Microbialdiversityexam2.txt

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Microbialdiversityexam2.txt
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microbial exam
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microbial exam 2
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  1. Who discovered the Archae?
    Carl Woese
  2. Archae is the greek root for...
    Ancient things
  3. T/F Archaea are more closely related to Eukarya than to bacteria
    True
  4. T/F Archaea have cytoplasmic membrance full of straight chain fatty acids
    False they are made of branced hydrocarbons
  5. T/F archae can have monolayer cytoplasmic membranes
    True
  6. T/F Archaea are extremophiles, but bacteria are not
    False, some bacteria are extremophiles and some archaea are mesophiles
  7. what are the three phyla of archaea?
    Euryarchaeaota, Crenarchaeota and Korarchaeota
  8. methanogens are _________ anerobes
    Obligate
  9. Euryarchaeota include what two groups
    Methanogens and extreme halophiles
  10. Crenarchaeota include what two groups
    Hyper- and hypothermophiles
  11. In what 4 ways do hyperthermic archaea survive high temperatures?
    Saturated lipids in membranes, Produce heat resistant enzymes, Use chaperonins to refold proteins, use DNA stabilizing mechanisms.
  12. what are some whaty for DNA to stablilize?
    positive supercoiling of DNA using reverse gyrase, salts prevent chemical damage to DNA, DNA binding proteins: archeal histones
  13. what sets the upper temp limit for archaea?
    ATP, bc it destabilizes at high temps
  14. T/F extremophiles evolved at a slower rate then mesophiles
    True
  15. What is the best known phylum of the archaea
    Euryarchaeota
  16. which group in the Euryarchaeota is most responsible for the oil pipe line bursts
    archaeoglobales
  17. the only sulfur reducing amoung archaea
    Archaoglobales
  18. Describe the halobacteriales
    Extreme halophiles, non motile gram negative, obligate anaerobes, Great DNA repair abilities, use light mediated ATP synthesis (not photosynthesis)
  19. what are the habitiats of the methanogenic archaea
    hydrothermal vents, as symbionts of protozoa, in sewage, in animal disgestive tracts
  20. what is the only methanogen that is hyperthermophile
    methnopyrus
  21. what shape do the methanopyrus have
    rods
  22. Crenarchaeota stain gram negative or gram positive
    gram negative
  23. what is the most abundant phylum of archaea in marine enviornments
    crenarchaeoata
  24. What is the most hyperthermophilic organism known
    Pryolobus
  25. what type of respiration do the crenarchaeota do? and what habitat do they live?
    faculatative aerobe, submarine volcanic
  26. describe the sulfolobales
    terrestrial volcanic habitat and hot springs, aerobic, acidiophilic, herpthermic and chemolithotrophic,
  27. what is the model system in archaeophage biology?
    sulfolobales
  28. what is the habitat and respiration style thermoproteales?
    terrestial volcanic habitats, mildly acidic, hyperthermophiles, chemolitotrophs anaerobes,
  29. what are the guidlines for compenstion on bioprospecting
    requires prior informed consent form source country, sharing benefits and promoting sustainable use of biodiversity.
  30. what is a new class of antibiotics
    archeocins
  31. where are the Korarchaeota found
    yellowstone hotspring
  32. What is the smallest organism known and how big is it?
    nanoarchaeum, 400nm diameter
  33. Explain how the nanoarchaeum is an obligate symbiont
    it is an obligate sybiont with another archaen ignioccus, it must be in contact wit ingnicoccus to survive
  34. Do archaea have viruses?
    yes.
  35. What is an example of the archaea viruses
    STIV.
  36. What was the first archaeophage described?
    STIV
  37. what type of enviornment does it prefer?
