EWM MCB 102 SP 19 PRACTICE + Study guide

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Feb 20, 2024

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Dear MCB 102, I’m providing this previous midterm to aid in your preparations for our Spring 202 3 mid-term #2. Please bear in mind that mid-terms change from year to year, and the precise content I cover changes from year to year. How should you use this practice exams? Some suggestions: 1) DO sit down, read the questions, commit to an answer on paper, and then check the key. 2) Do NOT look at the exam, think about the answer, and then consult the answer key. This is waste of your time; it is more valuable to take a nap. 3) It may also be useful to do one of the exams in a “timed” fashion to pract ice working through the problems under a time constraint. Below are my thoughts on preparing for exam #2 and a few answers to specific questions I’ve received about things to know for the exam. Like Exam 1, you will be able to bring in a 3 x 5 inch notecard with anything written on it. Any topic I have discussed in lecture will be considered “fair game” on the exam. That being said, your guiding principle for learning and studying is (and you’ve probably heard me say this before): I will hold you most accountable for topics/themes/concepts we have encountered the most. This principle will be really helpful as you study and place the topics we’ve learned into a hierarchy. You will not be responsible for structures introduced during the Molecule of the Day (unless they appeared again during the main part of lecture). You will not need a calculator for the exam. For the purposes of the exam, you should be able to identify (draw out, name, or otherwise recognize) the intermediates along the pathways we have discussed. For the metabolic pathways we have studied in the course, you should know the logic and sequence of the chemical transformations that give rise to the products and which cofactors/strategies cells take to do these reactions. We have used arrow pushing mechanisms as a tool to guide our understanding. There will be an arrow-pushing mechanism question on the exam, but your thinking should be guided by which intermediates, compounds, and mechanisms we have spent more time on or seen repeatedly. You do not need to be able to reproduce the entire structures of all high energy intermediates, cofactor s, etc., but you should be able to draw the “business end” or functional parts of these molecules. You should also be able to recognize or identify these structures, if provided to you on the exam. Thank you for your hard work with me over these last few weeks. Stay strong as we head into the last few lectures/weeks together. -Prof. Miller

Page 2 of 19 MCB 102 | Exam 2 | Wednesday, April 3, 2019 Instructions. Please read all instructions/questions carefully and provide answers to the questions in the space provided. Please be neat. If we can’t read your answers, we won’t be able to give you credit. To grade this exam, we will separate the pages and scan them. Therefore, please take a moment to put your name and SID number on every page. If your name is not on the pages, it may be lost when we separate the pages, and then it will not be graded. So, please be sure to put your name and SID on all pages. NAME Student ID Number There should be 18 total pages, containing 12 questions. The first page is this coversheet, and the last page is intentionally left blank. You may use this last page as scratch paper, but be sure to transfer any answer you wish to receive credit for to the spaces provided in the main portion of the exam. Remember that whenever you take an exam, you are really taking two tests. The first is a test of your knowledge from the class. The second, and more important, is a test of integrity: that the answers you put down represent your answers and not someone else’s. Please make sure to pass the more important test! You will not need any calculators, phones, electronic devices, headphones, etc. to complete this exam (indeed, they will slow you down), so please make sure these are put away. Thank you for a wonderful semester and good luck! -Prof. Miller Question Points 1 25 2 23 3 18 4 37 5 10 6 11 7 49 8 12 9 19 10 15 11 21 12 14 Total 254

NAME_____________________________SID_____________________________ Page 3 of 19 Question 1. (25 points) a. Early in Prof. Miller’s section, we discussed the use of adenosine triphosphate (ATP) as a universal energy carrier inside cells. Indicate which of the compounds below is ATP. (1 points) b. One of the reasons that ATP is a good, universal energy source is… ( pick one ) (2 points) - small, positive ΔG'° of hydrolysis - large, positive ΔG'° of hydrolysis - large, negative ΔG'° of hydrolysis - small, negative ΔG'° of hydrolysis c. In the space below, provide three reasons supporting the answer you chose in part ( b ) (one sentence each). On the molecule you selected for part ( a ), draw a box around the portion of ATP that accounts for this. (7 points). d. Provide a value of the ΔG'° for the hyd rolysis of ATP. (3 points) e. Another reason that ATP is a good, universal energy source is that it is kinetically stable. Explain, in 1-2 sentences, what helps to make ATP kinetically stable. (6 points) f. Finally, ATP is “universally accepted,” that is, many enzymes have evolved to be able to bind to ATP, making it a versatile molecule. In 1-2 sentences, explain what makes ATP compatible with a wide range of enzymes. (6 points)

