DNA

1. DNA • The Universal Code of Life

2. Early History • 1869: Friederich Mieschner isolates “nuclein” from nuclei of cells. His student Richard Altman later renames the substance “nucleic acid.” • Mid 1800s: Biochemists identify two distinct nucleic acids. • 1929: Phoebus Levine identifies four distinct bases in DNA.

3. Heredity as a Science • Genetics arose as a new science in the late 19th and early 20th centuries, spurred by questions raised by Darwin’s On the Origin of Species: • Are there patterns to inheritance? • Are traits handed on intact (particle theory) or blended together in each generation (blending theory)?

4. Mendel’s Answers • Gregor Mendel’s work was rediscovered in 1900, answering both questions: • Inheritance of many traits follows predictable patterns. • Traits are handed on intact via some kind of particle: “elementen.”

5. Hereditary Molecule? • Question in the 20th century: What is the hereditary molecule? • Cell nucleus associated with inheritance. • Both proteins and nucleic acids are in the nucleus. Which contains information coding for traits?

6. Protein or DNA? • Linus Pauling favored protein: DNA has only four bases, protein has over 20 amino acids. Seemed like protein could store more information. • Others favored DNA, which is found only in the nucleus.

7. Frederick Griffith • In 1928, Frederick Griffith carried out experiments on pneumonia bacteria, trying to create a vaccine against pneumonia. Among his findings were early clues about hereditary factors.

8. Griffith’s Experiment Bacterial strain(s) injected into mouse Results Conclusions Mouse remains healthy. R-strain does not not cause pneumonia. Living R-strain Mouse contracts pneumonia, dies. S-strain causes pneumonia. Living S-strain Mouse remains healthy. Heat-killed S- strain does not cause pneumonia. Heat-killed S-strain A substance from heat-killed S-strain can transform the harmless R-strain into a deadly S-strain. Mouse contracts pneumonia, dies. Living R strain, heat-killed S-strain

9. Oswald Avery • Avery learned of Griffith’s experiment and thought it might hold a clue to the identity of the hereditary molecule. • Avery isolated carbohydrates, proteins, lipids, and nucleic acids from the bacteria to discover which, if any, would transform the non-virulent R-strain bacteria.

10. Of the substances isolated and tested, only DNA from killed S-strain bacteria transformed R-strain bacteria.

11. Hershey & Chase • Early 1950’s: Alfred Hershey and Martha Chase used the bacteriophage virus in another series of experiments to identify the hereditary material. • Bacteriophages, like other viruses, contain both protein and DNA, but are non-living.

12. DNA Bacteriophage head Protein coat tail 1 Phage attaches to bacterium. 6 Bacterial wall destroyed; phage released. 2 Phage injects its DNA into bacterium. 5 Complete phages assembled. 3 Phage DNA is replicated. 4 Phage parts synthesized, using bacterial metabolism.

13. Radio-tagged DNA Radio-tagged Protein Radioactive phosphorus (P32) Radioactive sulfur (S35) Radioactive DNA (blue) Radioactive protein (yellow) 1 Label phages with P32 or S35. 2 Infect bacteria with labeled phages; phages inject genetic material into bacteria. 3 Whirl in blender to break off phage coats from bacteria. 4 Centrifuge to separate phage coats (low density: stay in liquid) from bacteria (high density: sink to bottom as a “pellet”) 5 Measure radioactivity of phage coats and bacteria. Results: Bacteria are radioactive; phage coats are not. Results: Phage coats are radioactive; bacteria are not. Conclusion: Infected bacteria are labeled with radioactive phosphorus but not with radioactive sulfur, supporting the hypothesis that the genetic material of bacteriophages is DNA, not protein.

14. DNA Structure? • While many research teams were trying to discover the hereditary molecule, other researchers were working to discover the nature of DNA.

15. Erwin Chargaff • Chargaff took apart DNA into its component nucleotides and studied the proportions. • Found consistent ratios between certain nucleotides.

16. In DNA, Chargaff consistently found equal amounts of adenine compared with thymine, and equal amounts of cytosine compared with guanine. Did that mean the bases were always paired?

17. Franklin and Wilkins • Rosalind Franklin worked in Maurice Wilkins’ lab in the late 1940s, using X-ray crystalography to find clues about the structure of DNA. • Franklin’s images were the first to suggest a helical structure.

18. The X-shape on the radiograph was characteristic of helical molecules. Franklin also measured distances between bases and other dimensions using her images.

19. Watson and Crick • James Watson and Francis Crick worked at the same time as Franklin and Wilkins. • Applying Chargaff’s rule, they concluded that A pairs with T, C with G. • Used their knowledge of molecular geometry to try to discover the structure of DNA.

20. Wilkins consulted with Watson and Crick. Without Franklin’s knowledge, he handed them several of Franklin’s X-ray images. • Watson immediately recognized their significance, though he’d criticized Franklin’s work earlier.

21. By adding Franklin’s data to their own (without her permission!), Watson and Crick assembled the first plausible model of DNA and published an article on the structure of DNA in 1953.

