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FinalexamCHMI2227 21April2007
FinalExamination
CHMI2227EBiochemistryI
Prof:EricR.Gauthier,Ph.D.
YOURNAME:____________________________
YOURSTUDENTNUMBER:_______________
GUIDELINES:
1) Duration:3hours2) 90questions,on19pages.3) Totalof220marks.Countsfor45%ofthefinalmark.4) Questions189(multiplechoice/trueorfalse):usetheanswersheetprovidedtoyou.5) Question90:writeyouranswerdirectlyonthisquestionnaire,limitingyourselftothe
allottedspace.
6) TheuseoftheUniversityapprovedcalculatorisauthorized.7) Theuseofbooks,notesisforbidden.8) Haveagoodsummer!
1
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MULTIPLECHOICESECTIONA.
Choosetheonealternativethatbestcompletesthestatementoranswersthequestion.2marksperquestion.
1)Thelastcommonancestorofmodernorganismsmusthaveused
A)eitherDorLaminoacids. B)Laminoacids.
C)Daminoacids. D)bothDandLaminoacids.
2)Aminoacidswithnonionizablesidechainsarezwitterionswhentheyare________.
A)inalkalinesolutionsonly
B)inanysolution
C)atphysiologicalpH,pH=7.4
D)inacidicsolutionsonly
E)Alloftheabove
3)Tyrosineandtryptophanarelesshydrophobicthanphenylalaninebecause
A)phenylalaninehasnopolargroupinthesidechain.
B)phenylalanineisaphenol.
C)tyrosineandtryptophanhavesmallerRgroups.
D)phenylalaninehasanindolegroup.
E)Alloftheabove
4)Proteinscanbemodifiedbyadding________toproteinresidues.
A)sugarsandphosphategroups
B)polypeptides
C)cystine
D)AandB
E)Alloftheabove
5)Whichaminoacidisidealforthetransferofprotonswithinthecatalyticsiteofenzymesdueto
thepresenceofsignificantamountsofboththeprotonatedanddeprotonatedformsofitsside
chainatbiologicalpH(i.e.pH~7.4)?
A)Lysine
B)Cysteine
C)Histidine
D)Asparagine
E)Tyrosine
6)ThepKasofargininesCarboxylgroup,Aminogroupandsidechainare1.8,9.0and12.5,respectively.Calculatetheisoelectricpoint.
A)7.2 B)10.8 C)5.4 D)7.8
7)ThepKaofacertainweakacidis4.0.Calculatetheratioofprotonacceptortoprotondonorat
pH7.0.
A)3:1 D)1000:1
B)20:1 E)Theratiocannotbecalculatedwithoutknowingthestructureoftheacid.
C)1:1
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8)TheisoelectricpointofalanineispH=6.15. Itismixedwithproline(pKaCOOH=2.0;pKaNH2=
10.6),andthemixtureisspottedonapieceoffilterpaperandplacedinanelectricfieldatpH
6.15. Whichstatementistrue?
A)Bothaminoacidswillmovefromthespotandbeseparated.
B)Neitheraminoacidwillmoveintheelectricfield.
C)Thetwoaminoacidswillbeseparated.
D)Thetwoaminoacidswillnotbeseparated.
9)AccordingtotheHendersonHasselbalchequation,whentheconcentrationsofprotonacceptor
andprotondonorarethesame,then
A)onlysaltformsarepresent.
B)pKa=log[protonacceptor]/[protondonor].
C)pH=pKa.
D)thecarboxylicacidistotallyneutralized.
10)Theprimarystructureofaproteindescribesthe________.
A) and anglesforeachaminoacid
B)numberofeachtypeofaminoacid(percentcomposition)
C)linearsequenceofaminoacids
D)overallthreedimensionalshape
11)Thepeptidebondiswhichofthefollowing?
A)anesterbond B)anetherbond C)anamidebond D)anaminebond
12)WhatisthenetchargeonthedipeptideArgProatpH9.0?ThetablebelowgivesthepKasof
theionizablegroupsonthefreeaminoacids.
