.2

21.5

1.02

0.95

1.38

Yeast

31.3

18.7

32.9

17.1

0.95

1.09

1.79

Clostridium
perfringens

36.9

14.0

36.3

12.8

1.01

1.09

2.70

Sarcina
lutea

13.4

37.1

12.4

37.1

1.08

1.00

0.35

Organism

Ratio(A+T)/(G+C)

Inasecondcriticalstudy,AlfredHersheyandMarthaChaseshowedthatwhenabacteriumisinfectedandgeneticallytransformedbyavirus,atleast80%of
theviralDNAentersthebacterialcellandatleast80%oftheviralproteinremainsoutside.TogetherwiththeChargafffindingsthisworkestablishedDNAas
therepositoryoftheuniquegeneticcharacteristicsofanorganism.
.

2.TheChemicalNatureofDNA

ThepolymericstructureofDNAmaybedescribedintermsofmonomericunitsofincreasingcomplexity.Inthetopshadedboxofthefollowingillustration,the
threerelativelysimplecomponentsmentionedearlierareshown.Belowthatontheleft,formulasforphosphoricacidandanucleosidearedrawn.
CondensationpolymerizationoftheseleadstotheDNAformulationoutlinedabove.Finally,a5'monophosphateester,calledanucleotidemaybedrawn
asasinglemonomerunit,shownintheshadedboxtotheright.Sinceamonophosphateesterofthiskindisastrongacid(pKaof1.0),itwillbefullyionized
attheusualphysiologicalpH(ca.7.4).NamesfortheseDNAcomponentsaregiveninthetabletotherightofthediagram.Isomeric3'monophospate
nucleotidesarealsoknown,andbothisomersarefoundincells.TheymaybeobtainedbyselectivehydrolysisofDNAthroughtheactionofnuclease
enzymes.Anhydridelikediandtriphosphatenucleotideshavebeenidentifiedasimportantenergycarriersinbiochemicalreactions,themostcommon
beingATP(adenosine5'triphosphate).

NamesofDNABaseDerivatives
Base

Nucleoside

5'Nucleotide

2'Deoxyadenosine

2'Deoxyadenosine5'monophosphate

Cytosine

2'Deoxycytidine

2'Deoxycytidine5'monophosphate

Guanine

2'Deoxyguanosine

2'Deoxyguanosine5'monophosphate

Thymine

2'Deoxythymidine

2'Deoxythymidine5'monophosphate

Adenine

AcompletestructuralrepresentationofasegmentoftheDNApolymerformedfrom5'nucleotidesmaybeviewedbyclickingontheabovediagram.Several
importantcharacteristicsofthisformulashouldbenoted.
First,theremainingPOHfunctionisquiteacidicandiscompletelyionizedinbiologicalsystems.
Second,thepolymerchainisstructurallydirected.Oneend(5')isdifferentfromtheother(3').
Third,althoughthisappearstobearelativelysimplepolymer,thepossiblepermutationsofthefournucleosidesinthechainbecomeverylargeasthe
chainlengthens.
Fourth,theDNApolymerismuchlargerthanoriginallybelieved.MolecularweightsfortheDNAfrommulticellularorganismsarecommonly109or
greater.
InformationisstoredorencodedintheDNApolymerbythepatterninwhichthefournucleotidesarearranged.Toaccessthisinformationthepatternmust
be"read"inalinearfashion,justasabarcodeisreadatasupermarketcheckout.Becauselivingorganismsareextremelycomplex,acorrespondinglylarge
amountofinformationrelatedtothiscomplexitymustbestoredintheDNA.Consequently,theDNAitselfmustbeverylarge,asnotedabove.Eventhe
singleDNAmoleculefromanE.colibacteriumisfoundtohaveroughlyamillionnucleotideunitsinapolymerstrand,andwouldreachamillimeterinlengthif
stretchedout.Thenucleiofmulticellularorganismsincorporatechromosomes,whicharecomposedofDNAcombinedwithnuclearproteinscalledhistones.
Thefruitflyhas8chromosomes,humanshave46anddogs78(notethattheamountofDNAinacell'snucleusdoesnotcorrelatewiththenumberof
chromosomes).TheDNAfromthesmallesthumanchromosomeisovertentimeslargerthanE.coliDNA,andithasbeenestimatedthatthetotalDNAina
humancellwouldextendto2metersinlengthifunraveled.Sincethenucleusisonlyabout5mindiameter,thechromosomalDNAmustbepackedtightlyto
fitinthatsmallvolume.
Inadditiontoitsroleasastableinformationallibrary,chromosomalDNAmustbestructuredororganizedinsuchawaythatthechemicalmachineryofthe
cellwillhaveeasyaccesstothatinformation,inordertomakeimportantmoleculessuchaspolypeptides.Furthermore,accuratecopiesoftheDNAcode
mustbecreatedascellsdivide,withthereplicatedDNAmoleculespassedontosubsequentcellgenerations,aswellastoprogenyoftheorganism.The
natureofthisDNAorganization,orsecondarystructure,willbediscussedinalatersection.

3.RNA,aDifferentNucleicAcid
Thehighmolecularweightnucleicacid,DNA,isfoundchieflyinthenucleiofcomplexcells,knownaseucaryoticcells,orinthenucleoidregionsof
procaryoticcells,suchasbacteria.Itisoftenassociatedwithproteinsthathelptopackitinausablefashion.
Incontrast,alowermolecularweight,butmuchmoreabundantnucleicacid,RNA,isdistributedthroughoutthecell,mostcommonlyinsmallnumerous
organellescalledribosomes.ThreekindsofRNAareidentified,thelargestsubgroup(85to90%)beingribosomalRNA,rRNA,themajorcomponentof
ribosomes,togetherwithproteins.ThesizeofrRNAmoleculesvaries,butisgenerallylessthanathousandththesizeofDNA.TheotherformsofRNAare
messengerRNA,mRNA,andtransferRNA,tRNA.BothhaveamoretransientexistenceandaresmallerthanrRNA.
AlltheseRNA'shavesimilarconstitutions,anddifferfromDNAintwoimportantrespects.Asshowninthefollowingdiagram,thesugarcomponentofRNA
isribose,andthepyrimidinebaseuracilreplacesthethyminebaseofDNA.TheRNA'splayavitalroleinthetransferofinformation(transcription)fromthe
DNAlibrarytotheproteinfactoriescalledribosomes,andintheinterpretationofthatinformation(translation)forthesynthesisofspecificpolypeptides.These
functionswillbedescribedlater.

