Paper

Chemistry of Cells

U14505

Topic 4

Structure of Macromolecules

Tony Bradshaw

Lecture 4

Protein structure and function II

Secondary structure

The Peptide Bond

Each amino acid contributes 3 bonds the to polypeptide backbone

Polypeptide backbone

In a polypeptide the main chain N-Cα and Cα-C bonds are

relatively free to rotate. These rotations are represented by the

torsion angles phi (φ) and psi (ψ), respectively.

phi (φ) and psi (ψ), are both defined

as 0° when the two peptide

bonds flanking the α carbon are in

the same plane

The two torsion angles of the polypeptide chain, describe the

rotations of the polypeptide backbone around the bonds

between N-Cα (called Phi, φ) and Cα-C (called Psi, ψ).

The Primary Structure

Non-covalent interactions

H

H

O

CH3

O

H

N+

H

C

H

C

Peptide

bond

N

C

C

O–

H

H

Structural hierarchy of proteins

In discussing protein structure, FOUR levels of complexity

are invoked

Primary structure:

the linear sequence of amino acids

Secondary structure: the spatial arrangement of the

polypeptide backbone atoms without

regard for the side chains

Tertiary structure:

refers the three dimensional structure

of the entire polypeptide including side

chains

Quaternary structure: refers to the spatial arrangement of its

subunits

Secondary structure of proteins

A few elements of protein secondary structure are so

widespread that they are found associated with many

different proteins with widely differing amino acid

sequences.

1. The α helix

(a) Favourable hydrogen bonding pattern

(b) Values of the torsional angles Ψ and φ fall

within the allowed regions of the

Ramachandran plot

Secondary structure of proteins

A few elements of protein secondary structure are so

widespread that they are found associated with many

different proteins with widely differing amino acid

sequences.

1. The α helix

(a) Favourable hydrogen bonding pattern

(b) Values of the torsional angles Ψ and φ fall

within the allowed regions of the

Ramachandran...