Biol 120 Exam 2.txt

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Biol 120 Exam 2.txt
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  1. Bacteriostatic
    Bacteriocidal
    Bacterialydic
    GRAPHS
  2. Bacteriocidal
    • Kills bacteria
    • Viable count is less than total count
  3. Bacteriostatic
    • Stops bacteria from reproducing
    • Viable count and total count plateau
  4. Bacteriolydic
    • Bacterial cells burst
    • Viable and total count are similar. Both decrease.
  5. In Vitro Agents
    • External Use
    • -Sterilants
    • -Disinfectants
    • -Sanitizers
    • -Anticeptics
  6. Disinfectants
    Used on inanimate objects
  7. Ethanol
    • - lipid solvent, denatures proteins in membrane
    • - Disinfectant
  8. Cationic Detergents
    • - Qaurternary ammonium compounds (disrupt lipids in membranes)
    • -Disinfectant or Sanitizer
  9. 2% Gluteraldehyde
    • - Denature proteins and DNA
    • - Disinfectant
  10. Iodophor
    • - Iodine, effects tyrosene so effects proteins (can be topical solution)
    • - Disinfectant
  11. Mercurials
    • - effects SH groups so targets cystene and glutamine
    • - Disinfectant
  12. Phenolics
    • - Denatures proteins
    • - Disinfectant
  13. Chlorine Compounds / Gas
    • - Chlorine compounds are oxidizing agents
    • - Disinfectant or Sanitizer
  14. When to use sterilants
    • (where you can’t use heat/radiation/filtration)
    • - gaseous sterilants-Ethylene oxide, formaldehyde, peroxyacetic acid or hydrogen peroxide vapor
    • - liquid sterilants- sodium hypochlorite, amyl phenol
  15. Antiseptics
    • -handwashing
    • -treating surface wounds
  16. Antimicrobial Efficiency
    Ability to kill microbes. Depends on microbial load, amount of microbes present
  17. Biofilms
    • -surface attached communities
    • -single species or multiple species (polymicrobial)
    • -form when nutrients are plentiful and dissolve when conditions poor (individuals detach to find new sources of nutrients)
    • -environmental signals
  18. Examples of biofilms
    • Pseudomonas- cystic fibrosis (lungs)
    • Staphylococcus- catheters and medical valves
    • Polymicrobial plaque on teeth
    • Marine snow- suspended particles of biofilm in ocean
  19. Biofilm Formation
    • Planktonic cell adheres to surface
    • Secretes polysaccharides
    • Cell proliferation
    • Send chemical signals (Quorum sensing)
    • Attracts other bacteria
    • Triggers genetic change in those bacteria so they join biofilm
    • Exopolysaccharide (extracellular matrix of polysaccharides)
    • Large colony is formed
  20. 3 Key Features of Biofilms
    • 1- Attach to surfaces
    • 2-Protect the bacteria from host immune defenses.
    • 3- Are highly resistant to antibiotics
  21. chemotherapeutic agents (in vivo)
    • -chemical agents that can be used internally
    • - must depend on selective toxicity so host cell isn't harmed
  22. Synthetic agents used in vivo
    • Growth factor analogs
    • Quinolones
  23. Naturally occuring antimicrobial drugs: antibiotics
    • Broad spectrum
    • Narrow spectrum
  24. Broad spectrum antibiotics
    • Kill range of microbes
    • ex. Gram negative AND Gram positive
    • ex. Kill needed microbes in your body along with infectious microbes
  25. Narrow spectrum antibiotics
    • Kill just one group of organisms, however there is more chance of resistance
    • ex. Kill only Gram negative
  26. Bacteria produce antimicrobial compounds as a defense mechanism (4 Types)
    • Antibiotics
    • Bacteriocins
    • Toxins
    • Bacteriolytic enzymes
  27. Bacteriocins
    Ribosome synthesized proteins formed by bacteria or archaea to kill closely related microbes.
  28. Gram Negative Colicins
    What is it? How does it work?
    • Bacteriocin
    • Cause pore in cell membrane, disrupts proton motive force, allows ion influx
    • Can also attach nucleic acid activity if it enters cell
  29. Gram Positive Colicins
    What is it? How does it work?
    • Bacteriocin
    • Small heat-stable cationic proteins
    • Cause pores that cause cells to leak
  30. Make cards for slide 14 of lecture 1
  31. Antimicrobial drug resistanceis an acquired ability of an organism to resist the effects of a chemotherapeutic agent (6 methods)
    • 1. inherent resistance-lack the structure that the antibiotic inhibits
    • 2. may be impermeable to antibiotic
    • 3. alter the antibiotic to an inactive form (ex. Beta Lactomase)
    • 4. modify the target of the antibiotic (mutation changes target so no longer recognized by antibiotic)
    • 5. may develop an alternative biochemical pathway
    • 6. pump out antibiotics entering the cells
  32. Free energy
    ΔG°
