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AipotuI:Genetics&BiochemistryObjectives:

• ToreinforceyourunderstandingofGenetics,Biochemistry,andMolecularBiology• Toshowtheconnectionsbetweenthesethreedisciplines• Toshowhowthesethreeapproachescanbecombinedtogiveacompletepictureofa

biologicalphenomenon• Tofigureoutacompleteexplanationofabiologicalphenomenon• Toexperiencehowscientistsdevelopandtesthypotheses

Introduction:Aipotu(pronounced“āpōtoo“–thewordis“utopia”spelledbackwards)isasimulatedworldwhereuserscanexploreabiologicalphenomenonintermsofgenetics,biochemistry,molecularbiology,andevolution.TheBiologicalPhenomenonUnderStudyInthislab,youwillexplorethebiologicalmechanismsbehindtheexpressionofflowercolorinahypotheticalplant.Theseflowerscanbewhite,red,orange,yellow,green,blue,purple,orblack.Scenario:Youarethechiefbiologistforabreederoffineflowers.Yourcompanysellsseedsthatcustomersplantintheirgardens.Sincemostofyourcustomersexpectthattheflowerswillgroweachyearfromseedsproducedthepreviousyear,youtrytoproducetrue-breedingplantswheneveryoucan.You’vefoundanewspeciesofflowerwithanattractiveshape.You’vecollectedfourplantsfromthewild:twogreen,onered,andonewhite.Yourcustomerswouldreallyliketohavepurpleflowersfromthisplant.Yousetouttocreateatrue-breedingpurpleflower.HypothesisTestingInthethreeAipotulabs,youwilluseaprocessmuchlikethatusedbypracticingscientistsastheyconductresearch.Althoughthisprocessalmostneverfollowsaformula,itoftenproceedsasfollows:1. ObservePatterns.Observethenaturalworldandlookforpatterns,exceptionalevents,

etc.Forexample,youmightobservethatredflowerssometimeshavewhiteoffspring.2. Develophypotheses.Fromtheobservations,youdefinetestablehypotheses–statements

orquestionsthatcanbeaddressedexperimentally.Continuingtheexample,youmightreasonablyhypothesizethatredisdominanttowhite.

3. Testhypotheses.Youthensetupexperimentsorobservationsthatwillcollectdatathatbearonyourhypothesis.Intheexample,youmightcrosspure-breedingwhitewithpure-breedingred.Ifyourhypothesisiscorrect,alltheoffspringwillbered.Ifyougetanotherresult,yourhypothesisisincorrect.

4. Revisehypothesesasnecessary.Ifyourresultsdonotmatchyourprediction,youneedtoreviseyourhypothesisandgotoStep(3)againuntiltheydomatch.

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YouhavealreadybeendoingthisinformallyintheVGLlabs.Youshouldnotethatthisprocessneverreallyends–typicallythereismoretoinvestigateonceyou’vereachedasatisfactoryconclusion.The“answer”vsthe“point”Althoughthereisananswer–thecompletemodelofcolorformationintheseplants–andyoucanfinditwiththetoolsinAipotu,havingtheanswerisnotasimportantasfindingtheanswer.Wecouldjusttellyoutheanswer,butthatwouldleaveoutthemajorlearninggoalsofthislab:

• Experiencinghowscientifichypothesistestingworks.• Experiencinghowyoucanusethetoolsofmodernbiologytocompletelyunderstanda

phenomenon.So,whilewewillworktogethertofind‘theanswer’,therealpointofthelabisthejourney.UnifyingThreePartsofModernBiologyThethreemajorpartsofthiscourseare:

• Genetics=explainingbiologicalphenomenaintermsofgenes.Howisflowercolorinherited?

• Biochemistry=explainingbiologicalphenomenaintermsofproteinsandothermolecules.Howdoesproteinsequencedetermineproteinstructureandcolor?

• MolecularBiology=explainingtheconnectionbetweengenes(DNA)andprotein.HowdoestheDNAsequenceofthecolorgeneleadtoaparticularcolor?

TheconnectionsbetweenthesethreefieldsofbiologyareshownbelowinadiagramcreditedtoDavidBotstein(eachofthearrowscorrespondsto“canbeexplainedintermsof”,thewordsinthisfontarethedifferentdisciplinesofbiology): genes individual life functions Molecular oflivingthings Biology proteinsUnderstandinganybiologicalphenomenonrequiresinformationfromallthreeofthesedisciplines.Throughoutthiscourse,youwillre-visitthislabtocreateanincreasinglycompletepictureofthephenomenonunderstudy.Eachtime,youwilladdtothemodelofcolorproductionintheseflowers.GettingAipotu BecauseAipotuisunderconstantdevelopment,youshouldalwaysusethelatestversion.Asaresult,itisnotinstalledonthecomputers.Youshoulddownloaditfromhttp://intro.bio.umb.edu/aipotu/orthelinkontheOn-LineLabManualforthislab.Itwillthenbeinstalledonthedesktop.

