Examination II Key PHRM 836 Biochemistry for Pharmaceutical Sciences II October 31, 2013

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1 Examination II Key PHRM 836 Biochemistry for Pharmaceutical Sciences II October 31, 2013 Correct answers in multiple choice questions are indicated in RED and underlined. Correct answers to essay questions are indicated in RED in comic book font. In some cases and explanation is provided in BLUE/BLUE PHRM 836 Exam II key - 1 MATCHING. For problems 1 to 3, a set of numbered answers is provided immediately below. For each problem, select from the list of answers the single choice that best matches the item described in the problem. Mark that answer on your answer sheet. An answer may be used more than once or not at all. [3 points each] 1. A motif first known as a DNA binding motif but is also involved in protein-protein interactions

2 PHRM 836 Exam II key Distortion of an AT-rich sequence near a promoter site 3. Two helices bind the major groove. MULTIPLE CHOICE. For problems 4 to 28, select from the list immediately following each question the single most correct choice to complete the statement, solve the problem, or answer the question. Mark that answer on your answer sheet. [3 points each] 4. A suicide inhibitor of an enzyme is one that is competitive with substrate. is reversible. is activated by one type of enzyme for the purpose of inhibiting a second type of enzyme. looks like the transition state of the substrate. has high bioavailability. 5. Which of the following accurately describes the Michaelis-Menten model for inhibitor effects on enzyme kinetic behavior? A competitive inhibitor and substrate both bind free enzyme with the same affinity. V max is unaltered in the presence of an uncompetitive inhibitor The difference between an uncompetitive and noncompetitive inhibitors is whether or not the inhibitor molecule binds the ES complex. The inhibition can be overcome with high concentration of substrate. The rate of product formation distinguishes competitive, non-competitive and uncompetitive inhibition. At substrate concentrations much less than K M, the initial velocity is determined by k cat. The inhibitor concentration and substrate concentration are varied simultaneously to measure k cat and K M. Even when [S] is at saturating concentrations, the apparent V max is less than the value in the absence of inhibitor. 6. The degree of inhibition caused by a competitive inhibitor can be decreased by adding water to reduce the concentration of the EI complex increasing the substrate concentration increasing the enzyme concentration increasing both the enzyme and inhibitor concentration decreasing the inhibitor concentration both and both and both and 7. In the presence of a noncompetitive inhibitor of a particular enzyme toward a given substrate the enzyme is irreversibly inactivated. the potential maximum velocity will remain unchanged from that in the absence of the inhibitor. the interaction of the inhibitor with the substrate is a major factor leading the observed inhibition. the apparent Michaelis constant for the substrate will be the same with or without inhibitor present. sigmoidal kinetics would be expected if there is a change in protein conformation in the binding site for either S or I.

3 PHRM 836 Exam II key Which of the statements is NOT an accurate description of the inhibition described from the following plot? the slopes differ by an amount proportional to (1+[I]/K I ) competitive inhibition citrate inhibits this enzyme the apparent K M is increased the inhibitor does not bind to ES the fastest rate of product formation is shown by curve 1 the y-intercept corresponds to conditions where the substrate competes off the inhibitor 9. The lowering of cholesterol by statins is due to inhibition of HMG-coA reductase. In class, the crystal structure of a ternary complex of HMG-coA reductase with a CoA and a cofactor analogue was compared to the binary complex with Rosuvastatin. How did this crystal structure elucidate the structural basis of the competitive inhibition against CoA, but not NADP, exhibited by statin drugs? Rosuvastatin was found to bind the active site of HMG CoA reductase. Rosuvastatin binds in a site that does not overlap with the NADPH binding site. the Rosuvastatin binding site overlaps only part of the binding site of CoA. Rosuvastatin does not bind to an allosteric site. choice and choice and all of the above none of the above 10. Selective inhibitors against cyclooxygenase-2 (COX-2) are needed to reduce undesired side effects and achieve a more effective treatment of pain and inflammation from arthritis. A problem that arises from long-term use of COX inhibitors is the unwanted inhibition of COX-1 and reduced levels of good prostaglandins, which can lead to gastrointestinal bleeding. Which statement on selective inhibitors is correct? Selective inhibitors have very high-affinity. Selective inhibitors of COX-2 acetylate a Ser residue and are irreversible. Selective inhibitors exploit structural differences in the binding site between COX-1 and COX-2. For an inhibitor that is selective for COX-2 over COX-1, the EC 50 value for COX-2 is smaller than the EC 50 value for COX-1. Selective inhibitors target the transition state. Choices and Choices and Choices and Choices and All of the above

