Midterm Exam #2 : MB 451 Name _________Key__________

1. What are the 3 primary evolutionary branches of life? (5 points)

Bacteria (or eubacteria)
Archaea (or archaebacteria)
Eukarya (or eukaryotes)

2. __A__ A hot spring that produces only steam is a: (2 points)
A. fumarole
B. solfatara
C. humidor
D. geyser
E. travertine

3. __A__ The authors of the pink filamants rRNA analysis paper cloned their rRNA PCR products before sequencing them, rather than sequencing them directly like we did in lab. Why? (2 points)
A. Because they amplified from a population instead of a pure culture.
B. Because sequencing technology at the time required cloning.
C. Because they needed to separate bacterial from archaeal sequences.
D. To prevent the production of chimeras.
E. Because they wanted to make long-term stocks of their DNA samples.

4. __D__ Which of the following is not a way an organism can get the carbon it needs for growth? (2 points)
A. Reverse (reductive) TCA/Kreb’s cycle.
B. Hydroxypropionate pathway.
C. Calvin cycle.
D. Cyclic photophosphorylation.
E. Organics it takes in from the environment

5. __C__ Secondary metabolites are produced in: (2 points)
A. Lag phase
B. Log phase
C. Stationary phase
D. Telo phase
E. none of the above

6. __A__ Filamentous cyanobacteria produce heterocycts so they can physically separate what processes? (2 points)
A. photosynthesis and nitrogen fixation
B. nitrogen fixation and carbon fixation
C. photosynthesis and ATP synthesis
D. ATP synthesis and carbon fixation
E. ATP synthesis and electron transport

7. _B or E_ The electron transport chain does not : (2 points)
A. Contain both electron and hydrogen carriers
B. Directly generate ATP from ADP and inorganic phosphate
C. Move protons from one side of the membrane to ther other
D. Separate an oxidation/reduction reaction into half-reactions
E. Exist in every organism

8. __C__ Cyclic photophosphorylation generates: (2 points)
A. NADH/NADPH for fixing carbon
B. Oxygen for respiration
C. A proton gradient for ATP synthesis
D. Both a proton gradient and NADH/NADPH
E. NADH/NADPH, oxygen, and a proton gradient.

9. __E__ Which is not a mechanism used by Bacteria for motility: (2 points)
A. Rotation of an axial fiber
B. Gliding
C. Gas vacuoles
D. Flagella
E. Cilia

10. __E__ Which is not an issue that thermophiles need to deal with: (2 points)
A. Denaturation of DNA
B. Denaturation of proteins
C. Denaturation of RNA
D. Small molecule stability
E. None of the above

11. _C or D_ Which is not one of the important differences between endospores and the spores of Streptomyces? (2 points)
A. Endospores are non-reproductive
B. Endospores are extremely resistant to harsh environments
C. Endospores are the result of a developmental process
D. The endospore is separated from the “mother” cell by septation early in its development
E. Endospores are not typically “decorated” to aid in their dispersal in the wind

12. Describe the life cycle or developmental cycle of an organism we talked in about class, and include a diagram. Be aware that you cannot use a paper specifically describing this organism to answer the next question (question 13). (5 points)

For example:

Chlamydia have a life cycle with two phases: an inert 0.3-0.4um spore-like "elementary body" (EB) that floats around in the environment waiting to be phagocytized and infect a new host cell, and a metabolically-active "reticulate body" (RB) that exists only intracellularly. An EB infects a cell and develops into an RB, which grows & divides until the cell is used-up, then the RB's develop into EB's and the cell either lyses (C. psittaci) or exocytoses them (the rest) , releasing them to infect other cells.


13. Pick one paper we’ve talked about and describe it in detail. See the next question (question 14) for a list of these papers. Do not use a paper that describes the life cycle of the same organism that you used to answer the previous question (question 12). Be organized; tell me the purpose (or problem/question), the system (environment, organism, whatever), the approach (methods), the results, and conclusion. (10 points)

For example:

The task: Cultivate the pink filaments on the basis of its phylotype, and isolate it as a pure culture from a single cell.