AcompletestructuralrepresentationofasegmentoftheRNApolymerformedfrom5'nucleotidesmaybeviewedbyclickingontheabovediagram

4.TheSecondaryStructureofDNA
Intheearly1950'stheprimarystructureofDNAwaswellestablished,butafirmunderstandingofitssecondarystructurewaslacking.Indeed,thesituation
wassimilartothatoccupiedbytheproteinsadecadeearlier,beforethealphahelixandpleatedsheetstructureswereproposedbyLinusPauling.Many
researchersgrappledwiththisproblem,anditwasgenerallyconcededthatthemolarequivalencesofbasepairs(A&TandC&G)discoveredbyChargaff
wouldbeanimportantfactor.RosalindFranklin,workingatKing'sCollege,London,obtainedXraydiffractionevidencethatsuggestedalonghelical
structureofuniformthickness.FrancisCrickandJamesWatson,atCambridgeUniversity,consideredhydrogenbondedbasepairinginteractions,and
arrivedatadoublestrandedhelicalmodelthatsatisfiedmostoftheknownfacts,andhasbeenconfirmedbysubsequentfindings.
BasePairing
Carefulexaminationofthepurineandpyrimidinebasecomponentsofthenucleotidesrevealsthatthreeofthemcouldexistashydroxypyrimidineorpurine
tautomers,havinganaromaticheterocyclicring.Despitetheaddedstabilizationofanaromaticring,thesecompoundsprefertoadoptamidelikestructures.
Theseoptionsareshowninthefollowingdiagram,withthemorestabletautomerdrawninblue.

Asimplemodelforthistautomerismisprovidedby2hydroxypyridine.Asshownontheleftbelow,acompoundhavingthisstructuremightbeexpectedto
havephenollikecharacteristics,suchasanacidichydroxylgroup.However,theboilingpointoftheactualsubstanceis100Cgreaterthanphenolandits
acidityis100timeslessthanexpected(pKa=11.7).Thesedifferencesagreewiththe2pyridonetautomer,thestableformofthezwitterionicinternalsalt.
Furtherevidencesupportingthisassignmentwillbedisplayedbyclickingonthediagram.
Notethatthistautomerismreversesthehydrogenbondingbehaviorofthenitrogenandoxygenfunctions(theNHgroupofthepyridonebecomesa
hydrogenbonddonorandthecarbonyloxygenanacceptor).

Theadditionalevidenceforthepyridonetautomer,thatappearsabovebyclickingonthediagram,consistsofinfraredandcarbonnmrabsorptions
associatedwithandcharacteristicoftheamidegroup.Thedatafor2pyridoneisgivenontheleft.SimilardatafortheNmethylderivative,whichcannot
tautomerizetoapyridinederivative,ispresentedontheright.
Oncetheyhadidentifiedthefavoredbasetautomersinthenucleosides,WatsonandCrickwereabletoproposeacomplementarypairing,viahydrogen
bonding,ofguanosine(G)withcytidine(C)andadenosine(A)withthymidine(T).Thispairing,whichisshowninthefollowingdiagram,explainedChargaff's
findingsbeautifully,andledthemtosuggestadoublehelixstructureforDNA.
Beforeviewingthisdoublehelixstructureitself,itisinstructivetoexaminethebasepairinginteractionsingreaterdetail.TheG#Cassociationinvolvesthree
hydrogenbonds(coloredpink),andisthereforestrongerthanthetwohydrogenbondassociationofA#T.Thesebasepairingsmightappeartobearbitrary,
butotherpossibilitiessufferdestabilizingstericorelectronicinteractions.Byclickingonthediagramtwosuchalternativecouplingswillbeshown.TheC#T
pairingontheleftsuffersfromcarbonyldipolerepulsion,aswellasstericcrowdingoftheoxygens.TheG#Apairingontherightisalsodestabilizedbysteric
crowding(circledhydrogens).

Asimplemnemonicdeviceforrememberingwhichbasesarepairedcomesfromthelineconstructionofthecapitallettersusedtoidentifythebases.AandT
aremadeupofintersectingstraightlines.Incontrast,CandGarelargelycomposedofcurvedlines.TheRNAbaseuracilcorrespondstothymine,sinceU
followsTinthealphabet.

TheDoubleHelix
Aftermanytrialsandmodifications,WatsonandCrickconceivedaningeniousdoublehelixmodelforthesecondarystructureofDNA.TwostrandsofDNA
werealignedantiparalleltoeachother,i.e.withopposite3'and5'ends,asshowninpartaofthefollowingdiagram.Complementaryprimarynucleotide
structuresforeachstrandallowedintrastrandhydrogenbondingbetweeneachpairofbases.Thesecomplementarystrandsarecoloredredandgreenin
thediagram.Coilingthesecoupledstrandsthenleadstoadoublehelixstructure,shownascrosslinkedribbonsinpartbofthediagram.Thedoublehelixis
furtherstabilizedbyhydrophobicattractionsandpistackingofthebases.Aspacefillingmolecularmodelofashortsegmentisdisplayedinpartconthe
right.
Thehelixshownherehastenbasepairsperturn,andrises3.4ineachturn.Thisrighthandedhelixisthefavoredconformationinaqueoussystems,and
hasbeentermedtheBhelix.AstheDNAstrandswindaroundeachother,theyleavegapsbetweeneachsetofphosphatebackbones.Twoalternating
groovesresult,awideanddeepmajorgroove(ca.22wide),andashallowandnarrowminorgroove(ca.12wide).Othermolecules,including
polypeptides,mayinsertintothesegrooves,andinsodoingperturbthechemistryofDNA.OtherhelicalstructuresofDNAhavealsobeenobserved,and
aredesignatedbyletters(e.g.AandZ).

