Biochemical Engineering Fundamentals, Part 1 - Bailey J., Ollis D. 1989

The Chemical Basis of Life
Sugars and Polysaccharides
Structural components of nucleic acids; energy carriers and coenzymes

In addition to their role as structural Components of nucleic acids, NUCLEOTIDES and their derivatives are of independent biological interest. All nucleotides are composed of three components: phosphoric acid, an aldopentose (ribose or deoxyribose), and a nitrogenous base, typically a purine or pyrimidine derivative.

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These three components form Two Types of nucleotides, which differ in The Nature of the aldopentose residue (Fig. 2.7). Ribonucleic Acids (RNA) are polynucleotides containing a ribose residue, while the polymer chains of Deoxyribonucleic Acids (DNA) are built with the monosaccharide deoxyribose. Fig. 2.7 also shows the chemical structures of the five nitrogenous bases that make up DNA and RNA nucleotides. Three of these bases—adenine (A), guanine (G), and cytosine (C)—are typical of both DNA and RNA. In contrast, thymine (T) is found only in DNA, while the related pyrimidine base uracil (U) is specific to RNA. Both types of nucleotides are strong acids due to the presence of the phosphoric acid residue.

Cleavage of the phosphate group from the 5'-carbon atom of a nucleotide yields the corresponding nucleoside. As shown in Table 2.4, the names of Nucleosides and Nucleotides are derived from the names of their respective nitrogenous bases. It should be noted, however, that an alternative nomenclature is also used for nucleotides. For example, adenylate can also be called adenosine 5'-monophosphate. The latter type of nomenclature is typically applied to nucleoside derivatives in which the hydroxyl group at C-5' is esterified with a diphosphate or triphosphate group, such as adenosine 5'-triphosphate (ATP).

From a biological standpoint, the nucleoside adenosine, composed of ribose and adenine residues, is particularly important. Fig. 2.8 shows The Structure of adenosine 5'-monophosphate (AMP) and several of its key derivatives. One or two additional phosphoric acid residues can be attached to AMP, yielding ADP (adenosine 5'-diphosphate) and ATP, respectively. The Hydrolysis of the phosphodiester bonds linking the phosphate groups releases a large amount of energy. For example, The conversion of ATP to ADP and phosphate at 3°C and pH 7 (recall that pH = -log a_H, where a_H is the concentration of H⁺ ions in solution in mol/L) is accompanied by a standard Gibbs Free energy change of -7.3 kcal/mol.

Table 2.4. Nomenclature of nucleosides and nucleotides. As shown in the last row, the prefix "deoxy-" is used to denote compounds containing a deoxyribose residue

We are accustomed to evaluating the energy yield of reactions primarily in units of thermal energy, i.e., heat; however, The Cell is essentially an isothermal system in which chemical Pathways of Energy transformation are typically utilized. Later, in Chapter 6, we will look in much greater detail at ATP as the primary carrier of chemical energy in all Cells without exception. In essence, ATP acts as a storage battery for energy obtained from nutrients or sunlight, which is then expended in polymer Biosynthesis, Active Transport across membranes, and cell motility. The diphosphates and triphosphates of other nucleotides can also perform similar Functions in cellular chemistry, but adenosine phosphates remain the primary energy carriers.

FIG. 2.8. Adenosine phosphates. AMP, ADP, and ATP participate in energy transfer processes in the cell, while cyclic AMP performs regulatory functions.

The cyclic form of AMP, which contains an intramolecular ring involving the phosphate group (Fig. 2.8), functions as a regulator of numerous cellular reactions, including those involved in the synthesis of Polysaccharides and storage polymers (Lipids).

FIG. 2.9. Three important Coenzymes that are nucleotide derivatives.

A deficiency of cyclic AMP in Tissues is associated with a type of Cancer, i.e., a state of relatively uncontrolled cell growth.

Adenosine monophosphate is not only a structural component of Nucleic Acids but also serves as the backbone for several coenzymes, whose chemical structures are shown in Fig. 2.9. Enzyme kinetics will be discussed in the next chapter; here, it suffices to note that coenzymes are Organic compounds required for the activation of certain Enzymes, i.e., for converting them into the form in which they can perform catalytic functions. Since virtually all reactions in the cell are catalyzed by enzymes, altering coenzyme concentrations is a convenient way to regulate The activity of the corresponding enzymes in the cell, thereby modulating the rates of various intracellular processes.