Exam2key - UC Berkeley Chem 130MCB 100A Fall 2006 Mid-term Exam Name UNIVERSITY OF CALIFORNIA BERKELEY CHEM C130/MCB CIOOA MIDTERM EXAMINATION#2

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Unformatted text preview: UC Berkeley. Chem 130MCB 100A. Fall 2006, Mid-term Exam. Name UNIVERSITY OF CALIFORNIA, BERKELEY CHEM C130/MCB CIOOA MIDTERM EXAMINATION #2. OCTOBER 19, 2006 INSTRUCTOR: John Kuriyan THE TIME LIMIT FOR THIS EXAMINATION IS 1 HOUR AND 20 MINUTES SIGNATURE: Please SIGN your name (In Indelible Ink) on the line above. YOUR NAME: Please PRINT your name {In lndelible ink) on the line above (& on the top right hand corner of every page). Also, please write all of your answers as leginy as possible. PLEASE CIRCLE THE NAME OF THE GSI FROM WHOM YOU WILL PICK UP YOUR GRADED MID-TERM EXAM: Natasha Keith Kyle Simonetta Jonas Lee James Fraser Allen Liu This exam consists of 5 questions, each worth 20 points total, as Indicated below, for a total of 100 points. This exam counts for 200 points out of the final score of 1100 for the course, and so your score on this exam will be multiplied by 2.0 when the final score is calculated. Page 1 of 16 UC Berkeley. Chem 130MCB 100A. Fall 2006. Mid-term Exam. Name QI.(2O points) (1 .A) (10 points) One mole of an ideal monatomic gas is initially at 300K. 10 atm pressure inside a cylinder with a frictionless piston. The gas expands until the pressure is 1 atm (101 J L“). Calculate the values of (i) AU (change in energy), (ii) q (heat transferred to the system), (iii) work done (lwi) and (iv) entropy change (A8) for each of the following processes. Show all the steps of your calculation, and specify the units of your answers. (1 .A.1) An isothermal and reversible expansion (4 points) AU : 0 fl .. [g /o -._..——-'— ——- ..—-- fl '4 1' 1/3 :1 2'5, X/gla/a : éjmat’" 7 iti: W 4 Asvg c 5‘8 :0 ONE/~1ij If 30?) 7'" Page 2 of 16 UC Berkeley. Chem 130MCB100A. Fall 2006. Mid-term Exam. Name Q1.(20 points) (1 .A) (10 points) One mole of an ideal monatomic gas is initially at 300K, 10 atm pressure inside a cylinder with a frictionless piston. The gas expands until the pressure is 1 atm,, (/01 3%.")- Calculate the values of (i) AU (change in energy), (ii) q (heat transferred to the system), (iii) work done (lwl), (iv) enthalpy change (AH) and (v) entropy change (A8) for each of the following processes. Show all the steps of your calculation, and specify the units of your answers. (1 .A.1) An isothermal and reversible expansion (4 points) ML W :0 AU:Og.glzImec" U |W|=S’-8’lz3mo{" (I’M AH: 22-43ka = 0 or? Lmal‘k P2, v: _ _ _, ~ 0 = b-S’éJ/ml V -.—. ,2 s 206W k : r1 Mr V, it/ 9 W ,_ .. V— nET; 2'5kJIW’fl f -"""""""'" L... _ y. P IOl AH ' fi' L = 3.5. L #935; A .3 in .. X h AH 40’ MEL —~i 0., Q4151— W' = 22% kiwi Va W“ ,_ ,, AV == 227~7SW Page 2 of 16 UC Berkeley. Chem 130MCB 100A. Fall 2006. Mid-term Exam. Name 01 A, continued. (1 .A.2) Isothermai expansion against a constant external pressure of 1 atm (3 points) AU=O r ____.... R - Anna M W = 2935' Lin/we ' I 19019511“: AV: 2.2'3 'Lmyg —t A$ Maw” L'- Warh=°l01h3 L" xZZ-i Lb mm Min (i) = 2125‘ firmfl = (1 .A.3) Expansion against zero external pressure in an adiabatic system (no heat transfer to surrounding). When the system pressure reaches 1 atm a stopcock stops the piston. (3 points) Page 3 of 16 UC Berkeley, Chem 130MCB 100A. Fall 2006. Mid-term Exam. Name 01. continued. (LB) 10 points total. A system consists of a large number of identical molecules at equilibrium. Each molecule can be in one of a ladder of energy levels. As shown in the diagram below, the energy levels are uniformly spaced, and the difference in energy between adjacent energy levels is 1 kBT. Shown below are two instantaneous “snapshots” of the energies of three of the molecules, which are labeled 1. 