Bio 120 lecture 2 2011 2012

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  • 1. BIOLOGY 120 LECTURE 2 DIVERSITY OF MICROORGANISMS (Chapters 10-13 : Microbiology by Tortora 9th ed.) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 2. Lecture Outline •Classifications of Microorganisms •Prokaryotes •Eukaryotes •Viruses, Viroids, Prions Parungao-Balolong 2011Tuesday, June 21, 2011
  • 3. Lecture Outline •Classifications of Microorganisms •Prokaryotes •Eukaryotes •Viruses, Viroids, Prions Parungao-Balolong 2011Tuesday, June 21, 2011
  • 4. Classification of Microorganisms • Taxonomy (REVIEW) • Science of classifying organisms • Provides universal names for organisms • Provides a reference for identifying organisms Parungao-Balolong 2011Tuesday, June 21, 2011
  • 5. THE 3 DOMAIN SYSTEM Parungao-Balolong 2011Tuesday, June 21, 2011
  • 6. THE 3 DOMAIN SYSTEM Parungao-Balolong 2011Tuesday, June 21, 2011
  • 7. Prokaryotic vs Eukaryotic Organelles Parungao-Balolong 2011Tuesday, June 21, 2011
  • 8. The ENDOSYMBIOTIC Theory Parungao-Balolong 2011Tuesday, June 21, 2011
  • 9. Scientific Names Scientific Binomial Source of Genus Name Source of Specific Epithet Klebsiella pneumoniae Honors Edwin Klebs The disease Pfiesteria piscicida Honors Lois Pfiester Disease in fish Salmonella typhimurium Honors Daniel Salmon Stupor (typh-) in mice (muri-) Streptococcus pyogenes Chains of cells (strepto-) Forms pus (pyo-) Penicillium chrysogenum Tuftlike (penicill-) Produces a yellow (chryso-) pigment Trypanosoma cruzi Corkscrew-like (trypano-, Honors Oswaldo Cruz borer; soma-, body) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 10. Taxonomic Hierarchy Parungao-Balolong 2011Tuesday, June 21, 2011
  • 11. DEFINING “SPECIES” • Eukaryotic species: A group of closely related organisms that breed among themselves • Prokaryotic species: A population of cells with similar characteristics • Clone: Population of cells derived from a single cell • Strain: Genetically different cells within a clone • Viral species: Population of viruses with similar characteristics that occupies a particular ecological niche Parungao-Balolong 2011Tuesday, June 21, 2011
  • 12. DOMAIN EUKARYA •Animalia: Multicellular; no cell walls; chemoheterotrophic •Plantae: Multicellular; cellulose cell walls; usually photoautotrophic •Fungi: Chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments •Protista: A catchall for eukaryotic organisms that do not fit other kingdoms Parungao-Balolong 2011Tuesday, June 21, 2011
  • 13. PROKARYOTES: DOMAIN BACTERIA & ARCHAEA Parungao-Balolong 2011Tuesday, June 21, 2011
  • 14. NAMING YOUR UNKNOWN MICROBE Bergey’s Manual of Determinative Morphology, differential staining, Bacteriology biochemical tests Provides identification schemes for identifying bacteria and archaea Bergey’s Manual of Systematic Based on rRNA sequencing Bacteriology Provides phylogenetic information on bacteria and archaea Approved Lists of Bacterial Names Based on published articles Lists species of known prokaryotes Parungao-Balolong 2011Tuesday, June 21, 2011
  • 15. IDENTIFYING YOUR UNKNOWN MICROBE • Morphological characteristics: Useful for identifying eukaryotes • Differential staining: Gram staining, acid- fast staining • Biochemical tests: Determines presence of bacterial enzymes Parungao-Balolong 2011Tuesday, June 21, 2011
  • 16. USEFUL TESTS BIOCHEMICAL TESTS SEROLOGY (e.g. ELISA, AGGLUTINATION TESTS, WB) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 17. USEFUL TESTS PHAGE TYPING GENETIC TESTS (DNA base composition, PCR, RNA sequencing, etc) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 18. USEFUL TESTS FISH MICROARRAYS (uses DNA (Gene Expression Assays, probe, antibody, Metabolomics, etc) antigen, etc) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 19. WHICH TESTS SHOULD YOU USE? Parungao-Balolong 2011Tuesday, June 21, 2011