TheDoubleHelixStructureforDNA

SpaceFillingMolecularModel

AmodelofashortDNAsegmentmaybeexaminedby ClickingHere
Excellentsites,incorporatingChimeandJmolmodelsforvisualizingDNA,hasbeencreatedby:
EricMartz,Univ.Mass.Amherst.ClickHere.
FriedaReichsman,Univ.Mass.Amherst.ClickHere

1.DNAReplication
Intheir1953announcementofadoublehelixstructureforDNA,WatsonandCrickstated,"Ithasnotescapedournoticethatthespecificpairingwehave
postulatedimmediatelysuggestsapossiblecopyingmechanismforthegeneticmaterial.".Theessenceofthissuggestionisthat,ifseparated,eachstrandof
themoleculemightactasatemplateonwhichanewcomplementarystrandmightbeassembled,leadingfinallytotwoidenticalDNAmolecules.Indeed,
replicationdoestakeplaceinthisfashionwhencellsdivide,buttheeventsleadinguptotheactualsynthesisofcomplementaryDNAstrandsaresufficiently
complexthattheywillnotbedescribedinanydetail.
Asdepictedinthefollowingdrawing,theDNAofacellistightlypackedintochromosomes.First,theDNAiswrappedaroundsmallproteinscalledhistones
(coloredpinkbelow).Thesebeadlikestructuresarethenfurtherorganizedandfoldedintochromatinaggregatesthatmakeupthechromosomes.Anoverall
packingefficiencyof7,000ormoreisthusachieved.ClearlyasequenceofunfoldingeventsmusttakeplacebeforetheinformationencodedintheDNAcan
beusedorreplicated.


OncethedoublestrandedDNAisexposed,agroupofenzymesacttoaccomplishitsreplication.Thesearedescribedbrieflyhere:
Topoisomerase:Thisenzymeinitiatesunwindingofthedoublehelixbycuttingoneofthestrands.
Helicase:Thisenzymeassiststheunwinding.Notethatmanyhydrogenbondsmustbebrokenifthestrandsaretobeseparated..
SSB:Asinglestrandbindingproteinstabilizestheseparatedstrands,andpreventsthemfromrecombining,sothatthepolymerizationchemistrycan
functionontheindividualstrands.
DNAPolymerase:Thisfamilyofenzymeslinktogethernucleotidetriphosphatemonomersastheyhydrogenbondtocomplementarybases.These
enzymesalsocheckforerrors(roughlytenperbillion),andmakecorrections.
Ligase:SmallunattachedDNAsegmentsonastrandareunitedbythisenzyme.
Polymerizationofnucleotidestakesplacebythephosphorylationreactiondescribedbythefollowingequation.

Diandtriphosphateestershaveanhydridelikestructuresandareconsequentlyreactivephosphorylatingreagents,justascarboxylicanhydridesare
acylatingreagents.Sincethepyrophosphateanionisabetterleavinggroupthanphosphate,triphosphatesaremorepowerfulphosphorylatingagentsthan
arediphosphates.Formulasforthecorresponding5'derivativesofadenosinewillbedisplayedbyClickingHere,andsimilarderivativesexistfortheother
threecommonnucleosides.TheDNApolymerizationprocessthatbuildsthecomplementarystrandsinreplication,couldinprincipletakeplaceintwoways.
Referringtothegeneralequationabove,R1couldrepresentthenextnucleotideunittobeattachedtothegrowingDNAstrand,withR2beingthisstrand.
Alternatively,theseassignmentscouldbereversed.Inpractice,theformerprovestobethebestarrangement.Sincetriphosphatesareveryreactive,the
lifetimeofsuchderivativesinanaqueousenvironmentisrelativelyshort.However,suchderivativesoftheindividualnucleosidesarerepeatedlysynthesized
bythecellforavarietyofpurposes,providingasteadysupplyofthesereagents.Incontrast,thegrowingDNAsegmentmustmaintainitsfunctionalityover
theentirereplicationprocess,andcannotaffordtobechangedbyaspontaneoushydrolysisevent.Asaresult,thesechemicalpropertiesarebest
accommodatedbyapolymerizationprocessthatproceedsatthe3'endofthegrowingstrandby5'phosphorylationinvolvinganucleotidetriphosphate.This
processisillustratedbythefollowinganimation,whichmaybeactivatedbyclickingonthediagramorreloadingthepage.

Thepolymerizationmechanismdescribedhereisconstant.ItalwaysextendsthedevelopingDNAsegmenttowardthe3'end(i.e.whenanucleotide
triphosphateattachestothefree3'hydroxylgroupofthestrand,anew3'hydroxylisgenerated).Thereissometimesconfusiononthispoint,becausethe
originalDNAstrandthatservesasatemplateisreadfromthe3'endtowardthe5'end,andauthorsmaynotbecompletelyclearastowhichterminologyis
used.
Becauseofthedirectionaldemandofthepolymerization,oneoftheDNAstrandsiseasilyreplicatedinacontinuousfashion,whereastheotherstrandcan
onlybereplicatedinshortsegmentalpieces.Thisisillustratedinthefollowingdiagram.Separationofaportionofthedoublehelixtakesplaceatasitecalled
thereplicationfork.Asreplicationoftheseparatestrandsoccurs,thereplicationforkmovesaway(totheleftinthediagram),unwindingadditionallengths
ofDNA.Sincetheforkinthediagramismovingtowardthe5'endoftheredcoloredstrand,replicationofthisstrandmaytakeplaceinacontinuousfashion
(buildingthenewgreenstrandina5'to3'direction).Thiscontinuouslyformednewstrandiscalledtheleadingstrand.Incontrast,thereplicationfork
movestowardthe3'endoftheoriginalgreenstrand,preventingcontinuouspolymerizationofacomplementarynewredstrand.Shortsegmentsof
complementaryDNA,calledOkazakifragments,areproduced,andthesearelinkedtogetherlaterbytheenzymeligase.ThisnewDNAstrandiscalledthe
laggingstrand.

