NucleicAcids

Nucleicacidsaremoleculesthatstoreinformationforcellular
growthandreproduction
Therearetwotypesofnucleicacids:
deoxyribonucleicacid(DNA)andribonucleicacid(RNA)
Thesearepolymersconsistingoflongchainsofmonomers
callednucleotides
Anucleotideconsistsofanitrogenousbase,apentosesugar
andaphosphategroup:

NitrogenBases

Thenitrogenbasesinnucleotidesconsistoftwogeneraltypes:
purines:adenine(A)andguanine(G)
pyrimidines:cytosine(C),thymine(T)andUracil(U)

PentoseSugars
Therearetworelatedpentosesugars:
RNAcontainsribose
DNAcontainsdeoxyribose
Thesugarshavetheircarbonatomsnumberedwithprimes
todistinguishthemfromthenitrogenbases

NucleosidesandNucleotides

Anucleosideconsistsofanitrogenbaselinkedbyaglycosidic
bondtoC1ofariboseordeoxyribose
Nucleosidesarenamedbychangingthethenitrogenbase
endingtoosineforpurinesandidineforpyrimidines
Anucleotideisanucleosidethatformsaphosphateesterwith
theC5OHgroupofriboseordeoxyribose
Nucleotidesarenamedusingthenameofthenucleoside
followedby5monophosphate

NamesofNucleosidesandNucleotides

AMP,ADPandATP

Additionalphosphategroupscanbeaddedtothenucleoside5
monophosphatestoformdiphosphatesandtriphosphates
ATPisthemajorenergysourceforcellularactivity

PrimaryStructureofNucleicAcids

Theprimarystructureofanucleicacidisthenucleotidesequence
Thenucleotidesinnucleicacidsarejoinedbyphosphodiesterbonds
The3OHgroupofthesugarinonenucleotideformsanesterbond
tothephosphategrouponthe5carbonofthesugarofthenext
nucleotide

ReadingPrimaryStructure
Anucleicacidpolymerhasafree
5phosphategroupatoneendanda
free3OHgroupattheotherend
Thesequenceisreadfromthefree
5endusingthelettersofthebases
Thisexamplereads
5ACGT3

ExampleofRNAPrimaryStructure

InRNA,A,C,G,andUarelinkedby35esterbonds
betweenriboseandphosphate

ExampleofDNAPrimaryStructure

InDNA,A,C,G,andTarelinkedby35esterbonds
betweendeoxyriboseandphosphate

SecondaryStructure:DNADoubleHelix
InDNAtherearetwostrandsofnucleotidesthatwindtogether
inadoublehelix
thestrandsruninoppositedirections
thebasesarearearrangedinsteplikepairs
thebasepairsareheldtogetherbyhydrogenbonding
Thepairingofthebasesfromthetwostrandsisveryspecific
ThecomplimentarybasepairsareATandGC
twohydrogenbondsformbetweenAandT
threehydrogenbondsformbetweenGandC
Eachpairconsistsofapurineandapyrimidine,sotheyarethe
samewidth,keepingthetwostrandsatequaldistancesfrom
eachother

BasePairingintheDNADoubleHelix

StorageofDNA

Ineukaryoticcells(animals,plants,fungi)DNAisstoredin
thenucleus,whichisseparatedfromtherestofthecellbya
semipermeablemembrane
TheDNAisonlyorganizedintochromosomesduringcell
replication
Betweenreplications,theDNAisstoredinacompactball
calledchromatin,andiswrappedaroundproteinscalled
histonestoformnucleosomes

DNAReplication
Whenaeukaryoticcelldivides,theprocessiscalledmitosis
thecellsplitsintotwoidenticaldaughtercells
theDNAmustbereplicatedsothateachdaughtercellhasacopy
DNAreplicationinvolvesseveralprocesses:
first,theDNAmustbeunwound,separatingthetwostrands
thesinglestrandsthenactastemplatesforsynthesisofthenew
strands,whicharecomplimentaryinsequence
basesareaddedoneatatimeuntiltwonewDNAstrandsthat
exactlyduplicatetheoriginalDNAareproduced
Theprocessiscalledsemiconservativereplicationbecauseone
strandofeachdaughterDNAcomesfromtheparentDNAandone
strandisnew
Theenergyforthesynthesiscomesfromhydrolysisofphosphate
groupsasthephosphodiesterbondsformbetweenthebases

