Biological Chemistry - Berezov T. T., Korovkin B. F. 1998

Chemistry of Nucleic Acids
Structure of Nucleic Acids

To understand A number of features of Introduction/20.html">DNA Structure, the Regularities of the composition and quantitative content of nitrogenous bases, first established by E. Chargaff, were of great importance. It turned out that the nitrogenous bases of DNA usually vary among different species of organisms, yet remain almost unchanged within the same species during development, regardless of environmental changes or dietary habits. It has also been shown that DNA isolated from different Tissues of the same species has the same composition of nitrogenous bases. The quantitative ratios obtained were named Chargaff's rules. When analyzing the composition of purified DNA isolated from various sources, the following Conclusions were drawn:

1) the molar fraction of Purines* equals the molar fraction of Pyrimidines:

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2) The amount of adenine and cytosine equals the amount of guanine and thymine:

3) the amount of adenine equals the amount of thymine, and the amount of guanine equals the amount of cytosine: A = T and G = C; accordingly

4) essential for species characterization (taxonomic significance) proved to be the so-called Specificity coefficient, reflecting the ratio

* Here and hereafter, purine and pyrimidine bases are designated by the initial letters of their respective names.

This ratio is often expressed in molar percentages (G + C), or percentages of GC pairs. For animals and most plants, this coefficient is below 1 (from 0.54 to 0.94), whereas in microorganisms it varies within a significant range (from 0.45 to 2.57).

Data obtained by A. N. Belozersky and his students indicate the existence in nature of an AT type of DNA (in Chordates and invertebrates, higher plants, a number of Bacteria, and Yeast-like organisms) and a GC type of DNA (in non-yeast Fungi, actinomycetes, and a number of bacteria and Viruses).

It is known that the structural units of Nucleic Acids are monomeric molecules—mononucleotides. Consequently, nucleic acids are polynucleotides. These are polymerization products of mononucleotides, the number and sequence of which in DNA and RNA chains are determined in strict accordance with the program embedded in the template molecule (see Chapter 14). Mononucleotides are easily formed upon the Hydrolysis of DNA and RNA in the presence of Nucleases, and consist of three specific components: a nitrogenous base, a carbohydrate, and phosphoric acid. In this mononucleotide "triad," the carbohydrate occupies the middle position. Compounds of a nitrogenous base (any) and a carbohydrate (ribose or deoxyribose), designated as nucleosides, are easily formed from a mononucleotide upon the hydrolytic Cleavage of phosphoric acid in the presence of alkali or with the participation of specific Enzymes—nucleotidases.

Nucleosides contain a purine or pyrimidine base linked to a carbohydrate by an N-glycosidic bond. Only ß-nucleosides are found in the Composition of Nucleic acids. Examples include two mononucleotides: adenosine-5'-monophosphoric acid (AMP) and cytidine-5'-monophosphoric acid (CMP):

R at the 2' carbon is represented by an H or OH group depending on the type of nucleic acid—DNA or RNA. The formation of the N-glycosidic bond in purine NUCLEOTIDES involves N-9 of the purine and C-1' of the pentose, while in pyrimidine nucleotides it involves N-1 of the pyrimidine and C-1' of the pentose. To distinguish the carbon atoms of ribose or deoxyribose from the carbon atoms comprising purine and pyrimidine bases, the former are conventionally designated with a prime symbol: for example, the atoms at the 3rd and 5th carbons are designated as C-3' and C-5' or, more frequently, 3' and 5'.

It should be noted that among the products of Enzymatic hydrolysis of DNA and RNA, besides nucleoside-5'-monophosphates, nucleoside-3'-monophosphates are also detected. THE POSITION OF the phosphate is determined by the site of Cleavage of the phosphodiester bond between adjacent nucleotides, which indicates The Nature of nucleotide linkage via the phosphoric acid residue connecting the 3' and 5' carbon atoms of the pentose.