    • - energy released that can be used to do work
    • - ΔG°’ -release of free energy-exergonic
    • + ΔG°’-requires energy-endergonic
  33. ENZYMES
    • - increase the rate of reactions 1012 fold
    • - protein catalysts
    • - specific, bind via weak bonds
    • - some require energy (ex. ATP)
  34. Non-protein catalysts
    • a. prosthetic groups
    • b. coenzymes
  35. Prosthetic groups
    • Tightly bind to enzyme
    • ex. heme
  36. Coenzymes
    • Loosely bind to substrate
    • ex. NADH, FADH2, Chymotrypsin
  37. Oxidation and Reduction
    • oxidation
    • LEO- loss of electrons
    • oxidized
    • electron donor
    • reduction
    • GER-gains of electrons
    • reduced
    • electron acceptor
  38. Reduction potentials
    • -tendency to become oxidized or to become reduced
    • -more negative reduction potential donates electrons
    • ΔE°’-difference in potential
    • ΔE°’ is proportional to ΔG°’
  39. Redox Potentials refer to H2
    • Less electronegative than H2: negative redox potential
    • More electronegative than H2: positive redox potential
  40. Fluorine as an electron acceptor
    Although fluorine is the most electronegative atom, it has properties that prevent it from being an electron acceptor
  41. Nicotine Adenine Dinucleotide
    NAD+
    • Strong reduction potential: -.32V
    • 2 electrons & 2 protons donated to destroy double bond
    • NADP+ has a phosphate bond
  42. Electron Carriers
    (prosthetic and coenzymes)
    • transfer of electrons from donor to acceptor through intermediary (also source of protons)
    • 1) freely diffusible
    • 2) attached to enzymes in cytoplasmic membranes
  43. Energy released in redox reactions is highly conserved in high energy phosphate bonds
    ATP, ADP, AMP
    • ATP is a great source of energy
    • ADP is a good source of energy
    • AMP is a poor source of energy
  44. 3 Classes of catabolism
    • 1. Fermentation
    • 2. Respiration
    • 3. Photoheterotrophy
  45. Fermentation
    -partial breakdown of organic food without net transfer of electrons to a terminal electron acceptor
  46. Respiration
    -breakdown of organic molecules with electron transfer to a terminal electron acceptor
  47. Photoheterotrophy
    -energy from light absorption is used to breakdown an organic molecule
  48. Catabolism substrates
    • Lipids
    • Glycerol (glycolysis)
    • Fatty acids (oxidative breakdown to acetyl group)
    • Amino acids
    • Decarboxylation (glycolysis)
    • Deamination (excretion)
    • Aromatic compounds (acetyl groups- TCA cycle)
  49. Substrate level phosphorylation
    • ATP is synthesized during the catabolism of an organic compound
    • Transfers high energy bond from one group to another, converting loe energy bond to high energy
  50. Glycolysis
    Products
    • NAD+ reduced to NADH
    • Consume ATP, produce 3 ATP
    • Pyruvate
    • (all happens twice)
  51. Citric Acid Cycle
    Broad overview
    • There are 10 variatios in archaea & bacteria
    • Pyruvate is completely oxidized to CO2
    • Can sometimes go backward for making carbon skeletons
    • Intermediate molecules can be used for other processes
  52. Alpha ketogluterate
    • Citric Acid Cycle Precursor Molecules
    • -glutamate -> other AAs
    • -oxaloacetate-> asparate -> other AAs
  53. Pyruvate as Citric Acid Cycle
    Precursor Molecule
    Can be used to make alanine
  54. 3-phosphoglycerate
    • Citric Acid Cycle Precursor Molecules
    • Can be used to make serine
  55. Citric Acid Cycle overall reaction
    Pyruvate + 4NAD+ + FAD --> 3CO2 + 4 NADH + FADH2
  56. Electron Transport Phosphorylation
    Donors and ATP yield
    • 8 NADH = 24 ATP
    • 2 FADH2 = 4 ATP
    • 2 GTP = 2 ATP
  57. NADH dehydrogenase
    • Each level of chain is reduced by the product of the previous form
    • ATP synthase uses proton gradient to make ATP
  58. If asked to sterilize a heat sensitive material, which would you use:
    A) steam autoclave
    B) ethylene oxide
    C) pasteurization
    B) ethylene oxide
    (this multiple choice question has been scrambled)
  59. Which statement is incorrect?
    A) biofilms protect bacteria
    B) biofilms attach to surfaces
    C) biofilms are often polymicrobial
    D) biofilms are more sensitive to antibiotics
    D) biofilms are more sensitive to antibiotics
    (this multiple choice question has been scrambled)
  60. Which is not a chemical agent used to control microbes?
    A) halogens
    B) gluteraldehyde
    C) phenol
    D) filtration
    D) filtration
    (this multiple choice question has been scrambled)
  61. Aerobic Respiration
    (3 parts and overall reactions of each)
    • 1. Glycolysis
    • Glucose -> 2 Pyruvate

