I.MultipleChoice.Fillinthecircleonthetestformcorrespondingtothecorrectanswer.

ForthenextsixquestionsyouwillneedtorefertothestructuresoftheaminoacidRgroupsshownat
theendofthemultiplechoicequestions.
1.________typicallyforms________bondsbetweentwodifferentproteinsubunits?
a.Cysteine,covalentc.Cytosine,disulfide e.aandd
b.Glycine,H d.Methionine,disulfide

2.Whichofthetripeptidesbelowwouldbeleastsolubleinahydrophobicsolventlikebenzene?
a.NphenylalaninecysteineglycineC d.NleucineaspartateglycineC
b.NprolinephenylalanineleucineC e.NarginineprolinealanineC
c.NglutamateaspartatelysineC
3.Whichoftheaminoacidslistedbelowwouldbemostlikelytobefoundonlyontheinteriorofa
polypeptidethathasalreadyadopteditsactiveconformationandisincontactwiththecenterofalipid
bilayer?
a.phenylalanineb.candec.aspartated.leucinee.glutamate

4.Whichaminoacidwouldbelikelytohaveachargeof1atphysiologicalpH7.4?
a.arginineb.lysinec.aspartated.leucinee.aandb
5.Whichaminoacidwouldprobablybefoundintheexteriorofaproteininthecytoplasm?
a.aspartateb.methioninec.lysined.aandce.alloftheotheranswers
6.WhichaminoacidhasapositivechargeatphysiologicalpH?
a.methionineb.glutamatec.arginined.bandce.noneoftheabove
7.WhatproteinstructureinvolvesinteractionbetweentwoportionsofthesamechainintheformofH
bondsperpendiculartotheaxisofthemolecule?
a.helixb.secondaryc.aandbd.pleatedsheete.bandd

8.Whichofthefollowingmayoccurifanaminoacidinthemiddleofanhelixischangedfroma
helixindifferenttoahelixbreakingaminoacid?
a.Thehelixisstrengthened. c.Thehelixceasestoexist.e.candd
b.Thehelixbecomesapleatedsheet. d.Theprotein'sfunctionislost.

9.Nondenaturinggelelectrophoresishastheadvantagethatit________________.
a.cande
b.allowsthedetectionofproteinsinagelbytheirbiologicalactivity
c.separatesonthebasisofmorethanonepropertythustosomedegreeconfusingtheresults
d.separatessolelyonthebasisofmolecularweight
e.separatesonthebasisofmolecularweightandcharge
10.Aproteinappliedtoagelmovessteadilydownthegelandstopsbeforereachingtheendwhilethe
currentisstillon.Whydidtheproteinstopmoving?
a.Itschargebecamepositive.c.Itwasisometricallyaffected. e.Itisdenatured.
b.Itschargebecamenegative.d.Itschargebecomesneutral.
11.WhatkindofpolypeptidestructureinvolvesinteractionwithinthesamechainsintheformofH
bondsperpendiculartotheaxisofthemolecule?
a.primaryb.secondaryc.tertiaryd.helixe.bandd
12.Whichtechniqueeffectivelyseparatesproteinsonthebasisoftheirsize,shapeanddensityandalso
onthebasisofthemediumthroughwhichtheyaremoving?
a.ionexchangechromatographyc.nondenaturinggels e.SDSPAGE
b.sucrosedensitygradientcentrifugationd.aandb
13.Thefinalproteinconformation(the3Dshape)isultimatelydeterminedby_________.
a.theinteractionbetweentheRgroupswithinthenucleicacidbackbone
b.interactionbetweensphingolipidRgroups
c.theinteractionbetweenadjacentornearlyadjacentregionsofthecarbohydratebackbone
d.theprimarystructure
e.alloftheabove

14.Whichpropertybelowistypicalofhelicalstructure?
a.ahighdegreeofextensibility b.flexibility c.strength d.rigiditye.bandc

