Midterm exam #2 - MB 409 - Spring 2003 Name _________Key_______

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

1. Bacteria
2. Archaea
3. Eukarya

2. ___A__Which is not a method used by Bacteria to fix carbon: (3 points)
A. reverse electron flow
B. the Calvin cycle
C. the hydroxypropionate pathway
D. the reverse TCA cycle

3. ___B__ Taq polymerase used in PCR amplification is a DNA polymerase from _______ aquaticus: (3 points)
A. Trichomonas
B. Thermus
C. Treponema
D. Tetrahymena

4. ___D__ Gliding motility is based (at least where the mechanism is known) on the secretion of: (3 points)
A. polyaromatic hydrocarbons
B. protons
D. polysaccharide
E. carbon dioxide

5. ___C__ The heterocysts of filamentous cyanobacteria carrry out what process? (3 points)
A. oxygenic photosynthesis
B. photorespiration
C. nitrogen fixation
D. reverse electron flow

6. ___A__ What is the defining characteristic of the Gram-positive cell envelop? (3 points)
A. the absence an outer membrane
B. the thick layer of peptidoglycan
C. the periplasm
D. glycerol ethers

7. ___D__ Which of the following is not an issue that has to be dealt with for thermophilic growth? (3 points)
A. nucleic acid denaturation
B. protein denaturation
C. instability of some small molecules
D. low rates of diffusion
E. racemization of amino acids

8. ___E__ The three major methods of sulfur metabolism are: (3 points)
A. sulfur fermentation, thiolation, and decarboxylation
B. sulfur amidation, phosphorylation, and disproportionation
C. sulfur acidification, hydroxylation, and protonation
D. sulfur kination, carbonylation, and transamidation
E. sulfur oxidation, reduction, and respiration

9. ___C__ The electron transport chain is driven by... (3 points)
A. substrate-level phosphorylation
B. the TCA cycle
C. oxidation/reduction reactions
D. the dark reactions of photosynthesis

10. ___B__ RNase polymerase in Archaea resembles... (3 points)
A. bacterial RNA polymerase
B. RNA polymerase II in eukaryotes
C. T7 RNA polymerase
D. reverse transcriptase

11. ___A__ Archaeal membrane lipids are... (3 points)
A. glycerol ethers of 20 or 30 carbon isoprenyl alcohols
B. glycerol esters of 12-24 carbon fatty acids
C. sterols and fatty acids
D. polyaromatic hydrocarbons
E. Archaea do not have membrane lipids

12. List the three major possibilities for the origin of viruses (5 points)

1. Degenerate cellular parasites
2. genetic offshoots of their hosts
3. leftovers of the precellular life

13. Describe the two fundamentally different types of thermophiles. (5 points)

Ancestral thermophiles are thermophilic organisms that apparently only have thermophilic ancestors (at least back to the last common ancestor). These organisms have not adapted to life a high temperature because they have always been there.

Adaptive (recent) thermophiles are thermophilic organisms with mesophilic ancestry. The ancestors of these organisms presumably adapted to life at low temperature long ago, then readapted to life at high temperatures more recently.

14. Tell me in a sentence about something interesting you learned from the paper by John Reeve, "Archaebacteria then...Archaes now (Are there really no archaeal pathogens?)", other than the fact that there are no known archaeal pathogens or that the first archaeal genes were cloned by complementation of E. coli auxotrophs. (5 points)

e.g. Archaea have histones, and package their DNA in nucleosomes like those of eukaryotes.

15. Describe (include a diagram) one bacterial life/developmental cycle (10 points).

e.g. Myxxococcus. They grow individually in rich environments, but when starved, aggregate into 'slugs' than move as a single organism. The cells in the slug differentiate into fruiting bodies, with base, stalk, sporangium, and spores cells. Spores are released into the wind, & those that land in a better environment germinate to produce a new crop of free-living cells.

