Ebook MCAT biochemistry review 2019-2020: Part 2

InThisChapter
7.1

TheGeneticCode
TypesofRNA
Codons
Mutations

7.2

Transcription
MechanismofTranscription
PosttranscriptionalProcessing

7.3

Translation
TheRibosome
MechanismofTranslation
PosttranslationalProcessing

7.4

ControlofGeneExpressioninProkaryotes
OperonStructure
InducibleSystems
RepressibleSystems

7.5

ControlofGeneExpressioninEukaryotes
TranscriptionFactors
GeneAmplification
RegulationofChromatinStructure


ConceptSummary


ChapterProfile

Thecontentinthischaptershouldberelevanttoabout15%ofall
questionsaboutbiochemistryontheMCAT.
ThischaptercoversmaterialfromthefollowingAAMCcontent
categories:
1B:Transmissionofgeneticinformationfromthegenetotheprotein
5D:Structure,function,andreactivityofbiologically-relevant
molecules

Introduction
HepatitisCvirus(HCV)continuestobeamajorcauseofcirrhosisandliver
failureintheUnitedStates.Usuallyassociatedwithintravenousdruguse,


hepatitisCcausesongoingdamageandinflammationintheliver,leadingto
theformationofscartissuethatreplacesthenormalcellsoftheorgan.Over
time,thisbuildupofscartissuemakestheliverunabletokeepupwiththe
metabolicdemandsofthebody,andliverfailureensues.Tofightthisvirus,
infectedhepatocytesreleaseinterferon,apeptidesignalthat—asthename
suggests—interfereswithviralreplication.Becausevirusesmusthijackthe

hostcell’smachinerytoreplicate,onewaythebodycanlimitthespreadof
thevirusisbyshuttingofftheprocessesoftranscriptionandtranslation.
Interferonnotonlycurtailstheseprocessesinvirallyinfectedcells,butalso
inducestheproductionofRNaseL,whichcleavesRNAincellstofurther
reducetheabilityofthevirustoreplicate.Coupledwithotherimmune
defenses,interferonthusservesasanefficientmechanismtoprotectthe
bodyfromviralpathogens.
Eveninnormal,healthycells,thefirststepinexpressinggeneticinformation
istranscriptionoftheinformationinthebasesequenceofadouble-stranded
DNAmoleculetoformasingle-strandedmoleculeofRNA.Thesecondstepis
translatingthatnucleotidesequenceintoaprotein.Noteverycell,though,
expresseseverygeneproduct,andcontrolofgeneexpressionleadstothe
differentiationofthetotipotentzygoteintoallofthetissuesofthebody.In
thischapter,wewilldiscusstheprocessthroughwhichproteinsareproduced
alongwiththecontrolsthatmodulateeachstepofthepath.


7.1TheGeneticCode
LEARNINGGOALS
AfterChapter7.1,youwillbeableto:
DifferentiatebetweenthreedifferenttypesofRNA:mRNA,tRNA,
andrRNA
TranscribeaDNAsequencelike"GAATTCG"intoitsmRNAconjugate
Definetheconceptsofwobbleanddegeneracy
Identifythetranslationoutcomesofkeycodons,includingAUG,
UAG,UAA,andUGA
Predictthelikelyimpactofdifferentmutationtypesontheresulting
peptide

Anorganismmustbeabletostoreandpreserveitsgeneticinformation,pass

thatinformationalongtofuturegenerations,andexpressthatinformationas
itcarriesoutalltheprocessesoflife.WeknowthatDNAandRNAsharethe
samelanguage:theybothcodeusingnitrogenousbases.Proteins,however,
arecomposedofaminoacids,whichconstituteadifferentlanguage
altogether.Therefore,weusethegeneticcodetotranslatethisgenetic
informationintoproteins.


Whilenucleotidesplayacrucialroleinmaintainingourgeneticidentityfrom
generationtogeneration,itistheproteinstheyencodethathelporganisms
developandperformthenecessaryfunctionsoflife.Themajorstepsinvolved
inthetransferofgeneticinformationareillustratedinthecentraldogmaof
molecularbiology,asshowninFigure7.1.Classically,ageneisaunitofDNA
thatencodesaspecificproteinorRNAmolecule,andthroughtranscription
andtranslation,thatgenecanbeexpressed.Althoughthissequenceisnow
complicatedbyourincreasedknowledgeofthewaysinwhichgenesand
nucleicacidsmaybeexpressed,itisstillusefulasageneralworkingdefinition
oftheprocessesofDNAreplication,transcription,andtranslation.Wehave
alreadydiscussedDNAsynthesis,butwillcontinuelearningmoreaboutgene
expressionintherestofthischapter.