15.Nucleationismostcloselyassociatedwithwhichphenomenonbelow?
a.renaturationb.proteinfoldingc.transcriptiond.translatione.aandb
16.Whatbondsareinvolvedinholdingtogethertertiarystructureinproteins?
a.disulfidelinkagesc.Hbondse.aandc
b.hydronomicinteractionsd.peptidebondinteractions
17.Aproteinyouwishtostudyislocatedinthemitochondriaofratlivercellsandisreadilyextractable
frompartiallypurifiedmitochondria.IthasahighlynegativechargeatpH7.Youproposetousea
seriesoftechniquestopurifytheprotein.Inwhatorderwouldyouusethetechniquesafteryouhad
homogenizedthetissue?
a.sucrosedensitygradientcentrifugation(SDGF)extractionisoelectricfocussing(IEF)
precipitationbyammoniumsulfate
b.differentialcentrifugationSDGFextractionammoniumsulfateprecipitationCM
(carboxymethyl)cellulosechromatographyaffinitychromatography
c.ammoniumsulfateprecipitationSDGFextractionCMcellulosechromatographyIEFSDGF
d.IEFaffinitychromatographydifferentialcentrifugationextraction
e.differentialcentrifugationSDGFextractionammoniumsulfateprecipitationDEAE
(diethylaminoethyl)cellulosechromatographyaffinitychromatography
18.TheUnitMembranemodelwasshowntobeinaccuratebecause__________.
a.allmembraneswerenotexactlyalike d.membranesvaryincholesterolcontent
b.membranesaremadeupofphospholipids e.a,candd
c.membraneshavedifferentproteinandlipidcontent
19.Aproteinisassociatedwiththecellmembraneandfullyexposedtotheextracellularenvironmentof
thecell.Itcan,however,befreedfromthemembranebywashingthecellwithalowionicstrengthsalt
solution.Itisa________protein.
 a.peripheralb.extrinsicc.lipidanchoredd.transmembranee.aandb
20.Resonanceexplainsthe______ofthe_______bondthatrestrictstheabilityofapolypeptidetocoil?
a.extensibility,peptide c.highrotationalfreedom,peptide e.aandd
b.rigidity,phosphateester d.rigidity,peptide
21.Ifthereareonlydifferent20aminoacidsinsertedintoproteins,howdoaminoacids,whicharenot
amongthetwenty(likehydroxylysineandhydroxyproline),getintoproteins?
a.Theyareaddedaftersynthesis. d.Therereallyare22aminoacids.
b.Theyarepresentbeforesynthesis. e.noneoftheabove
c.Aminoacidsinsertedduringsynthesisarealteredlater.
22.Whichtechniquecouldbeusedformolecularweightdeterminationsinproteinsunderallcircumstances?
a.gelfiltrationd.aande
b.isoelectricfocusinge.SDSPAGE
c.carboxymethyl(CM)cellulosechromatography
23.Whatisthelowestlevelofpolypeptidestructureinaproteinexhibitingsubunitstructure?
a.quaternaryb.secondaryc.tertiaryd.helixe.primary
24.Youarepurifyingaprotein.Beforeyouhaveemployedanyprocedurestopurifyit,itsspecific
activityis300units/mgprotein.After5successivepurificationprocedures,thespecificactivityis
12,000,000units/mgproteinHowmuchhaveyoupurifiedtheprotein?
a.40,000timesb.4,000timesc.400,000timesd.0.00004timese..0004times
25.Whatpropertyofaproteincanbedetermineddirectlywithgelfiltrationchromatographyifthe
