1. DNA Chapter 2 – read principal points TimelineTimeline for genetics

2. Deoxyribonucleic acid Functional Properties 1. Replication – DNA is copied prior to cell division why?

3. 2. Storage of information DNA inherited from parent to offspring from cell to cell Gene expression – Genes encode proteins 3. Mutation – DNA changes to allow variation and adaptation, the basis of evolution

4. A six-legged green frog. (Reproduced by permission of JLM Visuals http://www.isogenic.info/assets/images/autogen/a_image16.jpg http://3quarksdaily.blogs.com/3quarksdaily/images/wolfe_seal_1.jpg Neutral, harmful, adaptive?

5. DNA History 1869 Meischer extracted nuclein from pus 1900s – chromosomes discovered The genetic material must have the 3 functional properties microscopy.bio.cmich.edu

6. Griffith finds “transforming factor” 1928 London Streptococcus pneumoniae bacterium pneumonia in mice, deadly to humans sputum with bacteria

7. Smooth strain (IIIS) virulent polysaccharide capsule capsule allows bacteria to evade immune system Fluorescent stain of capsule

8.  isolate live IIIS from mouse

9. S pneumococcus kills mouse in 24 hours. But 100 million IIR strain bacterial cells is harmless SRSR (Research photographs of Dr. Harriet Ephrussi-Taylor, courtesy of The Rockefeller University.) Appearance when grown on an agar plate

10. http://biology.kenyon.edu/courses/biol114/KH_lecture_images/How_DNA_works/how_ DNA-works.html

11. Rough strain IIR is avirulent IIR lacks capsule -> isolate live IIR

12. The experiment: Heat kill IIIS strain  mouse ?

13. Heat killed IIIS strain + live strain IIR  mouse ? Which strain is isolated?

15. Griffith’s experiment and conclusion A “transforming factor” in killed S strain transformed live R strain into S DNA or protein?

16. 1944 Avery, McCarty, Macleod 1. Heat kill IIIS 2. Remove lipids and sugars – how? FYI iGenetics: DNA as Genetic Material: Avery’s Transformation Experiment

17. 3. Divide into 3 and treat with: protease RNase DNase  next, add live R cells to each

20. 1952 Hershey and Chase Used T2 bacteriophage + E. coli A phage is a virus that infects bacteria

21. How phage work 1. phage adsorbs onto bacterial surface 2. Genetic material injected 3. Cell makes progeny phage IS the genetic material DNA, or protein?

23. Experiment 1. Label phage protein with 35 S  infect E. coli  strip phage off cell surface New phage are not radioactive

24. 2. Label phage DNA with 32 P -> infect E.coli -> blend -> New phage contain 32 P

26. http://osulibrary.orst.edu/specialcollections/coll/pauling/dna/pictures/hersheych ase-experiment.html

27. Hershey and Chase conclusion DNA is responsible for function and reproduction of phage virus = the genetic material

28. Structure of DNA = nucleotide polymers NUCLEOTIDES 1. Nitrogenous base Purines = guanine and adenine G A Purines attached to 1 carbon of sugar at 9 nitrogen, covalent bond, pyrimidines attached to 1 carbon at 1 nitrogen How big IS a nucleotide? UTAH cell scale

29. Pyrimidines Thymine T Cytosine C RNA contains uracil U

30. 2. Deoxyribose sugar RNA (ribose) 2’ OH makes RNA less stable than DNA Sugar + base = nucleoside

31. 3. Phosphate (PO 4 ) Nucleotide = base + sugar + phosphate Phosphate covalently (phosphodietster bond) attached to 5’C of sugar Phosphodiester bond - Covalent bond between phosphate of one nucleotide and 3’ sugar carbon of another 9 N (purine) or 6N (pyrimidine) covalently bonded to 1C of sugar

32. DNA is a polymer of nucleotides polarity 5’carbon to 3’hydroxyl

33. DNA (double helix) Watson and Crick 1953 X-ray diffraction data Rosalind Franklin, Maurice Wilkins

34. DNA properties include:

35. Complementary base pairing 1. Hydrogen bonds between complementary bases How many bonds in a G-C pair? A-T? Which is stronger?

