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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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Final 2227e