Final Exam 2005 : 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. __
E__ The “purple Bacteria and relatives” are also known as the “Proteobacteria” because: (2 points)
A. They use different photosynthetic pigments than the green and colorless sulfur Bacteria
B. They are able to grow on protein as their sole carbon and energy source
C. They contain more protein than Bacteria in other phylogenetic groups
D. They are the most primitive Bacteria known at the time they were named
E. They have changed their metabolic phenotypes frequently in their evolution

3. __
C__ Proteorhodopsin is: (2 points)
A. a light-driven chloride pump
B. a sensory opsin
C. a light-driven proton pump
D. a light-driven ATPase
E. All of the above

4. __
B__ Life on Earth has been entirely microbial for about _____% if its existence: (2 points)
A. 97
B. 85
C. 50
D. 17
E. 3

5. __
A__ Archaea can tell us a lot about the origins of Bacteria and Eukaryotes because: (2 points)
A. They are more primitive that either of these other groups
B. They are the ancestors of these other groups
C. They are more derived than either of these other groups
D. They are more thermophilic than either of these other groups
E. They are simpler than either of these other groups

6. __
B__ The Prion Theory for transmissible spongiform encephalopathies (TSEs) states that: (2 points)
A. The infectious agent lacks a protein coat and is therefore not a true virus
B. The infectious agent is composed entirely of protein
C. There is no infectious agent; TSEs are not contagious
D. The infectious agent is a combination of an infectious nucleic acid and a host protein (PrP)
E. None of the above

7. __
A__ Organic acids are toxic to acidophiles because: (2 points)
A. they acidify the cytoplasm and deplete the proton gradient
B. the stop electron transport at low pH
C. the unprotonated forms of organic acids aren’t recognized by metabolic enzymes
D. increase the acidity of the environment
E. all of the above

8. __
B__ Most methanogens carry out the following overall reaction (not necessarily balanced): (2 points)
A. CH3COOH -> CH4 + CO2
B. CO2 + H2 -> CH4 + H2O
C. CH4 + O2 -> CO2 + H2O
D. S° + O2 -> H2SO4
E. CH3COOH -> H2 + CO2

9. __
A__ Most Bacteria with prostheca are members of the: (2 points)
A. a-proteobacteria
B. b-proteobacteria
C. g-proteobacteria
D. d-proteobacteria
E. e-proteobacteria

10. __
C__ Cesium tetrafluoroacetate gradients are used to: (2 points)
A. Separate DNA or RNA by size
B. Separate DNAs of the same size by melting temperature
C. Separate DNA or RNA by density
D. Separate swarmers from mother cells
E. Separate labeled from unlabeled cells

11. __
B__ DGGE is used to: (2 points)
A. Separate DNA or RNA by size
B. Separate DNAs of the same size by melting temperature
C. Separate DNA or RNA by density
D. Separate swarmers from mother cells
E. Separate labeled from unlabeled cells

12. List and show the overall reaction for the three main forms of sulfur metabolism : (3 points)

Sulfur reduction : S° + H2 -> H2S (+ protons)
Sulfur oxidation : S° + O2 -> H2SO4
Sulfur respiration : S° + organics -> CO2 + H2S


13. List the three main important phenotypic groups of Archaea : (3 points)

Halophiles
Methanogens
Sulfur-dependent thermophiles (or thermoacidophiles)


14. Pick one paper we’ve talked about and describe it in detail. See the next question (question 15) for a list of these papers. 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 :

Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN and DeLong EF. 2000 Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science 289:1902-1906.

Purpose : The purpose of this paper was to attempt to learn something about the phenotype of or role played in the environment by SAR86 in the absence of the ability to cultivate it.

System : SAR86 is an organism known previously only by its “environmental” 16S rRNA sequence. It has not been cultivated, nor have any of it’s close relatives. It, and it’s relatives, are abundant in the surface ocean waters worldwide.

Approach : The approach taken in this paper was to sequence a large (130kbp) chunk of genomic DNA (from a cosmid clone) known to be from SAR86 because of the presence of a copy of the 16S rRNA gene. The hope was that some gene or genes on this genomic fragment would provide information about the phenotype or metabolic capabilities of the organism.

Results: They found a gene that looked like it would encode a bacteriorhodopsin. Bacteriorhodopsins are light-driven ion pores or pumps. Although the sequence couldn’t be clearly related to any particular kind of bacteriorhodopsin (sensory opsins, proton pumps, or chloride pumps), the biochemicaal properties of the protein expressed in E. coli show that it is a light-driven proton pump.

Conclusion: SAR86 is a phototroph, using “proteorhodopsin” to harvest the energy of light for ATP synthesis. Whether it is autotrophic (i.e. whether it is photosynthetic) remains to be determined.


15. 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)

Viollier PH, Thanbichler M, McGrath PT, West L, Meewan M, McAdams HH & Shapiro L. 2004 Rapid and sequential movement of individual chromosomal loci to specific subcellular locations. Proc. Natl. Acad. Sci. USA 101:9257-9262

For example:

The conclusion of this paper is that genes in the chromosome of Caulobacter (and by extension Bacteria in general) are arranged in a linear fashion in the nucleoid from one of the cell (with the origin of replication) to the other end of the cell (with the replication terminator), and every step in between.


Manefield M, Whitely AS, Griffiths RI and Bailey MJ 2002 RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl. Environ. Microbiol. 68:5367-5373

The purpose of this paper was to show that rRNA-based (as opposed to DNA-based) stable isotope probing is a practical method for identifying the organism(s) in a natural population that utilize some specific substrate (phenol, in this case).


Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN and DeLong EF. 2000 Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science 289:1902-1906.

Conclusion: SAR86 is a phototroph, using “proteorhodopsin” to harvest the energy of light for ATP synthesis.

Drancourt, M., Aboudharam, G., Signoli, M., Dutour, O., and Raoult, D. 1998 Detection of 400-year-old Yersinia pestis DNA in human dental pulp: An approach to the diagnosis of ancient septicemia. Proc. Natl. Acad. Sci. USA 95:12637-12640. and Raoult, D. et al. 2000 Molecular identification by "suicide PCR" of Yersinia pestis as the agent of Medieval Black Death. Proc. Natl. Acad. Sci. USA 97:12800-12803.

Approach : DNA was extracted from the dental pulp of the remains of people that died of Black Death, and used this DNA in PCR reactions in (successful) attempt to detect the presence of Yersina pestis sequences.

Hugenholtz, P., Goebel, B.M. and Pace, N.R. 1998 Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774.

Purpose : The purpose of this paper was to compile and review all of the various data from 16S rRNA-based analyses of microbial populations.


Huber H, Hohn MJ, Rachel R, Fuchs T Wimmer VC and Stetter KO. 2002 A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63-67.

Purpose : This paper is a monogram, describing Nanoarchaeum equitans, an obligate symbiont/parasite of Igniococcus.

Cobucci-Ponzano B, Rossi M and Moracci M. 2005 Recoding in Archaea. Mol. Microbiol. 55:339-348.

This is a review of translation oddities in Archaea, focusing on the use of selenocysteine (encoded by UGA), pyrrolysine (UAG) and an apparent programmed frameshift in Sulfolobus.

Soto C and Castilla J 2004 The controversial protein-only hypothesis of prion propagation. Nature Medicine 10:S63-S67 or Somerville RA 2002 TSE agent strains and PrP: Reconciling structure and function. TiBS 27:606-612

These two papers review the strengths and weakness of the data supporting the Prion Theory, focusing on “strains” of TSEs and progress toward fulfilling Koch’s postulates with PrP^Sc.

MacKay, D.S., et al
., 1996 Search for past life on Mars: Possible biogenic activity in martian meteorite ALH84001. Science 273:924-930

Conclusion : Meteorite ALH84001 contains specific fossil evidence for the presence of cellular life on Mars about 3.6 billion years ago.


16. List two genera that are members of these phylogenetic groups. Choose only 14 of the 16 blanks to fill in; if you fill in more than 14, I will grade only the first 14. 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, 14 points total)

Example answers :

a-proteobacteria Rhodomicrobium Caulobacter

b-proteobacteria Thauera Burkholderia

g-proteobacteria Escherichia Pseudomonas

d-proteobacteria Myxococcus Desulfovibrio

e-proteobacteria Campylobacter Helicobacter

Crenarchaea Sulfolobus Pyrodictium

Euryarchaea Haloarcula Methanobacterium

Bacterial groups with few Verrucomicrobium Acidobacterium
or no cultivated members

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

Thermophile Pyrodictium Methanobacterium

Obligate parasite Nanoarchaeum Neisseria

Autotroph Methanococcus Hydrogenophilus

Phototroph Rhodospirillum Halobacterium

Heterotroph Escherichia Myxococcus

Human pathogen Bordetella Campylobacter

Sulfur metabolizer Sulfolobus Thermococcus

Mesophile Salmonella Desulfovibrio

18. List the three potential origins for viruses: (3 points)

genetic offshoots ('satellites') of their hosts
remnants of precellular life
degenerate parasites


List of genera mentioned in this section of class:

Acidianus
Acidobacterium
Agrobacterium
Aquifex
Archaeoglobus
Azoarcus
Azotobacter

Bacillus
Bacteroides
Bdellovibrio
Beggiotoa
Bordetella
Bradyrhizobium
Burkholderia

Campylobacter
Caulobacter
Chlamydia
Chloroflexus
Chromatium
Citrobacter
Coprothermobacter

Dechloromonas
Dehalococcoides
Deinococcus
Desulfovibrio
Desulfurococcus
Desulfurolobus
Dictyoglomus

Enterobacter
Erwinia
Escherichia

Ferribacterium
Fibrobacter
Flexistipes
Fusobacterium

Gallionella
Geothrix

Haloarcula
Halobacteerium
Halorubrum
Helicobacter
Heliothrix
Herpetosiphon
Holophaga
Hydrogenophilus
Igniococcus

Klebsiella

Magnetospirillum
Metallosphaera
Methanobacterium
Methanococcus
Methanomicrobium
Methanopyrus
Methanosarcina
Mycobacterium
Myxococcus

Nanoarchaeum
Natronobacterium
Natronomonas
Neisseria
Neurospora
Nitrobacter
Nitrosococcus
Nitrosomonas
Nitrosospira
Nitrospira

Oxalobacter

Petrobacter
Propionivibrio
Prosthecobacter
Proteus
Pseudomonas
Pyrobaculum
Pyrococcus
Pyrodictium

Quadricoccus

Rhizobium
Rhodobacter
Rhodocyclus
Rhodomicrobium
Rhodopseudomonas
Rhodosprillum
Rickettsia

Salmonella
Shigella
Sphaerobacter
Spirillum
Staphylothermus
Stigmatella
Streptomyces
Stygiolobus
Sulfolobus
Synergistis

Thauera
Thermococcus
Thermodesulfobacterium
Thermodiscus
Thermofilum
Thermomicrobium
Thermoplasma
Thermoproteus
Thiobacillus
Treponema

Ultramicrobium

Verrucomicrobium

Yersinia

Zoogloea