2 and 3. (1.8.1) (5 points) Assuming that the molecules are independent and the systems are at equilibrium (i.e., the Boltzmann distribition is valid), what is the relative probability of seeing molecule 1 in the 0 level and molecule 3 in the 3 kBT energy level. as shown in A? .750 -3 @w ’6 47' :8 afl-OWS” Page 4 of I6 UC Berkeley. Chem 13DMCB 100A. Fall 2006. Mid-term Exam. Name Question 1, continued. (1.3.2) (5 points) Assuming again that the molecules are independent and at equilibrium, what is the relative probability of seeing molecules 1, 2 and 3 simultaneously in the energy levels shown in A, versus the probability of seeing them simultaneously in the energy levets shown in B? That is, calculate: probability of situation A _ . _ _ . Show all the steps of your calculation. probability of Situation B Page 5 of16 UC Berkeley. Chem 130210163 100A. Fall 2006. Mid-ten'n Exam. Name 02. (20 points) The potential energy of a hydrogen bond between an oxygen (acceptor) and a nitrogen (donor) depends on the distance, r. between the oxygen and nitrogen in the following way: v<~=elléi°-l%l‘l where s and o are parameters that are characteristic of the particular kind of hydrogen bond. 5 (2A) (4’ points) Sketch the approximate shape of U(r) as a function of r. Write down numbers near the grid points on the two axes of the graph so as to indicate a rough scale for U(r) and r. Specify the units for the axes. Indicate the value of the energy as r—> no, r —) O. Show roughly what happens when the ener is minimal. (2.8) (11 points) On the same diagram. indicate the rough shape of the curve describing the force on one of the atoms as a function of the interatomic distance. r. Show the approximate behavior of the force as r-—> oo.r ‘90. Show what happens to the force when the energy is minimal. Page 6 of 16 UC Berkeley. Chem 130M03100A. Fall 2006. Mid-term Exam. Name 02, continued. (2.0) (2 points) If the units of s and r are kJ mol" and A, respectively, what is the unit of o? O __ I W (2.0) points total) You re told that only of the following three values of o is correct: 25, 2.5 and 0.25 (using units compatible with energy in kJ mol‘1 and distance in A). (2.D.1)Without knowing anything about the value of aexplain clearly how you can decide which one of these is a physically reasonable value for 6, given what you know about the lengths and strengths of hydrogen bonds. Clearly explain the mathematical steps you would take to get the answer. (gpoints) MM l/W 94/? WYWW rm :5‘0 minimal/M; fig = 5Eé(,éfia _U {.4 a0) .. da ,7 _ 5- :? —érrb/Lo +4vgfio :0 7. 2v 44 % + 4 ‘ 0 _ ()— ZZZ-4 :2) 0—3/70X0'glé 77,0 3 (2.0.2) Based on your reasoning in part 2.0.1. which of the three values is the reasonable value for o? ggoints) m W145 9W0? We; 2’5” Page '7 of16 UC Berkeley. Chem 130MB 100A, Fall 2006. Mid-term Exam. Name 03. (20 points) bowel (3.A) (5 points) Shown below are the energy levels for two different kinds of molecules, A and B: /\ Energy — Energy Molecule A Molecule B Which molecule has higher heat capacity, A or B? Explain your answer. Page 8 of 15 UC Berkeley. Chem 130MB 100A. Fall 2006. Mid-term Exam. Name 03, continued. (3.3) 15 points total. Shown below is the Block Substitution Matrix (BLOSUM): HIE! x Inflammummmlmmmmmmmm -BEIEIEIEEEIEIEIEL .EEIIJII undulalmlnclmlmammammmlmnsl Iflflflflflflfllflflflfilfilflfl 1 -umummmmmmmnmal BE] . aria! mm HIE] nu:- Elm mm mm - :15! E 2 -Il Consrder the foilowrng alignment of 6 resrdue segments of sequences from three proteins: (Protein A) nggn 6 (Protein 3) WVFy§§>SDuA (Protein C) NCGLEK> SD 4 (3.3.1) What is the sequence identity (% identity) between proteins A a B, and between proteins B & C? (2 points). 7345.970 Bra 13732 (3.3.2) Is the evolutionary distance between proteins A & 3 the same or different when compared to the evolutionary distance between proteins 3 & C? Explain how you would use the BLOSUM matrix to work out the answer. (5 points) A-i’»: 1+ +('2>+4+2 @394” EMF» I 4 +2:2i 0%5WW‘ SW Jfifi g1 3‘ “if +0!) + (-3)” +5'"+5 (Mews; A '8 is m«..s~-m. 054%. M 8,0 Page9of15 UC Berkeley. Chem 130MB 100A. Fall 2006. Mid-term Exam. Name Question 3, continued. (3.3.3) Calculate the probability or likelihood that proteins A and B are rotated evolutionarily relative to the probability that proteins B and C are related. That is, calcu|ate: WW likelihood that B and C are related . 