Whenyouconsiderthatahumancellhasroughly109basepairsinitsDNA,andmaydivideintoidenticaldaughtercellsin14to24hours,theefficiencyof
DNAreplicationmustbeextraordinary.Theproceduredescribedabovewillreplicateabout50nucleotidespersecond,sotheremustbemanythousandsuch
replicationsitesinactionduringcelldivision.AgivenlengthofdoublestrandedDNAmayundergostrandunwindingatnumeroussitesinresponseto
promoteractions.Theunraveled"bubble"ofsinglestrandedDNAhastworeplicationforks,soassemblyofnewcomplementarystrandsmayproceedintwo
directions.ThepolymerizationsassociatedwithseveralsuchbubblesfusetogethertoachievefullreplicationoftheentireDNAdoublehelix.Acartoon
illustratingtheseconcertedreplicationswillappearbyclickingontheabovediagram.Notethattheeventsshownproceedfromtoptobottominthediagram.

2.RepairofDNADamageandReplicationErrors
OneofthebenefitsofthedoublestrandedDNAstructureisthatitlendsitselftorepair,whenstructuraldamageorreplicationerrorsoccur.Severalkindsof
chemicalchangemaycausedamagetoDNA:
Spontaneoushydrolysisofanucleosideremovestheheterocyclicbasecomponent.
Spontaneoushydrolysisofcytosinechangesittoauracil.
Varioustoxicmetabolitesmayoxidizeormethylateheterocyclicbasecomponents.
Ultravioletlightmaydimerizeadjacentcytosineorthyminebases.
Allthesetransformationsdisruptbasepairingatthesiteofthechange,andthisproducesastructuraldeformationinthedoublehelix..Inspectionrepair
enzymesdetectsuchdeformations,andusetheundamagednucleotideatthatsiteasatemplateforreplacingthedamagedunit.Theserepairsreduceerrors
inDNAstructurefromaboutoneintenmilliontoonepertrillion.

RNAandProteinSynthesis
ThegeneticinformationstoredinDNAmoleculesisusedasablueprintformakingproteins.Whyproteins?Becausethesemacromoleculeshavediverse
primary,secondaryandtertiarystructuresthatequipthemtocarryoutthenumerousfunctionsnecessarytomaintainalivingorganism.Asnotedinthe
proteinchapter,thesefunctionsinclude:
Structuralintegrity(hair,horn,eyelensesetc.).
Molecularrecognitionandsignaling(antibodiesandhormones).
Catalysisofreactions(enzymes)..
Moleculartransport(hemoglobintransportsoxygen).
Movement(pumpsandmotors).
Thecriticalimportanceofproteinsinlifeprocessesisdemonstratedbynumerousgeneticdiseases,inwhichsmallmodificationsinprimarystructureproduce
debilitatingandoftendisastrousconsequences.SuchgeneticdiseasesincludeTaySachs,phenylketonuria(PKU),sickelcellanemia,achondroplasia,and
Parkinsondisease.Theunavoidableconclusionisthatproteinsareofcentralimportanceinlivingcells,andthatproteinsmustthereforebecontinuously
preparedwithhighstructuralfidelitybyappropriatecellularchemistry.
Earlygeneticistsidentifiedgenesashereditaryunitsthatdeterminedtheappearanceand/orfunctionofanorganism(i.e.itsphenotype).Wenowdefine
genesassequencesofDNAthatoccupyspecificlocationsonachromosome.Theoriginalproposalthateachgenecontrolledtheformationofasingle
enzymehassincebeenmodifiedas:onegene=onepolypeptide.TheintriguingquestionofhowtheinformationencodedinDNAisconvertedtothe
actualconstructionofaspecificpolypeptidehasbeenthesubjectofnumerousstudies,whichhavecreatedthemodernfieldofMolecularBiology.

1.TheCentralDogmaandTranscription
FrancisCrickproposedthatinformationflowsfromDNAtoRNAinaprocesscalledtranscription,andisthenusedtosynthesizepolypeptidesbyaprocess
calledtranslation.TranscriptiontakesplaceinamannersimilartoDNAreplication.Acharacteristicsequenceofnucleotidesmarksthebeginningofagene
ontheDNAstrand,andthisregionbindstoapromoterproteinthatinitiatesRNAsynthesis.Thedoublestrandedstructureunwindsatthepromotersite.,and
oneofthestrandsservesasatemplateforRNAformation,asdepictedinthefollowingdiagram.TheRNAmoleculethusformedissinglestranded,and
servestocarryinformationfromDNAtotheproteinsynthesismachinerycalledribosomes.TheseRNAmoleculesarethereforecalledmessengerRNA
(mRNA).
Tosummarize:ageneisastretchofDNAthatcontainsapatternfortheaminoacidsequenceofaprotein.Inordertoactuallymakethisprotein,therelevant
DNAsegmentisfirstcopiedintomessengerRNA.Thecellthensynthesizestheprotein,usingthemRNAasatemplate.

Animportantdistinctionmustbemadehere.OneoftheDNAstrandsinthedoublehelixholdsthegeneticinformationusedforproteinsynthesis.Thisis
calledthesensestrand,orinformationstrand(coloredredabove).Thecomplementarystrandthatbindstothesensestrandiscalledtheantisense
strand(coloredgreen),anditservesasatemplateforgeneratingamRNAmoleculethatdeliversacopyofthesensestrandinformationtoaribosome.The
promoterproteinbindstoaspecificnucleotidesequencethatidentifiesthesensestrand,relativetotheantisensestrand.RNAsynthesisistheninitiatedin
the3'direction,asnucleotidetriphosphatesbindtocomplementarybasesonthetemplatestrand,andarejoinedbyphosphatediesterlinkages.Ananimation
ofthisprocessforDNAreplicationwaspresentedearlier.Acharacteristic"stopsequence"ofnucleotidesterminatestheRNAsynthesis.Themessenger
molecule(coloredorangeabove)isreleasedintothecytoplasmtofindaribosome,andtheDNAthenrewindstoitsdoublehelixstructure.
IneucaryoticcellstheinitiallytranscribedmRNAmoleculeisusuallymodifiedandshortenedbyan"editing"processthatremovesirrelevantmaterial.The
DNAofsuchorganismsisoftenthousandsoftimeslargerandmorecomplexthanthatcomposingthesinglechromosomeofaprocaryoticbacterialcell.This
differenceisdueinparttorepetitivenucleotidesequences(ca.25%inthehumangenome).Furthermore,over95%ofhumanDNAisfoundinintervening
sequencesthatseparategenesandpartsofgenes.TheinformationalDNAsegmentsthatmakeupgenesarecalledexons,andthenoncodingsegments
arecalledintrons.BeforethemRNAmoleculeleavesthenucleus,thenonsensebasesthatmakeuptheintronsarecutout,andtheinformationallyuseful
exonsarejoinedtogetherinastepknownasRNAsplicing.InthisfashionshortermRNAmoleculescarryingtheblueprintforaspecificproteinaresenton
theirwaytotheribosomefactories.
TheCentralDogmaofmolecularbiology,whichatfirstwasformulatedasasimplelinearprogressionofinformationfromDNAtoRNAtoProtein,is
summarizedinthefollowingillustration.ThereplicationprocessontheleftconsistsofpassinginformationfromaparentDNAmoleculetodaughter
molecules.ThemiddletranscriptionprocesscopiesthisinformationtoamRNAmolecule.Finally,thisinformationisusedbythechemicalmachineryofthe
ribosometomakepolypeptides.

