1. Warm-up- 5 minutes Quietly and on your own, answer the following questions in your notes for today. Be prepared to answer. 1.In what part of the cell cycle does DNA replication occur? 2.Define chromosome. 3.Define nucleotide.

2. Homework & reminders 1.Chi-square lab write-up due WEDNESDAY in the beginning of class. 1.ALL late write ups = automatic 50% and additional 10% points for each day that it’s late. No excuses will be accepted. 2.Chapter 16 quiz on Wednesday. Start studying TODAY.

3. Today’s Agenda 1.Warm up 2.Chi-square lab overview. Due tomorrow. Worksheet is bonus. 3.Review midterm exams. 4.Chapter 16 lecture. 5.Start DNA replication diagram.

4. Chapter 16: The Molecular Basis of Inheritance

5. Chapter 16 vocabulary list List of need to know words are provided on the class wiki page. This is for you to work on for yourself.

6. Objectives

10. Building a Structural Model of DNA After most biologists became convinced that DNA was the genetic material of life, the next challenge was to determine its structure. Rosalind Franklin produced a picture of the DNA molecule by using a technique called X- ray crystallography Franklin produced a picture of the DNA molecule using this technique

11. LE 16-6 Franklin’s X-ray diffraction photograph of DNA Rosalind Franklin

12. Based on the images, two other scientists named Watson and Crick were able to determine that DNA molecules took a double helix shape.

13. LE 16-7 5 end 3 end 5 end 3 end Space-filling modelPartial chemical structure Hydrogen bond Key features of DNA structure 0.34 nm 3.4 nm 1 nm

14. Sugar–phosphate backbone 5 end Nitrogenous bases Thymine (T) Adenine (A) Cytosine (C) DNA nucleotide Phosphate 3 end Guanine (G) Sugar (deoxyribose) Phosphodiester bond

15. How DNA is elongated: phosphodiester bonds

16. Watson and Crick built models of a double helix to match to the X-rays and chemistry of DNA o The side strands, or “backbones” of the DNA molecule are made of a sugar (deoxyribose) paired with a phosphate. o The deoxyribose backbones are joined together by a series of molecules called nitrogenous bases.

17. Nitrogenous Bases There are two types of nitrogenous bases: o Purines Much wider Include adenine and guanine o Pyramidines Much narrower Include cytosine and thymine

18. LE 16-UN298 Purine + purine: too wide Pyrimidine + pyrimidine: too narrow Purine + pyrimidine: width matches data from X-rays How do the four bases combine to form DNA?

19. Watson and Crick reasoned that the pairing was more specific – o Adenine paired only with Thymine o Guanine paired only with Cytosine

20. Base Pairing to a Template Strand DNA is a double-helix molecule made of two intertwining strands. The two strands of DNA are complementary, meaning each has a set of bases that corresponds with the other. In DNA replication, the molecule is be separated into its two strands. o Two new strands can be made from these templates, duplicating the molecule.

21. LE 16-9_1 The parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding with its specific partner, A with T and G with C.

22. LE 16-9_2 The parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding with its specific partner, A with T and G with C. The first step in replication is separation of the two DNA strands.

23. LE 16-9_3 The parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding with its specific partner, A with T and G with C. The first step in replication is separation of the two DNA strands. Each parental strand now serves as a template that determines the order of nucleotides along a new, complementary strand.

24. LE 16-9_4 The parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding with its specific partner, A with T and G with C. The first step in replication is separation of the two DNA strands. Each parental strand now serves as a template that determines the order of nucleotides along a new, complementary strand. The nucleotides are connected to form the sugar-phosphate back- bones of the new strands. Each “daughter” DNA molecule consists of one parental strand and one new strand.

25. Origins of Replication Replication begins at special sites called origins of replication. o The two DNA strands are separated, opening up a replication “bubble” o Each chromosome may have hundreds or even thousands of origins of replication o Replication proceeds in both directions from each origin, until the entire molecule is copied

26. LE 16-12 In eukaryotes, DNA replication begins at may sites along the giant DNA molecule of each chromosome. Two daughter DNA molecules Parental (template) strand Daughter (new) strand 0.25 µm Replication fork Origin of replication Bubble In this micrograph, three replication bubbles are visible along the DNA of a cultured Chinese hamster cell (TEM).

