microbiology unit 1

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amauerba
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294573
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microbiology unit 1
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2015-02-02 23:53:27
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microbioloy review unit
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microbiology unit 1 chapters 1,2,3,5,7,8
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  1. what we know and what we don't know
    • we do know that microbes are everywhere
    •       - 10times as many microbes as cells on/in the adult human
    •             -approximately 1.5 kg of your weight
    • we only know 1%-5%of all microbes
    •       - we can only culture 1-5% the rest we can cannot
  2. how do microbes impact our daily lives
    • microbes has greatly impacted ( good and bad) human history
    •       -food availability
    •              - destroy agricultural products
    •                     1/3 of global food  supply destroyed yearly by microbes
    •              - improve agricultural products
    •              - generate or preserve food
  3. microbes have impacted human populations and shaped our immune response
    • disease
    • - black plaque killed 25%of population of europe
    • -polio depicted on wall of the tomb of the pharaohs
    • -small pox decimated the Aztecs
    • -cholera recently killed more than 5000 people in Haiti
  4. what is microbiology?
    • 1. the study of organisms too small to be seen clearly with the unaided eye
    • 2. know a fair amount about the 1%-5% of all microbes
    •    - pathogens
    • 3.now there is a big push to find out about the other 95% to 99%5 and what they are doing
  5. prokaryote
    • -prenucleus
    • - in general: no membrane bound nucleus, or subcellular organelles
  6. viruses
    are acellular
  7. eukaryote
    • - true nucleus
    • - have membrane bound nucleus
    • - have subcellular organelles
    •       - some protest don't always have the full complement
    •        - parasites don't need them since they feed/steal from others
  8. planctomycetes
    • -are bacteria
    • - classified as bacteria due to
    •         - 16s sequence 
    •         - membrane structure
    • - some have a membrane bound nucleus
    • -some have a specialized organelle
  9. viruses are infected by other viruses
    • - mamavirus
    •       - infect amoebas, but also recovered from people
    •            - may trigger rheumatoid arthritis 
    • -mamavirus many be infected by another virus
    •        -sputnik is a viriophage
  10. who are the members if the microbial world?
    • viruses- acellular obligate parasites
    •   - exist in nature but cant reproduce without a host
    • prokaryotes: bacteria
    •   - no membrane bound nucleus or organelles
    •   - genome: one circular double-stranded DNA molecule
    •          -there are exceptions
    • Achaea: methanogens, halophiles(extremophiles)
    •   - no all exist in extreme environments
    • Eukaryotes: algae, fungi, protist
    •   -membrane bound nucleus
    •   - organelles
  11. how are prokaryotic and eukaryotic microbes assigned to taxonomic groups?
    • by 16s rRNA gene sequences
    • -"true " bacteria
    • - archaea are not bacteria but are considered prokaryotes
    • - eukarya- protest, fungi etc.
    • mitochondria have their own ribosomes: 16s
    • Eukaryotic nucleus has its own ribosomes: 18s
  12. are microbes fund in pure culture out in nature
    • -no .... life is s composite that is built upon symbiotic relationship
    • -different anatomical sites on/within the human body contain a universe of different microbes
    • -many of these microbes are specifically adapted to live in these sites and do not exist elsewhere
    •       -many of them are unculturable
    • -likewise a number of eukaryotic microbes contain prokaryotes that "presumably" perform an important function
  13. eukarya-prokarya  composites:
    • -Endosymbiont  theory
    • how did eukaryotes arise?
    •   -DNA similar to archaea's
    • - mitochondrial, chloroplast DNA
    •    similar to bacterial DNA
    • Endosymbiont Theory:
    • mitochondria WERE bacteria
    • chloroplasts WERE cyanobacteria
    • - infected or eated by other species
    • -ended up living together inside
    •      -endo-sym-biosis