1 we) _ 3’22"" IS“ I 2/7; mg .._—-—-—-—-' h- ___._._ :7. KO?) 2} 71% Z( 2' l'O’S' 7-5" = 3-7 ‘ Z = “t7 2 (3.3.4) What is the likelihood that A and B are related versus the likelihood of A being related to a random sequence? (2 points) We via/[w 7/4172 fur-w fl}; L'Aaé'Aaai. 2} , r /a )0 S A .::.:2_ :2- 3’44? M Page 10 of 15 UC Berkeley. Chem lac/MOB 100A. Fall 2006‘ Mid-term Exam. Name 04. (4.A) (6 points) Consider the following schematic diagram of a frictionless movable piston that separates two chambers. The chamber on the left contains two molecules, indicated by black dots, and the chamber on the right contains one molecule. N :— L M 3 g N 2 I We ID IDIIIIIDII Is the piston in the most liker position as shown? Explain how you check whether it is or not, showing all the steps at your answer. am:- Weir-i; M is WLE‘FF 3 ‘ Lm 510 '= 2.’ (0’ 2x7% 3?- : f; 4 .— -l/Umr_n_IL‘-' my its l fr a”, More barrel/t. 0m 1 +9 5/1 .. 2| .. )k ____ r h we” r. ‘7! 7 e Z 3 2' 5", Z 5 I" z S- :- wflié‘yr '* 3..." 5- l 4/ l f l, . ‘1 WW barrtEV We”: 1 F” 0% mad» . .. 0i! 10MB 21:236gwmmbz Mw'ifi 1 la ewe " "' 3; Z. G r. a ‘ "S. _____ WLWT -' ___.'—— pfillofm WLLHW UC Berkeley. Chem 130MCB 100A, Fall 2006. Mid-tenn Exam. Name (4.3) 14 points total. A system is divided into two chambers by a movable system, as shown in the diagram below. Initially the two chambers have the same volume, but the chamber on the left has twice as many atoms as the chamber on the right. A B P4l=‘|tt1l:ls N=tx1D’ M=1£XIO’° Maosltto’“ (48.1) (8 points) What is the total change in entropy upon going from the situation shown on the left (A) to the situation shown on the right (B)? N and M 2.. :r— ______...u 7 A" f. -— M R (M) NA.» "fi’" 5. I MS ’9 x1072x5/9‘ — NZ) * W *0”?! 7; :: ____... Q __g_~.__o_,- I NA 32 5w J'K 'mafdkmgxa'l‘,‘ Mime”; TWarAf’L/li‘ out 405 7' mloflmdeh' Mm Page 12 0f16 UC Berkeley, Chem 130MCB 100A. Fall 2006. Mid-term Exam. Name 043, continued. .. )5 -i As: Mwa ‘3” £8 Mos-x 049 (43.2) (6 points) What is the relative probability of seeing the situation on the right (B) compared to the situation on the left (A)? That is. calculate the value of W. Show how you work out the probability of (A) answer. Page 13 of 16 UC Berkeley, Chem 130MCB 100A. F3112006. Mid-term Exam. Name 05. (20 points) Multiple choice and True/False questions. Circle the correct option (or TRUE or FALSE). +2 points for each correct answer, -2 points for each wrong answer. To get the maximum score you do not need to answer all the questions, so be careful not to answer questions incorrectly. Maximum points: 20. Minimum points: 0. (5. ' - l.‘ . - o- o r in which all the variables are extensive variables . entropy, energy, volume, tepera ure (0) force, energy, pressure, entropy (d) enthalpy, mass, molar heat capacity, density system always increases in a spontaneous process. TRUE I N541: Zi— r'g fix 722m. [St/F rSUrek) wflcfi ' I " flair/W. (5.3) A piston containing chloroform gas expands from 10 atm pressure to 1 atm pressure in an isothermal process. Define the system to be the contents of the piston. The energy of the system stays constant during this process. TRUE’ 7%.) )5 24%: fi/Wgwx {WW/n a": mm A; ‘ Mt I‘M. (5.4) Only one of the to owing st tements about potential energy is true. Which one is it? (a) The potential energy of an ideal gas molecule is equal to its kinetic energy (D P tein foldin is driven b a decrease in potential ener c) The potential energy of an atom is the work done in moving the atom from infinity to its resent sition (d) Potential energy is always conserved (e) The potential energy is an intensive function (5.2) According