7.014 Quiz I Handout

Transcription

1 7.014 Quiz I andout Quiz I announcements: Quiz I: Friday, February 27 12:05 12:55 Walker Gym, rd floor (room 5040) **This will be a closed book exam** Quiz Review Session: Wednesday, February 25 7:00 9:00 pm room pen Tutoring Session: Thursday, February 26 4:00 6:00 pm room 66156

2 Question 1 Shown below are the structures of three amino acids; they are shown in alphabetical order. 2 2 Phenylalanine Threonine (Phe) (Thr) a) ircle the side chain group on each amino acid. Tyrosine (Tyr) b) Using the blanks below, rank these three in order of the hydrophobicity of their side chains. i) Most ydrophobic ii) Intermediate iii) Least ydrophobic c) Explain why (i) is more hydrophobic than (ii). d) Explain why (ii) is more hydrophobic than (iii). Question 2 From the diagram below, P P 2 2 Lys 2 2 Tyr Arg Asp Glu a) ircle the strongest interaction that exists between: i) the side chain of Lys and the phosphate group of GDP van der Waals covalent hydrogen bond ionic 2

3 Question 2, continued ii) the side chain of Glu and the ribose group of GDP van der Waals covalent hydrogen bond ionic iii) the side chain of Tyr and the guanine base of GDP van der Waals covalent hydrogen bond ionic b) You make mutations in the GDPbinding pocket of the G protein and examine their effects on the binding of GDP. onsider the size and the nature (e.g. charge, polarity, hydrophilicity, hydrophobicity) of the amino acid side chains and give the most likely reason why each mutation has the stated effect. onsider each mutation independently. i) Arg is mutated to a Lys, resulting in a G protein that still binds GDP. ii) Asp is mutated to a Tyr, resulting in a G protein that cannot bind GDP. Question Short answer. Some possibly useful equations can be found at the end of this exam. a) onsider the following reaction: (1) A B G = 1 kcal/mol o i) What is the G for this reaction when [A] = [B] = [] = 10 mm and T = 25 º? Show your work. ii) Suppose you add an enzyme that catalyzes reaction (1). Make each of the following statements true by circling the appropriate underlined phrase. (4 circles total) becomes more runs faster. The forward reaction stays just as thermodynamically spontaneous and proceeds at the same rate. becomes less runs slower. becomes more runs faster. The reverse reaction stays just as thermodynamically spontaneous and proceeds at the same rate. becomes less runs slower.

4 Question, continued b) onsider the reaction: (2) X Y K 2 = [Y] at equilibrium [X] Given the following: () ATP ADP P i (4) X ATP Y ADP P i G = 7.5 kcal/mol at 25 o o i) What is the K eq for the coupled reaction (4) in terms of the K eq of reaction (2), at 25? Show your work. ii) Provide a plausible mechanism by which the cell could couple the energy from reaction () to drive reaction (2). You need not go into chemical detail; just describe the process clearly. Question 4 Part 1. True or False. If false, explain why. a) Most of the ATP produced from the aerobic metabolism of glucose results from glycolysis. b) In yeast cells under anaerobic conditions (no oxygen), the rate of glucose consumption is less than that under aerobic conditions. c) Glycolysis (glucose >2 pyruvate) occurs under aerobic and anaerobic conditions. d) Under anaerobic conditions (no oxygen), the citric acid cycle degrades acetyl coenzyme A to 2 and 2, producing AD and FAD 2. e) Electron transport produces ATP directly from the transfer of electrons from AD to 2. f) In eukaryotic cells, glycolysis occurs in the cytosol, whereas the reaction of the citric acid cycle and oxidative phosphorylation take place only in the mitochondria. g) During fermentation, pyruvate is converted to ethanol and 2 to use up excess oxygen. h) During glycolysis and respiration, glucose reacts directly with 2 to form 2 and 2. 4

5 Question 4, continued Part 2. Short Answer a) Pyruvate is a very versatile molecule. Give three pathways for pyruvate. For each pathway list the end product and whether AD or AD is formed. PATWAY ED PRDUTS AD or AD ADDITIAL ATPs GEERATED b) Explain briefly how is ATP formed during photosynthesis. c) Explain briefly, what carbon fixation is and what process in plants leads to carbon fixation. Part 2. Short Answer, continued d) When exposed to light, plant cells show net absorption of 2 and net production of 2. In the dark, they show net production of 2 and net absorption of 2. i) What biochemical process is responsible for the plant's absorption of 2 and production of 2 in the dark? Explain briefly. ii) Does this process continue when the plant is exposed to light? If so, why aren't net production of 2 and absorption of 2 seen under these conditions? Explain briefly. 5

6 Shown below is the portion of the diagram from page 8 which shows the electron transport pathway. In this pathway, electrons are transferred from AD to 2 ; the energy of this reaction is coupled to pumping of. AD (FAD 2 ) AD (FAD) 2 e drug X 2 e electron transport proton pumping (in space A) (in space B) 2 e drug Y Two drugs, drug X and drug Y, can pick up electrons from particular intermediates in this pathway. This is shown above. 2 e 2 e) You treat cells carrying out respiration with a saturating dose of drug X, so that all the electrons which would normally continue along the pathway are captured by drug X. Under these conditions: Will the cells continue to consume 2? Will the cells continue to produce 2? Will the rate of ATP synthesis increase or decrease or stay the same? Explain your reasoning. 2 f) You treat cells carrying out respiration with a saturating dose of drug Y, so that all the electrons which would normally continue along the pathway are captured by drug Y. Under these conditions: Will the cells continue to consume 2? Will the cells continue to produce 2? Will the rate of ATP synthesis increase or decrease or stay the same? Explain your reasoning. 6

