pqs4-practice-test-questions

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PQS4 - Practice Test questions Biological Foundations I (The City College of New York) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university PQS4 - Practice Test questions Biological Foundations I (The City College of New York) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

Practice Questions Set 4 Membranes and Transport 1. In any given cell or membrane-bound organelle, the lipid bilayer surrounds an aqueous solution with other particles or units inside it. What is the primary function of the lipid bilayer membrane for any given cell or membrane-bound organelle? ● To protect the cell from the outside, keep all components inside the cell ● Controls the exchange of what goes in and out of the cell How does the structure of the lipid bilayer relate to this function? Consider the role of the phosphate heads, the fatty acid tails and the embedded proteins. ● It is composed of phosphate heads (polar and hydrophilic) and fatty acid tails (nonpolar and hydrophobic) . The embedded proteins are used for transport and receiving cellular signals. 2. Compare and contrast simple diffusion, facilitated diffusion, and active transport. ● Simple Diffusion : Goes with the concn gradient (high -> low). This is the diffusion of water and small uncharged molecules without the use of proteins. (Passive Transport) ● Facilitated Diffusion : Use of the proteins to allow polar molecules like amino acids, sugars and ions into the cell (Passive Transport) ○ Concn gradient has no charge but the electrochemical has a charge and you need proteins ● Active Transport : ○ Primary active Transport: Phosphorylation of ATP to transport substances through a protein ○ Secondary Active Transport: No ATP to transport ions. Usually shoot electrons or protons to shoot substances in or out ○ From low -> high concn 3. Biological membranes are described as both fluid and a mosaic. Explain what these terms mean in terms of the components of the membrane. The fluid mosaic model proposes that the membrane consists of a fluid phospholipid Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

bilayer in which proteins are embedded and float freely The “fluid” part of the fluid mosaic model refers to the phospholipid molecules, which vibrate, flex back and forth, spin around their long axis, move sideways, and exchange places within the same bilayer half. The “mosaic” part of the fluid mosaic model refers to the membrane proteins, most of which float individually in the fluid lipid bilayer, like icebergs in the sea. Membrane proteins are larger than membrane lipids, and those that move do so much more slowly than do lipids. 4 . Explain why lateral drift of lipids in a membrane happens so much more often than transverse flip-flop. ● Lateral drift happens more than transverse flip-flop because it requires energy .to flip it. Because the hydrophilic heads need to go through the hydrophobic tails, which requires energy. 5. Review the figure relating to the experiment by Frye and Edidin (membrane fusion experiment). State: a. What is the big question being asked? ● Do the membrane proteins move laterally in the phospholipid bilayer? b. What is one alternative hypothesis? ● Membrane proteins move laterally in the phospholipid bilayer c. What is the null hypothesis for the alternative hypothesis you wrote above? ● Membrane proteins DO NOT move laterally in the phospholipid bilayer d. What is the experimental prediction based on the alternative hypothesis you wrote above? ● If we take two cells (1 human cell and 1 mouse cell) that have their membrane proteins tagged with antibodies with fluorescent dyes that show different colors, and fuse the cells than we will observe that the colors over time will mix throughout the cell membrane Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

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6. List 1 example of the types of molecules that can cross the membrane on their own. ● Small molecules with no charge can pass through the membrane. (C02, uncharge small lipids, and cholesterol) :) 7. Look at the figure for aquaporins from the lecture notes. Explain which parts of the protein have to be hydrophilic versus hydrophobic. What in the protein structure allows for these differences? ● The blue middle part is the hydrophilic part because that is where the water flows. The 2 side regions with the curly lines is the hydrophobic parts because that is in the lipid part of the membrane. ● The R-groups differ in the amino acids which allows for the change in shape of the protein channel 8. Explain the difference between channels and carrier proteins. ● Carrier proteins form passageways through the lipid bilayer. They each bind a specific single solute and transport it across the lipid bilayer. It binds the solute and changes the shape. Releases the substrate then changes back to its former shape. ● Channel proteins forms hydrophilic channels in the membrane through which water and ions can pass. It has charged side chains. Ex: Includes aquaporins and ion channels. 9. Explain why the sodium-potassium pump in animals and the proton pump in plants are considered to be electrogenic. ● The Sodium-Potassium pump in animals and the proton pump in plants are Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