to the second law of thermodynamics, the entr! of an isolated (5.5) A molecule has two conformations that are separated in energy by 25 kJ moi“. What are the ratios of their populations at 300 K? (a) 1: 0.000005 __. Z S» (b)1:0.1 /_ FJO 2'5 a 95 00005 (d) 1: 0.0001 '6 g 0 (e) 1: 0.0005 Page 14 of 16 UC Berkeley, Chem 130MCB 100A, Fall 2006. Mid-tam": Exam. Name (5.6) A protein molecule is negatively charged, but it binds to a negatively charged small molecule much faster than it binds to a positively charged small molecule. The most reasonable explanation for this phenomenon is: (a) the protein molecuie attracts substrates by hydrogen bonds, and it happens to form stronger hydrogen bonds with the negatively charged molecule (b) the negatively charged molecule has more hydrophobic groups (c) the shape of the active site is more complementary to that of the negativeiy charged—mmufi-yVR‘ (d) even though the protein is negatively charged overall, electrostatic focusing effects provide a pathway for negatively charged molecules to enter the active site (e) the presence of water molecules screens the effects of charges, making electrostatic effects irrelevant (5.7) Tryptophan, histidine and cysteine are the most highly conserved residues in proteins, while leucine is not TFiUE I FALSE (5.8) Even though the globin told is very hih conserved. only one or two residues are invariant across evolution! FALSE (5.9) In the BLOSUM substitution matrix the score is related to the probability of one amino acid being substituted by another. In the SD~1 D profile method, the score is given by: (a) the rms deviation between equivalent Cot atoms in homologous structures (b) the probability of substitution of one amino acid by the amino acid at the corres ndin sitiggflrelatedstwucjgggfi (c) the probability of finding an amino acid In onmental class corresponding to a position in a threeidimensional structure J e urie su ace areao the amino acid inathree—dimensional structure (e) the energy of the amino acid at a particular position in a three-dimensional structure Page 15 of 16 UC Berkeley, Chem 130MCB 100A. Fall 2006. Mid-term Exam. Name (5.10) Consider a piston containing a solution of protein molecules (the system). The quantity (absolute magnitude) of work done by the system is denoted le, the quantity of heat transferred is denoted lql and the change in energy of the system is given by AU. During an isothermal process the system expands against a constant pressure while a quantity of heat lql is transferred into the system. Which of the following statements is consistent with the first law of thermodynamics? (a) lql = AU - lwl (b ||=-lwl b (d) lql = 0 (e) |w| = -AU (5i The units of entropy are: (D) J K (c) J mol‘1 (d) kJ mol‘1 (5.12) Which of the following is a statement of Stirling's approximation? (a) lnN!=lnN—N (b) lnN!—I=NlnN-N (c) lan=NlnN+N /? W: / 3 lit/"fin N f” A” (dWJIJJLEEV—l M ‘ é) inN:=IHN_l\ N (5.13) According to the thermodynamic definition of the entropy. the change in ennpr for a process decreases as the temperature increases. @UJ‘IFALSE 418 z 2- 7.. (5.14) The enthalpy change for a process is equal to the heat transferred to the system under which of the following conditions: (a) constant volume (b) ccnstantjem re (0) constant pressure reversible expansion (5.15) Energy is a good indicator of the direction of spontaneous change for macroscopic objects but not for molecular processe TRUE / FALSE -END OF EXAM- Page 16 of 16 ...
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This note was uploaded on 01/12/2010 for the course MCB 100A taught by Professor Kuryian during the Fall '09 term at University of California, Berkeley.

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Exam2key - UC Berkeley Chem 130MCB 100A Fall 2006 Mid-term Exam Name UNIVERSITY OF CALIFORNIA BERKELEY CHEM C130/MCB CIOOA MIDTERM EXAMINATION#2

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