bio3 - Now a few questions on enzymes and a bunch on...

Unformatted text preview: Now a few questions on enzymes and a bunch on cellular respiration. These should keep you busy for a while. EAW 1. Compare irreversible inhibition and reversible competitive and reversible non- competitive inhibition of asingle-subunit enzyme. Where does the inhibitor bind and what determines whether or not it is reversible and what determines whether or not it is competitive? Draw all the appropriate graphs of reaction rates with or without inhibitor present. Which of these types of inhibition might also apply to allosteric enzymes? 2. Draw a generic allosteric enzyme and name two types of subunits of which it is composed. Indicate and name the binding site of each subunit and state what binds to each. Draw a graph of reaction rate vs. [substrate]. 3. How and why is the equilibrium between active and inactive forms of an allosteric enzyme altered when lots of substrate is added? What is “cooperativity”? 4. Why do we say that glucose (C6H1206) is oxidized during cellular respiration? 5.. What compound is most important for short term energy storage in cells? What bonds in this molecule store the energy? 6. What compounds are most important for long term energy storage in cells? What bonds in these molecules store the energy? 7. What are the two major mechanisms by which cells produce ATP? Which of the two mechanisms is responsible for producing most of the ATP? 8. Draw a mitochondrion. Label all of the following parts: outer membrane inner membrane (cristae) intermembrane space matrix location of electron transport chain molecules location of ATP synthase molecules location of highest acidity (high [H+]) location of ATP formation 9. Describe the process of chemiosmosis in a mitochondrion. 10. What is substrate-level phosphorylation? What kind of a reaction generally provides the energy to power substrate-level phosphorylation? 11. Contrast anabolism and catabolism. 12. What are the three components of cellular respiration? 13. In what part of the cell does each of the following processes occur? If within an organelle, name the specific part of the organelle involved. glycolysis citric acid cycle electron transport chain and oxidative phosphorylation 14. During glycolysis, 1 molecule of glucose is broken down to 2 molecules of . In addition, how many total molecules of each of the following are produced? How many n_et molecules of each of the following are produced? NADH+H+ ATP H20 15. What determines whether conditions are aerobic or anaerobic? 16. Following glycolysis, a cell can continue along either of two routes depending upon whether the conditions are aerobic or anaerobic. Under aerobic conditions, the cell will continue onto . Under anaerobic conditions, the cell will continue onto 17. Is the following an oxidation or reduction reaction? Is it exergonic or endergonic? NAD+ + 2H —> NADH + H+ 18. Which of these enzymes catalyzes the major feedback regulated reaction of glycolysis? A) hexokinase B) aldolase C) isomerase D) phosphofructokinase E) triose phosphate dehydrogenase 19. In aerobic respiration, the junction step between glycolysis and the citric acid cycle converts each molecule of pyruvate to a molecule of after an oxidation step in which — is removed from pyruvate and coenzyme A is added to the remaining fragment of pyruvate. At the same time, in an endergonic reaction, e" are added to another coenzyme (whose main function is to carry a) reducing this coenzyme to 20. The complete oxidation of 1 molecule of pyruvate results in the formation of how many NADH + H“? how many FADHZ? How many CO2 are released during this process? 21. The complete oxidation of 1 molecule of glucose results in the formation of how many NADH + H“? how many FADH2? How many 002 are released during this process? 22. Release of e' from 1 (NADH + H”) results in the formation of how many ATP during oxidative phosphorylation? 23. Release of e‘ from 1 FADH2 results in the formation of how many ATP during oxidative phosphorylation? 24. The complete oxidation of 1 molecule of pyruvate results in the formation of how many ATP? How many ATP are formed by oxidative phosphorylation? How many ATP are formed by substrate-level phosphorylation? 25. The complete oxidation of 1 molecule of glucose results in the formation of how many ATP? How many ATP are formed by oxidative phosphorylation? How many ATP are formed by substrate-level phosphorylation? 