Microbiology test 2

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  1. What is the difference between a biological and chemical process?
  2. What types of reactions are favored under oxic and anoxic conditions?
    • Oxic: oxidation
    • anoxic: reduction
  3. Explain mineralization:
    decomposition of organic matter into simpler inorganic molecules.
  4. What occurs in nutrient immobilization?
    Nutrients are converted into biomass, and are not available for nutrient cycling.
  5. Describe Carbon fixation.
    • CO2 turned into organic molecules.
    • step 1
  6. Describe oxidation of organic matter
    • Organic carbon is burned for energy (glycolysis, fermentation)
    • step 2.
  7. Describe methanogenisis
    Coming from oxidation of organic matter, an alternate pathway produces methane.
  8. Describe lignin degradation:
    • Oposite of forming of peat bogs and muck soils.
    • Must occure in Aerobic conditions.
  9. What are the steps in the carbon cycle?
    • Carbon fixation
    • oxidation of organic molecules
    • methanogenesis
  10. What are the steps in the Nitrogen cycle?
    • ammonification
    • anammox reaction
    • assimilation
    • denitrification
    • nitrification
    • nitrogen fixation
  11. Describe Nitrogen fixation:
    • N2 into NH3
    • the nitrogen is now useable
  12. Describe nitrification:
    Taking amonia (NH4) into a nitrite NO3
  13. Describe denitrification:
    taking a nitrite and turning it into N2
  14. describe ammonification:
    taking organic N into ammonia NH4
  15. describe anammox:
    NO2 and NH4 get turned into N2.
  16. Describe the general features of the Phosphorous cycle:
    • No gaseous component.
    • Environmental phos is ususally the limiting factor.
  17. Describe the Iron cycle:
    Iron is reduced and oxidized as it changes between anaerobic and aerobic conditions.
  18. Which form of mercury is less toxic than the other?
    • de methylated.
    • with a methyl group it is lipid solluble and very toxic.
  19. Describe the importance of biomagnification in the mercury cycle.
    The toxic mercury builds up in the fats of successive levels of predation.
  20. Describe biodegredation:
    • 3 outcomes:
    • 1. minor change.
    • 2. fragmentation
    • 3. mineralization.
    • : can produce more toxic products.
    • Can degrade things we don't want, like metal
  21. Describe bioremediation:
    • Takes toxic and turns it into non toxic forms.
    • Involves many intermediates.
    • May need artificial supplimentation of the limiting factor.
  22. How can oil spills be cleaned?
    • Through bioremediation.
    • The hydrocarbons are degredated naturally.
  23. Describe phytoremediation:
    • it is a form of bioremediation.
    • Using plants and bacteria to degrade and use the toxic materials.
  24. Describe bioleaching of Copper:
    • Copper is pulled off of the minerals, it then undergoes a change in oxidation and is precipitated out.
    • Fe2+ is used.
    • Bacteria facilitate changes in oxidation.
  25. Describe bioaugmentation:
    • Adding more microbes to microbial communities.
    • Has only shown short term increases in degredative activity.
  26. What is Chemolithotrophy?
    Using inorganic molecules as an energy source
  27. Discuss the general features of chemolithotrophy
    litho denotes inorganic molecules as an energy and electron source.
  28. Identify the major energy sources used by chemolithotrophic bacteria
    Hydrogen, reduced nitrogen compounds, reduced sulfur compounds, ferrous Iron.
  29. Describe the stages of chemolithotrophy in nitrifying bacteria
    • 2 different genera needed.
    • 1. ammonia to nitrite
    • 2. nitrite to nitrate.
  30. Discuss the adaptability of chemolithotrophs
    many can switch between chemolithotrophy to chemoorganotrophy
  31. What is phototrophy?
    • Light energy trapped and converted into chemical energy.
    • 2 parts: light and dark reactions.
  32. Define photosynthesis
    • light reaction.
    • light absorbing pigments.
  33. Discuss the requirements and the products from the Light reactions
    • Only ATP produced and NaDH.
    • H20 not used so no O2 produced.
  34. Discuss the requirements and the products from the Dark reactions
    • Energy from Light reaction (ATP and NADH) used to turn CO2 into organic molecules.
