Which part of the polypeptide chain or amino acid participat

Solution

Protein can be defined as a polymer of amino acids. Fundamental structure of amino acid is NH3-CHR-COO^-. Each amino acid will differ in the above R group. eg. Alanine will have a methyl as R group and if R is H or a hydrogen its a glycine.

Peptide bond is a bond that forms due to the dehydration reaction between two amino acid molecules, where the carboxyl group of one amino acid reacts with the amino group of the other releasing a water molecule and resulting in the peptide bond. This covalently linked amino acid structure is called the primary structure. the protein back bone has a sequence of NCCNCCNCC...or NH₃⁺-CHR-CO-NH-CHR-CO-NH-CHR-CO...so on.

When segments of the amino acids fold locally to form a stable structure its called as a secondary structure. It is two types i.e. alpha helix and beta sheet. In the alpha helix Hydrogen bond forms between oxygen of the C=O of the carbonyl group and the H of NH in the next helix. Due to partial positive charge on the H and weak negative charge on the O, there is a hydrogen bond formed and R groups project out of the helix or protrude out. So in the secondary structure the backbone participates in the formation of hydrogen bond. In beta sheets which is the other form of secondary structure, the hydrogen bonds are placed laterally between the carbonyl oxygen and the amino hydrogen, Strands often appear parallel, nonetheless the secondary structure is formed by the carbonyl oxygen and H of the amino group of the backbone.

Tertiary Structure

When the protein molecule folds or bends to go to a least energy state or also called as maximum stability state, its the tertiary structure of the protein. It is predominantly stabilized by weak interactions, like hydrogen bonds or Vanderwaals forces, ionic bonds between side chain groups of amino acids, or the disulfide bonds. Usually the interactions are between the side chain groups or R groups of the amino acids. Eg. alanine, valine, leucine and isoleucine interact by hydrophobic bonds, whereas in cysteine there is disulfide bridge formation by oxidation of sulfhydryl groups.