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NAME_____________________________SID_____________________________ Page 4 of 19 Question 2. (23 points) The amino acid serine is synthesized in cells according to the following reaction scheme: a. This metabolic pathway belongs to what general class of metabolic pathways (anabolic or catabolic)? (1 point) b. The carbon skeleton of 3-phosphoglycerate is derived from what molecular fuel source (name or structure)? (1 point) c. Name the pathway(s) that we have associated with 3-phosphoglycerate. (2 points) d. In the box provided, write the abbreviation of the co-factor likely required for Step 1 . (1 points) e. In the box provided, write the abbreviation of the by-product produced in Step 1 . (1 points) f. In the space provided below, draw a reasonable arrow-pushing mechanism for the transformation of 3- phosphoglycerate to 3-phosphohydroxypyruvate shown in Step 1 . Be sure to indicate how the co-factor you indicated in part (d) is involved in this reaction. (8 points)

NAME_____________________________SID_____________________________ Page 5 of 19 Question 2 (continued) The second step in the synthesis of serine involves the conversion of 3-phosphohydroxypyruvate to 3- phosphoserine, according to the reaction scheme depicted below: g. In the box above, provide the name or structure of the additional reactant required for Step 2 . (1 points) h. In the box above, provide the name or structure of the additional product generated in Step 2. (1 points) i. Based on our discussions in class, in what other pathways have we seen the “additional product” that you identified in part ( h )? (1 points) j. The enzyme that catalyzes the reaction described in Step 2 is phosphoserine transaminase. This general class of enzymes is mostly closely associated with which metabolic pathway? ( circle one ) (1 point) Calvin cycle | gluconeogenesis | β -oxidation | amino acid catabolism | fatty acid synthesis | Krebs cycle k. The enzyme phosphoserine transaminase requires a unique co-factor to carry out the conversion of 3- phosphohydroxypyruvate to 3-phosphoserine. Provide the name or abbreviation of this co-factor. (1 points) l. What is the ΔG'° for the reaction described by Step 2 ? Briefly explain your reasoning in 1-2 sentences. (4 points)

NAME_____________________________SID_____________________________ Page 6 of 19 Question 3. (18 points) The B-vitamins are a group of vitamins that are incredibly important for human health, especially metabolism. Shown below are the structures of some common B vitamins. For each B vitamin, identify which important cofactor it will give rise to. You may identify the cofactor by name or abbreviation. (2 points each) a. Vitamin B 1 : b. Vitamin B 2 : c. Vitamin B 3 : d. Vitamin B 5 : e. Vitamin B 6 : f. People with a Vitamin B 1 deficiency suffer from a serious disease called beriberi, which can result in swelling, pain, paralysis and even death. Fortunately, the disease can be managed with Vitamin B 1 supplementation. People who suffer from beriberi have elevated levels of pyruva te and α -ketoglutarate. How are the symptoms of elevated pyruvate and α -ketoglutarate related to a Vitamin B 1 deficiency? (2-3 sentences) (8 points)

