NAME:& &&&&&&&&&&&&&&&&&&&&&&&&&&&&ID&#&!BME50A&–&EXAM&1&–&January&21,&2015&–&40&minutes&(While!I!don’t!expect!a!major!time!crunch,!you!should!still!think!intensely!and!work!briskly.!Please!use!a!pen.!Use!your!scratch!paper!to!work!out!your!answer!before!writing!it!on!the!test.!If!you!must!cross!out!an!answer!on!the!test,!you!can!write!the!answer!on!the!back!of!that!page,!provided!you!note!it!clearly.)&&Question&1&(20&points):&!For!the!following!statements,!circle!TRUE!or!FALSE!or!LEAVE!IT!BLANK.!(For!each!correct!choice,!you!will!receive!2!points.!For!each!incorrect!choice,!you!will!lose!2!points.!For! each!choice!left!blank,!you!will!neither!receive!or!lose!points.)!!a)!By!reading!the!hydrogen!bonding!patterns!in!the!minor!groove!of!duplex!DNA,!it!is!possible!to!distinguish!all!four!possible!base!pairs!(AT,!TA,!CG,!GC)!from!each!other.!!TRUE! ! FALSE!!b)!Rotation!around!a!carbonRcarbon!double!bond!takes!much!more!energy!than!rotation!around!a!carbonRcarbon!single!bond.!!!TRUE! ! FALSE!!c)!Ionic!bonds!between!two!ions!are!much!stronger!in!water!than!in!air.!!!TRUE! ! FALSE!!d)!A!nucleosome!contains!a!stretch!of!doubleRstranded!DNA!wrapped!around!a!single!histone!protein.!!TRUE! ! FALSE!!e)!The!four!peptide!chains!of!an!antibody!are!held!together!by!disulfide!bonds.!!TRUE! ! FALSE!!f)!Telomeres!contain!repeated!nucleotide!sequences.!!TRUE! ! FALSE!!g)!Protein!phosphatases!are!enzymes!that!add!a!phosphate!group!to!a!cognate!protein.!!TRUE! ! FALSE!!h)!The!phospholipids!in!the!plasma!membrane!are!amphipathic.!!TRUE! ! FALSE!!i)!The!addition!of!cholesterol!into!a!human!cell’s!plasma!membrane!increases!the!fluidity!of!the!membrane.!!TRUE! ! FALSE!!j)!When!a!molecule!of!glucose!and!a!molecule!of!fructose!join!to!form!the!disaccharide!sucrose,!two!molecules!of!water!are!lost.!!TRUE! ! FALSE! !Question&2&(20&points):!!At!high!enough!temperatures,!duplex!DNA!melts,!meaning!that!the!WatsonRCrick!base!pairs!break!apart.!This!is!called!the!melting!temperature!of!DNA.!For!example,!if!I!boil!a!duplex!DNA!sequence!such!as!ATCCATTAG,!I!will!get!two!single!strands!of!DNA:!ATCCATTAG!and!CTAATGGAT.!!a)!Consider!the!following!sequences!of!duplex!DNA.!Which!has!the!higher!melting!temperature?!Why?!Circle!the!one!with!the!higher!melting!temperature!and!explain!your!choice.!(4!points)!!ATAATTT! OR! CAGTAAC!!Explanation0(One0sentence0max.0We0will0only0grade0your0first0sentence.):0!!!b)!Consider!the!following!sequences!of!duplex!DNA.!Which!has!the!higher!melting!temperature?!Why?!Circle!the!one!with!the!higher!melting!temperature!and!explain!your!choice.!(4!points)!!ATAATTA! OR! ATAATTAAA!!Explanation0(One0sentence0max.0We0will0only0grade0your0first0sentence.):0!!!c)&Now!consider!the!following!system!where!all!A’s!are!replaced!with!a!nucleotide!called!X.!X!is!like!A!but!has!an!extra!ring!in!the!middle.!Just!like!A,!X!hydrogen!bonds!to!T,!as!shown.!!Consider!the!following!sequences!of!duplex!DNA.!Which!has!the!higher!melting!temperature?!!Why?!Circle!the!one!with!the!higher!melting!temperature!and!explain!your!choice.!