Asmorehasbeenlearnedabouttheserelationships,thecentraldogmahasbeenrefinedtotherepresentation
displayedontheright.Thedarkbluearrowsshowthegeneral,welldemonstrated,informationtransfersnotedabove.
ItisnowknownthatanRNAdependentDNApolymeraseenzyme,knownasareversetranscriptase,isableto
transcribeasinglestrandedRNAsequenceintodoublestrandedDNA(magentaarrow).Suchenzymesarefoundin
allcellsandareanessentialcomponentofretroviruses(e.g.HIV),whichrequireRNAreplicationoftheirgenomes
(greenarrow).DirecttranslationofDNAinformationintoproteinsynthesis(orangearrow)hasnotyetbeenobserved
inalivingorganism.Finally,proteinsappeartobeaninformationaldeadend,anddonotprovideastructuralblueprint
foreitherRNAorDNA.
Inthefollowingsectionthelastfundamentalrelationship,thatofstructuralinformationtranslationfrommRNAto
protein,willbedescribed

2.Translation
Translationisamorecomplexprocessthantranscription.Thiswould,ofcourse,beexpected.Afterall,thecodedmessagesproducedbytheGerman
Enigmamachinecouldbecopiedeasily,butrequiredaconsiderabledecodingeffortbeforetheycouldbereadwithunderstanding.Inasimilarsense,DNA
replicationissimplyacomplementarybasepairingexercise,butthetranslationofthefourletter(bases)alphabetcodeofRNAtothetwentyletter(amino
acids)alphabetofproteinliteratureisfarfromtrivial.Clearly,therecouldnotbeadirectonetoonecorrelationofbasestoaminoacids,sothenucleotide
lettersmustformshortwordsorcodonsthatdefinespecificaminoacids.Manyquestionspertainingtothisgeneticcodewereposedinthelate1950's:
HowmanyRNAnucleotidebasesdesignateaspecificaminoacid?
Ifseparategroupsofnucleotides,calledcodons,servethispurpose,atleastthreeareneeded.Thereare43=64differentnucleotidetriplets,
comparedwith42=16possiblepairs.
Arethecodonslinkedseparatelyordotheyoverlap?
Sequentiallyjoinedtripletcodonswillresultinanucleotidechainthreetimeslongerthantheproteinitdescribes.Ifoverlappingcodonsareusedthen
fewertotalnucleotideswouldberequired.
IftripletsegmentsofmRNAdesignatespecificaminoacidsintheprotein,howarethecodonsidentified?
Forthesequence~CUAGGU~arethecodonsCUA&GGUor~C,UAG&GU~or~CU,AGG&U~?
Areallthecodonwordsthesamesize?
InMorsecodethemostwidelyusedlettersareshorterthanlesscommonletters.Perhapsnatureemploysasimilarscheme.
Physicistsandmathematicians,aswellaschemistsandmicrobiologistsallcontributedtounravellingthegeneticcode.Althoughearlierproposalsassumed
efficientrelationshipsthatcorrelatedthenucleotidecodonsuniquelywiththetwentyfundamentalaminoacids,itisnowapparentthatthereisconsiderable
redundancyinthecodeasitnowoperates.Furthermore,thecodeconsistsexclusivelyofnonoverlappingtripletcodons.
Cleverexperimentsprovidedsomeoftheearliestbreaksindecipheringthegeneticcode.MarshallNirenbergfoundthatRNAfrommanydifferentorganisms
couldinitiatespecificproteinsynthesiswhencombinedwithbrokenE.colicells(theenzymesremainactive).AsyntheticpolyuridineRNAinducedsynthesis
ofpolyphenylalanine,sotheUUUcodondesignatedphenylalanine.Likewiseanalternating~CACA~RNAledtosynthesisofa~HisThrHisThr~
polypeptide.
Thefollowingtablepresentsthepresentdayinterpretationofthegeneticcode.NotethatthisistheRNAalphabet,andanequivalentDNAcodontablewould
havealltheUnucleotidesreplacedbyT.Methionineandtryptophanareuniquelyrepresentedbyasinglecodon.Attheotherextreme,leucineisrepresented
byeightcodons.Theaverageredundancyforthetwentyaminoacidsisaboutthree.Also,therearethreestopcodonsthatterminatepolypeptidesynthesis.

RNACodonsforProteinSynthesis
SecondPosition
U

F
i
r
s C
t
P
o
s
i
t A
i
o
n

UUU Phe [F]

UCU Ser [S]

UAU Tyr [Y]

UGU Cys [C]

UUC Phe [F]

UCC Ser [S]

UAC Tyr [Y]

UGC Cys [C]

UUA Leu [L]

UCA Ser [S]

UAA Stop

UGA Stop

UUG Leu [L]

UCG Ser [S]

UAG Stop

UGG Trp [W]

CUU Leu [L]

CCU Pro [P]

CAU His [H]

CGU Arg [R]

CUC Leu [L]

CCC Pro [P]

CAC His [H]

CGC Arg [R]

CUA Leu [L]

CCA Pro [P]

CAA Gln [Q]

CGA Arg [R]

CUG Leu [L]

CCG Pro [P]

CAG Gln [Q]

CGG Arg [R]

AUU Ile [I]

ACU Thr [T]

