Midterm exam #2 - Spring 1999

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

Bacteria, Archaea, and Eukarya

2. What are the 2 major phylogenetic branches of the Archaea? What are the general phenotypes present in these groups? (5 points)

Crenarchaea - all sulfur-metabolizing thermophiles

Euryarchaea - methanogens, halophiles, and sulfur-metabolizing thermophiles

3. What are the three major types of sulfur metabolism? What are the electron donors, acceptors, and products in each of these reactions? (5 points)

1. Sulfur reduction : Sulfur + H2 ---> H2S + protons

Hydrogen is the electron donor and elemental sulfur (or sulfur compounds such as thiosulfate) is the terminal electron acceptor. H2S is the product.

2. Sulfur respiration : Sulfur + organics ---> CO2 + H2S

Organics are the electron donor and sulfur (or sulfur compounds) is the terminal electron acceptor. CO2 and H2S are the products.

3. Sulfur oxidation : Sulfur + O2 ---> H2SO4

Sulfur (or sulfur compounds) is the electron donor, and molecular oxygen is the electron acceptor. Sulfuric acid is the product.

4. What do cyanobacteria get from their 2-photosystem photosynthesis that other Bacteria, with a single photosystem, do not? (5 points)

reducing power - NADH or NADPH

5. Name an electron donor and an electron acceptor that can be used to drive electron transport for the generation of ATP. (5 points)

example electron donors: H2S, NH4+, Fe++, organics, CH4, H2O, activated photosystems

example electron acceptors: SO4--, Fe+++, NO3-, H2, organics, oxidized photosystems

6. Chlamydia cannot make amino acids, purines, pyrimidines, sugars, cofactors, any metabolic intermediates, or even ATP. How, then, is it possible for them to survive? (5 points)

They are energy parasites, getting all of the small molecules they need, including ATP, from their hosts.

7. How are the stalks of Planctomycetes different than those of the appendaged alpha-purple Bacteria? (5 points)

Planctomycete stalks are a bundle of external fibers, whereas 'appendages', the stalks of alpha purple Bacteria, are cytoplasmic extensions.

8. Why is energy production via electron transport particularly difficult for life at high pH's? (5 points)

Because protons pumped into the alkaline environment react quickly with hydroxide (to make water), and are not available for ATPase.

9a. Give an example genus from 15 of these 19 phylogenetic groups: (1 point each)

Example answers:

 Chloroflexus
Chlorobium
Treponema
Anacystis
Thermotoga
Cytophaga
Aquifex
Chlamydia
Deinococcus
Planctomyces
Rhodospirillum
Alcaligenes
Escherichia
Myxococcus
Helicobacter
Bacillus
Arthrobacter
Sulfolobus
Thermoplasma

green non-sulfur Bacteria
green sulfur Bacteria
spirochaetes
cyanobacteria
Thermotogales
Cytophagales
Aquificales
Chlamydiae
Deinococci
Planctomycetes
a-purple Bacteria
b-purple Bacteria
g-purple Bacteria
d-purple Bacteria
e-purple Bacteria
low G+C Gram-positive Bacteria
high G+C Gram-positive Bacteria
Crenarchaea
Euryarchaea

9b. Now name two bacterial groups that are defined primarily by ssu-rRNA sequences from environmental samples, and contain few or no cultivated species. (5 points)

e.g. Verrucomicrobium, Acidobacterium, OP11

10. What are the 4 mechanisms used by Bacteria for motility? Describe 2 of them. (10 points)

1. gas vacuoles
2. gliding
3. flagella
4. 'spirochaete'-type

Gas vacuoles are organelles that can be inflated or deflated to adjust bouyancy to move up or down in the water column.

Flagella are helical protein fibers that extend from the cell, wih an ATP-driven moter at the base (in the cell envelop) that rotates the fiber, which acts like a propeller.

11. Describe any bacterial species, genus, or phylogenetic group you find interesting. (10 points)

e.g. Thermus aquaticus - the organism that proved the utility of thermophiles

Thermus is a thermophilic heterotrophic rod found in thermal environments around the world (even household water heaters). It was first isolated from a Yellowstone hot spring. Thermus aquaticus is the source of Taq polymerase used in PCR. It was the use of Taq polymerase that lead to the widespread use of PCR, and demonstrated the general utility of thermophilic enzymes, now a huge industry.

12. Describe any archaeal species, genus, or phylogenetic group you find interesting. (10 points)

e.g. Archaeoglobus

This organism has been isolated only from deep-sea hydrothermal vents & heated marine sediments. It is a thermophilic (85C) coccus; some species are motile with tufted flagella (much like Thermococcus) and others are nonmotile.

Archaeglobus can be grown either of two ways. It can grow heterotrophically by a unique pathway - it uses the methanogenic pathway in reverse!

lactate or acetate ---> H2 + CO2

It also grows autotrophically by sulfate reduction:

H2 + SO4= ---> H2S (carbon fixed from CO2)

13. How did Dr. Anna-Louis Reysenbach show that one of the ssu-rRNA sequence (EM17) obtained from a sample of pink filaments in the outflow of Octopus spring really was that of the 'pink filaments' organism (now Thermocrinus ruber)? (5 points)

By "in situ hybridization". Dr. Reysenbach made a fluorescently-labeled oligonucleotide probe complementary to a unique sequence in EM17, and probed a sample from the pink filements environment. She showed at only the pink filaments could be labeled with the sequence-specific fluoresecent probe.

14. How was the EM17 sequence information generated by Dr. Reysenbach used by Dr. Robert Huber to 1) design culture conditions in attempt to cultivate the pink filaments organism, and 2) pick this organism (Thermocrinus ruber) out of successful enrichments and get it into pure culture? (5 points)

First, the phylogenetic placement of EM17 in the tree near Aquifex lead Dr. Huber to use media based on the growth requirements for Aquifex, as well with the chemical composition of the outflow stream.

Second, a specific fluorescent probe based on the EM17 sequence (the same one used by Dr. Reysenbach) was used to screen and monitor enrichment cultures.

Third, this same fluorescent probe was used to label cells in an enrichment during the isolation of a single cell using optical tweezers.

Fourth, the identity of the pure culture was confirmed by comparing the sequence of its ssu-rRNA, which is almost exactly the same as EM17.


Last updated March 19, 1999 by JWBrown
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