lesson plan carrying cargo: exploring non-covalent
TRANSCRIPT
pdb101.rcsb.org
LessonPlanCarryingCargo:Exploringnon-covalentinteractionsbetweenproteinsandsmallmoleculesinbloodtransportGradelevel:9-12Objectives:Aftercompletion,studentswillunderstandhowthehydrophobicandhydrophilicinteractionsbetweenproteinsandsmallmoleculesareutilizedintransportingoflipidsandothersubstancesinthebloodSummary:StudentsusethedataandtheinformationfromtheRCSB.organdPDB101.RCSB.orgwebsitestolearnaboutthefunctionofserumalbuminandtoexaminetheproteinin3D.Theyexplorethestructuralfeaturesandthenon-covalentinteractionsthatareemployedbytheproteintocarryfattyacidsintheblood.NGSSStandardsScience&EngineeringPractices:â Engaginginargumentfromevidenceâ Obtaining,evaluatingandcommunicatinginformationâ Developingandusingmodels
DisciplinaryCoreIdeas:â LS1A:StructureandFunction
CrosscuttingConcepts:â Patterns
Inaddition:Studentsgainexperienceincollectinginformationfromadatadrivenwebsite.Theypracticeanalyzingandcollectinginformationthroughapplyingvariousvisualizationtechniquestothesamesetofdata.Theyexploremodelsgeneratedbyscientificexperimentsandusetoolsdesignedforadvancedscientificanalysis.Materials/resources:⢠ComputerwithInternetaccess.Resourcestobeaccessedthroughoutthelesson
⢠MoleculeoftheMonthonSerumAlbumin:fromthetopmenuofpdb101.rcsb.org,chooseMoleculeoftheMonthandaccessSerumAlbuminarticlebytitleDirectaccesslink:https://pdb101.rcsb.org/motm/37
⢠SerumAlbuminStructure1e7i:gotorcsb.organdenter1e7iintothesearchbarDirectaccesslink:https://www.rcsb.org/structure/1E7I
⢠Mol*tutorial:fromthetopmenuofpdb101.rcsb.orgchooseBrowse,gotoStructureandStructureDeterminationthentoVisualizingMoleculesandlocateamongtheLearningResources:ExploringPDBstructuresin3DwithMol*(MolStar)Directaccesslink:http://pdb101.rcsb.org/learn/videos/exploring-pdb-structures-in-3d-with-molstar
â˘Studentworksheet(providedwiththelessonplan)â˘Possibleuseofprojected/sharedcomputerscreen
pdb101.rcsb.org
Preexistingknowledge:Studentsunderstand:⢠proteinsarepolymersmadeupofaminoacidsandthatthepolymerchainformstheelementsofsecondarystructureandfoldsintoaspecific3Dshape
⢠aminoacidssidechainsfallintothreedistinctivegroups(hydrophobic,hydrophilic,charged)dependingonhowtheyinteractwithwater,andothersidechainsandmolecules
⢠basicsofthehydrophilicandhydrophobicinteractionsandtheconceptofcovalentandnon-covalentinteraction(thisinformationmightbealsoreviewedbeforethefirststepoftheactivity)
⢠themainconventionsin3Drepresentationsofproteins(cartoon,surface)andatoms(ballandstick,spacefill)
Note:Thisinformationmightbetaught/reviewedusingPDB-101videoWhatisaProtein?(pdb101.rcsb.org>Learn>Videosorhttp://pdb101.rcsb.org/learn/videos/what-is-a-protein-video)Inaddition,TedEdlessoncreatedbyAlisonAckroydhttps://ed.ted.com/on/xdk2WHce#watchoffersquestionsforassessment.Preparation:
StudentsfamiliarizethemselveswiththecontentsofthetutorialExploringPDBstructuresin3DwithMol*toallowforfullfocusontheactivityduringclasstime.Thiscanbeassignedashomework.Thetutorialshouldbeusedasaidthroughoutthelessonaswell.
