A nucleotide is an organic compound consisting of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups. Nucleotides are the building blocks of nucleic acids, including DNA and RNA, whose sequences carry biological information. They also function independently as energy carriers, metabolic intermediates, and signaling molecules within the cell. Their structural diversity allows the same general class of compounds to support both information storage and biochemical reactions. (genome.gov)
Chemical structure
A nucleotide contains three distinguishable components. The nucleobase is usually a nitrogen-containing heterocyclic compound; the sugar is typically ribose or 2-deoxyribose; and the phosphate component supplies the phosphorylated portion. A base joined to a sugar without phosphate is a nucleoside, rather than a nucleotide. Thus, adenine is a base, adenosine is its ribose-containing nucleoside, and adenosine monophosphate is a nucleotide. This distinction is important because the three terms identify chemically different substances. (genome.gov)
The sugar’s carbon atoms are numbered with primes—1′ through 5′—to distinguish them from positions in the base. In the standard nucleotides of DNA and RNA, the base attaches at the sugar’s 1′ position, while phosphate commonly attaches at the 5′ position. Ribose has a hydroxyl group at its 2′ carbon; deoxyribose has hydrogen instead. This small structural difference distinguishes ribonucleotides from deoxyribonucleotides and contributes to differences in nucleic-acid chemistry and conformation. (ncbi.nlm.nih.gov)
The principal bases belong to two families. Purines, represented by adenine and guanine, have two fused rings. Pyrimidines, represented by cytosine, thymine, and uracil, have a single ring. Adenine, guanine, and cytosine occur in both standard DNA and RNA; thymine is characteristic of DNA, whereas uracil replaces it in standard RNA. The letters A, G, C, T, and U denote these bases and, in sequence notation, the corresponding nucleotide residues. (goldbook.iupac.org)
Naming and phosphorylation states
Nucleotides are commonly named according to their nucleoside and phosphate content. Adenosine monophosphate, diphosphate, and triphosphate are abbreviated AMP, ADP, and ATP. The corresponding guanosine compounds are GMP, GDP, and GTP. Cytidine and uridine give the analogous C- and U-series compounds. A nucleotide therefore need not contain only one phosphate group. (ncbi.nlm.nih.gov)
The prefix deoxy- or the abbreviation d identifies compounds containing deoxyribose: dATP, for example, is deoxyadenosine triphosphate. RNA synthesis uses ATP, GTP, CTP, and UTP, whereas DNA synthesis uses dATP, dGTP, dCTP, and dTTP. These free triphosphates must be distinguished from the nucleotide residues incorporated into a nucleic-acid chain, which no longer retain the incoming molecule’s complete triphosphate group. (ncbi.nlm.nih.gov)
Nucleotides in nucleic acids
DNA and RNA are polymers whose adjacent nucleotide residues are connected by phosphodiester bonds. A phosphate bridges the 3′ oxygen of one sugar and the 5′ oxygen of the next, producing a repeating sugar–phosphate backbone. The bases project from this backbone, and their order constitutes the molecule’s sequence. Chains have chemically distinct 5′ and 3′ ends; sequences are conventionally written in the 5′-to-3′ direction. (ncbi.nlm.nih.gov)
During DNA replication, DNA polymerase extends a growing strand using deoxyribonucleoside triphosphates. During transcription, RNA polymerase performs the corresponding reaction with ribonucleoside triphosphates. Addition occurs at the growing chain’s 3′ hydroxyl group, and each incorporation releases inorganic pyrophosphate. The substrates thus supply both the nucleotide units and chemical potential that supports chain formation. (ncbi.nlm.nih.gov)
Complementary base pairing allows a nucleic-acid strand to guide synthesis of another strand. In standard double-stranded DNA, adenine pairs with thymine and guanine with cytosine through hydrogen bonds. RNA commonly uses adenine–uracil pairing. These interactions are distinct from the covalent backbone bonds: pairing connects complementary regions, whereas phosphodiester bonds join successive residues within a strand. (ncbi.nlm.nih.gov)
Energy transfer, cofactors, and signaling
Adenosine triphosphate is a major carrier of chemical energy in cellular metabolism. Its conversion to ADP and inorganic phosphate can be coupled to otherwise unfavorable reactions. ATP frequently transfers a phosphoryl group to another molecule, linking energy transfer with chemical modification. It is continually regenerated rather than serving primarily as a long-term energy reserve. Other nucleoside triphosphates also support metabolic reactions; GTP, for example, participates in protein synthesis. (ncbi.nlm.nih.gov)
Nucleotide-containing compounds also carry electrons or chemical groups. NAD and NADP participate in oxidation–reduction reactions, alternating between oxidized and reduced forms. FAD is another nucleotide-containing electron carrier. UDP-glucose is an activated sugar donor, illustrating how attachment to a nucleotide can facilitate transfer of a chemical group during biosynthesis. These functions extend well beyond nucleic-acid construction. (ncbi.nlm.nih.gov)
Cyclic AMP and cyclic GMP act as intracellular second messengers. In these compounds, one phosphate forms a cyclic linkage with the sugar. Cyclic AMP is synthesized from ATP by adenylyl cyclase and can regulate proteins, including protein kinase A. Phosphodiesterases convert cyclic nucleotides to their noncyclic monophosphates, helping control signal duration. (ncbi.nlm.nih.gov)
Biosynthesis and recycling
Cells obtain nucleotides through de novo synthesis and salvage pathways. De novo pathways construct nucleotide components from simpler precursors, including amino acids and carbon-containing compounds. Salvage pathways reuse available bases or nucleosides. In purine biosynthesis, the ring is assembled on an activated ribose-containing precursor; in pyrimidine biosynthesis, the ring is formed before attachment to the ribose component. Recycling generally requires less energy than construction from simpler molecules. (pmc.ncbi.nlm.nih.gov)
Phosphate-transfer reactions interconvert nucleotide mono-, di-, and triphosphates. Ribonucleotide reductase supplies deoxyribonucleotide precursors by reducing ribonucleotide substrates. Biosynthesis, salvage, interconversion, and degradation are regulated through enzyme activity and gene expression, coordinating nucleotide supply with cellular requirements for nucleic-acid synthesis and other metabolic functions. (pubmed.ncbi.nlm.nih.gov)