SemiConservativeDNAReplication

DirectionofReplication

TheenzymehelicaseunwindsseveralsectionsofparentDNA
AteachopenDNAsection,calledareplicationfork,DNA
polymerasecatalyzestheformationof53esterbondsofthe
leadingstrand
Thelaggingstrand,whichgrowsinthe35direction,is
synthesizedinshortsectionscalledOkazakifragments
TheOkazakifragmentsarejoinedbyDNAligasetogivea
single35DNAstrand

EnzymesandProteinsInvolvedinDNAReplication

RibonucleicAcid(RNA)
RNAismuchmoreabundantthanDNA
ThereareseveralimportantdifferencesbetweenRNAandDNA:
thepentosesugarinRNAisribose,inDNAitsdeoxyribose
inRNA,uracilreplacesthebasethymine(UpairswithA)
RNAissinglestrandedwhileDNAisdoublestranded
RNAmoleculesaremuchsmallerthanDNAmolecules
TherearethreemaintypesofRNA:
ribosomal(rRNA),messenger(mRNA)andtransfer(tRNA)

TypesofRNA

RibosomalRNAandMessengerRNA
Ribosomesarethesitesofproteinsynthesis
theyconsistofribosomalDNA(65%)andproteins(35%)
theyhavetwosubunits,alargeoneandasmallone
MessengerRNAcarriesthegeneticcodetotheribosomes
theyarestrandsofRNAthatarecomplementarytothe
DNAofthegenefortheproteintobesynthesized

TransferRNA

TransferRNAtranslatesthegeneticcodefromthemessengerRNA
andbringsspecificaminoacidstotheribosomeforproteinsynthesis
EachaminoacidisrecognizedbyoneormorespecifictRNA
tRNAhasatertiarystructurethatisLshaped
oneendattachestotheaminoacidandtheotherbindstothemRNA
bya3basecomplimentarysequence

ProteinSynthesis
Thetwomainprocessesinvolvedinproteinsynthesisare
theformationofmRNAfromDNA(transcription)
theconversionbytRNAtoproteinattheribosome(translation)
Transcriptiontakesplaceinthenucleus,whiletranslationtakes
placeinthecytoplasm
GeneticinformationistranscribedtoformmRNAmuchthesame
wayitisreplicatedduringcelldivision

Transcription
Severalstepsoccurduringtranscription:
asectionofDNAcontainingthegeneunwinds
onestrandofDNAiscopiedstartingattheinitiationpoint,
whichhasthesequenceTATAAA
anmRNAissynthesizedusingcomplementarybasepairing
withuracil(U)replacingthymine(T)
thenewlyformedmRNAmovesoutofthenucleusto
ribosomesinthecytoplasmandtheDNArewinds

RNAPolymerase
Duringtranscription,RNApolymerasemovesalongtheDNA
templateinthe35directiontosynthesizethecorresponding
mRNA
ThemRNAisreleasedattheterminationpoint

ProcessingofmRNA
GenesintheDNAofeukaryotescontainexonsthatcode
forproteinsalongwithintronsthatdonot
BecausetheinitialmRNA,calledapreRNA,includesthe
noncodingintrons,itmustbeprocessedbeforeitcanbe
readbythetRNA
WhilethemRNAisstillinthenucleus,theintronsare
removedfromthepreRNA
TheexonsthatremainarejoinedtoformthemRNAthat
leavesthenucleuswiththeinformationforthesynthesisof
protein

