Levels of protein structure

A protein is a polymer of amino acids linked with peptide bonds. The amino acids are made of amino group, carboxyl and side chain.

1. Primary: determined by the peptide bond formation. The Phi and Psi angles determine conformation of the polypeptide.

2. Secondary: stabilization of phi and psi angles of the primary structure by H-bond.

   - Alpha helix; peptide bonds rotate and form a helical structure.

   - Beta sheet; peptide plane lies side and form parallels.

   - 3_10 helix; longer, more unfavorable and less frequent than alpha helix.

   Others include; pi-helix, polyprolin helix.

3. Tertiary: 3D structure formed by conformation of secondary structure, several bonds in it(ionic bond, hydrogen bond, disulfide bridge).

4. Quaternary: formed by interaction between individual protein subunits.

Example is folding up till Hemoglobin.

Anfinsens experiment

He chose an enzyme Ribonuclease-A and checked the 3D conformation can be reversibly denatured to get original function. He stated the 3D conformation (tertiary structure)is determined by the primary structure, he put the enzyme in high molar concentration of Urea(disrupts noncovalent bond) and high amounts of mercaptoethanol(disrupts disulfide bonds). The protein got unfolded and denatured then he put it in a dialyzing membrane that is permeable for the urea and mercaptoethanol gradually they were replaced and the protein was renatured.

Levinthals Paradox, if each bond could only have 2 conformations the time for one state may be 1ns then the protein will need 10^10 years to reach optimal conformation.

Conclusion: The folding is under kinetic control.

Folding funnel theory

Free energy of molecule against degree of conformation freedom of the protein. The funnel being wide at the top means there is the unfolded protein with highest entropy and as it narrows and starts folding then less opportunities of conformation.

In the bumpy the chaperones are needed to prevent wrong folding of the protein.

Protein misfolding

Cells try to clear away the misfolded proteins so less amount of functional proteins. But if it is not cleared there can be malfunction(Sickle-cell) , accumulating in tissues(Alzheimer’s) pharmacological chaperones help in folding.

Gibbs energy change of enzyme catalyzed reactions

Enzymes have no effect on the thermodynamics of the reaction. They do not supply energy for the reaction so do not determine whether a reaction is favorable or unfavorable.

The reaction can be described in terms of the rate of product formation as a function of the substrate concentration supplied.