Which hydrophobic amino acids with long alkyl side chains are typically found inside proteins?

The selection of isoleucine, valine, and phenylalanine as the correct answer highlights the nature of hydrophobic amino acids and their typical localization within proteins. These amino acids possess long alkyl side chains, making them nonpolar and thereby hydrophobic. In the context of protein structure, hydrophobic amino acids are usually found in the interior of proteins, where they tend to avoid contact with the aqueous environment, stabilizing the protein's three-dimensional structure through hydrophobic interactions.

Isoleucine and valine both contain branched aliphatic side chains, while phenylalanine has a large aromatic side chain, which also conveys hydrophobic characteristics. This propensity for hydrophobic amino acids to cluster within the protein interior is fundamental to the protein folding process and helps to maintain structural integrity.

In contrast, the other options consist of amino acids that either do not possess sufficiently hydrophobic side chains or have polar characteristics that would not typically lead them to reside within the hydrophobic core of proteins. Cysteine contains a thiol group that can participate in hydrogen bonding, while lysine and arginine are positively charged and thus polar. Similarly, threonine and asparagine have polar side chains due to their hydroxyl and amine