proteinisanoblatespheroid(cigarshaped)?
a.molecularchargeb.molecularweightc.molecularshaped.Stokes'radiuse.bandd
26.IfasolutioncontainingthefollowingtripeptideswerepassedthroughacolumnpackedwithCM
celluloseatpH7,whichofthemwouldbindmosteffectivelytotheCMcellulosecolumn?(seedrawing
atendofMultipleChoicesectionforRgroups)
a.NargininelysineprolineCd.NleucinealanineglycineC
b.NaspartateglutamateaspartateCe.NaspartatephenylalanineleucineC
c.NphenylalanineaspartateglycineC
27.Whichtechniquewouldbeleastlikelytoresultinahighdegreeofpurification?
a.differentialcentrifugationc.precipitatione.affinitychromatography
b.ionexchangechromatographyd.homogenization
28.WhichtechniquewouldbeusedtodetectthedifferencesinconformationseeninDNAsplacedin
differentchemicalenvironments?
a.Xraydiffractiond.isoelectricfocussing
b.SDSpolyacrylamidegelelectrophoresise.DEAEcellulosechromatography
c.spectrophotometry
29.Theeffectof________oneukaryoticcellmembranesistoabolishtransitiontemperature.
a.phospholipidsb.cholesterolc.gangliosidesd.lipidanchoredproteinse.aandb
30.___________arespecializedproteinsthatprovideanenvironmentinwhichproteinsthathave
denaturedcanrenaturewithoutinterference.
a.Foldasesb.Chaperoninsc.Molecularchaperonesd.Ubiquitinse.bandc
31.Redbloodcellswithasurfaceareaof_______arelysedandthelipidsoftheirmembranesaretotally
extracted.Theselipidsarethenspreadoverthesurfaceofawatertankandthesurfaceareacoveredis
foundtobe4502.
a.902b.452c.1502d.2252e.9002
32.Artificialmembranes______________.
a.donotresealspontaneouslyifpiercedd.bandc
b.possessmanypropertiesincommonwithnaturalmembranese.a,bandc
c.lacksomepropertiesthatnaturalmembraneshave
33.Whichofthefollowingmembranecomponentsisamphipathicatleasttoasmalldegree?
a.cholesterolb.gangliosidesc.transmembraneproteinsd.phospholipidse.alloftheabove
34.Whichofthepropertiesbelowfavorthepassageofamoleculethroughacellmembrane?
a.largeMWb.hydrophobicc.banddd.highnegativechargee.hydrophilic
35.Whichofthefollowingmoleculeswouldpassleasteasilythroughalipidbilayer?
a.waterb.carbondioxidec.oxygend.sodiumchloridee.a,bandc
36.Whichoneofthefollowingmoleculeswillelutelastfromagelfiltrationcolumn?(Assumethatall
aminoacidshavethesamemolecularweight.)
a.aglobularproteincomposedof187aminoacidsd.aglobularproteinwith165aminoacids
b.averylowmolecularweightdyee.aproteinconsistingof120aminoacids
c.acigarshapedproteinof188aminoacids
37.Whichofthetechniquesbelowmightbeusedtoeffectarapidpurificationandwouldbebasedon
thesolubilityofthemoleculetobepurified?
a.sucrosedensitycentrifugation d.selectiveprecipitation
b.sodiumhydroxideprecipitation e.candd
c.ammoniumsulfateprecipitation
38.Whichtechniquebelowisbestfordeterminingtheprecisequantityofradioactiveisotopelocatedina
specimen?
a.canddc.liquidscintillationcountinge.ultracentrifugation
b.atomicforcemicroscopyd.autoradiography