Genetics

Biochemistry

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ToolsAvailableinAipotuForeachofthethreedisciplines,thereisadifferenttoolinAipotuthatwillallowyoutoexplorethesamesetofcreaturesusingadifferentsetoftechniques:

• Genetics.Theflowersinthissimulationarediploids.Aswithmostflowers,theyareallhermaphrodites(bothmaleandfemale).Withthistool,youcanperformthefollowingexperiments:

o Crossanytwoorganisms.Anewwindowwillappearwiththeoffspringofthiscross.o Self-crossanyorganism.Inthiscase,thesingleselectedorganismisbothmother

andfathertotheresultingoffspring.o Mutateanyorganism.Anewwindowwillappearwithasetofflowersthatare

mutantversionsoftheselectedorganism.

• Biochemistry.Thecolorintheseflowersresultsfromtheform(s)ofpigmentproteinspresentinanindividualplant.Withthistool,youcanperformthefollowingexperiments:

o Examinethepigmentproteinspresentinaplant.Thetoolshowsyoutheaminoacidsequenceandtwo-dimensionalstructureofthepigmentproteinspresentinagivenplant.

o Designyourownproteins.Youcaneditanexistingproteinsequenceortypeinanentirelynewsequence.Theprogramwillthenpredictthetwo-dimensionalstructureoftheresultingproteinaswellasitscolor.Itwillalsopredictthecolorresultingfromthecombinationofanytwoproteins.

• MolecularBiology.Thepigmentproteinsintheseplantsareproducedbypigmentprotein

genes.Withthistool,youcanperformthefollowingexperiments:o Examinethepigmentproteingenespresentinaplant.ThetoolshowstheDNA,pre-

mRNA,maturemRNA,andproteinsequencespresentinagivenplant.Youcanexploretheintrons,exons,etc.ofthesegenes.

o Designyourowngenes.YoucaneditanexistingDNAsequenceortypeinanentirelynewsequence.TheprogramwillthenpredictthemRNA,proteinsequence,two-dimensionalstructureoftheresultingproteinaswellasitscolor.Itwillalsopredictthecolorresultingfromthecombinationofanytwoproteins.

o Designyourownplants.YoucansaveeditedDNAsequencesasneworganismsforfurtherstudy.

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WhenyoustartAipotu,theprogramwillloadthefourstartingflowertypesintotheGreenhouse,youwillthenseeascreenlikethis:

ThesearetheMenus;theyapplytoallthetools.

TheseButtonsselectthetoolyouwillbeusing.

TheGreenhousecontainsthestartingsetoforganisms.

UpperWorkPanel.Resultsofcrosses,etc.willappearhere.

LowerWorkPanel.Resultsofcrosses,etc.willappearhere.

TheHistoryListstorestheresultsofeachofyourexperiments.Theseresultscanbesenttotheupperorlowerpanes(seelater).

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Eachorganismisshownasaflower:

Thecolorofthepictureshowsthecoloroftheflower.Theseflowerscanbewhite,red,orange,yellow,green,blue,purple,orblack.Whenanyorganismisselected,theblackborderturnsgreentoshowthatithasbeenselected.Thenextsectionsofthismanualwillshowyouthevarioustoolsandthetasksthatyouwillneedtocarryout.PartI:GeneticsTasks:(specificquestionscanbefoundonpages9and10)

• Determinehowcolorisinheritedintheseflowers.NOTE:thecoloriscontrolledbyonegeneonly.

o Determinethecolorsoftheallelespresentintheoriginalsetoforganisms.o Whichallelesaredominant?o Whichallelesarerecessive?o Howdotheallelescombinetoproducetheoverallcoloroftheplant?

• Constructapurpleorganismtodemonstrateyourunderstandingofthisprocess.Usingthetool:Youcanswitchtothistoolbyclickingthe“Genetics”tabnearthetopofthewindow.Therearethreekindsofexperimentsyoucanperformwiththistool.Thefollowingsectionsuseexamplestoshowyouhowtodoeach;youwillneedtodeviseyourownexperimentstocarryoutthetasksabove.I)CrossTwoOrganisms.SupposethatyouwantedtocrossGreen-1andWhite: 1)ClickonGreen-1andthenonWhiteintheGreenhouse.Therectangularbordersof bothshouldturngreentoshowthattheyhavebeenselected.The“CrossTwo Organisms”buttonsintheUpperandLowerWorkPanelsshouldbeactivated.