Figure7.1. TheCentralDogmaofMolecularBiology
Therelationshipbetweenthesequencefoundindouble-strandedDNA,
single-strandedRNA,andproteinisillustratedinFigure7.2foraprototypical
gene.MessengerRNAissynthesizedinthe5′→3′directionandis
complementaryandantiparalleltotheDNAtemplatestrand.Theribosome
translatesthemRNAinthe5′→3′direction,asitsynthesizestheproteinfrom
theaminoterminus(N-terminus)tothecarboxyterminus(C-terminus).

Figure7.2. FlowofGeneticInformationfromDNAtoProtein

TYPESOFRNA
TherearethreemaintypesofRNAfoundincells:mRNA,tRNA,andrRNA.Each
ofthemaintypesisdescribedbelow,butregulatoryandspecializedformsof
RNAarealsodescribedlaterinthechapter.

MessengerRNA(mRNA)
MessengerRNA(mRNA)carriestheinformationspecifyingtheaminoacid
sequenceoftheproteintotheribosome.mRNAistranscribedfromtemplate
DNAstrandsbyRNApolymeraseenzymesinthenucleusofcells.Then,mRNA
mayundergoahostofposttranscriptionalmodificationspriortoitsrelease
fromthenucleus.mRNAistheonlytypeofRNAthatcontainsinformationthat
istranslatedintoprotein;todoso,itisreadinthree-nucleotidesegments
termedcodons.Ineukaryotes,mRNAismonocistronic,meaningthateach
mRNAmoleculetranslatesintoonlyoneproteinproduct.Thus,ineukaryotes,
thecellhasadifferentmRNAmoleculeforeachofthethousandsofdifferent
proteinsmadebythatcell.Inprokaryotes,mRNAmaybepolycistronic,and


startingtheprocessoftranslationatdifferentlocationsinthemRNAcan
resultindifferentproteins.TheprocessofcreatingmaturemRNAwillbe
discussedinthenextsectionofthischapter.

KEYCONCEPT
mRNAisthemessengerofgeneticinformation.DNAcodesforproteins
butcannotperformanyoftheimportantenzymaticreactionsthat
proteinsareresponsibleforincells.mRNAtakestheinformationfrom
theDNAtotheribosomes,wherecreationoftheprimaryprotein
structureoccurs.

TransferRNA(tRNA)


Figure7.3. TheStructureoftRNA


TransferRNA(tRNA)isresponsibleforconvertingthelanguageofnucleic
acidstothelanguageofaminoacidsandpeptides.EachtRNAmolecule
containsafoldedstrandofRNAthatincludesathree-nucleotideanticodon,as
showninFigure7.3.Thisanticodonrecognizesandpairswiththeappropriate
codononanmRNAmoleculewhileintheribosome.Thereare20aminoacids
ineukaryoticproteins,eachofwhichisrepresentedbyatleastonecodon.To
becomepartofanascentpolypeptideintheribosome,aminoacidsare
connectedtoaspecifictRNAmolecule;suchtRNAmoleculesaresaidtobe
chargedoractivatedwithanaminoacid,asshowninFigure7.4.MaturetRNA
isfoundinthecytoplasm.

Figure7.4. ActivationofAminoAcidforProteinSynthesis
Eachtypeofaminoacidisactivatedbyadifferentaminoacyl-tRNA
synthetasethatrequirestwohigh-energybondsfromATP,implyingthatthe
attachmentoftheaminoacidisanenergy-richbond.Theaminoacyl-tRNA
synthetasetransferstheactivatedaminoacidtothe3′endofthecorrect
tRNA.EachtRNAhasaCCAnucleotidesequencewheretheaminoacidbinds.


Thehigh-energyaminoacyl-tRNAbondwillbeusedtosupplytheenergy
neededtocreateapeptidebondduringtranslation.

