Structure, of dna Molecule

DNA is the genetic material in all organisms. In certain viruses, such as the AIDS virus and the tobacco mosaic virus (TMV), RNA is the genetic material.

History. Nucleic acid was first isolated in 1868 by a Swiss physician Friedrich Miescher from the nuclei of pus cells. He called it nuclein. In 1884, Oskar Hertwig wrote "nuclein is the substance responsible for the transmission of hereditary char­acters". Nuclein was renamed nucleic acid by R. Altman in 1889. He discovered the existence of two types of nucleic acids. Kornberg synthesized DNA in vitro in 1961.

Location. In the prokaryotic cells, DNA is circular and occurs in the cytoplasm as a component of the prochromosome and plasmids. In the eukaryotic cells, DNA is linear and largely confined to the nucleus as a component of the chromosomes. It is called nuclear DNA. A small quantity of DNA also occurs in the mitochondria and plastids. This is called extranuclear or organeller DNA. It is circular like the prokaryotic DNA. DNA is present in the chromosome of some viruses too.

Quantity. The DNA content is fairly constant in all the cells of a given species. Just before cell division, however, the DNA amount is doubled. The gametes have half the amount of DNA as they contain half the number of chromosomes.

Chemical Composition. Chemical structure of DNA was explained by P.A. Levene. DNA is the largest biomolecule, also the largest macromolecule. DNA molecule is a long, double chain of deoxy- ribonucleotide or deoxyribotide units. The two deoxyribo- nucleotide chains are unbranched and are twisted around a common axis to form at right-handed double helix (spiral) that encloses a cylindrical space inside it. Each deoxyribonucleotide unit, in turn, consists of 3 different molecules: phosphate (P0₄), 5-carbon deoxyribose sugar (C₅ H₁₀ 0₄) and nitrogenous base.| Nitrogen gives the base its basic nature. The nitrogenous base may be a 9-membered, double-ringed purine, i.e., adenine (A) or guanine (G) ; or a 6-membered, single-ringed pyrimidine, viz., thymine (T) or cytosine (C). In each chain, the phosphate component carried by the carbon atom at position 5' of the sugar in one nucleotide unit is joined by a phosphodiester bond to the hydroxyl component of the carbon atom at position 3 of the sugar in the next nucleotide unit. These 3', 5' phosphodiester bonds provide a con­siderable stiffness to the polynucleotide. The alter­nating sugar-phosphate-sugar components form the "backbones" of the DNA double helix. The nitrogenous base molecules are joined to the sugar molecules by glycosidic bonds and project into the space enclosed in the helix at about 90° to the long axis of the helix. The glycosidic bond develops between 1' carbon of the sugar and the nitrogen at position 1 in case of pyrimidine base and at position 9 in case of purine base. The two deoxyribonucleotide chains are held together by hydrogen bonds. Adenine of one chain is always joined to thymine of the other chain by 2 hydrogen bonds (A = T). Cytosine of one chain is always linked to guanine of the other chain by 3 hydrogen bonds (C = G). Thus, there are only 4 possible base pairs :A — T, T—A, G — C and C—G, in DNA. The phosphate groups provide acidity to the nucleic acid. Both glycosidic and phos-phodiester bonds are formed by condensa­tion reactions that involve elimination of; water.

Polarity. The polynucleotide chains show polarity (direction). One end of each DNA strand is called 5' end. The last; deoxyribose unit at this end has carbon at position 5 free. The other end of the strand; is termed 3' end. The last deoxyribose unit: at this end has the carbon at position 3 free.;

Variety. Although only four types of base pairs are involved in the formation of a DNA molecule, these base pairs may occur in any sequence and there maybe any number of sequences in a molecule. This I gives an infinite variety to the ;DKA molecule (Fig. 25.5). ; However, each individual has a specific sequence of base pairs ! in its DNA.

Complementarity of Base Pairs. The two| polynucleotide chains of DNA : molecule are not identical, but complementary to each other with respect to base pairs. This is due to restrictions on base pairing. A base pair must con­sist of a purine and a pyrimidine. There are two reasons for this limitation.

(i). The space available between the two sugar-phos­phate chains of DNA, i.e. 2nm (20 A), can accommodate one purine and one pyrimidine, but not two purines, which would be too wide, and not two pyrimidines, which would not be close enough to form proper hydrogen bonds (Fig. 25.6). It may be noted that the purine

bases, with two carbon rings, are about twice as wide as pyrimidine bases (Fig. 25.4).

(ii) A specific purine pairs with a specific pyrimidine because of a perfect match between hydrogen donor and acceptor sites on the two bases. Only adenine and thymine and also guanine and cytosine have the proper spatial arrangements to form correct hydrogen bonding (Fig. 25.7). Adenine and cytosine, and also guanine and thymine do not form proper hydrogen bonds and can not pair.

This concept of specific base pairing provides that an adenine in one chain must be matched with a thymine in the other chain ; and a guanine in one chain must have cytosine opposite to it in the other chain. Thus, the two chains are complementary to each other. Hence, from the base sequence in one DNA chain, the base sequence in its complemen­tary chain can be easily predicted. For example, if the base sequence in one chain is A, T, C, G, G, C, T, A that in the other chain will be T, A, G, C, C, G, A.T.

