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Your Name: Bioinformatics Take Home Test #1 –Due 9/19/16 Pleasesubmitahardcopyofyouranswers(withorwithoutthequestions),ifpossible.Ifyou haveanemergencyandcannotsubmitaquizinperson,emailitinbythestartofclassonthe duedate.Ifyoudoso,onlyemailyouranswers. Latequizzeswillnotbeacceptedaftertheanswershavebeenreleased. Allquestionsworth1ptifnototherwiseindicated 1.GiveaonesentencedescriptionofthefieldknownasBioinformatics. 2.BioinformaticsdoesNOTincludewhichofthefollowingactivities? A.Analyzinggenomedatausingcomputers B.FiguringoutaproteinstructurefromX-raycrystallography C.Detectinghomologsusingprimarysequencesimilarity D.Detectinghomologsusingsecondarysequencesimilarity 3.ATP,GTP,NAD,NADP,FMN,andFADareexampleofwhattypeofcofactor? A.Nucleotideormodifiednucleotide B.LipidormodifiedLipid C.Aminoacidormodifiedaminoacid D.oligosacharides 4.Thecofactorslistedinquestion3providesupportforwhichhypothesisregardingthe earlyevolutionoflife? A.DNAWorld B.CompartmentalizedCellsFirst C.RNAWorld D.ProteinWorld E.MetabolismFirst 5.Proteinsthatevolvedfromthesameancestralprotein A.ALWAYShavesignificantsimilarityintheirprimarysequence. B.Cannothavedifferentfunctions C.Candivergesothattheyhaveonlylimitedhomology. D.Donotnecessarilyretaindetectablesimilarityisprimarysequence. E.WillALWAYShavedetectablelevelsofprimarysequencesimilarity 6.Whatmightbethereasonforproteinsthatshowsignificantsimilarityintheirprimary sequence(whennosimplerepeatsorlowcomplexityregionsarepresent)tobehomologous. A.Sequencespaceissobigthatstumblingontoasignificantlysimilarsequencebychanceis veryunlikely B.Thisisatrickquestion,becauseNOTallcurrentlyknownproteinsthatsharesignificant similarityarehomologous C.Thereisadirectlinkbetweensequencesimilarityandpercenthomology D.Homologoussequencesshareafunctionandthereisonlyasmallregionofproteinspace thatcanaccomplishanyonefunction E.Alloftheabove 7.WhichofthefollowingisNOTconsideredstrongevidenceforhomology? A.Thearrangementofsecondarystructureelementsinspaceisthesameorverysimilar. B.Significantprimarysequencesimilarity C.Significantprimarysequenceidentity D.Identicalfunction E.Noneoftheabove 8.WhichofthefollowingistheBESTworkingdefinitionoflife? A.Acontainedmetabolicsystemcapableofevolutionwithheredity. B.Cells.Lifecouldonlyexistinaformcompartmentalizedbyalipidbilayer. C.Self-sustainedmetabolicsystemthatdoesnotrequireinputfromanyotherlivingsystem. D.Aninteractingwebwithintricatefeedbackloopstoensurehomeostasis. E.Anythingthatcanreproduceitselfperfectlywithnoerrors. F.Alloftheaboveareequallygoodanswers. 9.Whatishomology? A.Thecreationofartificiallifebyanymeans. B.Adifferencefoundbecauseofdivergingevolutionarypathssincethelastcommon ancestor. C.Similarityduetosharedancestry,i.e.bothgotitfromacommonancestor. D.Whentwoproteinsshareafunction,suchasnucleotidebinding,theyalsosharesequence similarities,becauseofthelimitedsizeofproteinspace. E.Sharedsequencesimilaritybasedonconvergentevolution,i.e.theancestordidnothaveit. 10.Canaproteinbe84%homologoustoanotherprotein? A.Yes. B.Mostlyno,withtheexceptionofcasesofdomainshuffling. C.Yes,iftheyshare84%sequenceidentity. D.No,withoutexception. 11.TheSwissProteindatabankfileviewer,akaDeepViewcanNOTbeusedtodowhichof thefollowingthings? A.Visualizewhereanucleotidecofactorbinds. B.Comparethestructuresoftwosequences. C.Colorastructurebyhowcloselyitmatchesanother. D.Detecthomologywith100%certainty. E.VisualizetheconformationalchangethattheATPsynthaseundergoesduringitscatalytic cycle. 12.Whichelementsmakeupthesecondarystructureofproteins? A.Hydrophobicdomains,nucleotidebindingmotifs,andproteinchannels. B.Betabarrels,alphacorkscrews,anddeltaturns. C.Betasheets,alphahelices,andloops. D.VanderWaalsinteractions,hydrogenbonds,anddisulfidebridges. E.Multipleproteinchainsinteractingtoformonemacromolecule. 