RemovingIntronsfrommRNA

RegulationofTranscription
AspecificmRNAissynthesizedwhenthecellrequiresa
particularprotein
Thesynthesisisregulatedatthetranscriptionlevel:
feedbackcontrol,wheretheendproductsspeedupor
slowthesynthesisofmRNA
enzymeinduction,whereahighlevelofareactantinduces
thetranscriptionprocesstoprovidethenecessaryenzymes
forthatreactant
Regulationoftranscriptionineukaryotesiscomplicatedand
wewillnotstudyithere

RegulationofProkaryoticTranscription
Inprokaryotes(bacteriaandarchebacteria),transcriptionof
proteinsisregulatedbyanoperon,whichisaDNAsequence
precedingthegenesequence
Thelactoseoperonconsistsofacontrolsiteandthegenes
thatproducemRNAforlactoseenzymes

LactoseOperonandRepressor
Whenthereisnolactoseinthecell,aregulatorygene
producesarepressorproteinthatpreventsthesynthesis
oflactoseenzymes
therepressorturnsoffmRNAsynthesis

LactoseOperonandInducer
Whenlactoseispresentinthecell,somelactosecombineswith
therepressor,whichremovestherepressorfromthecontrolsite
Withouttherepressor,RNApolymerasecatalyzesthesynthesis
oftheenzymesbythegenesintheoperon
Theleveloflactoseinthecellinducesthesynthesisofthe
enzymesrequiredforitsmetabolism
RNA Polymerase

TheGeneticCode
Thegeneticcodeisfoundinthesequenceofnucleotidesin
mRNAthatistranslatedfromtheDNA
AcodonisatripletofbasesalongthemRNAthatcodesfora
particularaminoacid
Eachofthe20aminoacidsneededtobuildaproteinhasatleast2
codons
Therearealsocodonsthatsignalthestartandendofa
polypeptidechain
Theaminoacidsequenceofaproteincanbedeterminedby
readingthetripletsintheDNAsequencethatarecomplementary
tothecodonsofthemRNA,ordirectlyfromthemRNAsequence
TheentireDNAsequenceofseveralorganisms,including
humans,havebeendetermined,however,
onlyprimarystructurecanbedeterminedthisway
doesntgivetertiarystructureorproteinfunction

mRNACodonsandAssociatedAminoAcids

ReadingtheGeneticCode
Supposewewanttodeterminetheaminoacidscodedfor
inthefollowingsectionofamRNA
5CCUAGCGGACUU3
Accordingtothegeneticcode,theaminoacidsforthese
codonsare:
CCU=Proline
GGA=Glycine

AGC=Serine
CUU=Leucine

ThemRNAsectioncodesfortheaminoacidsequenceof
ProSerGlyLeu

TranslationandtRNAActivation
OncetheDNAhasbeen
transcribedtomRNA,the
codonsmustbetranlatedtothe
aminoacidsequenceofthe
protein
Thefirststepintranslationis
activationofthetRNA
EachtRNAhasatripletcalled
ananticodonthatcomplements
acodononmRNA
AsynthetaseusesATP
hydrolysistoattachanamino
acidtoaspecifictRNA

InitiationandTranslocation
InitiationofproteinsynthesisoccurswhenamRNAattachesto
aribosome
OnthemRNA,thestartcodon(AUG)bindstoatRNAwith
methionine
ThesecondcodonattachestoatRNAwiththenextaminoacid
Apeptidebondformsbetweentheadjacentaminoacidsatthe
firstandsecondcodons
ThefirsttRNAdetachesfromtheribosomeandtheribosome
shiftstotheadjacentcodononthemRNA(thisprocessiscalled
translocation)
Athirdcodoncannowattachwherethesecondonewasbefore
translocation

Termination
Afterapolypeptidewithalltheaminoacidsforaproteinis
synthesized,theribosomereachesthethestopcodon:
UGA,UAA,orUAG
ThereisnotRNAwithananticodonforthestopcodons
Therefore,proteinsynthesisends(termination)
Thepolypeptideisreleasedfromtheribosomeandthe
proteincantakeonits3Dstructure
(someproteinsbeginfoldingwhilestillbeingsynthesized,
whileothersdonotfoldupuntilafterbeingreleasedfrom
theribosome)