hem 499 inal Exam pring, 2016 eauchamp ame: 1 Topic Total Points Exam Points Problem 1 6 Problem 2 6 Problem 3 5 Problem 4 5 Problem 5 14 Problem 6 14 Problem 7 5 Problem 8 13 Problem 9 9. Problem 10 8. Problem 11 6. Problem 12 11. Problem 13 9. Problem 14 10. Problem 15 18. Problem 16 8. Problem 17 8. Problem 18 12. Problem 19 8. Problem 20 10. Problem 21 4. Problem 22 6 Total 195 redit Make sure you show all of your work. Draw in any lone pairs of electrons, formal charge and curved arrows to show electron movement when required. nly write answers in the space available. Thank you for sharing this course with me. I learned a lot and I hope you did too. ave a productive summer.
2 1. The normal pka of the histidine in solution is about 6.0. In enzyme A it was found to be 5.1 and in enzyme it was found to be 7.9. What can you say about possible other amino acid residues near the binding site to rationalize these observations? (3 pts each = 6 pts) pka = 5.1 histidine pka = 7.9 histidine 2. a. ydrolysis of compound A occurs 10 8 times faster than compound. Provide a possible explanation. (3 pts each = 6 pts) 2 2 3 3 P compound A P compound b. Explain the relative reaction rates indicated. k rel. = 1.0 M -1 s -1 k rel. = 51,000 M -1 s -1 k rel. = 12,000,000 M -1 s -1
3 3. Valinomycin (shown below) is an antibiotic which is able to transport ions into and out of cells. Would you expect valinomycin is better at transporting anions, cations or both? Explain your reasoning. Propose an explanation for how this can occur considering the polarity of all the interacting components (blood, membranes and cytosol). Why might a microorganism make such a compound? (5 pts) 4. Adrenaline and estrone are signaling hormones. The hormone adrenaline interacts with proteins located on the surface of cells and does not cross the cell membrane. owever, the larger steroid estrone can cross cell membranes and interact with proteins located in the cell nucleus. Why is a larger steroid molecule able to cross the cell membranes while a smaller molecule, such as adrenaline cannot? (5 pts) 3 2 adrenaline estrone
4 5. riefly, discuss how epinephrine activates a cell from the time it is released into the blood stream. Make a series of simple sketches to show this. Why might there be a need for an inhibitor of epinephrine? (14 pts)
5 6. Discuss how vitamin and vitamin E can work together to protect cells throughout the body from free radical damage. represents a long hydrocarbon chain. Use a hydroxyl radical ( ) to provide a simple mechanistic explanation for how these 2 vitamins can repeatedly quench free radicals and eliminate the danger from the body. (14 pts) vitamin simplified vitamin simplified oxidized vitamin Me simplified vitamin E ( = long hydrocarbon chain) dangerous hydroxyl radical
7. a. Write a simple arrow pushing mechanism to show hydration of a ketone. (2 pts) 6 ketone carbonyl hydrate b. how oxidation of the ketone hydrate to a carboxylic acid using either AD+ or AD (whichever one works). (3 pts) carbonyl hydrate AD or AD+ carboxylic acid AD+ AD 8. a. Physostigmine is an alkaloid found in the alabar plant in Africa. In 1846 its main use was as a poison, though today it is used as a medicine. It is a reversible acetylcholine inhibitor. What overall charge would you expect on physostigmine at physiological p (= 7.4)? If you think charge is present, redraw the structure to show this and explain your reasons. (4 pts) 3 physostigmine
