Lesson Plan Carrying Cargo: Exploring non-covalent ...
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pdb101.rcsb.org Lesson Plan Carrying Cargo: Exploring non-covalent interactions between proteins and small molecules in blood transport Grade level: 9-12 Objectives: After completion, students will understand how the hydrophobic and hydrophilic interactions between proteins and small molecules are utilized in transporting of lipids and other substances in the blood Summary: Students use the data and the information from the RCSB.org and PDB101.RCSB.org websites to learn about the function of serum albumin and to examine the protein in 3D. They explore the structural features and the non- covalent interactions that are employed by the protein to carry fatty acids in the blood. NGSS Standards Science & Engineering Practices: – Engaging in argument from evidence – Obtaining, evaluating and communicating information – Developing and using models Disciplinary Core Ideas: – LS1A: Structure and Function Crosscutting Concepts: – Patterns In addition: Students gain experience in collecting information from a data driven website. They practice analyzing and collecting information through applying various visualization techniques to the same set of data. They explore models generated by scientific experiments and use tools designed for advanced scientific analysis. Materials/resources: • Computer with Internet access. Resources to be accessed throughout the lesson • Molecule of the Month on Serum Albumin: from the top menu of pdb101.rcsb.org, choose Molecule of the Month and access Serum Albumin article by title Direct access link: https://pdb101.rcsb.org/motm/37 • Serum Albumin Structure 1e7i: go to rcsb.org and enter 1e7i into the search bar Direct access link: https://www.rcsb.org/structure/1E7I • Mol* tutorial: from the top menu of pdb101.rcsb.org choose Browse, go to Structure and Structure Determination then to Visualizing Molecules and locate among the Learning Resources: Exploring PDB structures in 3D with Mol* (MolStar) Direct access link: http://pdb101.rcsb.org/learn/videos/exploring-pdb-structures-in-3d-with-molstar • Student worksheet (provided with the lesson plan) • Possible use of projected/shared computer screen
Transcript of Lesson Plan Carrying Cargo: Exploring non-covalent ...
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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
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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.
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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
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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.
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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.
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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
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• Theoxygensinthe“head”formhydrogenbondswithneighboringpolarandchargedaminoacidsidechainsandwaters.Thecarbonsinthetailformhydrophobicinteractionswithhydrophobicsidechainscarbons.Thenumberofinteractionsandthespecificaminoacidsaredifferentforeachligand,althoughtheheadalwaysinteractswithpolarandchargedamioacidsandthetailsalwaysinteractswithhydrophobicaminoacids.
• Theligandsfitverytightlywiththeprotein(asseenintheexampleofanimagethatcanbesavedusing
suggestedmolecularrepresentation).Possibleimagesavedforthisstagebelow.
Studentsreviewtheanswersinclasswithteacher’sfacilitationandpointtosupportingdata.FINALCONCLUSIONSStudentsanswerquestion12,inclassdiscussionfollows
• Summarizehowtheshapeofserumalbuminisoptimalforitsfunctionoftransportingoffattyacidsinthebloodplasma.Comparewithyourhypothesis.
Answer:
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• Theproteinhashydrophilicaminoacidsontheoutsideandisfairlysmallwhichhelpsittointeractwithwaterintheblood.Thehydrophobicaminoacidscreatetunnelsthataccommodatethehydrophobictailsoftheligand.Thefactthatitcantransportupto7ligandsmakesitveryefficient.
REVIEWANDEXPANDONTHEKNOWLEDGEStudentsfinishreadingtheMoleculeoftheMontharticle.Muchoftheinformationinthearticleprovidesisareviewoftheobservationsmadewhileinteractingwiththe3Dmodel.Studentsthenanswerquestion13whichhighlightsthenewinformationtheyobtained
• Whatothersubstancecanserumalbumincarryintheblood?WhatotherbloodtransportproteinsdoestheMoleculeoftheMontharticlementionandwhatligandsdotheytransport?UsethePDBIDstoaccesstheseproteinsonrcsb.organdobservetheinteractionswiththeligandsin3D.
Answer• Theproteincanalsocarryibuprofenandarachidonicacid.Otherexamplesoftransportproteinsare
transferrincarryingironandtransthyretinwhichcarriesthyroidhormone.
Optional:Studentscanexploreadditionalserumalbuminstructuresinteractingwithotherligands(e.g.PDBID6u4x–withibuprofen,orPDBID6mdq-withtestosterone)andexplorethe3Dinteractions.
