MB 451 : Microbial Diversity : Final Exam 2006
Honor Pledge: I have neither given nor received unauthorized aid on this test.
Signed ____
Key_______________________________________________
Date ___
5/8/06______
Print name _______________________________________________________________________________
-------------------------------------------------------------------------------------------------------------------------------------1) What are the 3 primary evolutionary branches of life? (5 points)
2) __
1. ___
Archaea________________________________________
2. ___
Bacteria________________________________________
3. ___
Eukarya________________________________________
D_ “Environmental” Clamydiae are ...
C
(2 points)
A. commonly detected in hydrothermal environments
B. free-living heterotrophs
C. faculatative parasites of insects
D. obligate intracellular parasites of protists
E. none of the above
3) __ _ Specialized parasites ... (2 points)
A. have often completely dispensed with their genome
B. have large, complex genomes with specialized pathogenicity genes
C. have reduced, simplified genomes with only the bare essentials
D. have large amounts of “junk” DNA and pseudogenes
E. none of the above
A
4) __ _ The two fundamentally different types of thermophiles are ... (2 points)
A. ancestral and recent thermophiles
B. moderate and extreme thermophiles
C. Gram-negative and Gram-positive thermophiles
D. bacterial and archaeal thermophiles
E. none of the above
B
5) __ _ The genome of Thermotoga maritima provides strong evidence for ... (2 points)
A. pathogenicity islands
B. horizontal gene transfer
C. transfer of genes to the nucleus
D. intraspecific recombination
E. all of the above
B
6) __ _ Nitrogen fixation by cyanobacteria is a problem because ... (2 points)
A. Z-scheme photosynthesis doesn’t generate reducing power
B. oxygen generated by photosynthesis inhibits nitrogenase
C. sulfide required for reverse electron flow inhibits nitrogenase
D. the product of nitrogen fixation is highly-reactive hydrazine
E. all of the above
Page 1
D
7) __ _ A metagenome is ... (2 points)
A. the complete metabolic pathways of an ecosystem
B. the complete metabolic potential of a genome
C. the complete genome sequence of an organism
D. the complete genetic composition of an ecosystem
E. none of the above
8) __
A_
E
Arthromitis, the filamentous spore-forming intestinal symbionts of insects, are ... (2 points)
A. Bacillus cereus
B. Streptomyces antibioticus
C. Myxococcus xanthus
D. just Arthromitis
E. none of the above
9) __ _ Which are real sulfur-based metabolisms? (2 points)
A. sulfur reduction : sulfur + organics -> CO2 + H2S
B. sulfur respiration : sulfur + O2 -> H2SO4
C. sulfur oxidation : sulfur + H2 -> H2S
D. all of the above
E. none of the above
10) __
11) __
A_
Energy from light is harvested by halophilic Archaea via ... (2 points)
A. bacteriorhodopsin
B. cyclic photophosphorylation
C. Z-scheme photosynthesis
D. the photoelectric effect
E. all of the above
D_
The stalks of Planctomycetes ... (2 points)
A. raise their eyes above the surface
B. aid in the dispersal of spores
C. are cytoplasmic appendages
D. are bundles of external fibers
E. none of the above
C
12) __ _ The stalks of Caulobacter ... (2 points)
A. raise their eyes above the surface
B. aid in the dispersal of spores
C. are cytoplasmic appendages
D. are bundles of external fibers
E. none of the above
B
13) __ _ In a resting bacterial cell, the origin of replication (ori) of the genome is located ... (2 points)
A. in the center of the cell, at the division plane
B. at the “old” end of the cell
C. at the “new” end of the cell
D. at both ends of the cell
E. any of the above
C
14) __ _ Secondary metabolites are produced predominantly... (2 points)
A. during lag phase
B. during log phase
C. during stationary phase
D. during senescence
E. none of the above
Page 2
15) __
D_
16) __
The C-signal in swarming Myxococccus is triggered by ... (2 points)
A. starvation
B. ppGpp
C. a phermone
D. end-to-end contact
E. all of the above
A_
Which is not an accepted view on the origin of some viruses? (2 points)
A. prions
B. remains of the RNA World
C. degenerate intracellular parasites
D. genetic offshoots of their hosts
E. all of the above
17. Label the electron micrograph (a thin-section) of Gemmata obscuriglobus below: (5 points)
Spaces:
PARYPHOPLASMA
RIBOPLASMA
Membranes:
NUCLEAR ENVELOPE
INTERNAL CELLULAR
MEMBRANE (ICM)
CYTOPLASMIC MEMB.
