BIOL+200+-+2024+Winter+-+Practice+Questions+-+Exam+2

3 7. (11 pts). You discover a drug that blocks the transport of NAD+ out of the mitochondrial matrix but still allows transport of NADH into the mitochondria. You add this drug to a culture of human cells grown in the presence of oxygen. A. (2 pts.) What is the mechanism by which ATP is normally produced during glycolysis? (circle one) substrate-level phosphorylation oxidative phosphorylation? B. (3 pts.) What specific effect will this drug have on glycolysis? (1-2 sentences, max) C. (3 pts.) What could the cell do to continue to make ATP in the presence of this drug over a long period of time? D. (3 pts.) Would you expect this drug to have an immediate impact on the function of the Krebs cycle? Explain your reasoning. 8. (9 pts) Below is a chemical reaction. Which molecule(s) is/are being oxidized? ________________ Which molecule has the highest potential energy?__________________ Methane Oxygen Carbon dioxide Water

6 Q10 (CONT) F. (8 pts) You add the poison Metablock (from part D) to the plant cell. You follow a single molecule of glucose after it enters the cell. For each of the four items in the table below, place an X in one of the columns (No energy or Some energy) indicating whether any energy from the original glucose molecule will be stored in each molecule/location in the poisoned cell. Assume that glucose metabolism has proceeded as far as it can go in the presence of the poison . Amount of Energy Stored in: No energy Some energy 1. ATP 2. Proton gradient 3. NADH 4. Glucose Q11(16 pts). You discover a new organism that uses GTP instead of ATP for energy. For each of the following steps in cellular respiration state whether or not you would expect this step to be different in this organism. i. Glycolysis: No change Different (circle one) Explanation (if no change, explain why; if different, explain how this step would be different): ii. Electron Transport Chain: No change Different (circle one) Explanation (if no change, explain why; if different, explain how this step would be different): iii. ATP synthase: No change Different (circle one) Explanation (if no change, explain why; if different, explain how this step would be different):

9 Q15. You have discovered single-celled organisms on Mars! These organisms have 3 interconnected organelles which you call A, B and C. Based on what you know about eukaryotes on earth, you propose that these organelles play a role in protein processing. You perform a pulse/chase experiment where you label newly made proteins with a radioactive amino acid. You then chase with unlabeled amino acids. You see the results shown in the graph. A. Based on the graph, in which of these organelles do you predict you would find the most mature, completely processed proteins? (circle one) A B C B. Approximately how many minutes does it take for a protein to pass through organelle B? a. 5 minutes c. 30 minutes d. 60 minutes C. You add a drug to the Martian cells and repeat the pulse chase experiment. You find that the labeled proteins end up entirely in the cytoplasm. No labeled proteins appear in organelles A, B or C. Fill in the blanks below. Based on what you know about protein trafficking in eukaryotes on earth, you predict the drug is disrupting a binding interaction between the ______________ on the labeled protein and the __________________ resulting in no docking of ribosomes on organelle ____ (A, B or C). Pulse Chase Experiment .

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15 Q22. (A-E) (19 pts) You discover a new species of aerobic bacteria that, similar to E. coli , oxidizes glucose through cellular respiration to generate ATP. You identify the enzyme responsible for catalyzing the first step in the citric acid cycle in this new bacteria and name the enzyme Funky Chickenase. A. Based on your general understanding of feedback inhibition, fill in the table below with your prediction for Funky Chickenase activity under the conditions listed: Condition Predicted Activity of the Funky Chickenase Enzyme (Write HIGH or LOW for each condition) High concentration of NADH Low concentration of ATP B. Explain your reasoning for your answer in the table above for High concentrations of NADH (1-2 sentences). You follow a single molecule of glucose after it enters the new strain of bacteria: Answer (2-3 words each) C. At the end of 2 rounds of the citric acid cycle, in what molecules and/or gradients would you expect to find the majority of the potential energy that originated in glucose? D. At the end of 2 rounds of the citric acid cycle, in what cellular location would you expect to find the majority of energy stored that originated in glucose (be as specific as possible)? E. In what form (thermal, kinetic etc.) would you expect the majorit y of energy to be stored at the end of 1 round of the citric acid cycle? Q23. (5 pts). You isolate several enzymes from E. coli and from a tomato plant that catalyze steps in the citric acid cycle. You find that although the corresponding enzymes from E. coli and tomato are very similar, the enzymes from tomato include an extra 20 amino acids . Based on your general understanding of cellular respiration and structure function, what is a possible explanation for this difference (1-2 sentences)? Q24. (A-B) (10 pts) You are studying a poison called fumarin that decreases the rate of cellular respiration in mice. Within minutes after adding fumarin to a mouse cell you find the results shown in Table 1.

