comparing dna sequences to understand evolutionary...
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ComparingDNASequencestoUnderstandEvolutionaryRelationshipswithBLAST
INVESTIGATION3BIGIDEA1
AdaptedbyC.Hollinger fromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard ©,revised2015,2017.
LabInvestigation3:BLASTPre-Lab
EssentialQuestion:Howcanbioinformaticsbeusedasatooltodetermineevolutionaryrelationshipsandtobetterunderstandgeneticdiseases?
1AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
LabInvestigation3:BLASTPre-Lab
LearningObjectives:Youwillbeableto-• createcladogramsthatdepictevolutionaryrelationships
• analyzebiologicaldatawithasophisticatedbioinformaticsonlinetool
• usecladogramsandbioinformaticstoolstoaskotherquestionsofyourownandtotestyourabilitytoapplyconceptsyouknowrelatingtogeneticsandevolution
2AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
LabInvestigation3:Pre-LabBackgroundInformation:ReadpagesS41toS44.
Answerthefollowingonyourpre-labhandout.1. Explainwhybeingabletoidentifythelocationand
sequenceofgenesisimportant.2. Whyisbioinformaticsconsideredapowerfultool?
Provide2piecesofevidencetosupportyourclaim.3. Whatisacladogram?Howarecladogramsused?4. Drawacladogramthatdepictstheevolutionary
relationshipamonghumans,chimpanzees,fruitflies,andmosses.
3AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
LabInvestigation3:Pre-Lab5.UsedatainTable1toconstructacladogramofthemajor
plantgroups.(pageS43)6. LookatTable2.PercentageSimilarityBetweentheGAPDH
GeneandProteininHumansandOtherSpecies onpageS44thatcomparesthe%similaritybetweentheGAPDHgeneandproteininhumanswiththeotherspeciesinthetable.a. Whyisthepercentagesimilarityinthegenealwayslowerthan
thepercentagesimilarityintheproteinforeachofthespecies?(Hint:Thinkabouthowageneisexpressedtoproduceafunctionalgeneproduct,inthiscaseaprotein.)
b. Drawacladogramdepictingevolutionaryrelationshipsamongthe5speciesaccordingtopercentsimilarity
4AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017. 5
ComparingDNASequencestoUnderstandEvolutionaryRelationshipswithBLAST
INVESTIGATION3BIGIDEA1
AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard ©,revised2015,2017. 6
LabInvestigation3:BLASTLabProcedure–ReadtheparagraphsatthebottomofpageS44.ThisisanenlargedphotoofFigure3.ThisfossilspecimenwasfoundneartheLiaoningProvinceinChina.Itisanewlydiscoveredspecies.
(Remember:DNAnucleotidesequenceswereextractedfromsofttissueinthisfossil.)
Source:AmericanMuseumofNaturalHistory,MickEllison
7AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
LabInvestigation3:BLASTLab
• Procedure– It’suncommonforanysofttissuetosurvivefossilization,butDNAnucleotideswereextractedfromsmallamountsofsofttissueinthisfossil.Scientistsusedthatinformationtosequenceseveralgenes.
– YourtaskistouseBLASTn toanalyzethesegenesanddeterminetheplacewherethefossilspeciesismostlikelytobeplacedonthecladogram.
AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017. 8
LabInvestigation3:BLASTLabSTEP1:UsingFigure4.FossilCladogram,formaninitialhypothesisastowhereyouthinkthefossilspecimenshouldbeplacedonthecladogrambasedonthemorphology(formandstructureofanorganism)youmadeearlier.• Writeyourhypothesistotherightofthecladogram.• RemembertodrawwhereyouthinkthefossilspecimenshouldbeonthecladograminFigure4onpage2ofyourlabhandout.
9AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
LabInvestigation3:BLASTLab
STEP2:Highlightandcopyoneofthe4genes*onthehandoutprovided.STEP3:Uploadone ofthegenesequencesintoBLASTbygoingtotheBLASThomepage.https://blast.ncbi.nlm.nih.gov/Blast.cgi
*4differentDNAnucleotidesequencesextractedfromsofttissueinthefossil.
10AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
HomepageforBLAST atNCBI
THISISWHATTHEBLASTHOMEPAGELOOKSLIKE.11AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard ©,revised2015,2017.
HomepageforBLAST atNCBI
BEGINbyClickingonNucleotideBLAST.
12AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
Thisisthenextpageyou’llsee.
13AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
UploadingaGeneSequence
Chooseyourfirstgene.Copyandpastethenucleotidesequenceofthatgene(1,2,3,or4)intotheEnterQuerySequencebox.
14AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
UploadingaGeneSequence
* Besuretoaddajobtitlesoyouknowwhichgenenucleotidesequenceyouuploaded.
Here’sthenucleotidesequence.
*
15AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
ClickonBLASTScrolltothebottomofthepage.ClickonBLASTbutton.
16AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
ResultsYou’llseetheresultsin2forms– asaDiagram,whichyouseebelow,andaTable.ClickonGraphicSummarytoseetheTableofyourBLASTresults.
17AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
Results
Thelistofspeciesthatappearsinthissectionarethosewithsequencesidenticalto ormostsimilar, tothegeneyouuploaded.ThesequencesbecomeLESSsimilarareyougodownthelist.
18AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
ResultsClickonaparticularspeciestofindoutmorespecificinformation,includingtheclassificationscheme(scientificname),theproteinthatthesequencecodesfor,andthesequenceofbasesthatappeartoalignwithyourgeneofinterest.
Copyandpastethescientificnameofthatspeciesandgoogleittofindoutthecommonname.
19AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
ResultsYoumustclickontheboxofthespeciesyouwanttousetocreatethe“DistanceTreeofResults.”Seethenextslide.
20AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
MakeaDistanceTreeofResults
ScrollbacktothetopofthepageandclickonDistancetreeofresults.Watchwhathappens!
21AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
TheCladogram
AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
Thisisthegeneyouuploaded.
TheLegendYouwillbeprovidedwithalegendwiththatincludesa“LabelColorMap”anda“BLASTnamescolormap”sothatyoucanbetterunderstandthecladogramyoursearchproduced.
Thisisthegeneyouuploaded.
23AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
ModifyingtheView
ChangetheMaxSeqDifferencefrom
ChangetheMaxSeq Differencefrom0.75to0.15toseeaclose-upofthetree.Yourgeneishighlightedinyellowbelow.
Usingthelegend,youcandetermineevolutionaryrelationships.24
AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
What’snext?• Youwill– Repeatthisprocessfor2othergenesofinterest.– Analyzeyourresults.– DecidewhetherornotthedatafromtheBLASTsearchsupportsyourhypothesisabouttheplacementofthefossilspeciesonthecladogram.
– Compareanddiscussyourcladogramwithotherstudents.
25AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
DesignandConductInvestigation
• Youwill– FindandBLASTyourowngenesofinterest.– Useexampleprocedureprovided.– Possiblyuseoneormoreofthesuggestedgenestoexplore.
26AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.
AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.27
FOR TEACHERS:YoucanuseotherresourceslikethosefoundattheENSI,UCMP,andBioInteractive sitesbeforeorafterdoingthislab.
28AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,
2017.