Lecture 32 Flashcards
What is the formula for N2 fixation in the nitrogen cycle?
N2 -> NH4+
N2 fixation is catalyzed by what enzyme?
Nitrogenase
What is the formula for ammonium assimilation?
NH4+ -> R-NH2
Ammonium assimilation is catalyzed by what enzyme?
GS-GOGAT system
GS = glutamine synthetase
GOGAT = glutamine oxyglutarate aminotransferase
Describe how ammonium assimilation works and the energy input involved.
Ammonium is put into the GOGAT enzyme system. The result of the reaction is a glutamate from 2-oxoglutarate + NH4+. It requires input of ATP and NADH to function, making it very energetically expensive - this is often a limiting step to growth.
Once the cell has glutamate, this can be used to produce all the other amino acids.
What is the formula for ammonification?
R-NH2 -> NH4+
Describe how ammonification works.
Many enzymes are capable of ammonification across plants, animals, microbes, etc. The process is the reverse of ammonium assimilation - ammonium gets released.
What is the formula for nitrification?
NH4+ -> NO2- -> NO3-
Describe the typical organisms that do nitrification and where they are found.
Nitrifiers are ubiquitous in aerobic environments, such as soil and water. In deep oceans, nitrification of ammonium is the source of nitrate upwelling. They are usually autotrophs.
Bacteria and archaea can do nitrification. Bacteria can do aerobic nitrification, ammamox, commamox, etc. Archaea nitrifiers are mainly Thaumarchaeota.
Describe the nitrogen cycle that takes place in the open ocean.
Particulate nitrogen sinks down to the bottom of the ocean, where it gets mineralized into NH4+. Nitrification then takes place, converting it to NO2- then NO3-. The NO3- then undergoes upwelling to the surface, where it can get assimilated as R-NH2.
Name and state the formulas for the two steps of nitrification. Are these done by the same or separate organisms?
- Ammonium oxidation: done by ammonium monooxygenase (AMO).
NH4+ -> NO2- - Nitrite oxidation: done by nitrite oxidoreductase (NOR or NXR)
NO2- -> NO3-
They is usually done in separate organisms. The exception to this is comammox bacteria.
What is comammox?
It is complete ammonium oxidation by a single species.
What is the formula for comammox?
NH4+ -> NO3-
Under what conditions does comammox occur?
It occurs under low O2 and low NH4+ conditions.
Describe the genes that comammox bacteria posseses.
They contain amoA genes, which encode the enzyme AMO.
Describe how
a) ammonium
b) nitrite
c) nitrate
d) nitrogen balance
Change over time during comammox
a) Ammonium will drop to zero
b) Nitrite will rise as ammonium gets converted, then drop again as it turns into nitrate.
c) Nitrate will grow.
d) The total nitrogen balance will remain the same.
What is the formula for nitrate assimilation?
NO3- -> R-NH2
Describe the 3 steps of assimilatory nitrate reduction, including the enzymes involved.
- NO3- -> NO2- by assimilatory nitrate reductase
- NO2- -> NH4+ by assimilatory nitrite reductase
- NH4+ assimilated via GS-GOGAT
What limits the process of assimilatory nitrate reduction?
It is inhibited by cellular [NH4+]. ANR is limited by end-product inhibition, as cells only need a limited amount of N (in the form of NH4+) to grow
What is the function of assimilatory nitrate reduction?
Cellular growth (synthesis of amino acids)
What is the purpose of dissimilatory nitrate reduction?
Anaerobic respiration (breathing nitrogen)
What is the formula for dissimilatory nitrate reduction? What enzyme executes this?
NO3- -> NO2-
Done by dissimilatory nitrate reductase
What types of organisms typically do dissimilatory nitrate reduction?
It is characteristic of facultative anaerobic that can use NO3- as a terminal electron acceptor when O2 is not available.
Dissimilatory nitrate reduction can lead to the production of […]
- N2 or N2O via denitrification
- NH4+ via dissimilatory nitrate reduction to ammonia (a form of ammonification)
