MicroBiology Chapter 3 (V2)

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MicroBiology Chapter 3 (V2)
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MicroBiology Chapter 3 (V2)
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  1. Define: ABC (ATP-bindign cassette) Transport System
    a membrane transport system consisting of three proteins, one of which hydrolyzes ATP; the system transports specific nutrients into the cell
  2. Define: Basal body
    the “motor” portion of the bacterial flagellum, embedded in the cytoplasmic membrane and wall
  3. Define: Capsule
    a polysaccharide or protein outermost layer, usually rather slimy, present on some bacteria
  4. Define: Chemotaxis
    directed movement of an organism toward (positive chemotaxis) or away from (negative chemotaxis) a chemical gradient
  5. Define: Cytoplasmic Membrane
    the permeability bar- rier of the cell, separating the cytoplasm from the environment
  6. Define: Dipolinic Acid
    a substance unique to endospores that confers heat resistance on these structures
  7. Define: Endospore
    a highly heat-resistant, thick- walled, differentiated structure produced by certain gram-positive Bacteria
  8. Define: flagellum
    a long, thin cellular appendage capa- ble of rotation and responsible for swimming motility in prokaryotic cells
  9. Define: Gas Vesicle
    gas-filled cytoplasmic structures bounded by protein and conferring buoyancy on cells
  10. Define: Gram-negative
    a bacterial cell with a cell wall containing small amounts of peptidoglycan, and an outer membrane containing lipopolysaccharide, lipoprotein, and other complex macromolecules
  11. Define: Gram-positive
    a bacterial cell whose cell wall consists chiefly of peptidoglycan; it lacks the outer membrane of gram-negative cells
  12. Define: Group Translocation
    an energy-dependent transport system in which the substance transported is chemically modified during the process of being transported by a series of proteins
  13. Define: lipopolysaccharide (LPS)
    a combination of lipid with polysaccharide and protein that forms the major portion of the outer mem- brane in gram-negative Bacteria
  14. Define: Magnetosome
    a particle of magnetite (Fe3O4) enclosed by a nonunit membrane in the cyto- plasm of magnetotactic Bacteria
  15. Define: Morphology
    the shape of a cell—rod, coccus, spirillum, and so on
  16. Define: Outer Membrane
    a phospholipid and polysaccharide containing unit membrane that lies external to the peptidoglycan layer in cells of gram-negative Bacteria
  17. Define: Peptidoglycan
    a polysaccharide composed of alternating repeats of N-acetylglucosamine and N-acetylmuramic acid arranged in adja- cent layers and cross-linked by short peptides
  18. Define: Periplasm
    a gel-like region between the outer surface of the cytoplasmic membrane and the inner surface of the lipopolysaccharide layer of gram-negative Bacteria
  19. Define: Peritrichous Flagellation
    having flagella located in many places around the surface of the cell
  20. Define: Phototaxis
    movement of an organism toward light
  21. Define: Pili
    thin, filamentous structures that extend from the surface of a cell and, depending on type, facilitate cell attachment, genetic exchange, or twitching motility
  22. Define: Polar Flagellation
    having flagella emanating from one or both poles of the cell
  23. Define: Poly-B-hydroxybutyrate (PHB)
    a common storage material of prokaryotic cells consist- ing of a polymer of β-hydroxybutyrate or another β-alkanoic acid or mixtures of β-alkanoic acids
  24. Define: S-layer
    an outermost cell surface layer com- posed of protein or glycoprotein present on some Bacteria and Archaea
  25. Define: Simple Transport System
    a transporter that consists of only a membrane-spanning pro- tein and is typically driven by energy from the proton motive force
  26. Define: Teichoic Acid
    a phosphorylated polyalcohol found in the cell wall of some gram-positive Bacteria
  27. Define (or draw) the major morphologies:

    1. Coccus
    2. Rod
    3. Spiral
    4. Spirillum 
    5. Spirochete
    6. Vibrio
    • Coccus: spherical or ovoid
    • Rod or bacillus: cylindrical
    • Spiral: rods that twist
    • Spirillum: rod twists or spirals
    • Spirochete: long, helically coiled (spiral-shaped) cells
    • Vibrio: half moon (bottom)
  28. Define that various clusters Cocci can present
    • Diplococcus: divide in 1 plane & stay together for 1 division; pairs
    • Streptococcus: divide in one plane & remain together for many divisions; chains
    • Staphyloccus: divide in many planes and remain attached; like bunch of grapes
    • Tetracocci: 1 plane & perpendicular plane
    • Sarcinae: like tetra & plane cross sections behind; cuboidal packets

