Key for Midterm #2 - MB 409 - April 7, 2003

1. What are the three primary evolutionary branches of life? (5 points)

Bacteria, Archaea, and Eukarya

2. __B_ Which of the following is not used by Bacteria for motility? (3 points)
A. gas vacuoles
B. cilia
C. flagella
D. spirochaete-type corkscrewing
E. gliding

3. __C__ Which of the following is the fundamental distinguishing feature of Gram-positive type cell envelopes? (3 points)
A. thick peptidoglycan layer
B. fatty-acid glycerol-phosphate ester lipids
C. no outer membrane
D. lipopolysaccharide
E. paryphoplasm

4. __C__ Cyanobacteria can vary their ratio of Z-scheme vs cyclic photosynthesis in order to.... (3 points)
A. maximize the amount of ATP they synthesize
B. make the no more oxygen than is needed for photorespiration
C. adjust the ratio of ATP:NADPH they synthesize
D. adjust to differences in the intensity of available light
E. adjust to differences in the available wavelengths of light

5. __C__ Which of the following genera are not phototrophs? (3 points)
A. Halobacterium halobium
B. Heliobacterium gestii
C. Helicobacter pylori
D. Anabaena variabilis
E. Chlorobium limicola

6. __E__ Most methanogens make methane from: (3 points)
A. H2 + O2
B. acetate or methanol
D. H2 + lactate
E. H2 + CO2

7. __D__ A cyanobacterial heterocyst can... (3 points)
A. reproduce
B. photosynthsize
C. resist harsh environments
D. fix nitrogen
E. all of the above

8. __B__ A hydrothermal vent in which all (or nearly all) of the water is vaporized before emerging to the surface is a... (3 points)
A. solfatara
B. fumarole
C. black smoker
D. geyser
E. mud volcano

9. __A__ Which of the following is not thermophilic? (3 points)
A. Deinococcus radiodurans
B. Aquifex pyrophilus
C. Pyrodictium occultum
D. Chloroflexus aurantiacus
E. Thermomonospora viridis

10. __E__ Which is an unlikely electron donor for electron transport? (3 points)
A. H2S
B. photosystem I
C. H2
E. glucose

11. __C__ Which do you think could not be the terminal electron acceptor in sulfur respiration? (3 points)
A. elemental sulfur
B. thiosulfate
C. sulfide
D. sulfite
E. sulfate

12. __C__ Which one of these does Chlamydia make for itself? (3 points)
A. glucose
C. ribosomes
D. alanine
E. riboflavin

13. __A__ Magnetotactic Bacteria use the earth's magnetic field to... (3 points)
A. distinguish up from down
B. physically pull them so they don't need to use energy to swim
C. guide their asteroid to Earth on the trip from Mars
D. eliminate friction by levitation
E. distinguish north from south

14. __B__ During log phase, Arthrobacter globiformis is rod-shaped. In stationary phase it is .... (3 points)
A. pleomorphic
B. a coccus
C. still rod-shaped
D. filamentous
E. sporulated

15. __B__ Deinococcus radiodurans is resistant to UV and gamma radiation because... (3 points)
A. it protects it's DNA from damage
B. it is efficient at repairing it's DNA
C. it's DNA exists normally in a large number of small fragments
D. it's DNA is modified so that it doesn't absorb at these wavelengths
E. it doesn't have DNA

16. __A__ Halophilic Archaea harvest light using.... (3 points)
A. bacteriorhodopsin
B. photosystem I
C. photosystem II
D. both photosystems
E. none of the above

17. __A__ How do we know about the existence phylogenetic groups of organisms that can't be cultured? (3 points)
A. from rRNA gene sequences obtained directly from the DNA of microbial communities
B. from genome sequencing and comparative genomics
C. by fluorescent in situ hybridization using probes against ribosomal RNAs
D. from the direct observation of organisms with unique cellular morphologies
E. from biochemical identification of new metabolic phenotypes

18. __C__ Which of the following is not a typical form of sulfur metabolism? (3 points)
A. sulfur respiration
B. sulfur oxidation
C. sulfur hydrolysis
D. sulfur reduction

19. __A__ Which if the following is the least of a problem for thermophiles? (3 points)
A. water vaporizes at 100°C
B. DNA denatures at about 65°C
C. membranes become more fluid at higher temperatures
D. chemical reaction occur faster at higher temperatures
E. many small biomolecules are short-lived at high temperatures

20. __D__ What is not true about the nucleii of eukaryotes and Gemmata? (3 points)
A. both nuclear envelops are comprised to 2 lipid bilayers
B. the Gemmata nucleus contains functional ribosomes, those of eukaryotes do not
C. both have pores or openings in their envelops that allow movement of material in and out
D. both contain all of the cells DNA
E. the nuclear envelop is continuous with the other internal membranes of the cell

21. __E__ Thermotoga adapted to life at high temperatures... (3 points)
A. before the main radiation of bacterial diversification
B. after Aquifex but before Thermoleophilum
C. when it's habitat (the Bay of Naples) became hydrothermally active
D. during enrichment culture at high temperatures
E. Thermotoga never adapted to life at high temperatures

22. What, in one sentence, was the most important thing other than getting samples out aseptically that the authors (Russ Vreeland, et al.) of the paper entitled "Isolation of a 250-million-year-old halotolerant bacterium from a primary salt crystal" tried to convince you of? (5 points)

That the aqueous inclusions in the salt crystals were trapped there 250 million years ago, and do not originate more recently.

23. Briefly describe the symbiosis in the phototrophic Chlorobium consortium. Draw a picture of one. (5 points)

Chlorobium participates in symbiosis with an uncultivated rod-shaped heterotroph (a beta-proteobacterium). The motile heterotroph is bound by several non-motile green sulfur bacteria - the heterotroph is provided resources by the green bacteria, which in turn are provided motility by the heterotroph. The two cell types divide synchronously, and the heterotroph swims around to follow the optimal light (phototaxis): the cells are in close communication. The green bacteria can often be cultivated alone but the heterotrophs have not.

24. Tell me about something interesting you learned from the paper by John Reeve, "Archaebacteria then...Archaes now (Are there really no archaeal pathogens?)", other than the fact that there are no known archaeal pathogens. (5 points)

For example:

That the first protein-encoding genes from Archaea were cloned by complementation of E.coli auxotrophs.

25. Give an example genus for each of the phylogenetic groups below. (20 points)

For example:

Aquifex Aquifex & relatives

Thermotoga Thermotoga & relatives

Chloroflexus green non-sulfur Bacteria & relatives

Deinococcus Deinococccus group

Gemmata Planctomycetes

Treponema spirochaetes

Flavobacterium Cytophagales

Rhodospirillum alpha subdivision of the purple Bacteria & relatives

Alcaligenes beta subdivision of the purple Bacteria & relatives

Escherichia gamma subdivision of the purple Bacteria & relatives

Desulfovibrio delta purple subdivision of the purple Bacteria & relatives

Helicobacter epsilon subdivision of the purple Bacteria & relatives

Bacillus low G+C Gram positive Bacteria

Streptomyces high G+C Gram positive Bacteria

Sulfolobus Crenarchaea

Methanobacterium Euryarchaea

Giardia Diplomonads

Trypanosoma Euglenoidozoans (Mastigophorans)

Aspergillus fungi

Acidobacterium a bacterial group with few or no cultivated species (not one of the above groups)