Structure of DNA
- 2. ✓ Although the name nucleic acid suggests their location in the nuclei of cells, certain of them are, however, also present in the cytoplasm. ✓ The nucleic acids are the hereditary determinants of living organisms. ✓ They are the macromolecules present in most living cells either in the free state or bound to proteins as nucleoproteins. ✓ Like the proteins, the nucleic acids are biopolymers of high molecular weight with mononucleotide as their repeating units, just as amino acids are the repeating units of proteins.
- 3. ✓ There are two kinds of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). ✓ Both types of nucleic acids are present in all plants and animals. ✓ DNA is found mainly in the chromatin of the cell nucleus whereas most of the RNA (90%) is present in the cell cytoplasm and a little (10%) in the nucleous. ✓ It may be added that extranuclear DNA also exists; it occurs, for example, in mitochondria and chloroplasts.
- 4. Hydrolytic products of nucleic acid
- 5. Components RNA DNA Acid Phosphoric acid Phosphoric acid Pentose sugar Ribose 2-deoxyribose Nitrogenous bases Purines Adenine Guanine Adenine Guanine Pyrimidines Cytosine Uracil Cytosine Thymine Components of nucleic acids
- 6. Phosphoric Acid ✓ The molecular formula of phosphoric acid is H3PO4. ✓ It contains 3 monovalent hydroxyl groups and a divalent oxygen atom, all linked to the pentavalent phosphorus atom
- 7. Pentose Sugar ✓ The two types of nucleic acids are distinguished primarily on the basis of the 5-carbon keto sugar or pentose which they possess. ✓ One possesses D-2-deoxyribose, hence the name deoxyribose nucleic acid or deoxyribonucleic acid, while the other contains D-ribose, hence the name ribose nucleic acid or ribonucleic acid.
- 8. ✓ An important property of the pentoses is their capacity to form esters with phosphoric acid. ✓ In this reaction the OH groups of the pentose, especially those at C3 and C5, are involved forming a 3′, 5′- phosphodiester bond between adjacent pentose residues. ✓ This bond, in fact, is an integral part of the structure of nucleic acids.
- 10. Nitrogenous Bases ✓ Two types of nitrogenous bases are found in all nucleic acids. ✓ The nitrogenous bases are derivatives of pyrimidine and purine. ✓ Pyrimidine bases – Uracil, Thymine and Cytosine ✓ Purine bases – Adenine and guanine
- 11. Pyrimidine Derivatives ✓ These are all derived from their parent heterocyclic compound pyrimidine, which contains a six membered ring with two-nitrogen atoms and three double bonds. ✓ It has a melting point of 22°C and a boiling point of 123.5°C.
- 12. Uracil (C4H4O2N2), found in RNA only, MW = 112.10 daltons, M.P - 338°C. Thymine (C5H6O2N2), found in DNA only, MW = 126.13 daltons, M.P - 335°C. Cytosine (C5H4ON3), found in both DNA and RNA, MW = 111.12 daltons, M.P – 320-325°C
- 13. Purine Derivatives ✓ These are all derived from their parent compound purine, which contains a six-membered pyrimidine ring fused to the five-membered imidazole ring and is related to uric acid. ✓ It has a melting point of 216°C.
- 14. Adenine (C5H5N5), found in both RNA and DNA, with MW = 135.15 daltons and M.P. 360-365°C. Guanine (C5H5ON5), also found in both RNA and DNA, with MW = 151.15 daltons and M.P. 360°C
- 15. ✓ The nucleosides are compounds in which nitrogenous bases (purines and pyrimidines) are conjugated to the pentose sugars (ribose or deoxyribose) by a β- glycosidic linkage. ✓ The β-glycosidic linkage involves the C-1′ of sugar and the hydrogen atom of N-9 (in the case of purines) or N- 1 (in the case of pyrimidines), thus eliminating a molecule of water. Nucleosides
- 16. Nucleosides
- 18. ✓ Nucleotides are the phosphoric acid esters of nucleosides. ✓ These occur either in the free form or as subunits in nucleic acids. ✓ In the ribose moiety of a ribonucleoside, phosphorylation is possible only at three positions (C2′, C3′, C5′) since C1′ and C4′ are involved in the furanose ring formation. ✓ In the deoxyribose component of a 2′- deoxyribonucleoside, only two positions (C3′, C5′) are available for phosphorylation, since in this sugar C1′ and C4′ are involved in the furanose ring and C2′ does not bear a hydroxyl group. Nucleotides
- 19. Nucleotides
- 20. Deoxyribonucleic Acid ✓ A nucleic acid may be visualized as a polymer of a nucleotide monomer. ✓ In other words, it may be considered as a polynucleotide. ✓ DNA as .... (base-deoxyribose-phosphate)n ✓ RNA as .... (base-ribose-phosphate)n
- 21. Base Composition of DNA-Chargaff Rule ✓ The sum of purines (Pu) is equal to the sum of pyrimidines (Py), i.e., Pu/Py = 1. In other words, A + G = T + C ✓ The ratio of adenine to thymine is also one, i.e., A/T = 1. ✓ The ratio of guanine to cytosine is also one, i.e., G/C= 1. ✓ Bases with 6-amino groups are equal to bases with 6- keto (hydroxyl) groups, i.e., A + C = G + T. ✓ The ratio of A + T/G + C, known as dissymmetry ratio, varies greatly from one species of DNA to the other and is characteristic of that species. ✓ Chargaff’s data suggest that A is always paired with T and G is always paired with C.
- 22. Primary structure ✓ Primary structure of DNA refers to the phosphodiester bond backbone. ✓ In nucleic acid strands, nucleotides are linked by phosphodiester bond. ✓ The bond is formed between the 5’-phosphate group of one nucleotide and 3—hydroxyl group of adjacent nucleotide. ✓ A single nucleic acid strand formed by phosphodiester bond has two termini namely 5’ end with phosphate group and 3’ end with hydroxyl group.