  29. What sort of size variance can be seen in cells?
    Prokaryotes vary in size from cells as small as about 0.2um in diameter to those more than 700um in diameter
  30. What is the relationship between a cell’s size and it’s metabolism?
    The metabolic rate of a cell varies inversely with the square of its size
  31. If a prokaryotic cell has a larger surface area, is it more or less efficient in taking up nutrients & expelling waste? Why?
    • The larger the prokaryotic cell, the less efficient it will be at taking up nutrients and expelling waste.
    • For very large cells nutrient uptake eventually limits metabolism to the point that the cell is no longer competitive with smaller cells. This is because transport rates are a function of the amount of membrane surface area available in comparison to volume
  32. Describe why a larger prokaryotic cell surface is less efficient at metabolsim (Demonstrate this mathematically!)
    Because a cell’s growth rate depends, among other things, on the rate of nutrient exchange, the higher S/V ratio of smaller cells supports a faster rate of nutrient exchange per unit of cell volume compared with that of larger cells. The volume of each cell is a function of the cube of it's radius (V= 4/3r3), while its surface area is a function of the 32 square of the radius (S = 4r2). Therefore, the S/V ratio of a spherical coccus is 3/r. Thus, as a cell increases in size, its S/V ratio decreases.

  33. Characterize the molecular structure and function of phospholipids
    A phospholipid two fatty acid chains esterified to a glycerol head. The fatty-acid chains display hydrophobic properties, while the glycerol-phosphate head displays hydrophilic properties. The function of phospholipids is to form the cytoplasmic membrane, separating the cytoplasm from the cell’s environment.

  34. How do the ester bonds of a phospholipid form?
    These ester bonds form by combining the alcohol group on glycerol and the carboxyl group of fatty acid (two) or phosphoric acid, resulting in a loss of an H20 molecule
  35. What is the average width of a cell’s cytoplasmic membrane?
    6 - 8nm wide
  36. Is the cytoplasmic membrane rigid?
    Although in a diagram the cytoplasmic membrane may appear rather rigid, in reality it is somewhat fluid, having a consistency approximating that of a low-viscosity oil.
  37. Describe Sterols and where they are found
    Sterols are rigid planar molecules & the association of these with the membrane serves to stabilize its structure and make it less flexible (fatty acids more flexible)