    Acidic hyperthermal enviornment
  38. All currently known archaeophage have what type of DNA?
    dsDNA
  39. Are Archaephage monophyletic?
    we dont know yet, but we can say no for now bc its branched off myoviridae
  40. what evidence supports the primordial hypothesis?
    the fact that viruses from different domains are similar suggests that viruses may have evolved prior to LUCA
  41. what is the eocyte hypothesis?
    that crenarchaeota are sister to eukaryotes not euryarchaeota
  42. with the eocyte hypothesis what two ways are beleived that crenarchaeota developed a nucleaus?
    spontaneaous origin, endosymbiotic origin with gram negative bacterisum the aquired the crenarchaeota endosymbiont which later becaome nucleus
  43. Name the 6 steps to cloning a DNA molecule.
    • DNA extraction
    • PCR
    • Ligation to plasmid
    • transformation of E. Coli
    • E. Coli culture on antibiotic medium
    • Individual colonies sequenced
  44. After sequencing what is done in order to identify a DNA molecule
    BLAST analysis
  45. what is the problems that arise from phylogenetic analysis
    some DNA does not have universal markers
  46. what is an alternative to cloning?
    sanger sequencing
  47. name and explain the three methods of the phylogenetic analysis
    • neighbor joining which looks a the percentge of similarity.
    • Parsimony seeks the tree with the least evolutionary step
    • Likelihood based methods looks at the actual data to seek the most likely hypothesis.
  48. Explain the Sanger sequence
    ssDNA is mixed with primer and mixed with DNA polymerase, dNTPs, replications terminatiors and primerss for replication. they replicated, they are loaded onto a gel and electrophoresis is done,
  49. What is the noncloning based second generation method
    pyrosequencing
  50. Summarize the Fierer et al study.
    they clonned SSUrDNA for bacteria (16s), archaea (16s) and fungi (18s), clones genomes of vurs sampled soil, Found that there is higher diversity of viruses and bacteria vs archaea, fungi, Higher diversity of Praries bacteria and viruses relative to the rainforest.
  51. The human body hosts how many species of bacteria
    100k
  52. How long does it take for a child to stabilize its flora?
    1 to 6 months depending if a child was born c section or non c- section
  53. Chilren who are breast fed have primaryly what type of bacteria, gram positive or gram negativce
    gram positive
  54. T/F formula fed babies have a less incidence of E. coli and low diversity of microbes
    False, Babies who are fomula fed have higher incidence of proteobacteria and higher diversity of microbes overall
  55. T/F E.coli is the dominate bacteria in human body
    false it is the most common but not dominant
  56. what is the bacillus shape? what does streptobacillus mean?
    rod shaped. chain of rods
  57. name 2 examples of bacillus bacteria.
    E.coli and anthrax bacteria
  58. what is the coccus shaped bacteria.
    They are sphereical
  59. what shape is staphylococcus?
    graped shaped
  60. what is the name of tbe bacteria that is formed into a cube with the round shaped coccus cells.
    sarcina
  61. what is an example of a disease that is caused by coccus bacteria?
    gonorrhea
  62. what coccus bacteria causes tooth decay
    streptococcus
  63. what shape of bacteria is part of out normal flora but also causes hospital acquired infection, food poisoning and toxic shock syndrome?
    stapylococcus aureus.
  64. what bacteria is part of out normal flora on our skin? what shape is it?
    micrococcus luteus, it is sarcina shaped
  65. what are comma shaped bacteria called?
    vibrio
  66. what is the largest and most physiologically diverse clade of bacteria?
    Proteobacteria
  67. T/F All Proteobacteria are gram positive
    False they are all gram negative
  68. T/F Proteobacteria are polyphyletic
    False they are monophyletic
  69. what are the5 major divisions of proteobacteria?
    alpha, beta, gamma, delta, epsilon
  70. what are the 4 groups of proteobacteria covered?
