Practice Questions Set 5 PDF

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© 2021 City College of New York Biology 101: Biological Foundations I

Practice Questions Set 5 Enzymes and Metabolism 1. During a laboratory experiment, you discover that an enzyme-catalyzed reaction has a G of -20 kcal/mol. If you double the amount of enzyme in the reaction, what will be the G for the new reaction? Explain. 2. Review Figures 6.9, 6.10, and 6.15 in the textbook. Be able to draw similar figures and identify the parts. 3. With or without the enzyme, there is a requirement for input of energy to start a reaction. Why is the reaction more likely to happen with the enzyme than without the enzyme? Where is that initial energy needed for the enzymatic reaction coming from? 4. Review the figure showing the effect of pH on activity of Pepsin and Trypsin. What are the optimal pH and the pH ranges for these enzymes? Explain why an enzyme has an optimal pH and if the pH goes above or below that optimum the rate of the reaction goes down. 5. Graph the effects of substrate concentration on the rate of an enzymatic reaction given a fixed concentration of enzymes (without any inhibitor). On your graph mark Vmax and Km. 6. Suppose you have two variants of the same enzyme. For the same reaction, they have the same Vmax, but different Km values. What does that tell you about the two variants? Draw the curves. 7. Suppose you have two variants of the same enzyme. For the same reaction, they have different Vmax and Km values, similar to slide 26 from lecture notes. Draw the curves. 8. What is a cofactor as opposed to a coenzyme? 9. Kuvan® is a commercially available drug to help treat some patients with PKU. It is the cofactor for the enzyme phenylalanine hydroxylase. When given to PKU patients, it showed effect in some patients but no effect in some patients. How come some patients did not benefit at all from this drug? 10. One trial using Kuvan® involved patients 8-48 years old given a dose of 10 mg/kg a day for 8 days. Another trial involved patients aged 4-12 given a dose of 20 mg/kg a day for 8 days. The 2nd trial led to a higher percentage of patients seeing a positive effect (≥30% reduction in blood phenylalanine levels). Can the researchers claim the higher dose (20 mg/kg) is more effective than the lower dose (10 mg/kg)? How would you design an experiment to determine whether the higher dose cofactor therapy will help with treatment of the disease PKU? 11. Explain why increasing temperature can increase the rate of an enzymatic reaction up to a certain temperature, but above that increasing temperature reduces the rate of the reaction. 1

© 2021 City College of New York Biology 101: Biological Foundations I

12. Sucrase has a temperature range of 30-45C and an optimum of 37C. Draw a graph showing the activity curve for this enzyme to show how temperature affects its activity. 13. Review the figure from Adesioye et al. (2018) showing the temperature curves for the activity of 2 variants of a cell wall degrading enzyme. What is the difference between the two variants WT and H2? What do the curves tell us about the two variants? Why are the curves different? 14. The Vmax and Km values for a cell wall degrading enzyme isolated from different strains of the same bacteria species are not identical, even though they are the same enzyme carrying out the same reaction. Why are the values different? 15. Review the slide about the muscle M4 LDH enzyme in Fundulus fish. The muscle M4 LDH enzyme in Fundulus fish has two subtypes (two different forms of the same protein) produced by two different versions (alleles) of the same gene. One subtype has an optimal temperature of 20C, while the other has an optimal temperature of 30C. As you study the subtypes of this enzyme in different fish populations in the US going from North to South, explain based on natural selection what subtypes you would expect to find in these populations. 16. Describe how allosteric inhibitors and activators carry out their functions. 17. Consider competitive and non-competitive inhibitors. How does each affect the enzyme? X 18. A series of enzymes catalyze the reaction: A → B → C → D. Product D binds to enzyme X, which converts A to B, at a position remote from its active site. This binding decreases the activity of enzyme X. What type of inhibitor is A for enzyme X? Inhibition of this pathway by product D is called _________________. 19. Review the figure showing regulation of the activity of the enzyme chorismate mutase. Explain how Phe, Tyr, and Trp regulate the pathways that lead to their own synthesis. 20. Review the figures showing the role of the enzyme TMPRSS2 in infections by SARS-CoV2. Explain how the action of this enzyme helps the virus infect a cell. 21. Consider the experiment using knockout mice to study the role of the enzyme TMPRSS2 in infections by SARS-CoV2. Identify the independent and dependent variables. 22. Consider the experiment using Camostat Mesylate as a potential drug to prevent viral infection of cells. Identify the independent and dependent variables. Be able to interpret the graphs.