    Eukaryotes have sterols in their membranes (5-25%) while these are usually absent in prokaryotic Bacteria
  38. What molecule found in bacterial cells stabilize their membrane? What does it resemble that is found in eukaryotes?
    • Hopanoids are a stabilizing molecule found in bacterial membranes
    • These somewhat rigid planar molecules are structural analogs of sterols, compounds that strengthen the membranes of eukaryotic cells, many of which lack a cell wall
  39. What molecule similar to sterols can be found in Bacterial membranes?
    Molecules similar to sterols, called hopanoids (such as diplotene), are present in the membranes of many Bacteria and may play a structural role.
  40. What are the two main types of membrane proteins
    • Integral Membrane Proteins and Peripheral Membrane Proteins
  41. Describe Peripheral Proteins
    • (extrinsic proteins) They are not embedded in the membrane, but nevertheless are still associated with the membrane surface
    • Some are easily removed with changes in pH, ionic strength, e.t.c.
    • Typically found on surface and some may be bound to integral proteins
    • Some are lipoproteins and have been shown to have a lipid tail on the amino terminus of protein that serves to anchor one portion of protein to the membrane
  42. Describe Integral Proteins
    • (intrinsic proteins) Are tightly bound and are fully embedded in the membrane
    • Many integral proteins span the bilayer and have surfaces exposed on both the inside and outside of the cell.
    • These must have hydrophobic external surfaces in the regions of the protein that make close contact with the highly nonpolar fatty acid chains & hydrophillic regions that associate with the hydrophillic external and internal environments.
    • Thus, integral proteins are ampipathic (they display both hydrophobic and hydrophillic regions)
    • Not easily removed.
    • Other proteins have one portion anchored in membrane & extramembrane regions pointing into or out of cell.
  43. How are Archaeal membranes different from eukaryotic membranes?
    • In contrast to the lipids of Bacteria and Eukarya in which ester linkages bond the fatty acids to glycerol, the lipids of Archaea contain ether bonds between glycerol and their hydrophobic side chains
    • Archaeal lipids lack true fatty acid side chains and instead, the side chains are composed of repeating units of the hydrophobic five-carbon hydrocarbon isoprene
    • Many archaeal lipids also contain rings within the hydrocarbon chains
    • The cytoplasmic membrane of Archaea can be constructed of either glycerol diethers, which have 20-carbon side chains (the 20-C unit is called a phytanyl group), or diglycerol tetraethers which have 40-carbon side chains
  44. What causes the formation of a monolayer rather than a bilayer in certain Archaea?
    In tetraether lipids, the ends of the phytanyl group side chains that point inward from each general molecule are covalently linked. This forms a lipid monolayer
  45. What are the three main functions of the cytoplasmic membrane?
    • Permeability Layer: prevents leakage and functions as a gateway for transport of nutrients into, and wastes out of, the cell
    • Anchor: Site of many proteins that participate in transport, bioenergetics, and chemotaxis (some of which are enzymes that catalyze bioenergetic reactions and others transport solutes into and out of the cell)
    • Site of Energy Conservation: Site of generation and use of the proton motive force (which protons (H+) are separated from hydroxyl ions (OH-) across its surface and is responsible for driving many energy requiring functions in the cell, including some forms of transport, motility, and biosynthesis of ATP)
  46. What sort of molecules may or may not pass through the cytoplasmic membrane?
    • Although some small hydrophobic molecules pass the cytoplasmic membrane by diffusion, polar and charged molecules (eg: amino acids, organic acids, and inorganic salts) do not readily diffuse but instead must be transported. Even a substance as small as a proton (H+) cannot diffuse across the membrane.
    • Water may pass through the cytoplasmic membrane, as it is weekly polar but sufficiently small to pass between phospholipid molecules in the lipid bilayer
    • Some small nonpolar and fat soluble substances like fatty acids, alcohols, and benzene may enter or exit cell by dissolving in lipid phase & diffusing through it.
  47. How might the passing of water through the cellular membrane be accelerated? give an example
    It can be accelerated by dedicated transport proteins called Aquaporins; form membrane spanning channels that can specifically transport water.