    • "Calvin cycle"
  35. Describe the main features of oxygenic photosynthesis
    • H20 is present as final electron acceptor,
    • O2 produced.
  36. Describe the main features of anoxygenic photosynthesis
    • Strict anaerobes.
    • No H20 or O2.
    • Only ATP produced.
  37. Discuss phototrophy in Archaea and identify the differences with photosynthesisin other phototrophs
    • Uses bacteriorhodopsin.
    • light driven proton pump.
    • NO ETC
    • ATP only produced by chemiosomoiss.
  38. Characterize a Photolithoautotroph
    • C source: CO2
    • Energy Source: light
    • e- source: inorganic e- donor.
  39. Characterize a Photoorganoheterotroph
    • C source: organic carbon
    • energy source: light.
    • e- source: organic e- donor.
  40. Characterize a Chemolithoautotroph
    • C source: CO2
    • energy source: inorganic chemicals
    • e- source: inorganic e- donor.
  41. Characterize a Chemolithoheterotroph
    • C source: organic carbon
    • energy source: inorganic chemicals
    • e- source: inorganic e- donor.
  42. Characterize a Chemoorganoheterotroph
    • C source: organic carbon
    • energy source: organic chemicals (often same as C source)
    • e- source: organic e- donor.
    • (most non photosynthetics)
  43. Why is Nitrogen required and how do microorganisms obtain it?
    • Nucleic and Amino acids.
    • Org. mol.
    • ammonia.
    • N2, nitrate.
  44. Why is Phosphorous required and how do microorganisms obtain it?
    • Phospholipids, nucleic acids.
    • inorganic phosphate.
  45. Why is Sulfur required and how do microorganisms obtain it?
    • Amino Acids, vitamins.
    • Sulfate.
  46. What are micronutrients, and how are they obtained?
    Trace elements, needed in very small amounts.
  47. What are growth factors and how are they obtained?
    • Essential cell component precursers that the cell cannot synthesise.
    • Amino Acids,
    • Purines, pyrimidines
    • vitamins.
  48. Describe passive diffusion
    • High Conc. to Low.
    • H2O, O2, CO2.
  49. Describe Facilitate diffusion
    • From High to Low, via "facultative" pores.
    • Sugar transport.
    • More promenant in Eukariotic cells.
  50. Describe active transport
    • ATP dependent. Against conc. gradient.
    • Concentrates molecules.
    • involves carrier proteins.
  51. Describe group translocation
    • Chemically modified molecule is brought into cell.
    • PEP is an example.
  52. describe iron uptake
    • Ferric iron is very insolluble.
    • Siderphore complex used to pick it up and then transport into cell.
  53. With respect to the chemical composition, describe Defined culture media:
    We know exactly what is in the medi.
  54. With respect to the chemical composition, describe complex culture media:
    we don't know everything exactly about the media
  55. What is mean by a supportive (general purpose) media?
    supports growth of many microorganisms.
  56. What is mean by an Enriched media?
    • general purpose media augmented with something special
    • blood, special nutient.
  57. Describe a selective media:
    Favors growth of some, inhibits growth of others.
  58. What is mean by a differential media?
    distinguishes between different groups of microorganisms.
  59. Describe the 3 methods of isolating pure cultures:
    • 1. Streak Plate
    • 2. Spread Plate
    • 3. Pour Plate.
  60. How do colonies develop in solid culture media?
    From a single cell
  61. Describe the events in the bacteria cell cycle.
    • replicates chromosome,
    • divides, septum forms
    • grow and repeat.
  62. In bacteria, how are chromosomes replicated and partitioned?
    • through an origin of replication and terminus.
    • Only 1 point of replication per cycle.
    • Multiple repication going on at same time because of rapid division.
  63. Describe the chromosomal sites involved in bacterial DNA replication
    • Origin of replication.
    • Terminus.
  64. What is a replisome?
    Group of proteins needed for DNA synthesis.
  65. What roles to MreB and FtsZ play in cytokinesis?
    • MreB: Determining cell shape, and moving chromosomes to opposing ends of the cell.
    • FtsZ: Z ring formation to form cross wall.
  66. Image UploadDescribe a typical growth curve:
    Image Upload
  67. What events occur during the lag phase?
    • The cell is synthesizing new components.
    • time frame depends.
  68. What is happening during the exponential phase?
    • Constant growth rate.
