MB 451 Microbial Diversity
Midterm Exam #2
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1. What are the 3 primary evolutionary branches of life? (5 points)
Bacteria, Archaea, Eukarya
__B__ 2. The root of the Universal phylogenetic tree was
identified using analysis of . . . (2 points)
__ E__ 5. Which of the following is not a process by which a
photoautotroph can fix CO2? (2 points)
A. small subunit ribosomal RNA sequences
A. the Calvin cycle
B. ancient duplicated genes
B. the reverse (reductive) TCA cycle
C. ribosomal RNA spacer sequences
C. the reductive acetyl-CoA pathway
D. antibiotic resistance genes
D. the hydroxypropionate pathway
E. none of the above
E. all of the above can be used to fix carbon
__ C__ 3. The deep branches of the bacterial phylogenetic tree
are both thermophilic and . . . (2 points)
__ A__6. Proteobacteria, regardless of their phenotype, obtain
their energy from . . . (2 points)
A. pathogenic
A. oxidation/reduction reactions & electron transport
B. autotrophic
B. light & photosynthesis
C. primitive
C. NADH, oxygen, & oxidation photphorylation
D. anthropomorphic
D. organics & substrate-level phosphorylation
E. none of the above
E. all of the above
__ E__ 4. Which of the following phototrophic groups is/are
capable of cyclic photophosphorylation? (2 points)
A. Cyanobacteria
B. Chloroflexi
C. Chlorobi
D. purple photosynthetic Bacteria
__ D__ 7. The term “Gram-positive” refers to . . . (2 points)
A. a particular phylogenetic group
B. a particular staining pattern
C. a particular envelope structure
D. it can mean any of these things
E. none of the above
E. all of the above
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__ B__ 8. Which of the following is not a likely notion of what
viruses might be? (2 points)
__ C__ 13. Which of the following is not true. Archaea can be
thought of as . . . (2 points)
A. degenerate parasites
A. a missing link between Bacteria and Eukarya
B. spontaneous generation
B. reflections of early life on Earth
C. genetic offshoots of their hosts
C. the ancestors of Eukarya
D. remnants of precellular life
D. a deep branch of the Eukarya
E. all of the above are reasonable
E. all of the above are true
__ D__ 9. Obligate parasites are usually _________ compared
to their non-parasitic relatives. (2 points)
__ B__ 14. Secondary metabolites are produced during . . .
(2 points)
A. slimy and underhanded
A. during logarithmic growth
B. morphological and biochemically complex
B. during stationary phase
C. small with simple life cycles
C. during lag phase after reinoculation
D. simplified and rapidly-evolving
D. all of the above - they are constitutive
E. none of the above
E. none of the above - they are synthetic
__ A__ 10. How do we know about the many phylogenetic
groups with no cultivated species? (2 points)
__ A__ 15. The two fundamentally different types of thermophiles are . . . (2 points)
A. rRNAs sequences PCR-ed from the environment
A. ancestral and adapted
B. from direct microscopic observations
B. autotrophic and heterotrophic
C. by statistical analysis of cultivated organisms
C. Gram-positive and Gram-negative
D. phenotypic analysis of environmental samples
D. eukaryotic and prokaryotic
E. all of the above
E. none of the above
__ D__ 11. Which of the following is not a general phenotype
found in the Archaea? (2 points)
A. sulfur-metabolizing thermophiles
B. methanogens
C. extreme halophiles
D. opportunistic pathogens
E. all of the above are common in the Archaea
__ A__ 12. Which of the following does not describe a common
sulfur metabolism in Archaea? (2 points)
__ D__ 16. The electron transport chain is used to create a
proton gradient, which is harvested by ATPase to make
ATP. What do organisms without the electron transport
chain use ATPase for? (2 points)
A. to pump protons into the cells
B. to generate ATP directly from NADH
C. to generate ATP from glycolysis
D. to generate a proton gradient
E. none of the above
A. Sulfide + light + CO2 --> sulfate + organics
B. Sulfur + hydrogen --> hydrogen sulfide
C. Sulfur + oxygen --> sulfuric acid
D. Sulfur + organics -> carbon dioxide + hydrogen sulfide
E. all of the above are common in Archaea
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17. Briefly describe any bacterial species of your choosing from the phyla Aquificae or Thermotogae. Be sure to include metabolism, morphology, habitat, and any other interesting facts about the organism you choose. (5 points)
Example answer:
Thermocrinus ruber (phylum Aquificae)
T. ruber is (like all members of this phylum) a thermophilic (80-90°C) hydrogen oxidizer. It is microaerophilic and autotrophic (fixing CO2 via the reverse TCA cycle) as well. It can also grow heterotrophically using formate or formamide. In
culture, this organisms grows as long rods (with numerous flagella at one end of the cell), but in its natural habitat it
grows as pink filaments. This pink filamentous growth is common in the neutral pH hot springs of Yellowstone, and early
unsuccessful attempts to cultivate it lead, by chance, to the cultivation of Thermus aquaticus and so, indirectly, to PCR
technology.
