![Page 1: Lesson Plan Carrying Cargo: Exploring non-covalent](https://reader030.vdocuments.us/reader030/viewer/2022012714/61ac8c850af509414b7c3a14/html5/thumbnails/1.jpg)
pdb101.rcsb.org
LessonPlanCarryingCargo:Exploringnon-covalentinteractionsbetweenproteinsandsmallmoleculesinbloodtransportGradelevel:9-12Objectives:Aftercompletion,studentswillunderstandhowthehydrophobicandhydrophilicinteractionsbetweenproteinsandsmallmoleculesareutilizedintransportingoflipidsandothersubstancesinthebloodSummary:StudentsusethedataandtheinformationfromtheRCSB.organdPDB101.RCSB.orgwebsitestolearnaboutthefunctionofserumalbuminandtoexaminetheproteinin3D.Theyexplorethestructuralfeaturesandthenon-covalentinteractionsthatareemployedbytheproteintocarryfattyacidsintheblood.NGSSStandardsScience&EngineeringPractices:– Engaginginargumentfromevidence– Obtaining,evaluatingandcommunicatinginformation– Developingandusingmodels
DisciplinaryCoreIdeas:– LS1A:StructureandFunction
CrosscuttingConcepts:– 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
•Studentworksheet(providedwiththelessonplan)•Possibleuseofprojected/sharedcomputerscreen
![Page 2: Lesson Plan Carrying Cargo: Exploring non-covalent](https://reader030.vdocuments.us/reader030/viewer/2022012714/61ac8c850af509414b7c3a14/html5/thumbnails/2.jpg)
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.
![Page 3: Lesson Plan Carrying Cargo: Exploring non-covalent](https://reader030.vdocuments.us/reader030/viewer/2022012714/61ac8c850af509414b7c3a14/html5/thumbnails/3.jpg)
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.
Studentsreviewtheanswersinclasswithteacher’sfacilitationandpointtosupportingdataEVALUATINGINFORMATIONANDCREATINGPREDICTIONSStudentsevaluatethesmallmoleculemodelstructureandpredictthekeyfeaturesofitscomponentsandanswerquestion5:
• Ifyouweretousethewords“head”and“tail”todescribetheligand,howwouldyoudescribethearrangementoftheatomswithinthem?ThesmallmoleculeiscalledstearicACID.Whichpartmakesitan
![Page 4: Lesson Plan Carrying Cargo: Exploring non-covalent](https://reader030.vdocuments.us/reader030/viewer/2022012714/61ac8c850af509414b7c3a14/html5/thumbnails/4.jpg)
pdb101.rcsb.org
ACID?Howwouldtheacidbehaveinwatersolution?Whatchargewoulditcarry?Howwouldthetailbehaveinthewater?Woulditcarryanycharge?
Answer
• The2oxygenscovalentlyboundtothecarbonatomscouldbedescribedasthe‘head’,thecarbonatomsarrangedinalongchainmightbedescribedasthe‘tail’.TheACIDpartistheCOOhead.Itwillbeionizedandcarrynegativechargeandinteractstronglywithwater.Thetailwouldnotcarryanycharge.Thetailwouldbenotinteractingwithwaterandwouldtrytofindotherhydrophobicparticlestoshielditselffromwater.
Basedonthefirsthypothesis,studentspredictthetransportenvironmentfortheligandandanswerquestion6.Theteachermightdisplaytheimagebelowontheoverheadprojectorforreference.Theteacherexplainsthatthestudentswillcreateaschematicmodeloftheinteractionstheypredict.Themodelcanbehand-drawnorcreatedusinganycomputersoftware.
• Whydoesthislipidneedatransportproteintobecarriedinthewater-basedbloodplasma?Whattypeofaminoacids(hydrophobic,hydrophilic,orcharged)wouldneedtobepresentontheoutsideoftheprotein?Whataboutinthecoreoftheprotein?Whattypesofaminoacidsidechainsinthecarrierproteinwouldthe‘head’interactwith:polar,charged,orhydrophobic?Whattypesofaminoacidsidechainsinthecarrierproteinwouldthe‘tail’interactwith:polar,charged,orhydrophobic?Explainwhy.Drawamodelofatransportproteinwithstearicacidandhighlighttheseinteractions.