RibosomalRNA(rRNA)

RibosomalRNA(rRNA)issynthesizedinthenucleolusandfunctionsasan
integralpartoftheribosomalmachineryusedduringproteinassemblyinthe
cytoplasm.ManyrRNAmoleculesfunctionasribozymes;thatis,enzymes
madeofRNAmoleculesinsteadofpeptides.rRNAhelpscatalyzethe
formationofpeptidebondsandisalsoimportantinsplicingoutitsown
intronswithinthenucleus.Thecomplexstructureoftheribosomeis
describedlaterinthischapter.

CODONS
Ifagenesequenceisa“sentence”describingaprotein,thenitsbasicunitisa
three-letter“word”knownasthecodon,whichistranslatedintoanamino
acid.Geneticcodetables,suchastheoneinFigure7.5,serveasaneasyway
todeterminetheaminoacidthatistranslatedfromeachmRNAcodon.Each
codonconsistsofthreebases;thus,thereare64codons.Notehowallcodons
arewritteninthe5′→3′direction,andthecodeisunambiguous,inthateach
codonisspecificforoneandonlyoneaminoacid.


Figure7.5. TheGeneticCode
Notethat61ofthecodonscodeforoneofthe20aminoacids,whilethree
codonsencodefortheterminationoftranslation.Thiscodeisuniversal
acrossspecies(althoughtherearesomeexceptionsinthemitochondriathat
arenotnecessarytoknowfortheMCAT).

KEYCONCEPT
Eachcodonrepresentsonlyoneaminoacid;however,mostamino
acidsarerepresentedbymultiplecodons.


Duringtranslation,thecodonofthemRNAisrecognizedbyacomplementary

anticodononatransferRNA(tRNA).TheanticodonsequenceallowsthetRNA
topairwiththecodoninthemRNA.Becausebase-pairingisinvolved,the
orientationofthisinteractionwillbeantiparallel.Forexample,theaminoacyl
tRNAIle-tRNAIlehasananticodonsequence5′—GAU—3′,allowingittopair
withtheisoleucinecodon5′—AUC—3′,asseeninFigure7.6.

Figure7.6. BasePairingofanAminoacyl-tRNAwithaCodoninmRNA
Everypreprocessedeukaryoticproteinstartswiththeexactsameaminoacid:
methionine.Becauseeveryproteinbeginswithmethionine,thecodonfor
methionine(AUG)isconsideredthestartcodonfortranslationofthemRNA
intoprotein.Therearealso3codonsthatencodeforterminationofprotein


translation;therearenochargedtRNAmoleculesthatrecognizethese
codons,whichleadstothereleaseoftheproteinfromtheribosome.The
threestopcodonsareUGA,UAA,andUAG.

MNEMONIC
Stopcodons:
UAA—UAreAnnoying
UGA—UGoAway
UAG—UAreGone

MUTATIONS
DegeneracyandWobble
Thegeneticcodeisdegeneratebecausemorethanonecodoncanspecifya
singleaminoacid.Infact,allaminoacids,exceptformethionineand
tryptophan,areencodedbymultiplecodons.ReferringbacktoFigure7.5,we
canseethatfortheaminoacidswithmultiplecodons,thefirsttwobasesare
usuallythesame,andthethirdbaseinthecodonisvariable.Werefertothis

variablethirdbaseinthecodonasthewobbleposition.Wobbleisan
evolutionarydevelopmentdesignedtoprotectagainstmutationsinthe
codingregionsofourDNA.Mutationsinthewobblepositiontendtobecalled
silentordegenerate,whichmeansthereisnoeffectontheexpressionofthe
aminoacidandthereforenoadverseeffectsonthepolypeptidesequence.
Theaminoacidglycine,forexample,requiresthatonlythefirsttwo


nucleotidesofthecodonbeGG.ThethirdnucleotidecouldbeA,C,G,orU,
andtheaminoacidcompositionoftheproteinwouldremainthesame.

KEYCONCEPT
ThedegeneracyofthegeneticcodeallowsformutationsinDNAthat
donotalwaysresultinalteredproteinstructureorfunction.Usually,a
mutationwithinanintronwillalsonotchangetheproteinsequence
becauseintronsarecleavedoutofthemRNAtranscriptpriorto
translation.