The system: The pink filaments of Octopus Spring, which had previously been shown to be closely related to Aquifex.

The approach: Since the pink filaments organism (EM17) is closely related to Aquifex, and all of the cultivated members of this group are physiologically similar, enrichment media were based on the optimal growth conditions for Aquifex. These enrichments were innoculated with pink filaments from Octopus Spring. The enrichments was assessed by microscopic examination and by testing samples for hybridization with the EM17 probe (i.e. FISH). In order to isolate this organism in pure culture from successful enrichments, an infrared laser was used as 'optical tweezers' to capture single cells, which were used to try to start pure cultures. Of course, many cells were collected and cultured in this way, and the resulting growth, if any, was tested using the EM17 probe. With pure cultures in hand that hybridized to the EM17 probe, the ssu-rRNA sequences were determined.

The results: Some enrichments yielded good growth of a rod-shaped pink bacterium that hybridized strongly to the EM17-specific probe, and their 16S rRNA sequences awere found to be nearly identical to the EM17 sequence. The organism grows as rods in suspension, but when cultivated in media prepared to match the composition of Octopus Spring water in an artificial 'creek', grows as nice pink filaments that are just like those seen in the wild.

Conclusion: The pink filaments were successfuly isolated (at least it is a near relative of EM17) and named Thermocrinus ruber.

14. Summarize in one sentence the purpose, or the results, or the conclusion of only 6 of these 10 papers. Be sure your answers are carefully worded and to the point. Answer only 6 of the these; if you fill in more than 6, I will grade only the first 6. Rewording the title of the paper is not acceptable. (5 points each, 30 points total)

Example answer :

Reysenbach, A.L., Wickham, G.S. and Pace, N.R. 1994 Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park. Appl. Env. Microbiol. 60:2133-2199.

The purpose of this paper was to determine the identity (16S rRNA sequence) of the pink filamentous organism of Octopus Spring.

Huber, R., et al. 1998 Thermocrinus ruber, gen. nov., sp. nov., a pink-filament-forming hyperthemophilic bacterium isolated from Yellowstone National Park. Appl. Env. Microbiol. 64:3576-3583.

The purpose of this paper was to cultivate the pink filaments on the basis of its phylotype, and isolate it as a pure culture from a single cell.

Hugenholtz P, Pitulle C, Hershberger KL and Pace NR 1998 Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring. J. Bacteriol. 180:336-376.

The purpose of this paper was to take a census of the microbial (bacterial adn archaeal) population of Obsidian Pool.

Feltens R, Goessringer M, Willkomm DK, Urlaub H and Hartmann RK. 2003 An unusual mechanism of bacterial gene expression revealed for the RNase P protein of Thermus strains. Proc. Natl. Acad. Sci. USA 100:5724-5729

The conclusion of this paper was that the gene for RNase P protein completely overlaps the preceeding gene for ribosomal protein L34 in Thermus.

Horn M, et al., 2004 Illuminating the evolutionary history of Chlamydiae. Science 304:728-730

The result of this paper was the complete genome sequence of the Entamoeba symbiont Parachlamydia UWE25.

Lindsey MR, Webb RL, Strous M, Jetton MW, Butler MK, Forde RJ and Feurst JA 2001 Cell compartmentalization in planctomycetes: novel types of structural organization for the bacterial cell. Arch. Microbiol. 175:413-429.

The purpose of this paper was to definitively characterize the internal cytoplasmic membranes in each of the genera of Planctomycetes, looking for both commonalities and variations on the theme.

Suau A, Bonnet R, Sutren M, Godon J-J, Gibson GR, Collins MD and Doré J. 1999 Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Env. Microbiol. 65:4799-4807.

Venter JC, et al., 2004 Environmental genome shotgun sequencing of the Sargasso sea. Science 304:66-74.

