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. Note the one-letter abbreviations (C, T, S, and L) that will be used for questions 1–13 on this exam.
CH2SH
Cysteine (C)
1.
OH
Tyrosine (T)
CH2OH
CH2CH2CH2CH2 NH2
Serine (S)
Lysine (L)
(2) Complete this statement by adding no more than ten words: A standard amino acid is an amino acid that...
CH2SH
2.
(2) Complete this drawing of cysteine:
N
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...
4.
(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 'N' (for none).
(a) Which amino acid has the most signals in its C-NMR spectrum? _________
(b) Which amino acid has the most deshielded carbon atom in its C-NMR spectrum? ________
(c) Which amino acid fits the following C-NMR 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 'N' (for no) if it cannot be proven or measured directly.
(a) Cysteine's S–H bond length: _____
(c) Cysteine's H–S–C bond angle: _____
(b) Whether or not cysteine can form a hydrogen bond _____
(d) If tyrosine is R or S: _____
(e) If tyrosine has resonance: _____
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Chemistry 14C
Winter 2017
Final Exam Part A
Page 2
OH
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 'N' of the answer
is none. If you write 'N' 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...
8.
(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) Now 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 pKa of water is 15.7. In the answer blank write the letter(s) (C, T, S, or L) of all amino acid side chain(s)
whose pKa is distinctly less than the pKa of water: _________
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Chemistry 14C
Winter 2017
Final Exam Part A
Page 3
13. (6) Write one or more amino acid side chain letter(s) (C, T, S, or L) in each blank.
Has a hydrophobic side chain:___________
Has a basic side chain: ______________
Fentanyl is an opioid analgesic (pain reliever) but often results in addition. It is believed that changing the way the opioid
binds to the receptor may reduce or eliminate its potential for addition. The extent to which the opioid is protonated (i.e.,
its basicity) plays a role in binding. With this in mind, fentanyl analog NFEPP 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
(C6H5X).
O
PhCH2CH2 N
N
F
PhCH2CH2 N
O
F
N
PhCH2CH2 N
O
N
H
Fentanyl (F)
NFEPP (N)
Protonated NFEPP
14. (2) In the blank write the letter (F or N) 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 NFEPP to bind to the receptor, but are absent in NFEPP.
Lorenzo's oil has been used to treat adrenoleukodystrophy, a genetic disease. The oil gained widespread publicity due to
the 1992 film Lorenzo's Oil. The oil consists of about 20% of the lipid shown below.
O
CH3(CH2)7CH=CH(CH2)11
O
O
O
O
(CH2)11 CH=CH(CH2)7CH3
(CH2)11 CH=CH(CH2)7CH3
O
Lorenzo's oil lipid
16. (2) By writing no more than twenty words, provide a precise yet concise definition of lipid. Note 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...
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Chemistry 14C
Winter 2017
Final Exam Part A
Page 4
19. (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
CH3F
F2
(b)
F2
FCl
FBr
FI
(c)
CH4
CH3OH
CH3CH2OH
HOCH2CH2OH
(d)
F2
Cl2
Br2
I2
22. (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
O
(a)
CH3OH
OH
OH
N
OH
O
(b)
HF
HCl
HBr
HI
(c)
HOF
HOCl
HOBr
H 2O
(d)
H 2O
HF
NH3
CH4
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Chemistry 14C
Winter 2017
Final Exam Part A
Page 5
23. (2) In the answer blank write the letter of the most acidic, boxed hydrogen atom. Answer: _______
O
(a)
H
O
H
(b)
H
O
(c)
H3C
H2C
H
O
(d)
CH3
H
H3C
O
O
H
N
N
Questions 24 and 25 refer to this DNA nucleobase:
N
N
NH2
24. (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.
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