Since Tyrosine and Tryptophan are amino acids, their polarity is determined on their side chains or R groups. If their R groups are polar, the amino acid is polar. Both Tyrosine and Tryptophan are listed as non-polar molecules. However, Tryptophan has nitrogen in its side chain and Tyrosine has oxygen, both of which have a high electronegativity compared to the carbon that makes up the bulk of both molecules, which is something commonly seen in polar amino acids like Serine, which has oxygen in its side chain. This should mean that Tyrosine and Tryptophan are polar, so why are they non-polar, even with an electronegative atom in their side chains?
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2 Answers
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Unlike that in organic chemistry, polar and non-polar compounds determination is done differently in biochemistry, probably because most biochemical reactions are done in aqueous medium. Therefore, the classification of them as polar and non-polar is somewhat different from source to source. In general, amino acids, which can make hydrogen bonding in aqueous solutions are called polar, and ones repel from water are non-polar. According to Ref.1:
All polar amino acids have either an $\ce{OH}$ or $\ce{NH2}$ group (when in aqueous environment), and can therefore make hydrogen bonds with other suitable groups.
Following image shows 20 amino acids categorized to polar (10) and non-polar groups (10):
All 10 non-polar amino acids are hydrophobic and 10 polar amino acids are hydrophilic. Polar amino acid residues have a tendency to be on the outside of a protein, due to the hydrophilic properties of the side chain (Ref.1). Keep in mind that tryptophan has indole function, but its lone pair of nitrogen is involved in the aromatic system. Thus, it make only weal H-bonding, which are not good enough to categorize as "polar."
References:
- Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter, In Molecular Biology of the Cell; 5th edition, Garland Science: New York, NY, 2008, p. 125-129 (ISBN-13: 978-0815341055).
answered Aug 9, 2020 at 9:04
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Tryptophan is less hydrophobic than phenylalanine and as a whole tryptophan is considered non polar although it has an additional N-H group at its side chain.. Look at the side chain of tryptophan which is more hydrophobic and large so if a tiny part (N-H) in its side chain is polar than still it can not influence the hydrophobicity of the entire side chain which is so large.. and secondly, although it has N-H group at its side chain so we accept that it will offer the hydrogen ion their lone pair electron to get charged but that is not happing actually ..because the lone pair electrons of tryptophan are busy in the resonance of the two fused ring so these electrons do not even try to look at the hydrogen ions in water so its neutral