  • 20. DICHOTOMOUS KEYS VIDEO: DICHOTOMOUS KEY Parungao-Balolong 2011Tuesday, June 21, 2011
  • 21. CLADOGRAMS Parungao-Balolong 2011Tuesday, June 21, 2011
  • 22. Lecture Outline •Classifications of Microorganisms •Prokaryotes •Eukaryotes •Viruses, Viroids, Prions Parungao-Balolong 2011Tuesday, June 21, 2011
  • 23. THE PROKARYOTES Parungao-Balolong 2011Tuesday, June 21, 2011
  • 24. PROTEOBACTERIA • includes most of the Gram negative, chemoheterotrophic bacteria • presumes to have risen from a common photosynthetic ancestor • largest taxonomic group of bacteria • 5 classes: alphaproteobacteria, betaproteobacteria, gammaproteobacteria, deltaproteobacteria, epsilonproteobacteria Parungao-Balolong 2011Tuesday, June 21, 2011
  • 25. ALPHAPROTEOBACTERIA Parungao-Balolong 2011Tuesday, June 21, 2011
  • 26. IMPORTANT GENERA Caulobacter (found in lakes) Hyphomicrobium (found in lakes) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 27. IMPORTANT GENERA Agrobacterium Rhizobium (nodules) (tumor) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 28. BETAPROTEOBACTERIA Parungao-Balolong 2011Tuesday, June 21, 2011
  • 29. IMPORTANT GENERA & Features Sphaerotilus Spirillum Fimbriae and (forms sheaths) (forms sheaths) Capsules = Pathogenicity Parungao-Balolong 2011Tuesday, June 21, 2011
  • 30. GAMMAPROTEOBACTERIA Parungao-Balolong 2011Tuesday, June 21, 2011
  • 31. IMPORTANT GENERA & Features Pseudomonas Legionella (opportunistic) (cooling towers) Vibrio (marine) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 32. IMPORTANT GENERA & Features Proteus (swarming; peritrichous flagella) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 33. DELTAPROTEOBACTERIA Bdellovibrio (prey on other bacteria) Myxococcus (aggregates) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 34. EPSILONPROTEOBACTERIA Helicobacter (stomach cancer) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 35. NON-PROTEOBACTERIA; GRAM NEGATIVE BACTERIA Chlorobium Fusobacteria Parungao-Balolong 2011Tuesday, June 21, 2011
  • 36. FIRMICUTES Parungao-Balolong 2011Tuesday, June 21, 2011
  • 37. IMPORTANT GENERA & Features Clostridium Epulopiscium Lactobacillus/ Streptococcus Staphylococcus Parungao-Balolong 2011Tuesday, June 21, 2011
  • 38. ACTINOBACTERIA Parungao-Balolong 2011Tuesday, June 21, 2011
  • 39. IMPORTANT GENERA & Features Actinomycetes (Actinomyces, Frankia, Nocardia, etc) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 40. THE PROKARYOTES Parungao-Balolong 2011Tuesday, June 21, 2011
  • 41. THE PROKARYOTES Parungao-Balolong 2011Tuesday, June 21, 2011
  • 42. • Hyperthermophiles DOMAIN •Pyrodictium ARCHAEA •Sulfolobus •Methanogens •Methanobacteriu m •Extreme halophiles •Halobacterium Parungao-Balolong 2011Tuesday, June 21, 2011
  • 43. SMALLEST AND BIGGEST BACTERIA •Thiomargarita (750 µm) •Nanobacteria (0.02 µm) in rocks Parungao-Balolong 2011Tuesday, June 21, 2011
  • 44. ISSUES: NON-CULTIVABLE PROKARYOTES •Use of Culture- Independent methods (e.g. PCR) •Pelagibacter ubique (Discovered by FISH technique) •Extremophiles Parungao-Balolong 2011Tuesday, June 21, 2011
  • 45. Lecture Outline •Classifications of Microorganisms •Prokaryotes •Eukaryotes •Viruses, Viroids, Prions Parungao-Balolong 2011Tuesday, June 21, 2011
  • 46. WHO ARE THEY? Parungao-Balolong 2011Tuesday, June 21, 2011
  • 47. THE FUNGI Parungao-Balolong 2011Tuesday, June 21, 2011
  • 48. DIMORPHISM & REPRODUCTION IN FUNGI Parungao-Balolong 2011Tuesday, June 21, 2011
  • 49. VARIOUS FUNGAL SPORES •ASEXUAL •SEXUAL SPORES SPORES •Zygospore •Sporangiosphore •Ascospore •Conidiospore •Basidiospore •Arthrospore •Blastoconidium •Chlamydospore Parungao-Balolong 2011Tuesday, June 21, 2011
  • 50. VARIOUS FUNGAL SPORES Parungao-Balolong 2011Tuesday, June 21, 2011
  • 51. VARIOUS FUNGAL SPORES Parungao-Balolong 2011Tuesday, June 21, 2011
