Nucleotides

General structural framework of nucleic acids

The evolutionary advancement of molecules led to the need for specialized chemical carriers of hereditary information. Deoxyribonucleic acids (DNA) became the primary molecular carriers of this genetic program, whereas protein synthesis processes are mediated by ribonucleic acids (RNA).

The relationship among all components during the formation of these nucleic acids is characterized by a strict sequence of chemical transformations:

1. First, nitrogenous bases combine with a carbohydrate—a pentose (which may be ribose or deoxyribose). This process occurs via substitution of a hydrogen atom, and the resulting intermediate is called a nucleoside.
2. Phosphate groups are then attached to the formed nucleosides. The product of this reaction is a complete nucleotide.
3. At the final stage, nucleotides undergo a polycondensation reaction. As the monomers link together, water ($H_2O$) is released, forming polymer chains—polynucleotides (DNA and RNA macromolecules).

Chemical nature of nitrogenous bases

The nitrogenous bases found in nucleic acids are substituted derivatives of two nitrogen-containing heterocyclic compounds:

• Pyrimidine;
• Purine.

Pyrimidine and purine bases bond to the carbohydrate moiety (ribose or deoxyribose) to become the core structural components of nucleic acids.

Three major compounds are distinguished among pyrimidine derivatives. They are characterized by the following systematic names:

• Uracil — 2,4-dihydroxypyrimidine.
• Thymine — 2,4-dihydroxy-5-methylpyrimidine.
• Cytosine — 2-hydroxy-4-aminopyrimidine.

Nomenclature of nucleosides

The names of nucleosides depend directly on the specific nitrogenous base and carbohydrate in their structure. Based on the type of pentose, two large groups are distinguished:

1. Ribonucleosides (RNA components). The name is formed by adding a specific suffix to the base name. The suffix -idine is used for pyrimidine derivatives, and the suffix -osine is used for purine derivatives.
2. Deoxyribonucleosides (DNA components). The prefix deoxy- is added to the base name of the nucleoside.

Important exception: the nucleoside derived from thymine is simply called thymidine (without the "deoxy-" prefix). This is because thymine is not found in RNA, eliminating any confusion with a ribose analog.

Correspondence of nitrogenous bases and nucleosides:

• Uracil $\rightarrow$ Uridine (U)
• Thymine $\rightarrow$ Thymidine (dT)
• Cytosine $\rightarrow$ Cytidine (C), Deoxycytidine (dC)
• Adenine $\rightarrow$ Adenosine (A), Deoxyadenosine (dA)
• Guanine $\rightarrow$ Guanosine (G), Deoxyguanosine (dG)

Physicochemical Properties of Nucleotides

From a chemical standpoint, nucleotides are phosphoric acid esters of nucleosides. The formation of these structures occurs through the esterification reaction of nucleosides with phosphoric acid ions.

Key physicochemical characteristics:

• Bond localization: Esterification typically occurs at the hydroxyl group located at the C-3' or C-5' carbon atoms of the pentose.
• Acid-base state: Phosphoric acid is triprotic. When it forms an ester within a nucleotide, the resulting compound retains the properties of a diprotic acid.
• Salt formation: Under the slightly alkaline conditions of living cells, nucleotides do not exist as free acids, but rather in the form of salts. The charge of the phosphate group is neutralized by cations, predominantly potassium and magnesium ions. For instance, in the structure of magnesium deoxyguanosine-5'-phosphate, the $Mg^{2+}$ ion completely compensates for the charge of the phosphoric acid residue.
• Hydrolysis: Nucleosides themselves are capable of slow hydrolytic cleavage, which proceeds in an acidic environment.

Biological Role and Functions of ATP

The biological significance of nucleotides is not limited solely to their structural role (acting as monomers for the synthesis of DNA and RNA). Individual nucleotides have an independent metabolic role, actively participating in biochemical transformations within the cell.

A special place is occupied by the energetic function. The most important molecules here are high-energy (macroergic) compounds — ATP (adenosine-5'-triphosphate) and ADP (adenosine-5'-diphosphate). Chemically, they are esters of triphosphoric and diphosphoric acids, respectively.

Role of ATP in biochemical processes: Energy is accumulated in ATP molecules and ions, which is released during the breakdown and oxidation of organic substances. The mechanism of ATP action consists in the phosphorylation of other organic molecules — thus ATP transfers the energy necessary for complex reactions to occur.

ATP energy is expended on various cellular syntheses:

• Formation of peptide bonds during protein synthesis.
• Synthesis of starch from glucose molecules.
• Formation of carboxylic acids necessary for subsequent fat synthesis.

Briefly: answers to topical questions

Class and exam questions

What else to study on this topic

• Polycondensation reaction mechanisms in polynucleotide formation
• Structure of purine nitrogenous bases
• Conditions and kinetics of nucleoside hydrolysis in an acidic environment
• The process of organic molecule phosphorylation using ATP

Other topics in "Chapter 18. Major Classes of Bioorganic Compounds"

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