Molicular Biology

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Molicular Biology

  1. 1. Types of Molecules <ul><li>DNA: code for genetic information </li></ul><ul><li>RNA </li></ul><ul><ul><li>mRNA intermediates in protein synthesis </li></ul></ul><ul><ul><li>rRNA carry out protein synthesis </li></ul></ul><ul><ul><li>tRNA translate info on mRNA into a.a. </li></ul></ul><ul><li>Gene </li></ul>www.freelivedoctor.com
  2. 2. Nucleotide Components <ul><li>Bases + sugar + phosphate </li></ul><ul><li>Bases </li></ul><ul><ul><li>purine </li></ul></ul><ul><ul><ul><li>adenine </li></ul></ul></ul><ul><ul><ul><li>guanine </li></ul></ul></ul><ul><ul><li>pyrimidines </li></ul></ul><ul><ul><ul><li>thymine </li></ul></ul></ul><ul><ul><ul><li>cytosine </li></ul></ul></ul><ul><ul><ul><li>uracil </li></ul></ul></ul>www.freelivedoctor.com
  3. 3. Bases www.freelivedoctor.com
  4. 4. Nucleotide Components <ul><li>Sugars </li></ul><ul><ul><li>ribose </li></ul></ul><ul><ul><li>Deoxyribose </li></ul></ul><ul><ul><li>Rings numbered using primes </li></ul></ul><ul><ul><ul><li>C1 = 1’ etc </li></ul></ul></ul><ul><li>PO 4 3- </li></ul>www.freelivedoctor.com
  5. 5. Nucleotide Structure <ul><li>Base-sugar-phosphate </li></ul><ul><li>Base attached to C1 of sugar </li></ul><ul><li>Phosphate attached to C5 of sugar </li></ul><ul><li>Usually nucleotides are triphosphates, but can be mono or di </li></ul>www.freelivedoctor.com
  6. 6. Nucleic Acid, a polymer of nucleotides www.freelivedoctor.com
  7. 7. Nucleic Acids <ul><li>Polymer of nucleotides </li></ul><ul><li>Phosphodiester linkage </li></ul><ul><ul><li>3’ of one sugar to 5’ of other </li></ul></ul><ul><ul><li>vectorial </li></ul></ul><ul><li>Sequence read 5’ -  3’ </li></ul><ul><li>Previous slide is C-A-A </li></ul><ul><li>Next slide (a cartoon drawing) is A-T-G-C </li></ul>www.freelivedoctor.com
  8. 8. Phosphodiester Bond www.freelivedoctor.com
  9. 9. Chain elongation <ul><li>3’ hydroxyl on chain has unshared pair on oxygen </li></ul><ul><ul><li>attacks phosphorus on first phosphate of new nucleotide </li></ul></ul><ul><ul><li>Nucleophilic attack </li></ul></ul><ul><li>Driven by hydrolysis of PPi </li></ul>www.freelivedoctor.com
  10. 10. Chain elongation www.freelivedoctor.com
  11. 11. Base pairs <ul><ul><li>Bases are planar </li></ul></ul><ul><ul><ul><li>sp 2 hybridization </li></ul></ul></ul><ul><ul><ul><li>Bases nonpolar </li></ul></ul></ul><ul><ul><li>In Nucleic acids, there is base pairing </li></ul></ul><ul><ul><li>Complementarity </li></ul></ul><ul><ul><ul><li>Purines always base-pair with pyrimidines </li></ul></ul></ul><ul><ul><ul><ul><li>Cytosine hydrogen bonds with guanine </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Thymine hydrogen bonds with adenine or uracil </li></ul></ul></ul></ul><ul><ul><ul><li>Due to distancing and proximity of unshared pairs and hydrogens </li></ul></ul></ul>www.freelivedoctor.com
  12. 12. GC base pair www.freelivedoctor.com
  13. 13. AT base Pair www.freelivedoctor.com
  14. 14. A-U base Pair (RNA) www.freelivedoctor.com
  15. 15. Base Pairs (Cartoon drawing) www.freelivedoctor.com
  16. 16. DNA structure <ul><li>Double helix </li></ul>www.freelivedoctor.com