    Purple phtotrophic bacteria, nitrifying bacteria, methanotrophs and methyltrophs, and spirilla
  71. what are the two functional groups of purple phototrophic bacteria.
    purple sulfur bacteria, puple non sulfu bacteria
  72. All Purple phototrophic bacteria carry out what type of phtotsynthesis?
    Anoxygenic
  73. what pigments are used in the anoxygenic photosynethesis of purple phototrophic bacteria
    bacteriochlorophylls and carotenoid
  74. Purple Sulfur bacteria use ______ are electron donor and _______ is stored inside of cells and are phylogenetically united in _________ proteobacteria and are found commonly in _________
    Hydrogen sulfide, sulfur, gamma, merimetic lakes
  75. spirilium proteobacteria look like
    have ridged spiral shape
  76. what is meromictic lakes
    lakes with permanet stratification (no mixing)
  77. T/F Purple non sulfur bacteria can use Hydrogen sulfide.
    true
  78. purple nonsulfur bacteria are __________ and do not require light. They use _____ to obtain C. They represent _____ and ______ proteobacteria.
    photoheterophic, organic molecules, alpha and beta
  79. what are the proteobacterial chemolithotrophs
    nitrifying bacteria
  80. what are the two functional groups of nitrifying bacteria
    True nitrifying bacteria, nitrosifying bacteria (ammonia oxidizing bacteria)
  81. ______ is converted to ________ in nitrite oxidizing bacteria
    Nitrate, nitrite.
  82. what are the three groups of proteobactieral chemolithotrophs
    Nitrifying bacteria, sulfur and iron oxidizing bacteria and hyrdogen oxidizing bacteria
  83. what is an example of sulfur-iron oxidizing bateria? where does is live? what type of shape does it have?
    beggioatoa. sulfur springs. filamentous
  84. what source of E does the Beggiatoa use.
    sulfur.
  85. T/F Beggiatoa are mixotropic
    False they are generally chemolitothrophs but some are mixotrophic and can switch to chemoorganotrophy
  86. Hydrogen oxidizing bacteria belong to what groups of proteobacteria?
    alpha, beta and gamma
  87. what is the theory of endosymbiosis?
    a seperate prokaryotic organism is taken into a eukaryotic cell
  88. what are the 6 chracteristic of the bacteria phylum
    • Prokaryotic cells
    • peptidoglycan cell wals
    • ester linkage in membrane
    • Simple RNA polymerase
    • Protein Synthesis
    • Unique SSUrDNA sequences
  89. Archae do not share all characteriscts except
    that they do have prokaryotic cells
  90. Eukaryontes do not share all characterictsic with bacteria except
    they have ester linkages in the membrane lipids
  91. what are the 2 funcitonal classifications of bacteria
    Gram posistive and Gram negatice
  92. what is the difference between gram positive and gram negative bacteria?
    gram positive have a cell wall that is mainly peptidoclycan and they retain the gram stain color. Gram Negative do not retain the gram stain color and there out wall does not contain much peptidoglycan. they have two layers to outer membrane it have inner phospholipid layer and out lipopolysaccharide layer
  93. T/F Gram negative bacteria have porins which are little pores in the outer membrane
    true
  94. what is the sister group of the gram positive bacteria?
    cyanobacteria
  95. What is polytomy?
    when there are many branching off events that happen at the same time
  96. what is the earliset arising bacteria
    aquifex
  97. T/F proteobacteria are monophyletic
    true
  98. T/F Alpha and Beta proteobacteria are monophyletic but the rest are not
    False they are all monophyletic
  99. Explain the species accumulation curve
    It shows the species richness of a given species sample
  100. what are shared characteristics of the all the bacterial lineages?
    SSUrDNA, Common ancestor, gram negative
  101. what is the sister group of the alpha proteobacteria?
    whe dont know because they all branch out at the sam etim
  102. what are the 7 major proteobacteral chemoorganotrophs
    methylotrophs, pseudomonads, acetic acid bacteria, neisseria, enteric bacteria, vibrio, rickettsias
  103. _________ consume simple one C organic molecules and some can be symbiotic in mussels
    Methlyotrophs
  104. __________ include serveral pathogens and attacks burn victims and the immunocomprimised
    Pseudomonads
  105. _________ can use ethanol to make __________. They are gram negative and can synthesize cellulose
    Acetic acid bacteria, acetic acid
  106. ________ is one cause of meningitis and gonorrhea
    Neisseria
  107. _______ is the best known proteobacteria exampls include.....
