dna rna structure 1


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  • dna rna structure 1

    1. 1. Genetics: Analysis and Principles By Robert J. Brooker CHAPTER 9 Molecular structure of DNA and RNA
    2. 2. Roles of the genetic material “ The genetic material must carry out two jobs: duplicate itself and control the development of the rest of the cell in a specific way” Francis Crick
    3. 3. <ul><li>To fulfill its role, the genetic material must meet several criteria </li></ul><ul><ul><li>1. Information: It must contain the information necessary to make an entire organism </li></ul></ul><ul><ul><li>2. Transmission: It must be passed from parent to offspring </li></ul></ul><ul><ul><li>3. Replication : It must be copied </li></ul></ul><ul><ul><ul><li>In order to be passed from parent to offspring </li></ul></ul></ul><ul><ul><li>4. Variation: It must be capable of changes </li></ul></ul><ul><ul><ul><li>To account for the known phenotypic variation in each species </li></ul></ul></ul>
    4. 4. Miescher Discovered DNA <ul><li>1868 </li></ul><ul><li>Johann Miescher investigated the chemical composition of the nucleus </li></ul><ul><li>Isolated an organic acid that was high in phosphorus </li></ul><ul><li>He called it nuclein </li></ul><ul><li>We call it DNA (deoxyribonucleic acid) </li></ul>
    5. 5. Mystery of the Hereditary Material <ul><li>Originally,they thought this was a protein </li></ul><ul><li>The underlying idea was: </li></ul><ul><ul><li>hereditary characteristics are very various </li></ul></ul><ul><ul><li>The resposible molecules should be various too </li></ul></ul><ul><ul><li>Peptides conist of 20 amino acids and therefore they are various in structure. </li></ul></ul>
    6. 6. Discovery of a “transforming principle” Frederick Griffith, 1928 Pneumonia ( Diplococcus pneumoniae ) infecteren muizen. Muizen krijgen longontsteking en sterven . Twee type bacteriën : R bacterie “rough coat”: - geen ontsteking S bacterie “smooth coat”- wel ontsteking “ Coat type is associated with virulence”. Healthy Mouse
    7. 7. Griffith’s experiment identifying the “transforming principle” Injection Bacterial colonies Rough nonvirulent (strain R) Results Mouse healthy Smooth virulent (strain S) Mouse dies Heat-killed smooth virulent (strain S) Live strain S bacteria in blood sample from dead mouse Mouse dies Mouse healthy + Rough nonvirulent (strain R) Heat-killed smooth virulent (strain S)
    8. 8. What is the “transforming principle”? Conclusion: DNA is the transforming principle allowing R bacteria to make a smooth coat and allow infection. Oswald Avery, Colin MacLeod and Maclyn McCarty, 1944 Heat-killed S bacteria “transformed” the R bacteria to a form that causes pneumonia
    9. 9. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 9.3 <ul><li>Avery et al also conducted the following experiments </li></ul><ul><ul><li>To further verify that DNA, and not a contaminant (RNA or protein), is the genetic material </li></ul></ul>
    10. 10. 05_04_Avery_MacLeod.jpg
    11. 11. Hershey and Chase Results
    12. 12. Bacteriophages <ul><li>Viruses that infect bacteria </li></ul><ul><li>Consist of protein and DNA </li></ul><ul><li>Inject their hereditary material into bacteria </li></ul>cytoplasm bacterial cell wall plasma membrane
    13. 13. virus particle labeled with 35 S DNA ( blue ) being injected into bacterium 35 S remains outside cells virus particle labeled with 32 P DNA ( blue ) being injected into bacterium 35 P remains inside cells Fig 9b 225 Hershey and Chase Results
    14. 14. RNA Functions as the Genetic Material in Some Viruses <ul><li>In 1956, A. Gierer and G. Schramm isolated RNA from the tobacco mosaic virus (TMV), a plant virus </li></ul><ul><ul><li>Purified RNA caused the same lesions as intact TMV viruses </li></ul></ul><ul><ul><ul><li>Therefore, the viral genome is composed of RNA </li></ul></ul></ul><ul><li>Since that time, many RNA viruses have been found </li></ul>
    15. 16. Structure of the Hereditary Material <ul><li>Experiments in the 1950s showed that DNA is the hereditary material </li></ul><ul><li>But how does it look like? </li></ul><ul><li>Scientists competed strongly to determine the structure of DNA </li></ul>
    16. 17. Structure of Nucleotides in DNA <ul><li>Each nucleotide consists of </li></ul><ul><ul><li>Deoxyribose (5-carbon sugar) </li></ul></ul><ul><ul><li>Phosphate group </li></ul></ul><ul><ul><li>A nitrogen-containing base </li></ul></ul><ul><li>Four bases </li></ul><ul><ul><li>Adenine, Guanine, Thymine, Cytosine </li></ul></ul>
