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The Making of the Fittest: Natural Selection and Adaptation

Lesson The Making of the Fittest Natural Selection and Adaptation Educator Materials

PublishedFebruary,2017

Page1of8

INTRODUCTIONTOTHEMOLECULARGENETICSOFTHECOLORMUTATIONSINROCKPOCKETMICE

OVERVIEWTheselessonsserveasanextensiontotheHowardHughesMedicalInstituteshortfilmTheMakingoftheFittest:NaturalSelectionandAdaptation.Studentswilltranscribeandtranslateportionsofthewild-typeandmutantrockpocketmouseMc1rgene.BycomparingDNAsequences,studentsidentifythelocationsandtypesofmutationsresponsibleforthecoat-colorchangedescribedinthefilm.StudentswillansweraseriesofquestionstoexplainhowachangeinaminoacidsequenceaffectsthefunctionalityoftheMC1Rprotein,andhowthatchangemightdirectlyaffectthecoatcoloroftherockpocketmousepopulationsandthesurvivalofthatpopulation.KEYCONCEPTSANDLEARNINGOBJECTIVES

• Amutationisarandomchangetoanorganism’sDNAsequence.• Mostmutationshavenoeffectontraits,butsomemutationsaffecttheexpressionofageneand/orthe

geneproduct.• Theenvironmentcontributestodeterminingwhetheramutationisadvantageous,deleterious,orneutral.• Naturalselectionpreservesfavorabletraits.• Variation,selection,andtimefueltheprocessofevolution.• Boththetypeofthemutationanditslocationdeterminewhetherornotitwillhaveaneffecton

phenotype(advancedversiononly).Studentswillbeableto:

• transcribeandtranslateaDNAsequence.• connectDNAchangestophenotype.• analyzeandorganizedata.

CURRICULUMCONNECTIONSCurriculum StandardsNGSS(April2013) HS-LS1-1,HS-LS3-1,HS-LS3-2,HS-LS4-2,HS-LS4-4,HS-LS4-5

HS.LS1.A,HS.LS4.B,HS.LS4.CCommonCore(2010) CCSS.ELA-Literacy.RST.9-10.3,CCSS.ELA-Literacy.RST.9-10.4,

CCSS.ELA-Literacy.RST.9-10.7APBiology(2012–13) 1.A.1,1.A.2,3.A.1,3.C.1,4.B.1IBBiology(2009) 3.5,4.1,4.3,5.4,7.3,7.4,D.2,G.1

KEYTERMSevolution,naturalselection,variation,trait,mutation,adaptationTIMEREQUIREMENTTheseactivitiesaredesignedforone50-minuteclassperiodincludingshowingthefilm.Additionaltimefortheanalysisquestionsmightberequiredforhomeworkdependingonstudents’pace.Bothactivitiescoverthesamematerial,butactivity2hasadditionalmaterialcoveringintracellular,transmembrane,andextracellulardomains.



The Making of the Fittest: Natural Selection and Adaptation Educator Materials

Lesson The Making of the Fittest Natural Selection and Adaptation

PublishedFebruary,2017Page2of8

SUGGESTEDAUDIENCEActivity1:Theactivityisdesignedforhighschoolbiology(primarilyfirst-yearbiology,bothregularandhonors).Activity2:TheactivityisdesignedforAPandIBhighschoolbiologyandintroductorycollegebiology.PRIORKNOWLEDGEStudentsshouldbefamiliarwiththedefinitionsof“gene”and“protein.”Theyshouldalsobecomfortablewithbasicmoleculargenetics,includingafamiliaritywiththeprocessesoftranscriptionandtranslation.Finally,studentsshouldunderstandthataprotein’saminoacidsequencedeterminesitsstructure,whichdeterminesitsfunction.MATERIALSStudentswillneed:geneticcodechart(providedinstudentmaterials)blue,red,andgreencoloredpencilsTEACHINGTIPS

• Ifyoudonothaveaccesstoacolorprintertoprintthechartonpage2ofthisdocument,youshouldcomparestudents’worktohowthechartsbelowappearonyourcomputerscreen.

• Youcouldassignanalysisquestionsashomeworktoreducetheamountofclasstimerequiredforthislesson.