LESSONACTIVITIES:Studentscanentertheiranswerandevaluations/predictionsontheenclosedStudentWorksheet.Studentscanworkindividuallyoringroups.Theteacherhelpsstudentsalongandmakessuretheystayontrack.TheteacheralsofacilitatesinclassdiscussionsandassessmentactivitiesCOLLECTINGINFORMATIONIntroducingtheFUNCTIONofserumalbuminwithMoleculeoftheMontharticleStudentsaccesstheMoleculeoftheMontharticleSerumAlbuminonPDB-101.TheyreadonlytheIntroductionandCarryingFattyAcidssectionsandanswerquestion1(asnumberedonstudentworksheet):
⢠Whatisthefunctionofserumalbumin?Whyisitimportanttohaveappropriatelevelsofthisproteininthebloodplasma?
Answer:
⢠Serumalbuministhecarrieroffattyacidsintheblood.Fattyacidsarethebuildingblocksforlipids.Lipidsformthelipidbilayermembranesaroundandinsidethecells.FattyacidsmayalsobebrokendowninsidecellstoformATP,animportantsourceofenergyforourbodies.Whenweneedenergyorbuildingmaterialsforbilayermembranes,fatcellsreleasefattyacidsintotheblood.Serumalbuminpicksthemupanddeliversthemtodistantpartsofthebody.
pdb101.rcsb.org
UsingtheRCSB.orgStructureSummarypagetocollectinformationabouttheSTRUCTUREofserumalbuminInthispartofthelesson,studentswillexplorea3DmodelfromtheProteinDataBank(PDB).IfstudentsarenotfamiliarwiththeProteinDataBank,theteachermayintroduceitbrieflytouchingonthefollowingpoints:
⢠PDBisadatabasecollectinginformationaboutthe3Dcoordinatesofatomsmakingupproteinstructures
⢠ThestructuresaredeterminedallovertheworldbydifferentscientificexperimentsthensubmittedtothePDBarchive
⢠Thereare4PDBdatacentersallovertheworldthatcuratethedata,maintainthearchive,andprovideaccesstothemalongwithtoolsforsearchandanalysisfreeofcharge.OneofthecentersisRCSBprovidingaccessthroughrcsb.org
⢠Rcsb.orgisahigh-levelresearchresourcesostudentsshouldnotfeeldiscouragedifinformationishardtolocate
⢠PDB-101istheeducationalportalofRCSBthatcreateseducationalresourcesbuildingonthedatafromtheProteinDataBank
StudentsaccesstheStructureSummarypagefortheserumalbuminstructure1e7i.StudentsusetheMacromoleculessectiontoanswerquestion2:
⢠Howmanychainsdoestheproteinhave?
Answer:
⢠Theproteinhas1chain(chainA)IntroducingStearicAcidStudentsgototheSmallMoleculessectionontheStructureSummarypage,analyzetheinformation,andanswerquestion3:
⢠Howmanytypesofsmallmolecules(ligands)interactwiththepolymer?Answer:⢠Onetype,stearicacid
StudentsaccesstheLigandsummarypagethroughtheligandIDlink,analyzetheinformation,andanswerquestion4:
⢠Whatatoms/howmanyofthemistheligandmadeof?Howaretheyarranged?Answer:⢠Theligandismadeupof2oxygenatomsand18carbonatoms.Theoxygenatomsarecovalentlyboundto
oneterminalcarbonatom,andthecarbonatomsarearrangedinalongchain.
StudentsreviewtheanswersinclasswithteacherâsfacilitationandpointtosupportingdataEVALUATINGINFORMATIONANDCREATINGPREDICTIONSStudentsevaluatethesmallmoleculemodelstructureandpredictthekeyfeaturesofitscomponentsandanswerquestion5:
⢠Ifyouweretousethewordsâheadâandâtailâtodescribetheligand,howwouldyoudescribethearrangementoftheatomswithinthem?ThesmallmoleculeiscalledstearicACID.Whichpartmakesitan
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ACID?Howwouldtheacidbehaveinwatersolution?Whatchargewoulditcarry?Howwouldthetailbehaveinthewater?Woulditcarryanycharge?
Answer
⢠The2oxygenscovalentlyboundtothecarbonatomscouldbedescribedastheâheadâ,thecarbonatomsarrangedinalongchainmightbedescribedastheâtailâ.TheACIDpartistheCOOhead.Itwillbeionizedandcarrynegativechargeandinteractstronglywithwater.Thetailwouldnotcarryanycharge.Thetailwouldbenotinteractingwithwaterandwouldtrytofindotherhydrophobicparticlestoshielditselffromwater.