    17. 18. DNA ( d eoxyribo n ucleic a cid) and RNA ( r ibo n ucleic a cid) are chains of nucleotides <ul><li>Base - one of four types: adenine (A), thymine (T) or uracil (U) in RNA </li></ul><ul><li>guanine (G), cytosine (C) </li></ul>Sugar - deoxyribose (DNA) or ribose (RNA) Phosphate Nucleotides are composed of:
    18. 19. 9-27 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display <ul><li>Base + sugar  nucleo s ide </li></ul><ul><ul><li>Example </li></ul></ul><ul><ul><ul><li>Adenine + ribose = Adenosine </li></ul></ul></ul><ul><ul><ul><li>Adenine + deoxyribose = Deoxyadenosine </li></ul></ul></ul><ul><li>Base + sugar + phosphate(s)  nucleo t ide </li></ul><ul><ul><li>Example </li></ul></ul><ul><ul><ul><li>Adenosine monophosphate (AMP) </li></ul></ul></ul><ul><ul><ul><li>Adenosine diphosphate (ADP) </li></ul></ul></ul><ul><ul><ul><li>Adenosine triphosphate (ATP) </li></ul></ul></ul>
    19. 20. 9-26 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display A, G, C or T <ul><li>These atoms are found within individual nucleotides </li></ul><ul><ul><li>However, they are removed when nucleotides join together to make strands of DNA or RNA </li></ul></ul>A, G, C or U Figure 9.9 The structure of nucleotides found in (a) DNA and (b) RNA
    20. 21. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 9.10 Base always attached here Phosphates are attached there
    21. 22. Biochemical experiments of Chargaff <ul><li>% adenine = % thymine </li></ul><ul><li>% guanine = % cytosine </li></ul>
    22. 23. <ul><li>% adenine = % thymine </li></ul><ul><li>% guanine = % cytosine </li></ul><ul><li>Complementary bases pair: </li></ul><ul><li>A and T pair </li></ul><ul><li>C and G pair </li></ul>An explanation of the data : Model
    23. 24. Rosalind Franklin <ul><li>She worked in the same laboratory as Maurice Wilkins </li></ul><ul><li>She used X-ray diffraction to study wet fibers of DNA </li></ul>The diffraction pattern is interpreted (using mathematical theory) This can ultimately provide information concerning the structure of the molecule
    24. 25. 09_06.jpg James Watson Francis Crick
    25. 26. DNA nucleotide bases phosphate group deoxyribose ADENINE (A) THYMINE (T) CYTOSINE (C) GUANINE (G)
    26. 27. Figure 9.11
    27. 28. Phosphodiester bond
    28. 29. Watson-Crick Model <ul><li>DNA consists of two nucleotide strands </li></ul><ul><li>The nucleotides are connected by phoshodiester bonds </li></ul><ul><li>The 2 strands run in opposite directions </li></ul><ul><li>Strands are held together by hydrogen bonds between bases </li></ul><ul><li>A binds with T and C with G </li></ul><ul><li>Molecule is a double helix </li></ul>
    29. 30. Esscher A The strands are Anti-parallel B The strands are complementary C The mechanism for copying lies within its structure Three important features of DNA
    30. 31. 9-29 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display <ul><li>Nucleotides are covalently linked together by phosphodiester bonds </li></ul><ul><ul><li>A phosphate connects the 5’ carbon of one nucleotide to the 3’ carbon of another </li></ul></ul><ul><li>Therefore the strand has directionality </li></ul><ul><ul><li>5’ to 3’ </li></ul></ul><ul><li>The phosphates and sugar molecules form the backbone of the nucleic acid strand </li></ul><ul><ul><li>The bases project from the backbone </li></ul></ul>
    31. 32. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 9.17
    32. 33. 9-49 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 9.18
    33. 34. The Three-Dimensional Structure of DNA 9-55 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display <ul><li>To fit within a living cell, the DNA double helix must be extensively compacted into a 3-D conformation </li></ul><ul><ul><li>This is aided by DNA-binding proteins </li></ul></ul>
    34. 35. 9-56 Figure 9.21 DNA wound around histone proteins
    35. 36. DNA Can Form Alternative Types of Double Helices <ul><li>The DNA double helix can form different types of secondary structure </li></ul><ul><ul><li>The predominant form found in living cells is B-DNA </li></ul></ul><ul><ul><li>However, under certain in vitro conditions, A-DNA and Z-DNA double helices can form </li></ul></ul>
    36. 37. 9-51 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display <ul><li>A-DNA </li></ul><ul><ul><li>Right-handed helix </li></ul></ul><ul><ul><li>11 bp per turn </li></ul></ul><ul><ul><li>Occurs under conditions of low humidity </li></ul></ul><ul><ul><li>Little evidence to suggest that it is biologically important </li></ul></ul><ul><li>Z-DNA </li></ul><ul><ul><li>Left-handed helix </li></ul></ul><ul><ul><li>12 bp per turn </li></ul></ul><ul><ul><li>Its formation is favored by </li></ul></ul><ul><ul><ul><li>GG-rich sequences, at high salt concentrations </li></ul></ul></ul><ul><ul><ul><li>Cytosine methylation , at low salt concentrations </li></ul></ul></ul><ul><ul><li>Evidence from yeast suggests that it may play a role in transcription and recombination </li></ul></ul>
