micro bio test 3 and 5 study guide

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micro bio test 3 and 5 study guide
2014-02-16 01:03:41
micro bio test study guide

micro bio test 3 and 5 study guide
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  1. Do work
  2. How do we categorize cells according to their requirement for a carbon source?
    • Chemoorganotrophs-obtain energy from oxidation of organic molecules
    • Chemolithotrophs-obtain energy from oxidation of inorganic molecules
    • Photolithotrophs-contain pigments allowing them to use light as an energy source
    • Autotrophs-use carbon dioxide as their carbon source
    • Heterotrophs-require one or more organic molecules for their carbon source
  3. What is an extremophile? In what domain classification do they generally reside?
    Organisms that generally inhabit extreme environments are extremophiles. They are generally Archaea.
  4. What structures/appendages comprise the cell envelope?
    Generally there is a phospholipid bilayer that allows for hydrophobic and hydrophilic components to function together.
  5. Why does the structure of a typical prokaryotic cytoplasmic membrane pose a problem for ions and large polar molecules?
    The permeability barrier prevents leakage and functions as a gateway for transport of nutrients into and wastes out of the cell. The membrane is also a phospholipid bilayer so it has hydrophilic heads on the outside and hydrophilic tails on the inside.
  6. What are three basic functions of a typical cytoplasmic membrane?
    The membrane serves as a permeability barrier, preventing leakage and functions as a gateway for transport of nutrients into, and wastes out of the cell. It acts as a protein anchor; it is the site of many proteins that participate in the transport, bioenergetics, and chemotaxis. It also acts to conserve energy; it is the site of generation and the use of the proton motive force.
  7. What would be the problem if simple diffusion represented the only means for nutrient entry?
    There would not be enough nutrients able to enter the cell, because the proton motive force would be exhausted.
  8. Why do transporters determine “the saturation effect” when considering nutrient import into the bacterial cell?
    Many substances cannot diffuse into the cell, so transport is used frequently, so it is highly specific and highly regulated.
  9. What three classes of prokaryotic membrane transport did we discuss in lecture? Where does the energy for transport come from in each system?
    • Simple transport: driven by the energy in the proton motive force
    • Group translocation: chemical modification of the transported substance driven by phosphoenolpyruvate
    • ABC transporter: periplasm binding proteins are involved and energy comes from ATP.
    • The energy from each transport comes from the proton motive force or ATP.
  10. What common secondary structures do membrane transport systems commonly exhibit?
    Beta pleated sheets
  11. Why is Gram negative molecule transport generally more complex than Gram + molecule transport?
    Gram positive just has one thick layer of peptidoglycan; however gram negative has an inner and outer membrane, and space in between (periplasm) so there is more maneuvering involved with gram negative bacteria.
  12. What is the function of a microbial cell wall? What are the key differences between the two basic bacterial cell walls: Gram + and Gram -.
    Cell walls provide structural integrity to protect cells from lysis. The major differences between the two walls are the sole thick layer of peptidoglycan in gram positive bacteria and the thin inner membrane, outer membrane, and periplasm in gram negative bacteria.
  13. How can LPS be used as a means of identification at the bacterial species level? (Hint – think about the strain E. coli 0157::H7)
    Lipopolysaccharides (LPS) are used to look fro Gram negatives. It replaces much of the outer phospholipid layer in the bacteria and when the cell lyses endotoxin is released.
  14. What are some functions of fimbriae? Pili?
    They are hollow cylinders of protein. They help with conjugation, adhesion, and twitching motility.
  15. How are flagella characterized? (Hint: think location and distribution on the bacterial cell)
    Flagella are characterized by the location and distribution on bacterial cells.
    • Polar: contains single flagella
    • Peritrichous: contains multiple flagella all around
    • Lophotrichous contains many flagella in one location
    • Amphitrichous: contains two flagella opposite from each other
  16. What type of motor powers the flagellar rotation? From where does it get its energy? Is the rotation a static process or a dynamic one?
    Motility proteins help power flagella. The motion is circular and the energy comes from the movement of protons across the membrane. It takes around 1000 protons for 1 turn of the rotor. Rotation is a dynamic process.
  17. What is the difference between a “run” and a “tumble”? How does this determine directed movement?
    Runs are directed movements and Tumbles are Brownian motion movements. This shows the speed of the flagella and depending on the environment the ratio of runs: tumbles.
