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BIBC 110 dutnall midterm1

BIBC 110 dutnall midterm1 - 14:thth STUDENT ID Question...

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Unformatted text preview: 14%:thth STUDENT ID: --._.. Question 1. {2i} pts total) {a} Name till examples for each of the following types of amino acid. For each example write the full name of the amino acid and its one letter abbreviation {(1.5 points each): a: nun—polar. aliphatic amino acids {2 as}: a can we (a), Ufiuma (v), assume a.) ' Pee Luce (a) . H e Tate-mm. (a) iii] non-polar. aromatic amino acids [2 no}: Pas N'rt th’thNe (F), “T"tfiaema (‘1). “WE.“ FTDPH-QN (- N) {iii} polar. uncharged amino acids {2 pts}: ' etL‘i'CIME [a L EE-IE'lME (cl { THfEEoNIMe (:r] , {WE-Etna (a) CaLlaJ‘l'FIHwt [a] . . . . . asmcaoimetwj {th negatively charged amino acids at pH 'l'JJI {2 pta). Pr-EPRETRR: {cl , Guumme. ta L E) {v} positively;r charged amino acids at pH 7.0 {2 pts}: misuse (In) Blade-lime (:2) (also t: we , H) {h} For the 3111-1310 acids glycine and proline. describe one general stereochemical feature that is diffemnt from the other amino acids conunonly found in proteins {2 pts}. ,_ .. e . t Glycine: P‘QHtRAL (lP'r-l Praline: lHlM-fi Rub (Ugh #:15an {c ) N- R D (mmeEHpfifiz-fi M ) fl" fi'L. Hole Lithium To C lpi) Fem-i ‘1'? - Peering ‘35-ch; {c} Suppose you compare the amino acid sequence of two vet}.r similar. but not identical. proteins {for example. cytochrome c from human and cvmchtmne c hum tuna) and that you find the following fotn' exenrplcs where the amino acid found at a particular location in the sequence differs between the two proteins: I pl'ttaolr" l '1' win Em M Similar‘iI {YesorNo} Wh '3 {'J Cyste’ne Set-inc SEEM Shaft 1-5.. e. t I YE": (‘1th W .m 35-1.: iii} Alanine mania: Mo rim-Poles:- vs. Chen-deal (iii) Aspartate Glutamate ‘19s: Eul’k -tr-€_ (Acidit) CW (iv) Glutamate Lysine :3 "”5 fl “"3 *1}; Earn [Haemolf’ccee For each of the differences {i1 - {iv} above. indicate in the next column whether you consider the amino acid properties to be similar or not [yes or no] and hriefl}.r state the basis for your decision {2 pts each). PageZofB NAME: MM STUDENT 1]): Question 2 {20 pts total}. {a} Briefly describe {using pictures} the experiment performed by Antinsen in 1955 that demonstrated that the “information" required to specify the three»dinrensional structure and activity of a protein is contained within the amino acid sequence {5 pts}. dc not.er E W Mali” M . an sea. It _ Belaac: l‘iiptlfc urilifl'tJ-Ecl [moths-I m 9M5 Pfflhsn (“both-rituals) firs"r cacti :1: our l'LvFfi HRH—reel {b} What ty of non-covalent interaction plays a principle role in determining secondary stnrcture in proteins {helices an sheets] and base pairs in nucleic acids? (2 pts} “:3de bonci )a-bw' (c) In proteins, which parts of the polypeptide backbone are involved in the interactions described in (b)? [2 pta) Con-broil are-4f:- H}: :‘3 a. mi :13. a may: M - H (d) For a “Watson—Crickfltype of base pair found in DNA, what characteristic of the type interaction described in (b) determines that adenine {A} pairs with thymine [T] and that guanine [G] pairs with cytosine (C)? [3 pts] DtFELfim radish-:1 GI: H "bone; and For. king] or, dot-u}..