    • Population most uniform.
  69. What is going on during the stationary phase?
    • Constant viable number of cells.
    • reproduction may stop, or
    • reproductive rate=death rate.
  70. Why do cultures enter a stationary phase?
    • This phase is entered because of:
    • Nutrient limitations,
    • O2 available,
    • waste accumulation,
    • population density critical.
  71. How do bacterial cells respond to starvation?
    • Endospore formation,
    • Decrease in size: protoplast shrinks, nucleoid condenses.
    • Produces starvation proteins.
  72. Describe the Death phase:
    • 2 ideas:
    • 1. viable, but not culturable. (VBNC)
    • 2. Part of population undergoes programmed cell death.
  73. What is the generation time?
    • The doubling time.
    • ranges from 10min to several days by species and environmental conditions.
  74. How would you calculate the number of cells from exponential growth?
    • Image Upload
    • P1 (origional population)
    • n (number of cycles)
  75. Define direct cell count:
    • counting chambers
    • electronic counters
    • membrane filters
    • counting actual cell bodies.
  76. Describe counting chambers:
    • Like a net, just count what is in the square.
    • Cheap and easy.
  77. Describe electron counters:
    • cells move through and disturb current.
    • Disturbances counted.
    • Usefull for large cells.
  78. describe direct count on membrane filters:
    • Dark membrane & fluorescent stained cells.
    • can distinguish living and dead.
    • good for bacteria.
  79. Define viable cell count:
    • Expressed in CFU's colony forming units.
    • dilute, let grow, count colonies.
    • count=colonies x dilution factor.
  80. How can one use a measurement of cell mass to estimate the cell numbers?
    • By dry weight,
    • By how much of particular component.
  81. Characterize continuous culture:
    Chemostat or turbidostat.
  82. Characterize chemostat
    • Limiting nutrient.
    • inflowing media=outflowing media.
  83. characterize turbidostat
    • No limiting nutrient.
    • flow rate determined by cell density or turbidity.
    • Operates best at high dilutions.
  84. What is water activity?
    • aw
    • amount of water available to organisms.
    • reduced by solute molecules.
    • ex: pure water vs. blood vs. dried fruits.
  85. Identify specific microbe adaptations to maintain tonicity:
    • compatible solutes to increase osmotic concentrations
    • proteins and membranes require high concentrations for stability and activity.
  86. What are compatible solutes?
    • they keep plasma firmly pressed against cell wall.
    • they do not interfere with metabolism or growth at high concentrations.
  87. What are:
    Extreme halophiles
    • Halophiles: optimal growth @ 0.2M
    • Extreme Halophiles: og@ 2M
    • osmotolerants: can grow over wide ranges of water activity.
  88. What are:
    • acidophile: og between pH 0-5.5
    • neutrophile: og between 5.5-8
    • alkalophiles: og between 8-11.5
    • producing a "buffer" waste.
    • protection proteins
    • proton impermiable membrane.
  89. What are the 3 cardinal tempuratures?
    • Minimum, optimum, maximum.
    • On a graph they show the relation between growth and temp.
  90. What are
    • psychrophiles: og -5-15
    • psychrotrophs: og 0-35
    • mesophiles: 15-40
    • thermophiles: 50-75
    • Hyperthermophile: 80-100
  91. describe superoxide dismutase
    2 O2 +2H into peroxide and O2
  92. Describe catalase
    peroxide into water and O2
  93. Describe the need for/response to oxygen, applicable enzymes, & type of metabolism for obligate aerobe:
    • Only grows in O2 presence.
    • SOD+Catalase
  94. Describe the need for/response to oxygen, applicable enzymes, & type of metabolism for falcultative anaerobe:
    • Can do without O2, but does best in it's presence.
    • SOD Catalase
  95. Describe the need for/response to oxygen, applicable enzymes, & type of metabolism for aerotolerant anaerobe:
    • Ignores O2 alltogether.
    • Has SOD, but no catalase.
  96. Describe the need for/response to oxygen, applicable enzymes, & type of metabolism for strict anaerobe:
    • Only grows away from O2.
    • No SOD, No Catalase.
  97. Describe the need for/response to oxygen, applicable enzymes, & type of metabolism for microaerophile:
    • Can only live in certain concentrations of O2.