  14. example : other Eukarya-prokarya composites
    • -protest that are moves by bacteria
    • -other bacteria live within the protist
    • -this protest is composed of 5 different microbes
  15. how did microbiology start?
    • the idea that disease was caused by invisible  creatures existed long before microorganisms were observed
    •   -danger of dog bites that could lea to rage and fear of water recognized in Mesopotamia
  16. the origins of the study of microbiology
    • 2 ideas led tot he development if microbiology as a scientific discipline
    • 1. cell theory
    • -attack on the theory of spontaneous generation
    • 2.germ theory
    • -awareness of the nature of infectious diseases
  17. Van Leeuwenhoek
    • -microscope started controversy
    • invented another small microscope (1677)
    • - first to describe bacteria
    •    - teeth scraping, rain water, food
    •    - motile organism
    • - findings heightened controversy surrounding spontaneous generation
  18. Cohn
    • - heat-resistant forms of bacteria
    •    - bacillus endospores
  19. Pasteur
    • -many accomplishments
    • -famous swan-necked flasks
    •       -showed microbes were airborne
    • -microbiology; pasteurization of food
    • -immunology; vaccine:rabies
    •        - 13 injections over 10 days saved the life of 9 year old joseph meister
  20. Koch
    • -pure culture, postulates, and germ theory
    •   - pure culture of "causative agent" of tuberculosis
    •    - Koch's postulates lead to germ theory
  21. Pasteur's swan necked flasks
    • - swan necked flasks: offered proof of biogenesis
    • -showed that cells do not grow in liquid until introduced from the outside
    • - final disproof of spontaneous generation
    • -led to development of cell theory
  22. germ theory of disease
    • Pasteur's theory:
    • - transmission of germs causes disease
    • - worked with rabies and rabits
  23. Koch's Postulates
    • -"proved Pasteur's theory that microbes cause disease: worked perfectly for Anthrax
    • - provided means of testing the hypothesis
    •     - "does this germ cause that disease?"
  24. Koch's Postulates criteria
    • must meet 4 criteria
    • 1. microbe always present in disease individual (human or animal)
    •      - microbe absent in healthy individaul
    • 2. microbe grows in pure culture
    •       - no other microbes grow
    • 3. introduce pure microbe into healthy animal
    •      - animal becomes sick
    • 4. same microbe re-isolated from now sick animal
  25. Koch's Postulates issues
    • -postulates worked nicely for anthrax
    • -the postulates were developed using animals not humans

    •  there are expectations to all 4 criteria
    • exception 1:healthy carriers
    • - MRSA, Typhoid
    • exception2: may be normal flora
    • - strep. pneumonia
    • exception 3: ethics
    • -human pathogens.... can you challenge humans
    • exception 4: first 3 exceptions preclude number 4
  26. modification of Koch's postulates
    • presence of virulence factors
    •    - bacterial gene products/components that promote disease
    •       examples
    •            -antibiotic resistance gene
    •            - toxin gene
  27. the importance of controlling disease
    • - microbes grow to high densities very quickly
    • - stop germ transmission, stop spread of disease
    • major development in the control of disease
    • vaccination (cowpox/small pox)
    • antiseptics (antiseptic surgery)
    • sanitation: drinking water and sewage treatment
    • antibiotics (penicillin)
  28. microbial ecology
    • - microbes comprise largest biomass (C,N,P)-microbes cycle most elements on earth
    •   -nitrogen cycle and carbon cycle
    • -significant control over ecosystems in nature
    • -significant control over ecosystems in and on the human body
    •    -bacteriotherapy
  29. genetics and recombinant  technology
    • -molecular genetics depends on bacteria
    •    -concept of "gene" first proposed for bacteria
    •    - DNA structure
    •    - genetic code
    •    - transcription and translation
    •    - restriction enzymes
    •    - recombinant DNA
    •    - cloning 
    •    - PCR reactions
    • - E.coli has the best understood genome

    •  basic model, used in biotechnology; recombinant technology
    •    - medicine, agriculture, food production, energy production , bioremediation
  30. bacterial genomic: the power of virtual
    • - once the genome of bacteria had been sequened it can be annotated or "mapped"
    • - computer software enables researchers to find "candidate" genes (virtual vs. real)
    • - the candidate genes can be used to infer different metabolic pathways, transport systems and other physiological features