    AqpZ in Escherichia coli is an example
  48. Describe in detail three characteristics of transport proteins
    • Saturation Effect: If the concentration of substrate is high enough to saturate the transporter, which can occur at even the very low substrate concentrations found in nature, the rate of uptake becomes maximal and the addition of more substrate does not increase the rate (is an essential characteristic for a system that must concentrate nutrients from an often very dilute environment)
    • High Specificity of the Transport Event: Many carrier proteins react only with a single molecule, but some show affinities for closely related molecules (ex. sugars or amino acids); reduces the need for separate transport proteins for each different amino acid or sugar.
    • Biosynthesis is Highly Regulated: the specific complement of transporters present in the cytoplasmic membrane of a cell at any one time is a function of both the resources available and their concentrations; Biosynthetic control of this type is important because a particular nutrient may need to be transported by one type of transporter when the nutrient is present at high concentration and by a different, higher-affinity transporter, when present at low concentration.
  49. Describe the three classes of active transport
    • Simple Transport: consists only of a membrane-spanning transport protein; Driven by the energy in the proton motive force
    • Group Translocation: involves a series of proteins in the transport event; Chemical modification of the transported substance driven by phosphoenolpyruvate
    • ABC System: consists of three components: a substrate-binding protein, a membrane-integrated transporter, and an ATP-hydrolyzing protein; Periplasmic binding proteins are involved and energy comes from ATP
  50. Describe the structure of Membrane Transporters
    12 alpha-helices that wind back and forth through membrane to form a channel through which solute enters cell.
  51. Where do the active transport systems get their energy?
    All transport systems require energy in some form, either from the proton motive force, or ATP, or some other energy-rich organic compound.
  52. What are the three classes of transport system events?
    • Uniporter: proteins that transport a molecule unidirectionally across the membrane, either in or out
    • Symporter: frequently proton (H+) cotransporters; they typically transport one molecule along with another substance
    • Antiporter: proteins that transport a substance across the membrane in one direction while at the same time transporting a second substance in the opposite direction.
  53. Describe the process by with EColi transports Lactose through the membrane
    E Coli metabolizes the disaccharide sugar, lactose, by the activity of a simple transport lac permease, a type of symporter
  54. Describe Group Translocation, and give an example
    • Group Translocation is a process in which the transported substance is chemically altered during the passage across the membrane
    • The best studied model of group translocation involves the transport of the sugars glucose, mannose and fructose, which are phosphorylated during transport by the phosphotransferase system (which are modified by phosphorylation during transport by the phosphotransferase system)
  55. List the two nonspecific enzymes and the three specific enzymes found in the phosphotransferase system
    • Enz I & HPr: nonspecific and shared by all three sugars
    • Enz IIa: specific to glucose
    • Enz IIb: specific to fructose
    • Enz IIc: specific to maltose
  56. Describe the three components of the ABC System
    • Periplasmic binding protein: high affinity for substrate [solute]. Bind solute even when in very low concentration.
    • Membrane-spanning proteins: is a carrier or transmembrane protein that serves as channel.
    • ATP hydrolyzing protein: [kinase] provides the energy
  57. Do Gram(+) bacteria lack an ABC Transport system?
    Even though gram-positive bacteria lack a true periplasm, they do have ABC transport systems. In gram-positive bacteria, however, substrate-binding proteins are anchored to the external surface of the cytoplasmic membrane. Nevertheless, once these proteins bind substrate, they interact with a membrane transporter to catalyze uptake of the substrate at the expense of ATP hydrolysis, just as they do in gram-negative bacteria
  58. How do macromolecules like protein exit or enter a prokaryotic cell?
    Proteins are exported through and inserted into prokaryotic membranes by the activities of other proteins called translocases, a key one being the Sec (sec for secretory) system. The Sec system both exports proteins and inserts integral membrane proteins into the membrane. Proteins destined for transport are recognized by the Sec system
  59. What is the distinction between Gm(+) and Gm(-) bacteria?
    • The distinction between gram-positive and gram-negative bacteria is based on the Gram stain reaction 

    • The walls of Bacteria have a rigid layer that is primarily responsible for the strength of the wall. In gram-negative bacteria, additional layers are present outside this rigid layer. This rigid layer is called peptidoglycan

  60. Describe the structure of peptidoglycan
    Peptidoglycan is a polysaccharide composed of two sugar derivatives, N-acetylglucosamine and N-acetylmuramic acid, and a few amino acids, including L-alanine, D-alanine, D-glutamic acid, and either lysine or the structurally similar amino acid analog, diaminopimelic acid (DAP). These constituents are connected to form a repeating structure, the glycan tetrapeptide