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2)Clickthe“CrossTwoOrganisms”buttonintheUpperWorkPanel.Youshouldsee somethinglikethis:

Ifyoudouble-clickontheTrayintheHistoryList,yougetapop-upmenuwithalistofusefuloptions:

• SendtoUpperPanel:SendsthisTraytotheUpperPanelsoyoucancrossthoseorganisms.

• SendtoLowerPanel:SendsthisTraytotheLowerPanelsoyoucancrossthoseorganisms.

• AddNotes...:AllowsyoutoaddnotestotheTrayintheHistoryList.ThesenoteswillappearifyouleavethecursorovertheTrayforafewseconds.

• DeletefromHistoryList:deletestheTrayfromtheHistoryList;thisiscannotbeundone.

Thesearetheoffspringofthecross.Youcanselectanyoftheseforcrossing,etc.

ThisrepresentstheTrayofplantscontainingtheoffspringyoujustproduced.Thecoloredsquaresrepresentthedifferentcolorsoftheoffspringproduced.

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II)Self-crossasingleOrganism.Supposethatyouwantedtoself-crossoneoftheoffspringinTray1: 1)SelectanyoneorganismfromTray1intheUpperWorkPanel.Youcande-selectan organismbyclickingonit.Whenyouhaveonlyoneorganismselected,the “CrossTwoOrganisms”buttonswillbegrayedoutandthe“Self-CrossOne Organism”and“MutateOneOrganism”buttonswillbeactivated. 2)Clickthe“Self-CrossOneOrganism”buttonintheLowerWorkPanel.Youshould seesomethinglikethis(sinceoffspringaregeneratedbyrandomchoiceof parentalalleles,youwilllikelyseeslightlydifferentnumbersofredandwhite offspring):Youshouldseesomethinglikethis:

Theoffspringofthisself-crossareintheLowerWorkPanel.NotetheadditionofTray2totheHistoryList.

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Atthispoint,thereareseveralotherthingsyoucando:A)Ifyoufindaninterestingorganism,youcansaveittotheGreenhouse: 1)Clickthe“Add…”buttonatthetopoftheGreenhouse. 2)Youwillbepromptedtogivetheorganismaname.Giveitadescriptivenameand click“OK”.YouwillseeyourneworganismappearintheGreenhouse.You cannowaccessitusingtheothertoolsinthisprogram. 3)Atthispoint,theorganismissavedintheprogram,butnotonthedisk.Tosavethe contentsoftheGreenhousetodisk,clickontheGreenhouseMenuandselect “SaveGreenhouse”.B)YoucancrossormutateanyoftheorganismsvisibleintheGreenhouse,UpperWork Panel,orLowerWorkPanel.C)YoucanbringanyTrayfromtheHistoryListtoaWorkPanelbydouble-clickingtheTrayandselectingtheappropriateiteminthepop-upmenu.D)YoucanaddnotestoanyTrayintheHistoryListbydouble-clickingtheTrayandchoosingthe“AddNotes...”itemfromtheresultingpop-upmenu.ThesenoteswillappearifyouleavethecursorovertheTrayforafewseconds.IMPORTANTNOTE:Thissoftwareisunderdevelopment.Pleasetreatitgentlyandbepatient.PleasereportanybugstoyourTA.YoushouldsaveyourGreenhouseregularly,especiallyifyousavealargenumberoforganisms.SpecificTaskstodowiththistool:

a) Howmanydifferentallelesarethere?Whichcolorsdotheyproduce?Itwillbeusefultousemultiple-allelenotationlikethis:CR=red;CG=green,etc.

b) Whicharedominantandwhicharerecessive?c) Howdothecolorscombinetoproduceanoverallcolor?Forthis,itmayhelptomakea

genotype-phenotypetableandthentrytoabstractrulesfromthat.Youshouldbesurethatyouhavetriedallthepossiblecombinationsoftheallelesyoufoundinpart(a).

d) Usingthesymbolsyouhavedeveloped,givethegenotypesofthefourstartingorganisms.e) Usingthisknowledge,constructapurpleflower.f) Canyouconstructapure-breedingpurpleflowerwiththestartingsetoforganisms?g) Postyourfindingstoyoursection’sLabDataBlog.

HowtogoaboutaccomplishingthesetasksFollowtheprocedurefrompage(1)–lookforpatterns,makehypotheses,testhypotheses,revisehypotheses.Today,wewillnotwritethemoutformally,butyoushouldbethinkinginthesetermsfortheAipotuIIlablaterinthesemester.

