Question

Examine the \(\alpha\)-helix conformation. Are amino acid side chains arranged all inside the helix, all outside the helix, or randomly?

Short answer

Answer: In an α-helix conformation, amino acid side chains are arranged outside the helix, projecting outward from the center of the helix, away from the helical axis. This arrangement allows for various interactions such as hydrophobic, electrostatic, and hydrogen bonds that contribute to the stability and function of the protein.

Step-by-step solution

Understanding an α-helix conformation

An α-helix conformation is one of the most common secondary structures in proteins. It is a right-handed coiled structure stabilized by hydrogen bonds between the peptide bonds in the backbone of the protein. It is important to know that each turn of the α-helix contains 3.6 amino acids, and the spacing between these amino acids in the helix is around 1.5 Å.

Examine the side chains arrangement in the α-helix

Side chains of amino acids in an α-helix don't remain inside the helix core but rather project outward from the center of the helix, away from the helical axis, due to steric hindrance that would happen if they were inwards.

Conclusion about the arrangement

Based on the projection of amino acid side chains from the central axis of the α-helix, we can conclude that amino acid side chains are arranged outside the helix, allowing for various interactions such as hydrophobic, electrostatic, and hydrogen bonds that contribute to the stability and function of the protein.