Microbiology Exam 2 Cards 2

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Microbiology Exam 2 Cards 2
2010-11-07 14:00:43

Micro Exam 2 Part 2
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  1. Archaea: Haobacterium Salinarium
    • Example of phototrophic archaea
    • Has pigment becteriorhodopsin
    • Appears purple: abosrbs green light and reflects blue and red
    • Absorbs e- and shifts from cis to trans
    • Going from trans to cis releases photon
  2. Photosythnesis
    • e- donor is H20
    • Makes ATP to fix CO2, making glucose or sucrose in Dark Reaction
  3. Light Reaction of Photosythesis
    • P2 excites e- to split H20
    • Drops in energy to P1
    • NADP+ is the electron carrier
  4. Antenna System
    Chlorophylls and Accessory Pigments : Collect photons
  5. Calvin Cycle
    • Rubisco binds CO2
    • Large, slow enzyme: Can react with O2 or CO2
    • 18 ATP required to fix 6 CO2 into glucose
    • 12 NADPHs are also required
  6. Anoxygenic Photosythesis
    • Green & purple bacteria, Purple bacteria
    • e- donor is H2S, Sulfide Ions, H2, or Ferrous Ions
    • Chlorophylls absorb infrared light, less energy = less ATP
    • Only one photosystem
    • Slow growth
  7. Denitrification
    Nitrate -> Nitrite -> Nitric Oxide -> Nitrous Oxide -> N2
  8. Nitrification
    NH3 -> Nitrite -> Nitrate
  9. Nitrobacter
    • O2 is e- acceptor to oxidize nitrite
    • Can perform nitrification under anoxic conditions. Has organelle to protect it from toxic byproduct
  10. Nitrogen Fixation
    • N2 -> NH3
    • Ammonia is then used to make amino acids
  11. Nitrogen (N2)
    • Has a triple bond (980 kJ to make/break bond)
    • Requires 6 e- to reduce
  12. Nitrogenase
    • Iron containing enzyme
    • There are alternate forms of nitrogenase
    • Dinitrogenase- enzyme w/ Moliptonone (Mo) cofactor
    • Dinitrogenase reductase- Inactived by O2 so used only in anoxic envir.
    • Not too specific, can break other triple bonds
  13. Nitrogen Fixation
    • Anaerobic process (must be done in absense of oxygen)
    • Can be performed by aerobes or anaerobes
  14. Rhizobium
    • Found in root nodule, very low O2 concentration
    • Both plant and bacteria secrete chemicals
    • -Rhizobia factors make root hairs curl so that bacteria can penetrate
    • -Plant factors cause bacteria to grow, nodule forms
    • Bacteria then changes to bacterioid
  15. Nutrient exchange between rhizobia and plant
    • Bacterioid membrane is surrounded by symbiosome membrane
    • Plant gets ammonia/amides, Bacteria gets sugars and organic acids
    • Leghemoglobin (Lb) produced by plant keeps O2 levels low in infected area
  16. Populations
    Arise from a single cell
  17. Guild
    Populations of metabolically related organisms
  18. Microbial Community
    Set of guilds that interact together
  19. Ecosystem
    Communities of organisms + Their natural environment
  20. Biogeochemical Cycle
    Biologically and chemically mediated chemical transformations of elements
  21. Niche
    Physical habitat. Resources available for growth
  22. Prime Niche
    Best conditions for fastest doubling time
  23. Microenvironments
    • Small environments of microbes
    • Ex. Bacillus = 3mm microenvironment
  24. Major Impact of Microbial Ecology & Interaction
    • Act as primary producers, consumers, decomposers, food
    • Biochemical cycles, transform things from gas to mineral or vice versa
  25. Enrichments can be selective or counterselective
    • Have resources for growth / prevent growth
    • ex. fungicide to prevent fungal growth
  26. Islation of microbes in lab
    Can not isolate all microbes. The ones we do isolate don't always act the same in lab setting (ex. lose capsule)
  27. Isolation to obtain pure culture
    • 1. Streak plates to obtain single colonies
    • 2. Agar shake- Can make agar, add sample, then place on more agar for anaerobes
    • 3. Liquid Dilution- Successive dilutions until the last tube shows no growth (10 or fewer cells) = Most Probable Number
  28. Confirmation of Purity- Axenic Culture
    • 1. Microscopy - Gram stain should only show one type of cell
    • 2. Look at colony characteristics
    • 3. Growth in media in which cultures grow poorly and contaminants grow well (should be no growth)
  29. Growth Rate In Environment vs Lab
    Microbes don't get nearly as many nutrients in natural environment. Growth rate can be as low as 1% in natural environment what it is in lab setting