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Putyourdatainthetablesbelow:(a)and(b) allele color(c)Genotype PhenotypeWhatrulescanyoufindtoexplainthedataabove?

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(d)Usingtheallelesymbolsabove,whatarethegenotypesofthestartingstrains? Green-1: Green-2: Red: White:(e)HaveyourTAcheckoffthatyouhaveconstructedapurpleflower.Forfullcredit,youmustbeabletoexplaintoyourTAwhytheflowerispurple.(f)Canyouconstructapure-breedingpurpleflowerusingonlythefourstartingstrains?Whyorwhynot?(g)Haveonegrouppostyourresultstoyoursection’sLabDataBlog.

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PartII:BiochemistryITasks:Worktogetherasaclassto:

• Explain,intermsoftheproteinspresent,theinteractionsbetweentheallelesyoufoundinPartI.

o Whyisthecolorphenotypeofsomepigmentproteinsdominantwhileothersarerecessive?

o Howdothepigmentproteinscombinetoproducetheoverallcoloroftheplant?• Determinethedifferencesinaminoacidsequencebetweentheproteinsproducedbythe

allelesyoufoundinPartI.• Begintodeterminehowtheaminoacidsequenceofapigmentproteindeterminesitscolor

–youwillcompletethistaskintheAipotuIIlablaterinthesemester.Asinrealscience,thesetasksaretoobigtobesolvedbyonegroupalone.Ifyouthinkofrealresearchassolvinganenormousjigsawpuzzle,eachresearcherworksononlyonelittlecornerofthepuzzle.Scientistspublishpapersandpresentfindingsatconferencesinordertoconnectthecornersofthepuzzlethateachisworkingon.ImportantNote:Itisalwaysimportanttokeepinmind,the‘scientist’smantra’:alwaysbeaskingyourself“HowcouldIbebeingfooledbythis?”Tocontinuetheexamplefromthepreviouspage,considerthefollowing:Supposethatthelongthinproteinwerered,youmightcongratulateyourselfthatyouhadfoundtheconnectionbetweenshapeandcolor.However,whatiftherealmechanismisthatproteinscontainingarginineareredandyourlongthinproteinjusthappenedtobemadewitharginine.Theredcolorwouldbefoolingyouintothinkingyouhaditright.Howdoyouavoidthistrap?Eventhebestscientistssometimesfallintotrapslikethis.Theansweristoalwaysbethinkingofalternativeexplanationsforyourresults.Inthecaseabove,onelongthinredproteindoesnotmeanthat“long&thin=red”.Youhavetocollectmoredata:proteinsthataren’tlongandthin;longandthinproteinswithdifferentaminoacids;etc.Inthispartofthelab,morethaninthefirstpart,itistheprocessofscienceratherthantheanswerthatismostimportant.Youwilluseablogtocollaborateasaclasstosolvethisscientificproblem.Inthislab,youwilluseaweblogor‘blog’tosharehypotheses,data,andconclusionsamongyourlab-matessothatyoucansolvethisprobleminthethreehoursofthelabperiod.Individualcontributionscanbesmall,orevennegative(“Iknowthatitcan’tbe…”),butyouwillbeabletoaccomplishthetasksaboveifyouworktogether.Inresearch,noone‘owns’data–thepointistofigureouthowtheworldworks,notwhogottheresult.Thisblogwillalsobeavailableonthewebforwhenyouwriteyourlabreports.

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Usingthetool:OnceyoustartAipotu,youcanswitchtothetoolforthissectionbyclickingthe“Biochemistry”tabnearthetopofthewindow.Youwillseesomethinglikethis:

Thispartoftheprogramusestheone-lettercodeforthe20aminoacids:

AminoAcid 3-lettercode

1-lettercode

Mnemonic

Alanine Ala A AlanineArginine Arg R aRginineAsparagine Asn N asparagiNeAsparticacid Asp D asparDicacidCystine Cys C CystineGlutamine Gln Q Q-tamineGlutamicAcid Glu E glu-tE-amicacidGlycine Gly G GlycineHistidine His H HistidineIsoleucine Ile I IsoleucineLeucine Leu L LeucineLysine Lys K lysinKMethionine Met M MethioninePhenylalanine Phe F FenylalanineProline Pro P ProlineSerine Ser S SerineThreonine Thr T ThreonineTryptophan Trp W tWptophanTyrosine Tyr Y tYrosineValine Val V Valine

Thisisareferenceforthenamesandpropertiesoftheaminoacids.• Thesingle-lettercodeisshownbelowthethree-lettercode.• Whitecirclesarehydrophilic;grayareintermediate;andblackare

hydrophobic.• Ared(-)indicatesanegatively-chargedsidechain• Ablue(+)indicatesapositively-chargedsidechain• Agreen(*)indicatesasidechainthatcanmakeahydrogenbond.

