7.3. Nucleotides
This chapter focuses on the uses of nucleotides in genetic material (DNA/RNA). However, not all applications of nucleobases/nucleotides are in DNA/RNA. For example, the cyclic adenosine monophosphate (cAMP; Figure 7.8) nucleotide is not involved in nucleic acid synthesis. Instead, it is used by cells for a number of purposes including regulating enzymes. Another classic example is the role of adenosine triphosphate (ATP) in cell metabolism. While not directly relevant to this chapter it is important to remember that other nucleotides exist and that nucleotides perform other functions than information storage in genetic code.
Figure 7.8 – Structure of Cyclic Adenosine Monophosphate (cAMP) Nucleotide.
7.3.1. The Eight Common Triphosphate Nucleotides
In principle the five common nucleobases would result in ten nucleotides: five with ribofuranose and five with 2-deoxyribofuranose. In practice only eight of these are commonly used in organisms (Figure 7.9). Four contain ribofuranose and are involved in ribonucleic acid (RNA) polymers and four contain deoxyribofuranose and are involved in deoxyribonucleic acid (DNA) polymers. These each have their own trivial names and letter shorthand notations.
Figure 7.9 – Structure, Trivial Name, and Letter Code for The Eight Common Triphosphate Nucleotides.
Both sets of common nucleotides incorporate adenosine, guanosine, and cytidine (from adenine, guanine, and cytosine respectively). However, ribofuanose nucleotides (for RNA) use uridine (from uracil) while deoxyribofuranose nucleotides (for DNA) use thymidine (from thymine) instead. This results from the differences in biological function for ribonucleic and deoxyribonucleic acid (see Section 7.5.2).
Other compounds can be used as nucleotides for nucleic acids. Often these are small modifications to the main eight structures. For example, some ribonucleic acids incorporate inosine (Figure 7.10) in certain applications. Many of these also have letter shorthand notations. This text will not use these letter codes but they may be encountered in other sources.
Figure 7.10 – Structure and Three-Letter Code for Inosine Triphosphate with Comparison to Adenosine and Guanosine Triphosphate.
7.3.2. Base Pairs by Hydrogen Bonding
Each of the nucleobases in the nucleotides has multiple groups capable of acting a hydrogen bond donors and/or acceptors. Based on the relative positions of these groups each nucleobase has a matching nucleobase that aligns with its donor(s)/acceptor(s) when oriented the opposite direction (Figure 7.11). These are often referred to as “base pairs” (a pair of nucleobases that align well for hydrogen bonding). The pairing is evident when in the standard resonance forms, but the “aromatic” resonance forms make the hydrogen bonding more accurate; the partial positive and negative charges make the hydrogen bonds even stronger than they would normally be.
Figure 7.11 – Adenine-Thymine and Guanine-Cytosine Base Pairs Highlighting Hydrogen Bonding Between Pairs in Two Resonance Forms.
The pairings are specific. For example, thymine has three potential hydrogen bonding groups. It would seem to be able to pair well to guanine, which also has three. However, they do not align properly and efficient hydrogen bonding between the two is not possible (Figure 7.12).
Figure 7.12 – Hypothetical Guanine-Thymine Pair Highlighting Lack of Efficient Hydrogen Bonding Between the Two.
Each purine nucleobase pairs with a pyrimidine nucleobase. This is significant for several reasons. The most important is that it keeps the distance between the two polymer strands relatively consistent; pairings of two purine and two pyrimidine nucleobases have significantly different distances between the two polymer backbones (Figure 7.13). The distance between the two halves would change significantly based on the sequence and the double strand helix structure of DNA would not be possible.
Figure 7.13 – Simplified Representation of Interstrand Distance Comparing Purine-Pyrimidine with Hypothetical Purine-Purine and Pyrimidine-Pyrimidine Base Pairs.
While base pairs are especially important for forming the structure of DNA (see Section 7.4.3) they are also important in other processes, including accurately forming specific RNA strands using the DNA template.
