120-201-fa21-practice-questions-exam-2-2

120-201 FA21 Practice Questions Exam 2-2 Foundations of Cellular & Molecular Biology (Rutgers University) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university 120-201 FA21 Practice Questions Exam 2-2 Foundations of Cellular & Molecular Biology (Rutgers University) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Faith Remias (6kpyhthdbk@privaterelay.appleid.com) lOMoARcPSD|20331520

120:201 Foundations of Biology CMB PRACTICE QUESTIONS FOR EXAM N° 2 Fall 2021/Prof. Cervantes • This practice set is a mix of several types of questions. Exam questions will cover the content in class and these practice questions show you the depth of knowledge and understanding that you should have to tackle the exam. • Exam 2 will consist of multiple choice (single-answer) questions. • Please note that there are no answers to the questions here, but if you send email with specific questions, I’ll guide you to the answer. The graph on the right illustrates the relationship between reaction rates and substrate concentration for an enzyme-catalyzed reaction. What does the K m value indicate with respect to enzyme-substrate interactions? A. the maximum rate of catalysis B. the number of enzyme active sites C. the enzyme-substrate binding affinity D. the equilibrium rate of catalysis The graph above illustrates the change in the rate of an enzyme-catalyzed reaction as the concentration of substrate is increased. Which of the values listed below is used to calculate the enzyme turnover number? (Remember that the turnover number of an enzyme reflects the number of molecules of product formed per unit of time.) A. ½Vmax B. Km C. Vmax D. Vmax – Km A certain enzyme can catalyze a reaction with either of two substrates (S A or S B ). The initial reaction rate (v 0 ) for each of the substrates was measured (in nmoles/min of product formed) as a function of the substrate concentration [S] (µM), and the following results were obtained: [S] v 0 S A S B 0.0001 33 17 0.0002 50 29 0.0005 71 50 0.001 83 67 0.002 91 80 0.005 96 91 0.01 98 95 0.02 99 98 0.05 100 100 5.0 100 100 Use these values to answer the next three questions. Which of the following is a correct conclusion from this data? A. the Km for both S A and S B is 100 B. the Km for both S A and S B is 50 C. the Km for both S A and S B is 5.0 D. the Km for S A is 0.0002 and for S B is 0.0005 E. the Km for S A is 50 and for S B is 29 K m rate of reaction substrate concentration V max ½ V max Downloaded by Faith Remias (6kpyhthdbk@privaterelay.appleid.com) lOMoARcPSD|20331520

120:201 Practice questions for Exam 1 Page 3 Use the Lineweaver-Burk graph above to answer the next three questions regarding enzyme inhibitors. Molecule A is a ___________ inhibitor whereas B is a _______________ inhibitor. A. competitive, non-competitive B. non-competitive, competitive C. competitive, uncompetitive D. None of the above E. There is not enough information. You know this because F. The reaction without inhibitor and the one with molecule A display the same Vmax. G. The reaction without inhibitor and the one plus molecule B show different values of Vmax. H. The reaction without inhibitor and the one with molecule A have different Km values for S. I. The reaction without inhibitor and the one plus molecule B have the same Km values for S. J. All of the above The intercept to the abscissa axis (X) for curve A is different for the curve of the activity assayed without inhibitor. This value is the Ki or inhibition constant. Is this correct? K. Yes L. No What is an allosteric site? How does an allosteric site differ from an enzyme’s active site or a receptor’s binding site? An enzyme’s K m is the concentration of substrate at which v o reaches ½ V max . M. True N. False Downloaded by Faith Remias (6kpyhthdbk@privaterelay.appleid.com) lOMoARcPSD|20331520

120:201 Practice questions for Exam 1 Page 4 Estimation of V max and K m by (visual) inspection. Although graphical methods are available for accurate determination of the V max and K m of an enzyme-catalyzed reaction, sometimes these quantities can be quickly estimated by inspecting values of v o at increasing [S]. Estimate the V max and K m of an enzyme-catalyzed reaction for which the following data were obtained (do not neglect the units): [S] (M) v 0 (µM/min) 2.5 X 10 -6 28 4.0 X 10 -6 40 1.0 X 10 -5 70 2.0 X 10 -5 95 4.0 X 10 -5 112 1.0 X 10 -5 128 2.0 X 10 -3 139 1.0 X 10 -2 140 What type of inhibitor (red line) is represented in the following Lineweaver-Burk graph? How do you know? Use the Michaelis-Menten equation to calculate the missing values of [S] given below if V max = 5 mmol/min. If necessary, you may plot [S] versus v o (not the reciprocals!). Draw a line parallel to the X-axis near V max (asymptote) and extend your plotted line to show its approach to V max . [S] (mM) v o (mmol/min) 10 1.2 [S] 1 1.7 [S] 2 2.1 [S] 3 2.2 [S] 4 2.5 Vmax = _________ Km = _________ Downloaded by Faith Remias (6kpyhthdbk@privaterelay.appleid.com) lOMoARcPSD|20331520

