Chemistry 14C Winter 2017 Final Exam Part A Page 1

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1 Chemistry 14C Winter 2017 Final Exam Part A Page 1 Please use the backs of the exam pages for scratch space. Please do not use the exam margins for this purpose. The active site of an enzyme is a cleft or hole in the enzyme's structure where the enzyme's chemical reactions take place. The active site is lines with amino acid side chains. Imagine an active site containing these standard amino acid side chains. ote the one-letter abbreviations (C, T, S, and L) that will be used for questions 1 13 on this exam. C 2 S C 2 C 2 C 2 C 2 C 2 2 Cysteine (C) Tyrosine (T) Serine (S) Lysine (L) 1. (2) Complete this statement by adding no more than ten words: A standard amino acid is an amino acid that... C 2 S 2. (2) Complete this drawing of cysteine: 3. (2) Complete this statement by adding no more than ten words: Cysteine is unique, or one of only two among the twenty standard amino acids because cysteine (6) Answer each question by writing one amino acid letter (C, T, S, or L) in each answer blank. In case of a tie write two or more letters. If none of the amino acid choices are correct, write '' (for none). (a) Which amino acid has the most signals in its C-MR spectrum? (b) Which amino acid has the most deshielded carbon atom in its C-MR spectrum? (c) Which amino acid fits the following C-MR spectrum: 175 ppm (singlet), 55 ppm (doublet), 40 ppm (triplet), 31 ppm (triplet), 27 ppm (triplet), and 22 ppm (triplet). Answer: 5. (5) For each part of this question write 'Y' (for yes) in the blank if the listed property can be proven (measured directly) by x-ray crystallography, or '' (for no) if it cannot be proven or measured directly. (a) Cysteine's S bond length: (b) Whether or not cysteine can form a hydrogen bond (c) Cysteine's S C bond angle: (d) If tyrosine is R or S: (e) If tyrosine has resonance: Page 1 score =

2 Chemistry 14C Winter 2017 Final Exam Part A Page 2 It was found that the enzyme mentioned on page 1 binds to phenol using noncovalent attractive forces. Phenol 6. (5) For each amino acid listed below, write all of the noncovalent attractive forces that might occur between that amino acid's side chain and phenol. If no noncovalent attractive forces can occur write 'none'. (a) Cysteine: (b) Tyrosine: 7. (6) For each statement below write one amino acid side chain letter (C, T, S, or L) in each blank, or '' of the answer is none. If you write '' you are done with that part of the question. If you write an amino acid letter complete the statement by adding no more than fifteen words of explanation. The explanations must be different for each part. Be precise and specific. If more than one amino acid applies, it does not matter which one you pick. (a) Amino acid cannot be a hydrogen bond donor because this amino acid... (b) Amino acid cannot be a hydrogen bond acceptor because this amino acid (4) Rank the water solubility of the four amino acids by writing one amino acid letter (C, T, S, or L) in each blank. Most soluble in water: Least soluble in water: The chemical reaction that occurs on the bound phenol might involve protonation by an amino acid side chain so predicting the relative acidity of these side chains can provide useful information. 9. (6) We learned in lecture of the various aspects of molecular structure that control acidity. For each structural factor listed below, write the letter (C, T, S, or L) of one amino acid side chain whose acidity is most enhanced or most increased by this factor. If more than one amino acid's acidity is enhanced, write just one letter. Resonance: Atomic radius: Electronegativity: 10. (4) Write the names of two structural features not mentioned in question 9 that might also enhance the acidity of a any molecule (not necessarily just the four amino acids mentioned on the first page). 11. (4) ow rank the acidity of the four enzyme amino acid side chains by writing one amino acid letter (C, T, S, or L) in each blank. In case of a tie write just one letter in each blank. Most acidic: Least acidic: 12. (4) The pk a of water is In the answer blank write the letter(s) (C, T, S, or L) of all amino acid side chain(s) whose pk a is distinctly less than the pk a of water: Page 2 score =

