Question

1. What non-covalent interactions can (1) Alanine and (2) Threonine acid participate in, as part of tertiary structure at pH 7? Include an explanation of the charges involved (full or partial, permanent or temporary)?

2. Suggest one amino acid whose side chain can participate in a non-covalent interaction with the side chain of alanine, and one amino acid whose side chain can participate in a non-covalent interaction with the side chain of threonine.

Answer 1

The structures of alanine and threonine in proteins are as above.

1.From above it is clear that side chain of alanine is simply methyl group ( -CH3 ) This group is non-polar thus it will participate in tertiary structure through non-covalent hydrophobic interaction.

From above it is clear that the side chain of Threonine contains hydroxyl (-OH) group. This group is polar in nature in which hydrogen atom carries permanent, partial, positive charge and oxygen atom carries permanent, partial, negative charge. Thus this group has the ability to form Hydrogen Bond.  Thus it will participate in tertiary structure through non-covalent Hydrogen-Bonding.

Since the side chain of alanine is non-polar it will interact non-covalently with the amino acid which has non-polar side chain like valine, leucine, isoleucine, etc.

Similarly threonine will interact non-covalently with amino acids serine, tyrosine, etc which have polar uncharged side chains due to presence of hydroxyl (-OH) group in their side chain.