1. Chapter 18 Microbial Models: The Genetics of Viruses and Bacteria

2. What is a virus? u An infectious particle consisting of nucleic acid enclosed in a protein coat.

3. Virus Characteristics 1. Small size 2. Infectious 3. Reproduction 4. Alcohol Resistance 5. Crystallization

4. Size u Large - barely visible with the light microscope. u Small - down to 20nm. u Comment - Much smaller than cells including bacteria.

6. Infectious u Viruses cause many diseases. They can be spread from one organism to another.

7. Reproduction u Can not reproduce without a host. u Viruses are obligate parasites.

8. Alcohol Resistance u Not immediately killed by alcohol like cells are. u Reason - resistant to dehydration by osmosis.

9. Crystallization u Can form crystals. u Cells can't do this.

10. Viral Structure 1. Genome - the genetic information. 2. Capsids and Envelopes - the outer covering.

11. Viral Genomes u Are used to classify virus types. u I - ds DNA u II - ss DNA u III - ds RNA u IV-VI - ss RNA

12. Capsid u Protein shell that encloses the viral genome. u Made from a large number of protein subunits. u Number of kinds of subunits usually small. u Often geometric in shape.

14. Envelopes u Membranes cloaking the capsids of some viruses. u Made from host membrane, but may have virus originated glycoproteins added.

15. General Steps for Viral Replication 1. Cell Entry 2. Genome Replication 3. Capsid Protein formation 4. Self-assembly of offspring 5. Exit from Host

17. Cell Entry u Locate host by "Lock-and- Key” fit between virus proteins and cell receptor molecules. u Infection - Begins when viral genome enters the cell.

18. Genome Replication u Host is reprogrammed to copy virus genome. u Use host DNA polymerase. u Use virus enzymes to copy RNA to DNA. u Use host's resources to make copies.

19. Capsid Protein Formation u Host's protein synthesis machinery used to make virus proteins.

20. Self-Assembly of Offspring u genome + capsid -----> virus u Particles usually assemble spontaneous.

21. Exit From Host u Host cell may burst or lyse, releasing the virus. u May "bud-off" host membrane, forming envelopes around the capsids.

22. Bacterial Viruses u Best understood of all viruses. u May show two types of virus life cycles: u Lytic Cycle u Lysogenic Cycle

23. Lytic Cycle u Virus reproductive cycle that kills the host cell. u Note - the previously described virus life cycle was a Lytic Cycle.

25. Ex: T4 Virus on E. coli u Uses Lytic Cycle. u Example of an Virulent Virus (a virus that only uses the lytic cycle). u Has about 100 genes. u Completes cycle in 20-30 minutes.

26. Lysogenic Cycle u Virus reproduction that doesn't immediately kill the host cell. u Viral DNA is inserted into the host DNA, but not expressed.

27. Movie – Lysogenic Cycle

29. Temperate Viruses u Viruses with both lytic and lysogenic cycles.   phage - Temperate virus on E. coli.  = Lambda )

30. Prophage u Virus DNA inserted into the host's DNA. u Viral DNA is reproduced with host DNA. u "Timebomb" for lytic cycle.

31. Lytic Mode Triggers u Switches the host from Lysogenic to Lytic Cycles u ex: radiation, chemicals, stress

32. Animal Viruses u Belong to several viral classes. u Specific Interests: 1. Viruses with envelopes 2. RNA viruses

33. Envelopes made with Host Membranes from: 1. Plasma Membrane 2. Nuclear Membrane

34. Herpes Viruses u Use nuclear membrane. u Viral DNA integrated into Host DNA as a provirus. u Shows both lytic and lysogenic life cycles.

35. RNA Viruses u Classes III - VI u Class VI - Retrovirus - use Reverse Transcriptase to make DNA from an RNA template.

36. Human Immunodeficiency Virus u HIV - causes AIDS. u Retrovirus from chimps. u Destroys the body’s immune system, allowing other diseases to kill.

37. Movie - HIV

39. Other Viral Diseases u Measles u Polio u Smallpox u Influenza

40. Treatments for Viruses u Vaccines (preventative). u Some Drugs u Ex: Ara-A Acyclovin u Comment - some treatments are working on the reverse transcriptase.