AAU Asn [N]

AGU Ser [S]

AUC Ile [I]

ACC Thr [T]

AAC Asn [N]

AGC Ser [S]

AUA Ile [I]

ACA Thr [T]

AAA Lys [K]

AGA Arg [R]

AUG Met [M]

ACG Thr [T]

AAG Lys [K]

AGG Arg [R]

GUU Val [V]

GCU Ala [A]

GAU Asp [D]

GGU Gly [G]

GUC Val [V]

GCC Ala [A]

GAC Asp [D]

GGC Gly [G]

GUA Val [V]

GCA Ala [A]

GAA Glu [E]

GGA Gly [G]

GUG Val [V]

GCG Ala [A]

GAG Glu [E]

GGG Gly [G]

T
h
i
r
d
P
o
s
i
t
i
o
n

Thetranslationprocessisfundamentallystraightforward.ThemRNAstrandbearingthetranscribedcodeforsynthesisofaproteininteractswithrelatively
smallRNAmolecules(about70nucleotides)towhichindividualaminoacidshavebeenattachedbyanesterbondatthe3'end.ThesetransferRNA's
(tRNA)havedistinctivethreedimensionalstructuresconsistingofloopsofsinglestrandedRNAconnectedbydoublestrandedsegments.Thiscloverleaf
secondarystructureisfurtherwrappedintoan"Lshaped"assembly,havingtheaminoacidattheendofonearm,andacharacteristicanticodonregionat
theotherend.Theanticodonconsistsofanucleotidetripletthatisthecomplementoftheaminoacid'scodon(s).ModelsoftwosuchtRNAmoleculesare
showntotheright.Whenreadfromthetoptothebottom,theanticodonsdepictedhereshouldcomplementacodonintheprevioustable.

CloverleafcartoonsofthreeothertRNAmoleculeswillbeshown
ontherightbyclickingonthediagram.

Acell'sproteinsynthesistakesplaceinorganellescalledribosomes.Ribosomesarecomplexstructuresmadeupoftwodistinctandseparablesubunits
(oneabouttwicethesizeoftheother).EachsubunitiscomposedofoneortwoRNAmolecules(6070%)associatedwith20to40smallproteins(3040%).
TheribosomeacceptsamRNAmolecule,bindinginitiallytoacharacteristicnucleotidesequenceatthe5'end(coloredlightblueinthefollowingdiagram).
Thisuniquebindingassuresthatpolypeptidesynthesisstartsattherightcodon.AtRNAmoleculewiththeappropriateanticodonthenattachesatthe
startingpointandthisisfollowedbyaseriesofadjacenttRNAattachments,peptidebondformationandshiftsoftheribosomealongthemRNAchainto
exposenewcodonstotheribosomalchemistry.
Thefollowingdiagramisdesignedasaslideshowillustratingthesesteps.TheoutcomeissynthesisofapolypeptidechaincorrespondingtothemRNA
blueprint.A"stopcodon"atadesignatedpositiononthemRNAterminatesthesynthesisbyintroductionofa"ReleaseFactor".

TovisitaninformativeTouroftheRibosomesite,createdbyWayneDecatur,Univ.Mass.AmherstClickHere.

3.PosttranslationalModification
Onceapeptideorproteinhasbeensynthesizedandreleasedfromtheribosomeitoftenundergoesfurtherchemicaltransformation.Thisposttranslational
modificationmayinvolvetheattachmentofothermoietiessuchasacylgroups,alkylgroups,phosphates,sulfates,lipidsandcarbohydrates.Functional
changessuchasdehydration,amidation,hydrolysisandoxidation(e.g.disulfidebondformation)arealsocommon.Inthismannerthelimitedarrayoftwenty
aminoacidsdesignatedbythecodonsmaybeexpandedinavarietyofwaystoenableproperfunctioningoftheresultingprotein.Sincethesepost
translationalreactionsaregenerallycatalyzedbyenzymes,itmaybesaid:"Virtuallyeverymoleculeinacellismadebytheribosomeorbyenzymesmadeby
theribosome."
Modifications,likephosphorylationandcitrullination,arepartofcommonmechanismsforcontrollingthebehaviorofaprotein.Asshownontheleftbelow,
citrullinationistheposttranslationalmodificationoftheaminoacidarginineintotheaminoacidcitrulline.ArginineispositivelychargedataneutralpH,
whereascitrullineisuncharged,sothischangeincreasesthehydrophobicityofaprotein.Phosphorylationofserine,threonineortyrosineresiduesrenders
themmorehydrophilic,butsuchchangesareusuallytransient,servingtoregulatethebiologicalactivityoftheprotein.Otherimportantfunctionalchanges
includeiodinationoftyrosineresiduesinthepeptidethyroglobulinbyactionoftheenzymethyroperoxidase.Themonoiodotyrosineanddiiodotyrosineformed
inthismannerarethenlinkedtoformthethyroidhormonesT3andT4,shownontherightbelow.

Aminoacidsmaybeenzymaticallyremovedfromtheaminoendoftheprotein.Becausethe"start"codononmRNAcodesfortheaminoacidmethionine,
thisaminoacidisusuallyremovedfromtheresultingproteinduringposttranslationalmodification.Peptidechainsmayalsobecutinthemiddletoform
shorterstrands.Thus,insulinisinitiallysynthesizedasa105residuepreprotein.The24aminoacidsignalpeptideisremoved,yieldingaproinsulinpeptide.
Thisfoldsandformsdisulfidebondsbetweencysteines7and67andbetween19and80.Suchdimericcysteines,joinedbyadisulfidebond,arenamed
cystine.Aproteasethencleavesthepeptideatarg31andarg60,withlossofthe3260sequence(chainC).Removalofarg31yieldsmatureinsulin,with
theAandBchainsheldtogetherbydisulfidebondsandathirdcystinemoietyinchainA.Thefollowingcartoonillustratesthischainofevents.