4 PHRM 836 Exam II key Transcription factors are hetero-oligomeric complexes comprising up to 10 protein chains, DNA and RNA. recognize DNA via nonspecific interactions with the phosphodiester backbone in the major groove. are proteins with at least one, and sometimes multiple zinc-finger motifs. cleave DNA in a sequence specific manner. are DNA-binding proteins regulated by a variety of mechanisms one of which is protein-protein interaction have a total length of less than 50 residues. 12. The following are common to cytochrome P450s and nitric oxide synthase EXCEPT which phrase? heme prosthetic group binds oxygen their reductase enzymes are structurally similar molecular oxygen is a substrate mono-oxygenase activity absorbance at 450 nm homodimeric proteins choice and choice and choice and choice, and 13. Cytochrome P450s do NOT activate some drugs. cause carcinogen activation. make xenobiotics more lipid soluble. contribute to the metabolism of the majority of therapeutic drugs. detoxify some toxins. reduce bioavailability of some drugs. catalyze hydroxylation at multiple sites of one substrate. dealkylate compounds. contribute to the synthesis of steroid hormones. 14. Acetaminophen is a substrate of CYP2E1. Alcohol is both an inducer and a substrate of CYP2E1. Alcohol taken at the same time as acetaminophen may protect the liver from injury due to high doses of acetaminophen. Which of the following is correct? CYP2E1 is increased by alcohol and converts acetaminophen to a nontoxic form. CYP2E1 metabolizes approximately 50% of therapeutic drugs. Alcohol and acetaminophen compete for CYP2E1 so a lower amount of the toxic metabolite, NAPQI, is formed. If alcohol is taken later in time than acetaminophen, high doses of acetaminophen are not toxic. The toxic metabolite of acetaminophen, NAPQI, is conjugated by alcohol to produce a nontoxic form. If alcohol is taken sooner in time than acetaminophen, then the protective effects are increased.

5 15. ATP-binding cassette transporters PHRM 836 Exam II key - 5 have both a membrane-spanning domain that recognizes ATP and a cytoplasmic domain that binds substrate. are all P-glycoproteins. are secondary active transporters. are phosphorylated upon hydrolysis of ATP. have a nucleotide binding domain that has a distinct sequence known as the ATP cassette. include the multidrug resistance family of ABC transporters, which cause the genetic disease cystic fibrosis. 16. The following accurately describe the movement of Na + and K + across the plasma membrane by Na + K + -ATPase EXCEPT which statement? utilizes ATP hydrolysis in an antiport process. works against a gradient in both Na + and K +. is highly efficient and therefore only about 10% of the ATP synthesized by muscle cells is needed for this process. even though Na + and K + are simple ions, the transmembrane domain requires as many as 10 helices for translocation. the translocation mechanism includes two distinguishable conformations. 17. Amplification can occur in a signaling pathway only if the pathway involves several protein kinases the pathway involves a second messenger the pathway involves an ion, such as sodium or calcium one molecule that is an element in the pathway can signal to many molecules of its effector there are many substrates for a protein kinase in the pathway the pathway leads to increased gene expression Choices 1, 2, 3, and 5 indicate A way for amplification to occur, but each is just one of several possible ways for amplification to occur. Choice 6 is unrelated to pathway amplification since it is the cellular process affected by the signaling pathway. Choice 4 describes the necessary and sufficient requirement for signaling amplification: that for each instance of signal input the step produces many instances of signal output. 18. Ligand binding to heptahelical receptors initiates signaling by producing a conformational change that alters the receptor conformation on the inside of the cell. producing a conformational change that causes dimerization of the ligand binding domains. producing a conformational change that leads to enlarging the opening in the transmembrane channel. producing a conformational change that causes dimerization of the intracellular domains. producing a conformational change that causes dimerization of ligand binding and intracellular domains. producing a conformational change that causes receptor internalization. producing a conformational change that causes receptor phosphorylation. There is no dimerization or membrane channel with heptahelical receptors. Choices 6 and 7 describe processes that attenuate or regulate heptahelical receptor signaling, but at least for heptahelical receptors is not part of the signaling process itself.

6 PHRM 836 Exam II key Some cell surface receptors utilize a scaffold mechanism for initiating signaling. In this context, how does a scaffold mechanism initiate signaling? It always activates a heterotrimeric G-protein. Scaffold receptors never do this. The scaffold binds the cytoskeleton and thereby becomes internalized where it initiates signaling. Scaffold receptors such as integrins can bind to proteins that bind the cytoskeleton, this does not lead to internalization and signaling does not depend on internalization. When the receptor binds ligand, the proteins that are bound to the scaffold part are activated by their close proximity to each other. The scaffold part causes the receptor dimerization. The ligand binding domain (extracellular) binds ligand, never the scaffold. The cytoplasmic domain includes an enzyme activity that becomes activated. As taught in this course, there is no enzyme activity that is part of scaffold-type receptors. The scaffold is the linker region that is between the ligand-binding domain and the intracellular domain. 20. Several kinds of receptors initiate signaling that involves tyrosine phosphorylation, but only a subset of these are considered receptors with tyrosine protein kinase activity. What is the requirement that distinguishes those that are receptors with tyrosine protein kinase activity? The tyrosine kinase cannot be a Janus kinase. The tyrosine kinase domain must be encoded by the same gene as the ligand-binding domain. The receptor must be a dimeric or trimeric cell surface receptor. The receptor must not be a gated ion channel. The receptor must not initiate signaling that leads to apoptosis. The receptor must not be associated with serine/threonine kinase activity. The receptor must initiate signaling that involves activation of the MAP kinase cascade. 21. Besides their subcellular location, what feature or function is common to nearly all intracellular receptors AND is not common to nearly all cell surface receptors? Intracellular receptors have an enzyme activity. Intracellular receptors function as dimers. Several types of cell-surface receptors (including heptahelical) do not function as dimers, while all intracellular receptors function as dimers (either hetero or homo). Intracellular receptors function as heterodimers. Intracellular receptors function as homodimers. Intracellular receptors change conformation when they bind their ligand. Intracellular receptors function once then are degraded. Intracellular receptors can function many times before they are degraded. 22. Sildenafil (Viagra) inhibits guanylate cyclase NO production adenylate cyclase phosphodiesterase It inhibits PDE5, an isoform specific for cgmp found in certain anatomical locations. ras MAP kinase cascade hydrolysis of GTP by G-proteins phospholipase C phospholipase A 2 a calcium channel located in the endoplasmic reticulum membrane

