Microbiology Chapter 3.txt

  1. Ecotype
    Subgroups of species that have special characteristics to survive in their ecological surroundings
  2. Biosphere
    That part of the earth where life occurs, including air, soil and water
  3. Homeostasis
    • Maintain a relatively steady internal state
    • Homeo = similar
    • Statis = state
  4. Biofilm
    • Bacterial cells live in communal associations where survival requires chemical communication between cells.
    • The cells become embedded in a matrix of excreted polymeric substances
    • Consists of charged and neutral particles that hold the biofilm together and cement to surfaces
  5. Quorum sensing
    Ability of bacteria to sense their numbers and then communicate and coordinate behavior, including gene expression via signaling molecules
  6. Cell membrane
    AKA plasma membrane
  7. Cytoplasm
    The internal cell environment in which chemical reactions occur
  8. Cytosol
    If all the cell structures are removed from the cytoplasm, cytosol remains and consists of water, salts, ions and organic compounds.
  9. Ribosome
    • An RNA protein machine that cranks out proteins based on the genetic instructions it receives from the DNA.
    • Although the pattern for protein synthesis is identical, structurally bacterial ribosomes are smaller than their counterparts in eukaryotic cells
    • Reader of RNA to make protein
  10. Organelles
    Structurally discrete, often membrane enclosed, sub-cellular compartments that carry out specialized functions. Bacterial cells also have subcellular compartments that are not readily visible or membrane enclosed.
  11. Endomembrane system
    Designed to transport protein and lipids into an out of eukaryotic cells.
  12. Endoplasmic reticulum
    Consists of flat membranes to which ribosomes are attached (rough ER involved in protein and lipid synthesis) and tube like membranes without ribosomes (smooth ER involved in protein and lipid transport).
  13. Vesicles
    Membrane enclosed spheres involved with secretion and storage
  14. Golgi apparatus
    A group of independent stacks of flattened membranes and vesicles where the proteins and lipids coming from the ER are processed, sorted and packaged for transport.
  15. Lysomes
    Somewhat circular membrane enclosed sacs containing digestive (hydrolytic) enzymes and are derived from the Golgi apparatus and in protozoal cells break down captured food materials.
  16. Microcompartments
    Areas of bacteria cells that represent a type of organelle
  17. Cellular respiration
    • All cells convert chemical energy into cellular energy for cellular work.
    • In eukaryotic microbes, this occurs in the cytosol and mitochondria
    • In prokaryotic microbes this occurs in the cytosol and cell membrane
  18. Photosynthesis
    • Conversion of light energy into chemical energy.
    • Some bacteria such as cyanobacteria can do this
  19. Cytoskeleton
    Interconnected system of cytoplasmic fibers, threads, and interwoven molecules that give structure to the cell and assist in the transport of materials throughout the cell. Bacterial cells don't have a cytoskeleton.
  20. Centrosome
    Microtubules that are the main components of the cytoskeleton and originate from the centrosome and microfilaments, each assembled from different protein subunits.
  21. Flagella
    Mechanical force for motility
  22. Cilia
    • Protozoa movement.
    • Bacteria don't have
  23. Prokaryote/Eukaryote Similarities
    • Homeostasis is an organism's ability to maintain a stable internal state
    • Many prokaryotes live in communal associations called biofilms
    • Myxobacteria live in a social community dependent on cell-to-cell interaction and communication
    • Prokaryotes carry out many of the same cellular processes as eukaryotes
    • All organisms have similar genetic organization whereby heredity material is expressed
    • Both prokaryotic and eukaryotic cells have internal compartments
    • Metabolism occurs in the cytoplasm
    • Ribosomes are involved in protein synthesis
    • Both eukaryotes and prokaryotes use flagella for motility, though the flagella differ structurally and functionally in the two groups
    • Many prokaryotes and eukaryotes have a cell wall to help maintain water balance
  24. Prokaryotes and Eukaryotes Distinctions
    • Eukaryotes have membrane-enclosed organelles
    • Protein/lipid transport in eukaryotes is carried out by the endoplasmic reticulum and Golgi apparatus
    • Mitochondria perform cellular respiration in eukaryotes
    • Both eukaryotes and prokaryotes can perform photosynthesis
    • Prokaryotes and Eukaryotes: The Structural Distinctions
    • The eukaryotic cytoskeleton gives the cell structure and transports materials within the cell
  25. Prokaryotes and Eukaryotes Differences
    • Prokaryote
    • No organelles
    • 1 circular chromosome
    • Smaller ribosomes
    • Complex cell wall
    • Eukaryote
    • Organelles
    • More than one chromosome
    • Larger ribosomes
    • No or simple cell wall
  26. Prokaryotic cells contain
    • Cytoplasm
    • Ribosome
    • Chromosome (DNA)
    • Cell wall
    • Cell membrane
  27. Eukaryotic cells contain
    • Centrosome
    • Flagellum
    • Free ribosomes
    • Mitochondion
    • Nuclear evelope
    • Chromosomes (DNA)
    • Ribosomes attached to endoplasmic reticulum
    • Cilla
    • Smooth endoplasmic reticulum
    • Rough endoplasmic reticulum
    • Cytoskeleton
    • Plasma membrane
    • Lysosome
    • Cytoplasm
    • Golgi apparatus
    • Metabolism
    • All the chemical reactions occurring in an organism or cell
  28. Taxonomy
    Taxonomy is the science of classification, involving arranging related organisms into logical categories.
