Primary structure, peptide bonds and secondary structure of proteins

Primary structure of proteins

Linear sequence of amino acids - each protein has a unique sequence

Peptide bonds (amide bond)

Condensation of the alpha carboxyl of one amino acid with the alpha amino of another amino acid

Residues

Amino acids in the peptide chains

How are peptide chains numbered?

From N terminus to the C terminus

Backbone of the peptide bond

The repeating N-C alpha -C unit

The three representation of protein structure

• Space filling model

• Cartoon ribbon model

• Substrate binding site view

Native conformation

The polypeptide chain folds into a single stable shape

What factors contribute to protein structure?

1. Allowable bond rotations define the possible conformations of the polypeptide chain

2. Weak non-covalent interactions between backbone and side chain groups

Peptide group

6 atoms all lying in the same place to the no bond rotation around C — N bond

Trans conformation in comparison to cis conformation

Trans conformation are more common due to the steric interference of alpha carbon side chains

Phi bond

N — alpha C bonds

Psi bond

Alpha carbon — carbon bonds

Secondary structure

regions of regulatory repeating conformations of the peptide chain, such as a helices and B strands (local folding)

Types of secondary structure

• Alpha helix

• Beta strands and beta sheets

• Loops and turns

What is secondary structure favoured by?

• Allowable phi and psi bond angles

• Stabilising H bonds

Properties of alpha helix

• Right handed (backbone turns clockwise viewed from N-terminus)

• Rise

• Pitch

• Amphipathic

Rise of alpha helix

• The rise of each residue advances by 0.15 nm along the long axis of the helix

Pitch of the alpha helix

• The advance along the helix long axis per turn - 0.54 nm

How many amino acids per turn in an alpha helix?

3.6 amino acids per turn

Why is the alpha helix amphipathic alpha helix?

Hydrophobic residues directed inward

Hydrophilic residues directed outwards

How is the alpha helix formed?

• Each C double bounded to O (residue n) forms hydrogen bond with the amide hydrogen of residue n+4

• Helix is stabilised by many hydrogen bonds — nearly parallel to long axis of the helix

• All C double bonded oxygen groups point towards the C-terminus

• Dipole with + to - (N to C - termini)

Beta strands

Polypeptide chains that are almost fully extended

Beta sheets

Multiple b strands arranged side by side

How are beta sheets stabilised?

stabilised by h bonds between C double bonded to O and -NH on adjacent strands

Parallel beta sheets

Strands run in the same N- to C- terminal direction

Antiparallel beta sheets

Strands run in the opposite N- to C- terminal direction

H bonds in parallel beta sheets

Distorted H bond

H bonds in antiparallel beta sheets

H bonds approx perpendicular to the strands

Functions of alpha helices and beta strands

Allows a peptide chain to fold back on itself to make a compact structure

Loops

Often contains hydrophilic residues are found on protein surfaces

Turns

Loops containing 5 residues or less