considered to be electrogenic because the ionic charges from the molecules will impact the membrane potential of the cell. 10. Carbon dioxide molecules typically cross the cell membrane by way of a. simple diffusion b. a channel protein c. a cotransporter d. a carrier protein Explanation: CO2 is nonpolar and symmetrical. And nonpolar uses simple diffusion to cross. 11. Review the figure of the K+ voltage-gated channel in your textbook. Where is the mistake in the figure? ● Opposed to the concentration gradient it is actually an electrochemical gradients 12. Compare and contrast active transport of Na+ through a Na+/K+ pump and active transport of glucose through a Na+/glucose symporter. ● A symport uses the ions of Na+ to allow movement inside the cell so both molecules can be within. Does not use ATP. ● Na+ and K+ pump uses the Na to exchange itself with K+ with the use of ATP. Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

13. A cell has a potential of -70 mV (negative inside). Therefore, positively charged ions such as K+ will enter the cell through K+ channels via passive transport. Is this statement correct? Explain your answer. ● We need to know the concn gradient to determine whether or not it is high to low. If not it will not go through. Either it would go through with the electrical gradient or the opposite gradient. If it’s the opposite directions which one is more concentrated. (This is an example of active transport opposed to passive depending on concentration gradient.) 14. What is membrane potential? ● The unequal distribution of ions across the membrane created by passive transport contribute to the voltage. 15. What is meant by the “electrochemical” gradient? ● The electrochemical gradient is electrical charge difference on the two sides of Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

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the membrane 16. Compare and contrast symport and antiport. ● Symport- the solute moves through the membrane channel in the same direction as the driving ion. Sugars and amino acids are examples of molecules actively providing the energy for the active transport of another molecule through the membrane in the opposite direction 17. A mutation causes the amino acids that normally line the tunnel part of aquaporins in an organism to be replaced with the following amino acids: valine, isoleucine, and leucine. Review (do not memorize) the structure of these amino acids. What would this mutation do to the function of aquaporins? Design an experiment to answer this question. Consider the following methods for your experiment: It is possible to check the function of a channel protein by using artificial lipid vesicles. You can use lipid vesicles (basically a ball of a lipid bilayer with an artificial solution inside) and insert your protein of interest in the lipid bilayer of the vesicle. You can manipulate the solutions inside and outside of the artificial vesicle and check the function of the protein. Include all of the elements of experimental design in your answer. Valine, isoleucine, and leucine are nonpolar and hydrophobic amino acids, they will not allow water to go through the aquaporins. (experiment) By creating two artificial membranes, and putting aquaporins with amino acids (the nonpolar) facing the inside and in the other artificial membrane putting regular polar amino acids within. The concentration of water would be higher outside than inside so the concentration gradient would favor water to go in. The experiment would determine whether the mutation affects the transport of water in aquaporin. Independent Variable : Polar amino acids Dependent Variable : amount of water that can cross the membrane. Control variables: water concentration gradient, proteins inside the membrane, temperature, size of the experiment, and pressure. :) 18. A fungal cell has a potential of -180 mV (negative inside). There is more Ca2+ Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