7 23. The effector for most, but not all, the actions of intracellular calcium is PHRM 836 Exam II key - 7 camp adenylate cyclase cgmp guanylate cyclase PKA PKG PKC non-receptor tyrosine protein kinases STAT proteins calmodulin 24. Nitric oxide is an exception in that its receptor is intracellular when its ligand cannot cross the cell membrane signals increased production of camp by a mechanism that does not involve a G-protein signals increased production of cgmp via activation of a G-protein is intracellular and signals via its associated enzyme activity All other intracellular receptors lack enzyme activity activates transcription of guanylate cyclase functions as a heterodimer but activates a G-protein 25. Coumadin inhibits hydroxylation of proline and lysine in collagen carboxylation of glutamate in prothrombin and other factors in the clotting cascade carboxylation of the alpha subunit of heterotrimeric G-proteins aggregation of misfolded protein unfolding of CFTR protein with a deletion of F508 lipid peroxidation activation of PKC signaling by prostaglandins 26. The most recently developed DNA sequencing methods avoid having to use PCR by sequencing in a massively parallel manner using sequencing-by-hybridization instead of sequencing-by-synthesis sequencing individual molecules of DNA sequencing only the DNA that encodes the exons sequencing the RNA directly instead of the cdna no longer needing to separate the members of the nested set produced during the extension reaction 27. Whether caused pharmacologically or physiologically, mitochondrial uncoupling results primarily in decreased cellular levels of ATP decreased cellular signaling decreased levels of ROS liver toxicity due to depletion of phosphate progression of cancer generation of heat

8 28. Transmissible spongiform encephalopathies such as scrapie are transmitted by a PHRM 836 Exam II key - 8 lentivirus transposon replicon dicoumarol prion protein catalytic RNA ESSAY PROBLEMS. Write your answers to problems 29 to 30 in the space immediately below each problem. 29. [8 points] If a bacterial toxin acted in the same manner as V. cholera toxin except that it modified G αq, and this has the same impact on Gα q as the on the G-protein modified by V. cholera toxin, what would be the direct and indirect consequences on cellular signaling of this toxin-mediated modification? Cholera toxin ADP ribosylates GTP bound Gα S inhibiting its GTPase activity. The toxin in this question must therefore similarly inhibit the GTPase activity of Gα q. Inhibiting the GTPase prolongs the signaling activity of the G-protein, amplifying the signal that originally activated the G-protein. That is the direct effect. The indirect effects are those downstream of this step in the signaling pathway. In this case, Gα q activates phospholipase C β which cleaves PIP 2 in the membrane to produce IP 3 and Diacylglyerol. The elevated levels of IP 3 increase intracellar calcium. The intracellular levels of calcium activate calmodulin, which activates Ca-CAM protein kinase. Along with diacylglycerol in the membrane, the increased calcium and diacylglycerol activate protein kinase C (PKC). In summary, the important signaling endpoints that are increased by this bacterial toxin are intracellular calcium, Ca-CAM protein kinase activity, and PKC activity. Note that the other indirect effects are intermediates in the signaling pathway and are not as important to note as the indirect effects on the end points in the signaling pathways. 30. [8 points] The figure below, taken from the PDB-101 website, shows the active site of a cytochrome P450 with the protein backbone drawn as a line tracing. In the left panel is a structure with camphor and carbon monoxide bound in the active site shown as ball-and-stick. The structure on the right is from another crystal structure and shows camphor after reaction.

9 PHRM 836 Exam II key - 9 a. For the left panel, why were the crystallographers able to crystallize cytochrome P450 with carbon monoxide but not with molecular oxygen? CO binds the heme iron and forms a thermodynamically stable complex because it blocks reaction of the enzyme. That is, CO poisons P450. Alternative answer: Because molecular oxygen is a substrate, it would react and not form a stable complex. b. Use the right panel figure to describe the chemical change in camphor catalyzed by this P450. P450 is a monoxygenase, and adds an oxygen to camphor, shown as the dark sphere closest to the heme iron on the camphor molecule.