practice final key

practice final key - Name: 6 \ Last First Student ID:...

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Unformatted text preview: Name: 6 \ Last First Student ID: Please put your name on every page. BIS 102, Fall 2009 Practice Final Exam Professor Toney Name: Last First Short Answers oints as indicated‘ 100 ts total I V (6 pts) For each of the following, write the one letter code oftlie single common amino fltlwt best fits the description. Has no side chain. gal t i .( Has a total 01 two nitrogen atoms and four carbon atoms. Cl‘M Q The side chain readily react with iodoaeetate and iodoacetamide. , i The smallest amino acid that has an alcohol group. Z _ The amino acid with the side chain attached to the ot—amino group ML Side chain does not ionize, and includes an atom other than C, H. O, or N. 2. (5 pts) The hydrolysis on—phosphoglycerate (2-PG) to form glycerie acid and phosphate has a free energy change (AG°’) ofvlo kJ/mol. What is the Ku ’ for this reaction? ( fir AG“: Jo's??? , (7’ =é’fi69/ £5 5‘ éé/O 3t ( lo pts) You accidentally mixed up two samples of the enzyme dihydrofolate reductase (DI IFR). One sample had trimethopriin, an inhibitor of dihydrofolatc reduetase (DHFR). The other sample had no inhibitor, You label the tubes “A” and “B”. Protein quatitation shows that the two tubes contain equal amounts Qf'the DUFR protein. You proceed to perform enzyme assays on the DHl-‘R activities in the two tubes. The results for sample A are plotted below, and the results for sample B are given in the table. Use this information to answer the questions below iiwr U 7 [\J __l_ 70.2 ‘30 i", 2 Q4 0.8 [7'8 1.0 1/[3] (1/HM) 00‘! / Viv Name: a Last First Data for Sample B: ISIULM) V6 lw (uM/ min) 1 3 3 (a 3 I .. . 2 05 so 0.? 5 0.2 7.1 0,;1} It) 0~| 8.3 a, a 20 0‘95 9.1 0'” LI) Plot the data for sample B on the graph shown above. h) Whieli sample does not contain triinethoprim‘? 521m 5 e) What are the Km and me for DHFR in the assay that does not contain triinethoprim‘? include units for both values. (MM i/m: WWW ti) You determine that the concentration ol‘trimethoprini in the inhibited samples is l n M. What is the K, for methotrexate (include units)? / 7e fl KmobsSK/Mfl+ (1%“ WM-l’l :6?) {4: e) Which ol‘ the following mechanisms would best i1 ustrnte the interaction 01' methotrexute (l) with DH FR (E)? (circle one) A. Else; Es<—-E Eip B. FmSSl—ZSSFwP l l i [£81 1351 <——__)_ El ~P L (—- ns-(— ~+ -; L S _>E+~ _>E P +s<—) h3<—,L P + Lu Name: Last 4, (9 pts‘) Answer the following questions for the peptide ri’ shown below, O O O O 0 ll H H H ll i. H H II HN ~CH C A—Ll'irl C N TH C \l TH C N TH C OH CH1 TH; Cl l3 CH2 Cl I2 SH CH2 / ‘_ N \ |l L \ l NH TH OH (‘3:NH NH; it) Write the name ofthis peptide using one letter amino acid abbreviations, h) What would the charge on this peptide be at pH 1 e) What would the charge he at pH 0'? 3+ 4:» 5. t l2 pts‘) Answer the following questions for the phospholipid drawn below. ,flwe/x/wofi O O \ev/\ \\ if 0\ /\\\‘ lo\ //0 \ /,NH2 /p\\O/ \J HO First a) What is the name Ol'the 3—Carb0n molecule that forms the backbone of the lipid? G ljé‘élv l b) What are the names Gillie fatty acids in this lipid? Palm‘tfi C a (Cit; l lamic 0cm? (CH) e) What is the general name 01' this phopholipid (not considering the names of the fatty aeidsl‘? e) What is the net charge ofthis lipid at twiztralpH? 26-11 0 Pill l’e‘i'hfl'l’l/ljjt‘l'hfiwo i V\ Q. ink CQF kit/l t A) 4 Name: (>. ((7 pls) What volumes 0f0.l M acetic acid (pKa : 4.8) and ().l M sodium acetate must be used to make 1 L of().l M acetate buffer pH 5.1? Show all calculations, Ach-i :—“ Prob“ + H’r '5/0,lr14§9 {WWSV 2‘ X .’ ‘__; x3006 :Atow V [MW] q “66 5" " 4% + V K x f with; MOM: 0.0333 < 0.1—1 , e r K , ‘ 0 J' 1935.7"! ~ float. of mu mm; ’ 1’1" =’ Y jaw - f‘= , ‘ l ‘g 07:; Did m L «y 0 IM AToH 7. ( 12 pts) Answer the following questions on the schematic structure of an integral membrane protein shown below. a) What secondary stnlcture is likely to be found in the membrane-spanning regions? 0(7 '\ f b) Would lysine or phenylalanine be more likely to be found in the loops protruding out of the membrane? Ljiziwb e) Would asparagine or isoleucinc be more likely to he found within the membrane? :éolQMCme/ Name: Last First 8. (8 pts‘) An enzyme catalyzes a reaction zit (ID initial velocity oli20 uM/n 'n when the concentration ofthe substrate is 0.05 VI. The KM for this substrate is 1th M. What will the initial velocity with the following concentrations ofsubstrates‘? Show all calculations a) 1>: 104M? b] l 110'” M‘? [S] =' 0‘05M is 60»: KM ; Z'C’r‘M/w'w‘ WW ‘\ \ffi» : \JNA-«y ; Z‘AJ tM/w", : {MM/F KM ~i ['3] ioowi loop/t L) V; if ,M/MLMYJDFMEW : iiAMAiin [COMM “i iDOjA/M ‘), (8 pts) Use the following information to answer the questions below. Show all culoulntions. Phosphocreatine H creatinejwfl —9 G“ = -43.0 kJ/mol ATP H + i A“ W-..) Keq =10 M at pH=7 " ) .wm‘.