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NAME_____________________________SID_____________________________ Page 7 of 19 Question 4. (37 points) a. Many cancerous tumors grow under hypoxic conditions (low O 2 ), due in part to the fact that the rapid, uncontrolled growth of cancerous tumors does not allow for proper vascularization, leading to poor blood (and, therefore, O 2 ) supply. Given that tumors have a low O 2 environment, which metabolic pathway would you suspect provides the majority of ATP for a cancer cell? Is this the same pathway that is used by normal cells? Explain your answer in 1-2 sentences. (4 points) b. What key cellular co-factor is required to enable net ATP production in the pathway you identified for cancer cells in part ( a )? (name or abbreviation) (2 points) c. Speculate as to the way cancer cells regenerate the critical co-factor you identified in part ( b ). ( Hint : cancer cells don’t produce ethanol). More generally, this reaction is a n example of what type of metabolic process? (2 points) d. What is the consequence, in terms of ATP production, if the co-factor in part (b) is not available? Briefly explain your answer (1-2 sentences) (4 points) e. Cancer cells take up copious amounts of glucose in order to support their metabolic needs. In their rush to import glucose, analogs of glucose, such as 18 F-deoxyglucose ( 2-FDG , shown below), will also be allowed into cancer cells through glucose transporters (GLUT). What is the ΔG'° for the transport of 2-FDG into a cancer cell, depicted in the equilibrium below? Briefly explain your answer (1-2 sentences). (6 points)

NAME_____________________________SID_____________________________ Page 8 of 19 Question 4. (continued) f. 2-FDG is a substrate for hexokinase. In the space provided below please provide the structure of the product generated by the reaction catalyzed by hexokinase. (2 points) g. What additional co-factor do you think is used by hexokinase to catalyze this reaction? (1 points) h. Suppose the reaction catalyzed by hexokinase is so rapid that it consumes 2-FDG as soon as it enters the cell, so that it makes the concentration of intracellular 2-FDG very low relative to extracellular 2-FDG . If the ratio of 2-FDG (out) to 2-FDG (in) is approximately 1000 to 1, what is the value of ΔG'° for the transport of 2-FDG into a cancer cell (the equilibrium in part e and f )? Explain your answer (1-2 sentences). (8 points) i. Under the same conditions described in part ( h ) – a 1000 to 1 ratio of 2-FDG (out) to 2-FDG (in), what is the ΔG for the transport of 2-FDG into a cancer cell? Briefly explain your answer (1-2 sentences or equation). (8 points).

NAME_____________________________SID_____________________________ Page 9 of 19 Question 5. (10 points) In class, we learned that the enzyme, phosphofructokinase-1, or PFK- 1 was the “gatekeeper” of glycolysis. PFK - 1 carries out the phosphorylation of fructose-6-phosphate to generate fructose 1,6-bisphosphate. The step catalyzed by PFK-1 is highly regulated, and we discussed how PFK- 1 is a “smart” enzyme. a. When Prof. Miller says PFK- 1 is a “smart” enzyme, he most likely means ( circle one ) (2 points) … that PFK- 1 changes the ΔG'° for the reaction to allow it to proceed under cellular conditions. … that PFK-1 binds mostly tightly to the transition state of the substrate, rather than the products. … that binding of cellular metabolites at allosteric sites on PFK-1 alters the efficiency of PFK-1. …that changes in cellular energy supply change the ΔG'° for the reaction catalyzed by PFK-1. b. From the three reaction coordinate diagrams below, please indicate which one most accurately depicts the situation for the catalysis of fructose 6-phosphate phosphorylation by PFK-1 when cellular AMP levels are higher than normal. (Solid lines indicate the reaction under PFK-1 catalysis. Dashed lines indicate the reaction under PFK-1 catalysis when AMP concentration is high). (4 points) c. From the three reaction coordinate diagrams below, please indicate which one most accurately depicts the situation for the catalysis of fructose 6-phosphate phosphorylation by PFK-1 when cellular citrate levels are higher than normal. (Solid lines indicate the reaction under PFK-1 catalysis. Dashed lines indicate the reaction under PFK-1 catalysis when citrate concentration is high). (4 points)