Base Pair. The term base pair refers to two bases, one in each chain of DNA molecule, joined together by hydrogen bonds. Each base pair con­sists of one 2-ringed purine and one 1-ringed pyrimidine. Therefore, all the base pairs have equal width, and the DNA helix has a constant diameter.

Antiparallel Direction. The two chains of DNA molecule run in opposite or antiparallel direc­tions. This means that the carbon atom at position

5' in the sugar component is in one direc­tion in one chain and is in the opposite. direction in the other chain (Fig. 25.8). Thus, the two chains are parallel bul '.heir 5' —* 3' directions are opposite.

Basis For Replication. 'The com­plementarity of bases in and antiparallel directions of the two chains of UNA moleciile provide the-basis; for the precise replication of DNA and proper transcrip­tion of RNA.

ChargaiFs Rules. In 1950, Erwin Chargaff formulated important gene -aliza-tions about DNA structure. These generalizations are called ChargafFs rules in his honour. They are summarized below—

(i) The DNA molecule, irrespective of its source, always has the A —T base pairs equal in number to the G —C base pairs.

(//) The purines and pyrimidincs are always in equal amounts, i.e., A + G = T + C.

(i«) The amount of adenine is always equal to that of thymine, and the amount of guanine is always equal to that of cytosine, i'.e.,A = TandG = ^r:.

However, amount of A + T is not

However, amount of A + T is not

necessarily equal to G + C.

In human DNA, A = 30 • 9%, T = 29 ■ 4%, G = 19-9% and C = 19-8%.

(iv) The bass ratio A + T/G + C may vary from one species to another, but is constant for a given species. This ratio can be used to identify the source of DNA, and can help in classification.

(v) The deoxyribose sugar and phosphate components occur in equal proportions.

Denaturation and Renaturation. If DNA molecule is exposed to a high temperature or titra­tion with an acid or an alkali, the two strands unwind and separate by breakdown of hydrogen bonds be­tween the base pairs. This process is called denaturation, or melting. When the denatured DNA is incubated at a low temperature, the two separated strands reassociate to form a DNA duplex. This process is termed renaturation.

Absorbance. An intact DNA molecule ab­sorbs less light energy as its bases are packed into the interior of the double helix. A denatured DNA molecule absorbs more light as its bases in a single strand are exposed. This rise in light absorbance is called hyperchromatic shift.

Optical Rotation. DNA is dextrorotatory, i.e., it rotates the polarised light to the right.

Physical Structure. Astbury, by his X-ray dif­fraction studies, suggested three dimensional con­figuration for DNA molecule due to its high density. The purines and pyrimidines seemed to be flat rings arranged at right angles to the sugar-phosphate backbones and stacked one above another. The successive base pairs appeared to be 0.34 nm¹ (3.4 A) apart in the stack.

Maurice H.F. Wilkins and Rosalind E. Franklin confirmed Astbury's inference in 1953

with X-ray diffraction I photographs taken by passing X-\ rays through crystals of DNA : and suggested helical configura-\ tion for DNA molecule (Fig. \ 25.9). The helix² was found to jj have a constant diameter of 2 nm I (20 A) along its entire length. Its : one complete turn was 3.4 nm. (34 A) long, and, therefore, had I 10 base pairs. Since the helix is 2 | nm. wide, it can accommodate ; only two strands, and not three l as suggested by Pauling³.

The above investigations I helped Watson and Crick to design a model of DNA molecule in 1953. Incidently, the conclusions of Watson and Crick j and the findings of Wilkins and his associates were published in the same issue of the British jour­nal "Nature⁴". Just 1-page paper of Watson and Crick formed a cornerstone of modern molecular genetics. J.D. Watson, an American biologist, and F.H.C. Crick, an English Chemist, in 1953, designed the model of DNА molecule to explain its structure. This model, now named in their honour, got them the 1962 Nobel Prize⁵ (Medicine and Physiology) alongwith Wilkins. They did not perform any new experiment, but intelligently enough, synthesized the data provided by others (Wilkins, Franklin) about the chemical and physical aspects of DNA to develop a suitable model for its structure. Watson's book, The Double Helix, provides a fascinating insight into their work. According to Watson-Crick model, the DNA molecule consists of two long, parallel chains (strands) which are joined together by short crossbars at regular intervals. The two chains are spirally coiled around a common aixs in a regular manner to form a double helix. The double helix is of con­stant diameter of 2 nanometres (nm) or 20 Angstroms (A) and has a major groove about 22 A wide and a minor groove about 12 A wide alternately. One com­plete spiral (turn) of the helix is 3 • 4 nm (34 A) long and has 10 base pairs. The bases face the interior of the double helix and are slacked 0-34 nm (3-4 A) apart. The sugar and phosphate components form backbones on the outside. The helix is generally right handed, that is, its turns run clockwise looking along the helix axis.

In other words, the DNA molecule has the form of a twisted ladder (Fig. 25.10). The vertical bars of the ladder are formed of alternating phos­phate and deoxyribose sugar components. The horizontal rungs of the ladder are joined to the sugar components of the vertical bars, and are com­posed of purines and pyrimidines linked up by hydrogen bonds.

Potential of Watson and Crick Model. Wat­son-Crick model not only depicts the structure of DNA, but also shows that DNA molecule can repli cate itself faithfully, and remains relatively stable from generation to generation, and also explains how information is contained in DNA molecule. Watson and Crick were aware of this potential of their model and wrote in the journal Nature, "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material".