Three-Dimensional Models of a Five-Carbon Sugar Molecule and Nucleic Acids

Three-Dimensional Models of a Five-Carbon Sugar Molecule and Nucleic Acids

DOI: 10.4018/978-1-5225-9651-6.ch007

Abstract

Three-dimensional images of five-carbon sugar molecules and single-stranded nucleic acid molecules (DNA and RNA) were obtained. The geometrical cause of the formation of different form by molecules nucleic acids (right and left spirals with different number of D-ribose and ribose molecules in the period, including closed chains) has been determined. Substituting the known effective values of the lengths of chemical bonds (carbon-carbon, oxygen-oxygen, phosphorus-oxygen) into the structure of polytopes, the values of the characteristic geometric parameters of molecules nucleic acids were calculated: their effective diameter and period. It turned out that the calculated values of these parameters are in good agreement with their values, determined earlier experimentally. It is shown that the set of single-stranded nucleic acids (both DNA and RNA) is broken into two sets of chiral forms. Each form in one set contains a chiral form in another set. Moreover, in each set there are possible rotation of the spirals both in the right and in the left direction.
Chapter Preview
Top

Three-Dimensional Model Of A Five-Carbon Sugar Molecule

Deoxyribonucleic acid (DNA), as a chemical substance, it was isolated by Johann Friedrich Micher in 1869 from the remains of cells contained in the pus. He singled out a substance that includes nitrogen and phosphorus. When Misher determined that this substance has acid properties, the substance was called nucleic acid (Dahm, 2005). Gradually it was proved that it was DNA, and not proteins, as previously thought, and which is the carrier of genetic information. One of the first decisive proofs was the experiments of Oswald Avery, Colin MacLeod and McLean McCarthy (1944) on the transformation of bacteria.

The structure of the double helix DNA it was proposed by Francis Crick and James Watson in 1953 on the base of the X-ray structural data obtained by Maurice Wilkins and Rosalind Franklin and the “Chargaff rules” according to which in each DNA molecule the strict relationships connecting the quantity of nitrogenous bases of different (Watson, & Crick, 1953a, b). For outstanding contributions to this discovery, Francis Crick, James Watson and Maurice Wilkins were awarded the 1962 Nobel Prize in Physiology or Medicine. Deoxyribonucleic acid (DNA) is a biopolymer, the monomer of which is the nucleotide (Albert, et al., 2002; Butler, 2005). Each nucleotide consists of a phosphoric acid residue attached to sugar deoxyribose, to which one of the four nitrogen bases is attached also. The bases that make up the nucleotides are divided into two groups: purines (adenine [A] and guanine [G]) and pyrimidines (cytosine [C] and thymine [T]) are formed by combined five - and six - membered heterocycles.

They managed to show that the DNA isolated from the pneumococci corresponds to the so -called transformation (the acquisition of pathogenic properties by a harmless culture as result of the addition of dead pathogenic bacteria to it). The experiment of American scientists Alfred Hershey and Martha Chase (Hershey - Chase experiment, 1952) with radioactively labeled proteins and bacteriophage DNA showed that only the phage nucleic acid is transmitted to the infected cell, and the new generation of phage contains the same proteins and nucleic acid, as the initial phage (Hershey & Chase, 1952). Deciphering the structure of DNA (1953) has become one of the turning points in the history of biology.

In 1986, Frank - Kamenetskiy in Moscow showed how a double - stranded DNA folds into a so -called H - shape, composed not of two but three strands of DNA (Frank – Kamenetskiy, 1986, 1988). Deoxyribonucleic acid (DNA) is a biopolymer, the monomer of which is the nucleotide (Albert et al., 2002; Butler, 2005).

Nucleotides are long polynucleotide chains covalently linked. These chains in the overwhelming majority of cases (except for some viruses possessing single - stranded DNA genomes) are combined pairwise by means of hydrogen bonds into a secondary structure, called the double helix (Watson & Crick, 1953 a, b; Berg, Tymoczko & Stryer, 2002). Each base on one of the chains is connected to one definite base on the second chain. This specific binding is called complementary. Purines are complementary to pyrimidines (that is, they are capable of forming hydrogen bonds with them): adenine forms bonds only with thymine, and cytosine - with guanine. In a double helix, chains are also linked by hydrophobic interactions and stacking, which do not depend on the DNA base sequence (Ponnuswamy & Gromiha, 1994). Complementarity of the double helix means that the information contained in one chain is also contained in another chain. Different base pairs form a different number of hydrogen bonds. In the future, the existence of nucleic acids differing in the length of the period and shape with rotation of the spiral both to the right and to the left was experimentally established (Ha, et al., 2005; Cantor, & Schimmel, 1980; Frank – Kamenetskiy, 2010).

Watson and Crick postulated the spiral form of the DNA molecule, but they did not discuss the reasons for the formation of such a DNA molecule. Until now there have been no works explaining the existence of a spiral in the DNA molecule.

Key Terms in this Chapter

Simplex: A convex polytope, any two vertices of which are joined by an edge.

Dimension of the Space: The number of independent parameters needed to describe the change in position of an object in space.

Polytope: A polyhedron in the space of higher dimension.

Deoxyribonucleic Acid: A biopolymer, the monomer of which is the nucleotide.

Nucleotide: A phosphoric acid residue attached to sugar deoxyribose, to which one of the four nitrogen bases is attached also.

Complete Chapter List

Search this Book:
Reset