22. DNA Structure DNA contains four bases. RNA also has four bases, but has uracil instead of thymine.

23. How many rings? How many rings? How many H-bonds? How many H-bonds? As Chargaff’s work suggested, Adenine always pairs across the DNA ladder with Thymine, while Cytosine always pairs with Guanine.

24. 5’ end 5 4 6 3 5’ 1 2 1’ 4’ 2’ 3’ 3’ end Nucleotides are 3-dimensional, with an orientation that affects the shape of the entire nucleic acid.

25. 5’ end The 3’ end of one nucleotide binds with the 5’ end of the next nucleotide in the chain. 5 4 6 3 5’ 1 2 1’ 4’ 3’ 2’ 7 8 5’ 9 5 4 1’ 6 3 4’ 1 2 3’ 2’ 3’ end

26. 5’end 3’ end Two chains of DNA nucleotides are held together by hydrogen bonds between the bases of each strand. Notice that the strands run in opposite directions. They are antiparallel. 3’end 5’end

27. free phosphate free sugar The 3-dimensional shape of the nucleotides creates the helical structure of DNA.

28. Label the four bases in this diagram. (Look back several slides for a hint.) T A A T Circle one complete nucleotide on each side. (Hint: look back several slides to see which carbon on the sugar attaches to the phosphate.) C G G C

29. DNA Replication • When cells divide, the two resulting daughter cells must have exactly the same DNA as the original cell. • Therefore, before cell division happens, the cell must replicate (copy) its DNA.

30. replication bubbles DNA DNA helicase replication forks The enzyme DNA helicase “unzips” DNA by breaking hydrogen bonds holding the two strands together. “Unzipping” occurs at multiple points on the DNA strand.

31. DNA helicase replication forks DNA polymerase #1 3′ continuous synthesis 5′ 3′ discontinuous synthesis 5′ DNA polymerase #2 Within each replication bubble, the enzyme DNA polymerase builds a new strand of DNA, using the original strands as templates.

32. DNA polymerase #1 3′ 5′ continuous synthesis 3′ discontinuous synthesis 5′ DNA polymerase #2 DNA polymerase #1 continues along parental DNA strand 3′ DNA polymerase #2 leaves 5′ 5′ continuous synthesis 3′ discontinuous synthesis 3′ 5′ DNA polymerase #3 Because DNA polymerase always travels from the 3’ to the 5’ end of DNA, one polymerase is always moving away from the replication fork

33. DNA polymerase #1 continues along parental DNA strand 3′ DNA polymerase #2 leaves 5′ 5′ continuous synthesis 3′ discontinuous synthesis 3′ 5′ DNA polymerase #3 3′ 5′ 3′ 5′ DNA polymerase #3 leaves 3′ 5′ 3′ DNA polymerase #4 5′ DNA ligase joins daughter DNA strands together. Multiple DNA polymerase molecules are required for the strand where discontinuous replication is happening.

34. How does DNA polymerase “know” which bases to use when replicating? Remember Chargaff’s rule: A and T always match, C and G always match. Practice DNA base-pair matching: http://learn.genetics.utah.edu/content/begin/dna/builddna

35. Mutations • Though many enzymes patrol your DNA, looking for replication errors, some errors do creep in. • Most cells with a DNA error will die. A few may turn cancerous. • If mutated cells are sex cells, the mutation can be passed on and will affect all cells in the offspring.

36. Mutations may be harmful, helpful, or neutral. • Harmful mutations result in genetic disease or death. • Helpful mutations increase evolutionary “fitness” (i.e. having offspring). • Neutral mutations neither help nor harm at the present.

37. Nucleotide substitution Silent mutation: still codes for the same amino acid. original DNA sequence Missense mutation: codes for a different amino acid, which may or may not affect the final protein. substitution Nonsense mutation: codes for a “stop” in the middle of the sequence, producing a useless protein. nucleotide pair changed from A–T to T–A

38. Examples: • Sickle-cell anemia is caused by a missense mutation due to a nucleotide substitution. • Duschenne’s Muscular Dystrophy is caused by a nonsense mutation in a gene for a critical enzyme. • Lactose persistence may be caused by a single nucleotide substitution.

39. Insertion mutation original DNA sequence Example: Huntington’s disease, a loss of neural function in middle-age, is caused by a string of insertions. T–A nucleotide pair inserted

40. Deletion mutation original DNA sequence Example: a 32-base-pair deletion in the gene for a certain cell membrane receptor protein causes resistance to HIV. C–G nucleotide pair deleted

41. Inversion original DNA sequences Example: an inversion mutation is responsible for one form of hemophilia. breaks DNA segment inverted

42. Translocation original DNA sequences DNA segments Switched break break Examples: Several forms of leukemia, lymphoma and possibly schizophrenia are caused by translocation mutations.

43. What causes mutations? http://learn.genetics.utah.edu/archive/sloozeworm/mutationbg.html

44. Recap • DNA is a nucleic acid which contains coded hereditary information. • The base-pairing rule helps the information in DNA accurate. • All cells in the body have the same DNA containing the same information. DNA must be replicated before cell division.