MissenseandNonsenseMutations
Ifamutationoccursanditaffectsoneofthenucleotidesinacodon,itis
knownasapointmutation.Althoughwe’vealreadydiscussedthesilent
pointmutationinthewobbleposition,otherpointmutationscanhavea
severedetrimentaleffectdependingonwherethemutationoccursinthe
genome.Becausethesepointmutationscanaffecttheprimaryaminoacid
sequenceoftheprotein,theyarecalledexpressedmutations.Expressed
pointmutationsfallintotwocategories:missenseandnonsense.
Missensemutation—amutationwhereoneaminoacidsubstitutesfor
another
Nonsensemutation—amutationwherethecodonnowencodesfora
prematurestopcodon(alsoknownasatruncationmutation)

FrameshiftMutations


Thethreenucleotidesofacodonarereferredtoasthereadingframe.Point
mutationsoccurwhenonenucleotideischanged,butaframeshiftmutation
occurswhensomenumberofnucleotidesareaddedtoordeletedfromthe
mRNAsequence.Insertionordeletionofnucleotideswillshiftthereading
frame,usuallyresultinginchangesintheaminoacidsequenceorpremature
truncationoftheprotein.Theeffectsofframeshiftmutationsaretypically
moreseriousthanpointmutations,althoughitisheavilydependentonwhere
withintheDNAsequencethemutationactuallyoccurred.Asynopsisofthe
differenttypesofmutationscanbefoundinFigure7.7.

Figure7.7. SomeCommonTypesofMutationsinDNA

REALWORLD
Cysticfibrosisismostcommonlycausedbyaframeshiftmutation:a
deletionatcodon508inthepolypeptidechainoftheCFTRchloride
channelgene.Thesubsequentlossofaphenylalanineresidueatthis
positionresultsinadefectivechlorideionchannel.Thisaltered


proteinneverreachesthecellmembrane,leadingtoblockedpassage
ofsaltandwaterintoandoutofcells.Asaresultofthisblockage,cells
thatlinethepassagewaysofthelungs,pancreas,andotherorgans
produceanabnormallythick,stickymucusthattrapsbacteria,
increasingthelikelihoodofinfectioninpatients.

MCATConceptCheck7.1:

Beforeyoumoveon,assessyourunderstandingofthematerialwith
thesequestions.

WhataretherolesofthethreemaintypesofRNA?
mRNA:
tRNA:
rRNA:

Thethree-basesequenceslistedbelowareDNAsequences.Using
Figure7.5,whichaminoacidisencodedbyeachofthese
sequences,aftertranscriptionandtranslation?
GAT:


ATT:
CGC:
CCA:

WhichmRNAcodonisthestartcodon,andwhataminoaciddoes
itcodefor?WhichmRNAcodonsarethestopcodons?
Startcodon:__________;codesfor:__________
Stopcodons:__________

Whatiswobble,andwhatroledoesitserve?

Foreachofthemutationslistedbelow,whatchangesinDNA
sequenceareobserved,andwhateffectdotheyhaveonthe
encodedpeptide?
TypeofMutation

ChangeinDNASequence

EffectonEncodedProtein


Silent(degenerate)
Missense
Nonsense


7.2Transcription
LEARNINGGOALS
AfterChapter7.2,youwillbeableto:
ExplainhoweachoftheeukaryoticRNApolymerases(I,II,andIII)
impactstranscription
IdentifywhereRNApolymerasewouldbindtostarttranscriptionon
aDNAstrand
DeterminethemRNAthatresultsfromagivenhnRNAmolecule:

AlthoughDNAcontainstheactualcodingsequenceforaprotein,the
machinerytogeneratethatproteinislocatedinthecytoplasm.DNAcannot
leavethenucleus,asitwillbequicklydegraded,soitmustuseRNAto
transmitgeneticinformation.ThecreationofmRNAfromaDNAtemplateis
knownastranscription,andwhilemRNAistheonlytypeofRNAthatcarries
informationfromDNAdirectly,therearemanyothertypesofRNAthatexist,


twoofwhichwillplayimportantrolesduringproteintranslation:transferRNA
(tRNA)andribosomalRNA(rRNA).

MECHANISMOFTRANSCRIPTION
TranscriptionproducesacopyofonlyoneofthetwostrandsofDNA.During
initiationoftranscription,severalenzymes,includinghelicaseand
topoisomerase,areinvolvedinunwindingthedouble-strandedDNAand
preventingformationofsupercoils,asdescribedinChapter6ofMCAT
BiochemistryReview.Thisstepisimportantinallowingthetranscriptional
machineryaccesstotheDNAandtheparticulargeneofinterest.Transcription
resultsinasinglestrandofmRNA,synthesizedfromoneofthetwonucleotide
strandsofDNAcalledthetemplatestrand(ortheantisensestrand).The
newlysynthesizedmRNAstrandisbothantiparallelandcomplementaryto
theDNAtemplatestrand.