    • 1. beneficial processes: moved into harmless microbes or more easily manipulated microbes, to produce beneficial products
    • 2. harmful processes: identified and studied in order to find ways to inhibit or destroy the process thereby inhibiting or destroying the microbe
  31. bacterial genomic : example
    • - syphilis can not be cultured outside of the human host (metabolically crippled)
    • - the entire genome has been sequenced
    • -proposed genes (based only on sequence) show that 5% of genes are transport genes
    • - researchers may now be able to generate a vaccine against surface transport proteins
  32. who dealt the final blow to the theory of spontaneous generation?
    pasteur
  33. who first identified bacterial endospores?
    van Leeuwenhoek
  34. do humans have a 16s ribosomal sequence?
    No
  35. are all prokaryotes missing a nuclear membrane?
    no there are expections
  36. who theorized that disease was caused by the transmission of germs?
    Pasteur
  37. what are 2 ways to prevent the spread of disease?
    • 1.vacciantions
    • 2. antiseptics/disinfectants
    • 3. sanitation
    • 4.antibiotics
  38. true or false: 95% to 99% of microbes are non-culturable
    true
  39. what are "carriers"?
    an infected individual who is a potential source of infection for others and plays an important role in the epidemiology of a disease
  40. what does "normal flora " mean?
    Microorganisms that normally reside at a given site and under normal circumstances do not cause disease
  41. true or false: all microbes residing on/in the human body are culturable
    true
  42. what were/are the 4 major developments in response to the germ theory
    Koch's Postulates, Developments in the control of disease, Bacterial Genomics
  43. who proved germ theory
    Koch
  44. in an "extreme" environments would you expect to find more  or less diversity
    more
  45. Staphylococcus aureus is a
    common inhabitant of human skin, yet this microbe is an opportunistic pathogen
    that can cause disease.  Is this microbe
    part of the normal flora?  Yes or No
    yes
  46. What is the major entryway of carbon into the food chain? What is major process that
    “fixes” carbon into biomass?
    • 1. photosynthesis
    • 2. nitrogen cycle
  47. True or False. Orthohepadna virus, which is the causative agent of Hepatitis B, and only causes disease in humans, was
    identified using Koch’s postulates.
    true
  48.  Burkholderia is a BSL 3 (biosafety
    level 3) pathogen and is especially dangerous to cystic fibrosis patients.  However, this microbe is also able to breakdown cancer causing agents.  How could you use genomics to harness the beneficial processes that this microbe has?
  49. units of measurement
    • -the unaided eye can not visualize microbes smaller than 0.2mm
    • - meausurements in general:
    •     -viruses: nm
    •     - bacteria: um
    •     - protest :um and larger
  50. microscopes have what kind of lenses?
    • convex lenses collect, bend and focus light rays
    • - required to produce enlarged images of small objects
  51. lenses and the bending of light
    • objective lenses:
    •  1.  4x - low power
    •  2.  10x
    •  3.  40x - high power
    •  4. 100x - oil immersion
  52. If  I plate 0.1ml 0f a sample and discover 20 cfu the correction factor and count for the sample is?
  53. If I plate 0.5ml of a sample and discover 25 cfu the correction factor and count for the sample is?
  54. Which of the following describes a microbe that requires growth factors for growth?
    fastidious
  55. You wish to obtain isolated colonies from a sample. You can use which of the following?
    A)spread plate
    B)streak plate
    C) all choices
    D)  pour plate
    C) all choices
    (this multiple choice question has been scrambled)
  56. You want to select for an organism that lives in anoxic environment(swamp) so it is critical that you use which of the following?
    A) a growth chamber devoid of media
    B) selective media
    C) enriched media
    D) deferential media
    C)enriched
    (this multiple choice question has been scrambled)
  57. Define the following:
    a) chemoheterotroph
    b)chemoautotroph
    c)photoheterotroph
    d) photoautotroph
    • a)chemoheterotroph-an organism that uses organic compounds as sources of energy, electrons and carbon for biosynthesis
    • b)chemoautotroph- An organism that depends on inorganic chemicals for its energy and principally on carbon dioxide for its carbon
    • c)photoheterotroph- a microorganism that uses light energy, organic electron sources, and organic molecules as a carbon source
    • d)photoautotroph-an organism that uses light energy, an inorganic electron source (e.g., H2O, H2, H2S) and CO2 as its carbon source.
  58. Which of the following can you use to enumerate and isolate CFUs from and unknown sample?
    A) streaking for isolation
    B)serial dilutions followed by streaking for isolation
    C) pour or spread plate without serial dilutions
    D) serial dilutions followed by spread or pour plating
    D) serial dilutions followed by spread or pour plating
    (this multiple choice question has been scrambled)
  59. When testing compound using growth response assay why are the bacteria not diluted?
    so that you can generate a  standard growth curve with a known quantity of bacteria and so that I can be used for comparison when testing the system
  60. 4 Major Nutritional types
    • a) chemoheterotroph
    • b)chemoautotroph
    • c)photoheterotroph
    • d) photoautotroph
  61. the 5th nutritional types
    mixotrophic bacteria-alter their metabolic requirements in response to environmental changes

