Biochemistry: Amino Acids & Protein Structure

What are the three-letter and one-letter codes for the basic amino acid Lysine?

The three-letter code is Lys and the one-letter code is K.

Which amino acid is the only one that is not chiral and why?

Glycine (Gly, G) is not chiral because its side chain is a single hydrogen atom, meaning the alpha-carbon is bonded to two identical groups.

Define the primary structure of a protein and the bond that stabilizes it.

Primary structure is the linear sequence of amino acids in a polypeptide chain, stabilized by covalent peptide (amide) bonds.

Which two amino acids contain carboxylic acid functional groups in their side chains and are negatively charged at pH 7.4?

Aspartate (Asp, D) and Glutamate (Glu, E).

What type of covalent bond can form between the side chains of two Cysteine residues?

A disulfide bond (or disulfide bridge), which results from the oxidation of two thiol (-SH) groups.

Name the three amino acids that contain aromatic rings in their side chains.

Phenylalanine (Phe, F), Tyrosine (Tyr, Y), and Tryptophan (Trp, W).

What are the one-letter codes for Asparagine and Glutamine?

Asparagine is N and Glutamine is Q.

Why is Proline often referred to as a 'helix breaker' in protein secondary structure?

Proline has a rigid cyclic pyrrolidine side chain that is covalently bonded to the nitrogen of the peptide backbone, which prevents it from participating in the standard N-H hydrogen bonding required for an alpha-helix.

Describe the specific hydrogen bonding pattern that stabilizes a standard alpha-helix.

Hydrogen bonds form between the carbonyl oxygen (C=O) of residue 'i' and the amide hydrogen (N-H) of residue 'i+4'.

What is the approximate pKa of the imidazole side chain in Histidine, and why is this value biologically significant?

The pKa is approximately 6.0. This is significant because it is close to physiological pH, allowing Histidine to act as both a proton donor and acceptor in enzyme catalysis.