Four levels of Protein Structure

Primary

Sequence of amino acids in a polypeptide, stabilized by peptide bonds

peptide bond

bond between C- and N- terminus on amino acids

secondary

formation of a-helices and b-pleated sheets in a polypeptide, stabilized by hydrogen bonding between groups along the peptide bonded backbone (depends on primary structure)

tertiary

overall three-dimensional shape of a polypeptide. Stabilized by bonds and other interactions between R-groups, or between R-groups and the peptide-bonded backbone (depends on primary structure). Has H-bonds, ionic bonds, hydrophobic/Van der Waals interactions, and covalent disulfide bonds/bridges

quarternary

shape produced by combinations of polypeptides. Stabilized by bonds and other interactions between R-groups, and between peptide backbones of different polypeptides (depends on primary structure).

a-helix

H-bonds residue 1+3. 3.6 residues/turn, R groups point outward. Each carbonyl group in the backbone forms a hydrogen bond with an amide group 4 amino acids away.

b-pleated sheets

can be antiparallel (more stable) or parallel (less stable). R-groups project above and below strand. H-bonds between amide and carbonyl groups in adjacent strands. Typically 4-10 strands aligned side by side.

b-turn

Allows the peptide chain to change direction. Carbonyl C of one residue is H-bonded to the amide protein of a residue 3 residues away. glycine and proline contribute to it bc glycine can make H-bonds and proline cannot which causes a turn.

How proteins fold

Chaperonin protein:

1. an unfolded polypeptide enters the cylinder from one end

2. the cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide

3. the cap comes off, and the properly folded protein is releaseed.

angle about C(a)-C bond

Psi

angle about C(a)-N bond

Phi

denaturation

Unfolding of protein. Can be caused by heat, extreme pH, Urea/Guanidine hydrochloride