1. Welcome to Molecular Biology Through Discovery Tuesday, 18 September 2012 DNA Structure / Sanger & Tuppy

2. What would you like discussed in class, on any subject that has already come up? General Questions The mentor list and clarification on who, what, when, etc. Who can we pick, how many can we choose from? What are we turning in exactly on Thursday???

4. 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... TAGGCCACTGCCCAACCCTCCAT CATAAAACTTGGGCTTGGGAGG CAGAGCCTAACCTCTCTCACTCT AGACAGGTCTAAGATGATTGGG AACGAAATGAGCCGTCTCGACTT TTTCGCGAAGTGGCTAA... #1: Hello! #2: Complete description of our civilization

5. DNA Structure Biology Today and Tomorrow Starr, Evers, and Starr (2010)

6. DNA Structure Biology: Understanding Life Alters (2000)

7. DNA Structure E. How can the helical structure of DNA and internucleotide distance be discerned from Franklin and Gosling's x-ray photograph?

8. DNA Structure E. How can the helical structure of DNA and internucleotide distance be discerned from Franklin and Gosling's x-ray photograph?

9. DNA Structure It's necessary to be slightly underemployed if you are to do something significant. - Jim Watson

10. From the nucleotides shown above, construct a double-stranded DNA fragment with the sequence ACTG. You may: duplicate (Ctrl-d) horizontal flip (Alt-hgoh) vertical flip (Alt-hgov) and/or rotate (Alt-hgor) the nucleotides, but you may not change the relative positions of their atoms. NH 2 N N N N P O O O O - N N N O P O O O O - O N NH O P O O O O - NH 2 N N N NH O P O O O O -

11. DNA Directionality & Palindromes SQ10. If one strand of DNA had the sequence 5'-GGACT-3', what would be the sequence of the second strand?

12. DNA Directionality & Palindromes I understand what a palindrome is in English but when it comes to DNA how come 5'-AGTTGA-3' isn't a palindrome when it's anti-parallel strand is 3'-TCAACT-5' which is also a palindrome.

13. Palindromic Sequences What is it? What about with DNA? GCTATCG Backwards = forwards ROTATOR TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA DNA is double stranded

14. What is it? What about with DNA? GCTATCG Backwards = forwards ROTATOR DNA is redundant TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA DNA is double stranded Palindromic Sequences

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

16. TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA 5’- -3’ 3’- -5’ TA T G GC AT GC TA GC TTAAT TCATT AATTA AGTAA CG TA CG AT CG G T AT DNA: cruciform RNA: stem/loop Palindromic Sequences Palindromic sequences as structural RNA

17. TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA 5’- -3’ 3’- -5’ tRNA UA U G GC AU GC UA GC UUAAU UCAUU DNA: cruciform RNA: stem/loop Palindromic Sequences Palindromic sequences as structural RNA

18. Palindromic Sequences Palindromic sequences as protein binding sites why palindromes are targeted by DNA-binding proteins why [are] palindromes… targeted by DNA-binding proteins

19. recognizes GTGAGTT NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA Palindromic Sequences Palindromic sequences as protein binding sites

20. NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA Palindromic Sequences Palindromic sequences as protein binding sites

21. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

22. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

23. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

24. recognizes GTGAGTT Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

25. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNN NNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

26. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNN NNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

27. Palindromes: Serve as binding sites for dimeric protein Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNN NNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

28. GTA..(8).. TAC 5’-GTA..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN 3’-CAT..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN gene RNA Polymerase Palindromic Sequences Palindromic sequences as protein binding sites

29. GTA..(8).. TAC 5’-GTA..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN 3’-CAT..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN gene Transcription factor RNA Polymerase Palindromic Sequences Palindromic sequences as protein binding sites RNA Is the promoter a beginning string of nucleotides for RNA,

30. Sanger and Tuppy (1951) Phe-Val-Asp-Glu-His-Leu-Cys-Gly Thr-Pro-Lys-Ala Gly-Glu-Arg-Gly-Tyr-Leu-Val-Cys-Gly Ser-His-Leu-Val-Glu-Ala

31. Sanger and Tuppy (1951)

32. Insulin is a dimer, composed of one A chain (fraction A) and a B chain (fraction B). Sanger and Tuppy determined this experimentally by oxidizing insulin with performic acid. The sequence of fraction B was determined experimentally as being at least composed of phenylalanine, valine, aspartic acid, and glutamic acid, and well as threonine, proline, lysine, and alanine. This was done using a prepared sample of polypeptide fragments, which were separated through a process known as paper chromatography. A similar process was done for fraction A. From all the studies perform, the overall structure and cross linking between chains can be deduced. Cross-linking can occur on cysteine residues, because they contain sulfur atoms, capable of dimerizing with one another and forming stable covalent bonds. Overall, two phenylalanine and two glcyl chains were determined to be the subunits of this particular form of insulin.

33. Sanger and Tuppy (1951) Now, how this was deduced was through a number of chromatography tests where different chemicals were used in order to split insulin at different bond points and then examine the fragments. In the first section we can see Phe.Val.Asp.Glu.His.Leu.CySO3H.Gly which has been determined by the following: B4β2, B1α2, B2γ8, B1α1, B1β8, B1γ1, B1α6, B1β13, B1γ4, B1β10, B1α5, B1γ7, B1β12, B4β1, B1γ6, B1β5. Where B1α1 refers to the test number and type, then spot number.

34. Sanger and Tuppy (1951) 1. Cys-Gly B1a.1

35. Sanger and Tuppy (1951) 1. Cys-Gly B1a.1

36. Sanger and Tuppy (1951) 1. Cys-Gly B1a.1 2. Leu-Cys B1a.6

37. Sanger and Tuppy (1951) 1. Cys-Gly B1a.1 2. Leu-Cys B1a.6 3. Leu-Cys-Gly #1 & #2

38. Sanger and Tuppy (1951)

39. 1. Cys-Gly B1a.1 2. Leu-Cys B1a.6 3. Leu-Cys-Gly #1 & #2

40. Results vs Conclusions Shahroze Mandi Shaun Bobby Supriya Tayab Kaleigh Jonathan Michael Colleen Abdul Cailin Sue Kristen Abdallah Celeste Neda Yordanos Me And go to CyanoBIKE

41. Sanger and Tuppy (1951)

42. Coming Attractions

43. Benzer (1959)

44. Goodbye from Molecular Biology Through Discovery Tuesday, 18 September 2012 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... G-O-O-D-B-Y-E