Question

Choose the amino acid in the following pairs that would be more likely to appear on the solvent-exposed surface of a protein and explain why you choose that answer.

a) Lys or Leu

b) Ser or Ala

c) Phe or Tyr

d) Trp or Gln

e) Asn or Ile

Answer 1

There are 20 different naturally occuring amino acids. All these amino acids have specific characterestics that is determined by the nature of thier side chain or R group ( variable region in an amino acid ). It is the chemical nature of this R groUp that decides whether an amino acid should be burried inside the protien ( hydrophobic) or exposed on the surface of the protein ( Hydrophilic).

a) Lys ( lysine) will be more likely to be present on the solvent exposed surface of a protein than Leu (leucine). It is because, lysine is a basic amino acid with a positively charged R group which is capable of forming bond with water. On the otherhand, leucine has a non polar aliphatic R group.

b) Serine (Ser) is more likely to be present in protien surface than alanine. serine is a polar but uncharged amino acid. The presence of an OH group in its side chain often makes it react with solvent thus making it hydrophilic. But, alanine (ala) has a non polar aliphatic R group.

c) Tyrosine (tyr). Here both tyrosine and phenyl alanine (phe) are aromatic amino acids. That is they have a ringed structure. And these aromatic amino acids are generally hydrophobic in nature. But comparing phenyl alanine with tyrosine, tyrosine is more hydrophilic. This hydrophilicity to tyrosine is provided by the exocyclic hydroxyl group (OH) present which makes it reactive. But, benzene ring in phenyl alanine confers high hydrophobicity to it and therefore burried in a protein.

d) Glutaminie (Gln). It is because, glutamine has a polar but uncharged R group while tryptophan (Trp) is an aromatic amino acid with double ring which itself makes it highly hydrophobic.

e) Asparagine (Asn). It is because the side chain or R goup of asparagine is polar and uncharged while that of isoleucine (Ile) is a non polar, alipahatic.

Note : Usually the presence of methyl group ( CH₃) provides hdrophobicity to an amino acid. So, as the length or number of methy groups in the side of amino acids increases, the hydrophobicity of amino acids keeps on increasing and hence will be burried in a protiens interior. This is the care in aminoacids like alanine, valine, leucine, isoleucine.