ANSWERKEYACTIVITY1GENETABLE1:WILD-TYPEMC1RGENE(LIGHTCOAT-COLORPHENOTYPE)

015 022DNA TTG AGG TGG GCG TGT CCG CAA GGAmRNA AAC UCC ACC CGC ACA GGC GUU CCUAminoAcid Asn Ser Thr Arg Thr Gly Val Pro

105 112

DNA CGG GAC CGG TGG GCC CAC TGA CACmRNA GCC CUG GCC ACC CGG GUG ACU GUGAminoAcid Ala Leu Ala Thr Arg Val Thr Val

154 161

DNA TCA TAA CAC TGT GAC GGG GCC CGAmRNA AGU AUU GUG ACA CUG CCC CGG GCUAminoAcid Ser Ile Val Thr Leu Pro Arg Ala

209 212

DNA GTG TAC GAA CGTmRNA CAC AUG CUU GCAAminoAcid His Met Leu Ala






230 237

DNA GAA CAG GTG GTT CCA AAG GCT GAGmRNA CUU GUC CAC CAA GGU UUC CGA CUCAminoAcid Leu Val His Gln Gly Phe Arg Leu

GENETABLE2:MUTANTMC1RGENE(DARKCOAT-COLORPHENOTYPE)

015 022DNA TTG AGG TGG ACG TGT CCG CAA GGAmRNA AAC UCC ACC UGC ACA GGC GUU CCUAminoAcid Asn Ser Thr Cys Thr Gly Val Pro

105 112DNA CGG GAC CGG TGG ACC CAC TGA CACmRNA GCC CUG GCC ACC UGG GUG ACU GUGAminoAcid Ala Leu Ala Thr Trp Val Thr Val

154 161

DNA TCA TAA CAC TGT GAC GGG ACC CGAmRNA AGU AUU GUG ACA CUG CCC UGG GCUAminoAcid Ser Ile Val Thr Leu Pro Trp Ala

209 212

DNA GTG TAC GAG CGTmRNA CAC AUG CUC GCAAminoAcid His Met Leu Ala

230

237DNA GAA CAG GTG GTG CCA AAG GCT GAGmRNA CUU GUC CAC CAC GGU UUC CGA CUCAminoAcid Leu Val His His Gly Phe Arg Leu






QUESTIONSANSWERKEY1.Ingeneexpression,whichenzymeisresponsiblefortranscribingtheDNAsequenceintomRNAbyaddingcomplementaryRNAnucleotides?RNApolymerase2.Inaeukaryoticcell,wheredoestranscriptionoccur?Inthenucleus3.Describetheprocessoftranslation.TranslationistheprocessofturninginstructionsfrommRNAintochainsofaminoacids.ItoccursinthecytoplasmwiththehelpofribosomesandtRNA.4.Inaeukaryoticcell,whatmainorganelleisinvolvedintranslation?Ribosome5.ExplaintherelationshipbetweenDNAsequence,aminoacidsequence,andproteinstructureandfunction.StudentsmaysimplyrelateDNAsequencetoaminoacidsequence,andaminoacidsequencetothethree-dimensionalshapeoftheprotein.Anexampleofastudentresponsemaybe:“DNAsequenceprovidesthecodefortheaminoacidsequence.Theaminoacidsequencedeterminesthestructureoftheprotein,whichaffectsthefunctionoftheprotein.”6.TheMc1rgenecodesforthemelanocortin1receptor(MC1R)protein.7.IftheMC1Rproteinis317aminoacidslong,whyarethere954basepairsinthecodingregionofthegene?EachoftheaminoacidshasacorrespondingmRNAcodonandDNAtripletconsistingofathree-basesequence.Aproteinthathas317aminoacidsthereforehasaDNAbasesequenceconsistingof951basepairs(317×3=951basepairs).Thethreeadditionalbasepairscorrespondtoastopcodonforwhichthereisnocomplementaryaminoacid.Thestopcodonsignalstheterminationoftranslation.8.OfthefivemutationsyouidentifiedintheMc1rgene,howmanyare: 5substitutions;0insertions;0deletions9.OfthefivemutationsyouidentifiedintheMc1rgene,howmanyare: 1silent;4missense;0nonsense10.Micewiththewild-type(nonmutant)Mc1rgenehavelight-coloredfur.Whichpigmentisresponsibleforthiscoloration?Pheomelanin11.Usingtheinformationintheintroductiononmutationsandyourknowledgeofproteins,developahypothesistoexplainhowthechangesintheMC1Rprotein’saminoacidsequencemightaffectitsfunction.Sampleanswer:ThefourmissensemutationsintheMc1rgenechangetheaminoacidsequenceoftheMC1Rprotein,whichchangesthestructureoftheprotein.Thechangeinproteinstructurewillaffecttheproteinfunction.12.Explainhowsilentmutationsaffectthestructureandfunctionoftheprotein.Silentmutationsdonotchangetheaminoacid,andthereforewillnotchangethestructureoftheprotein.Becauseaprotein’sstructureisrelatedtoitsfunction,silentmutationsdonotaffectthefunctionoftheprotein.13.Usingtheinformationprovidedintheintroductionunder“MC1RGene,”explainhowthemutantMC1Rproteindirectlyaffectsarockpocketmouse’scoatcolor.TheaminoacidchangesintheMC1Rproteinmaychangethestructureandfunctionoftheprotein.Thisleadstoincreasedproductionofeumelanin,whichresultsinthedarkcolor.14.Mutationsareasourceofgeneticvariation.Inthefilm,Dr.Carrollsaysthatmutationsoccurrandomly.Whatdoesthatmean?Sampleanswer:Itmeansthatmutationsdonotoccurforapurposeorforanypredeterminedresult.15.Itisacommonmisconceptionthat“allmutationsarebad.”Usetheexampleofrockpocketmicetoexplainwhythisisnottrue.Inyouranswer,explainhowthedarkcoatcolormutationcanbeanadvantagetosomemiceandadisadvantagetoothers.Sampleanswer:Mutationscanresultinnewtraits.Theselectiveadvantageprovidedbyatraitdependsontheenvironment.Forexample,onalightsubstrate,individualswithdark-coloredcoatswouldbeatadisadvantage