26. Name the five major H/e- carriers of the electron transport chain (ETC). Which of these carriers also pumps H+ ions? What is the final electron acceptor of the ETC? 27. Which member of the ETC does not require a prosthetic group for carrying H atoms/e-? Name 3 of the prosthetic groups found associated with some of the other members of the ETC. Which 2 members of the ETC frequently move laterally within the membrane? 28. How many total ATP are produced by substrate-level phosphorylation during cellular respiration? How many total ATP are produced by chemiosmosis during cellular respiration? 29. Why does is require ATP to move e' inside the mitochondria from the cytosol? 30. Why will glycolysis and the citric acid cycle stop under anaerobic conditions? How can fermentation allow glycolysis to continue under anaerobic conditions? What generally happens to the rate of glycolysis under anaerobic conditions in which fermentation is occurring? 31. What are the two major products that can be produced by fermentation? 32. What is the purpose of fermentation? As one molecule of glucose is broken down to 2 molecules of lactic acid, how many n_et NADH + H+ are produced? how many n_et ATP are produced? 33. Name 2 molecules that decrease the rate of conversion of fructose 6-phosphate to fructose 1,6-bisphosphate during glycolysis. Name 2 molecules that increase this rate of conversion. 34. Name 2 molecules that decrease the rate of conversion of isocitrate to or- ketoglutarate during the citric acid cycle. Name 2 molecules that increase this rate of conversion. 35. Name 2 molecules that decrease the rate of conversion of acetyl CoA to citrate during the citric acid cycle. 4 Answers to questions on enzymes and cellular respiration: 1. Remember that this question addressed the effects of these types of inhibition on single-subunit enzymes. irreversible inhibition: inhibitor binds permanently to the active site of enzyme and completely inactivates it. Not competitive because inhibitor does not resemble substrate, but is generally a small molecule. Reversible competitive inhibition: inhibition is competitive because inhibitor closely resembles normal substrate and binds to active site of enzyme instead of normal substrate; it is reversible because inhibitor does not permanently bind to enzyme. Addition of lots of normal substrate prevents competitor from binding. See page 8 of enzyme handout for graph. Reversible non-competitive inhibition: inhibition is non-competitive because inhibitor is some molecule that binds to the enzyme somewhere other than the active site (we don’t use the words “allosteric site”) and thus changes the conformation of the enzyme so that the active site is also changed and can no longer bind the substrate as efficiently; it is reversible because the inhibitor can dissociate from the enzyme. See p. 8 of enzyme handout for graph. When we talk about inhibition of an allosteric enzyme, we talk of inhibitory molecules binding to the allosteric site of the regulatory subunit, BUT we could also see an allosteric enzyme inhibited by irreversible inhibition and by competitive reversible inhibition, although these are not the natural common mechanisms. 2. See p. 9 of enzyme handout for diagram and see p. 10 for graph. 3. See bottom half of p. 10 of enzyme handout for answers to both parts. 4. Electrons start out equally shared between atoms of glucose, but then 02 reacts with glucose and oxygen is very electronegative and the electrons released as glucose if broken down are found in CO2 and in H20 and in these molecules they are more closely associated with oxygen than with the C or the H, respectively. See p. 3 of redox handout. 5. Short-term energy = ATP. Energy stored in bonds between the phosphate groups. 6. Long term energy = starch in plants and fats in animals. Energy stored in C-H bonds. 7. ATP is produced by chemiosmosis (90% of ATP produced) and by substrate-level phosphorylation (10%). In terms of how we arrive at the percentages, think about the absolute numbers of ATP we calculated are produced as a result of glycolysis and the citric acid cycle. 8. See top of p. 6 of redox handout. 