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• ClickintheAminoAcidSequenceBoxatthetopoftheUpperFoldingWindow.Typeashortsequenceoflettersandyouwillseeashortaminoacidsequenceappearinthewindow.Thistoolconvertsthesingle-lettercodetothethree-lettercodeautomatically.

• Clickthe“FOLD”buttonandatwo-dimensionalversionofyouraminoacidsequencewillappearintheFoldedProteinwindow.

Thereareseveralimportantthingstonoteaboutthisfoldingprocess:ItisthesameasyouusedintheProteinInvestigator.Thisisahighly-simplifiedmodelofproteinfolding.Itisnotintendedtopredictthecorrectstructuresofanyproteins;itisdesignedtoillustratethemajorprinciplesinvolvedinthatprocess.Theimportantfeaturesofproteinsthatthissoftwareretainsareasfollows:

• Aminoacidshaveside-chainsofvaryinghydrophobicity,charge,andhydrogenbondingcapacity.

• Theaminoacidsareconnectedinanun-branchedchainthatcanbend.• Hydrophobicaminoacidswilltendtoavoidthewaterthatsurroundstheprotein;

hydrophilicaminoacidswillbindtothewater.• Aminoacidsthatcanformhydrogenbondswilltendtoformhydrogenbondsiftheycan.• Positively-chargedaminoacidswilltendtoformionicbondswithnegatively-charged

aminoacidsiftheycan.• Like-chargedaminoacidswillrepeleachotheriftheycan.• Ionicinteractionsarestrongerthanhydrogenbonds,whicharestrongerthanhydrophobic

interactions.Eventhoughthissoftwareprovidessomeimportantinsightsintoproteinfolding,youshouldalwayskeepinmindthatthisisanapproximation.Themostimportant"gotcha's"tobeawareofare:

• Thisprogramfoldsproteinsin2-dimensionsonly.• Thisprogramtreatsallaminoacidsasequal-sizedcircles.• Thisprogrammodelsanenvironmentwheredisulfidebondsdonotform.• Thisprogramfoldstheproteinbasedontheinteractionsbetweenthesidechainsonly.• Thisprogramdoesnotmodelsecondaryorquaternarystructure.• Thisprogramassumesthatallsidechainswithhydrogenbondingcapabilitycanbondwith

eachother.Thesesimplificationsarenecessaryfortworeasons.Thefirstistechnical:itturnsouttobeextremelydifficulttopredictthefull3-dfoldedstructureofaproteingivenonlyitsaminoacidsequence.Asofthewritingofthislabmanual,ittakesasuper-computerseveraldaystopredictthefully-foldedshapeofevenasmallproteinlikelysozyme.Eventhen,thepredictionsdon’talwaysmatchknownstructures.GiventhecomputerswehaveintheBio111labs,itmighttakeyears….Thesecondreasoniseducational.Proteinsarecomplex3-dimensionalmolecules;thus,itcanbehardtofindyourwayaroundwheninsideone.Likewise,itwouldbeverydifficulttovisuallycomparetwoproteinmoleculestoobservetheeffectsofchangestotheiraminoacidsequence.Itwouldbeeasytomisstheforest(theforcesthatcontrolproteinstructure)forthetrees(thetinydetailsofthestructures).

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Forthesereasons,wewillusethissimplification.Itretainsthepropertiesofaminoacidsthatareimportantforthislabwhilebeingsimpleandfast.Therearethreekindsofexperimentsyoucanperformwiththistool.Thefollowingsectionsuseexamplestoshowyouhowtodoeach;youwillneedtodeviseyourownexperimentstocarryoutthetasksfromthepreviouspage.I)ExaminethePigmentProteinsPresentinanOrganismfromtheGreenhouse.Thissimulatesextractingthepigmentprotein(s)producedbythetwoallelesofthepigmentproteingenethatanorganismpossesses,displayingtheirtwo-dimensionalstructures,anddisplayingtheircolors. 1)Double-clickontheGreen-2organismintheGreenhouse.Youshouldseethis:

