7.2. Nomenclature/Terminology: Nucleobases, Nucleosides, Nucleotides, and Nucleic Acids
As groups are added to the nucleobase the name for the class of compounds can change. Unfortunately there are often several synonyms and subdivisions for each of the different classes, the names for some of the groups are similar, and there are commonly used letter codes for each individual compound. This can quickly lead to confusion.
The nucleobase on its own is simply a nucleobase (sometimes “base”).
The nucleobase can be combined with a pentose using an enzyme (Scheme 7.1). The pentose is almost always ribofuranose (for ribonucleic acid [RNA]) or 2-deoxyribofuranose (for deoxyribonucleic acid [DNA]). The two parts are always connected in the same way: the carbon at position 1 of the saccharide is attached to the relevant nitrogen of the nucleobase to form the beta- (β-) anomer. This type of compound (a nucleobase + a pentose) is referred to as a nucleoside because of the glycoside bond between the two.
Scheme 7.1 – Simplified Formation of Nucleosides from Nucleobases.
Most nucleosides have trivial names (Scheme 7.2). Often these are similar to the trivial name for the nucleobase (e.g. adenine becomes adenosine or deoxyadenosine). However, many of the trivial names are not intuitive. Additionally, each of the nucleosides technically has one-, two-, and/or three-letter code abbreviations for them. This text will avoid trivial names and all codes for nucleosides. At an introductory level it is sufficient to know that there are trivial names and abbreviations. Memorization of the names/abbreviations is not required. However, they may be encountered in other sources.
Scheme 7.2 – Examples of Nucleosides from Nucleobases with Trivial Names and Letter Codes.
Most nucleosides are not made through this process. There are (several) other pathways available for the synthesis of nucleosides depending on what compounds the cell is using as starting materials. These paths tend to be significantly more complex and are commonly discussed in intermediate/advanced biochemistry courses.
The nucleoside can be combined with one, two, or three phosphates using enzymes (Scheme 7.3). Often the phosphate groups are added sequentially by different enzymes. For nucleotides used in genetic material the phosphates are always added to the same position: the alcohol at position 5 of the saccharide is attached to the phosphate and additional phosphates are added to the first. This type of compound (a nucleoside + phosphate(s)) is referred to as a nucleotide. As a mnemonic, it may be helpful to remember that phosphates are in nucleotides.
Scheme 7.3 – Simplified Sequential Formation of Nucleotides from Nucleosides.
Most nucleotides are not made through this process. There are (several) other pathways available for the synthesis of nucleotides depending on what compounds the cell is using as starting materials. These paths tend to be significantly more complex and are commonly discussed in intermediate/advanced biochemistry courses.
There are other structures that are also referred to as nucleotides. Typically, these place the phosphate group(s) at different positions and/or connect them to the nucleoside in slightly different ways. These types of nucleotides serve important biological functions but are not routinely part of genetic material.
Most nucleotides have trivial names (Scheme 7.4). Typically these are simply the name of the nucleoside followed by mono/di/triphosphate (e.g. adenosine with two phosphates becomes “adenosine diphosphate”). However, several of the compounds have multiple synonymous names. Additionally, each of the nucleotides technically has one or more letter code abbreviations for them. This text will avoid complex trivial names and abbreviations/codes for nucleotides. At an introductory level it is sufficient to know that there are trivial names and abbreviations. Memorization of the names/abbreviations is not required. However, because of how often they are encountered interpreting simple names/codes is required. More complex names and codes may be encountered in other sources.
Scheme 7.4 – Examples of Nucleotides from Nucleosides with Trivial Names and Letter Codes.
Many nucleotides have several different biological functions outside of being used to form DNA/RNA. While biologically important, these additional roles are not the focus of this text.
The nucleotides are monomers and can be combined to form polymers using enzymes (Scheme 7.5). Often the polymerization involves several different enzymes. The monomers are always connected in the same way: the phosphate of one monomer is attached to the alcohol at position 3 of the saccharide of the next monomer. The starting monomers are the triphosphate nucleotides but only one phosphate is incorporated into the polymer chain from each monomer. The other two phosphates are removed as part of the polymerization mechanism. This type of compound (a polymer of nucleotides) is referred to as a nucleic acid. They are subdivided by the pentose: ribofuranose for ribonucleic acid [RNA] or 2-deoxyribofuranose for deoxyribonucleic acid [DNA].
Scheme 7.5 – Simplified Formation of Nucleic Acids from Nucleotides.
Overall, nucleobases are used to form nucleosides, which are used to form nucleotides, which are used to form nucleic acids (Scheme 7.6).
Scheme 7.6 – Simplified Summary of Relationships Between Nucleobase, Nucleoside, Nucleotide, and Nucleic Acid.
