MB 451 Microbial Diversity Midterm Exam #2 Honor pledge: “I have neither given nor received unauthorized aid on this test.” Name : ____KEY___________________________________________________________ Signed : _________________________________________________________________ Date : _______________________________ 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 Page 1 of 7 __ 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 Page 2 of 7 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. Page 3 of 7 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 Page 4 of 7 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. Page 5 of 7 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. Page 6 of 7 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 Page 7 of 7