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AipotuI-1
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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AipotuI-2
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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AipotuI-3
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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AipotuI-4
WhenyoustartAipotu,theprogramwillloadthefourstartingflowertypesintotheGreenhouse,youwillthenseeascreenlikethis:
ThesearetheMenus;theyapplytoallthetools.
TheseButtonsselectthetoolyouwillbeusing.
TheGreenhousecontainsthestartingsetoforganisms.
UpperWorkPanel.Resultsofcrosses,etc.willappearhere.
LowerWorkPanel.Resultsofcrosses,etc.willappearhere.
TheHistoryListstorestheresultsofeachofyourexperiments.Theseresultscanbesenttotheupperorlowerpanes(seelater).
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AipotuI-5
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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AipotuI-6
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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AipotuI-7
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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AipotuI-8
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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AipotuI-9
Putyourdatainthetablesbelow:(a)and(b) allele color(c)Genotype
PhenotypeWhatrulescanyoufindtoexplainthedataabove?
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AipotuI-10
(d)Usingtheallelesymbolsabove,whatarethegenotypesofthestartingstrains?
Green-1: Green-2: Red:
White:(e)HaveyourTAcheckoffthatyouhaveconstructedapurpleflower.Forfullcredit,youmustbeabletoexplaintoyourTAwhytheflowerispurple.(f)Canyouconstructapure-breedingpurpleflowerusingonlythefourstartingstrains?Whyorwhynot?(g)Haveonegrouppostyourresultstoyoursection’sLabDataBlog.
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AipotuI-11
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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AipotuI-12
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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AipotuI-13
•
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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AipotuI-19
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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