  30. How to quantify microbes in microbial habitat
    • 1. PCR and DGGE
    • 2. Metagenomics
    • 3. Staining Methods (Fluorescent, Viability, Fluorescent Antibody, GFP)
  31. Fluorescent Staining
    • DAPI- colors microbe blue by binding nucleic acid
    • Acridine Orange- Also binds nucleic acid
    • *Both fluoresce under UV
    • **Problem- can't tell the difference between live and dead cells
  32. Viability Staining
    • Depends on whether or not cytoplasmic membrane in intact
    • 2 Dyes
    • - Propidium Iodide- penetrates only cells w/o intact membrane
    • - Green fluorescent dye- penetrates all cells
    • **See mix of green and orange/red (Green=living cells)
  33. Fluorescent Antibody Probes
    • Antibody is used in place of a nucliec acid for dying
    • Limited to specific strains or species (must be specific)
  34. Green Fluorescent Protein-TAG
    • Insert GFP into genome and add to natural population of microbe
    • Reporter Gene- Used to tell if gene is transcribed
    • Needs O2 to autofluoresce so useless in anoxic environment
  35. Fluorescence In Situ Hybridization (FISH)
    • Nucleic acid probe (oligonucleotide is complimentary to a sequence in target gene OR RNA-hybridize)
    • Tagged w/ fluorescent dye
    • Fluoresces under microscope
    • *Must use different nucleic acid prope to observe different species
  36. Syntrophy
    • Beneficial relationship
    • Cooperative transformation of one compound into a compound another organism needs
  37. Predation
    • Ex. Potists feed on bacteria
    • Ex. Bacteria infect other bacteria
  38. Amensalism
    • One species benefits while harming another species non-specifically
    • Ex. Streptomyces produce antibiotics to kill other microbes inhabiting soil
  39. Parasitism
    One species benefits while harming a specific host
  40. Synergism
    Both species benefit through growth in proximity, however both species are easily separated to grow independently
  41. Biofilms differ from colony
    because they secrete polysaccarides to encase cells
  42. Soil microbes
    Most live at the surface but some can be found 4-5 km deep
  43. O Horizon
    • Contains rhizosphere
    • Earliest stage of decomposition by fungi and bacteria so many nutrients available
  44. Aerated Horizon
    A Horizon
    Peat or top soil. Contains broken down organic material and minerals
  45. Eluviated Horizon
    B Horizon
    Experience periods of H20 saturation from rain which leaches some nutrients, so has fewer microbes than O and A Horizons
  46. C Horizon
    Increasing proportion of minerals and rock fragments broken off from bedrock
  47. Endolymphs
    • Microbes in crustal rocks (3 km deep)
    • Energy source - radioactive decay of atoms including uranium
    • Carbon source- Minerals
  48. Vampirella
    Protist that sucks nutrients out of fungal filaments
  49. How microbes contribute to soil formation
    • -Create CO2 which becomes carbonic acid to disolve rock into mineral components of soil
    • -Secrete organic acid
    • -Decompose organisms
  50. Prochlorophytes
    Marine ecosystem primary producers
  51. Marine Ecosystems
    Oligotrophic: Extremely low concentration of nutrients and orgnisms
  52. Trichodesmium
    • filamentous marine cyanobacteria in tropical and subtropical oceans
    • Nitrogen Fixing
  53. Organisms in 1ml of sea water
    • Zooplankton- not many
    • Phytoplankton (algae and protozoa)- 3,000-4,000
    • Photosythetic bacteria- 100,000
    • Heterotrophic bacteria- 1,000,000
    • Viruses- 10,000,000
  54. Light Penetration of Ocean
    Light can reach organisms 100-200m in open ocean / 1m in coastal region
  55. Benthos
    Where water column meets ocean floor and soil
  56. Archaea vs Bacteria in Marine Ecosystem
    Archaea usually found in extreme environments. Only become more numberous than bacteria in deep ocean (2,000 meters)
  57. Barotolerant vs Barophilic
    • Barotolerant- >3,000 m
    • Barophilic- 4,000-6,000 m (grow optimally in high pressure)
  58. Molecular Effects of High Pressure Environment
    • Proteins are folded in a way to minimilize effect of pressure
    • Membrane is high in unsaturatated fatty acids
    • Omph porins- play role in nutrient aquisition
  59. Riftia Pachyptila
    Tube worm at thermal vent. No digestive tract but has blood vessels w/ oxygen. Trophosome (bacteria) uses oxygen to fix CO2, making organic compounds for the tube worm.