Nisinisapolypeptide(34aminoacids)madebythebacteriumLactococcuslactis.Nisinkillsgrampositivebacteriabybindingtotheirmembranesand
targetinglipidII,anessentialprecursorofcellwallsynthesis.Suchantimicrobialpeptidesareagrowingfamilyofcompoundswhichhavereceivedthename
lantibioticsduetothepresenceoflanthionine,anonproteinogenicaminoacidwiththechemicalformulaHO2CCH(NH2)CH2SCH2CH(NH2)CO2H.
Lanthionineiscomposedoftwoalanineresiduesthatarecrosslinkedontheircarbonatomsbyathioetherlinkage(i.e.itisthemonosulfideanalogofthe
disulfidecystine).Lantibioticsareuniqueinthattheyareribosomallysynthesizedasprepeptides,followedbyposttranslationalprocessingofanumberof
aminoacids(e.g.serine,threonineandcysteine)intodehydroresiduesandthioethercrossbridges.Nisinistheonlybacteriocinthatisacceptedasafood
preservative.Severalnisinsubtypesthatdifferinaminoacidcompositionandbiologicalactivityareknown.Atypicalstructureisdrawnbelow,andaJmol
modelwillbepresentedbyclickingonthediagram.

Thebacterialcellwallisacrosslinkedglycanpolymerthatsurroundsbacterialcells,dictatestheircellshape,andpreventsthemfrombreakingdueto
environmentalchangesinosmoticpressure.Thiswallconsistsmainlyofpeptidoglycanormurein,athreedimensionalpolymerofsugarsandaminoacids
locatedontheexteriorofthecytoplasmicmembrane.Themonomerunitsarecomposedof
twoaminosugars,Nacetylglucosamine(NAG)andNacetylmuramicacid(NAM),shownon
theright.Transglycosidaseenzymesjointheseunitsbyglycosidebonds,andtheyarefurther
interlinkedtoeachotherviapeptidecrosslinksbetweenthepentapeptidemoietiesthatare
attachedtotheNAMresidues.Peptidoglycansubunitsareassembledonthecytoplasmicside
ofthebacterialmembranefromapolyisoprenoidanchor.LipidII,amembraneanchoredcell
wallprecursorthatisessentialforbacterialcellwallbiosynthesis,isoneofthekey
componentsinthesynthesisofpeptidoglycan.PeptidoglycansynthesisviapolymerizationofLipidIIisillustratedinthefollowingdiagram.Crosslinkingofthe
peptidesidechainsistheneffectedbytranspeptidaseenzymes.AmodelofLipidIIcomplexedwithnisinmaybeexaminedaspartofthepreviousJmol
display.

Inorderforbacteriatodividebybinaryfissionandincreasetheirsizefollowingdivision,linksinthepeptidoglycanmustbebroken,newpeptidoglycan
monomersmustbeinserted,andthepeptidecrosslinksmustberesealed.Transglycosidaseenzymescatalyzetheformationofglycosidicbondsbetween
theNAMandNAGofthepeptidoglycanmonomersandtheNAGandNAMoftheexistingpeptidoglycan.Finally,transpeptidaseenzymesreformthepeptide
crosslinksbetweentherowsandlayersofpeptidoglycanmakingthewallstrong.Manyantibioticdrugs,includingpenicillin,targetthechemistryofcellwall
formation.TheeffectivenessofchoosingLipidIIforanantibacterialstrategyishighlightedbythefactthatitisthetargetforatleastfourdifferentclassesof
antibiotic,includingtheclinicallyimportantglycopeptideantibioticvancomycin.Thegrowingproblemofbacterialresistancetomanycurrentdrugs,including
vancomycin,hasledtoincreasinginterestinthetherapeuticpotentialofotherclassesofcompoundthattargetLipidII.Lantibioticssuchasnisinarepartof
thisinterest.

ForaspeculativediscussionofwhynatureselectedthecomponentsandfunctionalgroupsfoundinthenucleicacidsClickHere.

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Beginningofsupplementarytopics

AnalysisofStructuralSimilaritiesandDifferencesbetweenDNAandRNA
1.Background
Weknowthatlivingorganismshavetheabilitytoreproduceandtopassmanyoftheircharacteristicsontotheiroffspring.Fromthiswemayinferthatall
organismshavegeneticsubstancesandanassociatedchemistrythatenableinheritancetooccur.Itisinstructivetoconsidertheessentialrequirementssuch
geneticmaterialsmustfullfill.
Information
Biologicallyusefulinformation,especiallyinstructionsforproteinsynthesis,mustbeincorporatedinthematerial.
Stability
Theinheritedinformationmustbestable(unchanged)overthelifetimeoftheorganismifaccuratecopiesaretobe
conveyedtotheoffspring.Infrequentchangesmaytakeplace(seemutability).
Reproduction
Amethodoffaithfullyreplicatingtheinformationencodedinthematerial,andtransmittingthiscopytotheoffspring
mustexist.
Mutability

Despitetheinherentstabilitynotedabove,thematerialmustbecapableofincorporatingstablestructuralchange,
andpassingthischangeontosucceedinggenerations.
SincethisgeneticsubstancehasbeenidentifiedasthenucleicacidsDNAandRNA,itisinstructivetoexaminethemannerinwhichthesepolymerssatisfy
theaboverequirements.

2.InformationStorage
Thecomplexityoflifesuggeststhatevensimpleorganismswillrequireverylargeinheritancelibraries.AlthoughthefournucleotidesthatmakeupofDNA
mightappeartobetoosimpleforthistask,theenormoussizeofthepolymerandthepermutationsofthemonomerswithinthechainmeetthechallenge
easily.Afterall,thewordsandgraphicsinthisdocumentareallpresentedtothecomputerascombinationsofonlytwocharacters,zerosandones(the
binarynumbersystem).DNAhasfourlettersinitsalphabet(A,C,G&T),sothenumberofwordsthatcanbeformedincreaseexponentiallywiththe
numberoflettersperword.Thus,thereare42or16twoletterwords,and43or64threeletterwords.
AssuringthestabilityofinformationencodedbytheDNAalphabetpresentsaseriouschallenge.Ifthelettersofthisalphabetaretobestrungtogetherina
specificwayonthepolymerchain,chemicalreactionsforattaching(andremoving)themmustbeavailable.Simplecarboxylicesteroramidelinksmight
appearsuitableforthispurpose(notestepgrowthpolymerization),buttheseareusedinlipidsandpolypeptides,soaseparateenzymaticmachinerywould
beneededtokeeptheinformationprocessingoperationsapartfromothermoleculartransformations.
Theoverallstabilityofsuchcovalentlinkspresentsamoreseriousproblem.Underphysiologicalconditions(aqueous,pHnear7.4&27to37C)estersare
slowlyhydrolyzed.Amidesaremorestable,butevenahydrolyticcleavageofonebondperhourwouldbedevastatingtoapolymerhavingtensofthousands
tomillionssuchlinks.Furthermore,shortdifunctionallinkinggroups,suchascarbonates,oxylatesandmalonatesshowenhancedreactivity,andtheirparent
acidsareunstableortoxic.
Phosphateisanubiquitousinorganicnutrient.Mono,diandtriestersofthecorresponding
acid(phosphoricacid)areallknown.Becauseoftheiracidity(pKa2),themonoand