Answer
• Thehydrophobictailwillhavetobeshieldedawayfromthewater,that’swhythismoleculeneedsacarrierprotein.Theproteinwouldneedmostlypolarorchargedresiduesontheoutsidetointeractwithsurroundingwatermoleculesandhydrophobicresiduesontheinsidetoaccommodatethetails.Theoxygensintheheadcanbeexposedtothesurroundingwaterinthebloodplasma,creatingH-Ohydrogenbonds,andcanalsocreatehydrogenbondswiththehydrogensonthepolarandchargedresidues.Examplehowamodeloftheseinteractioncanbedrawnisshownbelow.However,studentsshouldusetheircreativityandoriginalideastodevelopthemodel,soshowingthemanexampleisnotrecommended.
![Page 5: Lesson Plan Carrying Cargo: Exploring non-covalent](https://reader030.vdocuments.us/reader030/viewer/2022012714/61ac8c850af509414b7c3a14/html5/thumbnails/5.jpg)
pdb101.rcsb.org
ENGAGINGINARGUMENTFROMEVIDENCE:SharinganddiscussingpredictionsStudentssharetheirpredictionsandmodelsinclasswhiletheteacherfacilitatesthediscussionandasksadditionalquestions.TheteachercanshareaGooglepresentationwiththestudentsforthemtoinserttheirimages(ifcreateddigitally)orphotosoftheimagesifhand-drawntosharewiththeclassviaoverheadprojector.Theimagescanbeusedinsupportoftheirarguments.Atthisstagestudentsshareargumentsfortheirpredictions,buttheydon’tknowwhethertheirpredictionsarerightorwrong.COLLECTINGMOREDETAILEDINFORMATIONANDEVALUATINGPREDICTIONSExploringthe3DstructureofserumalbuminwithMol*Studentsaccessthe3DviewofserumalbuminfromtheStructureSummarypage.Theyexplorethefeaturesofthe3Dstructureandanswerthequestions7and8.StudentsmightsavetheimagesfromMol*touseinthenextstep.
• Whatelementsofsecondarystructurearepredominant?Whatdoestheoverallshapeoftheproteinresemble?
• Evaluateyourpredictionsfrompreviouspartofthelesson:whattypesofaminoacidsarepresentontheoutsideoftheprotein?Whatkindofaminoacidsmakeupthecoreoftheprotein?Why?Youcanchangethepolymerrepresentationtospacefillandthecolorthemetohydrophobicitytoevaluateyourpredictions(seeMol*tutorialsection7and10)
Answers:
• Alphahelicesarethepredominantelementofthe3Dstructure,theoverall3Dshaperesemblesaheart
• Theaminoacidsontheoutsidearemostlyhydrophilictointeractwiththesurroundingwaterinthebloodplasma.Theaminoacidsinthecorearepredominantlyhydrophobictoholdthe3Dstructurestableandtocreatetheenvironmentforthehydrophobictailsofthelipidstobetransported.Exampleimagebelowshowstheproteinwiththehydrophobicitycolorthemeapplied.Hydrophobicresiduesareinshadesofgreentolightyellow,theresiduesthataremorelikelytointeractwithwaterareshownindifferentshadesfromdarkyellowtored.
![Page 6: Lesson Plan Carrying Cargo: Exploring non-covalent](https://reader030.vdocuments.us/reader030/viewer/2022012714/61ac8c850af509414b7c3a14/html5/thumbnails/6.jpg)
pdb101.rcsb.org
Assessment:Studentsreviewtheanswersinclasswithteacher’sfacilitationandpointtosupportingdatausingsavedimagesasevidenceExploringthepolymerligandinteractionin3DAsthestudentsexploretheproteinin3D,theyanswerthequestions9,10,and11.Studentsmightsaveimagestouseinthenexttosharewiththeclasstosupporttheirargumentsintheassessmentstepthatfollows
• Howmanyligandscanyouspotinteractingwiththeprotein?(youmightchangetheligandrepresentationtospacefillandapplydifferentcolorstothemusingsectionsinordertohelpyouspotallofthem).Twoligandsareoverlapping.Doyouthinkbothofthoseorientationscanhappenatthesametime?Howmanyligandstotalcanthisproteintransport?Clickonanyoftheligandstozoominandobserveinteractions.