(12!points)!!XTXTTXX! OR! XTXCGXX!!Explanation0(Two0sentences0max.0We0will0only0grade0your0first0two0sentences.):0!!!! !HNOOOHOOHMOLECULE XHNOOOHONHONHdenotes where the restof the peptide continuesMOLECULE X joinedto the N-terminus of a peptideremember, dark wedgedbonds means coming outfrom the plane of the page and dashed wedged bonds meansgoing into the plane of the pageRR denotes a sidechainHNNOORR denotes rest of the nucleotideNNNH2NNRXTNNNH2NNRXQuestion&3&(30&points):&!To!refresh!your!memory,!below!is!the!structure!of!an!alphaRhelix!(R!denotes!amino!acid!sidechains).!!a)!As!drawn,!what!direction!is!N!to!C?!Top!to!bottom!or!bottom!to!top?!(5!points)!!!!!!!b)!Alpha!helices!with!fewer!than!five!amino!acids!aren’t!stable.!Why?!(Two!sentences!max.!We!will!only!grade!your!first!two!sentences.)!(10!points)!!!!!!!!!c)!Molecule!X,!when!linked!to!the!NRterminus!of!an!alpha!helix!peptide!in!the!manner!shown,!significantly!promotes!the!rate!of!helix!formation.!Why?!(Feel!free!to!annotate!the!molecule!and!refer!to!your!annotations!in!your!answer. !Three!sentences!max.!We!will!only!grade!your!first!three!sentences.)!(Hint:!answer!part!(b)!first.)!(15!points)!!!!! !HNOOOHOOHMOLECULE XHNOOOHONHONHdenotes where the restof the peptide continuesMOLECULE X joinedto the N-terminus of a peptideremember, dark wedgedbonds means coming outfrom the plane of the page and dashed wedged bonds meansgoing into the plane of the pageRR denotes a sidechainHNNOORR denotes rest of the nucleotideNNNH2NNRXTNNNH2NNRXQuestion&4&(30&points):&!a)&Proteins!that!span!the!lipid!bilayer!must!expose!predominantly!nonpolar!sidechains!to!the!membrane.!However,!the!peptide!backbone!itself!has!polar!groups!in!it!!Clearly,!these!need!to!get!at!least!partially!masked!to!avoid!the!potentially!disfavorable!interaction!with!lipids.!With!this!in!mind,!please!explain!why!alphaRhelices!are!much!more!commonly!found!crossing!the!membrane!than!betaRsheets.!(There!is!an!image!of!an!alpha!helix!in!question!3.!Three!sentences!max.!We!will!only!grade!your!first!two!sentences.)!(12!points)!!!!!!!!!b)!There!is!one!exceptional!class!of!betaRsheet!proteins!that!do!in!fact!span!the!lipid!bilayer.!These!are!the!bet aRbarrel!proteins,!which!are!some!of!the!most!beautiful!transmembrane!proteins!around.!(See!example!on!the!left.)!Of!the!following!sequences,!which!is!most!likely!to!correspond!to!the!partial!sequence!of!one!of!the!betaRsheet!segments!spanning!the!membrane?!Circle!the!most!likely!sequence!and!explain!your!choice.!(12!points)!! Seq 1: …Tyr Val Trp Met Leu Asp Lys Asn Asp Arg… Seq 2: …Tyr Asp Val Lys Trp Asn Met Asp Leu Arg… Seq 3: …Tyr Val Asp Lys Trp Met Asn Asp Leu Arg… Seq 4: …Tyr Val Trp Asp Lys Asn Met Leu Arg Asp... Explanation (Two sentences max. We will only grade your first two sentences): 0000c)!In!part!a),!you!identified!an!issue!with!betaRsheets!as!the!reason!why!fewer!betaRsheets!cross!the!membrane!compared!to!alphaRhelices.!How!does!the!betaRbarrel!structure!remedy!the!issue!you!identified?!(Two!sentences!max.!We!will!only!grade!your!first!two!sentences.)!(6!points)!As you may recall from your book, each ribbon represents a strand in a beta-sheet, and the direction of the arrow of the ribbon represents the direction of N to C. So here, you have a bunch of anti-parallel beta-sheets that form a