Download Test 3 Review Questions

Microbiology Test #3 Review Questions
More questions will be added after Tuesday’s lecture (when I know what I covered)
Definitions:
1. Be able to define and give the microbial/ecological significance of the
following terms:
a. syntroph
b. methane hydrates
c. nutrient reservoirs (carbon, nitrogen)
d. secondary fermenters
e. assimilation
f. nitrification
g. denitrification
h. ammonification
i. microbial leaching
j. xenobiotic
k. reductive dechlorination
l. symbiosis
m. microbial consortia
n. rhizosphere
o. rhizobia
p. cross-inoculation groups
q. rhicadhesin
r. nod factors
s. bacteroids
t. leghemoglobin
u. Ti Plasmid
v. opines
w. T-DNA
x. ectomycorrhizae
y. endomycorrhizae
z. arbuscular mycorrhizae
aa. planktonic
bb. benthic
cc. photic zone
dd. epilimnion
ee. hypolimnion
ff. thermocline
gg. eutrophic
hh. oligotrophic
ii. BOD
jj. Pelagic zone
kk. Prochlorophytes
ll. Bacteriophages
mm.
nn.
oo.
pp.
qq.
rr.
ss.
tt.
uu.
vv.
ww.
xx.
yy.
zz.
aaa.
bbb.
ccc.
ddd.
eee.
fff.
ggg.
hhh.
iii.
jjj.
kkk.
lll.
mmm.
nnn.
ooo.
ppp.
qqq.
rrr.
Piezophile
Black smoker
Lost city formation
Population
Community
Species richness
Species abundance
Ecosystem
Microbial guild
Niche
Microenvironment
Biofilm
c-di-GMP
microbial mats
O-horizon, A-horizon, B-horizon, C-horizon
primary metabolite
secondary metabolite
semisynthetic penicillins
biosynthetic penicillins
natural penicillins
zone of growth inhibition
immobilized enzymes
extremozymes
malolactic fermentation
wort
malt
mash
primary heritable symbionts
secondary heritable symbionts
trophosome
methanotrophs
light organ
Commercial Products:
1. Be able to describe the ideal characteristics that an industrial microbe must
posess.
2. How would your culture approach differ if you were trying to harvest a
primary versus a secondary metabolite?
3. Be able to describe a ‘typical’ scale-up operation: from bench-top to
production. What types of challenges might you encounter along the way?
4. Be able to describe a laboratory process by which you could screen soil
bacteria for the production of antibiotics.
5. Be able to compare and contrast the culture conditions used to produce
penicillin versus those used to produce tetracycline. Be able to discuss the
role of catabolite repression in the latter.
6. Be able to name a few amino acids that are produced microbially and to
discuss why making amino acids in this way can be tricky. How do industrial
microbiologists get around this challenge?
7. Be able to describe 3 enzymes that are made via industrial microbiology, and
to state what their function is.
8. Be able to describe how to make beer, white wine, red wine and distilled
spirits.
9. Be able to discuss what biofuels are, and the pros and cons of using them.
What role might Botrycoccus braunii play in biofuels development?
Major microbial habitats and diversity:
1. Be able to discuss environmental factors (5) that influence species richness
and abundance in ecosystems.
2. What are 4 characteristics of microenvironments that differentiate them
from typical ‘macro’ environments?
3. What are biofilms? How do they form? What are the advantages of living in
a biofilm? Be able to give 1 example of a biofilm.
4. Be able to discuss the roles of c-di-GMP and riboswitches in the formation of
biofilms.
5. What is quorum sensing, and how does it play a role in biofilm development?
6. Why are biofilms problematic to humans? Be able to give two specific
examples.
7. Be able to give the likely characteristics of microbes at different depths in a
cyanobacterial mat (with respect to light, O2, and H2S usage).
8. Be able to describe how soils form, and the roles that microbes play in this
process.
9. Be able to describe a ‘typical’ soil particle as a microenvironment. Discuss
factors such as the concentrations of oxygen, water, phosphorus and nitrogen
and how they relate to microbial community composition.
10. We looked at many phylogenetic snapshots..in different environments as well
as in different symbioses. Be prepared to compare and contrast those
snapshots with a focus on the big taxonomic differences between them, and
on how those big differences reflect the types of environments/nutrient
availability/etc. How are those snapshots generated?
11. What types of characteristics does a microbe need to have to live in the deep
subsurface?
12. Describe the unique way in which Desulforudis audaxviator survives
essentially by itself in deep gold mines.
13. Be able to discuss the types of microbes (energy sources utilized, aerobic or
not, phototrophic or not, etc.) that are likely to live in different layers of a
freshwater lake as you move from the surface down into the sediments at the
bottom.
