Essay Questions

Question 1.

Extremely halophilic Archaea require high levels of NaCl for growth, and store large amounts of K+ intracellularly as a compatible solute. Some species can generate ATP from light using a simple proton pump involving bacteriorhodopsin. Methanogenic Archaea are strictly anaerobic prokaryotes whose metabolism is tied to the production of methane (CH4).

  • How can organisms like Halobacterium survive in high salt solutions whereas an organism like Escherichia coli cannot?
  • How does bacteriorhodopsin allow for the synthesis of ATP?
  • What are the major substrates for methanogenesis?


Question 2.

Thermoplasma and Picrophilus are extremely acidophilic thermophilic archeans that form their own phylogenetic family of prokaryotes inhabiting coal refuse piles and highly acidic sofataras. Cells of Thermoplasma lack a cell wall, and thus, resemble the mycoplasmas in this regard.

  • In what ways are Thermoplasma and Picrophilus similar? In what ways do they differ?
  • How does Thermoplasma strengthen its cell membrane to survive life in absence of a cell wall?


Question 3.

Hyperthermophilic euryarchaeota include the Thermococcales,Archaeoglobales, and Methanopyrus. All organisms in this group have growth temperature optima above 80°C.

  • How does the metabolism of Thermococcales differ from that of Methanopyrus?
  • How does the metabolism of Archaeoglobales differ from that of the Thermococcales?
  • How does the metabolism of Ferroglobus differ from that of Archaeoglobales?


Question 4.

Hyperthermophilic Crenarchaeota inhabit the hottest habitats currently known to support life. Cold-dwelling phylogenetic relatives of these organisms are also known. A variety of different morphological types of Crenarchaeota are known, and several different metabolic strategies are used to support growth.

  • What are the major differences between the organisms Sulfolobus and Pyrolobus?
  • What is unusual about the metabolic properties of Acidianus regarding elemental sulfur (S°)?
  • What evidence links the cold-dwelling Archaea to the Crenarchaeota?
  • What energy class of organisms are those that use H2 as electron donor? What Crenarchaeota use H2 and what do they use as electron acceptors?


Question 5.

Although hyperthermophiles live at very high temperatures, in some cases above the boiling point of water, it is likely that there are limits in terms of temperature beyond which no living organism can survive. The study of modern day hyperthermophilic prokaryotes may yield clues to early life on earth and other planets like Mars.

  • How do hyperthermophiles keep important macromolecules like proteins and DNA from being destroyed by high heat?
  • List at least two reasons why an upper temperature limit to life undoubtedly exists. What is the likely upper temperature limit for life?
  • What evidence suggests that extant hyperthermophiles most closely resemble ancient organisms?
  • What form of energy metabolism was likely key to energy economies of ancient organisms?

Question 6. 

Archaeal transcription: The Archaea are a unique group of organisms that share properties with both the Eukarya and Bacteria. The Archaea share the simplicity, versatility, and adaptability of the Bacteria, but their fundamental cellular processes of DNA replication, transcription, and translation are more closely related to those in the Eukarya. The eukaryotic transcription machinery consists of a 10-15 subunit RNA polymerase and five basal transcription factors. The first step in eukaryotic transcription initiation is recognition of the TATA box, located aproximately 30 base pairs upstream of the initiation site, by the TATA-box-binding protein TBP. TBP then recruits TBP-associated factors (TAFs) to form the TFIID complex. Binding of the TFIID complex is stabilized by the addition of another transcription factor TFIIA. The transcription factors TFIIB and TFIIF then bind along with RNA polymerase to initiate transcription. Efficient transcription initiation also requires two additional factors, TFIIE and TFIIH, which facilitate melting of the double helix at the transcription start site. 
The discovery that archaeal transcription was more like that in the Eukarya than the Bacteria came from studies of Sulfolobus acidocaldarius. Purified RNA polymerase from this organism has at least 10 subunits, unlike bacterial core RNA polymerase which has only 4 subunits. The genes encoding most of the archaeal subunits have been cloned and sequenced and show high similarity to the genes encoding the eukaryal RNA polymerase subunits.  In addition to the resemblance between the eukaryal and archaeal RNA polymerases, the promoters are also similar. The typical archaeal promoter contains three important elements. The first element is the TATA box, known as Box A, where TBP binds. Box A is located approximately 30 base pairs upstream of the initiation site, similar to the eukaryal TATA box. The second element, Box B, is centered around the initiation site. The third element consists of two adenine nucleotides located upstream of Box A at positions -33 and -34 with respect to the transcription start site. This element binds TFB (the TFIIB homolog) and is called BRE (transcription factor B recognition element).  Although standard promoter elements and basal transcription factors have been identified, little is known about how archaeal transcription is regulated. Archaeal genes are arranged in operons, similar to bacterial genes, and it is expected that transcription and translation must be coupled in the Archaea due to the lack of a nucleus. Upstream activation elements and other regulatory elements found in eukaryotic transcription units have yet to be identified in the Archaea. It is expected that the archaeal regulatory elements and regulatory proteins may more closely resemble those in bacteria. In fact, homologs of some bacterial global regulators have been identified in the Archaea.  It is apparent that archaeal transcription has some features that are more eukaryotic-like and others that more closely resemble bacterial transcription. As more becomes known, it will be very interesting to see how the Archaea have managed to integrate features of both the eukaryotic and bacterial transcription systems. Expand on the above brief description by answering the following questions: 

(a) What are the evolutionary implications of Archaea having a transcription apparatus that more closely resembles that of the Eukarya?

(b) How might the Archaea benefit from a transcription system that has similarities to both eukaryotic and bacterial transcription?


Question 7. 

Explain the findings that support the evolutionary tree of life that shows the domain Archaea positioned between domain Bacteria and Archaea.


Question 8.

Explain this statement: Archaeoglobus may represent a metabolically transitional type of organism among Archaea, one that bridged the energy generating process of H2S production and methanogenesis.


Question 9.

Compare and contrast Pyrodictium and Pyrolobus. Include their natural habitat, physiological requirements and respiratory processes in your answer.


Question 10.

Where is the thermosome found and what is its apparent role?


Question 11.

Write an essay explaining the limits of microbial existence



Question 12.

Speculate on the possibility of life on other planets. Use the representatives of the kingdom Korarchaeota as a guide to this discussion.