becausetheywouldstandoutmorethanindividualswithlight-coloredcoats,makingthemeasierforpredatorstospot.However,inthedarklavaflowhabitat,thosesamedark-coloredindividualswouldhaveaselectiveadvantagebecausetheywouldbebettercamouflagedthanlight-coloredindividuals.So,thestatementthat“allmutationsarebad”isincorrect,becausetherearedifferentselectivepressuresonthetraitsproducedbymutationsdependingonthehabitat.Therearealsosilentmutationsthatdonotchangetheresultingprotein;theseareneutral,neithergoodnorbad.16.Useyourunderstandingofevolutionandtheinformationinthefilmtoexplainhowthedark-coloredmutationcametobesocommoninsomepopulationsofrockpocketmice.Bespecific.Sampleanswer:Thedark-coloredmousehasaselectiveadvantageinahabitatsuchasthePinacatelavaflow,whichhasadark-coloredsubstrate.Sincerockpocketmicereproducequicklyandoften,thefrequencyofthisfavoredtraitwouldspreadrapidlythroughthepopulation.Anylight-coloredmiceinthedark-coloredhabitatwouldbeataselectivedisadvantage,thusdecreasingtheirgenefrequencyinfuturegenerations.Inthisway,favorabletraitsaccumulateandincreaseinfrequency—justasDarwinexplained.ANSWERKEYACTIVITY2

GENETABLES

WILD-TYPEMC1RGENE(LIGHT-COLOREDCOATPHENOTYPE) 015 024

DNA TTG AGG TGG GCG TGT CCG CAA GGA GTG GAG

EXTR

ACELLU

LARDO

MAINI

mRNA AAC UCC ACC CGC ACA GGC GUU CCU CAC CUCAminoAcid Asn Ser Thr Arg Thr Gly Val Pro His Leu

MUTANTMC1RGENE(DARK-COLOREDCOATPHENOTYPE) 015 024

DNA TTG AGG TGG ACG TGT CCG CAA GGA GTG GAGmRNA AAC UCC ACC UGC ACA GGC GUU CCU CAC CUCAminoAcid Asn Ser Thr Cys Thr Gly Val Pro His Leu


DNA CGG GAC CGG TGG GCC CAC TGA CAC CAT GTC

EXTR

ACELLU

LARDO

MAINIII

mRNA GCC CUG GCC ACC CGG GUG ACU GUG GUA CAG

AminoAcid Ala Leu Ala Thr Arg Val Thr Val Val Gln


DNA CGG GAC CGG TGG ACC CAC TGA CAC CAT GTCmRNA GCC CUG GCC ACC UGG GUG ACU GUG GUA CAGAminoAcid Ala Leu Ala Thr Trp Val Thr Val Val Gln







