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)

A. small subunit ribosomal RNA sequences

B. ancient duplicated genes

C. ribosomal RNA spacer sequences

D. antibiotic resistance genes

E. none of the above

__ C__ 3. The deep branches of the bacterial phylogenetic tree are both thermophilic and . . . (2 points)

A. pathogenic

B. autotrophic

C. primitive

D. anthropomorphic

E. none 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

E. all of the above

__ E__ 5. Which of the following is not a process by which a photoautotroph can fix CO2? (2 points)

A. the Calvin cycle

B. the reverse (reductive) TCA cycle

C. the reductive acetyl-CoA pathway

D. the hydroxypropionate pathway

E. all of the above can be used to fix carbon

__ A__6. Proteobacteria, regardless of their phenotype, obtain their energy from . . . (2 points)

A. oxidation/reduction reactions & electron transport

B. light & photosynthesis

C. NADH, oxygen, & oxidation photphorylation

D. organics & substrate-level phosphorylation

E. all of the above

__ 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

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__ B__ 8. Which of the following is not a likely notion of what viruses might be? (2 points)

A. degenerate parasites

B. spontaneous generation

C. genetic offshoots of their hosts

D. remnants of precellular life

E. all of the above are reasonable

__ D__ 9. Obligate parasites are usually _________ compared to their non-parasitic relatives. (2 points)

A. slimy and underhanded

B. morphological and biochemically complex

C. small with simple life cycles

D. simplified and rapidly-evolving

E. none of the above

__ A__ 10. How do we know about the many phylogenetic groups with no cultivated species? (2 points)

A. rRNAs sequences PCR-ed from the environment

B. from direct microscopic observations

C. by statistical analysis of cultivated organisms

D. phenotypic analysis of environmental samples

E. all 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)

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

__ C__ 13. Which of the following is not true. Archaea can be thought of as . . . (2 points)

A. a missing link between Bacteria and Eukarya

B. reflections of early life on Earth

C. the ancestors of Eukarya

D. a deep branch of the Eukarya

E. all of the above are true

__ B__ 14. Secondary metabolites are produced during . . . (2 points)

A. during logarithmic growth

B. during stationary phase

C. during lag phase after reinoculation

D. all of the above - they are constitutive

E. none of the above - they are synthetic

__ A__ 15. The two fundamentally different types of thermo-philes are . . . (2 points)

A. ancestral and adapted

B. autotrophic and heterotrophic

C. Gram-positive and Gram-negative

D. eukaryotic and prokaryotic

E. none of the above

__ 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

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17. Briefly describe any bacterial species of your choosing from the phyla Aquificae or Thermotogae. Be sure to include metabo-lism, 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 auto-trophic (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, mor-phology, 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 gen-erated 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 in-side 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 pe-cies 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, mor-phology, 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 clus-ter 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 Plancto-mycetes, 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 me-tabolism, 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, morphol-ogy, 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 un-usually resistant. The genome sequence has been determined from these isolations, and they seem to be hydrogen-generating 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 ree-merge 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 fixa-tion. 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 path-way 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

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

Methanothermobacter thermoautotrophicus

Microcystis

Mycobacterium ulcerans

Mycoplasma hominis

Myxococcus xanthus

Nanoarchaeum equitans

Nitrospira marina

Opitutus terra

Oscillatoria

Paramecium

Pelodictyon phaeoclathratiforme

Prochloron

Prosthecobacter fusiformis

Protochlamydia amoebophila

Pyrococcus furiosus

Pyrodictium occultum

Ralstonia solanacearum

Rhizobium etli

Rhodomicrobium vannielii

Roseiflexus castenholzii

Sphaerotilus natans

Spiroplasma

Streptomyces antibioticus

Sulfolobus solfataricus

Thermocrinus ruber

Thermodesulfobacterium hydrogenophilum

Thermoleophilum album

Thermomicrobium roseum

Thermoplasma acidophilum

Thermoproteus tenax

Thermosipho africanus

Thermotoga maritima

Thermus aquaticus

Thiobacillus thioparus

Trichomonas vaginalis

Trypanosoma

Veillonella atypica

Verrucomicrobium spinosum

Wolbachia pipientis

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