Introduction to Bioorganic Chemistry and Chemical Biology 1 Answers to Chapter 5 (in-text & asterisked problems) Answer 5.1 Answer 5.2 PDB 3ZNF H27 H21 C8 C5 N H H N N H H N N H H N O O O O O O NH NH 2 + H 2 N O - NH NH 2 + H 2 N O N H H N N H H N N H H N NH NH 2 + H 2 N O - NH NH 2 + H 2 N O O O O O O O N H H N N H H N N H H N O O O O O O NH NH 2 + H 2 N O - NH NH 2 + H 2 N O IRGERA AREGRI ent-IRGERA
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Answers to Chapter 5 - Garland · PDF fileIntroduction to Bioorganic Chemistry and Chemical Biology: Answers to ChApter 5 3 Answer 5.6 Answer 5.7 Answer 5.8 Answer 5.9 A A1,3 strain
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Introduction to Bioorganic Chemistry and Chemical Biology 1
Answers to Chapter 5(in-text & asterisked problems)
a concerted, one-step E2 mechanism is also plausible
+
..
Ph Ph
Cys S Ph
H A
Ph Ph
Cys S PhH
++ +CPh3
Cys SH
Ph Ph
Ph
H
Sii-Pri-Pri-Pr
CF3COO
+-
i-Pr3SiO2CCF3 + Ph3C-H
Ka' < -8).
A Initial protonation occurs on the amide carbonyl, not the amide nitrogen.
C
D
E
B Protonation of N would disrupt the aromaticity of the imidazole ring. Therefore initial protonation occurs on the N not N .
Note that protonation of thioethers is extremely unfavorable (p
8 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to ChApter 5
*Answer 5.28
A KVKVKVKVKVKVK, because β-branched amino acids have high β-sheet propensities and low α-helix and turn propensities.
B GppGppGppGppGppGppGpp, because pro has low α-helix and β-sheet propensities.
C nLeDKAeeLLsKnYhLeneVArL, because it has a leucine zipper motif with Leu at every seven residues.
D GppGppGppGppGppGppGpp, because (Gpp)n forms a collagen triple helix.
E GppGppGppGppGppGppGpp, because pro has low α-helix and β-sheet propensities.
*Answer 5.31
A the calcium-binding loops are underlined: MADQLTEEQIAEFKEAFSLFDKDG-DGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMK-DTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDG-DGQVNYEEFVQMMTAK
B the first calcium-binding loop is positions 21–32, -DKDGDGtIttKe-. the first and last positions of the calcium-binding loop are the only positions conserved as ani-onic amino acids. therefore Asp21 and Glu32 are most likely to bind as anionic car-boxylates. In the crystal structure for pDB 1CFC, both of the side-chain carboxylate oxygens of Glu32 bind to the calcium ion. Because asparagines are also tolerated at the second and third ligand positions, Asp23 and Asp25 probably coordinate as neutral ligands through the side-chain carbonyls. Because phenylalanine is also tol-erated at the fourth ligand position, it is likely that the backbone carbonyl, and not the side chain, is coordinating to calcium. Because serine is a common ligand for the fifth position, thr29 probably binds through the side-chain hydroxyl. As a result of the high pKa of alcohols compared with carboxylic acids, thr29 probably binds as a neutral oh ligand.
C Glycine is highly flexible and can adopt tight turns. Isoleucine and valine are β-branched hydrophobic amino acids that limit the flexibility of the side chain and loop.
*Answer 5.32
A two types of dimers are known. the dimer based on swapping the s-peptide (pDB 1Bsr) has the s-peptide from the first molecule bound in the cleft of the second molecule, and vice versa.
Introduction to Bioorganic Chemistry and Chemical Biology: Answers to ChApter 5 9
B there may be many solutions to this problem. Any mutation to the loop that prevents the helix from binding to the cleft in residues 1–113 will favor the formation of the domain-swapped dimer. Investigators have induced dimerization by generating a deletion variant Δ(114:119) that lacks the flexible loop.
*Answer 5.36
*Answer 5.38
A Cys28 makes contacts with DnA (rendered as a brown surface).
B the nearby cysteine residue is Cys120.
C Cysteine thiols are efficient at conjugate addition reactions.