Good question Mary Katherine! So the R groups of amino acids are made up of functional groups. These functional groups largely influence the properties of the amino acids (a hydroxyl group makes it polar, an carboxylic group makes it acidic, a methyl makes it hydrophobic... etc). The interactions (both repulsive and attractive) between the R groups of amino acids within a protein are what govern protein folding and protein interactions with other molecules. We will look at this in much more depth in a few days during our unit on protein structure and function. It is okay to be a little confused right now 