Basedonthefirsthypothesis,studentspredictthetransportenvironmentfortheligandandanswerquestion6.Theteachermightdisplaytheimagebelowontheoverheadprojectorforreference.Theteacherexplainsthatthestudentswillcreateaschematicmodeloftheinteractionstheypredict.Themodelcanbehand-drawnorcreatedusinganycomputersoftware.
⢠Whydoesthislipidneedatransportproteintobecarriedinthewater-basedbloodplasma?Whattypeofaminoacids(hydrophobic,hydrophilic,orcharged)wouldneedtobepresentontheoutsideoftheprotein?Whataboutinthecoreoftheprotein?Whattypesofaminoacidsidechainsinthecarrierproteinwouldtheâheadâinteractwith:polar,charged,orhydrophobic?Whattypesofaminoacidsidechainsinthecarrierproteinwouldtheâtailâinteractwith:polar,charged,orhydrophobic?Explainwhy.Drawamodelofatransportproteinwithstearicacidandhighlighttheseinteractions.
Answer
⢠Thehydrophobictailwillhavetobeshieldedawayfromthewater,thatâswhythismoleculeneedsacarrierprotein.Theproteinwouldneedmostlypolarorchargedresiduesontheoutsidetointeractwithsurroundingwatermoleculesandhydrophobicresiduesontheinsidetoaccommodatethetails.Theoxygensintheheadcanbeexposedtothesurroundingwaterinthebloodplasma,creatingH-Ohydrogenbonds,andcanalsocreatehydrogenbondswiththehydrogensonthepolarandchargedresidues.Examplehowamodeloftheseinteractioncanbedrawnisshownbelow.However,studentsshouldusetheircreativityandoriginalideastodevelopthemodel,soshowingthemanexampleisnotrecommended.
pdb101.rcsb.org
ENGAGINGINARGUMENTFROMEVIDENCE:SharinganddiscussingpredictionsStudentssharetheirpredictionsandmodelsinclasswhiletheteacherfacilitatesthediscussionandasksadditionalquestions.TheteachercanshareaGooglepresentationwiththestudentsforthemtoinserttheirimages(ifcreateddigitally)orphotosoftheimagesifhand-drawntosharewiththeclassviaoverheadprojector.Theimagescanbeusedinsupportoftheirarguments.Atthisstagestudentsshareargumentsfortheirpredictions,buttheydonâtknowwhethertheirpredictionsarerightorwrong.COLLECTINGMOREDETAILEDINFORMATIONANDEVALUATINGPREDICTIONSExploringthe3DstructureofserumalbuminwithMol*Studentsaccessthe3DviewofserumalbuminfromtheStructureSummarypage.Theyexplorethefeaturesofthe3Dstructureandanswerthequestions7and8.StudentsmightsavetheimagesfromMol*touseinthenextstep.
⢠Whatelementsofsecondarystructurearepredominant?Whatdoestheoverallshapeoftheproteinresemble?
⢠Evaluateyourpredictionsfrompreviouspartofthelesson:whattypesofaminoacidsarepresentontheoutsideoftheprotein?Whatkindofaminoacidsmakeupthecoreoftheprotein?Why?Youcanchangethepolymerrepresentationtospacefillandthecolorthemetohydrophobicitytoevaluateyourpredictions(seeMol*tutorialsection7and10)
Answers:
⢠Alphahelicesarethepredominantelementofthe3Dstructure,theoverall3Dshaperesemblesaheart
⢠Theaminoacidsontheoutsidearemostlyhydrophilictointeractwiththesurroundingwaterinthebloodplasma.Theaminoacidsinthecorearepredominantlyhydrophobictoholdthe3Dstructurestableandtocreatetheenvironmentforthehydrophobictailsofthelipidstobetransported.Exampleimagebelowshowstheproteinwiththehydrophobicitycolorthemeapplied.Hydrophobicresiduesareinshadesofgreentolightyellow,theresiduesthataremorelikelytointeractwithwaterareshownindifferentshadesfromdarkyellowtored.
pdb101.rcsb.org
Assessment:StudentsreviewtheanswersinclasswithteacherâsfacilitationandpointtosupportingdatausingsavedimagesasevidenceExploringthepolymerligandinteractionin3DAsthestudentsexploretheproteinin3D,theyanswerthequestions9,10,and11.Studentsmightsaveimagestouseinthenexttosharewiththeclasstosupporttheirargumentsintheassessmentstepthatfollows
⢠Howmanyligandscanyouspotinteractingwiththeprotein?(youmightchangetheligandrepresentationtospacefillandapplydifferentcolorstothemusingsectionsinordertohelpyouspotallofthem).Twoligandsareoverlapping.Doyouthinkbothofthoseorientationscanhappenatthesametime?Howmanyligandstotalcanthisproteintransport?Clickonanyoftheligandstozoominandobserveinteractions.