MNEMONIC
Whenwetranscribeinformation,weusethesamelanguagetowriteit
down(likeincourt,whenthejudgeasksthecourtreportertoread
backthetranscript—thereporterspeaksthesamelanguageas
written).Translationisexactlywhatitsays:wearechangingthe
language.RNAtranslationchangesthelanguagefromnucleotidesto
aminoacids.

RNAissynthesizedbyaDNA-dependentRNApolymerase;RNApolymerase
locatesgenesbysearchingforspecializedDNAregionsknownaspromoter


regions.Ineukaryotes,RNApolymeraseIIisthemainplayerintranscribing
mRNA,anditsbindingsiteinthepromoterregionisknownastheTATAbox,
namedforitshighconcentrationofthymineandadeninebases.
TranscriptionfactorshelptheRNApolymeraselocateandbindtothis
promoterregionoftheDNA,helpingtoestablishwheretranscriptionwill
start.UnlikeDNApolymeraseIII,whichwereviewedduringDNAreplication,

RNApolymerasedoesnotrequireaprimertostartgeneratingatranscript.
Ineukaryotes,therearethreetypesofRNApolymerases,butonlyoneis
involvedinthetranscriptionofmRNA:
RNApolymeraseIislocatedinthenucleolusandsynthesizesrRNA
RNApolymeraseIIislocatedinthenucleusandsynthesizeshnRNA(preprocessedmRNA)andsomesmallnuclearRNA(snRNA)
RNApolymeraseIIIislocatedinthenucleusandsynthesizestRNAandsome
rRNA
RNApolymerasetravelsalongthetemplatestrandinthe3′→5′direction,
whichallowsfortheconstructionoftranscribedmRNAinthe5′→3′direction.
UnlikeDNApolymerase,RNApolymerasedoesnotproofreaditswork,sothe
synthesizedtranscriptwillnotbeedited.Thecodingstrand(orsensestrand)
ofDNAisnotusedasatemplateduringtranscription.Becausethecoding
strandisalsocomplementarytothetemplatestrand,itisidenticaltothe
mRNAtranscriptexceptthatallthethyminenucleotidesinDNAhavebeen
replacedwithuracilinthemRNAmolecule.

KEYCONCEPT


Transcriptionissubjecttothe5′→3′rule,justlikeDNAsynthesis.
Synthesisofnucleicacidsalwaysoccursinthe5′→3′direction.

Inthevicinityofagene,anumberingsystemisusedtoidentifythelocationof
importantbasesintheDNAstrand,asshowninFigure7.8.Thefirstbase
transcribedfromDNAtoRNAisdefinedasthe+1baseofthatgeneregion.
Basestotheleftofthisstartpoint(upstream,ortowardthe5′end)aregiven
negativenumbers:–1,–2,–3,andsoon.Basestotheright(downstream,or
towardthe3′end)aredenotedwithpositivenumbers:+2,+3,+4,andsoon.
Thus,nonucleotideinthegeneisnumbered0.TheTATAbox,whereRNA
polymeraseIIbinds,usuallyfallsaround–25.

TranscriptionwillcontinuealongtheDNAcodingregionuntiltheRNA
polymerasereachesaterminationsequenceorstopsignal,whichresultsin
theterminationoftranscription.TheDNAdoublehelixthenre-forms,andthe
primarytranscriptformedistermedheterogeneousnuclearRNA(hnRNA).
mRNAisderivedfromhnRNAviaposttranscriptionalmodifications,as
describedbelow.


Figure7.8. TranscriptionofDNAtohnRNA

POSTTRANSCRIPTIONALPROCESSING
BeforethehnRNAcanleavethenucleusandbetranslatedtoprotein,itmust
undergothreespecificprocessestoallowittointeractwiththeribosomeand
survivetheconditionsofthecytoplasm,asdemonstratedinFigure7.9.You
canthinkofthenucleusasthehappyhomeofthecell;theDNAstrandsare
theparents,andthehnRNAistheirchild.Thechildmustmatureifheorsheis
tosurvive.