starbiochem lysozyme exercise...

Name________________________

StarBiochem

Ver.1‐MR

1

LysozymeExerciseBackgroundInthisexercise,youwilluseStarBiochem,aprotein3‐Dviewer,toexplorethestructureoftheproteinlysozyme.Lysozymedegradesthecellwallsofbacteria,andisfoundinhumantears.GettingstartedwithStarBiochem• TogettoStarBiochem,pleasenavigateto:http://web.mit.edu/star/biochem.• ClickontheStartbuttontolaunchtheapplication.• ClickTrustwhenapromptappearsaskingifyoutrustthecertificate.• InthetopmenuunderFileclickonOpen/Importandselect“1GXX”andclickonOpen.

Youarenowviewingthestructureoflysozyme,witheachbondintheproteindrawnasaline.Practicechangingtheviewpointofthisproteinintheviewwindow:

Mac PCTOROTATE

clickanddragthemouse left‐clickanddragthemouse

TOMOVEUP/DOWNRIGHT/LEFT

apple‐clickanddragthemouse right‐clickanddragthemouse

TOZOOM

option‐clickanddragthemouse Alt‐left‐clickanddragthemouse

Takeamomenttolookatthestructureoflysozyme(1GXX)fromvariousanglesinthis"bondsonly"view.Beforeproceedingtoanswerthequestions,reviewthebasicstructuresandtermsonthenextpagewhichyoucanrefertoduringthisexercise.

Name________________________

StarBiochem

Ver.1‐MR

2

PROTEINSTRUCTUREBASICSEachproteinhasthefollowingthreelevelsofproteinstructure:PrimarystructureListstheaminoacidsthatmakeupaprotein’ssequence,butdoesnotdescribeitsshape.SecondarystructureDescribesregionsoflocalfoldingthatformaspecificshape,likeahelix,asheet,oracoil.TertiarystructureDescribestheentirefoldedshapeofawholeproteinchain.Inaddition,someproteinsinteractwiththemselvesorwithotherproteinstoformlargerproteinstructures.HowtheseproteinsinteractandfoldtoformalargerproteincomplexistermedQuaternarystructure.

CHEMICALSTRUCTURESOFTHEAMINOACIDSThe20aminoacidsshareacommonbackboneandaredistinguishedbydifferent‘R’groups,highlightedinvariouscolorsbelow.

Name________________________

StarBiochem

Ver.1‐MR

3

ProteinStructureQuestions1Otherthanhydrogen,proteinscontainfouradditionalatoms,Carbon,Nitrogen,Oxygen,andSulfur.Whichofthesefouratomsismostrarelyfoundinproteins?• ClickonViewControls.• UnderAtoms,clickonDraw.Underthisview,eachatomintheproteinisshown.Carbonisgrey,Nitrogenisblue,Oxygenisred,andSulfurisyellow.Note:hydrogenisnotshown.

Answer

2Howmanyofthesulfursintheproteinareclearlyexposedonthesurfaceofthisprotein?• ClickonViewControls.• WithinAtomsboxclickonFillSpace.Thisshowsaspace‐fillingviewoftheproteinsothatyoucanseehowmuchspaceistakenupbyeachatom.

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3Nowexplorelysozyme’ssecondarystructure.

a)Howmanyhelicesareinonelysozymeprotein?• ClickonViewandchooseResetMolecule.• GotoStructureandclickonSecondary.• ClickonHelices.

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b)Whichstructurepredominatesinthelysozymeprotein,helicalshapesorsheet‐likeshapes?• UnderSecondary,clickonSheetsandcomparethiswithyouranswertoparta).

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4Whicharemorecommoninlysozyme,acidicaminoacidsorunchargedpolaraminoacids?• ClickonViewandchooseResetMolecule.• GotoStructureandclickonTertiary.• ClickonbothAcidicandPolartohighlighttheacidicandthepolaraminoacidswithintheprotein.

Answer

Name________________________

StarBiochem

Ver.1‐MR

4

5Lysozymeconsistsof129aminoacids.Listinorderthe12aminoacidsnumbered4through15inlysozyme.• ClickonViewandchooseResetMolecule.• GotoStructureandclickonPrimary.

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6These12aminoacidsmakeupahelixinlysozyme.Howmanyfullturnsofthehelix(i.e.360° turns)doyouseeinthisonehelix?• ClickonViewandchooseResetMolecule.• GotoStructureandclickonSecondary.• UnderHelixSelectionclickontheboxnextto"1".Thiswillselectalltheaminoacidsinthefirsthelixinlysozyme,whichturnsouttobethe12aminoacidsyoulistedabove.

• ClosetheStructurepanelandopentheViewControlspanel.IntheViewControlspanel,movetheUnselectedtransparencyslidertozero.Thismakesalltheaminoacidsyouhavenotselecteddisappear.

• SettheSidechaintransparencyslidertozero.• UnderAtomsclickontheDraw.Rotatethehelixtolookatitfromavarietyofviewpoints.

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7Everyaminoacidismadeupoftwoparts,thebackbone(whichissharedbyallaminoacids,andconsistsofanaminogroupboundtoacentralcarbonboundtoacarboxylgroup)andasidechain(whichisdifferentforeachofthe20aminoacids).DothesidechainsoftheaminoacidsinahelixpointINTOorOUTofthecenterofthehelix?• Rotatethehelixsothatyoulookdownthecenteraxisofthehelix.• ClickonViewControlsandmovethesliderlabeledSidechainbackandforth,toturnthesidechainsonandoff.

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8Howmanyprolinesareinonelysozymeprotein?• ClickonViewandchooseResetMolecule..• GotoSelectionControlsandclickonSelectresiduebytype.Thisallowsyoutoseewhereeachofthetwentyaminoacids/residuesareintheprotein.

• ClickonProline.Answer