Freeaminoacid
pKaof
Carboxylgroup
pKaof
aminogroup
pKaofside
chain
Arginine 1.8 9.0 12.5
Proline 2.0 10.6
A)0 B)+0.5 C)+1 D) 1 E) 0.5
13)Whichisusedasthebasisofseparationofproteinsbyaffinitychromatography?
A)ThenetchargeandpIoftheproteinatthepHofthecolumn.
B)Theproteinsmolecularweight.
C)Theselectivebindingoftheproteintoaligandonthecolumnmatrix.
D)Theproteinsdensity.
14)The________isthesingleshapeaproteinadoptsunderphysiologicalconditions.
A)moststableenantiomer B)minimalconfiguration
C)primarystructure D)nativeconformation
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15)Whatistheapproximativemolecularmassofa200aminoacidprotein.
A)20,000 B)22,000
C)11,000 D)222,000
E)Noneofabove
16)Structuralproteinsthattypicallyassembleintolargecablesorthreadstoprovidemechanical
supporttocellsororganismsareclassifiedas________proteins.
A)enzyme B)fibrous C)globular D)strand
17)Whatdoesitmeantosayaproteinismultimeric?
A)Invivoitestablishesanequilibriumbetweentwoormoreactiveconformations.B)Theactiveproteininvolvestheassociationoftwoormorepolypeptidechains.
C)Theproteinhasmultiplehelices.
D)Ithasmorethanfiftyaminoacids.
18)Whichstatementisnottrueaboutthepeptidebond?
A)Thepeptidebondislongerthanthetypicalcarbonnitrogenbond.
B)Rotationisrestrictedaboutthepeptidebond.
C)Thecarbonyloxygenandtheamidehydrogenaremostofteninatransconfigurationwith
respecttooneanother.
D)Thepeptidebondhaspartialdoublebondcharacter.
19)Whichrepresentsthebackboneofaprotein?
Note: R=aminoacidsidechain
N=nitrogen
C=alphacarbon
C=carbonylcarbon
A)repeatingunitsofNCC B)repeatingunitsofCC
C)repeatingunitsofNC D)R1R2R3R4R5
20)Ramachandrandeterminedtheallowed valuesofthephiandpsianglesprimarilyby
considering________.
A)thehydropathyofaminoacids B)pKavaluesoftheaminoacids
C)hydrogenbondingeffects D)sterichindrance
21)Whatwouldyouexpectabouttheformationofanhelixforasegmentofaproteinchainthat
containslysineapproximatelyeveryfourthresiduewithallotherresiduesbeingmostly
hydrophobic?
A)HelixformationwouldneveroccurregardlessofpH.
B)HelixformationwouldbefavoredathighpH.
C)HelixformationwouldbefavoredatlowpH.
D)HelixformationwouldbefavoredatneutralpH.
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22)Supersecondarystructuresthatcontainrecognizablecombinationsofhelices,strandsand
loops(e.g.barrel)arecalled________.
A)homologousregions B)folds
C)domains D)motifs
23)WhichofthefollowingsupersecondarystructurescorrespondstoaGreekkey.
24)Whichstructurebelowindicatestheproperhydrogenbondingpatternbetweenaminoacidsin
anhelix?(Dashedlinesrepresentthehydrogenbonds.)
A B C D E
A)I B)II
C)III D)IV
25)Theprincipleforcesholdingsubunitsofanoligomericproteintoeachotherare________.
A)hydrophobicinteractions B)disulfidebonds
C)covalentbonds D)peptidebonds
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26)________isusedtoestimatethemolecularweightofoligomericproteins,while________isused
todeterminethemolecularweightofeachchain.
A)Meltingpoint;SDSgelelectrophoresis
B)Acrylamidegelelectrophoresis;isoelectricfocusing
C)SDSgelelectrophoresis;NMR
D)SDSgelelectrophoresis;gelfiltrationchromatography
E)Gelfiltrationchromatography;SDSgelelectrophoresis
27)Hemoglobinis
A)adimerofsubunitseachwithtwomyoglobinproteins.
B)anerythrocyte.
C)atetrameroffourglobinchainsandonehemeprostheticgroup.
D)atetramerof4myoglobinproteins.
E)adimerofsubunitseachwithtwodistinctproteinchains(alphaandbeta).
