Sept 14, 2011 new

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Sept 14, 2011 new

  1. 1. BT-202 Netaji Subhas Institute of Technology, Dwarka, New Delhi. Dr. Amita Pandey Sept 14, 2011
  2. 2. <ul><li>Nucleotide </li></ul><ul><li>Nucleoside </li></ul><ul><li>2’-deoxy-D-ribose </li></ul><ul><li>D-ribose </li></ul><ul><li>Pyrimidines </li></ul><ul><li>Purines </li></ul>
  3. 3. Deoxyribonucleotide: -dAMP -dGMP -dTMP -dCMP Ribonucleotide: -AMP -GMP -UMP -CMP Nucleoside: -Deoxyadenosine -Deoxyguanosine -Deoxythymidine -Deoxycytidine Nucleoside: -Adenosine -Guanosine -Uridine -Cytidine
  4. 4. <ul><li>Minor bases </li></ul><ul><li>-methylated </li></ul><ul><li>-hydroxymethylated </li></ul><ul><li>-glycosylated </li></ul>
  5. 5. <ul><li>Phosphodiester bond </li></ul>
  6. 6. Hydrolysis of RNA molecules Mixture of 2’- and 3’- monophoaphate derivatives
  7. 7. <ul><li>Oligonucleotide </li></ul><ul><li>-50 nucleotides polymer </li></ul><ul><li>Polynucleotide </li></ul><ul><li>-longer polymers </li></ul>
  8. 8. DNA structure by Watson and Crick 1953 -hydrophobic interactions -van der Waals interactions -dipole-dipole interactions -hydrogen bonds
  9. 9. <ul><li>Primary structure: </li></ul><ul><li>-nucleotide sequence </li></ul><ul><li>Secondary structure: </li></ul><ul><li>-stable structure taken up by nucleotides </li></ul><ul><li>Tertiary structure: </li></ul><ul><li>-folding of chromosomes </li></ul>
  10. 10. <ul><li>Frederich Miescher (1868 ): isolated and characterized DNA from leukocytes and called it “ nuclein ” . He found that it was rich in phosphorus and nitrogen. </li></ul><ul><li>O. T. Avery, C. MacLeod, and M. McCarty (1940s) : first time said DNA was the genetic material. </li></ul><ul><li>A.D. Hershey and M. Chase (1952) : confirmed that DNA not protein is the genetic material. </li></ul><ul><li>E. Chargaff (1940s) : “Chargaff’s rules” he said that A = T and G = C. </li></ul><ul><li>R. Franklin and M. Wilkins (1950s) : DNA molecules are helical with two periodicities along their long axis. </li></ul>
  11. 11. <ul><li>Watson and Crick (1953) : </li></ul><ul><li>-hydrophillic phosphate and deoxyribose on outside </li></ul><ul><li>-hydrophobic bases on inside </li></ul><ul><li>-two grooves </li></ul><ul><li>-hydrogen bonding between base pair </li></ul><ul><li>-antiparallel </li></ul><ul><li>-10.5 bp in each turn </li></ul><ul><li>-complementary </li></ul>
  12. 12. <ul><li>Complementarity laid the foundation for DNA replication </li></ul>
  13. 13. B-form is the most stable A form B-form Z-form -A-form arises dehydration -Z-form is detectable in both bacteria and eukaryotes
  14. 14. <ul><li>Palindrome </li></ul><ul><li>Mirror repeats </li></ul><ul><li>Hairpins </li></ul><ul><li>Cruciforms </li></ul>
  15. 15. <ul><li>Triplex DNA </li></ul><ul><li>G tetraplex </li></ul>Hoogstein pairing
  16. 16. <ul><li>F. Jacob and J. Monod (1961) : proposed the name messenger RNA. </li></ul><ul><li>Transcription: process of forming mRNA on DNA template. </li></ul><ul><li>Monocistronic: mRNA encoding a single polypeptide. </li></ul><ul><li>Polycistronic: mRNA encoding for more than one polypeptide. </li></ul>
  17. 17. mRNA G pairs with C and A pairs with U
  18. 18. <ul><li>A-form of RNA is predominant form </li></ul><ul><li>Hairpins are most common secondary structures </li></ul>