TheGreenorganismcontainstwoallelesofthepigmentproteingene.Eachoftheseallelesproducesadifferentprotein.OneoftheseproteinsisshownintheUpperFoldingWindow;itisablue-coloredproteinasshownbythebluesquarenexttothe“Color:”label.TheotherproteinisshownintheLowerFoldingWindow;thisisyellow-coloredprotein.ThecombinedcolorofthetwoproteinsisgreenasshownbytheCombinedColorinbetweenthetwoFoldingWindows.II.ExaminingPigmentProteinsFromtheMutantOrganism(s)YouMadeintheAipotuILab.Youcangobacktoyoursection’sLabDataBloganddownloadanysavedorganism(s)tothegreenhouse.Control-clickonthefilenamelinkandselectDownloadLinkedFileAs….NavigatetotheDesktop,intotheAipotufolder,andfinallysaveitintheGreenhousefolder.Ifyounowquitandre-startAipotu,youwillseetheneworganismintheGreenhouse.

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III)Comparetheaminoacidsequencesoftwopigmentproteins.Thisalignsthetwoaminoacidsequencessothatthehighestnumberofmatchingaminoacidsisobtainedandthenfindstheremainingdifferences. 1)Double-clickontheGreen-2organismintheGreenhouse.Youshouldseethatthe UpperFoldingWindowshowsablueproteinandtheLowerFoldingWindow showsayellowprotein. 2)Youcancomparetheaminoacidsequenceofthesetwoproteinsbyclickingonthe “Compare”menuandchoosing“Uppervs.Lower”.Awindowwillappear showingthedifferencesbetweenthetwosequences.Thisisshownbelow:

Thisshowsthattheonlydifferenceisthat,intheupper(blue)protein,aminoacid10is tyrosine,whileinthelower(yellow)protein,aminoacid10istryptophan. ÞYoucanalsocopythesequenceofaparticularproteintotheclipboardusingthe optionsintheEditmenu.YoucanthenCompareasequencetotheoneinthe clipboard.IV)EditaProteinSequenceorCreateaNewProteinSequenceandDetermineitsTwo-DimensionalStructureandColor.YoucaneditthesequenceineitheroftheAminoAcidSequenceboxesandclickthe“Fold”buttontopredictthetwo-dimensionalstructureandcoloroftheprotein.ThetoolwillalsogivethecolorthatresultsfromthecombinationofthecolorsintheUpperandLowerwindows.Forexample,clickanywhereinthe“Tyr”correspondingtoaminoacid10intheUpperAminoAcidSequencebox.Clickthe“delete”keyandthataminoacidwilldisappear.Typean“L”(theonelettercodeforleucine)andtheaminoacidsequenceshouldbe: MetSerAsnArgHisIleLeuLeuValValCysArgGlnClickthe“FOLD”buttonintheUpperFoldingWindow(orclickthereturnkey).Youwillseethatthecolorofthenewproteiniswhiteasshownbythe“Color:”intheUpperFoldingWindow.Youshouldalsonoticethat:

• the“CombinedColor”atthecenterofthewindowisnowyellow.• thereisnowanentryintheHistoryListwithyournewprotein.Thebackgroundof

HistoryListentryiswhitetoshowthecolorofthisprotein.Youcanalsoclickthe“LoadSampleProtein”button.Thiswillloadasampleaminoacidsequencethatfoldstoawhite-coloredproteinwithashapethatissimilartomanycoloredproteins.

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Ifyoudouble-clickanentryintheHistoryList,youwillyougetapop-upmenuwithalistofusefuloptions:

• SendtoUpperPanel:SendsthisTraytotheUpperPanelsoyoucancrossthoseorganisms.

• SendtoLowerPanel:SendsthisTraytotheLowerPanelsoyoucancrossthoseorganisms.

• AddNotes...:AllowsyoutoaddnotestotheTrayintheHistoryList.ThesenoteswillappearifyouleavethecursorovertheTrayforafewseconds.

• DeletefromHistoryList:deletestheTrayfromtheHistoryList;thisiscannotbeundone.

ÞYoucanalsotakeaSnapshotofeitherWorkPanelInordertomakeentriesinthedatablog,youwillneedtotakesnapshotsofparticularproteins.Atypicalsnapshotlookssomethinglikethis;itshowstheprotein’sshape,aminoacidsequence,andcolor:

Youcantakeasnapshotineitheroftwoways:

• Saveasnapshotasapicture.IntheFilemenu,chooseeitherSaveImageofUpperPanel…orSaveImageofLowerPanel….Youwillthenbeaskedtogivethefileanameanditwillbe(typically)savedtothedesktopasname.png;youcanthenimportthatfileintothedatablog.

• Takeasnapshottotheclipboard.IntheEditmenu,chooseeitherCopyImageofUpperPaneltoClipboardorCopyImageofLowerPaneltoClipboard.Youcanthenpastetheresultingimageintoanotherprogram,likeMicrosoftWord.