18 Q26. (A-E) (20 pts) You learn about a hydrophilic toxin called TTX produced by newts that can bind and block the activity of a plasma membrane sodium (Na+) channel in snakes. You are interested in determining if TTX also impacts the activity of a chloride (Cl- ) channel in the snake’s cells. You compare the amino acid sequence of the Na+ channel and the Cl- channel proteins and find: • Overall 90% homology (identical amino acids) between the two channels • 90% of the amino acids in the transmembrane domains are identical between the Na+ and Cl- channels and are hydrophobic • 10% of the amino acids in the transmembrane domain are different between the Na+ and Cl- channels but are hydrophilic in both channels. A. Using the numbers on the picture of the channel protein shown above, where do you expect the hydrophilic transmembrane domain amino acids to most likely be located (select all numbers that apply)? B. What type(s) of hydrophilic amino acids would you expect to find in the transmembrane domain of the chloride channel? Type of amino acid YES or NO Acidic Basic Polar C. What type(s) of hydrophilic amino acids would you expect to find in the transmembrane domain of the sodium channel? Type of amino acid YES or NO Acidic Basic Polar D. You discover that the chloride channel is located in the endoplasmic reticulum (ER) membrane. Would you expect the hydrophilic TTX toxin eaten by the snake to be able to bind and block the activity of this chloride channel in a snake cell? (YES or NO) : E. Explain your reasoning to D (1-2 sentences):

21 Importantly, presence of the radiolabeled carbon does not impact the normal process of cellular respiration. Fig. 1. Pulse Chase Experiment A. (2 pts) You can assume that the sharp increase in radiolabeled carbon seen in “Peak 1” at 10-15 minutes represents the transport of radiolabeled glucose from the media into the cells. Based on this, what specific cellular location does “Peak 1” likely represent (1-2 words)? B. (3 pts) Based on Fig 1, in which of the following molecules would you expect to find most of the radiolabeled carbon after 20 minutes (select ALL that apply)? a. Glucose b. Pyruvate c. Acetyl CoA d. Complex I e. ATP synthase C. (2 pts) Based on Fig 1, after 20 minutes, in what form is the majority of energy that was originally stored in the radiolabeled glucose (kinetic, gradient etc.) (1-2 words) D. (2 pts) What specific cellular location does “Peak 2” likely represent (1-2 words)? E. (4 pts) Explain your reasoning for your answer to Q3D (~2 sentences). F. (3 pts) Based on Fig 1, in which of the following molecules would you expect to find the majority of the radiolabeled carbon after 40 minutes (select ALL that apply)? a. Glucose b. Pyruvate c. Acetyl CoA d. Complex I e. ATP synthase G. (3 pts) What is a likely explanation for why you observe very little radiolabeled carbon associated with Peak 2 after 60 minutes? (1-2 sentences)

22 Q32. You are studying a toxin called Rotone that decreases the rate of cellular respiration in plant cells. You add Rotone to plant leaves and a few minutes after adding the toxin you find the following: Molecule measured Amount relative to normal NAD+ in mitochondrial matrix Normal FADH2 in mitochondrial matrix Significantly higher Glucose Normal Pyruvate Normal Citrate Normal A. (3 pts) Based on these results and your general understanding of cellular respiration, which of the following processes in cellular respiration is Rotone most likely directly inhibiting? (Select ONE answer: 1, 2, 3, 4 or 5): 1. Glycolysis 2. Pyruvate Processing 3. Citric acid cycle 4. Electron Transport Chain 5. ATP synthase B. (2 pts) Given your answer in Q4A, what short term impact do you expect Rotone to have on concentration of H+ in the mitochondrial intermembrane space relative to normal levels (Select ONE answer: 1, 2, 3, 4 or 5): 1. Significantly lower 2. Slightly lower 3. No difference 4. Slightly higher 5. Significantly higher C. (6 pts) Explain your reasoning for Q32B (~3-4 sentences).

23 Q33. You are studying a protein called FLO. You create a Green Fluorescent Protein (GFP)-FLO protein (similar to the GFP-actin protein used to study ATP synthase). You introduce the GFP-tagged FLO protein into a single celled eukaryote. You see the results shown below. Green = GFP fluorescence. A. (2 pts). What does the result shown in Fig 2A suggest about the normal cellular location of the FLO protein? (1 sentence) B. (4 pts). Based on the results shown in Fig 2A, which of the following is the most likely function of the normal FLO protein (Select ONE answer: a, b, c or d)? a. Translation initiation b. Transcription elongation c. Catalyzing the commitment step in glycolysis d. Catalyzing the linking step (pyruvate processing) C. (6 pts.) You repeat the experiment with a shortened FLO protein (GFP-FLO SHORT) that is missing 20 amino acids at the carboxy terminus and see the results shown in Fig 2B. What does this result suggest about this 20 amino acid region? Explain your reasoning (2-3 sentences). Fig 2A. GFP tagging experiment with GFP-FLO Fig 2B. GFP tagging experiment with GFP-FLO SHORT