Page 3
18. List two genera from each of these groups of organisms. (24 points)
Examples
Chlamydiae and relatives
Chlamydiae & Parachlamydiae
Thermotoga and relatives
Thermotoga & Caldotoga
Planctomycetes
Pirellula & Gemmata
Cyanobacteria
Nostoc & Prochlorococcus
Alpha Proteobacteria
Agrobacterium & Caulobacter
Delta Proteobacteria
Myxococcus & Desulfovibrio
Epsilon Proteobacteria
Helicobacter & Campylobacter
Firmicutes (low G+C Gram+)
Bacillus & Clostridium
Actinobacteria (high G+C)
Streptomyces & Frankia
Crenarchaea
Sulfolobus & Pyrodyctium
Euryarchaea
Halobacterium & Methanosarcina
Viruses
M13 & T4
Genera mentioned in class:
Acanthamoeba
Acetobacterium
Acidianus
Agrobacterium
Aquifex
Archaeoglobus
Arthrobacter
Arthromitis
Bacillus
Bdellovibrio
Blatta
Bradyrhizobium
Brocadia
Burkholderia
Caldotoga
Campylobacter
Caulobacter
Chalymdophila
Chlamydia
Clostridium
Copia
Corynebacterium
Criblamydia
Desulfovibrio
Desulfurococcus
Desulfurolobus
Enterococcus
Eubacterium
F plasmid
Fervidobacterium
Frankia
Gemmata
Geotoga
Haemophilus
Haloarcula
Halobacterium
Hartmanella
Helicobacter
Heliobacterium
Igniococcus
Isosphaera
Lactobacillus
Leuconostoc
Listeria
M13
Marinotoga
Metallosphaera
Methanobacterium
Methanococcus
Methanomicrobium
Methanosarcina
Methanpyrus
Micrococcus
Mimivirus
Mu
Mycobacterium
Mycoplasma
Myxococcus
Nanoarchaeum
Natronobacterium
Neochlamydia
Nitrobacter
Nitrosococcus
Nocardia
Nostoc
P-element
Page 4
Parachlamydia
Peptostreptococcus
Petrotoga
Pirellula
Planctomyces
Prochlorococcus
Prochloron
PrP^Sc
Pyrococcus
Pyrodictium
Rhabdochlamydia
Rhizobium
Rhodobacter
Rhodomicrobium
Rhodopseudomonas
Rhodospirillum
Rickettsia
Sarcina
Shewanella
Simkania
Sporomusa
Staphylococcus
Staphylothermus
Streptococcus
Streptomyces
Stygiolobus
Sulfolobus
T4
Thermococcus
Thermodiscus
Thermopallium
Thermoplasma
Thermoproteus
Thermosipho
Thermotoga
Ty
Ultramicrobium
Waddlia
19) Describe any one heterotrophic organism covered in this section of the class. (6 points)
e.g. Caulobacter
aquatic habitat
stalked
stalked mother cell produces flagellated swarmer
mesophilic
DNA replication has an interphase
Genus & species
trait #1
trait #2
trait #3
trait #4
trait #5
morphology : (text or drawing)
20) Describe any one autotrophic organism (not in the same major phylogenetic group as the one you used
in the previous question) covered in this section of the class. (5 points)
e.g. Methanosarcina
methanogenic
can use acetate instead of CO2 and H2
important in wastewater treatment
mesophilic
Genus & species
trait #1
trait #2
trait #3
trait #4
morphology : (text or drawing)
Page 5
21) Describe the life cycle of any bacterium that has a complex life cycle (not just lag/log/stationary
phases). (5 points)
e.g. Bdellovibrio
Grows freely in rich environments as long spirals, then divide
simultaneously into many cells. In nature develop into parasitic
attack-phase motile cells that are non-replicative. These invade
& grow in periplasm of host, tapping the hosts cytoplasm. They
grow as a spiral filament, then divide into many attack-phase
cells - host lysis releases new parasites.
22) Describe the life cycle of another bacterium (from a different phylogenetic group that the one above)
that has a complex life cycle (not just lag/log/stationary phases). (5 points)
e.g. Bacillus sporulation
Page 6
23) Describe the question/problem, approach, results and conclusion of any one of the papers discussed in
class since the last midterm exam. (10 points)
e.g. the Thermotoga genome sequence paper
The purpose of the paper is to report the complete genome
sequence from Thermotoga. The reason for focusing on this
organism is to try to understand bacterial ancestry and early
evolution. A lot of the paper is devoted to basic info about the
genome; size, number of genes, etc. The genome is a single
circle of 1.86Mbp, about average for a bacterial genome, with
1877 identified ORFs, a full complement of tRNAs and rRNAs.
They use the identifiable genes (along with the known properties
of the species) to infer the metabolic pathways it uses. There
isn't an electron transport chain, and the "ATP synthase" must
hydrolyze ATP to pump protons. This is how organisms that don't
have electron trasport make a proton gradient to drive their
active transport systems (which Thermotoga has a lot of). The
most interesting thing about the genome sequence was that
there is clear evidence for significant amounts of "foreign"
genes, from Archaea, in the Thermotoga genome. The authors
argue that up to about a fourth of the genome was acquired
from Archaea recently enough that it's foreign-ness can still be
detected. Thermotoga is, at least to some extent, an
evolutionary mosaic, and the implication is that maybe all
Bacteria are as well.
Page 7
24) In eukaryotes, ribosomal RNA is transcribed, processed, and assembled into ribosomes in a more-or-less
spherical region of the nucleus known as the nucleolus. Given that bacterial nucleoids are organized
structures, in many ways like the eukaryotic nucleus, you might hypothesize that bacteria might
likewise contain a “nucleolus-oid”, a region within the nucleoid in which all of the ribosomal RNA
operons (most Bacteria have several scattered about the chromosome) are brought together,
transcribed and ribosomes are assembled. How could you test this hypothesis? (5 points)
Add arrays of operator (e.g. the Tet or Lac operators) adjacent
to each of the rRNA operons in a bacterium you can do genetics
in that has several rRNA operons, e.g. E. coli. Probably you’d do
several or each of them separately and see if expression of GFPrepressor lights up a spot in the same cellular location, then
have all of them labeled and see if only one sharp spot appears.
You could also do this using FISH with probes made to large
chunks (10-25Kbp) of sequence adjacent to each rRNA operon.
You couldn’t use the actually rRNA sequence, however, without
lighting up the ribosome-filled cytoplasm.
Page 8