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NAME_____________________________SID_____________________________ Page 10 of 19 Question 6. (11 points) Multiple choice. Parts a and b go together; parts c and d stand alone. a. In glycolysis, the pair of reactions catalyzed by glyceraldehyde phosphate dehydrogenase and phosphoglycerate kinase, that is, the oxidation of glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate, followed by generation of ATP and 3- phosphoglycerate, is most similar to the conversion of … ( pick one ) -succinyl- CoA to succinate in the Krebs cycle… - generation of ATP from the conversion of phosphoenol pyruvate (PEP) to pyruvate… -synthesis of ATP from ADP and P i by ATP synthase… b. …because the pair of reactions in glycolysis … ( circle all that apply ) -captures the free energy of thioester hydrolysis to generate ATP -use inorganic phosphate as a nucleophile -generate an acyl phosphate intermediate -couple oxidation of a substrate to synthesis of a phosphoanhydride c . The first step of β -oxidation, or [ pick one ] anabolism / catabolism, of fatty acids is the synthesis of a fatty-acyl co-enzyme A thioester. To do this, the enzyme fatty acyl CoA synthetase couples the hydrolysis of ATP to the synthesis of a thioester, generating [ pick one ] ADP and inorganic phosphate (P i ) / AMP and pyrophosphate (PP i ) as a by-product. The advantage, energetically speaking, is that generation of [ pick one ] … -ADP/P i makes the overall reaction energetically favorable because of the large negative ΔG'° associated with ATP hydrolysis. -AMP/ PP i makes the overall reaction reversible because PP i can be readily re-combined with AMP to make ATP. -ADP/P i makes the overall reaction reversible because of the close match between ΔG'° for the hydrolysis of thioesters and ATP. -AMP/ PP i makes the overall reaction irreversible because of the additional negative free energy changes associated with pyrophosphate hydrolysis. d. The value of 1.4 kcal / mol is a useful metric, for the following reasons… ( circle all the apply ) -it allows a quantitative estimate of the magnitude of the equilibrium position - it is the value of the ΔG'° for the hydrolysis of ATP -it is the value of Gibbs free energy that accounts for a ten-fold change in K eq or in Q - it is derived the relationship ΔG'° = -RT ln K eq , where we solve for RT and convert ln to log 10 -none of the above -all of the above

NAME_____________________________SID_____________________________ Page 11 of 19 Question 7. (49 points) a. Where do the reactions of the Krebs, or citric acid, cycle take place? (1 points) b. How many HEEP equivalents are generated from one molecule of acetyl-CoA entering the Krebs cycle? Provide the abbreviations and amounts. (5 points) c. For the transformations below, indicate which, if any, both belong to the Krebs cycle and generate the HEEP equivalents identified in part ( b ). Place a “ C ” in the boxes of the reactions that mee t these criteria. (6 points) d. In the box(es) above, place a “ D ” in the boxes that depict reactions that generate NADH in the cytosol. In the space below, provide the name(s) of the metabolic pathway(s) associated with the reaction(s) you identified above. (3 points) e. Reducing equivalents, or HEEPs, generated in the Krebs cycle can enter the oxidative phosphorylation pathway, or electron transport chain, directly. However, the inner mitochondrial membrane is not permeable to HEEP carriers like NADH, and so, NADH generated in the cytosol cannot enter the electron transport chain directly. Consider the reaction below, which takes place in the cytosol and is catalyzed by a cytosolic form of malate dehydrogenase. What is the other reactant? The other product? (4 points) f. Although NADH cannot pass through the inner mitochondrial membrane, a transporter exists to bring malate into the mitrochondrial matrix. In the space below, draw out the reaction that malate undergoes inside the mitochondrial matrix. Please also indicate any additional co-factors that are consumed/generated in the reaction catalyzed by mitochondrial malate dehydrogenase. (6 points)