  61. Which axis do the Peptide Bonds give strength in for peptidoglycan? Glycosidic Bonds?
  62. What percentage of Gm(+) bacterial cell wall is peptidoglycan?
    roughly 90%
  63. What percentage of Gm(-) bacterial cell wall is peptidoglycan?
    roughly 10%
  64. Describe the difference in cross-linkages between Gm(+) and Gm(-) bacteria.
    • Gram negative: peptidoglycan cross-linkage occurs by peptide bond formation from the amino group of DAP (diaminopalimic acid) of one glycan chain to the carboxyl group of the terminal D-alanine on the adjacent glycan chain.
    • Gram positive: cross-linkage may occur through a short peptide inter-bridge, with the kinds and numbers of amino acids in the interbridge varying from species to species.
  65. Is peptidoglycan present in Archaea and Eukarya?
    • Peptidoglycan is present only in species of Bacteria
    • The sugar N-acetylmuramic acid and the amino acid diaminopimelic acid are never found in the cell walls of Archaea or Eukarya
  66. What is an unusual feature of Bacterial cell walls?
    An unusual feature of the bacterial cell wall is the presence of two amino acids that have the D-configuration, D-alanine and D-glutamic acid, as most amino acids found in nature are in L-form
  67. How does lysozyme affect the peptidoglycan of bacteria?
    Lysozyme cleaves the β-1,4-glycosidic bonds between N-acetylglucosamine and N-acetylmuramic acid in peptidoglycan, thereby weakening the wall; water can then enter the cell and cause lysis.
  68. Contrast Lysozyme with penicillin
    Lysozyme destroys preexisting peptidoglycan, whereas penicillin instead prevents it's biosynthesis (eventually leading to osmotic lysis)
  69. Do Gm(+) Cocci have DAP in their peptidoglycan?
    No, most Gram (+) cocci have lysine instead of DAP
  70. What is something special that Gm(+) bacteria have embedded in their cell walls?
    Many Gram(+) Bacteria have acidic polysaccharides called teichoic acids embedded in their cell wall.
  71. Describe the term Teichoic Acids
    • The term teichoic acids encompasses all of the wall, membrane, or capsular polymers containing glycerophosphate or ribitol phosphate residues (polyalcohols)
    • Are covalently bonded to muramic acid in the wall peptidoglycan
    • Teichoic acids are polyalcohols connected by phosphate esters and usually have other sugars and D-alanine attached
    • Because they are negatively charged, teichoic acids are partially responsible for the negative charge on Gm(+) cell surface as a whole
  72. What are Lipoteichoic acids?
    Lipoteichoic acids are those teichoic acids covalently linked to membrane lipids.
  73. Give two examples of bacteria with no cell wall
    • Mycoplasma: like protoplast & lives in osmotically protected environment; sterols add strength to membrane; pathogenic to humans
    • Thermoplasma: species of Archae; has a tough membrane;
  74. Name a bacteria that does have sterols
    One exception is Mycoplasma. This prokaryotic bacterium lacks cell walls and requires sterols to stabilize their membranes
  75. Besides peptidoglycan, what else do Gm(-) bacteria contain in their cell wall?
    • Besides peptidoglycan (makes only 10% of total cell wall), gram(-) Bacteria contain an additional wall layer (LPS) made of lipopolysaccharide and called the outer membrane.
    • This second lipid bilayer contains polysaccharides and phospholipids which are linked in the outer membrane to form lipopolysaccharide structures; outer layer is called the lipopolysaccharide layer (LPS) because of this
  76. Describe the components of the Lipopolysaccharide Layer of Gm- bacteria
    • Two Main Components 
    • 1. O-specific polysaccharides
    • 2. Core polysaccharides

    Lipid portion referred to as Lipid A: linked to Glucosamine through Amine gps

    Lipid layer (phospholipid) including Lipid A is inner component & the Lipid A portion of LPS is endotoxic. Lipid A actually embedded in the phospholipid portion

    The lipoproteins present on inner side of LPS anchor outer membrane to peptidoglycan

    LPS is still considered a lipid bilayer but structure distinct from cytoplasmic membrane

