Molecular and Applied Microbiology Exams 2000 BBS 3010 and 3010L

Total Marks allocated: 120

Total time Allocated: 1.30 hrs

Answer all 5 questions:


Question 1. Answer all the following multiple choice questions (13 marks)

  1. Compared to other organisms, hyperthermophilic crenarchaeotes tend to have

A. Slow evolutionary clocks.

B. Fast evolutionary clocks.

C. Evolutionary clocks that tend to move at about the same pace

as the evolutionary clocks of other organisms.

D. Very erratic evolutionary clocks.

2. The cytoplasmic proteins of Halobacterium are

A. Highly acidic.

B. Highly basic.

C. Generally neutral.

D. Variable, depending on the species.

3. Methanogens

A. Produce methane as a part of their energy metabolism.

B. Utilize methane as an energy source.

C. Process and store methane as a part of their repair mechanism.

D. Do none of the above.

4. Which of the following is not a methanogenic substrate?

A. CO2-type substrates

B. Methyl substrates

C. Acetate

D. All of the above are methanogenic substrates.

5. _______________________ is a strict anaerobe with an optimum

temperature of 105C that grows chemolithotrophically on H2 with so

as an electron receptor or chemoorganotrophically on complex

mixtures of organic compounds.

A. Pyrodictium

B. Pyrolobus

C. Pyrobaculum

D. Desulfurococcus

6. One factor which seems to aid in maintaining heat resistance is that

dibiphytanyl tetraether lipids form

A. A covalently bonded monolayer cytoplasmic membrane.

B. An interlocking bilayer cytoplasmic membrane.

C. An interlocking lattice with the cell wall.

D. A pseudo-membrane immediately inside the cytoplasmic membrane.

7. Identification of the three lines of descent, Bacteria, Archaea, and

Eukarya, has come about primarily as a result of

A. Advanced methods of morphological examination.

B. Biochemical assays.

C. Analyses of metabolic pathways.

D. Nucleic acid sequencing studies.

8. Lateral gene transfer

A. Occurs between related species.

B. Occurs between domains.

C. Was prevalent before the primary lines of descent were formed.

D. Is still an unknown factor in setting up phylogenetic trees.

9. The eukaryotic functional equivalent of the prokaryotic 16S rRNA is the

A. 5S rRNA.

B. 16S rRNA (the same as the prokaryotic 16S rRNA).

C. 18S rRNA.

D. 23S rRNA.

10. Protein synthesis studies using Sulfolobus (Archaea), yeast (Eukarya), and

Escherichia coli (Bacteria) indicate the ribosomal proteins of and are

more closely related to each other than they are to the ribosomal proteins

of _________________________

A. Archaea / Bacteria / Eukarya

B. Archaea / Eukarya / Bacteria

C. Bacteria / Eukarya / Archaea

D. None of the above because the studies indicate these proteins all seem

to be similar.

11. The genus found closest to the Archaea/Eukarya divergence point is

A. Agrobacterium.

B. Proteobacteria.

C. Aquifex.

D. An as yet unidentified cyanobacteria

12. Although the microsporidia and the diplomonads are eukaryotic, they lack

A. Mitochondria.

B. A true nucleus.

C. Identifiable ribosomes.

D. All of the above

13. Heat stable proteins tend to have which probably leads to more

    1. Hydrophilic cores / ionic dispersal of particles which would
    2. normally cluster.

    3. Hydrophobic cores / "salt bridges" between hydrophilic amino
    4. acids on the surface.

    5. Hydrophobic cores / ionic dispersal of particles which would
    6. normally cluster.

    7. Hydrophilic cores / "salt bridges" between hydrophilic amino

acids on the surface.


Question 2. State true or false (7 marks)

  1. Life can be considered an imperfect replicating system because evolution is
  2. an ongoing process.

  3. Most eukaryotic organisms lacking cellular organelles are found in the early branches of the evolutionary tree
  4. In doing comparative SSU rRNA sequencing, it is essential that pure cultures be used.
  5. The hyperthermophilic members of the Crenarchaeota seem to branch very close to the root of the universal tree.
  6. Archaeal RNA polymerases are generally less complex than those of Bacteria.
  7. The methanogens and the extreme halophiles are both Euryarchaeota.
  8. In chemolithotrophy in the Archaea, H2 is a common electron donor.


Question 3. Answer the following in brief: (20 marks)

  1. On the basis of the following sequences, calculate an evolutionary distance between these three organisms and predict which two of the three are most closely related.
  2. Organism 1: AGGUACGUUA

    Organism 2: UGCCACGGUU

    Organism 3: AGGUACGGUA

  3. Why are ribosomal RNAs better molecules for phylogenetic studies
  4. than proteins like ferrodoxin, cytochromes or specific proteins?

  5. What are signature sequences and of what value are they? How are signature sequences discerned?


Question 4. Answer any ONE question from the following three: (40 marks)

a) Briefly describe the different strategies available for obtaining a complete microbial genome sequence (ie. ordered clone approach, shotgun approach). Discuss one experimental approach in more detail including library construction, sequencing, gap filling etc.

b) Outline the processes involved in microbial genome sequence annotation. Discuss possible approaches for characterising predicted genes of unknown function.

c) Horizontal transfer is an important evolutionary process in microorganisms discuss how data obtained from microbial genome sequences has improved our knowledge of this process. Give a specific example of a sequenced microbial genome that appears to contain significant levels of horizontally transferred genes.

Question 5 Answer any ONE question from the following two: (40 marks)

  1. Microorganisms produce industrially important compounds as both primary and secondary metabolites of growth. Discuss the industrial production of
  2. (i) a primary metabolite and

    (ii) a secondary metabolite.

  3. Microorganisms can be beneficial and detrimental to industry. Discuss these beneficial and detrimental effects giving specific examples where appropriate.