  17. 17. DNA structure <ul><li>B-DNA is most common </li></ul><ul><li>Antiparallel </li></ul><ul><li>bases inside </li></ul><ul><ul><li>Hydrophobic </li></ul></ul><ul><ul><li>Perpendicular to helix </li></ul></ul><ul><li>stands complementary </li></ul><ul><ul><li>Very important for information transfer </li></ul></ul><ul><ul><li>Each strand a template for the other. </li></ul></ul><ul><li>right handed </li></ul><ul><li>major and minor groove </li></ul>www.freelivedoctor.com
  18. 18. Other forms of DNA <ul><li>Z - DNA left handed; structure not fully understood </li></ul><ul><li>A- DNA; tighter helix </li></ul>www.freelivedoctor.com
  19. 19. DNA Types B- DNA (most common) www.freelivedoctor.com
  20. 20. A-DNA (supercoiled) www.freelivedoctor.com
  21. 21. Z-DNA www.freelivedoctor.com
  22. 22. Look down Axis www.freelivedoctor.com
  23. 23. Sequence dependent structures <ul><li>palindromes </li></ul><ul><li>hairpins </li></ul><ul><li>inverted repeats </li></ul><ul><li>mirror repeats </li></ul>www.freelivedoctor.com
  24. 24. RNA <ul><li>codes for protein </li></ul><ul><li>no consistent secondary structure </li></ul><ul><li>single stranded </li></ul><ul><li>Ribose instead of deoxyribose </li></ul><ul><li>Thymine (T) replaced by Uracil </li></ul>www.freelivedoctor.com
  25. 25. RNA www.freelivedoctor.com
  26. 26. Transfer RNA www.freelivedoctor.com
  27. 27. Instability of RNA <ul><li>RNA unstable due to reactivity of 2’ hydroxyl on ribose </li></ul><ul><li>Very labile </li></ul><ul><li>DNA extremely stable </li></ul>www.freelivedoctor.com
  28. 28. Nucleic Acid Chemistry <ul><li>Denaturation </li></ul><ul><ul><li>unzip by heating </li></ul></ul><ul><ul><li>reannealing </li></ul></ul><ul><ul><li>CoT curves: more GC=higher temp </li></ul></ul><ul><li>Uses of DNA to find sequences </li></ul><ul><ul><li>probes </li></ul></ul><ul><ul><li>forensic </li></ul></ul>www.freelivedoctor.com
  29. 29. DNA probes <ul><li>Take DNA from crime scene </li></ul><ul><li>DNA from suspect, random other person etc </li></ul><ul><li>See what matches </li></ul>www.freelivedoctor.com
  30. 30. Nucleic Acid Chemistry <ul><li>Mutations </li></ul><ul><ul><li>changes in sequence/structure </li></ul></ul><ul><ul><li>nonenzymatic changes </li></ul></ul><ul><ul><ul><li>thymine dimers </li></ul></ul></ul><ul><ul><ul><li>deamination </li></ul></ul></ul><ul><ul><ul><li>oxidative damage </li></ul></ul></ul>www.freelivedoctor.com
  31. 31. Nucleic Acid Chemistry <ul><li>Sequencing </li></ul><ul><li>PCR </li></ul><ul><li>Southern Blotting </li></ul><ul><li>Probes </li></ul>www.freelivedoctor.com
  32. 32. DNA sequencing, Sanger dideoxy method <ul><li>4 samples </li></ul><ul><li>Each gets template and nucleotides </li></ul><ul><ul><li>One dideoxy nucleotide </li></ul></ul><ul><ul><li>Has no 3’ OH so chain can’t elongate </li></ul></ul><ul><li>Sample 1 </li></ul><ul><ul><li>ddTTP…stops at T </li></ul></ul><ul><li>Sample 2 </li></ul><ul><ul><li>ddATP…stops at A </li></ul></ul><ul><li>Sample 3 </li></ul><ul><ul><li>ddCTP…stops at C </li></ul></ul><ul><li>Sample 4 </li></ul><ul><ul><li>ddGTP…stops at G </li></ul></ul><ul><li>Run on Gel </li></ul><ul><ul><li>Read from bottom up </li></ul></ul>www.freelivedoctor.com
  33. 33. Sample Sanger Gel www.freelivedoctor.com

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