Solved by a verified expert:Questions for lecture 6
Be comfortable with the following terms:
Organotroph
Lithotroph
Chemotroph
Glycolysis
Entner-Doudoroff Pathway
Pentose Phosphate Pathway
b-oxidation
Krebs cycle
Methylotrophy
FAD/FADH2
Ferredoxin
Dehalorespiration (also known as reductive
dehalogenation)
Nitrification
Denitrification
Anammox
Methanogenesis
Acetogenesis
You should use the redox table for many of these questions…
Does respiration require oxygen?
Is there any real advantage of using the
Entner-Doudoroff pathway? Is it possible
that evolution can produce organisms that are not as good as theoretically
possible? How could this happen?
Compare the chemistry of the
Entner-Doudoroff pathway and Glycolysis.
What intermediates are common to both the Entner-Doudoroff pathway and
glycolysis? What are unique to
each?
How might you use a chemostat to tell the
difference between a fermenting cell using glycolysis and one using the
Entner-Doudoroff pathway? Describe the
experiment you would use, and the results that you would expect. Now do it with batch culture.
Could a fermenting cell grow on fatty
acids? What high-energy compound would
it be likely to use for substrate-level phosphorylation? What waste product would it be likely to produce?
Why was it very surprising to see a
fermenting bacterium that showed a reduced growth rate in the presence of an
uncoupling agent? How does the use of
both Fe- based e- carriers and organic e- carriers make this type of growth possible? How does this relate to the mechanism used in
ETCs to make a proton gradient?
The E for the
Ferredoxin(oxidized)/Ferredoxin(reduced) redox couple is -0.39V. Is the transfer of e- from reduced ferredoxin
to NAD+ spontaneous or non-spontaneous?
Many organisms live in environments where
many different types of sugars are available.
Why might these organisms have both the pentose phosphate pathway and
glycolysis? Why are enzymes in the
pentose phosphate pathway useful for tasks such as making DNA? (hint—what is
DNA made of?) What is the NADPH produced
in this pathway useful for?
Many organisms do not use phospholipids for
fuel, but still have enzymes that are used forb-oxidation. What cellular
component(s) could be made using these enzymes (hint: most reactions are reversible, and most
membrane fatty acids have an even number of carbon atoms).
Is glycolysis
a necessary precursor to the Krebs cycle?
Describe how carbon atoms from glucose, ribose (a 5-carbon sugar), oleic
acid (a fatty acid), and benzoic acid can be completely oxidized to CO2. How many “turns” of the Krebs cycle can a C18
fatty acid power? How many turns of the
Krebs cycle can a molecule of glucose power?
The Krebs
cycle produces both NADH and FADH2; the reduction potential (E) for the
FAD/FADH2 redox couple is -0.22V. Could a respiring organotroph use NADH
oxidase to take electrons from FADH2 and feed them into an ETC?
If a respiring
organotroph moved from an aerobic environment to one with only nitrate, what
components of its ETC would you expect to change? Why?
What makes
hydrogen such a good energy source? What
biological process makes hydrogen?
If an organism switches from using glucose to H2 as an e- donor, what
aspect(s) of its electron transport chain need modification, if any?
Methanogens
love H2 as an e- donor. Why are
methanogens often found in the company of fermenters?
Why is it that
methanogens can use H2 as an e- donor, but not hydrogen sulfide (H2S; use the
redox table to answer). Why is the E of
the CO2/methanol redox couple important for knowing whether or not
methanogenesis is possible?
Is Methylotrophy simply Methanogenesis in
reverse—the same enzymes and organism, just different conditions—or are they
different? Why do methanogens fluoresce
at a characteristic wavelength; do methylotrophs fluoresce?
How are methanogenesis and acetogenesis
similar? How are they different?
Farmers spend lots of money injecting
ammonia into their soil as a plant fertilizer.
What bacterial activity is responsible for nitrification? What is the e- acceptor for
nitrification? Is nitrification an
example of anaerobic respiration or an example of lithotrophy? What bacterial activity is responsible for denitrification (the conversion
of nitrate and nitrite to atmospheric N2)?
What is the e- donor for this process?
Is this an example of aerobic respiration or lithotrophy? Using the redox tabloe, which has the better
energy yield?
Why is lithotrophy using Fe2+ as an e-
donor challenging? At neutral pH, Fe2+
is soluble only under anaerobic conditions.
Using the redox table, which could yield more energy: anaerobic iron oxidation at neutral pH, or
aerobic oxidation at highly acidic pH?
Energetic lifestyles such as aerobic iron
oxidation and methanogenesis have very poor energy yields. Why are they so common?
