SID#: Also give full SID# (w/ 9) on your computer grid sheet (fill in grids under Student Number) BIO 315 Exam I

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1 SID#: Also give full SID# (w/ 9) on your computer grid sheet (fill in grids under Student Number) BIO 315 Exam I Choose an answer of A,B, C, or D for each of the following Multiple Choice Questions Give your answer on the computer scan sheet and in this exam booklet. (2 pts. ea.) 1) Which of the following properties of an atom affect its electronegativity: A) number of electrons in the outer shell B) number of protons in the nucleus C) distance between the protons of the nucleus and electrons of the outer shell D) both B and C x 2) Which of the same properties is responsible for the polarity of the C-O covalent bond: A) number of electrons in the outer shell B) number of protons in the nucleus x C) distance between the protons of the nucleus and electrons of the outer shell D) both B and C 3) Which atoms of a polypeptide participate in the H bonds stabilizing the β sheet: A) electronegative atoms of the peptide bonds x B) electronegative atoms of polar charged amino acid R groups C) electronegative atoms of polar uncharged amino acid R groups D) electronegative atoms of nonpolar amino acid R groups 4) Which of the following types of non-covalent bonds/interactions requires a specific ph range to form: A) H bond B) Hydrophobic Interactions C) Van der Waals Interactions D) Ionic bond x 5) Which of the following types of microscopy would provide the highest resolution information about where a specific protein is located within the lipid bilayer of the plasma membrane: A) immunoelectron microscopy x B) immunofluorescence C) fluorescence microscopy of a GFP-tagged version of the protein D) electron microscopy 1

2 6) Which of the following methods could be BEST used to quantitatively measure the rate of a membrane protein s movement within the plasma membrane: A) immunofluorescence B) fluorescence microscopy of a GFP-tagged version of the protein C) fluorescence microscopy of a GFP-tagged version of the protein in a cell created by fusion of a cell expressing the GFP-tagged protein with a cell not expressing it. D) FRAP analysis of a GFP-tagged version of the protein x 7) Use the Table of pk' values for various amino acids to determine which of the following amino acids pairs could form an ionic bond between their R groups at ph 5.0. A) Lysine and Histidine B) Glutamine and Histidine C) Glutamic Acid and Aspartic Acid D) Glutamic Acid and Lysine x 8) Which of the following conditions describes an exergonic reaction: A) one that produces products with higher bond energies than the reactants and that are more disordered than the reactants B) one that produces products with lower bond energies than the reactants and that are more disordered than the reactants x C) one that produces products with higher bond energies than the reactants and that are less disordered than the reactants D) one that produces products with lower bond energies than the reactants and that are less disordered than the reactants 9) A reaction with which of the following thermodynamic parameters would be MOST likely to occur without any external energy: A) ΔH<0 and ΔS=0 x B) ΔH=0 and ΔS<0 C) ΔH>0 and ΔS=0 D) ΔH=0 and ΔS=0 2

3 10) Use the Table of Standard Redox Potentials to the right to determine which of the following electron transfer reactions would occur spontaneously under standard conditions: A) from malate to NAD + B) from NADH,H + to Oxaloacetate x C) from Ubiquinol to FAD D) from cytochrome c (red) to Ubiquinone 11) Which of the following electron transfer reactions would release enough energy to produce 1 mole ATP under standard conditions: A) from NADH + H + to NADP + B) from FADH 2 to Oxaloacetate C) from Ubiquinol to cytochrome c (ox) x D) from lactate to Oxaloacetate 12) The reaction shown to the right is the final step in the TCA cycle, in which electrons are transferred from Malate to NAD + to form Oxaloacetate and NADH + H +. Use the Table of Standard Redox potentials and what you know about the activities of enzymes to determione which of the following is a correct statement about this reaction: A) The reaction would occur spontaneously under standard conditions, as well as in the cell. B) The reaction would not occur spontaneously under standard conditions, but the enzyme catalyzing the reaction could alter the thermodynamics and allow it to proceed in the cell. C) The reaction would not occur spontaneously under standard conditions, but a strongly exergonic reaction coming after it may keep oxaloacetate levels low to allow the reaction to occur in the cell. x D) Only the reverse reaction would be allowed to proceed in the cell. 3

4 13) In the portion of the TCA cycle shown on the right, which reaction involves the production of an energy storage molecule similar to ATP by substrate level phosphorylation: A) 14 B) 15 C) 16 x D) 17 14) In the same set of reactions, which reaction(s) generate products that can be used to generate ATP by oxidative phosphorylation: A) 14 and 15 B) 14, 15, and 17 x C) 16 D) 16 and 17 15) Which of the same set of reactions would be MOST likely to occur spontaneously under standard conditions : A) 14 B) 15 x C) 16 D) 17 16) Which of the following subunits of ATP synthase is primarily responsible for translocating H + across the inner mitochondrial membrane during ATP synthesis: A) a subunit B) c subunit x C) β subunit D) γ subunit 17) Which of the following mutations in the c subunit of ATP Synthase would you predict to have the LEAST deleterious effect on its ability to synthesize ATP. A) mutating Asp61 to Glu x B) mutating Asp61 to Ala C) mutating Asp61 to Arg D) mutating Asp61 to Lys 4