  60. Lake Communities
    O2 production and consumption
    Even though organisms produce O2, this causes more heterotrophs to grow and consume it, making an anoxic environment
  61. River Pollutants
    • Input of sewage causes spike in bacterial population
    • There is a lag in algae/cyanobacteria growth but O2 will inc. when they do
  62. Biochemical Oxygen Demand (BOD)
    • -microbial oxygen consuming property of a body of water
    • -the amount of organic matter that can be oxidized by microorganisms
    • *carbon and oxygen concentrations are inversely related in a freshwater environment
  63. Biostimulation
    When microbe population is big enough to remove pollutants, but require a limiting nutrient
  64. Bioaugmentation
    Add specific microbes to decompose specific pollutants
  65. Limitations of Bioremediations
    • 1. Toxicity of site
    • 2. Initial levels of contaminant / microbes
    • 3. Ability of contaminant to be biodegraded
    • 4. Soil properties
  66. Genome
    All genes present in cell or virus
  67. Vertical Transmission
    Transmit genetic material from parent to offspring
  68. Horizontal Transmission
    Genetic info transferred from one cell to another
  69. Griffith's Experiment
    Used smooth and rough streptococcus. Living rough cells took genetic info for capsule formation from dead smooth cells
  70. Avery, MacLeod, & McCarty
    Found that DNA was the source of info transmitted
  71. Minimal Genome
    480 proteins. Found this by using transposons to mutate genes and determine if they were essential.
  72. Transcription
    RNA Polmyerase and Promotors (DNA sequence in front of gene to activate expression)
  73. Monosystonic
    • In eukaryotic genes, 1 gene is generally used to make 1 protein
    • In prokaryotic genes, many genes can follow the promotor and all be expressed into mRNA at same time
  74. Operon
    Region of promotor and genes
  75. Non-coding DNA in eukaryotes and prokaryotes
    • Eukaryotes- 90% non-coding
    • Prokaryotes- 15% non-coding
  76. Eukaryotic Differences In Transcription
    • 1. Has to remove introns (splicing)
    • 2. Add poly A tail
    • 3. Add 7-methylguanosine to 5' end (capping)
  77. Ribosomal Subunits of eukaryotes and prokaryotes
    • Prokaryotes: 30S and 50S
    • Eukaryotes: 40S and 80S
  78. Extrachromosomal Elements (ex. Plasmids)
    • Can code as few as 2-30 genes or as many as a few hundred
    • Have genes that aren't necessary for living
    • Can be used to clone genes
  79. Plasmids used for cloning gends must have..
    • 1. Antibiotic resistance gene (to select for transgenic bacteria)
    • 2. Several unique restriction sites
    • 3. Promotors for replication of DNA
  80. Horizontal Transfer
    • Can be interspecies or intraspecies
    • 1. Transformation
    • 2. Transduction
    • 3. Conjugation
  81. Transformation
    • Take in DNA from environment
    • Must have DNA binding protein to bind single strand DNA
    • If DNA is not integrated into host genome it will be broken down
  82. Transduction
    • Genetic exchange mediated by a virus
    • Bacteriophage gets copy of bacterial DNA, is replicated, and inserts bacterial DNA into next host cell (rather than virul DNA)
  83. Plasmids
    • dsDNA, circular or linear
    • Episomes- plasmids that become integrated into the chromosome
    • Curing- Eliminates plasmids in host cell using heat
    • Can be passed via conjugation
  84. Conjugation
    • Donor= male / Recipient= female
    • Must have cell to cell contact through pillus
    • Transer single strand (not in circular form)
    • Once one bacteria has plasmid, will eventually transfer to all others