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DNA Structure

Welcome to Molecular Biology Through Discovery Tuesday, 17 September 2013 DNA Structure / Benzer (1959). Finally found a mentor! Is there anything that we should physically or electronically be turning in as proof?. DNA Structure.

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DNA Structure

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  1. Welcome toMolecular Biology Through DiscoveryTuesday, 17 September 2013DNA Structure / Benzer (1959) Finally found a mentor!Is there anything that we should physically or electronically be turning in as proof?

  2. DNA Structure A class discussion on the tetranucleotide hypothesis might help. ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ...

  3. DNA Structure ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ... TAGGCCACTGCCCAACCCTCCATCATAAAACTTGGGCTTGGGAGGCAGAGCCTAACCTCTCTCACTCTAGACAGGTCTAAGATGATTGGGAACGAAATGAGCCGTCTCGACTTTTTCGCGAAGTGGCTAA ... #1: Hello! #2: Complete description of our civilization

  4. DNA Structure

  5. DNA Structure SQ7. What would you expect to happen to the diffraction pattern if the helix shown in Fig. 8B-D were squashed, i.e. the helix were more tightly wound, more like a solenoid?

  6. DNA Directionality & Palindromes …would like to go into deeper discussion about palindromic sequences

  7. Backwards = forwards AGTTGA • DNA is double stranded ROTATOR TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA Palindromic Sequences SQ16. … why is AGTTGA not a DNA palindrome? What is it? What about with DNA?

  8. Backwards = forwards AGTTGA ROTATOR Palindromic Sequences What is it? What about with DNA? • DNA is double stranded • DNA is redundant TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  9. Backwards = forwards AGTTGA ROTATOR TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA Palindromic Sequences What is it? What about with DNA? • DNA is double stranded • DNA is redundant • DNA has direction (read 5’->3’) 5’- -3’ 3’- -5’ TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  10. TAT GGCATGCTAGCTTAAT TCATTAATTA AGTAACGTACGATCGG TAT DNA: cruciform RNA: stem/loop Palindromic Sequences The full biological roles of palindromic sequences is still a bit unclear to me Palindromic sequences as structural RNA 5’- -3’ 3’- -5’ TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA SQ18. What is the relationship between a palindromic sequence and a potential hairpin structure?

  11. UAU GGCAUGCUAGCUUAAU UCAUU tRNA DNA: cruciform RNA: stem/loop Palindromic Sequences Palindromic sequences as structural RNA 5’- -3’ 3’- -5’ TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  12. TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA recognizes GTGAGTT Palindromic Sequences Palindromic sequences as protein binding sites

  13. TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA Palindromic Sequences Palindromic sequences as protein binding sites

  14. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA

  15. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA

  16. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA

  17. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA recognizes GTGAGTT

  18. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA

  19. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA

  20. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA Palindromes: Serve as binding sites for dimeric protein

  21. RNA Polymerase Palindromic Sequences Palindromic sequences as protein binding sites gene 5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN GTA ..(8).. TAC

  22. gene 5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN Transcription factor RNA Polymerase Palindromic Sequences Palindromic sequences as protein binding sites RNA GTA ..(8).. TAC 5’- -3’ 3’- -5’ TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA How many 12-nt palindromes would you expect at random in the genome of Anabaena variabilis?

  23. Probability How often A-A-A-A-A-A?

  24. Probability How often 1-1-1-1-1-1?

  25. Probability How often A-A-A-A-A-A?

  26. Probability How often 1-1-1-1-1-1?

  27. Probability How often 1-2-1-1-1-1?

  28. Probability How often 1-1-1-1-1-1?

  29. Probability How often 1-1-1-1-1-1?

  30. Probability How often A-A-A-A-A-A?

  31. Probability How often A-T-G-G-T-A?

  32. Counting Probability How often A-T-G-G-T-A?

  33. gene 5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN Transcription factor Palindromic Sequences Palindromic sequences as protein binding sites RNA GTA ..(8).. TAC 5’- -3’ 3’- -5’ TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA How many 12-nt palindromes would you expect at random in the genome of Anabaena variabilis?

  34. Welcome toMolecular Biology Through DiscoveryTuesday, 17 September 2013DNA Structure / Benzer (1959)

  35. Fermi Problems What is the question?

  36. Fermi Problems • Focus on what is being asked • Estimate what can be estimated • Set limits on what can't How many piano tuners are there in Chicago?

  37. Fermi Problems • Focus on what is being asked • Estimate what can be estimated • Set limits on what can't What fraction of the cells in your body are bacterial?

  38. Fermi Problems What is the question?What do you need?

  39. Benzer (1959) Hoping you will go over the experiment.It is so hard to visualize what goes down in a lab without actually laying on hands.

  40. Wrinch (1936) – What is a Gene? Drosophila chromosome What are genes?... There is no consensus of opinion amongst geneticists as to what the genes are – whether they are real or purely fictitious... Morgan T (1934) Nobel Lecture

  41. Benzer (1959)

  42. Benzer (1959)

  43. Benzer (1959) Complementation Test

  44. Benzer (1959) Phage Complementation Test E. coli

  45. Benzer (1959)

  46. Benzer (1959) Phage Recomination Test (Cis-Trans Test) Measuredistance E. coli

  47. Benzer (1959) Phage Recomination Test (Cis-Trans Test) Measuredistance E. coli

  48. Benzer (1959) Phage Complementation Test? Recombination Test? E. coli

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