    • Has SOD, and maybe Catalase.
  98. What is required to culture anaerobes?
    Paladium pellets, sillica gel, sealed container and an o2 indicator.
  99. what distinguishes barotolerant and barophilic microbes?
    • barotolerant: hurt by pressure, just not as bad as others.
    • barophilic: require, or grow more rapidly at 400atm or higher.
  100. What effect does ionizing radiation have on microbes?
    • disrupts chemical structure.
    • DNA etc.
  101. What effect does UV radiation have on microbes?
    formation of thymine dimers through forbidden diels-alder reactions.
  102. what is the effect of visible light radiation on microbes?
    • at high intensities generates singlet oxygen.
    • caroteniods protect many light exposed microorganisms from photooxidation.
  103. What are biofilms and how do they form?
  104. what is quorum sensing and how does it work?
  105. Describe oligotrophic conditions in nature. How do microorganisms respond to these conditions?
  106. Energy source: chemoorganotroph, chemolithotroph, and phototroph
    • Organic molecules
    • inorganic molecules
    • light
  107. Carbon source: autotroph and heterotroph
    • CO2
    • organic molecules
  108. Electron source: organotroph and lithotroph
    • organic molecules,
    • inorganic molecules.
  109. describe fermentation
    • Uses endogenous electron acceptor like pyruvate.
    • No etc or pmf.
    • ATP only produced by substrate level phosphorylation.
  110. What is respiration? How does it differ between aerobic and anaerobic microorganisms?
    • Glycolytic pathways,
    • transition step,
    • tricarboxylic acid cycle
    • oxidative phosphorylation in ETC.
    • They vary in final electron acceptor.
  111. Describe the Embden-Meyerhof pathway:
    • Breaking down sugar.
    • occurs in cytoplasm of both prokaryotes and eukariotes.
    • most common.
  112. Describe the pentose phosphate pathway
    • can operate same time as other pathways.
    • can be aerobic or anaerobic.
    • Is amphibolic.
    • Produces NaDPH, and Sugars.
    • ATP can be made from intermediates.
  113. Describe the Entner-Doudoroff pathway
    produces 1 of everything vs 2 of glycolyses.
  114. Describe the reactants and products of the Tricarboxylic Acid Cycle
    • Common in aerobic microorganisms.
    • Piruvate in CO2 and NADH and ACoA.
    • Each ACoA:
    • 2 CO2
    • 3 NADH
    • 1 FAD2
    • 1 GTP
  115. Describe the reaction involved in the formation of acetyl CoA from pyruvate.
    • TAC,
    • Each pyruvate: 1 CO2, 1 NADH, 1 ACoA
  116. Identify the differences between the mitochondrial ETC and the prokaryotic ETC
    • Location, mitochondria vs. cell membrane.
    • Different electron carriers.
    • May have branches or be shorter.
    • May have lower P/O ratio.
  117. Explain the chemiosmotic hypothesis and function of the Electron transport chain.
    Pumps protons out to churn atp synthase on the way back in via PMF.
  118. Explain the chemiosmotic hypothesis and function of ATP synthase
    Proton diffusion through protein results in atp being formed.
  119. Summarize ATP production during aerobic respiration.
    • Glucose is oxidized and ETC creates most ATP
    • Oxygen is final e- acceptor.
    • 36-38 ATP.
    • actual closer to 30.
  120. What are some uses of the Proton motive force in the cell?
    • ATP Production
    • flagellar rotation
    • active transport.
  121. Discuss the differences anaerobic respiration and aerobic respiration
    • Inorganic Ions act as e- acceptor.
    • Organic receptors also work.
    • Less effective than aerobic.
  122. Identify the major electron acceptors used in anaerobic respiration
    • NO3-
    • SO4 2
    • CO2
    • Fe3+
    • SeO4 2-
  123. Describe overall processes of anaerobic respiration that occur in Paracoccus denitrificans
    • Image UploadImage Upload
    • reduction of nitrate to nitrogen gas inavailabile.
  124. Describe overall processes of anaerobic respiration that occur in Methanogens
    CO2 or CO3 2- is reduce to methane CH4
  125. Describe overall processes of anaerobic respiration that occur in Desulfovibrio
    SO4 2- is reduced to H2S
  126. Compare and contrasts the processes of respiration and fermentation.
    • NADH Produced, but is then oxidized.
