M03.01.02 Nucleotide Structure and Nomenclature

Nucleic acids, including DNA and RNA, are essential macromolecules in living organisms. They are assembled from nucleotides, composed of three key components: a nitrogenous base, a five-carbon sugar (pentose), and one or more phosphate groups.

Components of Nucleotides

Five-Carbon Sugars

The classification of nucleic acids (DNA and RNA) depends on the type of pentose sugar they contain:

• Ribose: Found in RNA (Ribonucleic acid)
• Deoxyribose: Found in DNA (Deoxyribonucleic acid)

Nitrogenous Bases

Nitrogenous bases are categorized into two types: purines and pyrimidines.

Purines

Purines have a double-ring structure. The purines commonly found in nucleic acids are:

• Adenine (A): Found in both DNA and RNA
• Guanine (G): Found in both DNA and RNA

Other purine metabolites include Xanthine, Hypoxanthine, and uric acid, which are not typically found in nucleic acids.

Pyrimidines

Pyrimidines have a single-ring structure. The pyrimidines found in nucleic acids are:

• Cytosine (C): Found in both DNA and RNA
• Thymine (T): Found only in DNA
• Uracil (U): Found only in RNA

Nucleosides and Nucleotides

Nucleosides

Nucleosides are formed by covalently linking a nitrogenous base to the number 1 carbon of a sugar. The carbon atoms in the sugar are labeled with “primes” to distinguish them from the carbons in the nitrogenous base.

Examples of Nucleosides

Nucleotides

Nucleotides are nucleosides with one or more phosphate groups attached to the 5′ carbon of the sugar. Nucleoside di- and triphosphates are high-energy compounds due to the hydrolytic energy of the acid anhydride bonds.

High-Energy Bonds

The high-energy bonds in a nucleoside triphosphate, such as ATP, are critical for cell energy transfer.

Nomenclature

The nomenclature for bases, nucleosides, and nucleotides is standardized as shown in the table below. The “deoxy” prefix is sometimes omitted when it is understood from the context (e.g., thymine is almost always found attached to deoxyribose).

Table: Nomenclature of Important Bases, Nucleosides, and Nucleotides

Names of nucleosides and nucleotides attached to deoxyribose are shown in parentheses.

Summary Points

1. Nucleotides are the building blocks of nucleic acids and consist of a nitrogenous base, a five-carbon sugar, and one or more phosphate groups.
2. DNA and RNA are classified based on the type of sugar present (deoxyribose or ribose).
3. Nitrogenous bases are categorized into purines (adenine and guanine) and pyrimidines (cytosine, thymine, and uracil).
4. Nucleosides form when a base is attached to a sugar, and nucleotides form when one or more phosphate groups are added to a nucleoside.
5. The nomenclature of nucleotides is essential for understanding genetic and biochemical processes.

Bibliography

• Watson, J.D., et al. (2017). Molecular Biology of the Gene. Pearson.
• Alberts, B., et al. (2014). Molecular Biology of the Cell. Garland Science.