  18. What does it mean to say that bacterial motility is determined by a temporal, not a spatial concentration gradient?
    Temporal sensing refers to sensing given periods of time, whereas as spatial sensing is sensing the space around.
  19. How does taxis differ in response to an attractant? A repellant?
    Movement towards an attractant is increased, increasing the ratio of runs: tumbles. Movement towards a reactant is decreased, decreasing the ratio of runs: tumbles.
  20. What is the function of a gas vesicle? A carboxysome? Magnetosome? Storage inclusions?
    A gas vesicle affects the buoyancy of a bacteria. It allows the bacteria to be at different levels in liquid. Carboxysomes fix carbon in the process of photosynthesis. Magnetosomes contain the mineral magnetite which facilitates magnetotaxis. Storage inclusion is storing energy or other carbon sources.
  21. What is an endospore? What two genera of endospore forming bacteria have been well studied? Why?
    Endospores are differentiated cells resistant to heat, harsh chemicals and radiation. They are the dormant stage of the bacterial life cycle.  The 2 genera well studied are Bacillus and Clostridium. They have been studied extensively because the germination and activation are rapid taking a few minutes each, and the sporulation is 8 hours.
  22. How do bacteria divide? What are the three basic steps of this particular process? What term is used to describe the time it takes for this process to occur?
    Bacteria divide through binary fission. 1st the cell elongates, then the septum forms, and the completion of the septum forms the cell walls thereby separating the two cells. Generation time is the time required for microbial cells to double in number.
  23. What are some factors that affect the rate at which a particular species will divide?
    The generation time is highly variable and is dependent on nutrition, genetics, and temperature.
  24. What is a divisome? Why are the proteins that make up a divisome called Fts proteins?
    A divisome is the cell division apparatus made up of interacting Fts proteins. Fts stands for filamentous temperature sensitive, which describes the properties of the cells that have mutations in the genes that encode Fts proteins.
  25. FtsZ mutant?
    The cell would not divide properly, if at all.
  26. MinC mutant?
    The divisome would not form at the cell center.
  27. MinD mutant?
    The divisome would not form at the cell center.
  28. MinE mutant?
    The divisome would not form at the cell center.
  29. FtsK mutant?
    The cell would not divide properly, if at all.
  30. FtsI mutant?
    The cell would not divide properly, if at all.
  31. MreB mutant?
    The shape of the cell would be altered.
  32. Why would a compound that acts on FtsZ be of medical relevance?
    It is a universal cell division protein and by understanding the bacterial division process it could lead to the development of new drugs that target specific steps it he growth of pathogenic bacteria.
  33. How does crescentin determine the shape of Caulobacter crescentus?
    Crescentin complexes with MreB and forms filments along the concave surface thereby affecting shape.
  34. How does MreB determine the sites for “new” peptidoglycan synthesis?
    The helical structures formed by MreB can rotate within the cytoplasm of a growing cell. Newly synthesized peptidoglycan is associated with MreB helices where it connects to the cytoplasmic membrane, so this allows for growth along the x-axis of the cell.
  35. How does the action of autolysin contribute to peptidoglycan synthesis?
    Autolysin creates gaps in cell walls to add new material.
  36. What would be the problem with increased autolysin activity in the absence of peptidoglycan synthesis?
    Too much autolysin activity could cause autolysis or cell lysis.
  37. What is the mode of action of penicillin? Why can it be bacteriostatic and bacteriocidal depending upon its concentration? In other words why can it inhibit cell growth at certain concentrations and also cause cell death at higher concentrations?
    Penicillin inhibits transpeptidation. At certain concentrations it allows for proteins to lose their catalytic activity, but with the continued activity of autolysins too much penicillin can cause cell bursts.
  38. How is new peptidoglycan synthesis different in rod shaped cells versus spherical shaped cells?
    In most cocci, cell walls grow in opposite directions outward from the FtsZ ring whereas the walls of rod-shaped cells grow at several locations along the length of the cell
  39. What is Lysozyme?  How does it affect the bacterial cell wall? How does the mode of action of Lysozyme compare to penicillin’s mode of action?
    Lysozyme is a protein tha cleaves glycosidic bonds between N-acetylglucosamine and N-acetylmuramic acid in peptidoglycan, thereby weaking the wall. Water can enter and cause lysis.
  40. What are the four phases of growth that occur in a batch culture?
    Lag phase, exponential phase, stationary phase, and death phase are the phases of growth in a batch culture.
  41. What is the theory behind the “phase of prolonged decline”? Which enzyme needs to be expressed by regulated bacterial cells during this phase?
