Do Now:

1. Do Now: • Pick up a whiteboard, marker, and paper towel from the back table • Take out or open up the “DNA as Genetic Material” stuff from last class

2. Test Friday • Cell Cycle and Cancer • Genetics • Study cell cycle packets, Quest…

3. DNA as Genetic Material – Structure and Replication Chapter 16

4. Brief Overview of the Timeline of DNA

5. Griffith

6. Avery, McCarty, and MacLeod

7. Hershey and Chase

8. Chargaff

9. Rosalind Franklin

11. Details of DNA Structure

12. From DNA to Chromosome chromosome nucleus • A strand of human DNA is about 3 m long… • How does it fit into all our cells?? • Supercoiling cell Proteins that DNA wraps around histones Nitrogen bases DNA

13. Details of DNA Structure • Nucleotides are the monomers of nucleic acids • 5 carbon sugar • Ribose • Deoxyribose • Nitrogen Base • Adenine • Thymine • Cytosine • Guanine • Uracil • Phosphate 5’ Carbon 5’ 4’ 1’ 2’ 3’ 3’ Hydroxyl

14. Details of DNA Structure 5’ Carbon 3’ Hydroxyl • What do you notice about the 5’ and 3’ ends of the two strands? • They’re ANTIPARALLEL!! • Why? For the nucleotide bases to line up 3’ Hydroxyl 5’ Carbon

15. Details of DNA Structure 5’ Carbon 3’ Hydroxyl • What holds the nucleotides together? 3’ Hydroxyl 5’ Carbon

16. Details of DNA Structure • Nucleotide Bases: Purines and Pyrimidines • PURINES • “Aggies are Pure” – A and G are Purines which have 2 rings • PYRIMIDINES • “TCU Cheerleaders build Pyramids” – T, C, and U (in RNA) are Pyrimidines have one ring

17. Details of DNA Structure 5’ Carbon 3’ Hydroxyl What do you notice about the number of hydrogen bonds between the different bases? 3’ Hydroxyl 5’ Carbon

18. CFU • Which letter represents the bonds that will be broken when a strand of DNA gets replicated?

19. CFU • What type of bonds are the bonds between the nucleotides? • Covalent • Ionic • Van der Waals • Hydrogen

20. CFU • Which letter represents the 3’ end of the DNA molecule?

21. CFU • Which letter represents a purine?

22. CFU • Which pair of nucleotides must be C and G?

23. CFU • Which base pairs are most likely easier to break and why? • A-T because they are held together by 3 hydrogen bonds • C-G because they are held together by 3 hydrogen bonds • A-T because they are both purines • C-G because one is a purine and the other is a pyrimidine

24. CFU • Which letter represents thymine?

25. DNA Replication Flashback! • When in the cell cycle does replication occur? • When does the cell check for mutations? • What should happen to the cell if mutations are detected? (2 things!)

26. DNA Replication

27. Meselson and Stahl

28. Meselson and Stahl

32. DNA Replication

33. DNA Replication • Coordinated by a large team of enzymes! • helicases • polymerases • ligases • primases

34. DNA Replication • Problem: Nucleotides can only be added to the 3’ end by DNA Polymerase III… • Solution: Okazaki • Leading and Lagging Strands • Leading Strand • Continuous synthesis • Lagging Strand • Okazaki fragments • Joined by ligase

35. 3’ Remember: DNA polymerase can only add nucleotides to the 3’ end, so DNA gets built in the 5’  3’ direction! 5’ Parental DNA 5’ Okazaki fragments 3’ DNA polymerase 3’ Ligase 5’ Leading and lagging have the same origin of replication, but since DNA polymerase can only add on the 3’ end, the lagging strand has to start backwards and make little pieces to link together Leading strand One piece of 5’  3’ Lagging strand Many little pieces of 5’  3’ linked together later

36. Priming DNA Synthesis • DNA polymerase can only extend an existing DNA molecule; it cannot start a new one • Short RNA primer is built first on parent DNA by primase • RNA primer later removed by DNA polymerase I

37. Priming DNA Synthesis • Closer look… Primase builds the RNA primer Replaces RNA nucleotides with DNA Primase DNA polymerase

38. DNA Replication

39. Model It! • Nucleic Acids • Parent/template strands DNA (blue beads) • Daughter strands DNA (orange beads) • Primer RNA (white beads) • Enzymes • Helicase (black pipe cleaner) • DNA polymerase III (yellow pipe cleaner) • Primase (white pipe cleaner) • DNA ligase (blue pipe cleaner)

40. Test your understanding…On some paper, write A – H and decide whether each letter represents the 3’ or 5’ end of DNA. Then, label the sections (A-B, C-D, etc) as “leading” or “lagging” A-B: Leading C-D: Lagging B C A D 5’ 3’ 3’ 5’ 3’ 5’ E H 3’ 5’ G F F-E: Leading H-G: Lagging

41. Editing and Proofreading DNA Why do we not always get cancer? DNA can repair itself!!! • Since DNA polymerase III does 1,000 base pairs/second, it makes a lot of errors • DNA Polymerase I (only 20 bp/sec) excises mismatched bases, repairs the DNA, and removes the primer • DNA polymerase I reduces error from 1 in 10,000 bp to 1 in 100 million bp!!

42. Problems at the end… • Ends of chromosomes are “eroded” with each replication (don’t get fully copied) • Telomeres are expendable, non-coding sequences at the ends of the DNA strand • short sequence of bases repeated 1000s of times • TTAGGG in humans

43. Telomeres and Aging • In the absence of telomerase, the telomere will become shorter after each cell division.  When it reaches a certain length, the cell may cease to divide and die. 

44. Putting it ALL together • Summarize the roles of the key enzymes • Label the diagram showing the steps of DNA replication • DNA Structure – Questions and Practice

45. Summary of Replication Enzymes Unzips DNA (breaks H-bonds between nucleotides) Builds RNA primer in leading strand and Okazaki fragments Adds DNA nucleotides (20 bp/s); replaces RNA primer with DNA; repairs errors in DNA Adds DNA nucleotides (1,000 bp/s) Joins Okazaki fragments (using phosphate groups)

46. In the diagram below, label the key enzymes and structures in DNA replication. Be sure to label 3’ and 5’ ends, too!