Question

Why does adenine pair with thymine and not cytosine?

Answer 1

The chemical structure of the molecules determine what they are most likely to pair with.

In this image you can see that the -NH and -OH groups of both Guanine and Cytosine are aligned and connect through hydrogen bridges. This is a favourable situation for both molecules to be in, as both have 3 usable groups and no groups are in the way.

Adenine and Thymine also have a favorable configuration for their bonds. They both have to -OH/-NH groups which can form hydrogen bridges.

When one pairs Adenine with Cytosine, the various groups are in each others way. For them to bond with each other would be chemically unfavorable.

I hope that helps!