7 b. how an arrow-pushing mechanism for acetylcholine binding and hydrolyzing at a receptor. Use : (base) and + - (acid) as needed. (3 pts) (base) (acid) choline (base) (acid) acetylcholine serine in receptor recycles into the presynaptic cell acetylserine in receptor serine in receptor c. The reason physostigmine inhibits the acetylcholine receptor is because it binds to the receptor much more strongly than acetylcholine (hydrolyzes off more slowly). how a mechanism for physostigmine binding to the receptor and provide an explanation for why it hydrolyzes more slowly than acetylcholine. (6 pts) 3? physostigmine serine in receptor 9. a. The methylation of cytosine residues in DA plays a role in the regulation of transcription and is catalyzed by the enzyme DA methyltransferase. Add in curved arrows to show how the reaction proceeds. (4 pts) Enz cytosine Enz Enz 3 Enz 3 Enz 3 methylcytosine
8 b. 5-fluoro-2 -deoxycytidine is a mechanism-based inhibitor of DA methyltransferase. Explain why. (5 pts) Enz Enz ibose 5-fluoro-2'-deoxycytidine 10. Proteins can turn on or turn off through phosphorylation by a kinase enzyme. Make a sketch showing how an enzyme might turn on and how an enzyme might turn off. (4 pts each = 8 pts) components to work with P ATP serine other aminoacid other aminoacid generic base active site closed (enzyme off) active site open (enzyme on) generic acid show turning on enzyme show turning off enzyme
9 11. Propose a mechanism for how thiamin (vit. 1 ) could decarboxylate an α-keto-acid. upply necessary mechanistic details (curved arrows, electron pairs, formal charge, etc.) in scheme below. (6 pts) 2 thiamin (vitamin 1) = thiamin (simplified) generic keto-acid 12. how how pyridoxal phosphate, vitamin 6, can allow any of the three groups attached to serine s alpha carbon to become a good leaving group. Use mechanism arrows. Explain how it allows each of these eliminations to occur so easy? What structural feature on an enzyme could orientate the specified leaving group to be in the correct position for elimination? The example structure(s) have been simplified (on the next page). 2 2 serine -2 3 P vitamin 6 (aldehyde) (- 2 ) enzyme 2-2 3 P vitamin 6 (imine) 2 leaving group = 2 leaving group leaving group
+ leaving group (2 pts) 10 2 What how and why? 2 2 2 leaving group (2 pts) 2 What how and why? 2 2 2 = leaving group (2 pts) 2 What how and why? 2 2 Explanation. (2 pts) Provide a mechanism for how an amine can be released from vit 6 (imine form). (3 pts) use these as needed 2
13. a. What does ADME stand for? Give a one sentence explanation of each word. (3 pts) 11 b. What is the difference between pharmacokinetics and pharmocodynamics? (3 pts) c. What percent of a drug is left after 6 half lives? how your work. (3 pts) 14. a. Match the log P values with the compounds below and explain your reasoning. What is the K P value for each compound? (log P values = -3.1, 1.0 and 3.6) (5 pts) paroxetine prednisolone mitoxantrone b. Provide an explanation for the observed log D plot. (5 pts) log D 1.5 3 3 3 omeprazole 3 1.0 0.5 0.0-0.5 2 4 6 8 10 12 14 p -1.0-1.5
12 15. ytochrom P-450 enzymes use iron in different oxidation states to change the oxidation state of many functional groups in biochemistry. e +3 (reduced) and e +4 - (oxidized) show simplified representations of these enzymes that are commonly used. 2 e +3 e +4 cytochrom P-450 oxidation states oxidizes organic molecules a. lavins, in their oxidized form can accept up to two electrons and two protons (1 electron at a time or 2 electrons at a time). how how these transformation might occur by adding in simple 1 electron arrows and proton transfers. Include mechanism arrows. (4 pts) l ox l ox -l ox -l ox -l- red l ox l ox -l ox 1 e _ add electron add proton add electron 1 e _ -l- red add proton -l ox b. how an appropriate flavin in any necessary steps below (write simplistically as l in an acceptable oxidation state as shown above). Also draw any mechanism arrows, acids (- + ), bases (:), water molecules ( 2 ), etc as needed. (4 pts) oxidizing iron -l-, red e +3 e +2 e +3 -l ox e +3 e +4 e +3 e +3