  77. Apart from structural aid, what is a second major function of the outer membrane of Gm(-) bacteria?
    • One of its important biological activities is its toxicity to animals. Gm(-) bacteria are pathogenic for humans and other mammals. Toxicity is associated with the LPS layer, in particular, lipid A. The term endotoxin refers to this toxic component of LPS
    • Endotoxins can produce fever, a decrease in blood pressure, activation of inflammation and coagulation of blood (learn in med school or hemostasis; called DIC disseminated intravascular coagulation)
    • Presence in blood can lead to septicemia.
  78. Describe the permeability of the lipopolysaccharide layer (LPS)
    • The LPS is not permeable to proteins or other large molecules. Thus, a major function of LPS is to keep proteins whose activity occurs outside of cytoplasmic membrane from diffusing away from the cell. (Ex. hydrolytic enzymes like amylase)
    • Proteins are present in the periplasm and reach it by way of Sec protein-exporting system (they don’t get out)
    • Hydrophobic molecules do not get through outer o-specific polysaccharides
    • Hydrophobic Antibiotics are not effective against gram negative bacteria
    • Hydrophillic small molecules normally do not get through Lipid regions (Lipid A phospholipid layer)
  79. Where is the Periplasm found?
    Gram(-) bacteria contain a region called the Periplasm that lie between the cytoplasmic membrane and a second membrane layer called the outer membrane (part of the gram(-) cell wall)
  80. What types of proteins are found in the Periplasm?
    • Hydrolytic Enzymes: function in the initial degradation of food
    • Binding Proteins: begin the process of transporting substrates
    • Chemoreceptors: proteins involved in the chemotaxis response
  81. How do hydrophillic molecules get through LPS and into periplasm of Gm(-) Bacteria?
    • The outer membrane of Gm(-) Bacteria is relatively permeable to small hydrophillic molecules, even though it is basically a lipid bilayer (membrane part is not permeable, but porins allow hydrophillic through)
    • These proteins called porins are present in the outer membrane and function as channels for entry and exit of low-molecular weight hydrophilic substances
  82. How are the cell walls of certain methanogenic Archaea similar to bacteria?
    The cell walls of certain methanogenic Archaea contain a molecule that is remarkably similar to peptidoglycan, a polysaccharide called pseudomurein. The backbone of pseudomurein is composed of alternating repeats of N-acetylglucosamine (also found in peptidoglycan) and N-acetyltalosaminuronic acid; the latter replaces the N-acetylmuramic acid of peptidoglycan. Pseudomurein also differs from peptidoglycan in that the glycosidic bonds between the sugar derivatives are β-1,3 instead of β-1,4, and the amino acids are all of the L stereoisomer.
  83. Describe the S-Layer
    • The most common cell wall in species of Archaea is the paracrystalline surface layer (S-Layer)
    • Consists of interlocking protein or glycoprotein molecules that show an ordered appearance when viewed with the electron microscope
    • Typically have hexagonal symmetry
    • When an S-layer is present along with other wall components, the S-layer is always the outermost wall layer, the layer that is in direct contact with the environment.
  84. What functions do the hexagonal symmetry of the S-layer allow?
    • Protection from osmotic lysis
    • A selective sieve, allowing the passage of low-molecular-weight solutes while excluding large molecules and structures (such as viruses)
    • Function to retain proteins near the cell surface, much as the outer membrane does in gram-negative bacteria.
  85. How is a capsule defined?
    Traditionally, if the layer is organized in a tight matrix that excludes small particles, such as India ink, it is called a capsule. Typically adhere firmly to the cell wall, and some are even covalently linked to peptidoglycan
  86. How is a slime-layer defined?
    In contrast to a capsule, if the layer is more easily deformed, it will not exclude particles and is more difficult to see; this form is called a slime layer; are loosely attached and can be lost from the cell surface.
  87. What are some additional structures apart from the cell wall prokaryotic cells may display?
    Many prokaryotes secrete slimy or sticky materials on their cell surface. These materials consist of either polysaccharide or protein. These are not considered part of the cell wall because they do not confer significant structural strength on the cell. The terms “capsule” and “slime layer” are used to describe these layers.
  88. Describe Fimbriae
    Filamentous structures composed of protein that extend from the surface of a cell and can have many functions; enable cells to stick to surfaces, including animal tissues in the case of pathogenic bacteria, or to form pellicles (thin sheets of cells on a liquid surface) or biofilms on surfaces.
  89. Describe Pili
    Similar to fimbriae, but are typically longer and only one or a few pili are present on the surface of a cell.
  90. What are two important functions of Pili?
    Two very important functions of pili include facilitating genetic exchange between cells in a process called conjugation and in the adhesion of pathogens to specific host tissues and subsequent invasion
  91. What is one important class of Pili?
    Type IV Pili: assist cells in adhesion but also allow for an unusual form of cell motility called twitching motility (a type of gliding motility, movement along a solid surface)

    Also been implicated as key colonization factors for certain human pathogens

    also thought to mediate genetic transfer by the process of transformation in some bacteria, which, along with conjugation and transduction, are the three known means of horizontal gene transfer in prokaryotes
  92. Describe one of the most common inclusion bodies
    One of the most common inclusion bodies in prokaryotic organisms is poly-β-hydroxybutyric acid (PHB), a lipid that is formed from β-hydroxbutyric acid units.
  93. How is poly-β-hydroxybutyric acid formed?
    The monomers of PHB bond by ester linkage through the removal of water between COOH (carboxyl) on one monomer and OH on β Carbon of another, to form the PHB polymer, and then the polymer aggregates into granules.
  94. Apart from PHB, what is another common storage molecule?
    • Another storage product is glycogen, which is a polymer of glucose. Like PHA, glycogen is a storehouse of both carbon and energy.
    • poly glucose α 1,4 and α 1,6 glycosidic bonds
  95. How do some microorganisms accumulate phosphate?
    • Many microorganisms accumulate inorganic phosphate (PO43-) in the form of granules of polyphosphate. These granules can be degraded and used as sources of phosphate for nucleic acid and phospholipid biosyntheses and in some organisms can be used to make the energy rich compound ATP
    • Phosphate is often a limiting nutrient in natural environments. Thus if a cell happens upon an excess of phosphate, it is advantageous to be able to store it as polyphosphate for future use.
  96. Can microorganisms oxidize sulfur compounds?
    Yes, many gram-negative prokaryotes can oxidize reduced sulfur compounds, such as hydrogen sulfide (H2S).
  97. Describe magnetosomes
    Magnetosomes are intracellular particles of Fe3O4 (iron mineral magnetite) that impart a magnetic dipole on a cell which orients it in a particular direction with regard to Earth’s magnetic field lines.
  98. What does it mean if a prokaryotic species is planktonic?
    If a prokaryote is planktonic, it means that they live a floating existence within the water column of lakes and the oceans. 

