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Structure of DNA

Structure of DNA - The widely accepted molecular model of DNA is the double helix structure proposed by Watson and Crick (1953). The DNA molecule consists of two helically twisted strands connected together by 'steps'.

Each strand consists of alterna­ting molecules of deoxyrib6se (a pentose sugar) and phosphate groups. Each step is made up of a double ring purine base and a single ring pyrimidine base.

The purine and pyrimidine bases are connected to deoxyribose sugar molecules. The two strands are intertwined in a clockwise direction, i.e. in a right hand helix, and run in opposite direc­tions. The strand completes a turn p-ach 34A. Each nucleotide occupies 3.4A.

Thus, there are 10 nucleotides per turn. Each successive nucleotide turns 36 degrees in the horizontal plane. The width of the DNA molecule is 20A. The twisting of the strands results in the forma­tion of deep and shallow spiral grooves.

The DNA molecule is a polymer consisting of several thousand pairs of nucleotide monomers. Each nucleotide consists of the pentose sugar deoxyribose, a phosphate group and a nitrogenous base which may be either a purine or a pyrimidine. Deoxyribose and a nitrogenous base together form a nucleoside. A nucleoside and a phosphate together form a nucleotide.

Nucleoside=Deoxyribose+ Nitrogenous base. Nucleotide=Deoxyribose+ Nitrogenous base+ Phosphate.

(1) Deoxyribose is a pentose sugar with five carbon atoms. Four of the five carbon atoms plus a single atom of oxygen form a five-mem­bered ring. The fifth carbon atom is outside the ring and forms a part of a -CH2 group. The four atoms of the ring are num­bered'!' 2,3' and 4'. The carbon atom of -CH2 is numbered 5'.

There are three -OH groups in positions 1', 3' and 5'. Hydrogen atoms are attached to carbon atoms 1',2,3' and 4'.

Ribose, the pentose sugar of RNA, has an identical structure except that there is an -OH group instead of H on carbon atom 2'.

All the sugars in one strand are directed to one end, i.e. the strand has polarity. The sugars of the two strands are directed in opposite directions.

(2) Nitrogenous bases. There are two types of nitrogenous bases, pyrimidines and purines. The pyri­midines are single ring compounds, with nitrogen in positions l' and 3' of a 6-membered benzene ring.

The two most common pyrimidines of DNA are cytosine Pyrimidine and purine rings.

(C) and thymine (T). The purines are double ring compounds. A purine molecule consists of a 5-membered imidazole ring joined to a pyrimidine ring at positions 4' and 5'. The two most common purines of DNA are adenine (A) and guanine (G).

Nucleoside=Deoxyribose+ Nitrogenous base. Nucleotide=Deoxyribose+ Nitrogenous base+ Phosphate.

Base pairing
Each 'step' of the DNA ladder is made up of a purine and a pyrimidine pair, i.e. of a double ring and a single ring compound. Two purines would occupy too much space, while two pyrimidines would occupy too little. Because of the purine-pyrimidine pairing the total number of purines in a double-stranded DNA molecule is equal to the total number of pyrimidines.

Thus A/T = I and G/C = I or A+G = C+ T. The ratio A+ T/G+C, how­ever, rarely equals 1, and varies with different species from 0.4 to 1.9. This ratio is commonly low in micro-organisms and high in higher animals.

The purine and pyrimindine bases pair only in certain combinations. Adenine pairs with thymine (A:T) and guanine with cytosine (G : C). The total width of the pair is 10.7 A. Adenine and thymine are joined by two hydrogen bonds through atoms attached to positions 6' and Cytosine and guanine are joined 1y three hydrogen bonds through positions 6', l' and 2'.

The hydrogen atom with its positive charge is shared between an oxygen atom and a nitrogen atom, both with slight negative charges. Although hydrogen bonds are weak, the fact that there are so many gives stability to the DNA molecule. The weak hydrogen bonding enables the two strands of the DNA to separate during replication.

The pyrimidine and purine bases are linked to the deoxyribose sugar molecules. The linkage in pyrimidine nucleosides is between position of deoxyribose and 3' of the pyrimidine. In purine nucleosides it is between position l' of deoxyribose and position 9' of the purine.

(3) Phosphate. In the DNA strand the phosphate groups alter­nate with deoxyribose. Each phosphate group is joined to carbon atom 3' of one deoxyribose and to carbon atom 5' of another.

Thus each strand has a 3' end and a 5' end. The two strands arc oriented in oppo­site directions.
The 3' end of one strand corresponds to the 5' end of the other. Consequently the oxygen atoms of deoxyribose point in opposite directions in the two strands.
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