28)Unliketypicalcatalyzedreactionsinorganicchemistry,enzymereactionsare
A)usuallystereospecific.
B)modulatedtochangeactivitylevels.
C)reactionspecific.
D)essentially100%efficient.
E)Alloftheabove
29)AnenzymethatcatalyzesconversionsofLaminoacidstoDaminoacidsiscalleda/an________.
A)hydrolase
B)isomerase
C)synthase
D)synthetaseE)lyase
30)Atthebeginningofanenzymecatalyzedreactionthe________isnegligible.
A)disappearanceofES B)formationofES
C)formationofE+P D)conversionofEStoE+S
31)Whichenzymebelowisfastest?
A)kinase,kcat=103 B)catalase,kcat=107
C)carboxypeptidase,kcat=102 D)papain,kcat=10
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32)Theenzymecarbonicanhydrasecatalysesthefollowingreaction:
Giventhefollowingdataforthisreaction,determinethenumberofCO2moleculesproducedby
theenzymepersecond:[HCO3]=3mM;Vmax: 0.12moles/min;carbonicanhydrase: 5x109
moles;Km:2.6x102
M,reactionvolume:1ml.
HCO3-
A)4x105s1 B)2.4x107s1 C)6.67x102s1 D)0.08s1
33)The(lower,higher)thevalueofKm,the(less,more)tightlytheenzymeisboundtothe
substrate.
A)lower,less
B)lower,more
C)higher,less
D)higher,more
E)BandC
F)AandD
34)Whichstatementistrueabouttheremovalofreversibleinhibitorsfromenzymesolutions?
A)Dialysisandgelfiltrationareoftenused.
B)Theseinhibitorscannotbeseparatedfromtheenzymewithouttreatmentwith
diisopropylfluorophosphate.
C)PAGEistheprimarytechniqueusedforthispurpose.
D)Removalofreversibleinhibitorsisextremelydifficultandcanbeachievedonlyaftermany
purificationsteps.
35)Whichequilibriumbelowappliestononcompetitiveinhibition?
A)I B)II C)III D)IV
H2O
Bicarbonate
+ H+
+ CO2
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36)Whattypeofinhibitionisindicatedbythedatagraphedbelow?
A)noncompetitive B)competitive
C)irreversible D)uncompetitive
37)Thefollowingdatawereobtainedinthepresenceandabsenceofinhibitor.Whattypeof
inhibitionisshown?
Substrateconcentration
(millimolar)
Ratewithoutinhibitor
(mmol/min)
Ratewithinhibitor
(mmol/min)0.100 2.5 1.6
0.200 4.2 2.9
0.500 6.6 5.1
0.750 7.4 6.2
A)uncompetitive
B)irreversible
C)noncompetitive
D)competitive
E)cannottellinhibitiontypefromtheinformationgiven
38)WhatistheKivaluefortheinhibitorshowninproblem37if[inhibitor]=0.01mM?
A)0.0045mM
B)0.0082mM
C)0.022mM
D)0.012mM
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39)Anenzymeisirreversiblyinhibitedbydiisopropylfluorophosphate(DFP).Whatdoesthisshow?
A)Serineislikelyanimportantresidueintheactivesite.
B)TheenzymehasbeendenaturedbyDFP.
C)DFPisananalogoftheenzymessubstrate.
D)DFPisanallostericmodulatoroftheenzyme.
40)Twocurvesshowingtherateversussubstrateconcentrationareshownbelowforanenzyme
catalyzedreaction.OnecurveisforthereactioninthepresenceofsubstanceX.Theothercurve
isfordataintheabsenceofsubstanceX.Examinethecurvesandtellwhichstatementbelowis
false.
A)Xisacompetitiveinhibitor.
B)TheenzymeexhibitsnonMichaelisMentenkinetics.
C)Xisanactivatoroftheenzyme.
D)Xislikelyanallostericmodulator.
41)Replacementoftheaminoacid________atornearanactivesiteofanenzymeismorelikelyto
changeenzymeactivitythanthereplacementof________atorneartheactivesite.
A)histidine;aspartate B)histidine;leucine
C)leucine;histidine D)leucine;isoleucine
42)Whichaminoacidisleastlikelytoparticipateinacidbasecatalysis?A)histidine B)aspartate C)tyrosine D)lysine
43)Ahistidinewasdeterminedtobethecriticalresidueinvolvedinanenzymecatalyzedreaction.
