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2.13: Nucleotides

Nucleic acids are linear, unbranched polymers of nucleotides. Nucleotides consist of three parts.

A five-carbon sugar (hence a pentose). Two kinds are found:

  • deoxyribose, which has a hydrogen atom attached to its #2 carbon atom (designated 2'), and
  • ribose, which has a hydroxyl group there.

Deoxyribose-containing nucleotides, the deoxyribonucleotides, are the monomers of deoxyribonucleic acids (DNA). Ribose-containing nucleotides, the ribonucleotides, are the monomers of ribonucleic acids (RNA).


The Purines                                                            The Pyrimidines

A nitrogen-containing ring structure called a nucleobase (or simply a base). The nucleobase is attached to the 1' carbon atom of the pentose. In DNA, four different nucleobases are found:

  • two purines, called adenine (A) and guanine (G)
  • two pyrimidines, called thymine (T) and cytosine (C)

RNA contains:

  • The same purines, adenine (A) and guanine (G).
  • RNA also uses the pyrimidine cytosine (C), but instead of thymine, it uses the pyrimidine uracil (U).


The combination of a nucleobase and a pentose is called a nucleoside.

One (as shown in the first figure), two, or three phosphate groups. These are attached to the 5' carbon atom of the pentose. The product in each case is called a nucleotide. Both DNA and RNA are assembled from nucleoside triphosphates.

  • For DNA, these are dATP, dGTP, dCTP, and dTTP.
  • For RNA, these are ATP, GTP, CTP, and UTP.

In both cases, as each nucleotide is attached, the second and third phosphates are removed.

Table 2.13.1: The nucleosides and their mono-, di-, and triphosphates
  Nucleobase Nucleoside Nucleotides
DNA Adenine (A) Deoxyadenosine dAMP dADP dATP
Guanine (G) Deoxyguanosine dGMP dGDP dGTP
Cytosine (C) Deoxycytidine dCMP dCDP dCTP
Thymine (T) Deoxythymidine dTMP dTDP dTTP
RNA Adenine (A) Adenosine AMP ADP ATP
Guanine (G) Guanosine GMP GDP GTP
Cytosine (C) Cytidine CMP CDP CTP
Uracil (U) Uridine UMP UDP UTP

The polymerization of nucleotides

The nucleic acids, both DNA and RNA, consist of polymers of nucleotides. The nucleotides are linked covalently between the 3' carbon atom of the pentose and the phosphate group attached to the 5' carbon of the adjacent pentose (Figure 2.13.3).


Figure 2.13.3: The polymer structure of DNA.

Most intact DNA molecules are made up of two strands of polymer, forming a "double helix". RNA molecules, while single-stranded, usually contain regions where two portions of the strand twist around each other to form helical regions. Alanine transfer RNA, shown on the left, is an example. The two strands of DNA and the helical regions of RNA are held together by base pairing. The polymerization of DNA is described more fully in DNA Replication.