What are the Three Parts of a Nucleotide? | Albert.io Nucleotides are made up of 3 parts. The first is a distinct nitrogenous base, which is adenine, cytosine, guanine or thymine. In RNA, thymine is replaced by uracil. These nitrogenous bases are either purines or pyrimidines. Base pairs are formed when adenine forms a hydrogen bond with thymine, or cytosine forms a hydrogen bond with guanine.