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A592974226_23691_25_2019_Lecture11 onwards NUCLEIC ACIDS 2.pdf

  1. 1. Nucleic acid
  2. 2. Nucleic Acids Components of Nucleic Acids Primary Structure of Nucleic Acids
  3. 3. Nucleic Acids • The molecular repositories of genetic Information: Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA). • The amino acid sequence of every protein in a cell, and the nucleotide sequence of every RNA, is specified by a nucleotide sequence in the cell’s DNA • A segment of a DNA molecule that contains the information required for the synthesis of functional biological product, whether protein or RNA, is referred to as a gene.
  4. 4. • RNAs have a broader range of functions, and several classes are found in cells. • Ribosomal RNAs (rRNAs) – components of ribosomes, the complexes that carry out the synthesis of proteins. • Messenger RNAs (mRNAs) – intermediaries, carrying genetic information from one or a few genes to a ribosome, where the corresponding proteins can be synthesized.
  5. 5. • Transfer RNAs (tRNAs) – adapter molecules that faithfully translate the information in mRNA into a specific sequence of amino acids. • In addition to these major classes there is a wide variety of RNAs with special functions e.g. regulatory, enzymatic etc.
  6. 6. Nucleic Acids The nucleic acids DNA and RNA are large molecules consisting of long chains of monomers called nucleotides. Nucleotides consist of a: • pentose sugar. • nitrogen-containing base. • phosphate. Nucleotide
  7. 7. Nitrogen Bases The nitrogenous bases are derivatives of two parent compounds: • Purine • Pyrimidine
  8. 8. Purine
  9. 9. Pyrimidine
  10. 10. Nitrogen-Containing Bases in DNA and RNA DNA contains the nitrogen bases • Cytosine (C) • Guanine (G) • Adenine (A) • Thymine (T) RNA contains the nitrogen bases • Cytosine (C) • Guanine (G) • Adenine (A) • Uracil (U)
  11. 11. Pentose Sugars The pentose (five-carbon) sugar in RNA is ribose and in DNA is deoxyribose with no “O” atom on carbon 2ʹ The carbon atoms numbered with primes (ʹ) to distinguish them from the atoms in nitrogen bases.
  12. 12. Nucleosides A nucleoside has a nitrogen base linked by a glycosidic bond to C1ʹ of a sugar (ribose or deoxyribose). HO
  13. 13. Nucleotides The base of a nucleotide is joined covalently (at N-1 of pyrimidines and N-9 of purines) in an N—glycosyl bond to the 1 carbon of the pentose, and the phosphate is esterified to the 5 carbon.
  14. 14. Formation of a Nucleotide A nucleotide forms when the −OH on C5ʹ of a sugar bonds to phosphoric acid. deoxycytidine monophosphate (dCMP) O- O- O P O CH2 O NH2 N N OH O O- O- O P OH + deoxycytidine and phosphate HO CH2 O NH2 N N OH O 5’ 5’
  15. 15. Nucleosides and Nucleotides with Purines
  16. 16. Nucleosides and Nucleotides with Pyrimidines
  17. 17. Names of Nucleosides and Nucleotides
  18. 18. Nucleotides • Constituents of nucleic acids (RNA and DNA) • Nucleotide triphosphate structural component of energy currency of the cell i.e. ATP • Structural components of enzyme cofactors Adenine nucleotides are components of the coenzymes, NAD(P)+, FAD, and CoA. • Activated intermediates in many biosyntheses: – UDP-glucose to glycogen, – CDP-diacylglycerol to phosphoglycerides, – S-adenosylmethionine as methyl donor
  19. 19. • Metabolic regulators: (a) c-AMP is the mediator of hormonal actions; (b) ATP-dependent protein phosphorylation - activates phosphorylase and inactivates glycogen synthase; (c) adenylation of a Tyr of bacterial glutamine synthetase - more sensitive to feedback inhibition and less active; (d) allosteric regulator - glycogen phosphorylase activated by ATP and inactivated by AMP.
  20. 20. Structure of Nucleic Acids
  21. 21. Discovery of DNA Friedrick Miescher (1869) , a Swiss chemist first identified nuclein from nuclei of human white blood cells which was later on renamed as Nucleic acid . It was rich in phosphorus having no sulphur so was different than protein. Russian Biochemist Phobebus Levene (1910) is credited to discover Phosphate-Sugar-Base as three components of Nucleotide . He also mentioned DNA as polynucleotide (Any one of four adenine,Cytocine,Thymine /Guanine ). He also stated difference between Ribose and Deoxyribose Sugar • From
  22. 22. HISTORY OF DNA William Astbury (1938) detected a periodicity of 3.4 angstroms Rosalind Franklin (1952) performed - X- ray diffraction analysis of DNA crystal Franklin and Wilkins (1950-1953) confirmed 3.4 periodicity and noted uniform diameter of 20A○ (2nm) The images of DNA taken by Franklin gave clue to Watson and Crick about the width of double helix and spacing of N-bases Watson and Crick (1953 ) proposed the DNA double helical model based on Franklin’s X-ray crystallography Analysis and other evidences
  23. 23. 1962: Nobel Prize in Physiology and Medicine James D. Watson Francis H. Crick Maurice H. F. Wilkins Rosalind Franklin
  24. 24. X-ray Crystallography of DNA by Franklin and Wilkins (1950-52) showing helical symmetry Franklin’s X ray diffraction Photograph of DNA In 1953 Watson and Crick postulated a 3D model of DNA structure
  25. 25. • Two helical DNA chains wound around the same axis to form a right handed double helix. • The hydrophilic backbones of alternating deoxyribose and phosphate groups are on the outside of the double helix, facing the surrounding water. The furanose ring of each deoxyribose is in the C-2 endo conformation. • The purine and pyrimidine bases of both strands are stacked inside the double helix, with their hydrophobic and nearly planar ring structures very close together and perpendicular to the long axis. • The offset pairing of the two strands creates a major groove and minor groove on the surface of the duplex.