39.Whichtechniquebelowdependsontheabilityofaproteinlikeahormonereceptortobindtoa
specificmoleculelikethehormoneitnormallybinds?
a.DEAEcellulosechromatographyc.gelfiltratione.homogenization
b.selectiveprecipitationd.affinitychromatography
40.Oneofthemoststrikingfeaturesofmembranesisexhibitedbythedistributionofmembrane
polysaccharides.Thispropertyiscalled__________.
a.asymmetryb.diffusionc.exocytosisd.asynchronye.effilosis
41.WhichtechniquecombinestheeffectsofisoelectricfocusingandSDSPAGEtopurifyproteins?
a.ionexchangechromatography d.autoradiography
b.threedimensionalgelelectrophoresis e.twodimensionalgelelectrophoresis
c.spectrophotometry

42.Thepleatedsheetisstabilizedby________________.
a.HbondsbetweenpolaraminoacidRgroups
b.covalentbonds
c.Hbondsbetweenamide(peptide)linkagesorientedparalleltothemolecule'saxis
d.acidobasiccombinations
e.Hbondsbetweenamidelinkages,orientedperpendiculartothemolecule'saxis
43.Aproteinthatcanbewashedoffofacellularmembranebyamoderateconcentrationofasalt
solutioniscalleda(n)______protein.
a.transmembraneb.lipidanchoredc.aandbd.peripherale.bandd
44.Duringthesummer,someorganismsadjustthefluidityoftheirmembranesby__________.
a.increasingphospholipidtaillengthd.decreasingphospholipidtaillength
b.increasingtailunsaturatione.increasingtailsaturation
c.aande
45.Whatistheminimumnumberofconsecutivehelixformingand/orhelixindifferentaminoacids
requiredtoformanhelix?
a.10b.14c.3d.7e.24.5
46.Whatbondsmaybeinvolvedinholdingtogethertertiarystructureinproteins?
a.peptidebondsb.ionicbondsc.Hbondsd.disulfidelinkagese.b,candd

47.Whatisthehighestlevelofstructureexhibitedbyaproteinconsistingofonesubunit?
a.primaryb.secondaryc.tertiaryd.quaternarye.pentary

48.Whatpropertyofapleatedsheetregionofaproteinderivesfromtheextendedarrangementofits
backbone?
a.strengthb.flexibilityc.extensibilityd.aandbe.hardness
H CH3
CH CH CH N C NH CH2 CH CH2 H
2 2 2 2
arginine NH CH3 glycine
leucine phenylalanine
O O
CH2 C HO CH CH CH C CH2 OH
2 2 2
OH OH serine
aspartate tyrosine glutamate
CH3 O
CH2 SH CH CH2 CH2 CH2 CH2 NH 2 CH2 C
cysteine valine CH
3
lysine asparagine NH2
H
CH3 CH CH S CH C CH 2 CH3 CH2 C CH
2 2 3
alanine methionine CH3 isoleucine +
O H histidine HN NH
C CH3 C
CH CH C CH CH H
2 2 2 2
glutamine NH 2 OH threonine
CH2 HC CH2 C
N proline tryptophan HC
H N
H
II.ShortAnswer.Pleasebeasbriefaspossible.
1.Whatisthehighestlevelofstructureexhibitedbyaproteinhavingmorethanonesubunit?(1point)
2.Ifyouareattemptingtoisolatemitochondriafromlivertissue,whatisthefirststepintheprocedure?
(1point)

Beforestartingthisprocedure,whywouldyouplacethelivertissueinacold,isotonicsolution?(2points)

BONUSQUESTIONSSHORTANSWER
1.JEOPARDYBONUSQUESTION(Youranswermustbeintheformofaquestion.)
Subsequentanswersneednotbeintheformofaquestion.(1point)
This"giant"oceandwellerhasthelargesteyesofanycreature.

2.DrawageneralizedtetrapeptideatphysiologicalpH(pH7.4).(3points)

3.Aproteinhasthreeglobularregions,onethatbindsaspecificligand,onethatbindstospecific
regionsofDNAandonethatunwindstheDNAdoublehelix.Theseglobularregionsareconnected
byflexiblehingelikeregions.Whataretheglobularregionsofthisproteincalled?(1point)

4.Inwhatpurificationtechniquedoestrichloroaceticacid(TCA)playaprominentrole?(1point)

5.Whatdoyoucallavesiclethatiscoveredbyalipidbilayerandisusedtodeliveradrugordrugsto
aspecifictargetforchemotherapyofdiseaseslikecancer?Itisdirectedtotheappropriatesitebythe
placementofspecificantibodiesinthebilayer.(1point)
6.Whatpropertydeterminesthespeedbywhichaproteinorlipidcandiffuselaterallythrougha
membrane?(1point)

7.Brieflynameanddefinethelevelsofstructureinproteins.Whattypesofbondsareinstrumentalin
holdingeachlevelofstructuretogether?(8points)
LevelofStructure Definition Bond(s)Involved