5 18) Which of the following amino acid sequences would be most likely to form an amphipathic helix in an ion channel protein: Amino Acid #: A) val ala gly val leu val leu ile gly met leu ile leu leu val gly leu B) his lys arg his his arg gly ile glu lys arg lys lys arg arg arg his C) ile pro lue pro val met pro gly pro ala val pro ile leu val pro gly D) met ala val lys gly val leu his leu ile leu lys leu val ile arg leu x 19) Which of the same set of polypeptide sequences in question #18 would be LEAST likely to form an alpha helix of any kind, because it contains helix-breaking amino acids: Amino Acid #: A) val ala gly val leu val leu ile gly met leu ile leu leu val gly leu B) his lys arg his his arg gly ile glu lys arg lys lys arg arg arg his C) ile pro lue pro val met pro gly pro ala val pro ile leu val pro gly x D) met ala val lys gly val leu his leu ile leu lys leu val ile arg leu 20) Which portion of the lipid diagramed below provides the backbone of this class of lipid: A) 1 B) 2 x C) 3 D) ) Which of the following lipid compositions would you predict to find in the plasma membrane surrounding a protein with very short FRAP time in the membrane: A) saturated phospholipids B) trans unsaturated phospholipids C) high cholesterol concentration throughout the membrane D) low cholesterol concentration throughout the membrane x 22) Which of the following membrane transport proteins becomes localized on the plasma membrane only in response to insulin signaling: A) glucose transporter (GLUT4) x B) CFTR ABC transporter C) Voltage-gated K + ion channel D) Na + /K + ATPase 5

6 23) Which of the following proteins is responsible for pumping H + concentration into the stomach in response to food consumption: A) H + /K + ATPase x B) Neuroreceptors C) Voltage-gated K + ion channel D) Na + /K + ATPase 24) Which of the following proteins is responsible for the depolarization of a postsynaptic membrane to threshold in generating an action potential: A) H + /K + ATPase B) Neuroreceptors x C) Voltage-gated Na + ion channel D) Na + /K + ATPase 25) Mutations in the gene for which of the following transporter proteins are thought to have conferred selective resistance to the cholera bacterium: A) H + /K + ATPase B) Glucose transporter (GLUT4) C) CFTR Cl - channel x D) Na + /K + ATPase 26) Which of the following membrane proteins functions in active transport across the membrane: A) Neuroreceptors B) Cytochrome oxidase x C) Voltage-gated K + channel D) Glucose transporter (GLUT4) 27) Prozac affects neurostimulation by affecting which of the following processes: A) activating release of a neurotransmitter B) inhibiting release of a neurotransmitter C) inhibiting destruction of a neurotransmitter in the synaptic cleft D) inhibiting reuptake of a neurotransmitter in the synaptic cleft x 28) Amphipathic detergents, such as SDS, are sometimes used to induce protein unfolding. Which of the following bonds/interactions would you MOST expect to be involved in this: A) Hydrogen bonds B) Hydrophobic interactions x C) Disulfide bonds D) Covalent bonds 6

7 29) Which of the following has been shown to extend life span of a species? A) over-expressing Superoxide Dismutase B) high calorie diet C) mutations in proteins of the insulin-signaling pathway D) A and C x 30) Which of the following findings was discussed in the Charlie Rose Brain Series segment on autism: A) Mutations in genes of immune system function are associated with autism. B) Mutations in genes of neural synaptic function are associated with autism. C) Autism and Williams Syndrome are associated with reciprocal Copy Number Variant mutations that arose spontaneously in the germline. D) Both B and C x 31) Which of the following findings was discussed in the Charlie Rose Brain Series segment on Multiple Sclerosis (MS): A) Mutations associated with MS are also associated with Diabetes Type I. B) Mutations associated with MS are also associated with autism. C) MS is associated with mutations in genes of the immune system. D) Both A and C x 32) Dinitrophenol (DNP) is a lipid-soluble H + -binding drug that equalizes the concentration of H + across the inner mitochondrial membrane. Which of the following would you predict to occur upon addition of DNP to an actively respiring preparation of isolated mitochondria with pyruvate as an oxidizable carbon substrate (assume that pyruvate is able to cross the mitochondrial membranes) A) halt in both pyruvate oxidation and ATP synthesis B) halt in pyruvate oxidation but continuation in ATP synthesis C) continuation in pyruvate oxidation but halt in ATP synthesis X D) continuation in both pyruvate oxidation and ATP synthesis 33) You used Na + -Azide in your lab to poison the normal flow of electrons through the Electron Transport Chain and force the electrons to an artificial electron acceptor that undergoes a color transformation upon accepting electrons. Which of the following would you predict to occur upon addition of Na + -Azide to the actively respiring preparation of isolated mitochondria of question #32: A) halt in both pyruvate oxidation and ATP synthesis X B) halt in pyruvate oxidation but continuation in ATP synthesis C) continuation in pyruvate oxidation but halt in ATP synthesis D) continuation in both pyruvate oxidation and ATP synthesis 7