‘ 21 i What is the observed Gibbs free energy change for the following reaction at pH:7 und 1 mM ofzill three species? ,‘ k 47 «g \‘ ATP H ADP+Pi ’lgémm T~ Mfr/31x l [551,1 Ag" ,.. if? (“My : 4211},ka (TM a? .i /O,U(')i M i A; 1w b) What is the equilibrium constant for phosphocrcatinc hydrolysis at pl [:7'.’ , U ’ w v “ . (n ’ “ ifi—lt/XJ’M lanai? u/ L Kg 3 “(Ag/i113. at C’ (i Name: a l/ Last First 10. ( I 8 pts) Serine Protease Mechanism :1) Draw the chemical structure of tlyatalytic triad of the serine proteases. ’ 4/ r , ks . tum. _ , ’ N ‘1?“ ‘1' \ /§< . H ,. X, 2’ 0’9 AS} Wt is? l—lns h) Draw the mechanism ofthis class of enzymes starting with the ES (:0/17/7/ex [mt/going I/zmug/zjmvmirimz offlw (mill—enzyme inrcmwdiate only. You need only show only the nmide bond of the substrate. with “R” groups for the rest of it. Show the “oxyanion hole“, Show any and all transition states. Label all complexes clearly. Include curved arrows to indicate electron flowi Indicate the mechanism for catalysis used in each step. s-%,: :1 , :w ,r . \\_,,_._,/O M’ \snla it; 3')“ ) a ll Riflm’ ms \ My ll“; , , /, < / / 7 "it"; .4' . 1Q L; , Name: Last First Multi le Choice 4 ts each“ 100 ts total 1. Fatty acids are all EXCEP f: either saturated or unsaturated commonly found 111 free form in the cell. c. mostly found with an even number of carbons. d. found in linear. branched and cyclic fonns. e. all are [1110. 3 2 Alkali hydrolysis oftriacylglycerols is called and yields and n. triacylation: fatty acids; glycerol b. saponification; tatty alcohols; fatty acids c. triesteration; salts of fatty acids, fatty alcohols @ saponilication; salts of fatty acids; glycerol e none are true 3.. Llpids are the biomoleculcs of choice for storage of metabolic energy because they: a. are soluble in water. @ yield a large amount ofencrgy upon oxidation. are highly oxidized. d. are easily hydrolyzed. c. are amphipathic. 4. lylembranes with unsaturated fatty acids in their components are more flexible and lluid because: Unsaturated fatty acids pack closely together to form ordered airays. '1. Q Unsaturated fatty acids bend at the double bond preventing close packing. Saturated fatty acids have a "kink" that produces more fluid aggregates. d. Unsaturated fatty acids have (is double bonds that prevent formation of the "kink." e. All ot'the above are correct. 3. Lipids that spontaneously form micelles. monolayers and bilayers have what property“? a. waxy polar amphipathic bipolar e. polyisoprenoid Name: o. Liposomes are all EXCEPT: a. used to introduce contrast agents into the body for diagnostic imaging procedures. b. able to fuse with cells. c. highly stable structures. d possible to prepare with different inside and outside solutions. @ all are true. Integral membrane proteins (intrinsic proteins) do NOT: 2 have hydrophobic surfaces as well as hydrophilic surfaces. dissociate from the membrane by treatment with salt solutions. e. get exposed to one or both aqueous surfaces ofthe membrane. d. insert into the membrane. e. have significant lateral mobility 8, W11» we say that biological membranes are asymmetric structures we mean that: The lipids are not evenly distributed transversely in the membrane. . The proteins are not evenly distributed over the surface ofthe membrane. c. Patches ofeholesterol and other lipids occur on the surface of the membrane. d, (Terrain membrane proteins seem to prefer association with specific lipids. c. All are true ‘), lin7ynies have active sites that have the greatest complementarity to the: a. substrate. @ transition state. . product. d both substrate and product. e. none oftlie above. it). All are catalytic mechanisms or factors that contribute to the performance of e izymes EXCEPT: entropy gain in ES formation. covalent catalysis. c, general acid or base catalysis. d. proximity and orientation. c. all are true, I l. 1\ucleophilic centers for covalent catalysis include all ofthe following amino acid side—chains in proteins EXCEPT: methyl. 