Lecture 5 - primary structure

how is a peptide bond formed

• condensation of alpha-carboxyl of one amino acid with the alpha-amino of another

which direction is the polypeptide read

n terminus to c terminus

residues

• the amino acids that compose of the peptide chains

backbone

repeating N-Cα-C unit of the peptide chain

secondary structure

regions of regularly repeating conformations of the peptide chain

• alpha helices

• beta strands

conformation of a protein

functional 3d structure

native conformation

• polypeptide chain folds into a single stable shape

what is the native conformation determined by and what does it determine

• determined by the sequence of amino acids

• determines biological function

3 representations of protein structure

• space-filling model

• cartoon ribbon model - shows secondary structure

• substrate-binding site view

what factors contribute to protein structure

• allowable bond rotations around the backbone of the polypeptide

• weak non-covalent bond interactions between backbone and sidechain groups

peptide bond properties

• lone pair on amide nitrogen

• electronegative oxygen will accept the double bond electrons

• creates intermediate bond length

• double bond character

why does C-N peptide bond have double bond character

resonance

peptide bond and rotation

nitrogen cant rotate

peptide group

• 6 atoms in the same plane

• half of one amino acid and half of another

trans conformation of peptide group

• Cα opposite sides

cis conformation of peptide group

C α same side

which conformation of the peptide group is more favourable and why

• trans conformation

• cis conformation has steric interference of alpha-carbon side chains

where is there bond rotation in peptide group

• N-Cα phi bonds

• Cα-V psi bonds

rotation of N-Cα bond (phi) in proline

• restricted

• due to ring structure

properties of secondary structures

• alpha helix

• beta strands beta sheets

• loops and turns favoured by allowable phi and psi bonds

  • and stabilising hydrogen bonds

alpha helix

• right handed

• backbone turns clockwise

• all side chains point outwards

• helix is stabilised by hydrogen bonds

• each C=O forms a hydrogen bond with an amide hydrogen of residue n+4

hydrogen bonding in alpha helix

• each C=O forms a hydrogen bond with an amide hydrogen of residue n+4

pitch of alpha helix

• advance along the helix axis per turn

• 0.54nm in length

rise in helix

each residue advances by 0.15nm along the axis of the helix

how many acids per turn in alpha helix

3.6

amphipathic alpha helix

• hydrophobic residues

• hydrophillic residues