amino acids, peptides and proteins

Question 1

What are amino acids?

Answer 1

Amino acids are the building blocks of peptides and proteins.

Amino acids are organic compounds that contain amine (–NH2) and carboxyl (COOH) functional groups, along with a side chain (R group)
▪ R group is specific to each amino acid.
▪ The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other elements are found in the side chains of certain amino acids, such as sulphur.

Question 2

what is the sequence for the start codon?

Answer 2

AUG
It codes for Met

Question 3

what kind of configuration do most amino acids form?

Answer 3

Usually the L configuration.

Question 4

what is the isoelectric point?

Answer 4

At the exact midpoint between the two pKa values, the amount of negative and positive ions exactly balance, so that average net charge of all forms present is zero
▪ This pH is known as the isoelectric point

Question 5

What bond holds together amino acids?

Answer 5

peptide bonds
(formed as a result of a condensation reaction)

Question 6

What is the difference between proteinogenic amino acids and non-proteinogenic amino acids?

Answer 6

non-proteinogenic amino acids are either not found in proteins or not produced directly from the genetic code while proteinogenic amino acids are components of peptides and proteins.

Question 7

what is the primary structure of proteins?

Answer 7

Linear sequence of amino acids in a polypeptide or protein

Question 8

What is the secondary structure of proteins?

Answer 8

Highly regular local structures (folding) on the polypeptide backbone chain.
▪ A polypeptide will spontaneously fold into a regular and defined shape – dependent on the
primary structure.
▪ Three main types of secondary structure have been found in proteins:
✓ Alpha helix
✓ Beta pleated sheet
✓ Beta bend/turn
▪ These secondary structures are defined by patterns of hydrogen bonds between the
polypeptide R groups.

Question 9

What is the tertiary structure?

Answer 9

3D structure created by a single polypeptide chain
▪ The secondary structures are folded into a compact
3D structure
▪ The folding is driven by the non- specific hydrophobic
interactions and the burial of hydrophobic amino acids in the inside of the protein
▪ The structure is stable only when the parts of a protein
domain are locked into place by specific tertiary interactions, such as salt bridges, disulphide bonds
and hydrogen bonds.

Question 10

What is the quaternary structure?

Answer 10

3D structure consisting of the aggregation of two or more individual polypeptide
chains (subunits) that operate as a single functional unit (multimer).
▪ It is stabilised by the same interactions that hold the tertiary structure together
▪ Forms two types of proteins
▪ Globular – polypeptide chains interact to form a spherical shape
▪ Fibrous – polypeptide chains lie parallel to each other to form a fibre
▪ Not found in all proteins

Question 11

What post-translational modifications can take place in a protein?

Answer 11

A wide variety of modifications can take place
▪ The N-terminal amino group of a protein can be modified
▪ Acetylation – addition of a –CH3 group
▪ Phosphorylation - a phosphate group can be attached to the sidechain hydroxyl group of
serine, threonine and tyrosine.
▪ Glycosylation – addition of sugars to sidechain hydroxyl groups of serine and threonine.