    37. 38. Bases substantially tilted relative to the central axis Bases substantially tilted relative to the central axis Sugar-phosphate backbone follows a zigzag pattern Bases relatively perpendicular to the central axis No details
    38. 39. <ul><li>Triplex DNA formation is sequence specific </li></ul><ul><li>The pairing rules are </li></ul><ul><li>Triplex DNA has been implicated in several cellular processes </li></ul><ul><ul><li>Replication, transcription, recombination </li></ul></ul><ul><li>Cellular proteins that specifically recognize triplex DNA have been recently discovered </li></ul>T binds to an AT pair in biological DNA C binds to a CG pair in biological DNA DNA can even form triple helixes
    39. 40. RNA Structure <ul><li>The primary structure of an RNA strand is much like that of a DNA strand </li></ul><ul><li>RNA strands are typically several hundred to several thousand nucleotides in length </li></ul><ul><li>In RNA synthesis, only one of the two strands of DNA is used as a template </li></ul>
    40. 41. Figure 9.22
    41. 42. RNAs can fold in to 3D structure:like proteins “ RNAs kink, bend, loop and twist themselves into a wonderful variety of shapes” (Doudna, Nature 388, 1997) <ul><li>RNAs lack the chemical diversity of proteins </li></ul><ul><li>but </li></ul><ul><li>Many conformational degrees of freedom of its </li></ul><ul><li>phosphate backbone </li></ul><ul><li>Unique hydrogen-bonding </li></ul><ul><li>stacking of nucleotide bases </li></ul><ul><li>>> Ample resources for 3D-folding: </li></ul>
    42. 43. 9-59 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display <ul><li>Although usually single-stranded, RNA molecules can form short double-stranded regions </li></ul><ul><ul><li>This secondary structure is due to complementary base-pairing </li></ul></ul><ul><ul><ul><li>A to U and C to G </li></ul></ul></ul><ul><ul><li>This allows short regions to form a double helix </li></ul></ul><ul><li>RNA double helices typically </li></ul><ul><ul><li>Are right-handed </li></ul></ul><ul><ul><li>Have the A form with 11 to 12 base pairs per turn </li></ul></ul><ul><li>Different types of RNA secondary structures are possible </li></ul>
    43. 44. <ul><li>Many factors contribute to the tertiary structure of RNA </li></ul><ul><ul><li>For example </li></ul></ul><ul><ul><ul><li>Base-pairing and base stacking within the RNA itself </li></ul></ul></ul><ul><ul><ul><li>Interactions with ions, small molecules and large proteins </li></ul></ul></ul>Molecule contains single- and double-stranded regions These spontaneously interact to produce this 3-D structure
    44. 45. Figure 9.23 Also called hair-pin Complementary regions Held together by hydrogen bonds Have bases projecting away from double stranded regions Noncomplementary regions
    45. 46. Example: 3D structure of tRNA-Phe from yeast
    46. 47. RNAs are folded into complex structures because of their ability to form internal duplexes M.McManus Hairpin Loops Stems Bulge loop Interior loops Multi-branched loop
    47. 48. Divalent cations, Mg ++ , are essential for correct folding, stability, and catalysis.  (example: >100 Mg 2+ ions needed for the folding of RNAse P
    48. 49. 1. Identification of DNA as the Genetic Material 1. Experiments with pneumococcus suggested that DNA is the genetic material 2. Hershey and Chase provided evidence that the genetic material injected into the bacterial cytoplasm is T2 phage DNA 3. RNA functions as the genetic material in some viruses 2. Nucleic acid structure 1. Nucleotides are the building blocks of nucleic acids 2. Nucleotides are linked together to form a strand 3. A few key events led to the discovery of the double helix structure 4. Chargaff found that DNA has a biochemical composition in which the amount of A equals T and the amount of G equals C 5. Watson and Crick deduced the double helical structure of DNA 6. The molecular structure of the DNA double helix has several key features 7. DNA can form alternative types of double helices 8. DNA can form a triple helix, called triplex DNA 9. The three-dimensional structure of DNA within chromosomes requires additional folding and the association with proteins 10. RNA molecules are composed of strands that fold into specific structures Summary : Outline of this chapter 9