⢠Whattypesofaminoacidsdoestheâheadâinteractwith?Whatnon-covalentinteractionsdoyouobserve?Whattypesofaminoacidsidechainsdoestheâtailâinteractwith?Whatnon-covalentinteractionsdoyouobserve?Clickonotherligandsandobservetheinteractions.Whatdoyounotice?
⢠Changetherepresentationforthepolymertogaussiansurfaceandtherepresentationofligandtospacefill(seeMol*tutorialsection7).Whatoverallstructuralfeaturesdoyouobservewhenlookingattheproteininthisrepresentation?
Answers:
⢠Thereare8ligandsshowninsidethemodel.Theoverlappingligandshavetheheadsontheoppositesidewhichmeanstheycanentertheproteinineitherorientation.Themodelcaneffectivelyinteractwith7ligands.Note:withthisquestiontheteachercouldprovideabitofbackgroundifstudentsareconfused:Crystallographycapturessnapshotsofmolecules,andsometimes,differentmoleculesinthecrystallatticecanbeboundindifferentorientations.Theoverlappedligandisanexample--insomealbuminmoleculesinthecrystallatticeitbindsoneway,inotheralbuminmoleculesitbindstheoppositeway.Thecrystallographersincludebothorientationsinthecoordinateset.Theimagebelowshowstheserumalbumincrystallatticeandcanbeusedasvisualaidintheclassroom
pdb101.rcsb.org
⢠Theoxygensintheâheadâformhydrogenbondswithneighboringpolarandchargedaminoacidsidechainsandwaters.Thecarbonsinthetailformhydrophobicinteractionswithhydrophobicsidechainscarbons.Thenumberofinteractionsandthespecificaminoacidsaredifferentforeachligand,althoughtheheadalwaysinteractswithpolarandchargedamioacidsandthetailsalwaysinteractswithhydrophobicaminoacids.
⢠Theligandsfitverytightlywiththeprotein(asseenintheexampleofanimagethatcanbesavedusing
suggestedmolecularrepresentation).Possibleimagesavedforthisstagebelow.
Studentsreviewtheanswersinclasswithteacherâsfacilitationandpointtosupportingdata.FINALCONCLUSIONSStudentsanswerquestion12,inclassdiscussionfollows
⢠Summarizehowtheshapeofserumalbuminisoptimalforitsfunctionoftransportingoffattyacidsinthebloodplasma.Comparewithyourhypothesis.
Answer:
pdb101.rcsb.org
⢠Theproteinhashydrophilicaminoacidsontheoutsideandisfairlysmallwhichhelpsittointeractwithwaterintheblood.Thehydrophobicaminoacidscreatetunnelsthataccommodatethehydrophobictailsoftheligand.Thefactthatitcantransportupto7ligandsmakesitveryefficient.
REVIEWANDEXPANDONTHEKNOWLEDGEStudentsfinishreadingtheMoleculeoftheMontharticle.Muchoftheinformationinthearticleprovidesisareviewoftheobservationsmadewhileinteractingwiththe3Dmodel.Studentsthenanswerquestion13whichhighlightsthenewinformationtheyobtained
⢠Whatothersubstancecanserumalbumincarryintheblood?WhatotherbloodtransportproteinsdoestheMoleculeoftheMontharticlementionandwhatligandsdotheytransport?UsethePDBIDstoaccesstheseproteinsonrcsb.organdobservetheinteractionswiththeligandsin3D.
Answer⢠Theproteincanalsocarryibuprofenandarachidonicacid.Otherexamplesoftransportproteinsare
transferrincarryingironandtransthyretinwhichcarriesthyroidhormone.
Optional:Studentscanexploreadditionalserumalbuminstructuresinteractingwithotherligands(e.g.PDBID6u4xâwithibuprofen,orPDBID6mdq-withtestosterone)andexplorethe3Dinteractions.