14. What is the phenomenon of ‘turning over’ and how would you expect it to
impact the microbial species locations that you described in #13 above?
15. Be able to describe, in general, how pelagic waters differ from coastal waters.
16. Be able to discuss 2 important roles that bacteriophages play in marine
systems.
17. Be able to describe the deep sea environment, and to discuss the adaptations
that deep sea microbes must have (in general, and molecular).
18. Be able to compare and contrast “Black Smoker” with “Lost City Formation”
environments. How do each form? What types of electron sources are most
common in each of these areas, and what metabolic types of bacteria live
there as a result?
Nutrient Cycles, Biodegredation and Bioremediation
1. Be prepared to discuss the roles of oxygenic phototrophs, chemolithotrophs,
methanotrophs, methanogens, acetogens, anoxygenic phototrophs and
heterotrophs (aerobic respiration, anaerobic respiration and fermentation)
in the carbon cycle (the types of carbon they use, whether they oxidize or
reduce it..use it as an energy source or ‘fix’ it from CO2, etc.)
2. What are methane hydrates? How do they fuel deep water ecosystems?
What impact might global warming have on them, and what impact would
they then potentially have on the globe?
3. Be able to describe how organic carbon levels impact nitrogen fixation, and
how NH4+ and NO3- levels impact primary production, nitrogen fixation,
nitrification and denitrification.
4. Decomposition of complex polymers in anoxic conditions often results in the
production of methane. Be able to discuss the roles of polymer-degrading
bacteria, primary fermenters, secondary fermenters, methanogens,
acetogens and syntrophs in this process.
5. Why do termites produce so much methane?
6. Be able to discuss the roles of ammonia-oxidizing, nitrifying, denitrifying,
ammonifying and nitrogen-fixing microbes in the nitrogen cycle.
7. What are the environmental impacts of each of the parts of the nitrogen cycle
discussed above?
8. Be able to discuss the roles of chemolithotrophs and anaerobic respiration in
the iron cycle.
9. Be able to discuss how acid mine drainage is generated (initiator reactions,
oxidation of Fe2+ and the propagation cycle), and to discuss its environmental
impacts. Which microbes catalyze the rate-limiting step (name 2)?
10. How can microbes be used to leach copper from ore?
11. Be able to compare and contrast bioremediation/biodegradation of three
different human products. In particular, tell how the microbes
detoxify/break down the product, if any particular environmental conditions
are required, and any drawbacks to the process.
12. How do microbes make plastic? What are the pros and cons to using this
plastic?
Symbiotic Relationships.
1. Be able to describe the general symbiotic relationships (taxa involved,
benefits to both) in lichens, Chlorochromatium aggregatum, soybean root
nodules, Crown Gall disease, mycorrhizae, the Bobtail squid, cows, tube
worms and termites.
2. Be able to describe the steps in root nodule formation, and the role of Nod
Genes, Nod Proteins and Nod Factors in that process.
3. Be able to describe the biochemical interactions between the Bacteroid
and its host legume.
4. Be able to describe the steps in A. tumefaciens infection and
transformation of its host plants. Include all genes/gene products and
their roles in the transfer and integration of T-DNA.
5. Be able to describe how arbuscular microrrhizae associate with their host
(the steps involved).
6. Be able to describe the general differences between monogastric
stomachs and those with foregut and hindgut fermentation chambers.
What types of nutrition (herbivore, carnivore, omnivore) are best suited
to each type of digestive system, and why?
7. Be able to describe how food is digested in a ruminant…what roles do the
rumen, the reticulum and the abomasum play?
8. Be able to describe the fermentations that happen in the ruminant gut.
What are the major products, and what role(s) to these products play in
ruminant nutrition? Which biochemical processes rely upon microbes?
9. Be able to discuss how the food given to a ruminant can impact the
microbes in its rumen, and to discuss how this can impact both ruminant
and human health.
10. Insect symbionts play a variety of roles. Be able to briefly discuss a few,
and to tell how these roles could be used to control insect pests.
11. Discuss 3 unique features of the genomes of primary symbionts in insects.
12. Be able to discuss the roles of Protistan and bacterial symbionts in
termites. What biochemical and biological roles do they play? How does
the structure of the termite gut play a role in the location/metabolism of
its symbiotic bacteria?
13. Be able to describe the symbiotic relationship between deep ocean tube
worms and their symbiotic bacteria.
14. Be able to describe two ecological roles of quorum sensing that we have
studied in this unit.
15. Be able to describe, in some detail, the establishment and propagation of
the Bobtail squid/Aliivibrio symbiosis. What does each species get out of
the relationship?