16. List 15 of the major evolutionary branches of Bacteria. Some of these will, of course, need to be groups that are mostly or entirely known only from rRNA sequences rather than cultivated species. (1 point each - 15 points total)

1. Aquifex & relatives
2. Thermotoga & relatives
3. Green non-sulfur Bacteria
4. Deinococci
5. spirochaetes
6. green sulfur Bacteria
7. Bacteroids/Flavobacteria
8. Planctomycetes
9. Chlamydia
10. Gram positive Bacteria
11. Cyanobacteria
12. Purple Bacteria
13. Acidobacterium & relatives
14. OP11 & relatives
15. Verrucomicrobium & relatives

17. List the two major branches of Archaea. (5 points)

1. Crenarchaea
2. Euryarchaea

18. Give one genus that possesses the phenotypic traits indicated. Choose 20 of these traits to answer - mark out the 4 you choose not to answer. A list of genera from the class notes is given at the end of this test for your reference. (1 point each for a total of 20 points)

(examples)

________________Beggiatoa___________________ chemoautotrophic

________________Nostoc___________________ oxygenic photosynthesis

________________Rhodospirillum___________________ anoxygenic photosynthesis

________________Thermus___________________ thermophilic

________________Herpetosiphon___________________ filamentous

________________Planctomyces___________________ budding division

________________Escherichia___________________ rod-shaped

________________Methanobacterium___________________ methanogenic

________________Sulfolobus___________________ sulfur respiration

________________Thermoproteus___________________ sulfur reduction

________________Chromatium___________________ sulfur oxidation

________________Cytophaga___________________ gliding motility

________________Escherichia___________________ flagella

________________Haloarcula___________________ gas vacuoles

________________Treponema___________________ spirochaete

________________Rhodospirillum___________________ spirillum

________________Sulfolobus___________________ acidophilic

________________Halobacterium___________________ halophilic

________________Mycoplasma___________________ obligate parasite

________________Bacillus___________________ Gram positive cell envelop

________________X___________________ appendaged

________________X___________________ fibrous stalk

________________X___________________ internal membranes

________________X___________________ anaerobic & eukaryotic


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Sign ______________Key_____________________ Date ____3/24/04___________

Acanthamoeba Acetobacterium Acidianus Acidobacterium Agrobacterium Anabaena Anaerolinea Aquaspirillum Aquifex Archaeoglobus Arthrobacter Bacillus Bacteroides Balnearium Barbulanympha Bdellovibrio Beggiotoa Borrelia Brachyspira Bradyrhizobium Brevinema Caldilinea Caldotoga Campylobacter Caulobacter Chlamydia Chlamydiophila Chlamydomonas Chlorobaculum Chlorobium Chloroflexus Chloroherpeton Chloronema Chlorothrix Chromatium Citrobacter Clathrochloris Clostridium Coprothermobacter Corynebacterium Cytophaga Dehalococcoides Deinococcus Desulforobacterium Desulfovibrio Desulfurococcus Desulfurolobus Dictyoglomus Dictyostellium Enterobacter Enterococcus Erwinia Escherichia Eubacterium Euglena Fervidobacterium Fibrobacter Flavobacterium

Flexistipes Frankia Fritschea Fusobacterium Gemmata Geothrix Geotoga Giardia Haloarcula Halobacterium Helicobacter Heliobacterium Heliothrix Herpetosiphon Holophaga Hydrogenivirga Hydrogenobacter Hydrogenobaculum Hydrogenothermus Isosphaera Klebsiella Kouleothrix Lactobacillus Leptonema Leptospira Leuconostoc Listeria Marinithermus Marinotoga Meiothermus Metallosphaera Methanobacterium Methanococccus Methanomicrobium Methanopyrus Methanosarcina Micrococcus Mycobacterium Mycoplasma Myxococcus Natronobacterium Neochlamydia Niesseria Nitrobacter Nitrospira Nocardia Nostoc Oceanothermus Oscillochloris Parachlamydia Paramecium Pelodictyon Persephonella Pfisteria Pirellula Planctomyces Plasmodium Prochloron

Prosthecobacter Prosthecochloris Proteus Pseudomonas Pyrobaculum Pyrococcus Pyrodictium Rhizobium Rhodobacter Rhodocyclus Rhodomicrobium Rhodopseudomonas Rhodospirillum Rickettsia Roseiflexus Saccharomyces Salmonella Shigella Simkania Sphaerobacter Spirochaeta Spirogyra Spironema Sporomusa Staphylococcus Staphylothermus Stella Streptococcus Streptomyces Stygiolobus Sulfolobus Sulfurihydrogenobium Synergistis Thermococcus Thermocrinus Thermodesulfobacterium Thermodiscus Thermofilum Thermomicrobium Thermopallium Thermoplasma Thermoproteus Thermosipho Thermotoga Thermovibrio Thermus Thiobacillus Treponema Trichomonas Trypanosoma Ultramicrobacteria Verrucomicrobium Vulcanithermus Waddlia Yersinia