The below mentioned article provides a notes on Nucleotides.
The monomeric units of DNA are called deoxyribonucleotides and those of RNA are ribonucleotides. Both the nucleic acids are long threadlike macromolecules made up of a large number of deoxyribonucleotides and ribonucleotides respectively.
The nitrogenous bases fall into two types—purines and pyrimidines. They are organic bases belonging to a series of related ring compounds in which the rings contain more carbon and nitrogen atoms. These bases are adenine, guanine, thymine, cytosine and uracil which are broadly categorised under purines and pyrimidines.
The purines, adenine and guanine, are made up of two interconnecting rings while the pyrimidines, cytosine, thymine and uracil, possess a single ring structure. Purines are in fact derivatives of pyrimidines with an imidazole ring. Parent structures of purine and pyrimidine are given below.
Both the heterocylic bases are water insoluble, slightly basic in nature and show aromatic character. Both pyrimidines and purines are planar molecules. The purine molecules have a slight pucker in three-dimensional structures. The molecular structure of the bases are given below.
The purine and pyrimidine bases of DNA carry genetic informations, whereas the sugar and phosphate groups perform a structural role. Not only the dimensions of the bases but also their hydrogen bonding capacity are crucial to the biological function of nucleic acids.
Hydrogen bonding takes place through the functional groups like amino groups, the ring -NH- groups, and the strongly electronegative oxygen atoms of the different bases. Depending upon the pH, the bases may exist in two or more tautomeric forms.
An equilibrium is maintained between the keto (or lactum) and the enol (or lactum) forms at a particular pH. It is the lactum form which participates in the glycosidic bond with ribose and deoxyribose and this form is common at physiological pH.
Besides the common bases mentioned above a large number of unusual purine and pyrimidine derivatives called the rare or minor bases, are found in nucleic acids particularly in tRNAs. Most of the rare bases are methyl derivatives but acetyl, isopentenyl or hydroxymethyl derivatives are also found. Over thirty different types of rare bases had been found in tRNAs.
Zachau et al. (1966) and Biemann et al. (1966) identified N6-(Δ2-isopentenyl) adenine as a constituent of yeast tRNA in which it was present as the nucleotide adjacent to the anticodon of serine. Later, it was also identified as the odd base next to the anticodon of tyrosine tRNA in the yeast (Madison etal., 1967).
From the tRNA of spinach, corn and peas N6 -(Δ2-isopentenyl) adenine has been isolated by Hall ef al. (1967). It was also detected in tRNA preparations of E. coli (Armstrong etal., 1969), Staphylococcus epidermidis (Armstrong etal., 1970) and Corynebacterium tumifaciens (Rothborneand Hall, 1972).
Methylthio-isopentenyl adenine (ms2i6Ade) has been isolated from E. coli tRNA (Burrows et al., 1970). It is also present in wheat germ tRNA (Hetch et al., 1969). It has been identified in Spinacea oleracea leaf and isolated from chloroplast tRNA (Vreman etal., 1978).
Ribosyl zeatin (ZR) has been isolated and identified as a constituent of soluble RNA of spinach leaves, corn and pea seeds (Hall et al., 1967).
Methyl thio-zeatin riboside (msZR) has been isolated and identified from wheat germ tRNA (Burrows etal., 1 970) and in pea shoot (Vreman etal., 1974) and spinach leaf blade tRNAs (Vreman ef al., 1978) where it exists both in the cis- and trans- forms.
All the above-mentioned rare bases found in tRNA have been reported to have cytokinin activity. All the purine and pyrimidine bases strongly absorb ultraviolet light at 250-280 nm.
The nucleosides are carbohydrate derivatives of purines and pyrimidines. D-ribose containing nucleosides are the ribonucleosides, and the 2-deoxy-D-ribose containing nucleosides are the deoxyrlbonucleosides. They are much more water soluble than their corresponding free bases. The sugar is attached to the base by its hydroxyl group on the C-l carbon atom.
The ribosides of adenine, guanine, cytosine, uracil and thymine are known as adenosine, guanosine, cytidine, uridine, and thymine riboside, respectively. Correspondingly their deoxyribosides are deoxyadenosine, deoxyguanosine, deoxycytidine, and deoxythymidine.
Nucleotides are the phosphate esters of nucleosides. So the nucleotide composition includes residues of the pyrimidine or purine base, a pentose and phosphoric acid. Both ribonucleotides and deoxyribonucleotides are obtained in the free form in cells. Nucleotides are also formed when nucleic acids undergo milder chemical or enzymatic hydrolysis. It follows that nucleotides are the monomeric units of nucleic acids.
In case of ribonucleotides the phosphate can be esterified at three positions of ribose, the 2′-, 3′- and 5′-hydroxyI groups, but only the 3′- and 5′- isomers can exist in the deoxy series. All these possible structures exist in nature. The nucleotides can also be regarded as monoesterified derivatives of phosphoric acids. They are, therefore, strong dibasic acids.
The nucleotide derived by esterification of the 5′- hydroxyl group of adenosine is adenosine-5′- phosphate or adenylate. The term adenylic acid is sometimes used, but adenylate is preferred because the phosphate group remains ionized at physiological pH.
Adenylate is abbreviated as AMP (adenosine monophosphate). Other 5′- deoxyribonucleotides are called deoxyadenylate (dAMP), deoxyguanylate (dGMP), deoxythymidylate (dTMP), and deoxycytidylate (dCMP).
The first reported nucleotide was 5′-phosphate of inosine, or inosine-5′-monophate (IMP), discovered by Liebig in 1847. Nucleotides have many roles to play in the cellular metabolism as coenzymes, energy source, and as building blocks of DNA and RNA.
The cyclical -2′: 3′- phosphates of all the ribonucleotides are formed as hydrolytic products. The cyclical -3′: 5′-phosphate of adenosine (cyclic AMP) is an important metabolic regulator.