DNA TCA TAA CAC TGT GAC GGG GCC CGA GCC ACC

INTR

ACELLU

LARDO

MAINI

mRNA AGU AUU GUG ACA CUG CCC CGG GCU CGG UGGAminoAcid Ser Ile Val Thr Leu Pro Arg Ala Arg Trp


DNA TCA TAA CAC TGT GAC GGG ACC CGA GCC ACCmRNA AGU AUU GUG ACA CUG CCC UGG GCU CGG UGGAminoAcid Ser Ile Val Thr Leu Pro Trp Ala Arg Trp


DNA CAC GTG TAC GAA CGTTR

ANSM

EMBR

ANEV

mRNA GUG CAC AUG CUU GCAAminoAcid Val His Met Leu Ala

MUTANTMC1RGENE(DARK-COLOREDCOATPHENOTYPE)

208 212DNA CAC GTG TAC GAG CGTmRNA GUG CAC AUG CUC GCAAminoAcid Val His Met Leu Ala


DNA GAA CAG GTG GTT CCA AAG GCT GAG TTT CCGINTR

ACELLU

LARDO

MAINIII

mRNA CUU GUC CAC CAA GGU UUC CGA CUC AAA GGCAminoAcid Leu Val His Gln Gly Phe Arg Leu Lys Gly


DNA GAA CAG GTG GTG CCA AAG GCT GAG TTT CCGmRNA CUU GUC CAC CAC GGU UUC CGA CUC AAA GGCAminoAcid Leu Val His His Gly Phe Arg Leu Lys Gly






QUESTIONSANSWERKEY1.Usingtheaminoacidlocationnumbersprovidedabovethefirstandlastcolumnofeachtable,listthelocationsofthefiveaminoacidsthatcontainamutation.Theaminoacidlocationsare018,109,160,211,and233.2.OfthefivemutationsyouidentifiedintheMc1rgene,howmanyarethefollowing: 5substitutions,0insertions,0deletions3.OfthefivemutationsyouidentifiedintheMc1rgene,howmanyarethefollowing: 1silent,4missense,0nonsense4. a.Whichfouraminoacidlocations(seeQuestion1above)containthemissensemutations?Theaminoacidsare018,109,160,and233.b.ExplainthelinkbetweenDNAsequenceandproteinstructureandfunction.StudentsmaysimplyrelateDNAsequencetoaminoacidsequence,andaminoacidsequencetothethree-dimensionalshapeoftheprotein.More-advancedstudentsshouldbeabletolinkthemutationtoachangeintheprotein’sprimarystructure,whichaffectsotherlevelsofstructure(secondaryandtertiary).AllstudentresponsesshoulddemonstrateanunderstandingofthelinkbetweenDNAandthesequenceofaminoacidsthatdeterminesthestructure,andthereforefunction,ofaprotein.5.Usingtheinformationonmutationsintheintroductionandyourknowledgeofproteins,developahypothesistoexplainhowthechangesintheMC1Rprotein’saminoacidsequencemightaffectitsfunction.StudentsmightsuggestthatsincethefourmissensemutationsintheMc1rgenechangetheaminoacidsequenceoftheMC1Rprotein,theproteinwillnotfunctionproperly,asaprotein’sfunctionisdeterminedbyitsstructure.6.Manyproteins,includingMC1R,containseveralstructuraldomainsthatcanfoldandfunctionindependentlyfromtherest.ThedomainnameswereprovidedforeachportionofDNAsequenceyoutranslatedearlier.Answerthefollowingquestions.a.WhereistheMC1Rproteinfound,andwhatisitsfunction?Bespecific.Itisareceptorproteinembeddedinthemembraneofmelanocytes.Itisspecializedforpigmentproduction.b.WhichproteindomainscontainthefourMc1rmissensemutations?(Refertothegenetablesyoucompletedearlier.)Themutationat018isinExtracellularDomainI,themutationat109isinExtracellularDomainIII,themutationat160isinIntracellularDomainI,andthemutationat233isinIntracellularDomainIII.c.Define“extracellular.”Extracellularmeans“somethingoutsideofacell.”d.Define“intracellular.”Intracellularmeans“somethinginsideofacell.”e.Whyisitsignificantthatthefourmissensemutationsarefoundintheextracellularandintracellulardomainsoftheprotein?Explainyouranswer.(Hint:ThinkaboutMC1R’sfunction.)Specificanswerswillvary,butstudentsshouldhavetheideathataproteinthatspansacellmembranehasaportionthatprojectsoutofthecell(extracellular)andaportionthatprojectsintothecell(intracellular).Thistypeofreceptorproteinusuallyfunctionsineithercelltransportorcellsignaling.Changesinthestructureofextracellularandintracellularportionscanchangethefunctionoftheproteininthesignalingpathwayorthetransportmechanism.(Note:Seethelesson“TheBiochemistryandCellSignalingPathwayoftheMc1rGene”formoredetailonthisconcept.)






