Chemistry of Drugs Week 9

Question 1

What are the first few letters of the greek alphabet?

Answer 1

alpha, beta, gamma, delta, epsilon, zeta

Question 2

What is the carbon next to a carboxylic acid called?

Answer 2

alpha carbon

Question 3

What is the carbon 2 carbons away from a carboxylic acid called?

Answer 3

beta carbon

Question 4

What is the difference between a L-amino acid and a D-amino acid?

Answer 4

L has the NH2 group on the left, D has NH2 group on the right

Question 5

What are the 2 most relevant side chain interactions?

Answer 5

salt bridges and hydrogen bonds

Question 6

When will an amino acid be protonated?

Answer 6

when pH is lower than pKa

Question 7

When will an amino acid be deprotonated?

Answer 7

when the pH is above the pKa

Question 8

What is a hydrogen bond donor?

Answer 8

the molecule that provides a hydrogen atom in a hydrogen bond

Question 9

What is a hydrogen bond acceptor?

Answer 9

a species that accepts a hydrogen atom in a hydrogen bond

Question 10

Which amino acid side chains are hydrogen bond donors?

Answer 10

arginine, lysine, tyrosine (remember mesomeric effect)

Question 11

Which amino acid side chains are hydrogen bond acceptors?

Answer 11

aspartic acid, glutamic acid

Question 12

Which amino acid side chains are hydrogen bond donors OR acceptors?

Answer 12

aspargine, glutamine, histidine, serine, threonine

Question 13

Which amino acid side chains undergo pi stacking?

Answer 13

phenylalanine, tyrosine, tryptophan, histidine

Question 14

Which properties stabilise the internal structure of a protein and therefore stabilise drug-protein binding?

Answer 14

hydrogen bonds, salt bridges, pi stacking

Question 15

What are the 4 amino acids that act as nucleophiles in chemical reactions at or near physiological pH?

Answer 15

cysteine, glutamic acid, aspartic acid, serine

Question 16

When may amino acid sidechains be modified?

Answer 16

at the post-translational level by enzymes

Question 17

How may amino acid sidechains be modified?

Answer 17

phosphorylation, methylation, acylation

Question 18

What is monomethylation, dimethylation and trimethylation?

Answer 18

adding 1,2,3 methyl groups to NH2-R group

Question 19

What are the 7 amino acids with aliphatic side chains?

Answer 19

alanine, glycine, isoleucine, leucine, methionine, proline, valine (a giant iguana likes many perfect vegetables)

Question 20

What are the 3 amino acids with aromatic side chains?

Answer 20

phenylalanine, tyrosine, tryptophan

Question 21

What are the 3 amino acids with acidic side chains?

Answer 21

aspartic acid, glutamic acid, cysteine

Question 22

What are the 3 amino acids with basic sidechains?

Answer 22

arginine, histidine, lysine

Question 23

What are the 4 amino acids with neutral but polar sidechains?

Answer 23

serine, threonine, aspargine, glutamine

Question 24

What 3 factors does specificity rely on in biology?

Answer 24

1. molecular shape
2. chemical complementarity (interactions)
3. spatiotemporal overlap

Question 25

What can specific interactions involving protein be with?

Answer 25

small molecules (substrates or neurotransmitters) or large molecules (other proteins)

Question 26

Where does specific protein-protein interaction occur?

Answer 26

on the protein surface

Question 27

Where does specific protein-substrate interaction occur?

Answer 27

in the active site

Question 28

What is an example of interactions in an active site?

Answer 28

class A beta-lactamases in antimicrobial resistance

Question 29

What are b-lactam antibiotics?

Answer 29

most prescribed antibiotic class, includes penicillin

Question 30

What do b-lactam antibiotics do?

Answer 30

target enzymes called pencillin-binding proteins (PBPs)

Question 31

What do pencillin-binding protein do?

Answer 31

they are involved in the biosynthesis of the cell wall in gram-negative bacteria and are irreversibly inhibited by b-lactam antibiotics

Question 32

What are b-lactamases?

Answer 32

a class of enzymes found in some gram-negative bacteria that hydrolyse the amide bond of the 4-membered b-lactam ring in antibiotics