Elementary plant Biochemistry and Biotechnology (2+1)

RNA & DNA

• There are two kinds of nucleic acids- ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). A nucleic acid is a polynucleotide i.e. a polymer consisting of nucleotides. Each nucleotide has the three following components (Fig).


1. A cyclic five-carbon sugar: this is ribose, in the case of RNA and deoxyribose, in deoxyribonucleic acid DNA. The structure of ribose and 2’-deoxyribose differ only in the absence of a 2’-OH group in deoxyribose, a difference that makes DNA chemically more stable than RNA.



2.A purine or pyrimidine base attached to the 1’-carbon atom of the sugar by an N-glycosidic bond. The purines found in nucleic acids are adenine (A) and guanine (G) and the pyrimidines are cytosine (C), thymine (T) and Uracil (U). DNA and RNA both contain A, G and C. however, T is found only in DNA and U is found only in RNA. There are exceptions to this rule- T is present in some tRNA molecules and there are few phages who’s DNA exclusively contains U rather than T.



3.A phosphate attached to the 5’ carbon of the sugar by a phosphoester linkage. This phosphate is responsible for the strong negative charge of both nucleotides and nucleic acids.



• A base linked to a sugar at position C1 is called as nucleoside. The sugar C1 carbon atom is joined to the N9 atom of purines and N1 atom of the pyrimidines by ß-N-glycosidic bond. When a nucleoside linked with phosphate then it is called as nucleotide.
The terminology used to describe nucleic acid components is listed in Table 1.


• * Note that the names of purine nucleosides end in –osine and the names of pyrimidine nucleosides end in –idine. Note that in shorthand notation, nucleoside and nucleotide derivatives of deoxyribose are distinguished by the prefix ‘d’ and ‘r’. Only the second shorthand notation can discriminate between 5’ and 3’ phosphates, with 5’ phosphate residues placed before the base (e.g. pA is adenosine-5’-monophosphate) and 3’ phosphates placed after the base (e.g. Ap is adenosine-3’-monophosphate).
• $ Guanosine should not be confused with guanidine, which is not a nucleic acid base. @ Thymidine is the deoxy-form. The ribo form, ribosylthymine, is not generally found in nucleic acids
• # Uridine is the ribo-form. Deoxyuridine is not commonly found, although deoxyuridylic acid is on the pathway for synthesis of thymidylic acid.


• The nucleotides in the nucleic acids are covalently linked by a second phosphoester bond that joins the 5’phosphate of one nucleotide and 3’ –OH group of the adjacent nucleotide (Fig). Thus, the phosphate is esterified to both 3’ and 5’ carbon atoms; this unit is often called a phosphodiester group. Thus a polynucleotide chain is formed.


• Two polynucleotides interact with one another and produce DNA double helix structure. This double helix structure was first proposed by James Watson and Francis Crick in 1953 based on the X –ray diffraction studies of M. Wilkins and R. Franklin on DNA fibers (which revealed that the polynucleotide is helical and the bases of the nucleotides are stacked with their planes separated by a spacing of 3.4 A) and Chargraff’s rule (the amounts of purine and pyrimidines present in the Organism are equal, i.e. A+T = G+C).