27. Figure 16.13 Topoisomerase Primase RNA primer Helicase Single-strand binding proteins 5 3 5 5 3 3

28. Antiparallel Elongation The antiparallel structure of the double helix affects replication DNA polymerases add nucleotides only to the free 3  end of a growing strand; therefore, a new DNA strand can elongate only in the 5  to  3  direction

29. To elongate the other new strand, called the lagging strand, DNA polymerase must work in the direction away from the replication fork The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase

30. DNA replication video https://www.youtube.com/watch?v=27TxKoFU2Nw

31. Animation: Lagging Strand Right-click slide / select “Play”

32. Questions 1.What bonds are formed between two nucleotides in the formation of a new DNA strand? 2.In what direction is a new DNA strand formed? 3.At what end are new nucleotides added by DNA Polymerase III?

33. Origin of replication Overview Leading strand Lagging strand Overall directions of replication Template strand RNA primer for fragment 1 Okazaki fragment 1 RNA primer for fragment 2 Okazaki fragment 2 Overall direction of replication 3 3 3 3 3 3 3 3 3 3 3 3 5 5 5 5 5 5 5 5 5 5 5 5 2 2 2 1 1 1 1 1 2 1 Figure 16.16

34. Figure 16.17 Overview Leading strand Origin of replication Lagging strand Leading strand Lagging strand Overall directions of replication Leading strand DNA pol III Lagging strand DNA pol I DNA ligase Primer Primase Parental DNA 5 5 5 5 5 3 3 3 3 3 3 2 1 4

35. Proofreading and Repairing DNA DNA polymerases also proofread newly made DNA, replacing any incorrect nucleotides. Two types of repair: o In mismatch repair, the enzymes replace incorrect bases with the correct ones. o In nucleotide excision repair, enzymes cut out and replace entire stretches of DNA that are damaged.

36. Replicating the Ends of DNA Molecules DNA polymerase has one significant limitation. The enzyme has no way to complete one of the ends. o Every time the DNA is copied, it becomes a little shorter. Cells will divide countless times over the lifespan of an organism. How can DNA be protected, given this limitation?

37. The shortened DNA problem https://www.youtube.com/watch?v=AJNoTmWsE0s

38. Eukaryotic chromosomal DNA molecules have at their ends repeating nucleotide sequences called telomeres. o Telomeres are DNA, but do not actually encode for any traits. o Telomeres do not prevent the shortening of DNA molecules, but they postpone it.

39. Eventually, the telomeres are worn down and essential genes begin to be lost from the chromosomes. o This is one of the hypothesized causes of aging. An enzyme called telomerase catalyzes the lengthening of telomeres in stem cells. o This enzyme cannot be produced indefinitely due to an increasing risk of the cell growing uncontrollably (cancer)

40. Chromosome and chromatin

41. Activity 1: DNA replication 1.Draw figure 16.13 on page 314 and include the four main blue labels showed in the diagram, the RNA primer and label the 3’ and 5’ ends. 2.Draw figure 16.15 and include the 2 main blue labels. Also label the origin of replication, RNA primer, sliding clamp, DNA pol III, parental DNA, and the 3’ and 5’ ends. 3.Draw figure 16.16 and label the steps of synthesizing the lagging strand. 4.Summarize DNA replication starting from unwinding of the DNA to the end of synthesizing the lagging strand. Include the important proteins and enzymes. Include the appropriate 3’ and 5’ labels.

42. Activity 2: DNA & Chromosomes 1.Draw one nucleotide using the figure 16.5 on page 308 for reference. In your diagram, include the labels: nucleotide, phosphate, deoxyribose, and nitrogenous base 2.Draw figure 16.7 A on page 309. Include the labels: double helix, nitrogenous bases, adenine, guanine, thymine, and cytosine. 3.Diagram chromatin packing in shown in figure 16.22 on page 321. Include in your diagram the labels: DNA, double helix, histones, chromatin, and chromosome 4.When you are done drawing, you will write a comprehensive story about the molecular unit of inheritance by including all of the words above.