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UsingtheBlogtocollaborateduringclassThedatablogwillallowallthemembersoftheclasstosharehypotheses,data,andconclusionsinascaled-downscientificcommunity.Asyouwork,youshouldposttotheblog.Youshouldnotpostallyourdata;justtheinterestingbits.Itisprobablybettertoerronthesideofincludingsomethingratherthannot;youneverknowifitwillturnouttobeinteresting.Youshouldalsoconsulttheblogfrequentlytoseeifthereisdatatherethatwillhelpyoufigureoutwhat’sgoingon.Periodically,yourTAwillaskyoutotakeabreaktohaveabriefresearchsymposiumwhereyouwillreviewtheblogasaclassanddiscusswhatyou’vefoundsofarandwhereyoushouldbegoing.Usingtheblogwillbetrickyatfirst,butitwillsoonbecomeeasier.I)LoggingIn–loginthroughyourBlackboardaccountandgototheBio111page.II)Posting–youshoulddothiswhenyouhaveaninterestingresulttosharewiththeclass.Again,itisbettertoerronthesideofpostingthannotposting.Usethefollowingprocedure:1)Clickthe“LabBlogs”linkinthenavigationlist:2)InthelistofLabBlogs,clickonthelinkforyourlabsection.3)Click“CreateBlogEntry”.4)Youwillseesomethinglikethis:

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Apostshouldcontainthefollowingelements:

• Title.EnterthisintheTitlebar.Itshouldcontainyourgroupnameandashortphraseindicatingthesubjectofyourpost.Forexample,“Brian,Tina,&Ling:Thislongproteinisred!”

• AnImageoftheprotein.

o First,savetheimagetothedesktop.UsingAipotu’s“SaveImageof…Panel…”fromtheFilemenu,saveanimageoftheinterestingproteintotheDesktop.Giveitadistinctivenamesoyoucanfinditeasily.Aipotuwilladd“.png”totheendofthefilenametocorrectlyidentifyitasanimage.

o Next,insertitintothepost.Usethe“Insert/EditImage”button.DONOTUSEthe“AttachFile”buttons.

• AHypothesis.Usingtheformatbuttons,selectboldtypeandtype“Hypothesis:”.Gotothe

nextlineand,usingregulartype,writethehypothesisyouwereexploring.Forexample,“Longthinproteinswillbered”.

• TheExperiment.“Experiment:”shouldbeboldandonit’sownline.Followwithabrief

descriptionoftheexperiment;forexample,“Wedesignedalongthinprotein”.

• TheResult.“Result:”shouldbeboldandonit’sownline.Followwithabriefstatementdescribingtheresult;forexample,“Theproteinwascolorless”.

• TheConclusion.“Conclusion:”shouldbeboldandonit’sownline.Followwithabrief

conclusion;inthiscase,“Thehypothesisisincorrect;longthinproteinsarenotnecessarilyred.”

Titlebar

Insertpicturebutton(USETHISONE)

Dangerdanger!(Donotusethisbutton)

Type text here

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ASamplepost:

IMPORTANTNOTES:(1)Thissoftwareisunderdevelopment.Pleasetreatitgentlyandbepatient.PleasereportanybugstoyourTA.YoushouldsaveyourGreenhouseregularly,especiallyifyousavealargenumberoforganisms.Youshouldalsopostpicturestotheblogassoonasyoucan.(2)Don’tshutdownorrestartthecomputeroryouwillloseallthepicturesyou’vesavedontheDesktopandalltheorganismsyou’vesavedintheGreenhouse.SpecificTasksforthissectionWorkasaclass,usingthedatablogto:

a) WhatarethedifferencesintheaminoacidsequencesoftheproteinsproducedbytheallelesyoudefineinPartI?Hint:usetheComparemenutofindthedifference(s)betweentheaminoacidsequences.

b) Howdothecolorscombinetoproduceanoverallcolor?Howdoesthisexplainthegenotype-phenotyperulesyoufoundinPartI?

c) Starttoworkonthese;postpreliminaryfindingsandquestionstolabblog.Youwillfinishthislaterinthesemester:

o Whatfeaturesoftheaminoacidsequencemakeaproteinpigmented?o Whatfeaturesoftheaminoacidsequencemakeaproteinaparticularcolor?o Whichproteinsarefoundineachofthefourstartingorganisms?o Usingthisknowledge,constructapurpleprotein.

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Hints:A) Itmaybeuseful,beforeformulatinganyhypotheses,tolookforpatternsinthedata.

