Download Bioinformatics Take Home Test #1 –Due 9/19/16

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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.