EsterHydrolysisat35CandpH7

diestersarenegativelychargedatphysiologicalpH,renderingthemlesssusceptibleto
nucleophilicattack.Theinfluenceofnegativechargeontherateofnucleophilichydrolysisof
Ester
RateofHydrolysis RelativeRate
somerepresentativeestersisshowninthetableontheright.Clearly,apolymerinwhich
monomerunitsarejoinedbynegativelychargeddiphosphateesterlinksshouldbe
EthylAcetate
substantiallymorestablethanonecomposedofcarboxylateesterbonds.Thenegative
1.0*102
5*106
CH3CO2C2H5
chargefoundonallbiologicalphosphatederivativesservesotherpurposesaswell.
ThediphosphateesterlinksthatjointhenucleotidesunitsofDNAareformedby
phosphorylationreactionsinvolvingnucleotidetriphosphatereagents.Thesereagentsarethe TrimethylPhosphate
3.4*104
2*105
(CH3O)3PO
phosphoricacidanalogsofcarboxylicacidanhydrides,afunctionalgroupthatwouldnot
survivetheaqueousenvironmentofacell.Thehighdensityofnegativechargeonthe
DimethylPhosphate
triphosphatefunctionnotonlysolubilizestheorganicmoietytowhichitisattached,butalso
1.0
2.0*109
(CH3O)2PO2()
reducestherateatwhichitishydrolyzed.
Livingcellsmustconserveandemploytheirchemicalreagentswithinavolumedefinedand
enclosedbyamembranebarrier.Theselipidbilayermembraneshavehydrophobicinteriors,whichresistthepassageofions.Indeed,specialtrans
membranestructurescalledionchannelsexistsothatcontrollediontransportacrossamembranemaytakeplace.Smallneutralorganicmolecules,such
asadenosine,cytidineandguanosine,maypassthroughlipidmembranes,albeitatareducedrate,buttheirmono,diandtriphosphatederivativesaremore
tightlysequesteredinthecell.

3.Whyis2'DeoxyribosetheSugarMoietyinDNA?
Commonperhydroxylatedsugars,suchasglucoseandribose,areformedinnatureasproductsofthereductivecondensationofcarbondioxidewecall
photosynthesis.Theformationofdeoxysugarsrequiresadditionalbiologicalreductionsteps,soitisreasonabletospeculatewhyDNAmakesuseofthe
lesscommon2'deoxyribose,whenriboseitselfserveswellforRNA.Atleasttwoproblemsassociatedwiththeextrahydroxylgroupinribosemaybenoted.
First,theadditionalbulkandhydrogenbondingcharacterofthe2'OHinterferewithauniformdoublehelixstructure,preventingtheefficientpackingofsuch
amoleculeinthechromosome.Second,RNAundergoesspontaneoushydrolyticcleavageaboutonehundredtimesfasterthanDNA.Thisisbelieveddueto
intramolecularattackofthe2'hydroxylfunctionontheneighboringphosphatediester,yieldinga2',3'cyclicphosphate.Ifstabilityoverthelifetimeofan
organismisanessentialcharacteristicofagene,thennature'sselectionof2'deoxyriboseforDNAmakessense.Thefollowingdiagramillustratesthe
intramolecularcleavagereactioninastrandofRNA.

StructuralstabilityisnotaseriouschallengeforRNA.ThetranscriptedinformationcarriedbymRNAmustbesecureforonlyafewhours,asitistransported
toaribosome.Onceintheribosomeitissurroundedbystructuralandenzymaticsegmentsthatimmediatelyincorporateitscodonsforproteinsynthesis.The
tRNAmoleculesthatcarryaminoacidstotheribosomearesimilarlyshortlived,andareinfactcontinuouslyrecycledbythecellularchemistry.

4.TheThyminevs.UracilIssue

4.TheThyminevs.UracilIssue
Structuralformulasforthethreepyrimidinebases,cytosine,thymineanduracilareshownontheright.
Thecarbonatomsthatarepartofthesecompoundsmaybecategorizedasfollows.Allofthese
compoundsareapparentlyputtogetherfromathreecarbonmalonatelikeprecursor(bluecolored
bonds)andasinglehighoxidationstatecarbonspecies(coloredred).Suchbiosyntheticintermediates
arewellestablished.Thymineisuniqueinhavinganadditionalcarbon,thegreenmethylgroup.
Biosynthesisofthiscompoundmustinvolveadditionalsteps,thusaddingconstructionalcomplexityto
theDNAmoleculesinwhichitreplacesuracil.
ThereasonforthesubstitutionofthymineforuracilinDNAmaybeassociatedwiththerepairmechanismsbywhichthecellcorrectsdamagetoitsDNA.
Onesourceoferrorinthecodeistheslowhydrolysisofheterocyclicenamines,suchascytosineandguanine,totheircorrespondinglactams.Thischanges
thestructureofthebase,anddisruptsbasepairinginamannerthatcanbeidentifiedandthenrepaired.However,thehydrolysisproductfromcytosineis
uracil,andthismismatchedspeciesmustsomehowbedistinguishedfromtheuracillikebasethatbelongsintheDNA.Theextramethylgroupservesthis
rolenicely.
Foramorecompletediscussionofsomeoftheissuestouchedonhereseeanarticletitled"WhyNatureChosePhosphates",
authoredbyF.H.Westheimer,whichappearedintheMarch6th,1987issueofScience.
Return

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