  29. Taxonomic Classification
    • Domain - ie Eukarya
    • Kingdom - ie Animalia
    • Phylum - ie Chordata
    • Class - ie Mammalia
    • Order - ie Primates
    • Family - ie Hominidae
    • Genus - Homo
    • Species - sapiens
    • Subspecies
    • Strain
    • Morphotype
    • Variety
  30. Kingdoms
    • Monera - Prokaryotae, bacteria
    • Protistas - make own food & move
    • Fungi - Don't make their own food
    • Plantae
    • Animalia
  31. Carolus Linnaeus
    In the mid-1700s, Carolus Linnaeus published Systema Naturae, establishing a uniform system for naming organisms
  32. Scientific Organism Names
    Each name includes two words, the genus and the specific epithet
  33. Binomial Classification, Nomenclature
    • Used by Linnaeus
    • Genus species
    • Underline if writing, italics if typing
  34. Classification
    • Uses a hierarchical system
    • Species (least inclusive) to kingdom (most inclusive)
  35. The five kingdom system
    • Monera (Prokaryote)
    • Protista
    • Fungi
    • Plantae
    • Animalia
  36. Who developed the five kingdom system?
    Robert H. Whittaker and Lynn Margulis developed the five-kingdom system, giving bacteria their own kingdom.
  37. List the hierarchy of classification
    • Kingdom
    • Phyllum (division)
    • Class
    • Order
    • Family
    • Species
    • Genus
    • Subgenus
    • Serotype
    • Strain
    • Morphotype
    • Variety
  38. The Three Domain System
    • Bacteria
    • Eukarya
    • Archaea
    • Proposed by Carl Woese based on data from ribosomal RNA sequences
  39. Bacteria taxonomy
    • Distinguishing between prokaryotes
    • Experiments on physical characteristics, biochemistry, serology (antibodies), and nucleic acids can be done to identify microbes
    • Molecular taxonomy is bases on sequences of nucleic acids in ribosomal RNA
    • The dichotomous key can be used identify microbes
  40. Measurements
    • 1000 mm = 1 meter
    • 1000 um = 1 mm - 1 millionth of a meter
    • 1000 nm = 1 um - 1 billionth of a meter
  41. Where can the proper taxonomic classification for Bacteria and Archaea be found?
    • Bergey's Manual of Systematic Bacteriology.
    • The first two volumes of this 5-volume compendium have been published.
  42. What is used to identify medical identifications?
    Bergey's Manual of Determinative Bacteriology
  43. What are the physical characteristics of microbes used for classification?
    • Shape - staining allows us to see the shape
    • Size
    • Growth requirements (Oxygen, Ph, Temp)
    • Staining Reactions
    • Biochemical Characteristics (fermentation of carbs, use of a specific substrate, waste products)
  44. Molecular Taxonomy
    • Based on the universal presence of ribosomes in all living organisms.
    • Ribosomal RNA (rRNA) is the basis for the three domain system (Bacteria, Archaea, Eukarya)
  45. Dichotomous key
    • A popular version is to construct a flow chart where a series of positive or negative test procedures are listed down the page.
    • Based on the dichotomous nature of the test (always positive or negative) the flow chart leads to the next test result.
  46. Size of organisms
    • Protozoa: 100 um
    • Molds: 10 x 40 um
    • Yeasts: 8 um
    • Bacteria: 1 - 5 um (.25-20um)
    • Viruses: 200 - 250 nm*
    • *250nm = .25 um
  47. Light Microscopy
    • Is Used to Observe Most Microorganisms
    • Visible light passes through multiple lenses and through the specimen
    • Light microscopes usually have at least 3 lenses: low-power, high-power, and oil-immersion
    • The lens system must have high resolving power to see the specimen clearly
    • Blue light has a short wave length therefore has more energy
  48. Parts of a microscope
    • Ocular lens
    • Objective lens
    • Stage
    • Condenser
    • Light source
  49. What does a microscope do?
    Increases resolution - the ability to see things that are close to each other.