13.Howmanytypesofsubunits(note:thisasksforthedifferenttypesofsubunits,encoded byseparategenes,notthenumberofsubunits)formthehexamer(thehead)ofnucleotide bindingsubunitsintheF1ATPase? 14.True/FalseInthecatalyticcycleoftheATPase,allofthecatalyticsubunitsworkin differentphasesofthecatalyticcycleatanyonepointintime. 15.True/FalseThedifferentATPbindingsubunittypesthatformthehexameroftheF1- ATPsynthasearehomologoustoeachother. 16.True/FalseTheancestralATPasecouldhavelookedlikeahomohexamerwithsix identicalsubunits. 17. True/FalseItisNOTpossibletocreateacomputerprogramtomimicevolutionbymeans ofartificialselection,becausecomputersprogramsareNOTcapableoffindingnewsolutions thatahumanhasneverthoughtofbefore. 18.WhatistheGaiahypothesis? A.Earth’splantscontroltheplanet’stemperaturebyselectionforflowercolor B.AlllifeonEarthdescendedfromONEcommonancestor C.TheunitoflifeistheentireEarthandtheentirebiosphereisalive,becausenosingle speciescanexistincompleteisolation.TheecosystemsontheEarthareprotectedby negativefeedbackloopsthathelpmaintainhomeostasis. D.MarscooledfasterthantheEarthandthereforewasamorehabitableplaceforlifeearlier. LifearosefirstonMarsandtraveledtoEarthonmeteorites E.Largeglaciersandiceagesresultfromarunawaycold-house,wheretheEarthgetscolder becauseglaciersreflectmorelightfromthesurface F.Zirconcrystalsin3.8billionyearoldrockswereproducedbyancientlifeover4billion yearsago.Thezirconcrystalsareformedbyrunningwaterandthebiasincarbonisotope ratiosindicatesthepresentsoflife. 19.Evolutionbynaturalselectionrequireswhichthreethingstooccur? A.Variationamongoffspring,aniche,andcompetitionforresources. B.Heredity,excessoffspring,andaniche. C.Excessoffspring,competitionforresources,andvariationamongoffspring. D.Aniche,ahumantonaturallyselectthebestoffspring,andoxygen. E.Noneoftheabove. 20.WhichofthefollowingisNOTpartoftheexplanationforhowcomplexfunctional moleculeswereassembled,despitethevastnessofproteinspace? A.Gaiadirectsproteinevolution,throughnegativefeedbackloops,tothecorrectregionof proteinspace. B.Therearemultipleunrelatedsolutionsforthesamefunctionality,exemplifiedbythefact thattherearenon-homologousenzymesinhabitingcompletelydifferentregionsofprotein spacewiththesamefunction. C.Anexactfunctiondoesnotneedtobehitupon,becausenaturalselectioncantakea proteinwithlimitedfunctionandmakeitbetter. D.Similarstructureshavesimilarfunction,sothereareentireregionsofproteinspace occupiedbyhomologsthatallfunctionequallywell,ornearlyso. E.Proteinspaceismadeslightlysmallerbyremovingallofthepossibilitiesthatcannotbe synthesizedortheywillcloguptheribosome. 21.Howmanypeptides(shortproteins)of70aminoacidsinlengtharepossible,giventhat thereare20possibleaminoacids?Foryouransweronlyconsidertheprinciplesof combinatoricsandignorepossibleincompatibilitiesbetweenaminoacids.Howdoesthis numbercomparetotheestimatednumberofprotonsintheuniverse? 22.Wehaveworkedwith3enzymesintheFridaycomputerlabs,whichareshownbelow. Pleaseidentifythem: a. b. c. 23. Arevirusesalive?Pleaseinclude2-4pointsofevidencetobackupyouranswer(simplyayes ornowillnotsuffice). Extracredit: 1.Theplotathttp://web.uconn.edu/gogarten/mcb221_2007/chapter1/0101.jpgcontainsacurvegivingtheincreaseofDNAsequenceavailableinthe databanks.Accordingtothedepicteddata,howlongwillittakeonaveragefor thenumberofnucleotidesequencesdepositedingenbanktodouble?(Rough estimationisok) Accordingtothisdiagram,howmanynucleotidesequenceswouldyouexpectin GenbankintheSpringof2015andFallof2016? Abouthowmanysequencesandhowmanynucleotideswereinthetraditional GenbankintheFallof2016?HowmanynucleotideswerepartofWhole GenomeSequencesaccessiblethroughtheNCBI 2. WhowasAlanTuring,andwhyshouldyoucare?Atleastthreeunique pointsofrelevancearerequired.