7.UsingtheinformationontheMc1rgeneintheintroductionandyourknowledgeofproteins,developahypothesistoexplainhowthechangeinMC1Rproteinfunctionmightdirectlyaffectarockpocketmouse’scoatcolor.Bespecificandconsiderboththelight-coloredanddark-coloredphenotypes.Specificanswerswillvary,butstudentsshouldsuggestthatthenormalMC1Rreceptorproteinwillproducerelativeamountsofeumelaninandpheomelaninthatwillresultinthelightcoatcolor.Inaddition,thedark-coloredmousepopulationcontainsthemutantMc1rgene,whichresultsinadifferentreceptorprotein.Thischangeinstructuremightleadtoincreasedproductionofeumelanin,whichresultsinthedarkcolor.8.Explainwhythemutationataminoacidlocation211isnotassignificantastheotherfourmutations.Itisasilentmutation,sotheaminoacidinthatpositiondoesnotchange,nordoesthestructureofthespecificdomain.Thisisimportantbecauseaprotein’sstructurerelatestoitsfunction.Nochangeinthestructuresuggeststhatthereisnochangeinthefunctionofthisparticulardomainoftheprotein.9.Mutationsareasourceofgeneticvariation.Inthefilm,Dr.SeanCarrollsaysthatmutationsoccurrandomly.Whatdoesthismean?Sampleanswer:“Itmeansthatmutationsdonotoccurforapurposeorforanypredeterminedresult.”10.Itisacommonmisconceptionthat“allmutationsarebad.”Usetheexampleofrockpocketmicetoexplainwhythisstatementisnottrue.Inyouranswer,explainhowthedarkcoat-colormutationcanbeanadvantagetosomemiceandadisadvantagetoothers.Sampleanswer:“Mutationscanresultinnewtraits.Theselectiveadvantageprovidedbyatraitdependsontheenvironment.Forexample,onalightsubstrate,individualswithdark-coloredcoatswouldbeatadisadvantagebecausetheywouldstandoutmorethanindividualswithlight-coloredcoats,makingthemeasierforpredatorstospot.However,inthedarklavaflowhabitat,thosesamedark-coloredindividualswouldhaveaselectiveadvantagebecausetheywouldbebettercamouflagedthanlight-coloredindividuals.Sothestatementthat“allmutationsarebad”isincorrect,becausetherearedifferentselectivepressuresonthetraitsproducedbymutationsdependingonthehabitat.Therearealsosilentmutationsthatdonotchangetheresultingprotein;theseareneutral,neithergoodnorbad.”11.Useyourunderstandingofevolutionandtheinformationinthefilmtoexplainhowthedark-coloredmutationcametobesocommoninsomepopulationsofrockpocketmice.Bespecific.Sampleanswer:“Thedark-coloredmousehasaselectiveadvantageinahabitatsuchasthePinacatelavaflow,whichhasadark-coloredsubstrate.Sincerockpocketmicereproducequicklyandoften,thefrequencyofthisfavoredtraitwouldspreadrapidlythroughthepopulation.Anylight-coloredmiceinthedark-coloredhabitatwouldbeataselectivedisadvantage,thusdecreasingtheirgenefrequencyinfuturegenerations.Inthisway,favorabletraitsaccumulateandincreaseinfrequency—justasCharlesDarwinexplained.”AUTHORAnnBrokawAPBiologyTeacherRockyRiverHighSchoolRockyRiver,Ohio

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