41. Problem u Since viruses work within a host cell, they are very difficult to treat. u Best Treatment - prevention.

42. Viruses u Can also cause cancer u Ex: HTLV-1 Papilloma Viruses

43. Plant Viruses u Can be an important agricultural problem. u Ex: Tobacco Mosaic Virus Tulip Flower Breakage

44. Viroids u Infectious particles of naked RNA. u Similar to viruses, but lack a capsid. u Ex: u Coconut Blight u Chrysanthemum Wilt

45. Viroids u Sequences are similar to Introns. u Connection?

46. Prions u Infectious protein particles. u Cause “mad-cow” and Creutzfeldt-Jakob disease. u Protein folding problem?

47. Prion Action

48. Bacteria Genomes u DNA circle (Chromosome). u Plasmids. - Small circle of DNA that is independent of the chromosome. u Carries a small number of traits.

49. E. coli Mutations u Binary Fission is not always perfect. Mistakes or mutations are made. u Rate: 1x10 -7 cell divisions. u Rare, but impact is high with the short generation time.

50. Importance u Mutations are the prime source of new alleles in bacteria.

51. Bacterial Genetic Recombinations 1. Transformation 2. Transduction 3. Conjugation 4. Plasmids 5. Transposons Be able to discuss a few of these methods.

52. Genetic Recombination u Mixes the genetic material into new combinations. u Will move new mutations through a population.

53. Transformation u Alteration of a cell's DNA by the uptake of foreign DNA. u Ex: Griffith's experiment and our lab last semester.

54. Transduction u Transfer of genes through phage infections.

55. Conjugation u Direct transfer of genetic material between two bacterial cells. u Bacterial "sex”. u Used to map genetic sequences in bacteria.

56. Plasmids u Small circular piece of DNA. u Carry many important traits. u Ex: Fertility Factor Antibiotic Resistance (R Plasmids)

57. Episome u Plasmid that has been incorporated into the bacterial chromosome.

58. Transponsons u Transposable genetic elements. u Also called "Jumping Genes”.

59. Transposons u May change locations within the chromosome, or they may copy into a new location. u Don't usually attach to DNA at specific locations, allowing them to scatter genes throughout the genome.

61. Gene Expression in Eukaryotes u Important for cellular control and differentiation. u Understanding “expression” is a key area in Biology. u More details in a future chapter.

62. General Mechanisms 1. Regulate Gene Expression 2. Regulate Enzyme Activity

63. Operon Model u Jacob and Monod (1961) - Prokaryotic model of gene control. u Always on the national AP Biology exam !

64. Operon Structure 1. Regulatory Gene 2. Operon Area a. Promoter b. Operator c. Structural Genes

65. If Lactose is absent

66. Regulatory Gene u Makes Repressor Protein which may bind to the operator.

67. Promoter u Attachment sequence on the DNA for RNA polymerase.

68. Operator u The "Switch”, binding site for Repressor Protein. u If blocked, will not permit RNA polymerase to pass, preventing transcription.

70. Structural Genes u Make the enzymes for the metabolic pathway.

71. Lac Operon u For digesting Lactose. u Inducible Operon - only works (on) when the substrate (lactose) is present.

72. If no Lactose u Repressor binds to operator. u Operon is "off”, no transcription, no enzymes made

73. If Lactose is absent

74. If Lactose is present u Repressor binds to Lactose instead of operator. u Operon is "on”, transcription occurs, enzymes are made.

75. If Lactose is present

76. Enzymes u Digest Lactose. u When enough Lactose is digested, the Repressor can bind to the operator and switch the Operon "off”.

77. Net Result u The cell only makes the Lactose digestive enzymes when the substrate is present, saving time and energy.

78. trp Operon u Makes Tryptophan. u Repressible Operon.

79. If no Tryptophan u Repressor protein is inactive, Operon "on” Tryptophan made. u “Normal” state for the cell.

80. Tryptophan absent

81. If Tryptophan present u Repressor protein is active, Operon "off”, no transcription, no enzymes u Result - no Tryptophan made

82. If Tryptophan present

83. Repressible Operons u Are examples of Feedback Inhibition. u Result - keeps the substrate at a constant level.

85. CAP - positive gene regulation u Catabolite Activator Protein u Accelerates the level of transcription by working with the RNA polymerase. u Uses cAMP as a secondary cell signal.

86. CAP - Mechanism u Binds to cAMP. u Complex binds to the Promoter, helping RNA polymerase with transcription.

88. Result u If the amount of glucose is low (as shown by cAMP) and lactose is present, the lac operon can kick into high gear.

89. Summary u Know the general structure of a virus and how a virus reproduces. u Know the components of bacteria genomes and some methods for genetic recombination.

90. Summary u Know Operon theory ! u Know the difference between inducible and repressible enzymes.