Chemistry of Drugs Week 9 Flashcards
What are the first few letters of the greek alphabet?
alpha, beta, gamma, delta, epsilon, zeta
What is the carbon next to a carboxylic acid called?
alpha carbon
What is the carbon 2 carbons away from a carboxylic acid called?
beta carbon
What is the difference between a L-amino acid and a D-amino acid?
L has the NH2 group on the left, D has NH2 group on the right
What are the 2 most relevant side chain interactions?
salt bridges and hydrogen bonds
When will an amino acid be protonated?
when pH is lower than pKa
When will an amino acid be deprotonated?
when the pH is above the pKa
What is a hydrogen bond donor?
the molecule that provides a hydrogen atom in a hydrogen bond
What is a hydrogen bond acceptor?
a species that accepts a hydrogen atom in a hydrogen bond
Which amino acid side chains are hydrogen bond donors?
arginine, lysine, tyrosine (remember mesomeric effect)
Which amino acid side chains are hydrogen bond acceptors?
aspartic acid, glutamic acid
Which amino acid side chains are hydrogen bond donors OR acceptors?
aspargine, glutamine, histidine, serine, threonine
Which amino acid side chains undergo pi stacking?
phenylalanine, tyrosine, tryptophan, histidine
Which properties stabilise the internal structure of a protein and therefore stabilise drug-protein binding?
hydrogen bonds, salt bridges, pi stacking
What are the 4 amino acids that act as nucleophiles in chemical reactions at or near physiological pH?
cysteine, glutamic acid, aspartic acid, serine
When may amino acid sidechains be modified?
at the post-translational level by enzymes
How may amino acid sidechains be modified?
phosphorylation, methylation, acylation
What is monomethylation, dimethylation and trimethylation?
adding 1,2,3 methyl groups to NH2-R group
What are the 7 amino acids with aliphatic side chains?
alanine, glycine, isoleucine, leucine, methionine, proline, valine (a giant iguana likes many perfect vegetables)
What are the 3 amino acids with aromatic side chains?
phenylalanine, tyrosine, tryptophan
What are the 3 amino acids with acidic side chains?
aspartic acid, glutamic acid, cysteine
What are the 3 amino acids with basic sidechains?
arginine, histidine, lysine
What are the 4 amino acids with neutral but polar sidechains?
serine, threonine, aspargine, glutamine
What 3 factors does specificity rely on in biology?
- molecular shape
- chemical complementarity (interactions)
- spatiotemporal overlap