120:201 Practice questions for Exam 1 Page 6 The proteins hemoglobin and myoglobin can bind oxygen. Their amino acyl sequences are very similar, but hemoglobin—as you may recall—is a tetramer whereas myoglobin is a dimer. The illustration above is missing a couple of labels. Can you tell which curve represents binding of oxygen (saturation) to hemoglobin and which one to myoglobin vs. p O 2 [concentration of oxygen]? A. A , hemoglobin; B , myoglobin B. A , myoglobin; B , hemoglobin Briefly explain your answer. What equation (below) represents the last step of oxidative phosphorylation? Recall that cyt c ox represents oxidized cyt c and cyt c red indicates the reduced form of cyt c. A. cyt c ox + glucose ⇌ cyt c red + CO 2 B. cyt c red + O 2 ⇌ cyt c ox + H 2 O C. cyt c ox + e – + H+ ⇌ cyt c red + H 2 D. cyt c ox + O 2 ⇌ cyt c red + H 2 O E. cyt c red + H 2 O ⇌ cyt c ox + O 2 The ultimate source of energy in our planet is sunlight. In the first stage of photosynthesis, light energy is captured in chlorophyll-containing reaction centers (PSII and PSI). What is the first step in the capture of light energy at PSII? A. CO 2 reacts with the C5 sugar ribulose-1,5-bis-phosphate in the first step of the Calvin cycle. B. Starch is synthesized. C. H 2 O is photolyzed and its electrons are captured by special chlorophyll molecules. D. The energy carriers ATP and NADPH + H + are synthesized The study of chemical reactions in cells is useful in the study of metabolism. What is metabolism? A. All reactions in the cells or an organism that produce energy. B. All biosynthetic (anabolic) reactions in a cell. C. Reactions taking place in the organelles of eukaryotic cells. D. The sum of all biochemical reactions that take place in cells, tissues, organs, or whole organisms. E. Those reactions in the cell in which macromolecules are digested to their monomer components. Regarding directionality, metabolic pathways can be linear. A. cyclic. B. branched. C. All of the above D. None of the above The energy used by the cell to generate specific biological molecules and highly ordered structures is stored in the form of A. Brownian motion. B. heat. C. light waves. D. chemical bonds. Downloaded by Faith Remias (6kpyhthdbk@privaterelay.appleid.com) lOMoARcPSD|20331520

120:201 Practice questions for Exam 1 Page 7 Indicate whether the following statements are true or false. If a statement is false, explain why it is false. True or False (why)? A. Photosynthetic organisms release only O 2 into the atmosphere, while non-photosynthetic organisms release only CO 2 . B. The cycling of carbon through the biosphere first requires the incorporation of inorganic CO 2 into organic molecules. C. The oxidation of one molecule is always coupled to the reduction of a second molecule D. During cellular respiration, carbon-containing molecules become successively more oxidized until they reach their most oxidized form, as CO 2 . Oxidation is a favorable process in an aerobic environment, which is the reason cells are able to derive energy from the oxidation of macromolecules. Once carbon has been oxidized to __________, its most stable form, it can only cycle back into the organic portion of the carbon cycle through __________. A. CO 2 ; photosynthesis B. CH 3 ; combustion C. CO 2 ; respiration D. CO; reduction Which of the following statements is incorrect? A. Catabolic pathways are generally oxidative; some catabolic reactions produce energy. Example: glycolysis. B. Anabolic pathways are generally reductive; some anabolic reactions consume energy. Amino acid biosynthesis is an example of anabolism. C. An amphibolic pathway is catabolic and anabolic simultaneously, for example, the Krebs Cycle. D. Gluconeogenesis is an amphibolic pathway. E. Metabolism is the sum of all the chemical reactions in a cell, a tissue, or an organism. Find the mismatched pair: A. Entropy ( D S) — measurement of disorder in a thermodynamic system B. First Law of Thermodynamics — Energy in a system is not created nor destroyed, only transformed C. Second Law of Thermodynamics — The entropy of a perfect crystal at 0 K is exactly equal to zero. D. D G > 0 — Energetically unfavorable (non-spontaneous) reaction E. D G < 0 — Energetically favorable (spontaneous) reaction In metabolic reactions the equilibrium constant (K) is modified by enzymes. A. True B. False At first glance, it may seem that living systems are able to defy the second law of thermodynamics. However, on closer examination, it becomes clear that although cells create organization from raw materials in the environment, they also contribute to disorder in the environment by releasing A. water. B. radiation. C. heat. D. photons. Which of the following reactions is unfavorable? A. NaCl dissolving in water ( D G < 0) B. Formation of peptide bonds during protein synthesis ( D G o values vary from +10 to +20 kJ/mol) C. Hydrolysis of ATP to ADP + ℗ ( D G o ¢ = –30.5 kJ/mol) D. Oxidation of a 16-carbon (C 16 ) fatty acid releases enough energy to synthesize 130 ATPs E. Oxidation of one molecule of glucose (C 6 ) yields up to 8 ATPs in eukaryotic cells Downloaded by Faith Remias (6kpyhthdbk@privaterelay.appleid.com) lOMoARcPSD|20331520