Whichfeaturesdocoloredproteinshaveincommonthatuncoloredproteinslack?• Trycomparingtheaminoacidsequencesofproteinswithdifferentcolors.• Herearesomeadditionalinterestingsequencestotry:

• FFFFFFFRRRRRR• RRRFFFFFFFRRR• KKKKKKLLLLLLF• KKKKKKLLLLLLL• SLQLNITMEVDFW• EEEWWWWWWWEEE

B) Scientists,includingyourselves,oftenfinditusefultousemutationtostudyphenomena

likethis.GotoGeneticsandmakesomemutants.SaveanyoneswithinterestingcolorstotheGreenhouse.SwitchbacktoBiochemistryandlookattheproteinstheyhave.

Procedure:

1. Comparetheproteinsfoundinthestartingstrainstoanswerquestions(a)and(b)onthefollowingpages.

2. YourTAwillassignyourgrouponeparticularcoloredproteintostudy.Compareitssequenceandshapetothe“sampleprotein”thatyougetbyclickingtheLoadSampleProteinbuttonononeoftheFoldingWindowsandthenchoosingfromtheComparemenu.

3. Arepresentativefromeachgroupwillcometotheboardtodescribethesequenceand

shapedifference(s)betweentheirproteinandthesample.Notethateachsubsequentgroupshouldrelatetheirfindingstothepreviously-presenteddata.

4. Basedonthesedata,asaclass,makeseveralspecifichypothesesthatcanbetested.

5. Eachgroupshouldworkononeormoreoftheirhypothesesandpostthemtotheblog.

6. YourTAmaystopforamini-symposiumtosharedataanddesignnewhypotheses.

7. Youwillthenbeabletocompleteparts(d)through(f).

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Putyourdatainthetablesbelow:(a)Whichproteinsarefoundineachofthefourstartingorganisms? Green-1 Green-2 Red White(b)allele color aminoacidsequence(highlightdifferences)Wewillstarttoworkonthesequestionstoday.WewillrevisitandfinishthemintheAipotuIIlablaterinthesemester.Besuretotakegoodnotesandposttothelabblogtokeeparecordofyourthoughts,conclusions,andquestions.(c)Whatfeaturesofaproteinmakeitcolored?

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(d)Whatfeaturesoftheaminoacidsequencemakeaproteinaparticularcolor?(e)Howdothecolorscombinetoproduceanoverallcolor?Howdoesthisexplainthegenotype-phenotyperulesyoufoundinpart(I)?(f)ShowyourTAthatyouhavemadeapurpleprotein.Forfullcredit,youneedtoexplaintoyourTAwhyitispurple.

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Labreport• Mustbetyped;handwrittenreportswillnotbeaccepted.• Dueduringtheweeklistedinthesyllabusatthestartofthelabsessionyouarecurrentlyin.

Thisisafirmdeadline.• Althoughyouwillperformtheseexperimentsasagroup,eachmemberofthegroupmustturn

inanindividuallabreportandthisreportmustbeinyourownwords.Yourlabreportmustinclude:Adescriptionofoneplacewhereonehypothesis(abouttherelationshipbetweensequence,structure,andcolor)andsomedatainteractedtoleadtoafirmconclusion.NotethatthehypothesismustbefromtheBiochemistrysectionofthislab.Youshouldnotdescribealltheexperimentsyoudid;justoneplacewhereyouwereabletodrawafirmconclusion.Theconclusioncanbepositive(“Myhypothesiswassupportedbecause…”)ornegative(“Myhypothesiswasnotsupportedbecause…”).Thisneednotbeanexperimentyoudid,butitmusthavehappenedduringyourlabsession.1)Hypothesis–thehypothesisbeingtested.Youmustpickaclearandspecifichypothesisthatcanbeclearlyanddecisivelytestedbytheexperiment(s)youdescribebelow.Yourhypothesisneednotbecorrect.2)Experiments–adescriptionoftheexperiment(s)youtriedthataddressedthehypothesis.Donotincludeallyourexperiments;onlythoserelevanttothehypothesisfrompart(1).Thesemustclearlyanddecisivelytestyourhypothesis.3)Results–picturesoftheresultsoftheexperiments.Youcangetthesefromyoursection’sblogpage.Justdragthepicturefromthewebpagetothewordprocessor.Youmayneedtonotethecolor(s)intextsincemostprintersprintinblackandwhite.4)Conclusions–dothedatasupportthehypothesisornot.Explainyourreasoning.Youwillbegradedonthequalityofyourargument:howclearlyyoudescribedyourhypothesis,experiment(s),andresult(s)aswellashowclearlyandcompletelyyourconclusionsareexplained.

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