7 STRUTURES F AMI AIDS ALAIE (ala) ARGIIE (arg) ASPARAGIE (as) 2 ASPARTI AID (asp) 2 S YSTEIE (cys) 2 2 GLUTAMI AID (glu) 2 2 GLUTAMIE (gl) 2 GLYIE (gly) 2 ISTIDIE (his) 2 ISLEUIE (ile) 2 LEUIE (leu) LYSIE (lys) 2 2 S METIIE (met) TREIE (thr) 2 2 PEYLALAIE (phe) TRYPTPA (trp) PRLIE (pro) TYRSIE (tyr) 2 SERIE (ser) VALIE (val) 7

8 Thermodynamics: For the reaction: A B K eq D with G o as its standard free energy at equilibrium: G o = _ RT ln [][D] [A][B] where: if T = 25 º then RT = 0.59 kcal mol if T = 7 º then RT = 0.61 kcal mol under any conditions: G = G o RT ln [][D] [A][B] Solutions to Practice Quiz I Question 1 a) 2 (Phe) (Thr) 2 (Tyr) b) i) most hydrophobic: phenylalanine ii) intermediate tyrosine iii) least hydrophobic threonine c) Phe is more hydrophobic than tyr because tyr has a hydrophilic group that phe lacks ( can form bonds). d) Tyr is more hydrophobic than thr because, although both have s, tyr has more nonpolar s than thr. 8

9 Question 2 a) i) van der Waals covalent hydrogen bond ionic ii) van der Waals covalent hydrogen bond ionic iii) van der Waals covalent hydrogen bond ionic b) i) Arg and Lys are both positively charged, thus the ionic interaction with the phosphate group is preserved. The side chains of both amino acids are also of similar size. Question ii) Tyr is much larger than Asp. Although Tyr can form a hydrogen bond, GDP will no longer fit into the binding pocket. The Tyr side chain is also much more hydrophobic than the Asp side chain. a) i) (remember that 10mM = 0.01M) G = G 0 RTln [] [A][ B] becomes : G = 1 (0.59) ln 0.01 (0.01)(0.01) = 1 (0.59) ln(100) = 1.71 kcal mol ii) Both the forward & reverse reactions stay just as thermodynamically spontaneous and both run faster. b) i) K 4 = [Y][ ADP][ P i ] [ X][ ATP] = K 2 [ADP][ P i ] [ ATP] = K 2 e G 0 RT = K 2 e =.x10 5 (K 2 ) Question 4 Part 1 ii) Several possibilities, here are 2: (1) common intermediate: ATP Q > ADP Pi Q* then X Q* > Y Q (2) both reactions catalyzed by the same enzyme so that the energy is coupled a) False. Most of the ATP produced from the aerobic metabolism of glucose results from respiration. b) False. In yeast cells under anaerobic conditions (no oxygen), the rate of glucose consumption is greater than that under aerobic conditions. c) True. d) False. The citric acid cycle does not occur under anaerobic conditions. The statement is true as written of aerobic conditions. 9

10 Question 4 Part 1, continued e) False. Electron transport from AD to 2 proceeds through many intermediates leading to the production of a proton gradient which drives ATP synthesis. f) True. g) False. Pyruvate is converted to ethanol and 2 to regenerate AD. h) False. Glucose and its derivatives are oxidized by AD and FAD. The resulting AD and FAD 2 carry electron to 2 via the electron transport chain, producing 2. Part 2 a) Pyruvate is a very versatile molecule. Give three pathways for pyruvate. For each pathway list the end product and whether AD or AD is formed. 1. fermentation Lactic acid AD none 2. fermentation ethanol AD none. respiration 2 AD 4 b) ATP is generated by photophosphorylation using the energy from the electrochemical proton gradient formed by the passing of electrons through the photosystems. c) arbon fixation is changing 2 to an organic form by covalently binding it to an organic molecule, usually a sugar. ne example is seen in mesophyll cells where a 2 is added to the sugar ribulose1,5bisphosphate (RuBP) by the enzyme rubisco to form phosphoglycerate. This is the first part of the alvinbenson ycle, also referred to as the dark reactions, because they are lightindependent. d) When exposed to light, plant cells show net absorption of 2 and net production of 2. In the dark, they show net production of 2 and net absorption of 2 i) What biochemical process is responsible for the plant's absorption of 2 and production of 2 in the dark? Explain briefly. Respiration. The plant cells are using 2 to oxidize stored carbohydrates to 2, in order to produce energy. ii) Does this process continue when the plant is exposed to light? If so, why is no net production of 2 and absorption of 2 seen under these conditions? Explain briefly. Yes, the plant always needs energy from respiration to perform cellular reactions. In the light, the rate of photosynthesis is greater than the rate of respiration, so result is net 2 production and net 2 absorption. In the dark, there is no photosynthesis, so the basal respiration level predominates ( 2 absorption and 2 production). e) won t consume 2 ; will produce 2 ; ATP will decrease because no pumped. f) won t consume 2 ; will produce 2 ; ATP will stay the same because still pumped. 10