— cello-t 0s£ * 3;: Far Ft". T (.th C1 is: right HUMW one! 94.3155 5} tit-mo! it OLEEE'i’Dhot s [e] What structural feature do helices found in proteins and helices found in nucleic acids have in connnon‘? [2 Fla) is calh tidal realest M Ma, s. (f) If a helix has 3 amino acid residues per turn and the horizontal rise per amino acid is 3.12 A. what is the pitch of this helix. (2 pts}? pack : 3e3ath = sees (3)11“ a fl-sheet in a protein is made up of B-sn-ands in which the sequence of amino acid side chains atternate between hydrophobic character and hydrophilic character Urydt‘ophobic-h drophilic-hydmphobic- hydrophilic...}, what will this mean for the general properties of the sheet. Explain why this is the case [4 pts). flthl-Pflhlts - firms, Page b} [l9]- fih-aa'lr r l‘xfrqnfphobic. alpha! [meat en's-Uh he Hédmpk'tli .. M 510L9— Lhcsins 5} fl rams cal Lermoiglj olni up o- chosen hjdalph'sloiu {shah-"e FHD‘F'L W PageBofE igdhprhvhc Win. [Gui- Nam: FH- MON‘F'i-twfir STUDENT ID: Question 3. {It} pta total] {a} Sketch a graph ta show the relationship between distance of separation and interactien energy for twe alums if the type of nen-ccralent interaction is effective user a short range, or effective ever ale-115 range (4 pts] \ 6e: ‘2‘; E lam?) Fete/‘31 filomrlc ("ea/1%! rL lion ener y for twe charged ions and use it te calculate the interaction ten separate h}; 3 nm in water [dielectric constant ~30). Eire year (ti pts}. {h} Define the equation that relates i energy between a Mg1+ ten and a 5 answer in KJmcIl" to 1 deci c _I ct; 5E = :1“;le “mid-1 xb-D‘l’liflfiflmel v. 1 a ,1 {Lac-late! CL 30 a Ealflfiqm = -—Z%rs-5'jma” _3 or —2+ 3“: 'thel-‘ %Mtalal:e 1-5.th haw. been -2 5.3 ”all “15,0 accep- 59=lfipb film leceleehlm matinee: bull? ....-x'2x-l~.gl-t.--v l‘u Cat-K Ember ... H.538“:t Umalri a: —i*15 elma” Page 4 cf 8 NAME: A. HDNIIH’r-tm} STUDENT ID: Question 4. [Ill pts total} (a) Sketch the typical interaction with water molecules observed when: {i} A hydtophilic molecule is dissolved in water {2 pts): . fl. Tar" " - i' “' 3a hffihm sin-flie- s, malt-cf mum-4M . "til-H 14 wwtr‘f} he: {mi-t ooh-U . -. Ed t:- CHEEDMGJ Molecule: I... (ii) A hydrophobic molecule is dissolved in water (2 pts) l. "' “- H _- o H H.‘ ,1“ Ca. DJ Load-er "anthem ,r- CI 0"“ O 3‘” H-W {'0 {od‘l oTEIJ bah fiat" . tJ Hal-T. “Ma/I fl) "alibi-E LEI-Ln- H (h) A graduate student is in a is]: late one night and is canying out a routine enzyme activity analysis that requires the presence of [1.1 M NaCl to maintain the ionic strength within the normal phlystologieal range. ' hu' l_'_‘ that no NaCl is available. and no one else is around, they decide to borrow a so ution of magnemum gClfl instead and so use this at ELI M in 'the assay. When they check the results of the may they find I t the protein has much less activity than expected. tilWhv?