- 24. Secondary Structure ✓ Double helical DNA model was proposed by Watson and Crick. ✓ This model is also called as B-form. ✓ DNA double helix is made up of two DNA strands running in opposite directions along a common axis. ✓ A pairs with T via two hydrogen bonds and G pairs with C via three hydrogen bonds. ✓ DNA will have 1:1 ratio of purine and pyrimidine bases (Chargaff’s rule).
- 26. Tertiary structure ✓ Supercoiled, DNA, chromosomes and chromatin are the three types of tertiary structures of DNA ✓ DNA can be twisted, coiled into compact structure which resembles a coiled telephone wire ✓ Supercoiling may be right handed or left handed.
- 28. Double Helical Structure of DNA (Watson-Crick Model) ✓ DNA molecule consists of two helical polynucleotide chains which are coiled around (or wrapped about) a common axis in the form of a right-handed double helix. ✓ The two helices are wound in such a way so as to produce 2 interchain spacing or grooves, a major or wide groove (width 12 Å, depth 8.5 Å) and a minor or narrow groove (width 6 Å, depth 7.5 Å).
- 30. ✓ The phosphate and deoxyribose units are found on the periphery of the helix, whereas the purine and pyrimidine bases occur in the centre. ✓ The planes of the bases are perpendicular to the helix axis. ✓ The planes of the sugars are almost at right angles to those of the bases.
- 31. ✓ The diameter of the helix is 20 Å. ✓ The bases are 3.4 Å apart along the helix axis. ✓ Therefore, the helical structure repeats after 10 residues on each chain, i.e., at intervals of 34 Å. ✓ In other words, each turn of the helix contains 10 nucleotide residues.
- 32. ✓ The two chains are held together by hydrogen bonds between pairs of bases. ✓ Adenine always pairs with thymine by 2 hydrogen bonds and guanine with cytosine with 3 hydrogen bonds. ✓ The individual hydrogen bonds are weak in nature but, as in the case of proteins, a large number of them involved in the DNA molecule confer stability to it. ✓ It is now thought that the stability of the DNA molecule is primarily a consequence of van der Waals forces between the planes of stacked bases.
- 33. ✓ The sequence of bases along a polynucleotide chain is not restricted in any way. ✓ The precise sequence of bases carries the genetic information. ✓ As a corollary, the entire structure of a DNA molecule resembles a winding staircase, with the sugar and phosphate molecules of the nucleotides forming the railings and the linked nitrogen base pairs (A-T and G- C) forming the steps.
- 34. A-DNA ✓ A-DNA appears when the DNA fibre (B-DNA) is dehydrated, i.e., relative humidity is reduced from 92 to 75% and Na+, K+ and Cs+ ions are present in the medium. In other words, in solution, DNA assumes the B form and after dehydration it assusmes the A form. ✓ This is because the phosphate groups in the A-DNA bind fewer water molecules than the phosphates in B- DNA.
- 36. C-DNA ✓ C-DNA is formed at 66% relative humidity in the presence of Li+ ions. ✓ This form of DNA is also right-handed, with an axial rise of 3.32 Å per base pair. ✓ There are 9.33 base pair per turn of the helix ; the value of helix pitch is, therefore, 3.32 × 9.33 Å or 30.97 Å. ✓ The rotation per base pair in C-DNA is 360/9.33 or 38.58°. ✓ The C-helix has a diameter of 19 Å, smaller than that of both B- and A-helix.
- 38. D-DNA ✓ D-DNA is an extremely rare variant with only 8 base pairs per helical turn. ✓ This form of DNA is found in some DNA molecules devoid of guanine. ✓ By contrast, A-, B- and C forms of DNA are found in all DNA molecules, irrespective of their base sequence.
- 40. Z-DNA ✓ Z-DNA is the more radical departure from B-DNA and is characterized by a lefthanded helical rotation. ✓ It was discovered by Rich, Nordheim and Wang in 1984. ✓ They found that a hexanucleotide, CGCGCG, forms a duplex of antiparallel strands held together by Watson- Crick base pairing, as expected. ✓ Surprisingly, they found that this double helix was left- handed and the phosphates in the DNA backbone were in a zigzag manner ; hence, they termed this new form as Z-DNA.
- 42. Palindromic DNA ✓ It has sequences with twofold symmetry. ✓ In order to superimpose one repeat (shaded sequence) on the other (unshaded sequence), it must be rotated 180° around the horizontal axis and then again about the vertical axis, as shown by arrows.
- 43. Mirror repeat ✓ It has a symmetric sequence on each strand. Superimposing one repeat on the other requires only a single 180º rotation about the vertical axis.
- 44. Bent DNA ✓ Some sequences cause bends in the DNA helix. ✓ Bends are produced whenever 4 or more adenine residues appear sequentially in one of the two strands. ✓ Six adenines in a row produce a bend of about 18°. ✓ Bending may be important in the binding of some proteins to DNA. Hairpin ✓ When only a single strand of palindromic DNA (or RNA) is involved, a hairpin is formed. Cruciform ✓ When both the strands of a double helical DNA are involved, a cruciform is formed.
- 46. H-DNA ✓ H-DNA is usually found in polypyrimidine or polypurine segments that contain within themselves a mirror repeat. ✓ One simple example is a long stretch of alternating T and C residues. ✓ A striking feature of H-DNA is the pairing and interwinding of 3 strands of DNA to form a triple helix. ✓ Triple-helical DNA is produced spontaneously only within long sequences containing only pyrimidines (or purines) in one strand. ✓ Two of the three strands in the H-DNA triple helix contain pyrimidines and the third contains purines.