Nomenclature for Pyrimidines and Purines
One of the important specialized pathways of a number of amino acids is the synthesis of purine and pyrimidine nucleotides. These nucleotides are important for a number of reasons. Most of them, not just ATP, are the sources of energy that drive most of our reactions. ATP is the most commonly used source but GTP is used in protein synthesis as well as a few other reactions.
Nitrogen Bases: There are two kinds of nitrogen-containing bases - purines and pyrimidines. Purines consist of a six-membered and a five-membered nitrogen-containing ring, fused together. Pyridmidines have only a six-membered nitrogen-containing ring. There are 4 purines and 4 pyrimidines that are of concern to us.
Purines
- Adenine = 6-amino purine
- Guanine = 2-amino-6-oxy purine
- Hypoxanthine = 6-oxy purine
- Xanthine = 2,6-dioxy purine
Adenine and guanine are found in both DNA and RNA. Hypoxanthine and xanthine are not incorporated into the nucleic acids as they are being synthesized but are important intermediates in the synthesis and degradation of the purine nucleotides.
Pyrimidines
- Uracil = 2,4-dioxy pyrimidine
- Thymine = 2,4-dioxy-5-methyl pyrimidine
- Cytosine = 2-oxy-4-amino pyrimidine
- Orotic acid = 2,4-dioxy-6-carboxy pyrimidine
Cytosine is found in both DNA and RNA. Uracil is found only in RNA. Thymine is normally found in DNA. Sometimes tRNA will contain some thymine as well as uracil.
Nucleosides: If a sugar, either ribose or 2-deoxyribose, is added to a nitrogen base, the resulting compound is called a nucleoside. Carbon 1 of the sugar is attached to nitrogen 9 of a purine base or to nitrogen 1 of a pyrimidine base. The names of purine nucleosides end in -osine and the names of pyrimidine nucleosides end in -idine. The convention is to number the ring atoms of the base normally and to use l', etc. to distinguish the ring atoms of the sugar. Unless otherwise specificed, the sugar is assumed to be ribose. To indicate that the sugar is 2'-deoxyribose, a d- is placed before the name.
- Adenosine
- Guanosine
- Inosine - the base in inosine is hypoxanthine
- Uridine
- Thymidine
- Cytidine
Nucleotides: Adding one or more phosphates to the sugar portion of a nucleoside results in a nucleotide. Generally, the phosphate is in ester linkage to carbon 5' of the sugar. If more than one phosphate is present, they are generally in acid anhydride linkages to each other. If such is the case, no position designation in the name is required. If the phosphate is in any other position, however, the position must be designated. For example, 3'-5' cAMP indicates that a phosphate is in ester linkage to both the 3' and 5' hydroxyl groups of an adenosine molecule and forms a cyclic structure. 2'-GMP would indicate that a phosphate is in ester linkage to the 2' hydroxyl group of a guanosine. Some representative names are:
- AMP = adenosine monophosphate = adenylic acid
- CDP = cytidine diphosphate
- dGTP = deoxy guanosine triphosphate
- dTTP = deoxy thymidine triphosphate (more commonly designated TTP)
- cAMP = 3'-5' cyclic adenosine monophosphate