What do the sides of a punnett square represent?

They represent the genotypes of the parent organisms.

Explanation:

As you can see in the picture, the genotype of the mother goes on one side while the genotype of the father goes on the other side. Let's create an example for this Punnett square. The letters represent alleles, which can be either dominant (capital letters such as B) or recessive (lowercase letters such as b).