120:201 Practice questions for Exam 1 Page 9 The small molecule cyclic AMP (cAMP) takes about 0.2 second to diffuse 10 μm, on average, in a cell. Suppose that cAMP is produced near the plasma membrane on one end of the cell; how long will it take for this cAMP to diffuse through the cytosol and reach the opposite end of a very large cell, on average? Assume that the cell is 200 μm in diameter. (Hint: Do not overthink this question.) A. 4 sec B. 16 sec C. 80 sec D. 200 sec The figure above is an energy diagram for the reaction X→Y. Which equation below provides the correct calculation for the amount of free-energy change when X is converted to Y? A. a + b − c B. a − b C. a − c D. c − a Enzymes facilitate reactions in living systems. The figure above presents an energy diagram for the reaction X→Y. The solid line in the energy diagram represents changes in energy as the reactant is converted to product under standard conditions. The dashed line shows changes observed when the same reaction takes place in the presence of a dedicated enzyme. Which equation below indicates how the presence of an enzyme affects the activation energy of the reaction (catalyzed versus uncatalyzed)? A. d − c versus b − c B. d − a versus b − a C. a + d versus a + b D. d − c versus b – a A chemical reaction is defined as spontaneous if there is a net loss of free energy during the reaction process. However, spontaneous reactions do not always occur rapidly. Favorable biological reactions require __________ to selectively speed up reactions and meet the demands of the cell. A. heat B. water vapor C. metal ions D. enzymes Downloaded by Faith Remias (6kpyhthdbk@privaterelay.appleid.com) lOMoARcPSD|20331520

120:201 Practice questions for Exam 1 Page 10 Activated carriers are small molecules that can diffuse rapidly and be used to drive biosynthetic reactions in the cell. Their energy is stored in a readily transferable form such as high-energy electrons or chemical groups. Which of the molecules below donates a chemical group rather than electrons? A. FADH 2 B. NADH + H + and NADPH + H + C. FMN D. ATP The amino acid histidine is often found in enzymes. Depending on the pH of its environment, sometimes histidine is neutral and at other times it acquires a proton and becomes positively charged. Consider an enzyme with a histidine side chain that is known to have an important role in the function of the enzyme. It is not clear whether this histidine is required in its protonated or its unprotonated state. To answer this question, you measure enzyme activity over a range of pH, with the results shown in the figure below. Explain why a fully protonated His molecule, favored at low pH, is necessary for the active enzyme. The variety and arrangement of chemical groups on monomer subunits contribute to the conformation, reactivity, and surface of the macromolecule into which they become incorporated. What type of chemical group is circled on the nucleotide shown below? A. pyrophosphate (PPi) B. phosphate (Pi) C. phosphoryl D. carbonyl E. carboxyl You are studying a biochemical pathway that requires ATP as an energy source. To your dismay, the reactions soon stop, partly because the ATP is rapidly used up and partly because an excess of ADP builds up and inhibits the enzymes involved. You are about to give up when the following table from a biochemistry textbook catches your eye. Substrates Products D G° (kJ/mol) Creatine + ATP Enzyme A Creatine-phosphate + ADP + 3 ATP + H 2 O Enzyme B ADP + Phosphate –7.3 Pyrophosphate + H 2 O Enzyme C 2 Phosphate –7.0 Glucose-6-phosphate + H 2 O Enzyme D Glucose + Phosphate –3.3 Downloaded by Faith Remias (6kpyhthdbk@privaterelay.appleid.com) lOMoARcPSD|20331520