NAME_____________________________SID_____________________________ Page 12 of 19 Question 7. (continued) g. Across the two reactions outlined in parts e and f , above, what is the net effect of NADH in the cytosol and mitrochondrial matrix? In 1-2 sentences, briefly explain how this solves the problem of getting HEEPs from cytosolic NADH into the mitochondrial matrix. (4 points) h. How many ATP can be generated from a molecule of NADH that is generated in the cytosol? Briefly explain your answer by tracing the path that electrons take from NADH to the final electron acceptor. Indicate at which stage protons (and how many) are moved from the matrix to inner membrane space. (10 points) i. In muscles and brain cells, an alternative strategy is employed to bring reducing equivalents from cytosolic NADH into the electron transport chain. On the cytosolic face of the inner mitochondrial membrane, a pair of enzymes work in tandem. The first, cytosolic glycerol 3-phosphate dehydrogenase catalyzes the reduction of dihydroxy acetone phosphate to glycerol 3-phosphate, consuming an equivalent of cytosolic NADH. Then, a mitochondrial glycerol 3-phosphate dehydrogenase catalyzes the re-oxidation back to dihydroxy acetone phosphate, ultimately generating QH 2 through an FAD/FADH 2 intermediate. The HEEPs derived from this cytosolic NADH next enter the respiratory chain at which complex? (2 points) j. Your classmate thinks that cytosolic NADH always generates the same amount of ATP, regardless of whether the malate pathway (parts e-h ) or the glycerol 3-phosphate dehydrogenase pathway (part i ) is used to bring reducing equivalents to the electron transport chain. Do you agree? If so, explain your reasoning. If not, which pathway produces more, and by how much? (1-2 sentences) (8 points)

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NAME_____________________________SID_____________________________ Page 13 of 19 Question 8. (12 points) The hydrogen isotope, deuterium, D , behaves nearly identically to hydrogen, H , thus making it incredibly useful as a tool for tracing the fate of metabolic products. Below are listed several palmitate molecules that differ only in their substitution patterns of deuteria atoms (indicated as “ D ”). For each palmitate derivative, circle the required building blocks/precursors that are needed for its synthesis, assuming this reaction is carried out in a test tube containing only fatty acid synthase and the precursors you select. a. b. c. d.

NAME_____________________________SID_____________________________ Page 14 of 19 Question 9. (19 points) A rare genetic disorder called maple syrup urine disorder (MSUD) results from the impaired metabolism of branched-chain amino acids, like leucine, isoleucine and valine. The branched- chain α -keto acid dehydrogenase complex normally responsible for catabolizing these amino acids doesn’t function properly in individuals affected by MSUD. In a healthy person, the catabolism of these aminos acids proceeds as follows: in a two-step process, the amino groups are removed from the branched-chain amino acids (valine is shown below) by a branched- chain amino transferase before the branched- chain α -keto acid dehydrogenase complex catalyzes the generation of the acyl-CoA derivative. a. In the space provided, write in the name/structure/abbreviation of one of the additional products made in the reaction catalyzed by the dehydrogenase complex. (2 points) b. In the space provided, write in the name/structure/abbreviation of the other additional products made in the reaction catalyzed by the dehydrogenase complex. (2 points) c. Please list the co-factors/co-enzymes that are likely used by branched- chain α -keto acid dehydrogenase comple x to catalyze the transformation of α -keto- β - methylbutyrate to α -methyl propionyl CoA. (7 points) The branched- chain α -keto acid dehydrogenase complex is similar to two other dehydrogenases we have discussed in class. Please provide the name of the complexes or the reactions (structures or names are fine) catalyzed by the two other dehydrogenase complexes. (6 points) d. Other dehydrogenase #1 e. Other dehydrogenase #2 Provide the name of the metabolic pathway or process where we have encountered each dehydrogenase. (2 points) f. Other dehydrogenase #1 g. Other dehydrogenase #2

NAME_____________________________SID_____________________________ Page 15 of 19 Question 10. (15 points) The figure below depicts a schematized structure of the mitochondrial ATP synthase. Please identify the following: a. The sub-unit or structure by Box (a). (1 points) b. The sub-unit or structure indicated by the arrow from Box (b). (1 points) c. The sub-unit or structure by Box (c). (1 points) d. The sub-unit or structure indicated by the arrow from Box (d). (1 points) e. The sub-unit or structure by Box (e). (1 points) f. ATP synthase couples the movement of protons down their concentration gradient to the synthesis of ATP. In the two boxes provided, indicate, by circling the appropriate choice, which side of the diagram has a higher concentration of H + and which sides correspond to the matrix and intermembrane space. (4 points) g. One of your classmates discovers a new species of yeast lurking in the dark corners of Dwinelle Hall. Working diligently, your classmate finds that this species uses a mitochondrial ATP synthase that contains ten (10) c subunits. Your classmate explains to you that this means the organism generates 10 molecules of ATP per turn of ATP synthase. Do you agree with your classmate’s explanation? Explain your reasoning ( 2-3 sentences). (6 points)