13 c. Write a simplistic mechanism for 2 electron reduction of the given lavin using the appropriate reagent, AD+ or AD, and any other necessary compounds. (2 pts) oxidized flavin reduced flavin d. how how the oxidized form of iron (cytochrom P-450s) could cause the indicated transformations below (write mechanisms) and provide an explanation for why this is useful to an organism. reaction 1 (2 pts) e +4 reaction 2 (2 pts) e +4 reaction 3 (2 pts) e +4 reaction 4 (additional hydration step for the epoxides) (2 pts)
14 16. Porphobilinogen synthase is a zinc-dependent enzyme (contains two zinc ions) that catalyzes the condensation of two molecules of 5-aminolevulinic acid to give porphobilinogen, a compound used to make porphyrin rings that complex metals, such as iron in cytochrom P-450. upply necessary mechanistic details (curved arrows, electron pairs, correct formal charge, etc.) in the scheme below. (8 pts) 2 Zn +2 2 Zn 2 2 Zn 2 Zn +2 2 3 2 Zn 2 2 2 2 2 2 Zn 2 2 2 2 2 2 2 2 2
15 17. Eflornithine (α-difluoromethylonithine) is used for treating African sleeping sickness. A possible mechanism for inactivating a key enzyme in the microorganism is shown below. Add in the necessary mechanistic details (curved arrows, formal charge, important lone pairs) to show how this might occur. (8 pts) simplified vitamin 6 2 Eflornithine 2 2 2 2 2 2 2 2 2
16 18. Indicate what kind of DA drug is shown below and how it interferes with DA function. upply necessary mechanism details. a. daunorubicin (3 pts) 2 daunorubicin 3 DA 3 DA b. esperamicins show formation of the reactive species (3 pts) duocarbycin A ugar ugar ugar ugar 3 3 diradical cleaves DA chain ugar ugar ugar ugar
17 c. fluphenazine has a short duration of activity of 6-8 hours in the body. luphenazine ethanate has a duration of about 1 month. Provide a possible explanation. (3 pts) 3 3 fluphenazine ethanate fluphenazine e. tolmetin sodium (Tolectin) has an activity of about 1 hour in the body. The glycine conjugate as an activity of about 9 hours. Provide a possible explanation. (3 pts) Tolmetin sodium a glycine conjugate of Tolmetin
18 19. Enzymes that use glutathione are an important part of the defense against toxic drugs and metabolites. Using simplistic arrow-pushing mechanisms, show how glutathione could protect against potent electrophiles, and how it could protect against reactive free radicals. You can write glutathione as --. Use : (base) and + - (acid) as needed. 2 3 2 i. Protection from electrophiles (2 pts each = 8 pts) a. r glutathione (you can write this as --) b. c. d. Protection from free radical
19 20. In large doses Tylenol causes severe liver necrosis, resulting from over 80% depletion of glutathione levels and depletion of P-450 capacity (so they cannot oxidize normal biological molecules and other drugs that might be taken). This is thought to occur from oxidation of acetaminophen by cytochrome P-450 enzymes, followed by conjugate addition of glutathione. how simplistic mechanisms for these processes. (10 pts) 3 Tylenol (aceaminophen) 2 glutathione (you can write this as --) 2 e P-450 enzyme Tylenol (metabolites) glutathione
20 21. An antibody was raised against a tumor cell line and was conjugated to a β-lactamase. A nitrogen mustard was conjugated to a cephalosporin for use in ADEPT (antibody directed enzyme prodrug therapy). Draw a mechanism for the activation of the prodrug by the ADEPT conjugate (elimination of the mustard drug. (4 pts) l l 2 serine 22. Propose a mechanism, using ATP, for each of the following transformations. Use for a base and - + for an acid, if necessary. What purpose might these transformations serve in a living organism? int: making a mixed anhydride might prove very helpful. (2 pts each = 6 pts) foreign alcohol in body glucoronic acid sulfate 3 glycine P ATP simplified ATP i. Glucoronic acid conjugation of an. glucoronic acid P simplified ATP ATP foreign alcohol in body ii. ulfonation of an. P sulfate simplified ATP ATP foreign alcohol in body iii. Glycination of a 2. 3 glycine P ATP foreign alcohol simplified ATP in body 3