Question

3. What kinds of amino acids are NOT favored in right handed helical structures, Why?

Answer 1

The secondary structure of proteins refers to the shape in which a long polypeptide chain can exist. The secondary structure exhibit two different types of structure:

1. α helix
2. β pleated sheet structure

These structures arises due to the regular folding of the backbone of the polypeptide chain due to the formation of hydrogen bonding between the C=O and NH group of the peptide bond.

The α helix is one of the most common ways in which a polypeptide chain forms all possible hydrogen bond by two string into a right handed screw helix with the NH group of each amino acid residue hydrogen bonded to the C=O of the adjacent turn off the help of the ellipse as shown in the given figure:

0 0넌 alus

The Alpha helix is stabilized by the two major factors: (i) the intermolecular hydrogen bonding (ii) Decrease of steric hindrance present in the polypeptide chain in between the side chains of thee amino acids.

The α helix contains about 10 amino acids and the  amino acids forming short polypeptides do not tend to form the alpha structure.

Certain amino acids like Proline and glycine are not able to form the α helix structure . The amino acid Proline has a cyclic structure. It has no backbone NH therefore formation of H Bonding to form helical structure is not favoured and forms β pleated sheet structure. The hydrogen bond of the α helix is weaker in comparison to the β pleated sheet structure. Trytophan has a bulky structure so it also not favours helix structure due to steric hindrance. Glycine is the simplest amino acid and the side chain is most sterically flexible.

Many amino acids like methionine, alanine,leucine, glutamate, and lysine tend to form the alpha helix. They form hydrogen bond in the between the electronegative oxygen of one peptide bond to the hydrogen of other amino acid along the helix.