When mine tailings containing iron sulfides
(Pyrites) are brought to the surface and exposed to the atmosphere, they are
attacked by bacteria to create hyperacidic runoff such as the Rio Tinto. The sulfur in the pyrite changes from an oxidation
state equivalent to –SH to an oxidation state of SO4. Is this an example of lithotrophy or
anaerobic respiration? How does the
utilization of sulfur make the utilization of Fe2+ possible under aerobic
conditions? Can the resulting Fe3+ serve
as an e- acceptor for the –SH under anaerobic conditions?
Thiomargarita
namibiensis (the current record holder for largest
Bacterium) has a vacuole that stores nitrate extracted from sea water
and lives in an anaerobic environment rich in sulfides; “thio-margarita”
translates to “sulfur pearl”, and refers to the blobs of elemental sulfur
that accumulate in the periplasm of this organism. How does this organism make its ATP? What would you call its oxidase? Its reductase? Is the elemental sulfur just accumulating
waste, or is it a snack that is saved for later? Would you expect the elemental sulfur to be
used if H2S were still available? What
difficulties might there be with using elemental sulfur, which is a solid? Why does the topology of the sulfur-using
oxidoreductases matter?
Acetogenic organisms can use glucose as a
growth substrate: essentially, they
ferment glucose to 2 mol acetate, 2 CO2, and hydrogen. They then use the hydrogen and the CO2 to produce
acetate. So, glucose goes in and acetate
comes out; the same occurs in some fermentations. How might you use batch cultures to tell the
difference between cells that are growing acetogenically, and cells that are
fermenting glucose to acetate? How would
uncoupling agents or ATPase inhibitors be useful in this determination?
Acetogens and aerobic hydrogen consumers
both love to consume H2 as an e- donor.
Acetogenesis produces Acetyl-CoA as an intermediate. How is the way acetogens produce ATP different
from the way an aerobic hydrogen consumer produces ATP?
How is it possible that the anammox process
can use N compounds both as e- acceptors and e- donors? Is it theoretically possible for an organism
to use Sulfur in the same way? How about
Carbon (remember to look at the redox table!
The answers are there!)
Consider the diagram of the anammox
process. How does the topology of the
nitrate reductase (NIR) help with ATP synthesis? Hydrazine (N2H4) is a deadly poison (as well
as a powerful rocket fuel). Why does
having the anammoxosome compartment help the cell?
What kind of microscopy was used for the
picture of Brocadiain the lecture
slides, and why is it useful for showing the anammoxosome? Could it be visualized by freeze-fracture
SEM? How could you use GFP technology to
demonstrate that the hydrazine oxidase (HZO) was located in the anammoxosome
membrane (AM)?
There are certain cases where the proper
orientation of an oxidoreductase (e.g. the oxidoreductases in anammox bacteria
or iron oxidizers) is very important.
Compose a paragraph about the importance of proper orientation of
oxidoreductases. Your paragraph should
have a topic sentence briefly introducing what a respiratory oxidoreductase is
and what is meant by its orientation.
The meat of the paragraph should explain exactly why the proper
orientation is critical, and what would happen if the oxidoreductase were
“upside-down.”
If you observe an organism living in
anaerobic conditions and producing CO2 and H2S, what would you conclude about
its metabolic lifestyle?
If you observe an organism living in
aerobic conditions and producing elemental sulfur, what would you conclude
about its metabolic lifestyle?
If you observe an organism living in an
aerobic environment and producing a lot of rust, what would you conclude about
its metabolic lifestyle?
If you observe an organism living in an
anaerobic environment, consuming H2S and Fe3+, what might it be producing?
If you observe an organism living in an
anaerobic environment, consuming H2 and tetrachloroethylene, what might it be
producing?
How do respiratory metabolic abilities
allow microbes to clean up man-made disasters?
How do respiratory metabolic abilities allow microbes to make man-made
situations worse?
There seems to be a lot to memorize in looking
at metabolism. It’s best to keep an eye
on the big picture, and not worry too much about the details of whata-keto-glutarate is doing in the Krebs cycle. Focus on the essentials of these processes,
and compare them with one another.
For instance, consider organotrophy:
Pathway
What is
consumed?
What is
produced?
Is O2
involved?
Is ATP
made? How?
Distinctive
to any group?
Glycolysis
Entner-Doudoroff
Pentose-Phosphate
Shunt
Krebs
Cycle
b-oxidation
Aromatic
catabolism (aerobic)
We can also consider different types of
respiration. Of course, “lithotrophy”
and “anaerobiosis” are very general terms; you can fill in the table with a
specific example, or just be very general.
Type of
respiration
e- donor
e-
acceptor
Waste
products
How is
ATP made?
Is O2
involved?
Unique to
any organism?
Aerobic
organotrophy
Anaerobic
organotrophy
Aerobic
lithotrophy
Anaerobic
lithotrophy
Methanogenesis
Acetogenesis
Reductive
dehalogenation
(dehalorespiration)
What YOU
do
Just for contrast, do the same for
fermentation.
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