  • 52. LICHENS (FUNGI + ALGAE) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 53. THE ALGAE Parungao-Balolong 2011Tuesday, June 21, 2011
  • 54. REPRESENTATIVE GROUPS Parungao-Balolong 2011Tuesday, June 21, 2011
  • 55. THE PROTOZOA Parungao-Balolong 2011Tuesday, June 21, 2011
  • 56. THE PROTOZOA Parungao-Balolong 2011Tuesday, June 21, 2011
  • 57. THE PROTOZOA Plasmodium Cryptosporidium Parungao-Balolong 2011Tuesday, June 21, 2011
  • 58. THE PROTOZOA Cellular Slime Molds Parungao-Balolong 2011Tuesday, June 21, 2011
  • 59. THE PROTOZOA Plasmodial Slime Molds Parungao-Balolong 2011Tuesday, June 21, 2011
  • 60. THE HELMINTHS Parungao-Balolong 2011Tuesday, June 21, 2011
  • 61. THE HELMINTHS TREMATODES Parungao-Balolong 2011Tuesday, June 21, 2011
  • 62. THE HELMINTHS TREMATODES Parungao-Balolong 2011Tuesday, June 21, 2011
  • 63. THE HELMINTHS CESTODES Parungao-Balolong 2011Tuesday, June 21, 2011
  • 64. THE HELMINTHS NEMATODES (egg infects humans) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 65. THE HELMINTHS NEMATODES (adult infects humans) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 66. VECTORS (Arthropods) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 67. Lecture Outline •Classifications of Microorganisms •Prokaryotes •Eukaryotes •Viruses, Viroids, Prions Parungao-Balolong 2011Tuesday, June 21, 2011
  • 68. VIRUSES • Contain DNA or RNA • Contain a protein coat • Some are enclosed by an envelope • Some viruses have spikes • Most viruses infect only specific types of cells in one host • Host range is determined by specific host attachment sites and cellular factors Parungao-Balolong 2011Tuesday, June 21, 2011
  • 69. VIRUSES : ARCHITECTURE Helical Viruses Enveloped Viruses Polyhedral Viruses Complex Viruses Parungao-Balolong 2011Tuesday, June 21, 2011
  • 70. HOW ARE THEY NAMED? • Family names end in -viridae.  EXAMPLE  Herpesviridae • Genus names end in -virus  Herpesvirus • Viral species: A group of  Human herpes virus viruses sharing the same genetic information and  EXAMPLE ecological niche (host)  Retroviridae • Common names are used  Lentivirus for species  Human immunodeficiency virus • Subspecies are designated HIV-1, HIV-2 by a number Parungao-Balolong 2011Tuesday, June 21, 2011
  • 71. GROWING VIRUSES Embryonated Eggs Plaques Cell Culture Parungao-Balolong 2011Tuesday, June 21, 2011
  • 72. LIFE CYCLE Parungao-Balolong 2011Tuesday, June 21, 2011
  • 73. LIFE CYCLE Parungao-Balolong 2011Tuesday, June 21, 2011
  • 74. LIFE CYCLE  Lytic cycle: Phage causes lysis and death of host cell.  Lysogenic cycle: Prophage DNA incorporated in host Parungao-Balolong 2011Tuesday, June 21, 2011
  • 75. LIFE CYCLE  Lytic cycle: Phage causes lysis and death of host cell.  Lysogenic cycle: Prophage DNA incorporated in host DNA. Parungao-Balolong 2011Tuesday, June 21, 2011
  • 76. VIRUS MULTIPLICATION Parungao-Balolong 2011Tuesday, June 21, 2011
  • 77. VIRUS MULTIPLICATION Parungao-Balolong 2011Tuesday, June 21, 2011
  • 78. VIRUS MULTIPLICATION (DNA Virus) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 79. VIRUS MULTIPLICATION (+ strand RNA Virus) Attachment Capsid Nucleus RNA Cytoplasm Host cell Entry Maturation and uncoating and release Translation and synthesis RNA replication by viral RNA- of viral proteins dependent RNA polymerase Uncoating releases – strand is transcribed viral RNA and proteins. from + viral genome. Capsid Viral Viral protein genome protein (RNA) (a) ssRNA; + + strand or sense strand; Picornaviridae mRNA is transcribed from the – strand. Parungao-Balolong 2011Tuesday, June 21, 2011
  • 80. VIRUS MULTIPLICATION (- strand RNA Virus) Attachment Capsid Nucleus RNA Cytoplasm Host cell Entry Maturation and uncoating and release Translation and synthesis RNA replication by viral RNA- of viral proteins dependent RNA polymerase Uncoating releases viral RNA and proteins. The + strand (mRNA) must first be transcribed from the – viral Viral Viral genome before proteins can genome protein be synthesized. (RNA) Capsid protein (b) ssRNA; – or – strands are antisense strand; incorporated Rhabdoviridae into capsid Additional – strands are transcribed from mRNA. Parungao-Balolong 2011Tuesday, June 21, 2011