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NAME_____________________________SID_____________________________ Page 16 of 19 Question 11. (21 points) Recent efforts by Fiedorczuk and co-workers ( Nature , 2016 , 538 , 406) revealed the nearly complete structure of ovine (sheep) Complex I using a powerful technique called cryo-electron microscopy, or cryo-EM. Shown below is the cryo-EM structure at approximately 3.9 Å resolution (far left). The middle panel shows a schematic version of the same, and the far right panel provides a detail of the electron transfer pathway within Complex I. a. What is the fuel source that enters at Complex I? Please provide the name or the common abbreviation. (1 points) b. Complex I catalyzes the net transfer of electron pairs into what molecule? In the space below, provide the structures of the business end of the electron accepting species and the product that is formed once electrons have been fully transferred. (5 points) c. As a result of this fuel entering Complex I and transferring its electrons to the species you identified, how many H + are moved from the N to the P side? (2 points)?

NAME_____________________________SID_____________________________ Page 17 of 19 Question 11. (continued) d. According to the scheme depicted in the far right side above, electrons from the fuel you identified in part ( a ) are initially transferred into FMN before proceeding into iron-sulfur (FeS) clusters and ultimately into the electron acceptor you identified in part ( b ). FMN is most similar to what common redox-active co-factor/HEEP carrier that we have discussed in class? Please provide the name and/or common abbreviation in the space below. (2 points) e. What does “HEEP” stand for? ( 2 points) f. How many electrons are transferred from the fuel source in part ( a ) to FMN? (1 points) g. How many electrons can iron-sulfur clusters accept at one time? (1 points) h. In light of your answers to parts ( e ) and ( f ), why is FMN uniquely capable of facilitating the transfer of electrons from the fuel in part ( a ) into iron-sulfur clusters. (4 points) (1-2 sentences) i. According to the diagram of electron flow The flow of electrons (indicated by arrows) from the fuel in part ( a ) into the acceptor in part ( b ) proceeds in the following manner: fuel → FMN → N3 → N1b → N4 → N5 → N6a → N6b → N2 → electron acceptor Based on this information, which iron-sulfur complex has the highest/most positive reduction potential overall? (2 points) j. Which iron-sulfur complex has the higher reduction potential, N4 or N6b? (1 points)\

NAME_____________________________SID_____________________________ Page 18 of 19 Question 12. (14 points) In the endoplasmic reticulum, an alternative pathway exists for the catabolism of fatty acids. a. What common high-energy compound or co-factor is generated during the reactions catalyzed by alcohol dehydrogenase and aldehyde dehydrogenase? (1 points) b. What is the name of the collective reactions catalyzed in steps 1- 4? (1 points) c. Steps 1-4 are analogous to a subset of reactions in another metabolic pathway. What is that pathway? (2 points) In the boxes below: d. Provide the structure of the compound produced by the reaction catalyzed at step 1. (1 points) e. Provide the abbreviation of the compound that is also generated at step 1. (1 points) f. Provide the structure of the compound produced by the reaction catalyzed at step 3. (1 points) g. Provide the abbreviation of the compound that is also generated at step 3. (1 points) h. Provide the abbreviation, name, or structure of the additional product generated at step 4 . (2 points) i. How many additional rounds of steps 1-4 would be required to generate succinyl Co-A as the final product? (4 points)

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NAME_____________________________SID_____________________________ Page 19 of 19 This page is intentionally left blank. You may use the space below for scratch work, a brief poem, or illustration. We will not grade this section, so please be sure to transfer any answer you wish to receive credit for to the appropriate portion of the exam. Sincerely, Prof. Miller

EWM MCB 102 SP 19 PRACTICE + Study guide

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