Biochemistry and Molecular Biology Resource


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Eric C. Niederhoffer, Ph.D.

Associate Professor of Biochemistry and Molecular Biology

Southern Illinois University School of Medicine
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Purines, Pyrimidines, Nucleosides, and Nucleotides

Purines and pyrimidines are the building blocks of the nucleic acids (deoxyribonucleic acid, DNA ; ribonucleic acid, RNA). The various forms also serve as second messengers for signal transduction pathways. Some serve as nucleotide sugar donors in metabolic pathways. There are five nitrogenous bases, the two purines adenine and guanine and the three pyrimidines cytosine, thymine (found primarily in DNA), and uracil (found primarily in RNA). Their structures appear as follows:


Building blocks: bases, nucleosides, nucleotides

Purines and pyrimidines representations


Adenine, A


Cytosine, C


Guanine, G


Thymine, T


Uracil, U

When the five-carbon sugar group (ribose or deoxyribose) is added to the nitrogenous base, we get what is denoted as a nucleoside. Note the position of the 2-C hydroxyl (OH) or hydrogen (H).

Generic deoxyribonucleoside and ribonucleoside representations



Nucleosides that have a phosphate group at the 3- or 5-C position are denoted nucleotides (nucleoside monophosphate). The following compares the structures of purines, pyrimidine, nucleosides, and nucleotides:

Purines, Pyrimidines, Nucleosides, and Nucleotides






Deoxyadenylate, A, dA, dAMP


Deoxyadenylate, A, dA, dAMP




Adenylate, A, AMP


Adenylate, A, AMP






Deoxyguanylate, G, dG, dGMP


Deoxyguanylate, G, dG, dGMP




Guanylate, G, GMP


Guanylate, G, GMP






Deoxycytidylate, C, dC, dCMP


Deoxycytidylate, C, dC, dCMP




Cytidylate, C, CMP


Cytidylate, C, CMP






Deoxythymidylate, T, dT, dTMP


Deoxythymidylate, T, dT, dTMP






Uridylate, U, UMP


Uridylate, U, UMP


The properties of purine and pyrimidine bases and phosphate groups of nucleic acids and those of proteins allows for hydrogen bonding, non-polar, and polar interactions. We can observe these interactions when DNA-binding proteins (transcription factors) and drugs associate with nucleic acids.

We also find the triphosphate form of nucleic acids involved in energy transfer reactions. The most common example is ATP. GTP can bind to proteins (enzymes), where they serve to facilitate signal transduction (G protein transducin).

Phosphorylated forms of nucleotides

adenosine-5'-monophosphate, AMP

adenosine-5'-diphosphate, ADP

adenosine-5'-triphosphate, ATP


Cyclic nucleotides as second messengers

Both ATP and GTP may be cyclized by their respective enzymes, adenylyl cyclase and guanylyl cyclase, to form cyclic AMP and cyclic GMP. The remaining phosphates are lost as pyrophosphate.

Cyclic nucleotides


cyclic AMP, cAMP


cyclic GMP, cGMP

Cyclic AMP binds to and activates protein kinase A, which is an important enzyme in the regulation of many signal transduction pathway such as those involved in glucose and glycogen metabolism and in taste sensation. Both cAMP and cGMP bind to cyclic nucleotide-gated channels, which allow the transport of ions across cell membranes.


Nucleotides as sugar donors

Nucleotide sugars are used to transfer sugars (monosaccharides) to polymer chains (glycogen or starch) or in the synthesis of other biomolecules (sucrose and lactose). The most important one is UDP, which transfers glucosyl units to growing glycogen chains. During lactation, UDP is used to transfer a galactosyl unit to glucose forming lactose


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