8.Identifythetechniquesdescribedbelow?(3points)
a.separationofproteinsonthebasisofmolecularchargeandmolecularweight

b.separationofproteinsonthebasisoftheirchargealone

c.accuratedeterminationofthepositionofradioactivemoleculestakenupbyculturedcells

9.HowischargeeliminatedasafactorintheseparationofproteinsbySDSPAGE?(1point)
10.NameonedifferencefoundbetweendifferentmembranesthatcontributedtothedownfalloftheUnit
Membranemodelofmembranestructure.(1pointed)

11.Whatisthenameoftheuncommonprocesswherebyamembranelipidmovesfromoneleafletofthe
membranetotheotherleaflet?Thismovementcansometimesbereversedbytheactionofanenzyme.
(1point)

12.Youfuseahumanandamousecelltogetherandthenlabeltheresultantcellwithfluorescently
labeledantibodiesagainsthumanandmousemembraneproteins.Theantimouseantibodiesarelabeled
withfluorescein(green)andtheantihumanantibodiesarelabeledwithrhodamine(red).Basedonits
appearance,whatisthecellcalledimmediatelyafterfusion?(1point)

Whatdoyoucallacellthatresultsfromthefusionoftwodifferentcelltypeslikeamousecellfusing
withanalligatorcell?(1point)

13.Youaredesigningadrugthatmustpassthroughalivercellmembraneeasilytocureaparticular
liverailment.Whattwopropertiesmustthatmoleculehaveinorderforittopasseasilythroughthe
membrane?(2points)

14.Scientistshavesequencedproteinsbyusingspecificproteasesto"clip"apurifiedproteinpreparation
betweentwospecificaminoacidsthusforminganumberofmoderatelysizedfragments;theyhaveused
acidhydrolysistoproducesmallerfragments.Eachfragmentcanthenbesequencedbybreakingthe
moderatefragmentsintodipeptides,whichareeasilysequenced.Thefragmentsbelowareobtainedafter
theinitialenzymaticcleavages.Canyoudeducethesequenceoftheoriginalpolypeptide?(HINT:the
originalcleavagesatspecificlocationsdifferdependingonwhichproteolyticenzymewasusedtocreate
eachfragment;thiscausesanoverlapinthefragments'sequences.)(2points)(Usethebackofthetestif
youneedto)

NphevalaspglyalaleutyrargC
NalatyrargphegluNaspNleuC
NleutyrargtyrgluNserglycysC
NalaalatyrargC
NgluNaspNleuvalalaphevalaspC
15.Lookatthefollowingexperimentalresultsobtainedbyadeepspaceprobeinvestigatinglifeonother
planets.MembraneproteinswereextractedwithSDSandsubjectedtoSDSpolyacrylamidegel
electrophoresisontubegels.TheresultantgelswerestainedwithCoomassieBlue,whichstainsproteins(a)
andPeriodicAcidSchiff(PAS)stain,whichspecificallystainscarbohydrates(b).

Whenwholecellsorinsideoutvesicleswereexposedtolactoperoxidaseand125I,theprofileinGraph
(c)wasobtainedwhenthegelswerecutinto1mmthickslicesandtheradioactivitywasmonitoredin
thescintillationcounter.InGraph(d),weseetheresultsofexposuretogalactoseoxidaseand3H
borohydride,aprocess,whichradioactivelylabelssugarresiduestowhichgalactoseoxidaseand3H
borohydrideareexposed.InGraphs(c)and(d),thesolidlineindicateslabelingofwholecellsandthe
dottedlineindicateslabelingofinsideoutvesicles.WhatkindofmembraneproteinsareA,B,Cand
D?(i.e.,Onwhichsurfacearetheyexposed?Dotheyhavepolysaccharidesandonwhichsideofthe
membranearethepolysaccharidesexposed,ifpresent?)Ignoreanypreconceivednotionsabout
membraneproteins!Justinterpretthedata!!!(Pleaseseethefollowingpageforthegraphs.)

Isitexposedontheintracellularor Whichleaflethasthesugargroups(if
Protein Isitaglycoprotein?
extracellularsurface? any)?

A
B
C
 D

Whichprotein,ifany,maybeinvolvedinmembranetransport?(4points)
Whichproteinhasthehighestmolecularweight?(1point)