Chemical nature of DNA /dna / What is DNA?

DNA is found in all plants , animals, prokaryotes and some viruses. In eukaryotes it is present inside the nucleus, chloroplast and mitochondria, whereas in prokaryotes it is dispersed in cytoplasm. In plant, animal and some viruses DNA is double stranded (ds) DNA molecules except some viruses such as fX174. IN TMV, influenza virus, polionylitis virus and bacteriophage the genetic material is single stranded (ss) RNA molecule (Table.1). The entire genetic message which control the chemistry of every cell of the body acting in a specific way is actually written in the language of four nitrogen bases of DNA i.e. purines and pyrimidines. The defined sequence of four bases constitutes a ‘gene’ which may be few or several hundred base pair long. Genes are the structure of the blue prints called protein which control the infinite variety of life.

Table.1 Nature of genetic material

DNA / RNA	Examples
Double stranded DNA (dsDNA)	Higher plants, animals, bacteria, animal viruse (polyoma virus, small pox ,herpes virus), Bacteriophage( T-even)
Single stranded DNA (ssDNA)	Bacteriophage (f X174 and other bacteriophage), animal viruses (parvovirus)
Double stranded RNA (dsRNA)	Retrovirus, reovirus, Hepatitis-B virus, anima virus, plant virus (tobacco mosaic virus)
Single stranded RNA (ssRNA)	Animal viruse (influenza virus, poliomylities virus), Bacteriophages (F_2’ ~ R₁₇)

Fig. DNA

1. 1. Chemical composition

Purified DNA isolated from plants, animals, bacteria and viruses has shown a complex form of polymeric compounds containing four monomers known as deoxyribonucleotide monomers or deoxyribotides (fig.1). Each deoxyribonucleotide consists of pentose sugar (deoxyribose), a phosphate group and a nitrogenous base (either purine or pyrimidine). Purines bases (adenine and guanine) are hetrocyclic and two ringed bases and the pyrimidines (thymine and cytosine) are one ringed bases. The following compounds are of deoxyribonucletide have been described:

Fig;- A typical nucleotide showing its components: Base, sugar and phosphate.

(a) A five carbon ring.

Deoxyribose is a pentose sugar consists of five carbon atom. Four carbon atoms (1’,2’,3’,4’) of this sugar combined with one oxygen atom and form a ring. The fifth atom (5’) forms –CH₂ group which is present outside the ring. Three –OH group are attached at the position 1’ ,3’ and 5’ and the hydrogen atom combined at position 1’, 2’, 3’ and 4’ of carbon atoms (Fig.1). In ribonucleotides, the pentose sugar is ribose which is similar to deoxyribose except that there is an –OH group instead of –H at 2’ carbon atom. The abence of –OH group in DNA make it chemically more stable than RNA.

(B) Nitrogenous bases.

There are two nitrogenous bases purines and pyrimidines. The purines are double ringed compounds that consists of 5-membered imidazole ring with nitrogen at 1’,3’, 7’ and 9’ position. The pyrimidines are one ring compounds, the nitrogen being at the position 1’ and 3’ in 6-membered benzene ring. A single base is connected to 1’-carbon atom of pentose sugar by N-glycosidic bond. Purines are of two types, adenine (A) and guanine (G), and pyrimidines are also of two types , thymine (T) and cytosine (C). Uracile (U) is the third pyrimidine (fig.2). A, G and C are common found in both DNA and RNA. U is found only in RNA.

(b) A phosphate group.

In DNA a phosphate group (PO₄^3- ) is attached to 3’-carbon of deoxyribose sugar and 5’-carbon of another sugar. Therefore, each and every strand contains 3’ end and 5’ end arranged in an alternate manner. Strong negative charges of nucleic acid are due to the presence of phosphate group. A nucleotide is a nucleoside phosphate which contains its bond to 3’ and 5’ carbon atom of pentose sugar that is called phosphodiester.