IfthepKaofthehistidineisknowntobe6.5intheactivesiteandthepHofmaximumcatalytic
activityis7.2,whatislikelytheprimaryroleofhistidineinthecatalyticreaction?
A)actsasaprotondonor B)reducestheentropyofthesubstrate
C)stabilizesachargedintermediate D)formsacovalentbondwiththesubstrate
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44)Theroleofserineattheactivesiteofserineproteasesistoactasa(n)________catalyst,whilethe
histidineresidueservesasa(n)________catalyst.
A)weak;strong
B)covalent;acidbase
C)strong;weak
D)anionic;ionic
E)acidbase;covalent
45)Thecatalytictriadofchymotrypsinandotherserineproteasesconsistsof
A)threeaminoacidresiduesadjacentintheprimarystructurewhichacttomakeserinea
strongnucleophile.
B)threeaminoacidresiduescloseenoughinspacetomakeserineastrongnucleophile.
C)threeenzymeswithverysimilarstructuralfeatures.
D)threesubunitsoftheenzyme.
E)Noneoftheabove.
46)InhibitionofATCasebya________nucleotideandactivationofATCasebya________
nucleotidekeepthebalanceofpurineandpyrimidinepoolsinE.coli.A)purine;purine B)pyrimidine;pyrimidine
C)purine;pyrimidine D)pyrimidine;purine
47)Whicharepurines?
A)adenineandthymine B)uracilandguanine
C)cytosineandthymine D)guanineandadenine
48)Whichofthefollowingisguanine?
N
N
N
N
O
H
H2N
N
N
N
N
H2NN
N
N
NO
H2N
HN
N
N
NO
H
A B C D
49)ATPisnotanucleosidebecauseit________.
A)isnotconnecttoacarbohydrategroup B)hasthreephosphatesinsteadofjustone
C)lacksthedeoxyribosylgroup D)hasphosphategroups
50)InDNA,phosphodiesterbondsformwithhydroxylgroupsofcarbonsnumber________and
________ofeachdeoxyribosesugar.
A)3;5 B)2;4 C)2;3 D)4;5 E)3;4
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51)MuchofthestabilityofthedoublestrandedDNAstructureistheresultof
A)theangleoftheplanesofthebaseswithrespecttothehelixaxis.
B)hydrogenbondingbetweenpurines.
C)thestackinginteractionsbetweenadjacentbasepairs.
D)thephosphodiesterbackbone.
52)TheriseandpitchofBDNAare0.33nmand3.40nm,respectively. Abouthowmanyhelical
turnsarethereinafragment1mminlength?
A)330
B)3030
C)294
D)0.0034
E)Cannotcalculatefromtheinformationgiven.
53)RegionsofDNAthataremosteasilyunwoundhave
A)greaterA:Tcontent. B)abouthalfGandhalfC.
C)greaterG:Ccontent. D)alternatingAandG.
54)Inproteins,aminoacidsarelinkedbypeptidebonds;inpolynucleotides,nucleotidesarelinked
by
A)phosphoanhydridebonds.
B)53phosphodiesterbonds.
C)35phosphodiesterbonds
D)Alloftheabove.
55)Fiveprimetothreeprime descriptionofaDNAstrandreferstoA)thelocationofthehydroxylgroups.
B)thephosphorylated5 carbonononesugarandthe3 carbononthenextsugar.
C)thephosphorylated5 carbonatoneend,the3 attheotherend.
D)thephosphodiesterbackboneofDNA.
56)AsBDNAisgraduallyheated,theabsorbanceat260nm
A)staysthesame.
B)decreases.
C)ishalfwaybetweenthatofpoly(ATandpoly(GC).
D)increases.
57)WhichisnotadifferencebetweenBDNAandADNA?
A)Botharehelical,butBDNAisrighthandedandADNAislefthanded.
B)Forpolynucleotidestrandscontainingthesamenumberofnucleotides,theADNAstrand
willbeshorterfromendtoendthanthecorrespondingBDNA.