18. Briefly describe any bacterial species of your choosing from the phylum Cyanobacteria. Be sure to include metabolism, morphology, habitat, and any other interesting facts about the organism you choose. (5 points)
Example answer:
Oscillatoria
Oscillatoria is a common mesophilic freshwater cyanobacterium. It is a large filamentous organism easily mistaken for a
eukaryotic alga. Often sheathed. Filaments are composed of individual short, disk-like cells that divide by binary fission.
There is no differentiation of cells, except for the rounded ends of filaments; no heterocysts, akinetes, or hormongonia
are produced. Filaments are rigid and fairly straight, and motile by gliding. Like cyanoabcteria in general, Oscillatoria is a
photoautotroph, generating both reducing power for carbon fixation (via the Calvin cycle) and ATP from light. Oxygen generated by photosynthesis.
19. Briefly describe any bacterial species of your choosing except Escherichia coli from the phylum Proteobacteria. Be sure to
include metabolism, morphology, habitat, and any other interesting facts about the organism you choose. (5 points)
Example answer:
Beggiotoa alba
B. alba is a gliding filamentous sulfur oxidizer. Sulfide is oxidized to elemental sulfur, which accumulates in globules inside the cell. These sulur granulaes are further oxidized to sulfate. They are microaerophilic and autotrophic. It is found
on the surface of freshwater and marine seiements, and especially freshwater sulfur springs. Unlike other filamentous
sulfur-oxidizing bateria, B. alba does not produce holdfasts or sheaths. B. alba is distinguished from other Beggiotoa pecies by diamter - 2-3 um.
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20. Briefly describe any bacterial species of your choosing from the phylum Planctomycetes. Be sure to include metabolism, morphology, habitat, and any other interesting facts about the organism you choose. (5 points)
Example answer:
Blastopirellula marina
B. marina is a common freshwater organism, oval with short stalks (fibrous and external to the cell membrane) that cluster cells together into rosettes. Like most Planctomycetes, it is a mesophilic heterotroph. B. marina has a simple for of
internal comprtmentalization compared to other Planctomycetes - the internal cytoplasmic memban separates the oval
riboplam compartment from the periperpheral paryphoplasm, which is thickest at one end of the cell. Like other Planctomycetes, B. marina lacks peptidoglycan, but has a cell wall made of plates of unknown composition.
21. Briefly describe any bacterial species of your choosing except any species of the genus Bacillus from the phyla Firmicutes or
Actinobacteria. Be sure to include metabolism, morphology, habitat, and any other interesting facts about the organism you
choose. (5 points)
Example answer:
Clostridium botulinum
C. botulinum is a mesophilic anaerobic heterotroph. It is rod-shaped and produces endospores. Also like its relatives, C.
botulinum lacks the electron transport chain, and so ferments organics by substrate-level phosphorylation. C. botulinum
produces a potent toxin known as Botox. Intoxication by this toxin is known as botulism, a flaccid paralysis. Botulism is
usually the result of the ingestion of the toxin from spoiled canned food, but in infants the organisms itself can sometimes
grow in the gut. It can also grow in gangrenous wounds. Botox is popularly and inexplicably used to to erase all signs of
personality from the faces of experienced people.
22. Briefly describe any bacterial species of your choosing from the phylum Bacteroids (Sphingobacteria). Be sure to include metabolism, morphology, habitat, and any other interesting facts about the organism you choose. (5 points)
Example answer:
Flavobacterium johnsoniae
F. johnsonae is an aerobic mesophilic heterotroph, growing by chitin degradation. It is rod-shaped with tapered ends.
common in freshwater & marine environments. It is a rapid glider; this gliding seems to be caused by adhesins that move
from the leading tip of the cell to trailing end. Colonies are yellow. Like other Sphingobacteria, the cell membrane of F.
johnsoniae contains sphingolipids
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23. Briefly describe any archaeal species of your choosing from the phylum Euryarchaea. Be sure to include metabolism, morphology, habitat, and any other interesting facts about the organism you choose. (5 points)
Example answer:
Thermoplasma acidophilum
T. acidophilum is a facultative anaerobe, moderately thermophilic, acidophilic and autotrophic. It can use either O2 or
sulfur for respiration. It is iregularly shaped, with pseudopod-like extensions, and also has a single flagellum for motility,
It lacks a cell wall, but protein in the cell membrane are cross-linked for rigidity. It is found in smoldering colad refuse
piles (tailings), and so perhaps the natural habitat is the subterranean coal deposit.