(3 tits) I“... ._ Sham Lieu = M Islam: t. .. ['qu :Qg‘f'l>flafill_ (J2— : 2.; H; ) Htfllur toot; swath 51‘ NfiC-ilf'S-dehom dimimemcj iflLOG-LfiéVHfi 9t ENE-EM £3 .Jih Sugififlt 3c:- mflvn‘fl‘b (ii) What concentration of magnesiutEsulfate should they have died? (3 pts] 0“”. /3 = O- 03?) M (of 33m”) E13 Malone—e [E 39cm. We] [”1333Mr Pagefioffl Nam; Ll. vanma STUDENT 1]): Question 5. (Ill pts total} {a} What atomic and structural properties determine if a molecule has a pennanent overall dipole? [2 pts} Sfimflmm (ELS- flmW‘EL) tidal eLLc‘l‘rofizfloLHo a% [[1] Sketch diagrams to illustrate thc following: {i} the overall dipole moment for a peptide bond and a water molecule. For each, indicate which end has partial negative and which has psartial positive charge. (4 pts} 5 - * .’ P o i l‘ I! I r; till.- I“ M (- liar 1' C " c. [.t f “EH. I. Mi" d, I 5' D l H s4 ’5‘ [ii] the overall dipole moment of a protein helix. Indicate the N-tenninal and lll'J-ten'ninal end of the helix and the direction of the dipole. What feature of the helix structure leads to this overall dipole? [4 pts) :3- C :1th'- 13¢!)th W S flnhn'rgi snail-4. Mass} height—st it? limits. 0.11 s all ht PD-thr —i.| N. *i-Htm at.“ E? —':a C -l-E.nM 8* M I'll: 1.5 {iii} a favorable interaction between a positively charged ion and a permanent dipole [2 pin) 5," 4- 69—4 {c} The graph below shows the interaction energy as a function of distance between two permanent dipoles arranged as so that their dipole moments are parallel and pointing in the same direction. Sketch on the graph the curve that would result if they were arranged in the antiparallel fashion shown (4 pts). Parallel Anti-parallel ”9 3 l ' ; Energy. E 0 distance. r % i 9 -"li'& {d} Is it possible to induce a dipole in a benzene ring by a positively charged ion or a permanent dipole as follows. State wafih—a'nT why [2 pts each). [1} [ii] 5‘ ~- <9 @ a \fieg indULflJ (kiwi... No - cun‘l' indoor} coin»? Foam-alas diacheem i2: MGM! a: hon-e bkuniike opposite is: airless; .r .L l1? 3? Wm on elm-oi f7. aha cf:- It“; 0m? labflfim Pagefiofli NAME: . Nos-‘- ‘fHDub STUDENT ID: Question 6. (21] pts total) (a) Define the isoelectric point (p1) of a molecule? (2 pts] F1! : Pp. at which ”if {Liar-3,1 : o {b} Draw a diagram to illustrate the typical relationship between net charge of a protein and pH. Indicate where the p1 of the protein is on your diagram. [4 pts] {c} The following table lists is different proteins {A through F) and describes their amine acid composition. cl pas at an amass it" “a “a ' M number of one letter abbreviation it“ it ( 1* mi) +t- ”F “'5? amino acids BREE-m THE lure ——--“.—El 5 i Si or E-mfllflll_ 5'? 23 '- 5* _IE_E.I§-IIIIIE_ i 3 its + 21 [_lsfl-Eunem s. it 55 — 3 _—---m_ l a t:- .- l3. _—--E-E-_ 5 i5 + to (if) Arrange the proteins in orderofmctessingespectedplvaiue. {5 pts} (=- rec-sir eel are +1 taut nor 4m) 8 «rt 1; a: D a. a a. F a. r; (ii) At pH '3 which proteints] would have a significant net positive charge? [3 pts] C F {iii} At pH 1 which proteinls} would have a significant not negative charge? (3 pts} 8 D E {iv} At pH 'i which proteints] would you expect might have limited solubility? How could you improve the solubilityr in such a situation? (3 pts] lil(+il<+t1-iib+e 5.... a: ma) lfitlrfioegg ionic malls, ho CA. (CS-Daria Page 1' offl ...
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