  • 81. VIRUS MULTIPLICATION (dsRNA Virus) Attachment Capsid Nucleus RNA Cytoplasm Host cell Entry Maturation and uncoating and release Translation and synthesis RNA replication by viral RNA- of viral proteins dependent RNA polymerase Uncoating releases RNA polymerase initiates production of mRNA is produced inside the viral RNA and proteins. – strands. The mRNA and – strands form the capsid and released into the dsRNA that is incorporated as new viral genome. cytoplasm of the host. Viral Viral genome protein (RNA) (c) dsRNA; + or sense Capsid proteins and RNA- strand with – or dependent RNA polymerase antisense strand; Reoviridae Parungao-Balolong 2011Tuesday, June 21, 2011
  • 82. VIRUS MULTIPLICATION (Comparing Notes : RNA Viruses) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 83. VIRUS MULTIPLICATION (Retrovirus) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 84. DNA vs RNA VIRUSES • DNA: Cellular enzyme • RNA – strand: Viral transcribes viral DNA in enzyme copies viral RNA nucleus to make mRNA in cytoplasm • DNA, reverse transcriptase: Cellular • RNA, double-stranded: enzyme transcribes viral Viral enzyme copies – DNA in nucleus; reverse strand RNA to make transcriptase copies mRNA in cytoplasm mRNA to make viral DNA • RNA, reverse • RNA, + strand: Viral RNA transcriptase: Viral is a template for enzyme copes viral RNA synthesis of RNA to make DNA in polymerase. cytoplasm. Parungao-Balolong 2011Tuesday, June 21, 2011
  • 85. VIRUSES & CANCER • CANCER • Activated oncogenes transform normal cells into cancerous cells. • Transformed cells have increased growth, loss of contact inhibition, tumor specific transplant and T antigens. • The genetic material of oncogenic viruses becomes integrated into the host cells DNA. Parungao-Balolong 2011Tuesday, June 21, 2011
  • 86. VIRUSES & CANCER • Oncogenic DNA • Oncogenic RNA viruses viruses • Adenoviridae • Retroviridae • Heresviridae • Viral RNA is transcribed to DNA • Poxviridae which can integrate into host DNA • Papovaviridae • Hepadnaviridae • HTLV 1 • HTLV 2 Parungao-Balolong 2011Tuesday, June 21, 2011
  • 87. • Latent viral infections • Virus remains in LATENT vs asymptomatic host cell PERSISTENT VIRAL for long periods INFECTIONS • Cold sores, shingles • Persistent viral infections • Disease processes occurs over a long period; generally is fatal • Subacute sclerosing panencephalitis (measles virus) Parungao-Balolong 2011Tuesday, June 21, 2011
  • 88. PRIONS • Infectious proteins • Inherited and transmissible by ingestion, transplant, and surgical instruments • Spongiform encephalopathies: Sheep scrapie, Creutzfeldt-Jakob disease, Gerstmann- Sträussler-Scheinker syndrome, fatal familial insomnia, mad cow disease • PrPC: Normal cellular prion protein, on cell surface • PrPSc: Scrapie protein; accumulates in brain cells forming plaques Parungao-Balolong 2011Tuesday, June 21, 2011
  • 89. VIROIDS • Infectious RNA; e.g., potato spindle tuber disease. Parungao-Balolong 2011Tuesday, June 21, 2011
  • 90. MAJOR PLANT VIRUSES Parungao-Balolong 2011Tuesday, June 21, 2011
  • 91. FAMILY OF VIRUSES ssDNA dsDNA Human Parvovirus Human Respiratory Infections Wart Viruses Smallpox; Cowpox Herpes Simplex 1 and 2 Hepatitis B Parungao-Balolong 2011Tuesday, June 21, 2011
  • 92. FAMILY OF VIRUSES ssRNA (-) Rabies Ebola Mumps Hepatitis D Influenza Hantavirus Lassa Fever ssRNA (+) Rhinovirus Hepatitis E Dengue Rubella SARS Parungao-Balolong 2011Tuesday, June 21, 2011
  • 93. FAMILY OF VIRUSES ssRNA, 2 strands dsRNA HIV Rotavirus Parungao-Balolong 2011Tuesday, June 21, 2011
  • 94. ISSUES: CROSSING BARRIERS Parungao-Balolong 2011Tuesday, June 21, 2011