Lecture 2: Protein structure - primary sequence

How are peptide bonds formed

Reaction between carboxyl and amino group of 2 amino acids

Amino acids linked by peptide bonds form a

Polypeptide (folds to form specific protein)

What is a residue

Each amino aid in a polypeptide chain

Why are polypeptides polar

Due to the oppositely charged ends, called the N-terminus (always positive) and C-terminus (always negative)

Carbonyl and NH groups are hydrogen bond…

Acceptors

Donors

Average mass of an amino acid

110 Da (g/mol)

Average mass of proteins

5500 Da and 220000 Da

Why do peptide bonds have partial double bond character

They are planar with limited rotation, also have a length between a C-N single and double bond

What is geometric isomerism

Explains how 2 alpha-carbon atoms are positioned around peptide bonds form

Cis/trans

Why do peptide bonds in proteins prefer trans configuration

Fewer steric clashes

Why is amino acid + proline peptide bond special

The steric clashes are equal so there is equal chance of forming cis/trans isomers

What are dihedral angles

Ways to specify rotation around the two types of bonds (i..e peptide and regular single)

What are the 2 different dihedral angles

Phi and Psi

What is Phi angle

Angle of rotation about the bond between nitrogen and a-carbon atom

What is the Psi angle

Angle of rotation about the bond between a-carbon atom and the carbonyl chain

What does the freedom of rotation allow

The protein to fold in many ways

Why may some combinations of Phi and Psi permitted

Steric hindrance/ collisions between atoms

What is used to assess these combinations

Ramachandran Plot, where patches of favoured angles define secondary structure (white areas = high steric hindrance so unfavourable)