Is tyrosine polar or non-polar

Confusion about the polarity and hydrophobicity of proline, tyrosine, and cysteine?

TL / DR: These are borderline cases, complicated cases. There is no broad consensus on whether cysteine ​​and tyrosine should be viewed as hydrophobic or polar. However, proline is clearly non-polar.

The reason for the confusion is that there are different ways to define and measure polarity and hydrophobicity for amino acids. First, the polarity and hydrophobicity of the free amino acid is very different from that of the amino acid side chain associated with a peptide (protein). I suppose you are interested in the latter.

The polarity is pretty hard to define for amino acids. The dipole moment is the usual measure of polarity, but this depends on the geometry of the molecule and is therefore only well defined for small molecules like water that cannot "wobble". Larger amino acid side chains can wobble quite a bit, and their dipole moment is difficult to define. Instead, the polarity is usually indicated by rules of thumb such as "hydroxyl groups are polar" and "aromatic rings are non-polar". But then there are borderline cases like tyrosine, which have both an aromatic ring and a hydroxy group.

The hydrophobicity is related to polarity, but is an experimentally measured quantity that is usually determined by how an amino acid distributes itself between water and non-polar solvents, or by observing how it orients itself in folded proteins (opposite or against the water solvent). Further information can be found here . However, the results of such experiments do not always agree, so it can be difficult to classify amino acids that are borderline hydrophobic / hydrophilic. For example, for two amino acids X and Y, we could find that X dissolves better in water than Y, so that X appears more hydrophilic in this sense; At the same time, however, X could also be better divided into a lipid bilayer, so that X appears more hydrophobic than Y in this sense. In such cases, the various hydrophobicity scales differ.

For these reasons, there is disagreement as to whether some amino acids are polar / hydrophobic. With that in mind, here are my two cents for the amino acids you mention:

Proline is special in that it does not have an -NH3 group. The amine nitrogen attaches to the side chain - it's more of a "loop" than a chain - and the peptide bond is different. But this "side loop" clearly does not have a polar group, and I think there is good agreement that proline should be considered non-polar. The Khan Academy site is likely wrong. Proline has a medium hydrophobicity.

Tyrosine: As mentioned earlier, the polarity of the tyrosine side chain is unclear as it is quite large and has both polar and non-polar groups. Tyrosine is somewhat hydrophobic, but among the amino acids it is near the middle on most hydrophobicity scales. So tyrosine is a borderline case that explains why different sources do not agree.

Cysteine is something special in connection with proteins, as cysteine ​​residues often pair via disulfide bonds and this changes their properties. As such, the -SH group is polar (although less than an -OH group) so the cysteine ​​side chain is somewhat polar. It has medium hydrophobicity as measured by solvent distribution. Cysteine ​​was considered hydrophobic based on the observation that cysteine ​​is often found inside proteins outside of the water solvent. However, this is mainly due to its ability to form disulfide bonds.

Tho H. Ho

Many Thanks. Very insightful and detailed explanation. Accepted and positively rated.