• Whattypesofaminoacidsdoesthe‘head’interactwith?Whatnon-covalentinteractionsdoyouobserve?Whattypesofaminoacidsidechainsdoesthe‘tail’interactwith?Whatnon-covalentinteractionsdoyouobserve?Clickonotherligandsandobservetheinteractions.Whatdoyounotice?
• Changetherepresentationforthepolymertogaussiansurfaceandtherepresentationofligandtospacefill(seeMol*tutorialsection7).Whatoverallstructuralfeaturesdoyouobservewhenlookingattheproteininthisrepresentation?
Answers:
• Thereare8ligandsshowninsidethemodel.Theoverlappingligandshavetheheadsontheoppositesidewhichmeanstheycanentertheproteinineitherorientation.Themodelcaneffectivelyinteractwith7ligands.Note:withthisquestiontheteachercouldprovideabitofbackgroundifstudentsareconfused:Crystallographycapturessnapshotsofmolecules,andsometimes,differentmoleculesinthecrystallatticecanbeboundindifferentorientations.Theoverlappedligandisanexample--insomealbuminmoleculesinthecrystallatticeitbindsoneway,inotheralbuminmoleculesitbindstheoppositeway.Thecrystallographersincludebothorientationsinthecoordinateset.Theimagebelowshowstheserumalbumincrystallatticeandcanbeusedasvisualaidintheclassroom
![Page 7: Lesson Plan Carrying Cargo: Exploring non-covalent](https://reader030.vdocuments.us/reader030/viewer/2022012714/61ac8c850af509414b7c3a14/html5/thumbnails/7.jpg)
pdb101.rcsb.org
• Theoxygensinthe“head”formhydrogenbondswithneighboringpolarandchargedaminoacidsidechainsandwaters.Thecarbonsinthetailformhydrophobicinteractionswithhydrophobicsidechainscarbons.Thenumberofinteractionsandthespecificaminoacidsaredifferentforeachligand,althoughtheheadalwaysinteractswithpolarandchargedamioacidsandthetailsalwaysinteractswithhydrophobicaminoacids.
• Theligandsfitverytightlywiththeprotein(asseenintheexampleofanimagethatcanbesavedusing
suggestedmolecularrepresentation).Possibleimagesavedforthisstagebelow.
Studentsreviewtheanswersinclasswithteacher’sfacilitationandpointtosupportingdata.FINALCONCLUSIONSStudentsanswerquestion12,inclassdiscussionfollows
• Summarizehowtheshapeofserumalbuminisoptimalforitsfunctionoftransportingoffattyacidsinthebloodplasma.Comparewithyourhypothesis.
Answer:
![Page 8: Lesson Plan Carrying Cargo: Exploring non-covalent](https://reader030.vdocuments.us/reader030/viewer/2022012714/61ac8c850af509414b7c3a14/html5/thumbnails/8.jpg)
pdb101.rcsb.org
• Theproteinhashydrophilicaminoacidsontheoutsideandisfairlysmallwhichhelpsittointeractwithwaterintheblood.Thehydrophobicaminoacidscreatetunnelsthataccommodatethehydrophobictailsoftheligand.Thefactthatitcantransportupto7ligandsmakesitveryefficient.
REVIEWANDEXPANDONTHEKNOWLEDGEStudentsfinishreadingtheMoleculeoftheMontharticle.Muchoftheinformationinthearticleprovidesisareviewoftheobservationsmadewhileinteractingwiththe3Dmodel.Studentsthenanswerquestion13whichhighlightsthenewinformationtheyobtained
• Whatothersubstancecanserumalbumincarryintheblood?WhatotherbloodtransportproteinsdoestheMoleculeoftheMontharticlementionandwhatligandsdotheytransport?UsethePDBIDstoaccesstheseproteinsonrcsb.organdobservetheinteractionswiththeligandsin3D.
Answer• Theproteincanalsocarryibuprofenandarachidonicacid.Otherexamplesoftransportproteinsare
transferrincarryingironandtransthyretinwhichcarriesthyroidhormone.
Optional:Studentscanexploreadditionalserumalbuminstructuresinteractingwithotherligands(e.g.PDBID6u4x–withibuprofen,orPDBID6mdq-withtestosterone)andexplorethe3Dinteractions.