  99. How are planktonic prokaryotes able to float?
    Planktonic prokaryotes can float because they contain gas vesicles. These structures confer buoyancy on cells, allowing them to position themselves in a water column in response to environmental cues.
  100. What is the most dramatic example of a planktonic prokaryote?
    The most dramatic examples of gas-vesiculate bacteria are cyanobacteria that form massive accumulations called blooms in lakes or other bodies of water 

  101. Describe the molecular structure of Gas Vesicles
    The conical-shaped gas vesicle is composed of two different proteins:

    • The major protein, called GvpA, forms the vesicle shell itself and is a small, hydrophobic, and very rigid protein which makes up 97% of the vesicle. The rigidity is essential for the structure to resist the pressures exerted on it from outside.
    • The minor protein, called GvpC, functions to strengthen the shell of the gas vesicle by cross-linking copies of GvpA
  102. Describe Endospores
    • Certain species of Bacteria produce structures called endospores during a process called sporulation. Endospores (the prefix endo means “within”) are highly differentiated cells that are extremely resistant to heat, harsh chemicals, and radiation. Endospores function as survival structures and enable the organism to endure unfavorable growth conditions, including but not limited to extremes of temperature, drying, or nutrient depletion.
    • Also, aid in dispersal of organism by wind & water
  103. Where are spore forming bacteria commonly found?
    Endospore-forming bacteria are found most commonly in the soil.
  104. What are the two most notable spore forming bacterial genera?
    Most notable genera include Bacillus and Clostridium (also in lab know Sporosarcinae)
  105. Describe the following Endospore Components:

    Exosporium
    Spore coat
    Cortex
    Core
    • Exosporium: a thin protein covering which comprises the outermost layer
    • Spore coat: composed of layers of spore-specific proteins; located in the exosporium
    • Cortex: located below the spore coat; consists of loosely cross-linked peptidoglycan
    • Core (spore protoplast): contains the core wall, cytoplasmic membrane, cytoplasm, nucleoid, ribosomes, and other cellular essentials

  106. Imagine the stages of endospore formation
  107. Imagine stage I and II of endospore formation
  108. Imagine stage III and IV of endospore formation
  109. Imagine stage V, VI, and VII of endospore formation
  110. Imagine the germination lifecycle
  111. Name a substance characteristic of endospores but absent from vegetative cells
    One substance that is characteristic of endospores but absent from vegetative cells is dipicolinic acid, which accumulates in the core
  112. What protein does an Endospore contain high levels of?
    The endospore core contains high levels of small acid-soluble proteins (SASPs). These proteins are made during the sporula- tion process and have at least two functions:

    • 1. SASPs bind tightly to DNA in the core and protect it from potential damage from ultraviolet radiation, desiccation, and dry heat.
    • 2. SASPs function as a carbon and energy source for the outgrowth of a new vegetative cell from the endospore during germination.
  113. Describe the function of a flagellum in prokaryotes
    Many prokaryotes are motile by swimming, and this function is due to a structure called the flagellum (plural, flagella). The flagellum functions by rotation to push or pull the cell through a liquid medium.
  114. Where are polar flagella attached?
    In polar flagellation, the flagella are attached at one or both ends of a cell.
  115. Describe the different types of Polar Flagella
    • Occasionally a group of flagella (called a tuft) may arise at one end of the cell, a type of polar flagellation called lophotrichous. When a tuft of flagella emerges from both poles of the cell, flagellation is called amphitrichous.
    • In peritrichous flagellation, flagella are inserted at many locations around the cell surface. The type of flagellation, polar or peritrichous, is a characteristic used in the classification of bacteria.
  116. What are the three basic subunit of prokaryotic flagellum?
    • The base, the hook, and the motor
  117. Describe the structure of the base of prokaryotic flagellum
    The base of the flagellum is structurally different from the filament. There is a wider region at the base of the filament called the hook.
  118. Describe the structure of the hook of prokaryotic flagellum
    The hook consists of a single type of protein and connects the filament to the motor portion in the base
  119. Describe the structure of the Motor of prokaryotic flagellum
    • The motor is anchored in the cytoplasmic membrane and cell wall. The motor consists of a central rod that passes through a series of 4 rings. In Gm(-) bacteria, an outer ring, called the L ring, is anchored in the lipopolysaccharide layer.
    • A second ring, called the P ring, is anchored in the peptidoglycan layer of the cell wall.
    • A third set of rings, called the MS and C rings, are located within the cytoplasmic membrane and the cytoplasm, respectively. In Gm(+) bacteria, which lack an outer membrane, only the inner pair of rings is present. 
    • Surrounding the inner ring and anchored in the cytoplasmic membrane are a series of proteins called Mot proteins.
    • A final set of proteins, called the Fli proteins, function as the motor switch, reversing the direction of rotation of the flagella in response to intracellular signals.
  120. Contrast a Gram- and Gram+ motor
    • In Gram- bacteria, an outer ring, called the L ring, is anchored in the lipopolysaccharide layer. A second ring, called the P ring, is anchored in the peptidoglycan layer of the cell wall. A third set of rings, called the MS and C rings, are located within the cytoplasmic membrane and the cytoplasm
    • In Gram+ bacteria, which lack an outer membrane, only the inner pair of rings is present. Surrounding the inner ring and anchored in the cytoplasmic membrane are a series of proteins called Mot proteins. A final set of proteins, called the Fli proteins, function as the motor switch, reversing the direction of rotation of the flagella in response to intracellular signals.
  121. Detail how flagellar movement occurs
    • The flagellum is a tiny rotary motor. How does this motor work? Rotary motors contain two main components; the rotor and the stator. In the flagellar motor, the rotor consists of the central rod and the L, P, C, and MS rings. Collectively, these structures make up the basal body. The stator consists of the Mot proteins that surround the basal body and function to generate torque.
    • Rotation of the flagellum is imparted by the basal body. The energy required for rotation of the flagellum comes from the proton motive force. Proton movement across the cytoplasmic membrane through the Mot complex drives rotation of the flagellum. About 1000 protons (H+) are translocated per rotation of the flagellum. Protons flowing through channels in the Mot proteins exert electrostatic forces on helically arranged charges on the rotor proteins. Attractions between positive and negative charges would then cause the basal body to rotate as protons flow though the Mot proteins.
  122. How do the swimming motions of polarly flagellated organisms differ from those of peritrichously flagellated organisms?
    • Peritrichous: move forward when flagella bundled and rotate counterclockwise. Clockwise causes cell to tumble, and then return to counterclockwise leads cell in new direction.
    • Polar: cells change direction by reversing flagellar rotation. Unidirectional (Ex. only clockwise); cells must stop periodically to reorient & then move forward.



  123. Do all prokaryotes have flagella?
    No, though many prokaryotes are motile, some lack flagella. These nonswimming bacteria move across solid surfaces in a process called gliding
  124. Describe the motile process of "Gliding"
    • Gliding is considerably slower than propulsion by flagella but provides a means of moving about
    • Gliding prokaryotes are filamentous or rod-shaped cells and the gliding process requires that the cells be in contact with a solid surface
    • May excrete slime (polysaccharide); some use “twitching motility” which uses pili extension and retraction.
  125. Do Gm+ or Gm- produce spheroplasts?
    • Gram positive: produces protoplast when treated with lysozyme in isotonic environment; is essentially cell membrane & internal constituents of cell )devoid of cell wall; IE: no residual wall left)
    • Gram negative: when treated with lysozyme produces a spheroplast which is similar to protoplast but has residual wall attached.

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