    Enteric, E.Coli and Salmonella
  108. T/F Yersenia causes Chron's disease
    False, ppl with Chron's carry Yersenia but it doesnt necesarily cause it
  109. What is the model endosymbiont with aphids
    Buchnera
  110. ________ causes cholera and some food poisoning
    Vibrio
  111. __________ are oblitgate intracellular parasites and cause typhus and rocky mountain spotted fever.
    Rickettsias
  112. What is the name of the proteobacteria that manipulates sexuality of insects in which it selectively kills males
    wolbachia
  113. spirilla include _________ which orient to north/ south axis based on internal magnets
    magnetotactic
  114. describe the 5 ways of reproducing as a bacteria.
    • binary fission- one cell splits into two
    • budding- bud formation, but forms another cell
    • buddding from hyphae- bud forms cells froms from hyphae, hyphae remains attatched to original and other cells is created
    • stalked formation- cell division on stalk produces 2 cells
    • polar growth- formation of secondary cells attatched (dont know how) and they split
  115. name the 3 ways in which polar flagella can be attached to a cell.
    • monotrichous- one end
    • ambitricous- one at ea. end
    • lophotrichous- many at one end
  116. what is it called when there are many flagella placed all around the cell surface?
    Peritrichous
  117. with polar flagellation clockwise rotation means the flagella is anterior/posterior?
    anterior
  118. when a flagella moves counterclockwise the flagellum is postition anterior or posterior?
    posterior
  119. counterclockwise flagellum cause what type of movements
    forward
  120. Bacteria flagella are driven by_______ and archae flagella are driven by________
    H ions, ATP
  121. T/F Bacteria flagella are tine and rotate independently
    False they are thick and rotate independently
  122. explain the ways in which bacteria move other than with flagella.
    gliding motility= non swimming movement, requires contact with solid surface
  123. What type of bacteria use gliding motility
    Myoxobacteria
  124. Explain the gliding motility used in myoxobacteria
    they use gliding motility to creat a fruiting bodie to use to eat
  125. what are the three High GC gram positive bactera?
    Coryneform, myobacteria and actinomycetes
  126. what type of bacteria using snappind division?
    coryneform
  127. what bacteria is characterized as the joint bacterium.
    arthrobacter
  128. T/F Myobacterium are non motile
    true
  129. the type of high GC gram positive bacteria that is used as major producers for antibiotics. with an example as the streptomyces
    actinomycetes
  130. Product of Streptomycen that is used in cancer treatment
    bleomycin
  131. Actinomycete bacteria that is a symbiont with roots that fixes N
    Frankia or Rhizobium
  132. what are the three non sporuolating Low GC gram positive bacteria
    staphylococcus, streptococcus, lactic acid bacteria
  133. what is the well know genus of the lactic acid bacteria that is used to make yogurt
    lactobacillus
  134. how can one distinguish the streptococccus?
    y the activity on blood agar. there is alpha and beta hemolytic
  135. T/F Not all Endopore producers in the Low GC gram positive bacteria are low GC
    True
  136. T/F Endopores are very sensitive to heat
    False they are very resistant to heat and can actually be isolate from soil but heating the soild to kill everything else
  137. _________are famous for the production of larvacides
    Endopore producers like bacillus
  138. Bacillus shaped organism in soil that causes botulism and tenanus
    Clostridium
  139. Low GC gram positive bacteria that lacks a cell is...
    mycoplasms
  140. smallest bacteria capable of autonomous growth
    mycoplasms

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