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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. 1.GiveaonesentencedescriptionofthefieldknownasBioinformatics.
Bioinformatics is the science at the intersection of Computer Sciences
(informatics) and Genomics and the analysis of other biological data sets related
to the acquisition of large amounts of data.
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.Countedascorrectforthisexam,becausewedidn'tdoprotein
domainsyet.
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?
2
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.(youmightbe
abletoarguewithme,ifyoucheckedsomethingelse,thisseemstomissthatthevariationis
heritable)
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?1.18*1091
Foryouransweronlyconsidertheprinciplesofcombinatoricsandignorepossible
incompatibilitiesbetweenaminoacids.Howdoesthisnumbercomparetotheestimated
numberofprotonsintheuniverse?Itislargerbyabouttenordersofmagnitude.
22.Wehaveworkedwith3enzymesintheFridaycomputerlabs,whichareshownbelow.
Pleaseidentifythem:
a.
b.
c.
LysozymewithNAGtrimerInteinwithHEboundtoDNAF1ATPase(partoftheF-ATPase)
23.
Arevirusesalive?Pleaseinclude2-4pointsofevidencetobackupyouranswer(simplyayes
ornowillnotsuffice).
Extracredit:
1.Theplotathttp://web.uconn.edu/gogarten/mcb221_2007/chapter1/0101.jpgcontainsacurvegivingtheincreaseofDNAsequenceavailableinthe
databanks.Accordingtothedepicteddata,howlongwillittakeonaveragefor
thenumberofnucleotidesequencesdepositedingenbanktodouble?(Rough
estimationisok)
1.5years
Accordingtothisdiagram,howmanynucleotidesequenceswouldyouexpectin
GenbankintheSpringof2015andFallof2016?
About4*109sequencesinSpringof2015and1010inFallof2016.
Abouthowmanysequencesandhowmanynucleotideswereinthetraditional
GenbankintheFallof2016?
Nucleotides217,971,437,647
Sequences196,120,831
HowmanynucleotideswerepartofWholeGenomeSequencesaccessible
throughtheNCBI
Nucleotides1,637,224,970,324
Sequences 359,796,497
2.
WhowasAlanTuring,andwhyshouldyoucare?Atleastthreeunique
pointsofrelevancearerequired.
• ProposedtheTuringtesttodetermineifacomputershouldbe
considereda"person".
• Providedamathematicaldescriptionforsymmetrybreakingcell
divisionsbasedonreactiondiffusionsystems.
• DevelopedtheconceptoftheTuringmachine(universalcomputing
machine)
• Solvedthe"halting"problem
(https://en.wikipedia.org/wiki/Halting_problem).
• BuildthefirstcomputerandusedittodecryptmessagesoftheGerman
armyandnavyinthesecondworldwar.
• DevelopedadecisiontheorybasedonBayesfactors(thatare
independentofpriors)