Introduction to Enzyme and Coenzyme Chemistry - E-Library Home

Appendix 4: Answers to
Problems
Chapter 2
(1) pH4. (a) Arginine, lysine, histidine. (b) None.
pH7. (a) Arginine, lysine, histidine (partially). (b) Aspartate, glutamate.
pH10. (a) Arginine. (b) Aspartate, glutamate, cysteine, tyrosine (partially).
(2) Donation of nitrogen lone pair into C5O bond requires nitrogen lone pair
to be parallel with p bond. In fact there is some double bond character in
the C2N bond, so the amide bond is planar and rigid. Trans-conformation
more favourable due to steric repulsions between a-carbons in cisconformation.
Proline forms a secondary amide linkage in which there is
a much smaller diVerence in energy between cis- and trans-conformations.
(3) 1st reading frame: Thr–Ala–Glu–Asn–Phe–Ala–Pro–Ser–Arg–Stop
2nd reading frame: Arg–Leu–Lys–Thr–Ser–His–Gln–Val–Asp–
3rd reading frame: Gly–Stop (–Lys–Leu–Arg–Thr–Lys–Ser–Ile)
Stop codon is impossible in the middle of a gene, so second reading frame
appears to be the right one.
(4) 1(Met) 4(Ala) 6(Leu) 6(Ser) 2(His) 2(Asp) 1(Trp) 2(Phe)
6(Arg) 4(Val) ¼ 27 648.
A primer based on the His–Asp–Trp–Phe sequence would have a 1 in 8
chance of being correct.
(5) (a) This a helix has 6 leucines on one face, forming a very hydrophobic
surface. This leads to self-aggregation in water to form a four-helix
bundle with hydrophobic side chains on the inside and hydrophilic side
chains on the surface. There are also favourable Glu 4 -Lys 8 and
Glu 5 -Lys 9 electrostatic interactions which stabilise the helix.
(b) This a-helix has Wve lysines on one face, designed to mimic the active
site of acetoacetate decarboxylase, where the proximity of a second
lysine residue leads to a lower pK a value and a more nucleophilic lysine.
This helix showed some catalytic activity as an oxaloacetate decarboxylase.
Chapter 3
(1) Intramolecular base catalysis, with the internal tertiary amine acting as a
base to deprotonate an attacking water molecule. Tertiary amines are good
bases and poor nucleophiles, so nucleophilic catalysis is not feasible.
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