37. Complementary base pairs Which are the G-C pairs?

38. 2. antiparallel stands 5’  3’ and 3’  5’

39. 3. Sugar phosphate backbones

40. 4. Base composition DNA 50% purine 50% pyrimidine A = TG = C A/T = 1C/G = 1 A +T does not equal C+G A + G = C + T Chargaff (1950)

41. 5. DNA can denature and renature Melt hydrogen bonds (chemical or heat)

42. And 5. Right handed helix 6. Complete turn of the helix is 0.34 nm, 10 bases per turn 7. Major and minor grooves

43. Major and minor grooves

44. Forms of DNA B DNA right helix 10 bp/ turn A DNA right helix 10.9 bp/ turn Z DNA left helix 12 bp/turn (role?) Cellular DNA closest to B DNA 10.4 bp/turn

45. Replication of DNA by Complementary Base Pairing HHMI interactive DNA replicationHHMI interactive DNA replication advanced

46. Organization of DNA in chromosomes Genome Full amount of genetic material in a single cell

47. Influenza ssRNAHIV ssRNA Bacteriophage ds DNA Viral chromosome Single or double stranded DNA or RNA Circular or linear Herpes ds DNA Parvovirus ssDNA

48. Genetic material in prokaryotes 1 (usually) chromosome Circular (most) chromosome Supercoiled DNA located in nucleoid region Neisseria gonorrhoeae

49. E. coli = 4.6 million bp, circular chromosome 1500 um genome stuffed into a 1 um cell via supercoiling E. Coli cellsE. coli DNA map of chromosome

50. Some bacteria contain extra-chromosomal DNA called a plasmid

51. Eukaryotic Chromosomes C value - Amount of DNA varies among species

52. The structure of chromatin DNA + proteins Highly conserved

53. Histones and non-histones Histone proteins basic net + charge interacts with – charged DNA Package DNA Highly conserved Non-histone proteins vary among species http://faculty.jsd.claremont.edu/jarmstrong/images/chromatin.gif

54. What do histones do? 1. pack DNA into chromatin Condense DNA 10,000X (2 meters  nanometers) 1. Modifications to histone proteins affect gene expression

55. 5 histone proteins Histone type #amino acidscontent_________________ H1 200-26527%lysine, 2%arginine H2A 129-155 11% lysine, 9% arginine H2B 121-155 6% lysine, 6% arginine H3 135 10%lysine, 15% arginine H4 102 11% lysine, 4% arginine Note: all are lysine/arginine rich, they contain other amino acids, but at small percentages. Basic, + charge

56. Gel electrophoresis

57. epigenetics Modification of histone proteins changes gene expression. Chemical tags can be inherited and are stable in cell division

58. Pbs: A Tale of Two Mice Pbs: A Tale of Two Mice Epigenetics with deGrassi http://www.pbs.org/wgbh/nova/scienceno w/3411/02.html http://www.pbs.org/wgbh/nova/scienceno w/3411/02.html Agouti Mice Epigenetics and gene silencing Mouse and twin studies Diet and the epigenome Methyl group tags

59. Chromosome packaging 1. Nucleosomes 1 nucleosome “beads on a string” The 10 um chromatin fiber 2(H2A).2(H2B) 2(H3).2(H4) octomer

60. Dual role of nucleosomes stable to shelter DNA and compact it labile to allow DNA information to be used

61. 2. The 30 nm chromatin fiber Histone H1 a ttaches linker DNA to nucleosomes

62. The 30 nm chromatin fiber (11nm string-> 30 nm helical fiber) See Science article

63. 3. Further packaging into loops and scaffolds……

64. Summary of DNA packaging 30nm chromatin fiber Nucleosomes DNA helix

65. Metaphase chromosome is 10,000 X condensed compared to double helix Condensed scaffold The scaffold with loops

66. Euchromatin and Heterochromatin

67. 1. Heterochromatin Condensed Transcriptionally inactive Ex. centromeres

68. Heterochromatin stains darkly

69. Heterchromatin example Barr body (facultative, extent of inactivity varies) Inactivated X chromosome in females

71. 2. Euchromatin Lighter staining regions of DNA that contain genes Transcriptionally active

72. Unique Sequences and Repetitive DNA

73. What genes are on a chromosome? http://www.dnalc.org/ddnalc/resources/chr11.html Chromosome 11 flyover Terms: Transposon Pseudogene Olfactory Polymorphism

74. 1. Unique Sequence DNA (1 to a few copies) a. Genes Encode proteins ~60% of DNA Only 2% of DNA is coding (H. sapiens) Estimated 20,000 genes in humans

75. b. Gene families  encodes embryonic beta globin  encode fetal beta globin  is a pseudogene (not functional)  encodes normal beta globin  encodes normal adult beta globin Example: Beta globin (encode subunits of hemoglobin)

76. 2. Repetitive DNA Repeated 10 – 1000sX in the genome a. Dispersed repeated DNA LINES = long interspersed elements 1000 – 7000 bp Ex. humans have 500,000 copies of L1 = 15 % of genome. some are transposons = copy and move

78. SINES 100 – 400 bp Ex. Alu repeats repeated 1 million times = 10% of genome

79. b. Tandem repeats 1 – 10 bp long tandemly repeated Centromeres, telomeres, rRNA genes Ex. telomere sequence repeated 2000X 5'...TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG..3' 3'...AATCCC AATCCC AATCCC AATCCC AATCCC AATCCC..5'

80. Ex. rRNA genes