outside the cell than inside the cell. What can we conclude about the movement of Ca2+ in this case? a. Ca2+ will enter the cell through open channels via passive transport. b. Ca2+ will exit the cell through open channels via passive transport. c. Ca2+ will enter the cell only through active transport. d. Ca2+ will exit the cell passively through a carrier protein. e. We need more information. Reasoning: Negative inside. Positive Outside. 19. Select all that apply: The proton pump in plant cells a. is considered to be an electrogenic pump b. moves two + charges into and three + charges out of the cell c. moves ions down their electrochemical gradient d. carries out facilitated diffusion of ions across the membrane e. moves ions against their electrochemical gradient Reasoning: It is electrogenic bc positive charges move out, and the sodium potassium pump moves AGAINST the gradient. 20. Select all that apply: The Na+-glucose symporter in animal cells a. is considered to be an electrogenic pump b. moves Na+ ions down their electrochemical gradient c. moves glucose down its concentration gradient d. moves Na+ ions against their electrochemical gradient Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

e. moves glucose against its concentration gradient f. carries out facilitated diffusion of ions across the membrane Reasoning: It is active transport bc sodium goes down the gradient which means this facilitated diffusion of an ion. The glucose is going against the gradient 21. Select all that apply: Both facilitated diffusion and active transport share the following characteristics: a. The use of transport proteins is required to move the solute. b. The rate of transport linearly increases with solute concentration. c. There is a concentration gradient across the membrane. d. The direction of transport is down the concentration gradient. Reasoning: When going down the gradient it is Passive transport, and when going against the gradient it is Active transport 22. Select all that apply: How are the membranes of many eukaryotic organisms able to remain fluid when the temperature becomes extremely cold? a. The percentage of unsaturated fatty acids in the membrane is increased. b. The percentage of saturated fatty acids in the membrane is increased. c. The percentage of sterols like cholesterol in the membrane is increased. d. The percentage of phospholipid molecules in the membrane is increased. Reasoning: Unsaturated is a double bond and a saturated is a single bond. Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

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23. Which of the following is/are amphipathi c (both h ydrophobic and hydrophilic) ? a. Channel protein b. Phospholipid c. Sterol d. a and b e. a, b, and c Enzymes and Metabolism 24. What is a catalyst? ● A chemical agent that accelerates the rate of a reaction without itself being changed by the reaction. 25. In enzymatic reactions, what is meant by “an induced fit”? ● When the substrate binds initially at the active site of the enzyme, both the enzyme and substrate molecules are distorted, which stabilizes the substrate molecule in the transition state and makes its chemical bonds ready for reaction 26. What is a cofactor as opposed to a coenzyme? ● Cofactor - a non protein group that binds precisely to the enzyme, for catalytic activity. (inorganic) ● Coenzyme - a small organic cofactor which are often derived from vitamins. Some coenzymes bind loosely to enzymes ● A catalyst can be an enzyme, enzymes may need a cofactor. Cofactors can be a coenzyme 27. Which of the following is (are) true for anabolic pathways? Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

a. They do not depend on enzymes as catalysts for reactions. b. They are usually highly spontaneous chemical reactions. c. They consume energy to build up polymers from monomers. d. They release energy as they degrade polymers to monomers. Anabolic pathway- (putting together) energy is used to build complicated molecules from simpler one. AN example would be dehydration synthesis {example of catabolic(taking apart) pathway would be hydrolysis} 28. Which of the following statements is (are) true about enzyme-catalyzed reactions? a. The reaction is faster than the same reaction in the absence of the enzyme. b. The free energy change is opposite from the reaction in the absence of the enzyme. c. The reaction always goes in the direction toward chemical equilibrium. d. All of the above Reasoning: Enzymes do not affect free energy. Enzymatic rxns usually are not reversible 29. During a laboratory experiment, you discover that an enzyme-catalyzed reaction has a ΔG of -20 kcal/mol. If you double the amount of enzyme in the reaction, what will be the Δ G for the new reaction? Explain. ● Enzyme doesn’t affect the free energy. Enzyme only affects activation energy (there will be no change in the G energy) 30. Review the figure regarding the synthesis of glutamine from glutamic acid. Why is energy coupling required for synthesis of glutamine? ● Coupled w/ ATP hydrolysis, the glutamine synthesis rxn is spontaneous bc net Δ G is negative. Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