24 Q34. You discover a new single-celled archaebacteria that can use a novel sugar called Creose as its only energy source (shown in Fig 3). Fig 3. Chemical Structure of Creose A. (3 pts) This archaebacteria grows in an environment with very low concentrations of Creose. Based on the chemical properties of Creose and what you know about membrane transport, what type of transport is most likely required for Creose to enter the eukaryotic cells (1-2 words)? B. (4 pts) List 2 structural properties of Creose you used to determine if this molecule has a high or low probability of crossing the cell membrane unassisted (1-2 words each)? 1. 2. C. (8 pts) These archaebacteria are found in both the cold waters (-2 to 10°C) of the Antarctic Ocean and in hot springs (60-65°C) in Yellowstone National Park. You find that the archaebacteria living in the Antarctic have a higher percentage of unsaturated phospholipids in their cell membranes compared to those living in Yellowstone National Park. Based on what you know about membrane structure and function, explain how this difference in phospholipid content would be an advantage in each of these climates. Antarctic Ocean (~2 sentences): Yellowstone National Park (~2 sentences): D. (8 pts) If you added a toxin to this archaebacteria that blocked both ATP synthase and ATP hydrolysis (ATP could not be converted into ADP + Pi) what immediate impact would you expect the toxin to have on each of these processes? Consider each step independently of the others. Fill in the chart below. Process Would still occur? (YES or NO) Creose Transport Glycolysis Citric acid cycle Electron transport chain

25 Fig. 4 Q35. (3 pts) Based on your general understanding of redox reactions, which of the following could be an additional product of the reaction shown in Fig 4? (Select ALL that apply: a, b, c, d, e and/or f)? a. NAD+ b. NADH c. FAD d. FADH 2 e. CO 2 f. None of the above Q36. You are studying a novel calcium (Ca ++ ) channel located in the plasma membrane. Fig. 5 A. (4 pts) Using the numbers on the picture of the Ca ++ channel protein shown in Fig 5, where do you expect to find nonpolar amino acids? (1, 2, 3 and/or 4)? (select ALL that apply) B. (8 pts) You discover a mutation that leads to a change from aspartate (Asp) to tyrosine (Tyr) in region 3 in the channel protein shown above. Using the amino acid chart on the next page, what impact would you expect that change to have on the structure and/or function of the calcium channel? Explain your reasoning. i. Structure (~2 sentences): ii. Function (~2 sentences):

37. Understanding cellular respiration challenges us to balance the “details” and the “big picture.” Your study partner asks you to illustrate the “big picture” by connecting different processes of cellular respiration via outputs and inputs. A. Which of the following molecules are both (1) outputs of glycolysis, linking step, and citric acid cycle and (2) inputs of electron transport chain? Mark all correct answers with an X. CO 2 _____, glucose _____, H 2 O _____, NAD + _____, NADH _____, O 2 _____ B. Which of the following molecules are both (1) outputs of electron transport chain and (2) inputs of glycolysis, linking step, and citric acid cycle? Mark all correct answers with an X. CO 2 _____, glucose _____, H 2 O _____, NAD + _____, NADH _____, O 2 _____ 38. To check your understanding of the core concept of transformations of energy and matter, your study partner asks, “Oxidative phosphorylation couples an endergonic (i.e., energetically unfavorable) process and an exergonic (i.e., energetically favorable) process. What are these processes?” A. Endergonic (i.e., energetically unfavorable) process? Limit: 1 sentence. B. Exergonic (i.e., energetically favorable) process? Limit: 1 sentence. 39. Given the evolutionary origin of the mitochondrion, where would you expect the electron transport chain of a bacterium to be located? Where? Why? Limit: 1 sentence. 40. The processes of cellular respiration can be “broken,” both in experiments and in nature. A species of bacteria naturally produces Molecule X that blocks the proton channel of the ATP synthase in the inner mitochondrial membrane of eukaryotes. A. In the absence of Molecule X, does movement of protons through the ATP synthase represent active transport, diffusion, or facilitated diffusion? Mark all correct answers with an X. active transport _____, diffusion _____, facilitated diffusion _____ B. In the presence of Molecule X, which of the following processes in eukaryotes would decrease? Mark all correct answers with an X. 26