C)ADNAformsundermoredehydratingconditionsthanBDNA.
D)TheplanesofthenitrogenousbasesarenotperpendiculartothehelixaxisinADNA.
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58)WhichisnotadifferencebetweenRNAandDNA?
A)RNAissinglestranded;DNAisdoublestranded.
B)ThesugarringofRNAismoreoxidizedthanthatinDNA.
C)RNAcannotformhelices.
D)RNAcontainsuracil;DNAusuallydoesnot.
59)Whichofthefollowingrepresentscorrectlypairedbases:
60)DNAthathasbeenliberallylabeledwithradioactive14Cisusedasthetemplateforreplication.
Replicationiscarriedoutinamediumcontainingonlyunlabelednucleotides.Aftertworounds
ofreplication,whatpercentofDNAmoleculesarestilllabeled?
A)25% B)50% C)75% D)100%
61)MeselsonandStahlsexperimentsinvolvedgrowingE.colionamediumcontaining15N(heavynitrogen)whichincreasedthedensityofthebacterialDNA. Cellswerethengrownona
mediumcontainingonly14N. DNAsampleswereobtainedforanalysisafterone,twoandthree
roundsofreplication(generations)andcentrifugedonadensitygradient. Thedoublehelical
DNAformsbandsinthegradientdependingonitsdensity. HowmanybandsdidMeselsonand
Stahlseeaftertwogenerationofcellsweregrownonthe14Nmedium?
A)Two,onewithDNAcontainingboth15Nand14NandonewithDNAcontainingonly
14N.
B)Two,onewithDNAcontainingonly15NandonewithDNAcontainingonly14N.
C)Three,onewithDNAcontainingonly15N,onewithDNAcontainingboth15Nand14N
andonewithDNAcontainingonly14N.
D)OnewithDNAcontainingboth15Nand14N.
62)Whichofthefollowingwouldbethebestprimerforreplicatinginitsentiretythefollowing
DNAstrand:
5TAGATAGCTAGATGCGATCCTATCGATATCGCGATATCTAGATATTCTTATCTATCGGAGCG
3
A)TAGATAGCTAGATG B)CGCTCCGATAGATA
C)TATCTATCGGAGCG D)CATCTAGCTATCTA
A B C D
N
N
N
N
H2NN
H2N
N O
HN
N
N
N
H2NN
N O
OH2N
N
N
N
N
H2NN
N O
O
HN
N
N
N
H2NN
N O
H
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63)Whatisthemeltingpoint(Tm)ofthefollowingdsDNAmolecule?
CATCTAGCTATCTA
GTAGATCGATAGAT
A)38oC B) 46oC
C)76oC D) 92oC
64)DNApolymeraseIIIrequiresa/an________forsynthesisofDNAtooccur.
A)RNAprimer B)DNAtemplate
C)free3OHendofaDNAstrand D)Alloftheabove
65)TheprocessivityofE.coliDNApolymeraseIIIholoenzymeaccountsforallofthefollowingexcept
A)thedirectionalityofpolymerization.
B)therelativelysmallnumberofenzymesneededtoreplicatetheentirechromosome.
C)therapidrateofpolymerization.
D)theabilityofasingleholoenzymetoaddmanynucleotidestoagrowingDNAchain.
66)TheRNAprimeratthebeginningofeachOkazakifragmentisremovedby
A)DNApolymeraseI.
B)DNApolymeraseII.
C)DNApolymeraseIII.
D)35 exonucleasesubunitofDNApolymeraseIII.
67)Okazakifragmentsare________.
A)shortstretchesofDNAformedonthelaggingstrandB)thesmallestsubunitsofDNApolymeraseIII
C)fragmentsofDNApolymeraseIthatlack53 exonucleaseactivity
D)shortRNAprimersneededforinitiationofpolymerization
68)WhatisareasonablelengthforanRNAprimerinE.coli?A)afewnucleotides B)50nucleotides
C)100nucleotides D)1000nucleotides
69)Fragmentsonthelaggingstrandarejoinedbytheenzyme________.
A)DNAligase B)DNAprimase
C)DNApolymeraseI D)DNAsynthase
70)ThetechniqueofSouthernblotisusedtoprobe_________
A)Nucleicacids B)DNA
C)Proteins D)RNA
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MULTIPLECHOICESECTIONB
Choosetheonerightanswerfromthechoicesprovided.10marksperquestion.