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© 2021 City College of New York Biology 101: Biological Foundations I

Respiration 23. Which process in eukaryotic cells will proceed normally whether oxygen (O2) is present or absent? a. electron transport in cristae b. glycolysis c. the citric acid cycle d. oxidative phosphorylation e. chemiosmosis in mitochondria 24. Where in the cell does each of the following take place? Glycolysis, Pyruvate Oxidation, Citric Acid Cycle, Electron Transport / Oxidative Phosphorylation. 25. What does the molecule that functions as the reducing agent in a redox or oxidationreduction reaction actually do? 26. Review the figure for the reaction between methane and oxygen. Explain how that reaction is a redox reaction. 27. The free energy for the oxidation of glucose to CO2 and water is -686 kcal/mole and the free energy for the reduction of NAD+ to NADH is +53 kcal/mole. Why are only two molecules of NADH formed during glycolysis when it appears that as many as a dozen could be formed? Consider what comes out of the reaction as a net product. Where is the rest of the potential energy? Where is glucose oxidized to CO2? 28. Review the structure of pyruvate. Pyruvate has to enter the mitochondria in order to enter the citric acid cycle. Will pyruvate cross the lipid bilayer membrane easily? Explain. 29. Consider the cotransport proteins involved in bringing Pyruvate into the matrix of the mitochondria. In the absence of oxygen, why won’t pyruvate enter the mitochondria? Consider the role of oxygen in electron transport and the proton gradient. 30. Review the figure showing the steps of glycolysis in the textbook and in the handout. Mark the specific energy investment and energy harvest steps. 31. What is substrate-level phosphorylation? 32. In the diagram showing the energy harvest phase of glycolysis, circle and identify the steps that show substrate-level phosphorylation. 33. Review the citric acid cycle. How many carbon atoms are fed into the citric acid cycle as a result of the oxidation of one molecule of glucose? 34. Review the citric acid cycle. How many molecules of ATP, NADH, and FADH2 are generated in the citric acid cycle as a result of the oxidation of one molecule of pyruvate? 3

© 2021 City College of New York Biology 101: Biological Foundations I

35. Review the citric acid cycle. Explain why step 8 is a redox reaction. Gaining or losing hydrogens (not just electrons) … 36. Review the citric acid cycle. Explain what happens if you add an inhibitor that inhibits malate dehydrogenase, the enzyme that carries out the reaction in step 8. 37. What has to happen to amino acids before they are fed into the catabolic pathways for carbohydrates (glycolysis, pyruvate oxidation, citric acid cycle)? 38. Fatty acids enter the catabolic pathways for carbohydrates (glycolysis, pyruvate oxidation, citric acid cycle) at the Citric Acid Cycle. In what form do they enter the cycle? 39. Both FADH2 and NADH donate electrons to the electron transport chain. Which does it at a lower energy level? 40. In electron transport, as electrons move from complex to complex, the energy level keeps dropping. What is happening to the energy being released by the electrons? 41. Review the slides for electron transport in the mitochondria. Explain how donation of electrons by NADH and FADH2 to the ETC leads to the synthesis of ATP. 42. Review the slides for electron transport in the mitochondria. It is possible to prepare vesicles from portions of the inner membrane of the mitochondrial components. For oxidative phosphorylation to be carried on by this isolated inner membrane with its protein complexes intact, we must provide the required substrates. What are these substrates? List all of the materials that are supplied on the matrix side of the membrane. Note that any aqueous solution in a normal room will have oxygen dissolved in it. 43. Review the slides for electron transport in the mitochondria from lecture notes. Mark the steps that contribute to the formation of the proton gradient across the membrane. Consider both movement of protons across the membrane and reactions that remove protons from the matrix. 44. What is the immediate source of energy for ATP synthesis by the ATP synthase in mitochondria? 45. One example of a mitochondrial disease is Leber hereditary optic neuropathy (LHON), a form of blindness that strikes in midlife as a result of mutations in Complex I. Some mutations leading to LHON block use of NADH, while other mutations leading to LHON block electron transfer to ubiquinone. What will be the consequences of these mutations for electron transport, the proton gradient, and ATP synthesis in the mitochondria that carry these mutations?

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© 2021 City College of New York Biology 101: Biological Foundations I

46. Cyanides attach to the iron within cytochrome c oxidase and inhibit its activity. What would that do to electron transport in the mitochondria? To the proton gradient? To ATP synthesis? Why would that make cyanides poisonous to us? Explain. 47. Plants have an alternative oxidase that allows them to bypass complexes III and IV. This means electrons from ubiquinone go to this alternative oxidase, which then passes the electrons to oxygen reducing it to water. Compare the proton gradient established across the inner mitochondrial membrane, the relative amount of ATP synthesized, and the energy released as heat when this alternative oxidase is used as opposed to when the normal electron transport pathway (including complexes III, IV, and cytochrome c) is used. Note: under normal conditions both systems are used.

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