    • * combine autrophic and heterotrophic process as need
    • *allows them to survive and grow in the environment outside the host
  62. macronutients
    N, K, Ca, Mg, P and S
  63. micronutrients
    Cl, Fe, B, Mn, Zn, Cu, Mo, and Ni
  64. trace elements
    Al, Cr, Li
  65. assimilation
    assimilation-mean obtained from a preformed source
  66. fastidious organism
    fastidious organism- require many growth factors when cultivated in lab

    *niche and microbe's genetic capabilities determine type and amount of growth factors needed
  67. Fe
    • Fe: cytochromes
    • - anaerobic environment- soluble ferric form
    • -aerobic environments- insoluble ferric form
    •     - many microbes have "siderophores" which are used to assimilate insoluble iron in aerobic environments
  68. Magnesium
    • - stabilizes cell structures
    •    - ribosomes, membranes nucleic acids
    •    - required by some enzymes for activity
  69. calcium
    • -required for spore formation
    •    - endospores ( stabilizes DNA during desiccated state
  70. sodium
    • - required by extremophiles and marine microbes
    •     - vibrio cholera ( etiologic agent of cholera'
    •     - similar to marine vs. freshwater fish
  71. siderophores
    • -secreted by the cell, bind insoluble Fe, complex taken back into cell , Fe released in soluble
    • form
    • - siderophores produced by pathogens are capable of "stealing" Fe from host transferrins and lactoferrins
    • -iron siderophores may also take-up other metals that are similar to Fe
  72. agar
    • solidifying agent; complex carbohydrate; kelp
    • - generally not metabolized by microbes
  73. defined or synthetic media
    exact chemical composition and concentrations known
  74. undefined or complex media
    • exact chemical composition and concentration unknown
    • - most media car complex thus contain one or more ingredients of unknown composition (molecular formula)
  75. synthetic (defined) vs. complex (undefined) media
    • - E.coli- defined
    • - leuconostoc fastidious- defined
    • - leuconostoc and E.coli -complex or undefined
  76. general media
    • supports growth of many organism
    • - nutrient broth/agar, Tryptic soy broth/agar
  77. enriched media
    • encourages growth of fastidious organisms
    • - fastidious: require complex media for growth
    • -yeast extract, blood or serum often added for pathogens
    •      -mimics nutrients and growth factors found in host
  78. selective media
    • favors growth of some, inhibits others
    • - Gram negative vs. gram positive
    • -salt tolerant vs. non-salt tolerant
  79. differential media
    • test for metabolic abilities
    • -often contains a pH indicator
    •     - ability to ferment a particular substrate(s)
    •     - ability to form particular patterns
    •  *many types of media can act as a combination of enriched, selective and/or differential*
  80. colony morphology and growth
    • morphology- shape, appearance, color, texture of colony is often species specific
    •    - does the bacteria produce a pigment or shine
    •    - does the growth show swarming effect
  81. pure culture
    a population of identical cells
  82. colony
    • is a population of cells arising  from a single or clump of cells
    •    - called a colony-forming unit (CFU)
  83. 3 basic methods: all require aseptic technique
    • - streak plate- isolation
    • - spread plate - isolation and enumeration( dilutions used)
    • - pour plate - isolation and enumeration( dilutions used)
  84. streak plate
    • a loop is required to streak the inoculum onto the plate
    •    - loop is sterilized before sampling innoculant
  85. spread plate
    • -isolation and enumeration
    • - sample is serially diluted and then inoculum of each dilution is spread over the surface of the plate
  86. pour plate
    • - isolation and enumeration
    • - sample is serially diluted. specified amounts o each dilution then placed in petri and mixed with molten agar

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