3 Chemistry 14C Winter 2017 Final Exam Part A Page (6) Write one or more amino acid side chain letter(s) (C, T, S, or L) in each blank. as a hydrophobic side chain: as a basic side chain: Fentanyl is an opioid analgesic (pain reliever) but often results in addiction. It is believed that changing the way the opioid binds to the receptor may reduce or eliminate its potential for addiction. The extent to which the opioid is protonated (i.e., its basicity) plays a role in binding. With this in mind, fentanyl analog FEPP was tested, and found that it binds less strongly (and therefore has less potential for abuse). Recall that Ph = phenyl = a benzene ring with one substituent (C 6 5 X). F F PhC 2 C 2 PhC 2 C 2 PhC 2 C 2 Fentanyl (F) FEPP () Protonated FEPP 14. (2) In the blank write the letter (F or ) of the molecule that is the weakest base: 15. (4) Binding to the opioid receptor occurs via various noncovalent interactions. Write the name(s) of all noncovalent molecular forces that might allow protonated FEPP to bind to the receptor, but are absent in FEPP. Lorenzo's oil has been used to treat adrenoleukodystrophy, a genetic disease. The oil gained widespread publicity due to the 1992 film Lorenzo's il. The oil consists of about 20% of the lipid shown below. C 3 (C 2 ) 7 C=C(C 2 ) 11 (C 2 ) 11 C=C(C 2 ) 7 C 3 (C 2 ) 11 C=C(C 2 ) 7 C 3 Lorenzo's oil lipid 16. (2) By writing no more than twenty words, provide a precise yet concise definition of lipid. ote this definition has two essential parts. 17. (2) In lecture we learned of seven general lipid categories. To which of these categories does the Lorenzo's oil lipid belong? 18. (6) Complete each statement below by writing the name of one of the seven general lipid categories in the blank, and then add no more than ten words of explanation. (a) The Lorenzo's oil lipid is not an example of a because the Lorenzo's oil lipid... (b) The Lorenzo's oil lipid is not an example of a because the Lorenzo's oil lipid... Page 3 score =

4 Chemistry 14C Winter 2017 Final Exam Part A Page (2) Complete this statement by writing C (for cis), T (for trans), or X (for cannot determine) in the blank. The alkenes present in the Lorenzo's oil lipid are most likely. 20. (2) Another lipid component of Lorenzo's oil contains 57 carbons. Write in the blank the letter of least likely number of oxygen atoms in the structure:. Answer choices: (a) zero oxygens; (b) six oxygens; (c) 57 oxygens. 21. (8) For each set of molecules, write the number of the molecule with the highest boiling point in the answer box. Choice 1 Choice 2 Choice 3 Choice 4 Answer Box (a) LiF ClF C 3 F F 2 (b) F 2 FCl FBr FI (c) C 4 C 3 C 3 C 2 C 2 C 2 (d) F 2 Cl 2 Br 2 I (8) For each set of molecules, write the number of the most acidic molecule in the answer box. Choice 1 Choice 2 Choice 3 Choice 4 Answer Box (a) C 3 (b) F Cl Br I (c) F Cl Br 2 (d) 2 F 3 C 4 Page 4 score =

5 Chemistry 14C Winter 2017 Final Exam Part A Page (2) In the answer blank write the letter of the most acidic, boxed hydrogen atom. Answer: (a) (b) (c) (d) 3 C 2 C C 3 3 C Questions 24 and 25 refer to this DA nucleobase: (4) In each blank write the letter of the best answer from among the given answer choices. This nucleobase is part of. Answer choices: A, C, G, T, or U. This nucleobase is a. Answer choices: (a) purine, or (b) pyrimidine This nucleobase is. Answer choices (a) aromatic, or (b) not aromatic 25. (2) Complete each sentence by writing a number in the blank: This nucleobase forms a Watson-Crick base pair involving hydrogen bonds. Page 5 score =