    The idea behind the “phase of prolonged decline” is how cells die at a lower rate than the rate of exponential growth so slowly cell populations will decrease in size.
  42. Why is a lag phase of bacterial growth necessary? Why can it vary?
    Lag phase essentially gets the biochemical machinery of the cell to become active. The older the cells are the longer they stay in lag phase. If cells move to an environment similar to their old environment, lag phase will become shorter.
  43. What induces entrance into the stationary phase of growth?
    This occurs when an essential nutrient of the culture medium is used up entirely, or a waste product of the organism accumulates in the medium and inhibits growth.
  44. Why are growth curves plotted in a semilogarithmic manner?
    The growth curve is plotted using cell number vs. time, so as time slowly increases, cells slowly increase and then rapidly increase.
  45. Why is exponential growth expressed as a geometric progression of two?
    During cell division one cell becomes two.During the time that it takes for this to occur, both cell number and mass double, so that is why exponential growth is shown as  a geometric progression of 2.
  46. What is a chemostat? How are both growth rate and growth yield controlled both independently and simultaneously in a chemostat?
    A chemostat is a device that can control growth rate and cell density simultaneously.  The growth rate and growth yield can be controlled by the dilution rate, which is the rate at which fresh medium is pumped in and spent medium is removed ,and the concentration of a limiting nutrient present in the sterile medium entering the chemostat vessel.
  47. What is the Great Plate Count Anomaly?
    Microscopic counts of natural samples typically reveal more organisms than are recoverable on plates of single culture medium. This is how plate counts can be highly unreliable when used to assess total cell numbers of natural samples.
  48. What is the difference in the serial dilution and plating method when spread plates versus pour plates are used?
    For serial dilutions less volume of a diluted culture is generally used in compared to a pour plate and with the spread plate the culture is placed on top of the agar, but with pour plates the culture is mixed in with the agar.
  49. How can OD values relate to the overall cell number present in a particular culture?
    Since cells are able to scatter light, their turbidity can be determined using optical density. With more cell density, there is a higher OD value.
  50. What are the cardinal temperatures for a particular organism?
    For every organism cardinal temperatures exist. There is a minimum temperature below which growth is not possible, an optimum temperature at which growth is most rapid, and a maximum temperature above which growth is not possible.
  51. How can we characterize microbes in relation to temperature?
    • Psychrophiles: grow in low temperatures
    • Mesophiles: grow in midrange temperatures
    • Thermophiles: grow in high temperatures
    • Hyperthermophiles: grow in very high temperatures
  52. What are some characteristics of microbes that grow at low temperatures?
    Psychrophiles grow at low temperatures and they contain several cold-active enzymes that have higher amount of alpha-helix and lesser amount of beta-sheet secondary structure than do enzymes that are inactive in the cold. This allows for more flexibility for catalyzing their reactions at cold temperatures.
  53. What are some characteristics of thermophilic organisms?
    Heat stability is bolstered by an increased number of ionic bonds between basic and acidic amino acids and often have hydrophobic interiors. There are also modifications in the cytoplasmic membrane to ensure heat stability.
  54. How is bacterial metabolism affected by pH?
    It depends on the bacteria, but generally metabolism of the bacteria will slow significantly and can sometimes lead to death.
  55. What is a halophile?
    A halophile is a salt-loving bacteria.
  56. How can we characterize microbes according to their oxygen requirements?
    • Obligate Aerobes: Grow in oxygenated conditions
    • Anaerobes: Cannot grow in oxygen, and need another source for growth
    • Facultative Aerobes: Can grow in either oxygenated or non-oxygenated conditions, but thrive in oxygen
    • Microaerophiles: Grow in oxygenated conditions, but less than the atmospheric concentration
    • Aerotolerant: Can grow in oxygenated and non-oxygenated conditions, but thrive in non-oxygenated
  57. Why can growth in the presence of oxygen be detrimental for aerobic bacteria? Anaerobic bacteria?
    Aerobes can be sensitive to high concentrations of oxygen, so generally if there are concentrations higher than atmospheric levels they will cease to grow or die. Anaerobic bacteria are sensitive to oxygen levels so they generally have trouble growing and can even die.
  58. oligate aerobe
    sod and catalase
  59. Facultative Anaerobes
    sod and catalyase
  60. Obligate/strict Anaerobes
    no sod no catalyase
  61. Aerotolerant
    no sod no catalase
  62. Microaerophiles
    yes sod but no catalase