Basic components of nucleic acids
Mononucleotide contains three components, namely a pentose, a phosphate and a nitrogenous base. The pentose has a central position among them, it is either β-D-ribofuranose (ribose) or 2'-deoxy-β-D-ribofuranose (deoxyribose). In nucleotides, the pentose carbons are numbered with an apostrophe (C2'..c two with a dash) to distinguish them from the base carbons. Depending on the type of pentose, we distinguish ribonucleic acids (RNA) and deoxyribonucleic acids (DNA). Pentose occurs in various conformations. If C2' protrudes above the plane of the furanose ring in the same way as C5', it is a 2'-endo conformation, if C3' protrudes like this, the conformation is called 3'-endo. The conformation of pentoses changes during functionally significant changes in the higher structure of nucleic acids.
A base is attached to C1 of pentoses by an N-β-glycosidic bond. Bases are derived either from a pyrimidine (cytosine, uracil, thymine) or from a purine (adenine, guanine). In RNA thymine occurs rarely, DNA does not contain uracil. The basic character of these compounds is given by heterocyclic nitrogens, which, however, are not protonated in the cell at pH close to 7.
Cytosine
Uracile
Thymine
Adenine
Guanine
The compound of a nitrogenous base with a saccharide is called a nucleoside, according to the pentose a ribonucleoside (specifically cytidine, uridine, thymidine) or a deoxyribonucleoside (adenosine, guanosine). The heterocycles of the bases are flat, their plane is approximately perpendicular to the plane of the furanose ring of the pentose. At first glance, it appears that the base can rotate around the glycosidic bond relative to the pentose. However, steric hindrances allow only the syn- or anti- conformation to be adopted, depending on whether the base around the glycosidic bond is turned over the pentose face (syn-) or to the opposite side (anti-). In natural dsDNA, the anti-conformation of purines and pyrimidines predominates.
A nucleotide is formed from a nucleoside by esterification of a saccharide with trihydrogenphosphoric acid. In ribonucleotides, phosphate can be attached in the 2', 3' or 5' position, in deoxyribonucleotides in the 3' or 5' position.
Due to the complexity of the formulas and the length of the names of the components of nucleic acids, the nomenclature commission of the International Union of Pure and Applied Chemistry (IUPAC) established rules for the use of names, abbreviations, one- or three-letter symbols. The table shows the most used of them:
| Base | Ribonucleoside | Deoxyribonucleoside | |||||
|---|---|---|---|---|---|---|---|
| N | dN | ||||||
| Pyrimidins | Pyr | -idine | Y | Pyd | Deoxy- -idine | dY | dPyd |
| Cytosine | Cyt | Cytidine | C | Cyd | Deoxycytidine | dC | dCyd |
| Uracile | Ura | Uridine | U | Urd | Deoxyuridine | dU | dUrd |
| Thymine | Thy | Ribosylthymine | T | Thd | (Deoxy)thymidine | dT | dThd |
| Purins | Pur | -osine | R | Puo | Deoxy- -osine | dR | dPud |
| Adenine | Ade | Adenosine | A | Ado | Deoxyadenosine | dA | dAdo |
| Guanine | Gua | Guanosine | G | Guo | Deoxyguanosine | dG | dGuo |
| Hypoxanthine | Hyp | Inosine | I | Ino | |||
| Xanthine | Xan | Xanthosine | X | Xao | |||
| Orotate | Oro | Orotodine | O | Ord | |||
Examples[edit | edit source]
| Uridine-5’-phosphate | Urd-5’-P | UMP |
| Uridine-3’-phosphate | Urd-3’-P | |
| Adenosine-5’-diphosphate | Ado-5’-PP | ADP |
| Adenosine-5’-triphosphate | Ado-5’-PPP | ATP |
| Cyclic adenosine-3’,5’-phosphate | Ado-3’,5’-P | cAMP |
| Deoxycytidine-5’-phosphate | dCyd-5’-P | dCMP |
| Isoacceptor RNAs | tRNA1AA, tRNA2AA, tRNA5AA | |
| Aminoacyl-tRNA | AA-tRNA | |
| Heterogeneous nuclear RNA | hnRNA | |
| Small nuclear RNA | snRNA | |
| Small nucleolar RNA | snoRNA | |
| Complementary DNA (to mRNA) | cDNA |
Table notes:
- The IUPAC Commission has reserved single-letter symbols C, T, A, G, etc. for nucleosides included in an oligo- or polynucleotide. It is written CpUpGpAp or C–U–G–Ap in the case of RNA and d(pApGpT) or d(pA–G–T) in the case of DNA. Phosphates (and terminal phosphates) are marked with the lowercase letter p. If the polarity of the chain is not indicated by numbers or arrows between the letters, then the 5'-end of the chain is on the left and the 3'-end is on the right. If there is a p symbol at either end, it means that the terminal 5'- or 3'-OH group is esterified with phosphate. Single-letter symbols are not used for mononucleotides; these can only be described with three-letter symbols, and phosphate is written as a capital letter P.
- The prefix deoxy- is usually omitted for thymidine, so dT is thymidine. T is ribosylthymine, found for example in transfer RNAs.
- The abbreviations ATP, CDP, dGMP are reserved only for nucleoside 5'-phosphates, not 3'- or 2'-phosphates. The first phosphate, referred to as α, is connected to the pentose by an ester bond, the second (β) and third (γ) phosphates form an anhydride with the previous phosphate.
- Phosphate can bind to two carbons of the same pentose through a phosphodiester bond, creating another heterocycle in the compound, which is why the compound is called a cyclic nucleotide. The abbreviations cAMP and cGMP denote the respective 3',5'-phosphates; have an important signaling function in the cell.
In addition to the listed basic components, nucleic acids also contain other so-called minor bases and nucleosides. They are mostly formed by additional methylation of a base or pentose after their incorporation into a polynucleotide, there are, for example, N-6-methyladenosine (m6A), 5-methylcytosine (m5C), 2'-O-methylguanosine (Gm). Dihydrouracil and thymine riboside are found in transfer RNAs. Minority bases and nucleosides probably participate in the formation of signal sites or their substituents protect the nucleic acid from cleavage by nucleases. Other bases are metabolites of basic bases, for example hypoxanthine (6-oxopurine), xanthine (2,6-dioxopurine) and uric acid (2,6,8-trioxopurine). Methylxanthines caffeine (1,3,7-trimethylxanthine), theophylline (1,3-dimethylxanthine) and theobromine (3,7-dimethylxanthine) are pharmacologically active substances of plant origin.
Among the properties of bases, their tautomerism is significant, where isomers differ in the distribution of electrons and protons in the molecule.
In the cell at pH around 7, the lactam form predominates for uracil, guanine and thymine, and the lactim form for cytosine and adenine. Tautomerism is important for correct base pairing in double-stranded nucleic acids. Another property of the bases is their characteristic spectrum with a maximum at λ=260 nm. It is used in a number of methodological approaches to the study of nucleic acids (purity of the nucleic acid preparation, their concentration, denaturation, etc.)
Links[edit | edit source]
Related articles[edit | edit source]
- Structure of DNA
- Denaturation of nucleic acids, molecular hybridization
- Topology of DNA
- Interaction of DNA with proteins
- Bacterial chromosome
- Eukaryotic Chromosomes
Bibliography[edit | edit source]
- ŠTÍPEK, Stanislav. Stručná biochemie : Uchování a exprese genetické informace. 1. edition. Medprint, 1998. 92 pp. pp. 8–11. ISBN 80-902036-2-0.
