The three molecules that make up a nucleotide are phosphate, pentose sugar, and nitrogenous bases. The four nitrogenous bases are adenine, guanine, cytosine, uracil, and thymine. The sugar in DNA is deoxyribose and that in RNA is ribose. Aphosphodiester bond is a linkage between the 3' carbon atom of one sugar molecule and the 5' carbon atom of another sugar.