Physicochemical properties of bases
In their pure form, nitrogenous bases are white crystalline substances. One of their important characteristics is a moderate solubility in aqueous media, which is of fundamental importance for their behavior in biological fluids.
Lactim-lactam tautomerism
In aqueous solutions, many nitrogenous bases are capable of a dynamic structural transition called lactim-lactam tautomerism. The essence of this phenomenon is the mutual conversion of hydroxyl groups (-OH) into oxo groups (=O) with the simultaneous migration of a proton.
There are two main forms:
- Lactim form: the molecule's structure features a pronounced hydroxyl group (-OH) while maintaining the aromatic bond system.
- Lactam form: the hydroxyl group is transformed into a keto group (oxo group =O), and the migrated hydrogen atom binds to a nitrogen atom in the ring (forming an NH group).
This process is characteristic not only of purines, but also of pyrimidine bases. In particular, a pyrimidine base in the lactam form possesses a mobile hydrogen atom attached to the nitrogen atom at position N-1. In chemical classification, such a nitrogen atom is conventionally called 'pyrrolic'.
Structural features of purine bases
Natural nucleic acids traditionally contain two main representatives of the purine series, which differ in their ability to undergo tautomeric transformations:
- Adenine. According to chemical nomenclature, it is 6-aminopurine. A key structural feature of adenine is the complete absence of hydroxyl groups. Due to this, adenine is fundamentally incapable of undergoing lactim-lactam tautomeric transformations.
- Guanine. Its chemical name is 2-amino-6-hydroxypurine. Unlike adenine, guanine contains a hydroxy group. This makes it structurally plastic: similar to pyrimidine bases, it readily undergoes lactim-lactam tautomerism. In the lactim form, guanine contains an –OH group and maintains a unified aromatic system, whereas in the lactam form, it transitions to a state with a keto group (=O) and a proton attached to the nitrogen (NH).
Structure and nomenclature of nucleosides
Chemically, nucleosides are classified as pentose $\beta$-glycosides. They are the direct products of the condensation reaction between nitrogenous bases and carbohydrates—ribose or deoxyribose.
A key element of the nucleoside structure is the N-glycosidic bond. The process of its formation is strictly specific:
- On the part of the carbohydrate (pentose), the first carbon atom—C-1'—always participates in bond formation.
- On the part of the nitrogenous base, a strictly specific nitrogen atom is involved: N-9 for purine bases and N-1 for pyrimidine bases.
> Important nomenclature rule: To avoid confusion when describing a nucleoside molecule, the carbon skeleton atoms in the sugar (pentose) are always numbered with primed numbers (e.g., 1', 2', 3', and so on). This clearly distinguishes them from the atoms of the nitrogenous base, which are numbered with plain numbers without primes.
Example of chemical interaction: The reaction between adenine and $\beta$-D-deoxyribose yields a water molecule ($H_2O$) and synthesizes the nucleoside deoxyadenosine. In this molecule, the N-glycosidic bond securely connects the N-9 nitrogen atom of adenine and the C-1' carbon of deoxyribose.
Briefly: answers to topical questions
Which bases are characterized by lactim-lactam tautomerism?
Lactim-lactam tautomerism is characteristic of pyrimidine bases and the purine base guanine. The process is characterized by the conversion of hydroxyl groups (-OH) into oxo groups (=O) and vice versa.
- Pyrimidine bases undergo tautomerism in solutions, forming the lactam form with a mobile hydrogen atom at the 'pyrrolic' N-1 nitrogen.
- Guanine possesses a hydroxy group and is therefore capable of tautomeric transformations (unlike adenine, which lacks one). The lactim form of guanine includes an –OH group, while the lactam form includes a keto group =O and a proton at the nitrogen (NH).
To avoid confusing the atom numbers that form the bond: Purines are large—the number is large (N-9). Pyrimidines are small (one ring)—the number is small (N-1). The sugar always attaches to the first hook (C-1').
Class and exam questions
Why does adenine not undergo lactim-lactam tautomerism?
Adenine (6-aminopurine) does not contain a hydroxyl group (-OH) or an oxo group (=O) in its structure. Without these functional groups, the transition between the lactim and lactam forms is impossible.
What is the difference between atom numbering in pentose and in the nitrogenous base?
Carbon atoms in the sugar (pentose) ring are designated with primed numbers (1', 2', 3'), whereas atoms in the nitrogenous base are designated with regular numbers (1, 2, 3). This is an international nomenclature rule.
Which atoms participate in the formation of the N-glycosidic bond in purine nucleosides?
The bond is formed between the C-1' carbon atom of the sugar (ribose or deoxyribose) and the N-9 nitrogen atom of the purine base.
What else to study on this topic
- Spatial structure of the N-glycosidic bond in nucleosides
- Mechanism of the water molecule formation reaction during nucleoside synthesis
- Chemical properties of pyrimidine bases (uracil, thymine, cytosine)
- Effect of lactim-lactam tautomerism on molecular stability
- Specificity of the pentose beta-glycosidic configuration
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