ETC _____, oxidative phosphorylation _____, substrate-level phosphorylation _____ C. Bacteria, even those that perform oxidative phosphorylation, are resistant to Molecule X. Based on your understanding of affinity and structure/function, propose a hypothesis to explain this difference between bacteria and eukaryotes. Limit: 2 sentences. 41. After yeast cells deplete the oxygen in their environment, they use alcohol fermentation, as illustrated in the following figure. A. In this reaction, which of the following molecules is in the more reduced state? Mark the correct answer with an X. acetylaldehyde _____ ethanol _____ B. Based on your understanding of cellular respiration and redox reactions, rather than memorization, what molecules are likely to be found at locations A, B, and C? For each location, mark the correct answer with an X. i. Location A: CO 2 _____, H 2 O _____, NAD + _____, NADH _____, O 2 _____ ii. Location B: CO 2 _____, H 2 O _____, NAD + _____, NADH _____, O 2 _____ iii. Location C: CO 2 _____, H 2 O _____, NAD + _____, NADH _____, O 2 _____ C. Given that ethanol is toxic, one might wonder about the possible benefits of alcohol fermentation for these yeast cells. In the absence of oxygen, which of the following processes can occur alongside alcohol fermentation? Mark all correct answers with an X. citric acid cycle _____, ETC _____, glycolysis _____, linking step _____, oxidative phosphorylation _____, substrate-level phosphorylation _____ 42. You and your study partner are explaining feedback regulation of the citric acid cycle to each other. Reminder: Consult the figures included at the end of this exam. 27

A. Explain to your study partner why this type of inhibition is referred to as feedback inhibition. Limit: 1 sentence. B. Based on your understanding of active sites and structure-function relationships, explain how NADH is able to regulate Enzyme 3 competitively. Limit: 2 sentences. 43. Fascinated by the concept of protein trafficking, you and your study partner are discussing both the signal hypothesis and the research that underlies our conceptual understanding. Reminder: Consult the figures included at the end of this exam. A. Your study partner encourages you to apply your understanding of the following core concepts of biology. i. Information flow, exchange, and storage: Where is the information that specifies the localization of a protein to the ER stored? Limit: 1 sentence. ii. Structure and function: What prevents cytosolic proteins, which lack an ER signal sequence, from diffusing into the lumen of the endoplasmic reticulum (ER)? Limit: 1 sentence. B. Continuing your discussion, your study partner asks you to “break” components and predict consequences. Where could the protein be observed? Mark all correct answers with an X. Cytosol ER Lumen Extracellular Space Nucleus i. For your favorite secreted protein, you remove, from the gene, the ER signal sequence. ii. For your favorite cytosolic protein, you add, to the gene, an amino-terminal ER signal sequence. iii. For your favorite cytosolic protein, you add, to the gene, a carboxy-terminal ER signal sequence. 28

C. Your study partner notes that the binding of the signal recognition particle to the signal sequence pauses translation. Explain to your study partner why this pause is important. Limit: 2 sentences. 44. Imagine: You are investigating a membrane protein within a cellular membrane. You label the membrane protein with GFP, as illustrated in the figure. Based on your understanding of cellular membranes and structure-function relationships, answer the following questions. Cellular Space #1 GFP | Cellular Space #2 A. At which location(s) would we be more likely to find nonpolar than polar amino-acid side chain(s)? Mark all correct answers with an X. Location A _____ Location B _____ Location C _____ B. After a long period of time, where would you expect to see GFP? Mark the correct answer with an X. cellular space #1 _____ cellular space #2 _____ equally in both spaces _____ 29

26 Create your own practice exam questions! See the next page for “madlib” templates you can use to create your own practice exam questions to answer with your study groups.

27 Below are templates for creating questions focused on different core concepts Core concept: Information Flow Possible Templates: You have discovered a ( bacteria, eukaryote ) that ( has a particular mutation ) in ( a particular step in the central dogma ). What phenotype will this organism have in response to this mutation? You have discovered a ( bacteria, eukaryote ) that ( has a particular phenotype ) in ( a step in the central dogma ). What mutation could cause this phenotype? Example Exam question addressing this concept: You have discovered a strain of E. coli in which many of its proteins contain leucines in place of isoleucines. What mutation could cause this phenotype? Core concept: Structure Function Possible Template: ( Name of a molecule/cellular component ) has ( a particular function ). How is the structure of ( molecule/cellular component ) optimized for its function? OR How would ( a specific change ) in the structure of ( this molecule/cellular component ) impact its function? Example Exam question addressing this concept: DNA is the information storage molecule in the cell. How does the structure of DNA make it a better storage molecule than RNA? Core concept: Evolution Possible Template: What is the molecular basis for how ( a particular allele ) impacts the fitness of an individual in ( a particular situation) ? Example Exam question addressing this concept: Streptomycin is an antibiotic that selectively blocks the interaction between the large and small subunit of bacterial ribosomes. How could a streptomycin-resistant population of bacteria arise? Core concept: Transformation of Energy and Matter Possible Templates: Where is energy stored ( before/after ) ( a particular step in cellular respiration )? How is energy transformed during ( a particular step in cellular respiration )? What makes ( this reaction ) energetically favorable? Example Exam question addressing this concept: After 1 round of glycolysis, in which molecules and/or gradients is the bulk of the energy that originated in glucose stored?