1, amines. e. carboxylate. d aryl and alkyl hydroxyls. e. lhiols. () Name: Last First l 2. The catalytic mechanism below is an example of: Mechanism (W H' D , t i (*3 Fat ll rage o _ no2 > mar ro \/ \ my > war: 0' 4 a' ..,\V t ._ \::/ I: (I‘ll an \” \,// a. covalent nucleophilic catalys' '. b. covalent electrophilic catalysis. c. specific base catalysis. @ )cneral base catalysis. ow barrier hydrogen bond catalysis. l3. The catalytic triad common to many serine proteases involves shuttling of protons between (sequence in the catalytic triad): scr-his-asp his-ser-asp c. scr—his—his d. ser—asp-his cys-his-ser F! r: l4. The initial bond formation in the covalent intermediate in the chyniotrypsin catalyzed reaction is between: a serine and the carbonyl carbon in the peptide backbone. ) serine and the nitrogen in the peptide backbone. c. histidine and the carbonyl carbon in the peptide backbone. ll. histidine and the nitrogen in the peptide backbone. c. aspartatc and the carbonyl carbon in the peptide backbone. l 5. The mechanism ofaspartate protease catalysis is proposed to be: a. covalent nucleophilic catalysis. b. covalent electrophilic catalySIs. c. specific base catalysis. 9 general base—general acid catalysis all ofthe above. 16. Recent data provide unequivocal evidence for the mechanism ofhen egg white lysozyme involving: @ covalent nucleophilic catalysis. . covalent electrophilic catalysis. c. specific base catalysis. d. general base—general acid catalysis. e. all ofthc above. Name: ‘ Last First [7, The tree energy ofactivation, AG. is defined as: a. The average free energy ofthe product formed. h The rate of a chemical reaction in relationship to the concentration ol’ reactant molecules. Q The energy required to raise the average energy of one mole ol‘ reactant to the transition state energy. ti. The amount ol‘energy released by a spontaneous reaction. c. The lowest point on a free energy diagram. 1 8. For the following irreversible reaction, the relationship between activation lree energy and the rate constant of the reaction can be found by using which ot’the to] lowing equations? A -—> P a. —d[A]dt = k b, Km 2 (K4 + Kg)/K| e. V ’ V.HH\[A]/Km V ti. K[A][P] = V @ k ’ lmT/h e'wi RT l t). All of the following statements about noncompetitive inhibition are true EXCEPT: :1. inhibitor interacts with the enzyme as well as the enzyme-substrate complex. @ Increasing the concentration of [S] can overcome the inhibition. c. The V"m value does not remain the same as that for an uninhibited reaction. d. The inhibitor can cause a conibrmalional change in the enzyme. e. The inhibitor binds to a different site than does the substrate. 20. Hydrogen bonds in ice are all EXCEPT: a. directional. 3 straight. a weak. L. responsible tor the lower density ol‘ice over liquid water. c. holding water molecules in ice apart. I l . Which ot‘the following pairs would he the best buffer at pH 10.0? a. Acetic acid and sodium acetate (pKU = 4.76) [13(703 and NaIlCOx (pK;»s are 3.77 and 10.4) c. Lactic acid and sodium lactate (pKa ‘7 3.86) d. N11H3PO4 and NagHPOa (pKUs are 2.1, 7.2, 12.4) Sodium succinate and succinic acid (13K;1 = 4.21) G l 4 'Jt Name: Last All ol’the statements about the classification ofthese aniin acids are corrcct LIX ‘ Ll’T: Aspartic acid and asparagine are acidic amino acids. Alanine and valine are neutral, nonpolar amino acids. c. Serine and glutannne are polar. uncharged amino acids. d. Lysine and arginine are basic amino acids. e. Tyrosine and phenylalanine are aromatic amino acids, All otthc information necessary for a protein to achieve its intricate architecture is contained Within its 7 structure 6‘ priinary ). secondary c. tertiary d . q u atern ary c. all are true Amino acid side chains capable of forming hydrogen bonds are usually located on the protein 7 and form hydrogen bonds primarily with the surface. water solvent , interiort water solvent c. surface, other amino acid side chains d, interior. other amino acid side chains c. all are true 77, between tightly packed amino acid side chains in the interior ofthe protein are a major ('rmlrllmfimz to protein structure. a. llydrogen bonds b, Electrostatic interactions ' Covalent ester bonds @ Van der Waals interactions L. All are true ...
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This note was uploaded on 01/10/2011 for the course BIS 102 taught by Professor Hilt during the Fall '08 term at UC Davis.

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practice final key - Name: 6 \ Last First Student ID:...

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