  50. What does the oil immersion lens do?
    Allows light to travel in a straight line from lens to specimen so that it can be seen clearly. Without the oil, light would bend away from the specimen.
  51. What color light has more energy?
    Blue. It has a shorter wave length
  52. How do you calculate resolving power?
    • Wavelength of light (550nm)/2*numerical aperture of the lens
    • i.e. 550/(2*1.25) = 55/2.5 = 220 nm or .22 um
  53. Magnification and resolution define the limits of what is visible
    The practical limits of an electron microscope is 2nm, 100x better than the resolving power of a light microscope
  54. Index of refraction
    A measure of the light bending ability of a medium
  55. Simple stain technique
    Just add dye
  56. Negative stain
    Stain everything but the cells. Looks like a negative photo
  57. Gram stain - 5 steps
    • Heat fix
    • Crystal Violet (purple) - 60 seconds
    • Grams Iodine (Blue/Purple) - 60 seconds
    • Alcohol wash (either loses stain or remainns Blue/Purple) - 14 seconds
    • Safranin - Gram negative - now orange red. Gram positive remains Blue/Purple - 30 seconds
  58. Acid fast stain
    • For tuberculosis, (mycobacterium) because of the waxy coating that resists other staining
    • Mycobacteria can be stained with carbol-fuchsin in the acid-fast technique
  59. Types of microscopes
    • Dark field
    • Phase contrast
    • Fluorescent
    • Electron - Transmission
    • Electron - Scanning
  60. Dark field microscopy
    • Provides good resolution and often illuminates parts of a specimen not seen with bright field optics
    • Preferred way to study motility of live cells
    • Uses a special condenser lens mounted under the stage.
    • The condenser scatters light and causes it to hit the specimen from the side
    • Only light bouncing off the specimen and into the objective lens makes the specimen visible as the surrounding area appears dark because it lacks background light
  61. Phase Contrast microscopy
    • Can see organisms alive and unstained
    • Typically for yeasts, molds, protozoa
    • Uses a special condenser and objective lenses
    • Splits a light beam and throws rays slightly out of phase
    • The separated beams of light then pass through and around specimen
    • Small differences in the refractive index show up as different degrees of brightness and contrast
  62. Fluorescence microscopy
    • Used in immunology
    • Microorganisms are coated with a fluorescent dye such as fluorescein and illuminated with UV light.
    • UV light excites electrons in fluorescein moving them up to a higher energy level
    • The electrons quickly drop back to original energy levels and give off excess energy as visible light
  63. Fluorescent antibody technique
    • Used to identify an unknown organism
    • Fluorescein is attached to antibodies, the protein molecules produced by the body's immune system.
    • The tagged antibodies are mixed with a sample of the unknown organism
    • If the antibodies are specific for that organism, they will bind to and coat the cells with dye.
    • When subjected to UV light, the organisms will fluoresce.
    • If the organisms fail to fluoresce, the antibodies were not specific to that organism and a different tagged antibody is tried.
  64. Electron microscopy
    • Allowed us to see that bacteria were cellular but their structure was different than eukaryotic cells
    • Electron Microscopy Provides Detailed Images of Cells, Cell Parts, and Viruses
    • Electrons are absorbed, deflected, or transmitted based on the density of structures in the specimen
    • The practical limit of an electron microscope�s resolution is about 2nm
    • Preparation method kills the specimen
    • Grew out of a design made in 1932 by German physicist Ernst Ruska
    • Electrons will flow in a sealed tube if vacuum is maintained to prevent electron scattering
    • Magnets pinpoint the flow onto an object where the electrons are absorbed, deflected, or transmitted depending on the density of the structures within the object
    • When projected on a screen underneath, the electrons form a final image that outlines the structures
  65. Transmission Electron Microscope
    • The transmission electron microscope visualizes structures in ultrathin section of cells
    • Used to view and record detailed structures within the cells
    • Ultrathin sections of the prepared specimen must be cut because the electron beam can only penetrate a short distance
    • 2 million x resolution (professor saw only 1 million x)
  66. Scanning Electron Microscope
    • The scanning electron microscope is used to visualize surfaces of unsectioned objects
    • Developed in late 1960s to see surfaces of objects in the natural state without sectioning
    • Specimen placed in vacuum chamber and thinly coated with gold
    • Electron beam scans across specimen and knocks loose showers of electrons that are captured by a detector
    • Image builds line by line like a TV
    • 100,000x resolution. Best the professor did was 50,000x. Book says 20,000x
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Microbiology Chapter 3.txt
Microbiology Three