Natures wonders: nitrogen cycle mechanism (Introduction)

by David Turell @, Thursday, November 26, 2015, 00:22 (1394 days ago) @ David Turell

An organism uses very toxic hydrazine to help the process of the nitrogen cycle which is a key part of providing nitrogen for plants and animals:

"Anammox, an abbreviation for ANaerobic AMMonium OXidation, is a globally important microbial process of the nitrogen cycle. The bacteria mediating this process were identified in 1999, and at the time were a great surprise for the scientific community. It takes place in many natural environments.


"Anaerobic ammonium oxidation (anammox) has a major role in the Earth's nitrogen cycle and is used in energy-efficient wastewater treatment. This bacterial process combines nitrite and ammonium to form dinitrogen (N2) gas, and has been estimated to synthesize up to 50% of the dinitrogen gas emitted into our atmosphere from the oceans. Strikingly, the anammox process relies on the highly unusual, extremely reactive intermediate hydrazine, a compound also used as a rocket fuel because of its high reducing power. So far, the enzymatic mechanism by which hydrazine is synthesized is unknown.


"Dinitrogen gas (N2) is a tough nut to crack. The atoms pair up with a triple bond, very difficult for humans to break without a lot of heat and pressure. Fortunately, this makes it very inert for the atmosphere, but life needs to get at it to make amino acids, muscles, organs, and more. Nitrogenase enzymes in some microbes, such as soil bacteria, are able break apart the atoms at ambient temperatures (a secret agricultural chemists would love to learn). They then "fix" nitrogen into compounds such as ammonia (NH3) that can be utilized by plants and the animals that eat them. To have a nitrogen cycle, though, something has to return the N2 gas back to the atmosphere. That's the job of anammox bacteria.

"Most nitrogen on earth occurs as gaseous N2 (nitrogen oxidation number 0). To make nitrogen available for biochemical reactions, the inert N2 has to be converted to ammonia (oxidation number ?III), which can then be assimilated to produce organic nitrogen compounds, or be oxidized to nitrite (oxidation number +III) or nitrate (+V). The reduction of nitrite in turn results in the regeneration of N2, thus closing the biological nitrogen cycle.


"What does the anammox enzyme look like? They say it has tunnels between the active sites. The "hydrazine synthase" module is "biochemically unique." Don't look for a common ancestor, in other words. It's part of a "tightly coupled multicomponent system" they determined when they lysed a cell and watched its reactivity plummet. Sounds like an irreducibly complex system.

"The paper's diagrams of hydrazine synthase (HZS) show multiple protein domains joined in a "crescent-shaped dimer of heterotrimers" labeled alpha, beta, and gamma, constituted in pairs. The machine also contains multiple haem units (like those in hemoglobin, but unique) and "one zinc ion, as well as several calcium ions." Good thing those atoms are available in Earth's crust.

"Part of the machine looks like a six-bladed propeller. Another part has seven blades. How does it work? Everything is coordinated to carefully transfer electrons around. This means that charge distributions are highly controlled for redox (reduction-oxidation) reactions (i.e., those that receive or donate electrons).


"So here's something you can meditate on when you take in another breath. The nitrogen gas that comes into your lungs is a byproduct of an exquisitely designed, precision nanomachine that knows a lot about organic redox chemistry and safe handling of rocket fuel. This little machine, which also knows how to recycle and reuse all its parts in a sustainable "green" way, keeps the nitrogen in balance for the whole planet."

Comment: Remember the bombardier beetle and how it handle the toxic stuff it made. This bug's machine is also irreducibly complex.

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