Is there a difference between polarity and hydrophobicity?

Question

From literature the two terms seem to be interchangeable when discussing protein domains and motifs. But biochemically, what are the specific differences between these two terms? For example what is the difference in these sentences:1. Generally globular protein cores have hydrophobic regions whilst the surface contains hydrophilic exterior facing residues. 2. Generally globular protein cores have non-polar regions whilst the surface contains polar exterior facing residues.

Answer 1

When these terms are applied to amino acids, polar and hydrophobic go hand-in-hand but they are opposite, as is the case in your example. There are polar/ hydrophilic amino acids and there are non-polar/hydrophobic amino acids. There are also charged/acidic/basic amino acids which are all hydrophilic. This is usually the case in biochemistry since much of it deals with amino acids.The bottom line here is that anything with partial positive or partial negative charge will be considered polar since it will have delocalized electrons that can bind to water and allow it to be soluble, thus classified as polar. In the case of hydrophobic compounds, usually they are C-H bonds or bonds that have a very slight electronegativity difference, hence there are not any delocalized electrons that can bind to water.

All in all, in Biochemistry the terms polar and hydrophobic can be used together but I would just stick to hydrophobic/hydrophilic or polar/nonpolar just to avoid any confusion.