!!Exam%%1%Study%Guide%!!MCB!354!–!Exam!1!Study!Guide!• Breakdown!for!Exam!1!o 200!points!o 8!–!Multiple!choice!questions!(5!points!each)!o 6!–!Short!answer!questions!o 4!–!Long!answer!questions!(multiFpart,!calculations/estimations,!etc.)!o Hint:!Be!prepared!to!do!calculations,!draw!structures,!and!interpret!data!!• The!following!material!listed!in!this!study!guide!is!fair!game!for!the!exam!!There!could!also!be!material!from!lectures,!textbook,!or!the!bonus!slides!present!on!the!exams!as!well!!Good!luck!!!!!!!!!!!!!!MCB!354!!!!!1st!Edition!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!• Example!problems!from!Quiz!1:!!1. The!secondary!structure!of!a!protein!is!determined!mainly!by:!!Incorrec t!B u r yin g !h y d ro p h o b ic !side!chain!in!the!inte rio r. !!Incorrec t!T h e !p rimary!seq u e n ce .!!Correct:!Hydrogen!bonding!between!main!chain!atoms.!!Incorrec t!T h e !p K a !o f!th e !a mino!and !c a rb o x y!t e rminus.!!Incorrec t!S id e !ch a in s !th a t!p r o tr u d e!f ro m!the!secondary!structure.!!2. What!would!a!(reasonably)!expected!value!for!the!pKa!of!a!Lys!residue!that!is!located!near!a!negatively!charged!patch!of!in!the!interior!of!a!protein?!!Incorrec t!6 .5 !!Incorrec t!9 .0 !!Incorrec t!1 0 .5 !!Correct:!12.0!!Incorrec t!C a n 't!b e !ionized!!3. In!a!mu ltip le !s eq uence!alig n ment,!wh ic h !o f!th e !fo llo wing!pair s!o f !amino!acid s !would!N O T !b e !considered!similar?!!Incorrec t!S !a n d !C !!Incorrec t!L !a n d !I!!Incorrec t!V !a n d !L !!Incorrec t!D!and!E!!Correct:!F!and!T!!4. Which!of!the!following!is!NOT!always!true!about!an!βFsheets?!!Incorrec t!A ntiparallel!s tr an d s !a re !o f!lo wer!energ y !th a n !p a ra llel!s tr an ds.!!Correct:!The!hydrogen!bonds!are!between!residues!that!are!close!in!primary!sequence.!!Incorrec t!It !is!in !a !fu lly !e xt en ded !configuration.!!Incorrec t!Multiple!P r o !ca n !d is ru p t!f o rmation!o f!s h ee t s.!!Incorrec t!C onsecut ive !sid e !c h a in s!in !a !st ra n d !a re !lo ca te d !o n !o pposite!fa c es !o f!th e !s tra n d .!!5. The!pKa!of!an!ionizable!group!in!a!protein!is!6.1.!At!what!pH!will!that!group!be!99%!protonated?!!Correct:!pH!4.1!!Incorrec t!p H!8.1!!Incorrec t!p H!5.1!!Incorrec t!p H!7.1!!Incorrec t!p H!6.1!!!!!!6. In!a!poly p e p tid e ,!ro ta t io n s!a re !p e rmitted!ab o u t :!!Incorrec t!T h e !N FC(alpha)!bond!only.!!Incorrect!The!C(alpha)FC!bond!only.!!Correct:!The!C(alpha)KC!and!NKC(alpha)!bonds.!!Incorrec t!T h e !p e p tid e !b o n d . !!Incorrec t!T h e !p e p tid e !b o n d !a n d !t h e!C ( alp h a )FC!bond.!!7. Which!of!the!following!statements!about!Lys!is!not!true?!!Correct:!It!is!unlikely!to!be!present!in!amphipathic!αKhelices.!!Incorrec t!It s!s id e !ch a in !c an !form!ion !p air s!with!D!an d !E !a t!p H!6.5.!!Incorrec t!In !a !p e p tid e ,!it!a d o p t s!a !smaller!ran g e!o f !P h i!an d !P s i!a n gle s !th a n !G ly .!!Incorrec t!It !h a s!a !n e t!p o s itive !c h a rg e!a t!p H!9.0.!!Incorrec t!It s!side !chain!contains!an!am ine.!!8. In!a!3(10 )Fhelix,!the!hydrogen!bonds:!!Incorrec t!A r e !ro u g h ly!p e rpendicu la r!to !t h e!a x is!of!the!helix .!!Correct:!Form!between!the!carbonyl!oxygen!of!a!peptide!linkage!to!amino!acid!residue!n!and!the!amide !pro ton !of!the !pe ptid e!bond!in!amino!acid!n+3.!!Incorrec t!F o r m !b e tween!th e !amide!pro ton!of!a!pe p t id e!lin k a ge !t o !amino!acid !r es id u e !n !a n d !th e !carbonyl!oxygen!of!the!peptide!bond!in!amino!acid!n+3.!!Incorrec t!F o r m !b e tween!th e !ca rb o n y l!o x yg e n !o f!a !p eptide!linka g e!t o !amino!acid !r e sidue!n !a nd !the!amide!pro to n!of!th e!pe ptid e!bo nd !in!am in o!ac id!n+4 .!!Incorrec t!F o r m !b e tween!th e !amide!pro ton!of!a!pe p t id e!lin k a ge !t o !amino!acid !r es id u e !n !a n d !th e