Structural Biochemistry/Proteins/Nitrogen Fixation

Nitrogen Fixation, or rather, the fixing of Nitrogen, is a process where N₂ is reduced into NH₃, either biologically or abiotically. The nitrogen in amino acids, pyrimidines, purines and other molecules all come from the N₂ in our atmosphere. The fixing of nitrogen can also be associated with the conversion of nitrogen into other forms, other than ammonia, such as nitrogen dioxide. The triple bond that is present in N₂ is very strong; it has a bond energy of 940 kJ/mol. Yet, it is thermodynamically favorable to form ammonia from hydrogen and nitrogen, yet the reaction is still very difficulty kinetically speaking since intermediates can prove to be unstable. It has been estimated that approximately 60 percent of the newly fixed nitrogen on Earth is produced by diazotrophic microorganisms, while lightning and ultraviolet radiation contribute another 15 percent and the rest 25 percent is done by industrial processes.

Nitrogen Fixation
The main avenue for entry of nitrogen into the biosphere is nitrogen fixation. In the nitrogen fixation, we basically fix the dinitrogen, or nitrogen gas into ammonia. Also, fixation of nitrogen requires lots of energy because the triple bond of nitrogen gas is stable. However, breaking the triple bond to generate ammonia requires a series of reduction steps involving high input of energy. Biologically speaking, the conversion of nitrogen into ammonia is usually done by bacteria and archaea. These organisms that are responsible for nitrogen fixation are called diazotrophic microorganisms. For example, the symbiotic Rhizobium bacteria, a diazotrophic microorganism, goes into the roots of leguminous plants to form root nodules where they fix nitrogen. Other examples include Cyanobacteria, Azotobacteraceae, and Frankia. Industrial Processes of Nitrogen Fixation include Dinitrogen complexes, Ambient Nitrogen reduction, and the most common process is the Haber process, invented in 1910. The Haber process involves high pressure, high temperatures, possibly an iron or ruthenium catalyst to produce ammonia. Nitrogen Fixation, in the biological sense, is run by an enzyme called nitrogenase. The reason why the nitrogenase complex is used is because it has multiple redox centers. In general though, nitrogenase complex contains two proteins. The first, a reductase, which provides electrons while the second part, nitrogenase, uses these electrons to turn nitrogen into ammonia. The transferring of electrons, from reductase to nitrogenase, in this process is coupled with the hydrolysis of ATP by the reductase. The reaction for this process is N2 + 8 H+ → 2 NH3 + H2. The reason why this process is an 8 electron process and not simply a 6 electron process is due to the extra mole of Hydrogen that gets generated along with the generation of the ammonia. Often the microorganisms that carry out nitrogen fixation, contain the 8 electrons from the reduced form of Ferredoxin, which can be made from photosynthesis or oxidative processes. Also, this process is coupled by two ATP molecules for each mole, which in turn, equals 16 molecules. The reason for this is not that the ATP hydrolysis is making the reduction thermodynamically favorable since the process is already thermodynamically favorable, but rather allows the reaction to be kinetically possible. Nitrogen fixing bacteria generally separate anaerobic nitrogen fixation from aerobic metabolism by one of several mechanisms. In the ocean and in the freshwater systems, cyanobacteria are the major nitrogen fixers. Within an ecosystem, nitrogen fixers ultimately make the reduced nitrogen available for assimilation by nonfixing microbes and plants. Besides, nitrogen fixation is extremely energy intensive; thus the rate of fixation usually fails to meet the potential demand of other members of the ecosystem.

Reference
Berg, Tymoczko, Stryer, Biochemistry Sixth Edition

Slonczewski, Joan L. Microbiology. "An Evolving Science." Second Edition.