1. PowerPoint Presentation Materials to accompany Genetics: Analysis and Principles Robert J. Brooker Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display CHAPTER 9 MOLECULAR STRUCTURE OF DNA AND RNA

2. INTRODUCTION In this chapter we will shift our attention to molecular genetics The study of DNA structure and function at the molecular level 9-2 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

3. 9.1 IDENTIFICATION OF DNA AS THE GENETIC MATERIAL

4. Frederick Griffith Born1879 Died1941 Frederick Griffith “Almighty God is in no hurry, why should I be? “ “Disappointment is my daily bread, but I thrive on it“ He found something in the lab but no in hurry for publication. This is his line. the first widely accepted demonstrations of bacterial transformation

5. 9-8 Figure 9.2 Griffith’s Experiment, 1927

6. Griffith studied a bacterium (pneumococci) now known as Streptococcus pneumoniae (ZATÜRE) S. pneumoniae comes in two strains S  Smooth Secrete a polysaccharide capsule Protects bacterium from the immune system of animals Produce smooth colonies on solid media R  Rough Unable to secrete a capsule Produce colonies with a rough appearance 9-5 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Frederick Griffith Experiments with Streptococcus pneumoniae

7. In addition, the capsules of two smooth strains can differ significantly in their chemical composition 9-6 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 9.1 Rare mutations can convert a smooth strain into a rough strain, and vice versa However, mutations do not change the type of the strain

8. Oswald Theodore Avery (1877-1955) For many years, genetic information was thought to be contained in cell protein. cellprotein He is best known for his discovery that deoxyribonucleic acid (DNA) serves as genetic material

9. Avery, MacLeod and McCarty realized that Griffith’s observations could be used to identify the genetic material They carried out their experiments in the 1940s At that time, it was known that DNA, RNA, proteins and carbohydrates are major constituents of living cells They prepared cell extracts from type IIIS cells containing each of these macromolecules Only the extract that contained purified DNA was able to convert type IIR into type IIIS Treatment of the extract with RNase or protease did not eliminate transformation Treatment with DNase did Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display The Experiments of Avery, MacLeod and McCarty 9-10

10. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 9-11 Figure 9.3 Avery et al also conducted the following experiments To further verify that DNA, and not a contaminant (RNA or protein), is the genetic material

11. 9-20 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display In 1956, A. Gierer and G. Schramm isolated RNA from the tobacco mosaic virus (TMV), a plant virus Purified RNA caused the same lesions as intact TMV viruses Therefore, the viral genome is composed of RNA Since that time, many RNA viruses have been found Refer to Table 9.1 RNA Functions as the Genetic Material in Some Viruses

12. 9-21

13. DNA and RNA are large macromolecules with several levels of complexity 1. Nucleotides form the repeating units 2. Nucleotides are linked to form a strand 3. Two strands can interact to form a double helix 4. The double helix folds, bends and interacts with proteins resulting in 3-D structures in the form of chromosomes Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 9.2 NUCLEIC ACID STRUCTURE 9-22

14. 9-23 Figure 9.7

15. 9-24 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display The nucleotide is the repeating structural unit of DNA and RNA It has three components A phosphate group A pentose sugar A nitrogenous base Refer to Figure 9.8 Nucleotides

16. 9-25 Figure 9.8

17. 9-26 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 9.9 The structure of nucleotides found in (a) DNA and (b) RNA A, G, C or T These atoms are found within individual nucleotides However, they are removed when nucleotides join together to make strands of DNA or RNA A, G, C or U

18. 9-27 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Base + sugar  nucleoside Example Adenine + ribose = Adenosine Adenine + deoxyribose = Deoxyadenosine Base + sugar + phosphate(s)  nucleotide Example Adenosine monophosphate (AMP) Adenosine diphosphate (ADP) Adenosine triphosphate (ATP) Refer to Figure 9.10

19. 9-28 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 9.10 Base always attached here Phosphates are attached there

20. 9-29 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Nucleotides are covalently linked together by phosphodiester bonds A phosphate connects the 5’ carbon of one nucleotide to the 3’ carbon of another Therefore the strand has directionality 5’ to 3’

21. 9-30 Figure 9.11

22. 9-31 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display In 1953, James Watson and Francis Crick discovered the double helical structure of DNA The scientific framework for their breakthrough was provided by other scientists including Linus Pauling Rosalind Franklin and Maurice Wilkins Erwin Chargaff Discovery of the Structure of DNA

23. Linus Pauling Linus Pauling (1901-1994) the only person to win two Nobel prizes 1954 Nobel Prize in Chemistry 1962 Nobel Peace Prize He elucidated a-helix structure, and he built ball-and-stick models

24. 9-32 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display In the early 1950s, he proposed that regions of protein can fold into a secondary structure  -helix Linus Pauling Figure 9.12 To elucidate this structure, he built ball-and-stick models

25. Rosalind Elsie Franklin (1920-1958) a British chemist and crystallographer who is best known for her role in the discovery of the structure of DNA It was her x-ray diffraction photos of DNA and her analysis of that data--provided to Francis Crick and James Watson without her knowledge--that gave them clues crucial to building their correct theoretical model of the molecule in 1953

26. 9-33 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display She used X-ray diffraction to study wet fibers of DNA Rosalind Franklin The diffraction pattern is interpreted (using mathematical theory) This can ultimately provide information concerning the structure of the molecule