(Fig.2) Nitrogen bases of nucleic acids.

2. 2. Nucletides and Nucleosides

The nitrogen bases combined with pentose sugar are called nucleosides. A nucleoside linked with phosphate forms a nucleotide (Fig.1)

Nucleoside = pentose sugar + Nitrogenous bases

Nucleotide = nucleoside + phosphate

On the bases of different nitrogenous bases the deoxynucleotide are of following types:

(a) Adenin (A) = deoxyadenosine-3’/5’-monophosphate (3’/5’ –d AMP)

(b) Guanin (G) = deoxyguanosine-5’-monophosphate (5’ –d GMP)

(c) Thyamine (T) = deoxythymidine-5’-monophosphate (5’ –d TMP)

(d) Cytocine (C) = deoxycytidine -5’-monophosphate (5’ –d CMP)

In addition to the presence of nucleosides in DNA helix, these are also present in nucleoplasm and cytoplasm in the form of deoxyribonucleotide phosphate e.g. deoxyadenosine triphosphate (dATP), deoxyguanosine triphosphate (dGTP), deoxycytidine triphosphate (dCTP) , deoxythmidine triphosphate (dTTP). The advantage of this four deoxyriboncletide in triphoshate form is that the DNA polymerase acts only on triphosphate of nucleotides during DNA replication.

Similarly, the ribonucleotides contains ribose sugar, nitrogenous bases and phosphate. Except sugar, the other components are similar. However, uracil (U) is found in RNA instead of thymine. Generally, RNA molecule is single stranded beside some exceptions.

3. 3. Polynucleotide

The nucleotides undergo the process of polymerization to form a long chain of polynucleotide. The polynucleotides are designated by prefixing ‘poly’ to each repeating unit such as poly A (polyadenylic acid), poly T (polythymidilic acid), poly C (polycytidilic acid), poly G (polyguanidylic acid) and poly U (polyuridylic acid). The polynucleotides that consists of the same repeating unit are called homopolynucleotides such as poly A, poly T, poly C, poly G and poly U.

4. 4. Chargaff-equivalent rule

By 1948, a chemist Erwin chargaff started using paper chromatography to analyse the base composition of DNA from a number of studies. In 1950, chargaff discovered that in DNA of different type of organisms the total amount of purines is equal to the total amount of pyrimidines, i.e. the total no. of A is equal to the total no. of T (A-T), and the total no. of G is equal to the total no. of C (G-C). It means that A/T = G/C, i.e. A+T/G+C = 1. In DNA molecules isolated from several organisms regularity exists in the base composition.

The DNA molecule of each species comprises of base composition which is not influenced by either environmental conditions or growth stage or age. The molar ratio i.e. [A] +[T]/[G]+[C] represents the characteristic composition of DNA of each species. However, in higher plants and animals A-T composition was found genetically high and G-C content low, whereas the DNA molicules isolated from lower plants and animals, and bacteria and viruse was generally rich in G-C and poor in A-T contents (Table 2). The two closely related species will have very similar molar % G+C values and vice versa. Thus, the use of base composition has much significance in estabilashing relationship between two species and in taxonomy and phylogeny of species.

Table 2. Relative amount of nitrogenouse bases in DNA isolated from different organisms.

Source	Adenine	Guanine	Thymine	Cytosine	A+T/G+C
Human sperm	30.9	19.1	31.6	18.4	1.62
Human thymus	30.9	19.9	29.4	19.8	1.52
Sea urchin sperm	32.8	17.7	32.1	18.4	1.85
Wheat germ	26.5	23.5	27.0	23.0	1.19
Yeast	31.3	18.7	32.9	17.1	1.79
Escherichia coli	26.0	24.9	23.9	25.2	1.00
Diplococcus pneumonia	29.8	20.5	31.6	18.0	1.59
Bacteriophage T₂	32.5	18.2	32.6	16.7	1.86
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