The one part of the nucleotide that differs among the different nucleotides is the nitrogenous base. There are four different nitrogenous bases: adenine (A), cytosine (C), guanine (G), and thymine (T) . In RNA, uracil (U) replaces thymine. The nitrogenous base is one of the three parts of a nucleotide, along with a phosphate group and a pentose sugar.