27. 9-34 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display She made marked advances in X-ray diffraction techniques with DNA The diffraction pattern she obtained suggested several structural features of DNA Helical More than one strand 10 base pairs per complete turn Rosalind Franklin

28. Erwin Chargaff (1905 – 2002) Chargaff discovered two rules that helped lead to the discovery of the double helix structure of DNA

29. 9-35 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 1- DNA the number of guanine units equals the number of cytosine units, and the number of adenine units equals the number of thymine units. 2- The relative amounts of guanine, cytosine, adenine and thymine bases varies from one species to another. This hinted that DNA rather than protein could be the genetic material. Erwin Chargaff’s Experiment

30. 9-41 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Familiar with all of these key observations, Watson and Crick set out to solve the structure of DNA They tried to build ball-and-stick models that incorporated all known experimental observations A critical question was how the two (or more strands) would interact An early hypothesis proposed that the strands interact through phosphate-Mg ++ crosslinks Refer to Figure 9.15 Watson and Crick

31. 9-42 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 9.15 This hypothesis was, of course, incorrect!

32. 9-43 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display They went back to the ball-and-stick units They then built models with the Sugar-phosphate backbone on the outside Bases projecting toward each other They first considered a structure in which bases form H bonds with identical bases in the opposite strand ie., A to A, T to T, C to C, and G to G Model building revealed that this also was incorrect Watson and Crick

33. 9-44 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display They then realized that the hydrogen bonding of A and T resembled that between C and G So they built ball-and-stick models with AT and CG interactions These were consistent with all known data about DNA structure Refer to Figure 9.16 Watson, Crick and Maurice Wilkins were awarded the Nobel Prize in 1962 Rosalind Franklin died in 1958, and Nobel prizes are not awarded posthumously Watson and Crick

34. 9-45 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display General structural features (Figures 9.17 & 9.18) The DNA Double Helix Two strands are twisted together around a common axis There are 10 bases and 3.4 nm per complete twist The two strands are antiparallel One runs in the 5’ to 3’ direction and the other 3’ to 5’ The helix is right-handed As it spirals away from you, the helix turns in a clockwise direction

35. 9-48 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 9.17

36. 9-47 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display General structural features (Figures 9.17 & 9.18) The DNA Double Helix There are two asymmetrical grooves on the outside of the helix 1. Major groove 2. Minor groove Certain proteins can bind within these grooves They can thus interact with a particular sequence of bases

37. 9-48 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 9.17

38. 9-49 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 9.18

39. 9-50 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display The DNA double helix can form different types of secondary structure The predominant form found in living cells is B-DNA However, under certain in vitro conditions, A-DNA and Z-DNA double helices can form DNA Can Form Alternative Types of Double Helices

40. 9-51 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display A-DNA Right-handed helix 11 bp per turn Occurs under conditions of low humidity Little evidence to suggest that it is biologically important Z-DNA Left-handed helix 12 bp per turn Its formation is favored by GG-rich sequences, at high salt concentrations Cytosine methylation, at low salt concentrations Evidence from yeast suggests that it may play a role in transcription and recombination

41. 9-52 Figure 9.19 Bases substantially tilted relative to the central axis Sugar-phosphate backbone follows a zigzag pattern Bases relatively perpendicular to the central axis

42. DNA Can Form a Triple Helix Edirne Selimiye Mosque

43. 9-53 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display In the late 1950s, Alexander Rich et al discovered triplex DNA It was formed in vitro using DNA pieces that were made synthetically In the 1980s, it was discovered that natural double- stranded DNA can join with a synthetic strand of DNA to form triplex DNA The synthetic strand binds to the major groove of the naturally-occurring double-stranded DNA Refer to Figure 9.20 DNA Can Form a Triple Helix

44. 9-54 Figure 9.20 Triplex DNA formation is sequence specific The pairing rules are Triplex DNA has been implicated in several cellular processes Replication, transcription, recombination Cellular proteins that specifically recognize triplex DNA have been recently discovered T binds to an AT pair in biological DNA C binds to a CG pair in biological DNA

46. stabilized by the presence of a cation, especially potassium

48. Model for quadruplex-mediated down-regulation of gene expression

49. 9-56 Figure 9.21 DNA wound around histone proteins

50. 9-57 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display The primary structure of an RNA strand is much like that of a DNA strand Refer to Figure 9.22 vs. 9.11 RNA strands are typically several hundred to several thousand nucleotides in length In RNA synthesis, only one of the two strands of DNA is used as a template RNA Structure

51. 9-58 Figure 9.22

52. 9-59 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Although usually single-stranded, RNA molecules can form short double-stranded regions This secondary structure is due to complementary base- pairing A to U and C to G This allows short regions to form a double helix RNA double helices typically Are right-handed Have the A form with 11 to 12 base pairs per turn Different types of RNA secondary structures are possible Refer to Figure 9.23

53. 9-60 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 9.23 Also called hair-pin Complementary regions Noncomplementary regions Held together by hydrogen bonds Have bases projecting away from double stranded regions

54. 9-61 Many factors contribute to the tertiary structure of RNA For example Base-pairing and base stacking within the RNA itself Interactions with ions, small molecules and large proteins Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 9.24 depicts the tertiary structure of tRNA phe The transfer RNA that carries phenylalanine Molecule contains single- and double- stranded regions These spontaneously interact to produce this 3-D structure Figure 9.24