120:201 Practice questions for Exam 1 Page 12 Globular proteins fold up into compact, spherical structures that have uneven surfaces. They tend to form multisubunit complexes, which also have a rounded shape. Fibrous proteins, in contrast, span relatively large distances within the cell and in the extracellular space. Which of the proteins below is not classified as a fibrous protein? A. elastase B. collage C. keratin D. elastin Which of the following statements is incorrect? A. We only need to consume vitamins in small amounts B. Vitamins are precursors to some coenzymes C. Some vitamins are fat-soluble whereas others are soluble in water D. All of the above E. None of the above The correct folding of proteins is necessary to maintain healthy cells and tissues. Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer’s, Huntington’s, and Creutzfeld–Jacob disease (the specific faulty protein is different for each disease). What is the ultimate fate of these disease-causing, unfolded proteins? A. They are degraded. B. They bind a different target protein. C. They form structured filaments. D. They form protein aggregates. Which of the following statements is true? A. Peptide bonds are the only covalent bonds that can link together two amino acids in proteins. B. The polypeptide backbone is free to rotate about each peptide bond. C. Nonpolar amino acids tend to be found in the interior of proteins. D. The sequence of the atoms in the polypeptide backbone varies between different proteins. Which of the following is not a feature commonly observed in a -helices? A. left-handedness B. one helical turn every 3.6 amino acids C. cylindrical shape D. amino acid side chains that point outward Which of the following is not a feature commonly observed in β sheets? A. antiparallel regions B. coiled-coil patterns C. extended polypeptide backbone D. parallel regions Protein structures have several different levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. Consider the definitions below and select the one that best fits the term “protein domain.” A. a small cluster of α helices and β sheets B. the tertiary structure of a substrate-binding pocket C. a complex of more than one polypeptide chain D. a protein segment that folds independently Downloaded by Faith Remias (6kpyhthdbk@privaterelay.appleid.com) lOMoARcPSD|20331520

120:201 Practice questions for Exam 1 Page 13 In the reaction 7-dehydrocholesterol + NADH + H + ⇌ cholesterol + NADP + , cholesterol is the product of the oxidation of 7-dehydrocholesterol with the concomitant reduction of NADH + H + to NADP + . A. True B. False For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. The a -helices and β-sheets are examples of protein ____________ structure. A protein such as hemoglobin, which is composed of more than one protein ________________, has ____________ structure. A protein’s amino acid sequence is known as its _______________ structure. A protein ____________ is the modular unit from which many larger single-chain proteins are constructed. The three-dimensional conformation of a protein is its ____________ structure. allosteric ligand subunit domain primary secondary helix tertiary quaternary Fill in the blanks: The protein ________ is involved in vision in higher organisms; its prokaryotic cognate, _________, is a light-activated proton pump involved in ATP production. The cofactor of these proteins is ________________. A. a [H + ]-ATP synthase; a sodium-channel, copper B. rhodopsin; bacteriorhodopsin, retinal/retinol C. hemoglobin; myoglobin, heme D. glutamate dehydrogenase; nitrogenase, molybdenum E. None of the above The following is correct regarding the oxidoreductase enzymes: A. NADH + H+/NAD+ are involved in catabolism and NADPH + H+/NADP+ participate in anabolism B. The oxidation of the reduced member of a redox pair is associated to a DG < 0 C. The reduction of the oxidized member of a redox pair is associated to a DG > 0 D. All of the above E. None of the above Which of the following is an alternative to ATP ( D G°’ = –31 kJ/mol) as an energy carrier? A. creatine-phosphate B. phosphoenolpyruvate C. diphosphoglycerate D. All of the above E. None of the above Complete the sentence with the best option provided below. The secondary structures of a protein are the A. regular, repeated folds present in a lowest energy conformation. B. temporary, unstable protein folding conformations. C. interactions between polar amino acid side groups. D. chemical modifications of amino acid side groups. Two or three a helices can sometimes wrap around each other to form coiled-coils. The stable wrapping of one helix around another is typically driven by __________ interactions. A. hydrophilic B. hydrophobic C. van der Waals D. ionic Downloaded by Faith Remias (6kpyhthdbk@privaterelay.appleid.com) lOMoARcPSD|20331520