Final exam - Fall 1997

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

Bacteria, Eukarya, and Archaea

2. List the 2 major phylogenetic branches of the Archaea, and the general phenotypes present in each of these groups. (5 points)

Crenarchea - sulfur metabolizers

Euryarchaea - sulfur meabolizers, methanogens, and extreme halophiles

3. Describe the structure of the major membrane lipids of Archaea, and how they differ from those of Bacteria and Eukaryotes. (5 points)

Archaeal membrane lipids are glycerol phosphate derivatives (like those of other organisms) that are ether-linked (not ester-linked, like those of Bacteria & Eukarya) to 20 or 40-carbon isoprenyl-based alcohols (not fatty acids). They are therefore branched, and unsaturations are often conjugated. The 20-carbon lipids are arranged in bilayers (like those of other organisms) wheras the 40-carbon lipids are linked at both ends to glycerol phosphate and span the entire width of the membrane.

4. The promoters of archaeal genes are similar to those of eukaryotic RNA polymerase II. (5 points)

5. Sulfur metabolism in Archaea can take several forms. Describe these metabolic processes, being sure to indicate electron donors & acceptors, and whether they occur aerobically or anaerobically, and autotrophically or heterotrophically. (10 points)

1. Sulfur reduction

Sulfur + H2 ---> H2S + protons

Sulfur is the electron acceptor & H2 is the electron donor
These organisms are autotrophic anaerobes

2. Sulfur respiration

Sulfur + organics ---> CO2 + H2S

Organics are the electron donor, sulfur is the terminal electron acceptor
These organisms are heterotrophic anaerobes.

3. Sulfur oxidation

Sulfur + O2 ---> H2SO4

Sulfur is the electron donor & O2 is the electron acceptor
These organisms can usually grow heterotrophically, but most can also be grown autotrophically. All are aerobes

6. Describe one way in which Archaea are similar to Bacteria, but not Eukaryotes, at the molecular biology level (5 points)

Genes in these organisms are arranged in operons. The clusters are co-transcribed, and there is a tight linkage between transcription of the operon and translation of the mRNA.

Other examples might include:

7. Describe one way in which Archaea are (in general) similar to Eukaryotes, but not Bacteria, at the molecular biology level (5 points)

The RNA polymerase of Archaea is quite similar to that of eukaryal RNA polymerase II in sequence, in promoters, and in how it recognizes promoters (via a homologous TATA-binding transcription factor).

Other examples might include:

8. Describe the process used by halophilic Archaea to gather light energy, or the process used by methanogenic Archaea to generate energy from CO2 and H2. (10 points)

Halophiles gather light using a single protein (bacteriorhodopsin) that is a simple light-driven proton pump. A proton gradient is therefore generated directly rather than by electron transport, and is harvestedd to generate ATP by the standard proton-riven ATPase.


Methanogens generate energy by oxidizing H2 using CO2 as the electron acceptor. There is an entire novel pathway for this process, with unique enzymes and cofactors, and methane is the final 'waste' product. The carbon is carried by a series of 1-carbon carriers and sequentially reduced.

9. If you answered your take-home question with a description of a crenarchaeal species or group, then describe the interesting features of any species or group of Euryarchaea you find interesting. On the other hand, if you answered your take-home question with a description of a euryarchaeal species or group, then describe the interesting features of any species or group of Crenarchaea you find interesting. (10 points)

e.g. Methanobacterium

These are nonmotile rod-shaped or filamentous organisms with pseudomurein cell walls. They can only use H2 + CO2 (sometimes CO and/or formate) to make energy and fix carbon. They are mostly thermophiles, and are more easily isolated that other methanogens because they are more resistant to exposure to oxygen.

10. Briefly describe an example of the phylogenetic characterization of an organism that could not be cultivated. (10 points)

The examples discussed in class were:

In the case of Epulopiscium, individual cells are big enough that they were picked directly from fih gut contents by micromanipulation. PCR was used to get rRNA sequence which was nalyzed phylogenetically & turned out to be Gram-positivein nature (related to Clostridium). A fluorescent probe was then made that would only anneal to the specific rRNA sequence & hybridized to fish gut contents, and sure enough only the Epulopiscium cells were labeled.

11. Briefly describe an example of the characterization of a microbial population using molecular phylogenetics. (10 points)

The examples discussed in class were:

In the case of ocean picoplancton, pelagic water samples were filtered to collect 0.2 to 1.0 micron cells, which were then hybridized with fluorescent rRNA probes specific to Archaea, Bacteria, & Eukarya. Interestingly, all samples contained large archeal populations (up to a third of the cells) evn though the environment isn't one in which arhaeas are known to grow.

12. What is (or was) a 'progenote'? (5 points)

Progenotes are (or were) organisms that existed before the translational machinery was accurate and eficient - in other words, before the linkage between genotype and phenotype was tight.

13. What is the difference between the evolutionary tempo and evolutionary mode. (5 points)

Evolutionary tempo is the same as evolutionary rate - the extent of change over time. Evolutionary mode is the quality of change - the types of changes that take place. The difference between tempo and mode are reflected in abrupt evolutionary events, such as evolutionary 'explosions'.