  19. 19. <ul><li>rRNA: provides peptidyl transferase activity during translation </li></ul><ul><ul><li>Large subunit (LSU): 18S rRNA </li></ul></ul><ul><ul><li>Small subunit (SSU): 5S, 5.8S, and 28S rRNAs </li></ul></ul>
  20. 20. Reversible denaturation and annealing of DNA -viscosity of DNA -pH -temperature -absorption of UV light -hypochromic effect -hyperchromic effect
  21. 21. <ul><li>Melting point t m </li></ul><ul><li>-higher GC content higher melting temp </li></ul>Partially denatured DNA
  22. 22. Hybridization <ul><li>Hybrid duplexes </li></ul><ul><li>- temperature </li></ul><ul><li>-evolutionary relationship </li></ul><ul><li>Southern hybridization </li></ul><ul><li>Northern hybridization </li></ul>
  23. 23. Mutations <ul><li>Alteration in DNA structure that produce permanent changes in the genetic information </li></ul><ul><li>-deamination </li></ul><ul><li>cytosine undergoes </li></ul><ul><li> deamination spontaneously </li></ul><ul><li>Adenine deaminates to Hypoxanthine </li></ul><ul><li>Guanine deaminates to Xanthine </li></ul>
  24. 24. <ul><li>-depurination </li></ul><ul><li>-apurinic or apyrimidinic </li></ul>
  25. 25. <ul><li>Radiation </li></ul><ul><li>- cyclobutane pyrimidine dimers </li></ul><ul><li>-6-4 photoproduct </li></ul><ul><li>Ionizing radiation </li></ul><ul><li>-ring opening </li></ul><ul><li>-fragmentation of bases </li></ul>
  26. 26. <ul><li>Chemicals </li></ul><ul><li>-deaminating agents eg. Nitrous acid </li></ul><ul><li>-alkylating agents </li></ul><ul><li>Oxidative damage </li></ul><ul><li>-hydrogen peroxide, hydroxyl radicals, and superoxide radicals </li></ul>
  27. 27. Learning check! <ul><li>Phosphatidylethanolamine has a net charge of </li></ul><ul><li> at pH 7.0. </li></ul><ul><li>zero </li></ul><ul><li>Lipids molecules are the only essential components of biological membranes. </li></ul><ul><li>True </li></ul><ul><li>False </li></ul><ul><li>Lipids in bilayer have high ratio of diffusion. </li></ul><ul><li>lateral </li></ul><ul><li>Palmitic acid is a acid. </li></ul><ul><li>fatty </li></ul>
  28. 28. <ul><li>Match </li></ul><ul><li>Glycerophospholipids Cholesterol </li></ul><ul><li>Sphingolipids Phosphatidylcholine </li></ul><ul><li>Steroid Spingomyelin </li></ul><ul><li>Lipids containing hydrocarbon chain serve as energy stores. </li></ul><ul><li>True </li></ul><ul><li>False </li></ul><ul><li>Ergosterol is a glucorticoid. </li></ul><ul><li>True </li></ul><ul><li>False </li></ul><ul><li>Polyunsaturated Fas contain multiple bonds. </li></ul><ul><li>double </li></ul><ul><li>Phospholipases are enzymes that catalyz e of glycophospholipids. </li></ul><ul><li>hydrolysis </li></ul>
  29. 29. <ul><li>Which of the following is not a complex lipid </li></ul><ul><li>Triacylglycerol </li></ul><ul><li>Glycolipids </li></ul><ul><li>Sphingolipids </li></ul><ul><li>Phospholipids </li></ul><ul><li>Sphingolipids are significant components of biological membranes. </li></ul><ul><li>True </li></ul><ul><li>False </li></ul><ul><li>Which FA would have a melting temperaturehigher than palmitic acid (16:0)? </li></ul><ul><li>Myristic acid (14:0) </li></ul><ul><li>Palmitic acid (16:1) </li></ul><ul><li>Oleic acid (18:1) </li></ul><ul><li>Stearic acid (18:0) </li></ul>
  30. 30. Assignment # 4 <ul><li>Lehninger: </li></ul><ul><li>Question 2, 5, 6, 8, and 9. </li></ul>

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