    • Pyruvate is electron acceptor.
    • No oxidative phosphorylation.
  127. Describe the two stages in the process of fermentation
    • NADH Produced, but is then oxidized.
    • Pyruvate is electron acceptor
  128. Describe alcoholic fermentation
    Alcohol and Co2 are produced as pyruvate degrades.
  129. Describe homolactic fermentation
    Only NADH is given off as pyruvate degrades to lactate.
  130. Describe heterolactic fermentation
    Lactic acid, ethanol and CO2 produced.
  131. Describe mixed acid fermentation
    Ethanol and other acids produced.
  132. How are monosaccharides catabolized?
    converted into glucose 6 phosphate to enter glycolysis.
  133. How are disaccharides catabolized?
    cleaved into monosacharides
  134. How are Glycogen and Starch catabolized?
    subunits cleaved by phosphorylases.
  135. How is PHB (poly-beta-hydroxybutyrate) catabolized?
    it is turned into ACoA for the TCA cycle.
  136. Describe the stages in the catabolysis of lipids
    • Turned into glycerol for glycolysis
    • or fatty acids, Then ACoA for TCA
  137. Describe deamination
    removal of amino group from AA,
  138. In the simplest way possible describe:
    • symbiosis: simple relationship between two or more.
    • Ectosymbiosis: one on top of another
    • Endosymbiosis: on inside another
    • Consortium: having more than one symbiont
  139. In the simplest way possible describe:
    • Mutualism: Obligatory ++
    • Cooperation: not obligatory ++
    • Commensualism: 0+
    • predation: x+
    • Parasitism: -+
    • Amensalism: 0-
    • Competition: --
  140. Describe Staph Food poisoning:
    • Staphylococcus aureus
    • GI probs, 6-36h
    • Contaminated Food.
    • Keep food hot or cold, in doubt throw out.
    • All people susceptible
  141. Describe Syphilis
    • The great pretender
    • Treponema pallidum - gramneg spirochete
    • Hypcrates and tuskegee
    • Human reservoir 21 day ave. (10-90)
    • infectus until latent stage
    • rashes and lesions
  142. Describe Listeriosis
    • Listeria monocytogenes grm+ rod. flagella
    • pigs, rodents, undercooked pork. melons
    • most asymptomatic
    • can penetrate epithelial lining.
  143. Describe Gonorrhea
    • Neisseria gonorrhoeae diplococci
    • 5 phase. human reservoir. Many asymptomatic carriers.
    • Lots of african americans 20-24.
    • 2-5d. men up to 1month.
    • Dysuria. or painfull discharge.
    • 2nd to chlymidia as bacterial STD.
  144. Describe Typhoid Fever
    • Salmonella enterica serovar Typhi Rod grm-
    • Falcultative anerobe, peritrichous flgella.
    • bile resistant, found only in humans.
    • Asymptomatic typhoid mary.
  145. Describe Botulism
    • Clostridium Botulinum. grm+ rod. anaerobic. endospore forming.
    • 7 neurotoxins. 3 types. food, infant, wound.
    • paralysis.
    • people and animals.
    • food, ingesting endospores.
    • infant, honey or airborn particles.
    • Wound, like tetanus.
  146. Describe Cholera
    • Vibrio cholerae 16 strains. grm- flgellum.
    • contaminated water or food.
    • LOTS of diarrhea
  147. Describe Pertussis
    • Bordetella pertussis. grm- aerobic coccobacillus.
    • binds to cillia in resp. sys.
    • Whooping cough.
    • person-person , dtap.tdap
  148. Describe Lyme disease:
    • Borelia burgdorferi. spirochete.
    • mice, ticks (lxodes scapularis), deer.
    • bruise with halo.
    • no more vaccine.
  149. What are macronutrients?
    Nitrogen, Phosphorous, Sulfur.
  150. Image UploadBased off the following graph, what type of metabolism do the following microorganisms exhibit?
    • Obligate aerobe
    • facultative anaerobe
    • aerotolerant anaerobe
    • obligate anaerobe
    • microaerophile
Card Set:
Microbiology test 2
2013-02-27 18:07:21
bio 321 test micro

Notes for Bio321 test 2
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