C4. Amino Acids and Drug-Target Interactions

Question 1

Describe the general structure of an amino acid

Answer 1

-Conventionally, amino acids and peptides are represented with the N-terminus on the left, and the C-terminus on the right.
-The stereochemistry at the α-carbon is nearly always (S).
ONE NOTE

Question 2

Protein Backbone and Sidechains?

Answer 2

-The ‘R’ groups of amino acids in a protein are known as sidechains.
-The rest of the amino acid forms the backbone of the protein
ONE NOTE

Question 3

Amino acid nomenclature?

Answer 3

ONE NOTE

Question 4

amino acids can be placed into what different categories?

Answer 4

-Alkyl amino acids
-(Neutral) Polar amino acids
-Sulfur-containing amino acids
-Aromatic amino acids
-Anionic amino acids
-Cationic amino acids

Question 5

Alkyl amino acids?

Answer 5

glycine, alanine, valine, leucine, isoleucine, proline
ONE NOTE

Question 6

Neutral and polar amino acids?

Answer 6

serine, threonine, asparagine, glutamine
ONE NOTE

Question 7

Sulfur containing amino acids

Answer 7

cysteine and methionine

Question 8

aromatic amino acid?

Answer 8

phenylalanine, tyrosine, trytophan
ONE NOTE

Question 9

Anionic amino acids

Answer 9

aspartic acid and glutamic acid
ONE NOTE

Question 10

cationic amino acids

Answer 10

histidine, lysine, arginine
ONE NOTE

Question 11

Angstroms (A)?

Answer 11

It is much easier to talk about distances between atoms in terms of Angstroms (Å).
1Å = 1 × 10-10 m
1Å = 0.1 nm
The length of a typical C-C bond is 1.54 Å

Question 12

non-covalent interactions?

Answer 12

Electrostatic interactions
Hydrogen bonds
Pi-Pi Interactions
Hydrophobic interactions

Question 13

electrostatic attraction?

Answer 13

attraction between positive and negative charge
ONE NOTE

Question 14

Describe hydrogen bonds

Answer 14

-A widely-observed example of a strong dipole-dipole interaction.
-Occur between a HBD and HBA.
-Distance and angle important.
-Typically 2.5 – 3.5 Å.
-Ideally linear

Question 15

an ideal hydrogen bond?

Answer 15

-An ideal hydrogen bond is linear (180°).
-Consider the two arrangements adjacent.
-Directionality of orbital containing lone pair is important!

Question 16

amides and hydrogen bonds?

Answer 16

-The nitrogen atom in an amide is not a HBA.
-The lone pair is delocalised and so not available to donate.
-The lone pairs on the oxygen are a HBA, they are not delocalised
ONE NOTE

Question 17

Aromatic interactions?

Answer 17

-Aromatic rings are planar.
-Pi system of electrons above and below the ring.
-A mix of van der Waals and electrostatic interactions.
ONE NOTE

Question 18

Describe Sildenafil

Answer 18

-Brand name is Viagra.
-Used to treat erectile dysfunction and pulmonary hypertension.
-Inhibitor of PDE5, leads to smooth muscle relaxation.

Question 19

Phosphodiesters and Phosphodiesterase?

Answer 19

one note

Question 20

Cyclic guanosine monophosphate (cGMP)?

Answer 20

-Cyclic nucleotide.
-‘Second messenger’ - triggers intracellular signal transduction cascades.

Question 21

cGMP-specific phosphodiesterase type 5?

Answer 21

one note

Question 22

Sildenafil – Drug-Target Interactions?

Answer 22

one note