Refer to the Figure below to answer the following questions. 31. Which curve represents the behavior of an enzyme taken from a bacterium that lives in hot springs at temperatures of 70°C or higher? a. curve 1 b. curve 2 c. curve 3 d. curve 4 e. curve 5 32. Which curve was most likely generated from analysis of an enzyme from a human stomach where conditions are strongly acid? a. curve 1 b. curve 2 c. curve 3 d. curve 4 e. curve 5 Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

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The following questions are based on the reaction A + B → C + D shown in the figure below. You should be able to draw a diagram similar to this for both exergonic and endergonic reactions if asked. 33. Which of the following terms best describes the reaction? a. endergonic b. exergonic c. anabolic d. allosteric e. nonspontaneous Reasoning: The free energy of C + D is lower than the free energy of A + B 34. Which of the following would be the same in an enzyme-catalyzed or noncatalyzed reaction? a. a b. b c. c d. d e. e 35. Explain your answer to the previous question. ● D is the only one staying consistent which is the total energy that is released. B Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

is the change in activation energy. C is the activation energy or the non catalyzed rxn. E is the rxn energy released from the non catalyzed rxn. Free energy is affected by the enzyme. A + B = substrate. The enzyme only affects the transitional state. 36. Which of the following represents the activation energy required for the enzyme- catalyzed reaction? a. a b. b c. c d. d e. e 37. With or without the enzyme, there is a requirement for input of energy to start this 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? ● More activation energy requires more work. The enzyme reduces this activation energy therefore making it easier to actually occur. Initial energy comes from the heat around the surroundings. This is where the ΔG comes into play. 38. 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. What does high temperature do to the hydrogen bonds? What does low temperature do in terms of the activation energy? ● The increase of temperature actually causes the hydrogen bonds to break leading to the reaction being unable to continue due to lack of things to react with. Plus the high temperature could denature the enzyme. The temperature decrease however, will not allow the reaction to occur as efficiently because there is lower amounts of heat causing the activation energy unable to go through. 39. Explain why an enzyme has an optimal pH and if the pH goes above or below that the rate of the reaction goes down. What do the extra H+ or OH- (depending on the pH change) do to the hydrogen bonds? The shape of the enzyme? Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

● Each enzyme has an optimal pH where it operates at peak efficiency in speeding the rate of its biochemical reaction ● If it is not the optimal pH, the enzyme will not function properly and denature Each enzyme has an optimal pH because a change in the pH would affect the shape of the enzyme. Depending on the function of the enzyme it might need a more acidic or more basic environment. H+ increases the acidity of the base and OH increases the basicity, both disrupt the hydrogen bond and the shape of the enzymes. (secondary, tertiary, quartiary shape of the protein) 40. Explain how noncompetitive inhibition differs from competitive inhibition. Remember that the competition is with substrates for binding to the active site, while non-competitive inhibitors bind somewhere else on the protein. ● Competitive slows down the reaction while the noncompetitive stops it ○ Competitive - Competes with the active site -Bind to the active site -Compete with the substrate ○ Noncompetitive - Binds outside the active site to change the shape of the enzyme -Bind somewhere other than active site -Enzyme changes shape -Active site less effective 41. Explain why increasing the substrate concentration in an enzymatic reaction could ● The more substrates there are, the more chances of meeting with an enzyme than a competitive inhibitor. However, a noncompetitive inhibitor does not need to bind to the active site so the noncompetitive can bind whenever completely changing the enzyme. 42. 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. See figure 4-12. Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

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43. Graph the effects of substrate concentration on the rate of an enzymatic reaction that is being inhibited by a competitive inhibitor versus one that is being inhibited by a noncompetitive inhibitor compared to the rate of reaction without any inhibitor. Make sure to label the axes. What is the dependent variable? What is/are the independent variable? Independent variable: what you change. You may have more than one. In that case, which one goes on the x-axis? Dependent variable: the effect you measure, on y- axis. Three lines on your graph, one for reaction with non-competitive inhibitor, one for reaction with competitive inhibitor, and one for reaction without any inhibitor. How do the lines look different? Refer to Figure 4-12 in the textbook. Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