    • 2. Tricarboxylic Acid Cycle
    • 2 Pyruvate -> 6 CO2

    • 3. Electron Transport Chain
    • 12 H+ + 3 O2 -> 6H20
  62. NADH dehydrogenase & ETC
    • -transfer hydrogen atoms from NADH
    • -inner surface of cell membrane
    • -in respiration, hydrogen atoms passed to flavoproteins
  63. FMN or FAD containing proteins (flavoproteins)
    • -riboflavin (vitamin B2)
    • -flavoprotein accept H atoms (2 electrons and 2 protons are transferred)
  64. Cytochromes
    • heme containing proteins (iron-porphyrin ring)
    • -different classes of cytochromes with different reduction potentials, but all have an iron section to be reduced and oxidized
  65. Porphyrin
    • Cytochrome example: heme group in blood
    • Porphyrin Degrading Enzymes get blood out of clothes
  66. Iron-sulfur proteins
    • -Fe2S2 and Fe4S4
    • -have a range of reduction potentials
  67. Quinones
    • -hydrophobic-lipid soluble-diffuse through membrane
    • -similar to vitamin K
  68. Proton motive force
    • -electon transport carriers-oriented in the membrane in such a way that a separation of proton from electrons occurs across the membrane during electron transport
    • -protons pumped to the outside
    • -electrons move down the electron transport chain until they reduce oxygen
    • -oxygen is reduced to water-hydrogen for the water come from inside the cytoplasm
  69. Gradients used in Proton Motive Force
    • Electrical and pH gradients
    • Protons are pumped out of cell and energy is stored in these gradients
    • NAD+ is the best electon donor
    • O2 is the best electron acceptor
    • Complex 1
    • 1. NADH donates 2H+ and 2e- to FAD
    • 2. FADH donates 2e- to iron-sulfur protein
    • but the 2H+ are released into the environment
    • 3. 2H+ from the cytoplasm and 2e- from Fe-S protein reduce coenzymeQ

    • Complex III
    • 4. Coenzyme Q passes e- to cytochrome bc1
    • 5. Fe-S protein (Rieske protein) passes the electrons to cytochrome c1 and eventually to cytochrome c (periplasmic protein)

    • Complex IV
    • 6. Cytochrome c diffuses to cytochrome aa3 and donates electrons
    • 7. O2 is reduced to water
    • ATP Synthase
    • Oxidative Phosphorylation