9. See p. 6 of redox handout. A few points to keep in mind: it requires energy to pump the H+ and this energy comes from constantly passing the e‘ on to increasingly electronegative molecules which therefore releases energy; think of the three things (see handout) that contribute to the “proton-motive force”; the only way the H+ can get back to the matrix is through the ATP synthase molecules in the presence of ADP in the matrix and this is how the mitochondrion couples the energy released by H+ moving down their three gradients with the energy required to form ATP. 10. Substrate-level phos’n refers to the enzyme-catalyzed transfer of phosphate groups from “donor molecules” (which have acquired a Pi from the cytosol or mitochondrial matrix - because enough energy was given off in an accompanying reaction - generally an oxidation reaction - to allow the addition of P.) to ADP in order to form ATP. See example on p. 8 of redox reaction. This is one of two substrate-level phosphorylation steps in glycolysis. There is also one such step during the citric acid cycle. 11. Anabolism - forming more complex molecules from simpler ones; overall=endergonic; Catabolism - breaking down complex molecules to obtain simpler ones and to release energy i.e. exergonic. 12. Cellular resp’n = glycolysis + citric acid cycle + electron transport chain 13. Glycolysis in cytosol; c.a. cycle in mitochondrial matrix; ETC on mitochondrial cristae (see diagram on p. 2 of cellular resp. handout) 14. 1 glucose broken down to 2 pyruvate; net output of other molecules: 2 H20, 2 (NADH + H“), 2 ATP 15. If 02 is present, this is aerobic. If no 02 is present, then this is anaerobic. 16. If aerobic, then continue onto c.a. cycle and ETC; if anaerobic, then continue onto fermentation. 17. NAD+ + 2H —9 NADH + H+ is an endergonic reduction reaction—because 2e‘ in the form of an e' and a whole H atom are added to NAD”. This involves the formation of new bonds. 18. D 19. acetyl CoA; COZ; NADH 20. complete oxidation of 1 pyruvate results in formation of 4 NADH+ + H+ 1 FADH2 release of 3 C 02 [2(NADH + H”) during glycolysis plus 2 (4NADH + H*) ring c.a. cycle] 2 FADH2 release of 6 CO2 21. complete oxidation of 1 glucose results in formation of €10 NADH + H+ u 22. 3 ATP 23. 2 ATP 24. complete oxidation of 1 pyruvate results in formation of 15 ATP 14 ATP by oxid. phosphorylation [3(4 NADH + W) + 2(1FADH2)] 1 ATP by substrate-level phos’n 25. complete oxidation of 1 glucose results in formation of 36 ATP 34 ATP by oxid. phosphorylation (6 during glycolysis; 28 during c.a. cycle) 4 ATP by substrate—level phos’n) (net of 2 during glycolysis; 2 during c.a. cycle) -but it requires 2 ATP to get e' generated during glycolysis and associated with NADH in cytosol into mitochondria, so subtract 2 ATP from 38 ATP and arrive at total of 36 ATP 26. NADH-Q reductase —> pumps H+ ubiquinone cytochrome reductase —> pumps H+ cytochrome c cytochrome oxidase —+ pumps H+ final e‘ acceptor of ETC is 02 27. ubiquinone has no prosthetic group; some associated prosthetic groups = flavins, FeS complexes, hemes, Cu; ubiquinone and cytochrome c move laterally between other ETC members to transfer 6‘ 28. 6 total ATP produced by substrate-level phos’n; 34 total ATP produced by chemiosmosis (see answer #25) 29. The inner mitochondrial membrane is not permeable to NADH, so e' (generated during glycolysis) must be released from NADH in the cytosol or in the mitochondrial intermembrane space and transported by a shuttle system across the mitochondrial cristae to NAD+ in the matrix. It always requires energy to move ions across membranes, so it requires ATP to move these e'. 30. Under anaerobic conditions when there is no 02 around to act as the final e‘ acceptor at the end of the ETC all or most of the NAD+ in a cell gets reduced to NADH and then the reduced NADH can not get rid of its e‘ and be oxidized back to NAD‘“. Therefore there is no NAD+ around to accept e' during glycolysis and the c.a. cycle and these pathways stop; similarly for FAD and FADHZ. Fermentation converts the NADH generated during glycolysis back to NAD“, thus allowing glycolysis to continue. In order for the cell to continue to generate a reasonable amount of ATP, the rate of glycolysis may increase up to 1 0-fold. 31. Produced by fermentation: lactic acid, ethanol 7 32. Purpose of fermentation is to allow the cell to continue to generate ATP and stay alive. As 1 glucose broken down to 2 lactic acid: 0 net NADH + H’“ produced; 2 net ATP produced. 33. ATP and citric acid decrease rate of conversion of F6-P to F1,6-P; AMP and ADP increase rate of conversion of F6-P to F1,6-P 34. ATP and NADH decrease rate of conversion of isocitrate to a-ketoglutarate. ADP and NAD+ increase rate of conversion of isocitrate to a-ketoglutarate. 35. ATP and NADH decrease rate of conversion of acetyl CoA to citrate. ...
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