Basic Atomic Structure

1. Basic Atomic Structure

2. A Whole New RealityThe Atomic Scale • In a word we’re talking small! • If an atom were the size of a BB, you’d be 23,000 miles tall! • Atoms are 99.9999999999999% empty space! • Can we “see” them?

3. Platinum and Oxygen Atoms

5. The Umbrellas Project

6. CurtainAcross Rifle Gap

7. Surrounded Islands

8. Wrapped Reichstag

9. Scanning Tunneling Microscope (STM) • The local geometric topography of a sample surface is “probed” • Overlap of electron wave functions for the tip and sample creates a “tunneling current” • Changes in the tip-sample distance are indicted by changes in the “tunneling current”

10. Scanning Tunneling Microscope (STM)

11. Scanning Tunneling Microscope (STM) The “Scan” reflects the density of the electron cloud. The Physical Object is Here

12. Do You Really “See” the Atoms?

14. STM Image of DNA The Image The Model

15. Nucleic Acids • The Stuff Upon Which Everything in Biology Ultimately Depends • Elemental Composition • Carbon, Hydrogen, Oxygen, Phosphorous, and Nitrogen • Subunits: • Ribose/Deoxyribose Sugars • Phosphates • Nitrogenous Bases • Purines: Guanine, Adenine • Pyrimidines: Cytosine, Thymine, Uracil

16. RNA versus DNA • Deoxyribonucleic acid (DNA) • (The shy and timid one) • Ribonucleic acid (RNA) • (The bold and shameless one) • Why does everything that is biologically significant revolve around nucleic acids?

17. Because……. • All organisms are fundamentally packages for the expression and replication of nucleic acids. • At its core, everything that an organism does is a reflection of the expression of its nucleic acids. • Our understanding of every area of modern biology has been touched by and has benefited from recombinant DNA technology.

19. DNA is Everywhere • Japanimation/Manga • Research • Forensics • Business and Marketing • Medicine

20. Nitrogenous Base Structure Pyrimidines Single Ring Bases (T and C) Purines Double Ring Bases (A and G)

21. DNA Building Blocks • Nitrogenous Base • Pentose Sugar • Triphosphate • 5’ Phosphate • 3’ Hydroxyl

22. DNA • Sugar-phosphate backbone serves as a “backbone”. • The “backbone” has directionality (PO4 / OH). • Bases encode the genetic information.

23. The First Clues to DNA Structure G A T C 22.1% 28.1% 30.1% 19.7% 15.4% 33.6% 37.1% 13.9 40.4% 9.0% 11.7% 38.9% 8.9% 42.6% 39.9% 8.6%

24. DNA Basepairing A pairs with T (2 bonds) G pairs with C (3 bonds) Almost no exceptions

25. 3’ OH 5’ PO4 Anti-parallel Bonding 3’ OH PO4 5’

26. The Big Bang Alfred Hershey and Martha Chase (1952) DNA is genetic material. • Watson and Crick (1953) DNA is a double helix.

27. The Big Bang 20Å Diameter 3.4Å between bases 34Å Turn

28. Right Handed 10.7-11 bp/turn 23A Diameter dsRNA and RNA-DNA Hybrids Right Handed 10-10.6 bp/turn 19A Diameter “Normal DNA” Left Handed 12 bp/turn 18A Diameter dinucleotide repeats Pu-Py (GCGCGCGC) From A to Z DNA

29. OH OH P P 3' 3' 5' 5' ... ... T A T A ... ... T A T A ... ... ... C G C G ... ... ... G C G C ... ... ... C G C G ... ... A T A T ... ... ... C G C G ... ... ... G C G C ... ... A T A T ... ... A T A T ... ... ... G C G C ... ... A T A T ... ... A T A T ... ... A A T T ... ... T A T A ... ... A T A T 5' 5' 3' 3' P P OH OH Denaturation / Renaturation The bonds that hold DNA strands together are easily broken and reformed.

30. DNA Structure • DNA exists as a double helix. • DNA strands are anti-parallel • If you know one strand, you can predict the other strand. • A pairs with T • G pairs with C

31. DNA Replication • Basepairing rules determine which nucleotide is added next. • DNA replication requires a template strand from which to copy. • Either stand can be used a template.

32. More building blocks for DNA? Nucleotide Analogs Dideoxyinosine Didehydro-dideoxythymidine Dideoxycytidine Azido-dideoxythymidine

33. CopyingDNA Semiconservative Replication Parent strands split to serve as templates for synthesis of daughter strands.

34. DNA Replication The Lagging Strand Primase synthesizes a start point on the lagging strand. DNA Polymerase extends the DNA from the start point. This process is repeated over and over. At the end all the small gaps in the new DNA strand are sealed up.

35. DNA Replication It’s not just smoke and mirrors! DnaB - Helicase unwinds DNA. Pol III Catalytic Core:  (polymerase) (dimerization component)  (dimeric clamp)  (clamp loader) DnaG - Primase SSB - Single stranded binding protein (straightens out the DNA)

36. Can you say Mechanical • Form follows function. The clamp part of DNA Polymerase keeps the replication machine on the DNA. Now that’s just cool!

37. DNA Replication and Mitosis http://www.stolaf.edu/people/giannini/flashanimat/celldivision/crome3.swf Normal Body Cell (2n Chromosomes) Replicate all the DNA (4n Chromosomes) Split all the DNA Divide into two Daughter Cells (2n Chromosomes in each cell) Repeat

38. DNA Replication and Mitosis http://www.stolaf.edu/people/giannini/flashanimat/celldivision/crome3.swf (2n Chromosomes in each Daughter Cell) (Splitting the 4n Chromosomes)

39. DNA Replication and Meiosis Normal Body Cell (2n Chromosomes) Replicate the DNA (4n Chromosomes) Split the DNA into two Daughter Cells (2n Chromosomes in each cell) Looks like Mitosis so far. Immediately split the cells (and the DNA) again into two sets of Daughter Cells (1n Chromosomes in each cell)

40. The Importance of Meiosis