    • FO portion crosses membrane
    • F1 portion is inside cell and catalyzes ATP synthesis

    Protons enter FO, cause conformation change of F1 and create ATP
  70. ATP Synthase Inhibitors
    • block electron flow and thus there is no proton motive force established
    • eg. CO, CN- -bind to cytochromes
  71. ATP Synthase Uncouplers
    • prevent ATP synthesis without affecting electron transport
    • eg. Dinitrophenol, dicumarol-make membranes leaky destroying the proton motif force
  72. ATP produced by glucose catabolism
    Efficiency
    –Efficiency of energy capture= 40%

    –Efficiency of an Internal combustion engine= 20%
  73. Aerobic respiration: oxygen as the terminal acceptor

    What happens without oxygen?
    Found: Wetland soils and water, human digestive tract


    • Environmental modulation of ETS
    • 1. Food is limiting- less NADH entering the system (alternative NADH dehydrogenase)

    2. Low oxygen conditions (different terminal electron acceptor)
  74. Chemoheterotrophs: Anaerobic respiration
    -alternative electron acceptors (6 of them)
    • Fe 3+
    • NO3-
    • NO2-
    • S
    • CO2
    • SO4 2-
  75. Chemoheterotrophs: Anaerobic respiration
    Proton gradient & energy yield
    Still have proton gradient and ATP synthase but energy yield is lower
  76. Assimilative metabolism
    -compounds that serve as terminal electron acceptors can be a nutrient source (ex. Nitrate, Nitrite are terminal electron acceptors also used for amino acid synthesis)
  77. Dissimilative metabolism
    • -electron acceptors
    • -large amounts of compounds reduced
    • -reduced electron acceptor is excreted into the environment
  78. Nitrate (NO3-) reduction
    • -obligate and facultative anaerobes
    • -reduced waste products (nitrite) are excreted in significant amounts
  79. Redox potential=+ 0.42 v (+ 0.82 v for oxygen).
    -Nitrate reduction is repressed by the presence of oxygen
  80. Nitrate Reduction
  81. Reduction of nitrate to nitrogen gas
    (Examples of microbes)
    • Examples:
    • Paracoccus dinitrificans
    • Pseudomonas stutzeri
    • Rhodobacter sphaeroides
  82. Sulfate (SO42-) sulfate reduction
    • -sulfate to sulfite to hydrogen sulfide
    • -marine environments, hydrothermal vents
    • -obligate anaerobes
    • **Not many protons are pumped through ATP Synthase
  83. Sulfate Reduction
  84. Carbonate reduction (CO2)
    Hydrogen gas is a strong electron donor, can be used to reduce CO2 to methane
  85. Hydrogenotrophy
    Carbonate reduction

    use of molecular hydrogen as an electron donor
  86. Methanogens
    • Carbonate reduction
    • most important group of CO2 reducers (Archaea)
    • Produce methane as waste product
    • Found in landfills and arctic poles, also found in digestive tract of cows
  87. Methanogens & Homoacetogens
    • Methanogens have electron acceptors (coenzymes) that differ from other bacteria and archaea.
    • -still have proton motive force but very low energy yield

    Homoacetogens- Not seen in eukaryotes. Use methane but produce acetic acid (acetogenesis)
  88. Metal Electron Acceptors
    Ferric Ion (Fe3+), Manganese, chlorate, uranium

    Fe2+ was likely the dominant electron acceptor in early Earth

    Geobacter metallireducens- can reduce metals by grabbing with pilli

    Can be used to clean environment
  89. Organic Electron Acceptors (example)
    Ex. Fumerate is reduced by succinate
  90. How do organisms decide if they should do fermentation or anaerobic respiration?
    Usually do fermentation when no final electron acceptor is present
  91. Fermentation Products
    • H2, butyrate, formate
    • Excreted from cell when produced
    • *Glycolysis is not the only way to get fermentation products
  92. What happens when there is not enough energy to synthesize ATP?
    Ion pumps can create a gradient (ex. Na+) that stores energy
  93. API-20E test
    • •System of 20 individual, miniaturized tests used to determine the metabolic capabilities of the organism.
    • Used to determine genus & species

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