Table 3.3 presents the composition and names (including trivial ones), as well as the abbreviated designations of Nucleosides and Nucleotides (for RNA they are called ribonucleotides, and for DNA—deoxyribonucleotides).

Table 3.3. Composition of Nucleosides and Mononucleotides

Mononucleotides and their derivatives, as well as dinucleotides, are present in Cells in a free state and play an important role in METABOLISM. In particular, many Coenzymes, including coenzymes of oxidoreductases, have a nucleotide structure. Mononucleotides, by attaching another phosphate residue, form a phosphoanhydride bond (similar to the bond present in pyrophosphate) and are converted into nucleoside diphosphates (accordingly abbreviated as ADP, GDP, UDP, CDP, and TDP). The latter, by attaching yet another phosphate residue, form nucleoside triphosphates (accordingly abbreviated as ATP, GTP, UTP, CTP, and TTP).

It should be specifically pointed out that only free nucleoside triphosphates in cells serve as precursors for the enzymatic synthesis of DNA and RNA (see Chapter 13). However, cells contain free, naturally occurring nucleoside triphosphates that do not participate in Protein Synthesis but perform vital Functions. In particular, one of the most important functions of nucleoside triphosphates, and especially ATP, is their Participation in the Bioenergetics of All living organisms (see Chapter 13). Below is the scheme of formation of adenosine diphosphate and adenosine triphosphate molecules (some hydrogen atoms, as well as carbon atoms, in the purine Nucleus and the ribose ring are omitted):

It is necessary to point out the existence in the Organism of two more types of phosphoric esters of nucleotides, where a phosphate links 2 oxygen atoms of the pentose residue within the same nucleotide and where a phosphate bridge unites two different mononucleotides. An example of the first type is Cyclic Nucleotides 2',3'- and 3',5'-, i.e., two possible classes of compounds in which oxygen atoms at C-2' and C-3' or at C-3' and C-5' participate in forming a cyclic structure:

The first of these compounds, 2',3'-AMP, is formed as an intermediate product of ribonucleic acid degradation, whereas cyclic 3',5'-AMP (cAMP) is a naturally occurring ribonucleotide (formed from ATP in a reaction catalyzed by the enzyme adenylate cyclase). cAMP possesses a number of unique functions and high biological activity in Metabolic Regulation, acting as a mediator of extracellular signals in animal cells. A similar function is performed by cGMP, UDP and CTP derivatives, and nucleotides as parts of Cofactors and Coenzymes (see Chapter 4).

An example where a single phosphate group links two different ribonucleoids is The structure of guanosylthymidine phosphate:

Although this compound has not been found in nature, it contains the type of linkage characteristic of natural nucleic acids. As can be seen, the C-3' of the ribose of one nucleotide is linked via a phosphodiester bond to the C-5' of the ribose of the second nucleotide.

In medical practice, particularly in oncology, synthetic analogues of nitrogenous bases, nucleosides, and nucleotides have found widespread application. These analogues, featuring minor modifications in the base or carbohydrate structure, are incorporated into the corresponding cellular components, exerting a noticeable cytotoxic effect. The most common drugs that are analogues of purine and pyrimidine bases (and their corresponding nucleotides) include 5-fluorouracil, 6-thio- and 6-mercaptopurine, 8-azaguanine, 6-azauridine, and 6-azacytidine, as well as the 5-iodo derivative of deoxyuridine.

In addition to the abbreviated names and designations of nucleosides and nucleotides (see Table 3.3), single-letter Abbreviations are adopted for nucleosides (and nucleotides): specifically, A for adenosine (and AMP), G for guanosine (and GMP), C for cytidine (and CMP), U for uridine (and UMP), and T for thymidine (and TMP). Using these symbols, the diribonucleoside monophosphate mentioned above can be designated as G—T. Note that both in Structure and properties, G—T and T—G will differ significantly from each other (just as in the case of dipeptides).