Nucleotide

Nucleotides are organic molecules built from three parts: a nitrogenous base, a five-carbon sugar, and a phosphate group. They are the monomeric units that make up the nucleic acid polymers DNA and RNA, both of which are essential biomolecules found in all life on Earth. The body obtains nucleotides from food and also synthesizes them from common nutrients, primarily in the liver.

Each nucleotide consists of a nucleobase, a five-carbon sugar (either ribose or deoxyribose), and a phosphate group that can contain one, two, or three phosphate molecules. In DNA, the four nucleobases are guanine, adenine, cytosine, and thymine (G, A, C, T); in RNA, uracil (U) replaces thymine.

Beyond building nucleic acids, nucleotides are central to cellular metabolism. They supply chemical energy in the form of nucleoside triphosphates—such as ATP, GTP, CTP, and UTP—which power many cellular functions, including the synthesis of amino acids, proteins, and cell membranes, cell movement, and cell division. Nucleotides also participate in cell signaling through molecules like cyclic GMP and cyclic AMP, and they are incorporated into important enzymatic cofactors, such as coenzyme A, FAD, FMN, NAD, and NADP+. In experimental biochemistry, nucleotides can be radiolabeled with radionuclides to create radionucleotides. Additionally, 5-nucleotides are used as flavor enhancers to boost umami taste, often added as yeast extract.

**Structure**

A nucleotide is made of three distinct chemical subunits: a five-carbon sugar, a nucleobase (together these form a nucleoside), and one phosphate group. Depending on the number of phosphates, a nucleotide is called a nucleoside monophosphate, diphosphate, or triphosphate. In nucleic acids, the nucleobase is either a purine or a pyrimidine, and the nucleotide is termed a ribonucleotide if the sugar is ribose, or a deoxyribonucleotide if the sugar is deoxyribose. Adjacent nucleotide monomers are linked by phosphate molecules connecting the sugar rings, forming a long chain. This sugar-phosphate backbone creates a strand with a directionality from the 5'-end to the 3'-end. In a double helix, the two strands run in opposite directions, allowing base pairing and complementarity essential for DNA replication and transcription.

The purine bases adenine and guanine, and the pyrimidine base cytosine, appear in both DNA and RNA. Thymine is found only in DNA, and uracil only in RNA. Adenine pairs with thymine via two hydrogen bonds, while guanine pairs with cytosine via three. Besides building nucleic acids, single nucleotides store and provide cellular energy, participate in signaling, supply phosphate groups to modulate protein activity, and act as enzymatic cofactors in redox reactions. Signaling cyclic nucleotides form when the phosphate group binds twice to the same sugar, bridging the 5'- and 3'-hydroxyl groups. Some signaling nucleotides have multiple phosphate groups attached at different positions on the sugar. Nucleotide cofactors can include additional chemical groups, such as nicotinamide or flavin, attached to the sugar via a glycosidic bond; in flavin’s case, the ribose sugar is linear rather than ring-shaped.

**Synthesis**

Nucleotides can be synthesized both in vitro and in vivo. In the lab, protecting groups are used to create a phosphoramidite from a purified nucleoside, which can then produce unnatural analogues or oligonucleotides. In living cells, nucleotides are made either from scratch (de novo) or recycled through salvage pathways. The raw materials for de novo synthesis come from carbohydrate and amino acid metabolism, ammonia, and carbon dioxide. Recent research shows that cellular bicarbonate metabolism can be regulated by mTORC1 signaling. The liver is the main site for de novo synthesis of all four nucleotides. Pyrimidines and purines are made via different pathways: pyrimidines are built first from aspartate and carbamoyl-phosphate in the cytoplasm, forming orotic acid, to which a phosphorylated ribosyl unit is attached. Purines, however, are synthesized starting from the sugar template, with the ring built onto it. Both pathways use several enzymes in the cytoplasm, not within a specific organelle. Nucleotides are also broken down so that useful parts can be reused in new synthesis reactions.