8 34) ATP and AMP have which of the following allosteric effects on key enzymes of the glycolytic and gluconeogenic pathways: A) High ATP inhibits the key enzyme of the glycolytic pathway, and high AMP activates it. B) High ATP stimulates the key enzyme of the glycolytic pathway, and high AMP inhibits it. C) High ATP stimulates the key enzyme of the gluconeogenic pathway, and high AMP inhibits it. D) Both A and C X 35) Which of the following is a true statement about how SIRT1 functions in the hormonal control of glucose oxidation and gluconeogenesis: A) High NAD + activates it to increase expression of both gluconeogenesis enzymes and mitochondrial proteins but to decrease expression of glycolysis enzymes. X B) High NADH activates it to increase expression of both gluconeogenesis enzymes and mitochondrial proteins but to decrease expression of glycolysis enzymes. C) High NAD + activates it to decrease expression of both gluconeogenesis enzymes and mitochondrial proteins but to increase expression of glycolysis enzymes. D) High NADH activates it to decrease expression of both gluconeogenesis enzymes and mitochondrial proteins but to increase expression of glycolysis enzymes. Use the following word bank to fill in the blanks for questions #36 and #37. WORD BANK All options may not be used, and some options may be used more than once. Na + /K + ATPase product (ATP) and substrates (ADP and Pi) Voltage-gated Na + channel one inner membrane Voltage-gated K + channel intermembrane space Neuroreceptors matrix space ligand-gated ion channel a subunit (s) voltage-gated ion channel c subunit (s) Na + α subunit (s) K + β subunit (s) 2 Na + γ subunit (s) 2 K + c ring 3 Na K + 3 depolarization to threshold 6 full depolarization 12 repolarization into out of 8

9 36) Use the word bank on the previous page to fill in the blanks in the description of how neurostimulation of a postsynaptic membrane generates an action potential. (14 pts) The Na+/K+ATPase establishes the resting membrane potential of -70 mv on the postsynaptic membrane by moving 3 Na+ out for every 2 K+ it moves in across the plasma membrane. This sets up a charge gradient and a concentration gradient for both ions across the membrane at rest. Neurotransmitters released from the pre-synaptic neuron bind to neuroreceptors on the plasma membrane of the post-synaptic cell, stimulating it to open a ligand-gated ion channel and allow some Na+ to flow into the cell to bring about a change in the membrane potential to - 50 mv, called the depolarization to threshold. This stimulates opening of voltage-gated Na+ channels, allowing even more Na+ to rush into the cell until the membrane potential reaches +50 mv, called the full depolarization. This membrane depolarization then stimulates voltage-gated K+ channels to open, allowing K+ to now flow out of the cell. This brings about a repolarization of the membrane to near its resting state of -70mV. 37) Use the word bank on the previous page to fill in the blanks in the description of how H + translocation through the F o base of ATP synthase drives the activity of the F 1 head.(12 pts) H + accummulated in the intermembrane space of the mitochondria bind to the Asp 61 of each of 12 c subunits of the c ring of the F o base embedded in the inner membrane of the mitochondria. This powers a conformational change that stimulates the c ring to rotate, allowing an H + picked up from the intermembrane space to be moved to the matrix space. The rotation of the c ring, causes rotation of the attached γ subunit projecting into the matrix space, which is surrounded by 3 catalytic β subunit of the F 1 head. Rotation of this subunit relative to the fixed catalytic subunits induces the catalytic subunits to undergo a series of conformations with different affinities for the product and substrates of the ATP synthesis reaction. Each 360 o rotation of the c ring, brings about the translocation of 12 H + across the inner membrane (1 per c subunit) and the production of 3 ATP (1 per β subunit). 38) List two treatments discussed in class that extend life span of a variety of species and explain what the cost of aerobic respiration is and how these treatments may affect this in extending life span. (4 pt) Overexpression of SOD (Superoxide Dismutase) or Sirt1, calorie-restricted diet, loss of function mutations in insulin signaling proteins, or treatment with the Sirt1-activator Resveratrol have life-span extending activities. These either remove (SOD) or minimize the production of superoxide free radicals, destructive by-products of aerobic respiration caused by single electrons escaping the Electron Transport Chain of mitochondria (cost of aerobic respiration). Caloric restriction and mutations in insulin signaling minimize the 9

10 production of these by reducing the amount of glucose oxidation. Sirt1 and its activator (Resveratrol) activate a starvation response that allows for more efficient oxidative phosphorylation. 10