24. Briefly describe any archaeal species of your choosing from any archaeal phylum other than Euryarchaea. Be sure to include
metabolism, morphology, habitat, and any other interesting facts about the organism you choose. (5 points)
Example answer:
Korarchaeum cryptophilum (phylum Korarchaea)
K. cryptophilum is the only korarchaeon about which much of anything is known. Although not in pure culture, it can be
isolated from thermophilic enrichment cultures predominated by this organism by treatment with SDS, to which it is unusually resistant. The genome sequence has been determined from these isolations, and they seem to be hydrogengenerating peptide-degrading heterotrophs. They are long very thin rods with an S-layer cell wall. These organism was
taken from Obsidian Pool, Yellowstone.
25. Briefly describe and diagram one mechanism other than flagella that Bacteria use for motility. (5 points)
Example answer:
Gliding by Bacteroids
Adhesins on the surface of the cells seem to move uniformly from
one end of the cell to the other. Presumably the adhesins are
internalized upon reaching the trailing end of the cell, and reemerge at the leading edge. Think of the tracks on a bulldozer, a
conveyor belt, or an escalator. These organisms can only glide if
in contact with a surface. It has been proposed that gliding in
Myxobacteria may be similar, except that the surface adhesins
follow a helical path along the surface of the cell, guided by the
cytoskeleton.
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26. Describe one mechanism/pathway by which an autotrophic photosynthesizer can get the reducing power needed for CO2 fixation. Be sure to specify the kinds of organisms that can use this pathway, and how (or if) this pathway uses elements of cyclic
photophosphorylation. (10 points)
Example answer:
In Chlorobi, the reaction center is very highly reduced, and so the electrons from it pass through an iron-sulfur protein
(via a chlorophyll a intermediate) before going to the electron transport chain during cyclic photophosphorylation. For
fixing carbon, electrons in the FeS protein are used instead to reduce ferridoxin, which is used in the reductive TCA pathway to reduce CO2 to acetyl-CoA. Electrons from sulfide are used to recycle the reaction complex chlorophylls.
27. Prions are thought by many to be protein-only infective agents, and you read a paper either for or against this view. Describe
the single most compelling point the authors made in their attempt to convince you that their view of prions is correct. (10
points)
Example answer:
I read the paper in favor of the prion hypothesis, and the best evidence I think they gave was that highly purified PrP(res)
protein could catalyze the conversion of PrP(c) to PrP(res) in vitro.
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Example organisms from the lectures:
Acidobacterium capsulatum
Anabaena
Anaerolinea thermophila
Aquifex pyrophilus
Archaeoglobus fulgidus
Arthrobacter globiformis
Azotobacter vinelandii
Bacillus cereus
Bacteroides thetaiotaomicron
Bdellovibrio bacteriovorans
Beggiatoa alba
Blastopirellula marina
Borrelia recurrentis
Brocadia anammoxidans
Buchnera aphidicola
Caulobacter crescentus
Chlamydia trachomatis
Chlorobium limicola
Chloroflexus aurantiacus
Chromatium vinosum
Methanothermobacter thermoautotrophicus
Sphaerotilus natans
Microcystis
Spiroplasma
Mycobacterium ulcerans
Streptomyces antibioticus
Mycoplasma hominis
Sulfolobus solfataricus
Myxococcus xanthus
Thermocrinus ruber
Nanoarchaeum equitans
Thermodesulfobacterium hydrogenophilum
Nitrospira marina
Thermoleophilum album
Opitutus terra
Thermomicrobium roseum
Oscillatoria
Thermoplasma acidophilum
Paramecium
Thermoproteus tenax
Pelodictyon phaeoclathratiforme
Thermosipho africanus
Prochloron
Thermotoga maritima
Prosthecobacter fusiformis
Thermus aquaticus
Protochlamydia amoebophila
Thiobacillus thioparus
Pyrococcus furiosus
Trichomonas vaginalis
Pyrodictium occultum
Trypanosoma
Ralstonia solanacearum
Veillonella atypica
Rhizobium etli
Verrucomicrobium spinosum
Rhodomicrobium vannielii
Wolbachia pipientis
Roseiflexus castenholzii
Clostridium botulinum
Crysomallon squamiferum symbiont
Cytophaga hutchinsonii
Deinococcus radiodurans
Dermocarpa
Desulfovibrio desulfuricans
Dictyostellium
Escherichia coli
Fervidobacterium islandicum
Fischerella
Flavobacterium johnsoniae
Fusobacterium nucleatum
Gemmata obscuriglobus
Giardia lamblia
Halobacterium salinarium
Helicobacter pylori
Heliobacterium chlorum
Herpetosiphon aurantiacus
Isosphaera pallida
Korarchaeum cryptofilum
Leptospira biflexa
Leptospirillum ferrooxidans
Leuconostoc mesenteroides
Magnetobacterium bavaricum
Methanocaldococcus jannaschii
Methanosarcina barkeri
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