71) Youwishtodeterminethesequenceofashortpeptide.Youdigestthepeptidewiththefollowingreagentsandobtaintheresultsshownbelow:
1) HClhydrolysis:A,D,I,K,M,S,T,V,W2) FDNBdigestion:A3) Carboxypeptidase:T4) Trypsin:a)A,D,K,M,S
b)I,T,V,W
5) CyanogenBromide:a)A,Mb)D,I,K,S,T,V,W
6) Cuttingfragment(5b)withFDNByields: S7) Thermolysin: a)V
b)W
c)I,T
d)A,D,K,M,S
8) Chymotrypsin:a)I,Tb)A,D,K,M,S,V,W
Howmanyaminoacidswouldbefoundineachofthefragmentsobtainedaftercuttingthispeptidewith
proteaseV8:
A)4and5 C)2and7
B)3and6 D)proteaseV8wouldnotcutthispeptide
72) Thetableshownbelowpresentsdataobtainedduringthepurificationoflactatedehydrogenase. Whichpurificationstepworkedbest(Note:extinctioncoefficientofNADH= 6.22x103M1cm1)?
PurificationStep Volume
(mL)
Dilution Absorbance
NADH@340
nm(1min
reaction)
Protein
concentration
(mg/mL)
Homogenate 10 1/100 0.323 33.02
Supernatantafter40%saltprecipitation
8.9 1/100 0.316 31.84
Gelfiltration
chromatography
9.1 1/100 0.274 26.51
Ionexchange
chromatography
5 1/100 0.345 12.07
A)Gelfiltration C)saltprecipitation
B)Ionexchange D)thepurificationdidnotwork
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TRUE/FALSE. Select A ifthestatementistrueand B ifthestatementisfalse. 2marksperquestion.
73)TheisoelectricpointofaminoacidsistheaverageofthevaluespKaCOOH+pKaNH2.
74)Ingelelectrophoresisthemoleculeswiththehighestmolecularweightmigratethefarthestfrom
thestartingwells.
75)Mostproteinscontainanapproximatelyequalamountofeachofthestandardaminoacids.
76)Thetwentystandardaminoacidsaretheonlyaminoacidsfoundinlivingorganisms.
77)Allproteinspossessprimary,secondary,tertiaryandquaternarystructure.
78)Oncedenatured,proteinscannotberenaturedorrestoredtothenativestate.
79)Ascorbicacidisnecessaryfortheformationofhydroxyprolineandhydroxylysineresidues
beforetheyareincorporatedintothecollagenproteinmolecule.
80)Theporphyrinprostheticgroupisheldintotheinteriorofglobinmoleculesbycovalentbondsto
specificaminoacidresidues.
81)Increasingtheconcentrationofaclassiccompetitiveinhibitorhasnoeffectonthemaximumvelocityofanenzymesubstratereaction.
82)Allostericmodulatorsbindcovalentlytotheregulatorysiteofanenzymeandchangeits
conformation.
83)ThetwostrandsofdoublestrandedDNAhavethesamecontentofeachofthebasesA,T,Gand
C.
84)ThemajorandminorgroovesarethesameinBDNAandADNA.
85)RNAdoesnothaveadoublestrandform.
86)The subunitsofE.coliDNApolymeraseformaslidingclampthatsurroundstheDNAstrandsatthereplicationfork.
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87)InE.colireplicationbeginsattheoriginofreplicationandproceedsinonedirectionuntiltheentirecircularDNAmoleculehasbeencopied.
88)DNAligaseenzymesuseATPasacofactor.
89)InDNAsequencing,readingfromthebottomtowardsthetopofthegelwillgiveyouthe
sequenceinthe3>5 orientation.
ESSAYQUESTION. Provideacompleteanswertothefollowingquestion.Writeyouransweronthis
questionnaire,limitingyourselftothespaceallotted.For26marks.
90)
16Continues on followin a e
ExplainwhyDNAreplicationcanonlyoccurinthe5 3directionandnotinthe35direction.
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uestion 90 (continued)
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