Cano, R.J., Borucki, M.K., Higby-Schweitzer, M., Poiner, H.N., Poiner, G.O., and Pollard, K.J. 1994 Bacillus DNA in fossil bees: An ancient symbiosis? Appl. Env. Microbiol. 60:2164-2167.

Miguélez EM, Hardissson C, and Manzanal MB. 1999 Hyphal death during colony development in Streptomyces antibioticus: Morphological evidence for the existence of a process of cell deletion in a multicellular prokaryote. J. Cell Biol. 145:515-525.

15. List two genera that are members of these phylogenetic groups. Choose only 20 of the 24 blanks to fill in; if you fill in more than 20, I will grade only the first 20. A list of all of the genera discussed in class or in the papers can be found on the last page of this test. (1 point each, 20 points total)

Example answer :

Aquifex & relatives Aquifex Thermocrinus
Thermotoga & relatives Thermotoga Thermosipho
Green non-sulfur Bacteria Chloroflexus Heliothrix
Deinococci & relatives Deinococcus Thermus
Chlamydia & relatives Chlamydia Parachlamydia
Planctomycetes Planctomyces Gemmata
Spirochaetes Treponema Borrrelia
Bacteroides Bacteroides Cytophaga
Green sulfur Bacteria Chlorobium Clathrochloris
Cyanobacteria Anabaena Nostoc
Firmicutes    
Actinobacteria    

16. List two genera from different phylogenetic groups that have these phenotypes or properties. Use each genus only once. Choose only 10 of the 12 blanks to fill in; if you fill in more than 10, I will grade only the first 10. A list of all of the genera discussed in class or in the papers can be found on the last page of this test. (1 point each, 10 points total)

Example answer :

Thermophile Thermus Thermotoga
Obligate parasite Chlamydia Mycoplasma
Autotroph Aquifex Chloroflexus
Obligate anaerobe Clostridium Bacteroides
Photosynthesizer Chloroflexus Chlorobium
Heterotroph    

 


List of genera mentioned in class:

Acanthamoeba
Acetobacterium
Anerolinea
Aquifex
Arthrobacter
Axinella
Bacillus
Bacteroides
Balnearium
Bartonella
Borellia
Brachyspira
Brevinema
Brocadia
Buchnera
Burkholderia
Caldilinea
Caldotoga
Calyptogena
Cenarchaeum
Chlamydia
Chlamydophila
Chlorobaculum
Chlorobium
Chloroflexus
Chloroherpton
Chloronema
Chlorothrix
Clathrochloris
Clostridium
Corynebacterium
Cytophaga
Dehalococcoides
Deinococcus
Desulfurobacterium
Enterococcus
Epulopiscium
Escherichia
Eubacterium
Fervidobacterium
Flavobacterium
Fritschea
Gemmata
Geotoga
Hartmanella
Heliobacterium
Heliothrix
Herpetosiphon
Hydrogenobacter
Hydrogenobaculum
Hydrogenothermus
Isosphaera
Kouleothrix
Lactobacillus
Lactobacillus
Lentispharea
Leptonema
Leptospira
Listeria
Marinotoga
Meiothermus
Marinothermus
Mycobacteruim
Mycoplasma
Neochlamydia
Nostoc
Oceanothermus
Oscillochloris
Parachlamydia
Paramecium
Pelodictyon
Persephonella
Petrotoga
Pirellula
Planctomyces
Prochlorococcus
Prochloron
Propeneia
Prosthecochloris
Rickettsia
Riftia
Rochalimaea
Roseiflexus
Sargassum
Shewanella
Simkania
Sphaerobacter
Spirochaeta
Spironema
Sporomusa
Staphylococcus
Streptococcus
Streptomyces
Sulfurihydrogenobium
Synechococcus
Thermocrinus
Thermomicrobium
Thermopallium
Thermosipho
Thermotoga
Thermovibrio
Thermus
Treponema
Verrucomicrobium
Vulcanothermus
Waddlia
Wolbachia