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The nucleotide molecule contains three functional groups: a base, a sugar, and a phosphate (see diagram). It may seem puzzling that a nucleic acid should contain a base. While the base portion does have weakly basic properties, the nucleotide as a whole acts as an acid, due to the phosphate group.

The names DNA and RNA are generated from the deoxyribose and ribose sugars found in these two polymers. Both are five-carbon sugars, whose carbons are numbered around the ring from 1′ to 5′ ("one prime" to "five prime"). The prime distinguishes the carbons on the sugar from the carbons on the base. The sugar in RNA nucleotides is ribose. The sugar in DNA is 2′-deoxyribose, which lacks an-OH group at the 2′ position. This small difference has some important consequences: The extra oxygen in RNA interferes with double helix formation between RNA chains (though it does not completely prevent it), and makes RNA more susceptible than DNA to base-catalyzed cleavage (breakdown into individual monomers).

A base attaches to the sugar at the sugar's 1′ position. Because of their nitrogen content, the bases are called nitrogenous bases, and are further classified as either purines or pyrimidines. Purine structures have two rings, while pyrimidines have one. The two purine bases found in both DNA and in RNA are guanine (G) and adenine (A). The two pyrimidine bases found in DNA are cytosine (C) and thymine (T), and the two pyrimidine bases found in RNA are cytosine and uracil (U). The only difference between thymine and uracil is the presence of a methyl group in thymine that is lacking in uracil. A base plus a sugar is called a nucleoside.

The phosphate groups are linked to the sugars at the 5′ position. The addition of one to three phosphate groups generates a nucleotide, also known as a nucleoside monophosphate, nucleoside diphosphate, or nucleoside triphosphate. For instance, guanosine triphosphate (GTP) is an RNA DNA double helix molecular model. The ball-and-stick models linking the backbones represent the nucleotides A, T, C, and G. DNA nucleotides hydrogen bond across the double helix. A pairs with T, and C with G, due to the specific positioning of the hydrogen bonds (dashes) they form. Each side of the helix has a directionality imposed by the differing characters of the 5′ and the 3′ ends of the nucleotides. The two sides are oriented in opposite, "anti-parallel" directions. A nucleotide consists of a nitrogen-containing base, a 5-carbon sugar, and one or more phosphate groups. Carbons occupy four vertices of the pentagon, and are numbered counterclockwise from 1′ ("one-prime"), the point of attachment of the base, to 5′, the point of attachment of the phosphate. The sugar depicted is ribose; Deoxyribose has an H instead of an OH at the 2′ position, indicated by the box. nucleotide with three phosphates attached. Deoxycytosine monophosphate (dCMP) is a DNA nucleotide with one phosphate attached.

Adenosine triphosphate, ATP, is the universal energy currency of cells. The breakdown of energy-rich nutrients is coupled to ATP synthesis, allowing temporary energy storage and transfer. When the ATP is later broken back down to ADP or AMP (adenosine diphosphate or monophosphate), it provides energy to power cell reactions such as protein synthesis or cell movement.

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Medicine EncyclopediaGenetics in Medicine - Part 3Nucleotide - Structure, Polymer Formation, The Double Helix Of Dna