  26. 26. • Each nucleotide base of one strand is paired in the same plane with a base of the other strand. • An antiparallel orientation produced the most convincing model. The original DNA model by Watson and Crick. Photo: Cold Spring Harbor Laboratory Archives Imaginary axis is shown by a line passing through the centre longitudinally The vertically stacked bases inside the double helix would be 3.4 Å apart; the secondary repeat distance of about 34 Å was accounted for by the presence of 10 base pairs in each complete turn of the double helix. In aqueous solution the structure differs slightly from that in fibers, having 10.5 base pairs per helical turn
  28. 28. DNA Double Helix
  29. 29. Two strands are coiled around a common axis in such a way ( like a rope ) that deep (major ) and shallow (Minor) grooves are resulted. Proteins can bind with DNA at these locations. Major grooves are 22A° and Minor grooves are 12 A°
  30. 30. •DNA is long, unbranched and spirally coiled in Eukaryotes and circular in prokaryotes as well as mitochondria and plastids • In Prokayotes DNA is present only in Nucleoid and is Monocistronic, but in Eukaryotes DNA is present in Nucleus, Mitochondria and Plastids and is Polycistronic. •DNA is genetic material ,carries heredity characters over generations through DNA Replication ( DNA  DNA )and Transcription ( DNA RNA ) followed by Translation
  31. 31. What chemical forces hold the two DNA strands together?  Two strands are connected to each other by means of base pairing which comprise the steps of the ladder. Base pairing takes place between one purine and one pyrimidine by H bonds. Although H bonds are weak but many H bonds give stability to the double helical structure.
  32. 32. The two strands of DNA are oriented in opposite directions. One strand runs in 3’-5’ direction and the other in 5’-3’ direction. This antiparallel orientation also supports the double helical nature of DNA molecule. There lies close similarity of measurements of AT and GC pairs, distance of A-T is about 1.11 nm and that of G-C is 1.08nm. The angle between C- 1 of deoxyribose sugar and N of base is about 51°.
  33. 33. Base Pairing • Hydrogen bonds Individually weak electrostatic bonds but collectively become strong and provide stability to double helix
  34. 34. Hydrogen bonds between bases Also important that the purine-pyrimidine base pairs are of similar size.
  35. 35. DNA strands also held together by base stacking: Van der Waals interactions with neighboring base pairs Double stranded helix structure is also promoted by having phosphates on outside ,interact with water and K+ and Mg+ + ions
  36. 36.  Bases are projected inwards and lie perpendicular to the long sugar & phosphate chains.  Bases are attached to C -1 of sugar and for attachment N at 3 position of pyrimidine and N at 9 position of Purine is used.  During base pairing Adenine always pairs with Thymine by 2 H bonds and Guanine pairs with Cytosine b y 3 H bonds. A=T G Ξ C
  37. 37. DNA Molecules Have Distinctive Base Compositions • Important clue to the structure of DNA came from the work of Erwin Chargaff and his colleagues. • They found that the four nucleotide bases of DNA occur in different ratios in the DNAs of different organisms and that the amounts of certain bases are closely related. • These data, collected from DNAs of a great many different species, led Chargaff to the some important conclusions.
  38. 38. Erwin Chargaff (1949-1953) Digested many DNAs and subjected products to chromatographic separation RESULTS  The sum of Purines is equal to sum of Pyrimidines A = T, C = G , A + G = C + T (purine = pyrimidine) but A+T ≠ G +C ( Not equal )  Base ratio A + T/ G+C varies from one species to other and is not always equal to one but is constant for a species.
  39. 39. Chargaff’s rule • Base composition of DNA varies from one species to another • Base composition of DNA from different tissues of same organism is same • Base composition of DNA not affected by age, environment etc.
  40. 40. Chargaff’s rule • In all cellular DNAs, regardless of the species, the number of adenosine residues is equal to the number of thymidine residues (that is, A T), and the number of guanosine residues is equal to the number of cytidine residues (G C). From these relationships it follows that the sum of the purine residues equals the sum of the pyrimidine residues; that is, A G T C. A=T and G=C or purines = pyrimidines
  41. 41.  DNA with high percentage of G ≡ C pairing ( Mitochondrial DNA ) have more density than those with high A = T pairing. (Nuclear DNA ) Upon heating upto 80-90 º C or more 2 strands of DNA uncoil and separate ( DNA Denaturation ). Increase in absorbance at 260 nm (hyperchromicity/ (hyperchromic effect ) On cooling the strands come closer and are held together ( DNA Renaturation or Annealing ). Deccrease in absorbance at 260 nm (hypochromicity/ hyperchromic effect)
  42. 42.  DNA is generally double stranded, but is single stranded exceptionally in some Viruses viz. ȹ- 174 & S-13  Both strands of DNA are right handed spirals except Z DNA ( Left handed spiral ) Alternative Forms of DNA DNA can exist in several conformational isomers B form is the “normal” conformation A form is found in high salt conc Z form Left-handed helix and 12 bp/turn (Z for zigzag)
  43. 43. Figure : DNA can assume several different secondary structures. These structures depend on the base sequence of the DNA and the conditions under which it is placed. Used with permission. © 2005 by W. H. Freeman and Company. All rights reserved
  44. 44. Right vs. Left Handed Helices B Z