44. A series of enzymes catalyze the reaction X → Y → Z → A. Product A binds to the enzyme that converts X to Y at a position remote from its active site. This binding decreases the activity of the enzyme. What is substance X? What is substance A? How does A function to regulate its own synthesis? Review feedback inhibition. Substance X is the first substrate to go through the enzymatic reaction. Substance A is the product of the reaction. When there is too much product build up, the product goes back to the commitment step (between X and Y) to inhibit the reaction and regulate it's own production. 45. Describe in your own words what allosteric inhibitors and activators do. Remember what matters is the change in the shape of the active site as the inhibitor or activator binds to the allosteric site. Allosteric inhibitors: converts an allosteric enzyme from the high- to low-affinity state and therefore decreases enzyme activity Allosteric activators: converts it from the low- to high-affinity state and therefore increases enzyme activity, and binding 46. Among enzymes, kinases catalyze phosphorylation, while phosphatases catalyze removal of phosphate(s). Explain how a cell's use of these enzymes can function as an Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

on-off switch for various processes. Consider how phosphorylation and dephosphorylation (adding and removing phosphate groups with their negative charges) would affect the shape of the enzyme and how that would affect the activity of the enzyme. https://www.youtube.com/watch?v=qOVkedxDqQo During phosphorylation and dephosphorylation the enzyme changes its shape which it would prevent the enzymes to work properly and regulate its behavior 47. Using a series of arrows, draw the branched metabolic reaction pathway described by the following statements, then answer the question at the end. · L can form either M or N. (+) · M can form O. (+) · O can form either P or R. (+ ) · P can form Q. (+) · R can form S. (+) · O inhibits the reaction of L to form M. ( -) · Q inhibits the reaction of O to form P. (-) · S inhibits the reaction of O to form R. (-) You should be able to draw this pathway based on the above information. Note: if the effect is to enhance, then a + sign is used. Note that the arrows are pointing to steps (leading from one compound to the next) not to individual, intermediate compounds. Which reaction would prevail if both Q and S were present in the cell in high concentrations? If Q is in high concentration, then it would inhibit production of P , which would mean lots of O would be around. If S is in high concentration, then that would inhibit production of R , which would also mean lots of O would be around. Therefore, conversion of L to M will be inhibited, and so L can be converted to lots of N . 48. Scopolamine is a drug commonly used to relieve nausea and dizziness. Scopolamine can bind to the enzyme sucrase and cause an increase in the number of beta-pleated sheets in the enzyme. This will inhibit sucrase activity. What type of inhibitor is Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

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scopolamine? Noncompetitive because the number of beta-pleated sheets IN THE ENZYME is increased. This shows that the structure of it changed. 49. 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 . *Note that the numbers were made up for enzyme activity (y-axis); however, the activity of it will roughly be the same. 50. Review the figure showing thermal denaturation half-times at 37°C for myofibrillar ATPase from fish species taken from 6 habitats. Why would the same enzyme extracted from these different organisms show such different thermal denaturation half-times? Consider both alternative protein folding and differences in amino acids. 51. Review the figure showing properties of LDH in barracuda species in the eastern Pacific. What do the data for Km tell us? What do the data for Kcat tell us? Make sure to consider the data at the temperature that is normal for the fish populations (how good is the enzyme for the fish where it lives) as well as the data at 25C (comparing the proteins). 52. The enzyme in the previous question is the same enzyme, but the properties of the enzyme extracted from the different fish are not the same. What about the enzyme can account for these observed differences? Consider the amino acid sequence and the folding of the polypeptide. 53. 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. Review lecture notes. Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

Make sure to discuss it in terms of Darwin’s 4 tenets. Downloaded by aye aljondi (ayealjondi@gmail.com) lOMoARcPSD|36425582

pqs4-practice-test-questions

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