The make of Nitrogenase enzymes: By evolution, or design ?
In order to have ammonia essential for the make of DNA, amino- acids and lipids, nitrogen in the air has to be fixed. The uptake of ammonia by microorganisms depends on the interdependent nitrogen cycle. The nitrogen cycle is interdependent with the carbon cycle, and the other energy cycles. Energy cycles, how did they "take off" ?https://reasonandscience.catsboard.com/t2660-energy-cycles-how-did-they-take-offNitrogen fixation is an amazingly complex process. https://reasonandscience.catsboard.com/t2590-origins-what-cause-explains-best-our-existence-and-why#5864
Only a few bacterias fix nitrogen. The most proeminent one are CyanobacteriaCyanobacterias, amazing evidence of designhttps://reasonandscience.catsboard.com/t1551-cyanobacteria-amazing-evidence-of-design
Nitrogen fixation is catalyzed by the nitrogenase complex, a very intricate system with nitrogenase reductase and dinitrogenase as the main components. Nitrogenase is central to life on our planet. Nitrogen fixation has always been considered of fundamental importance, not only for its significance in global nutrition, but also because of the relevance of nitrogenase as a model system for examining processes such as multiple electron oxidation-reduction reactions, complex biological metal assembly, and even nucleotide-dependent signal transduction. The process is highly energetically costly and thus tightly regulated. Nitrogenase is an extremely complex enzyme system composed of two proteins designated the Fe protein and the MoFe protein. With assistance from an energy source (ATP) and a powerful and specific complementary reducing agent (ferredoxin), nitrogen molecules are bound and cleaved with surgical precision. In this way, a ‘molecular sledgehammer’ is applied to the N=N bond, and a single nitrogen molecule yields two molecules of ammonia. The ammonia then ascends the ‘food chain’, and is used as amino groups in protein synthesis for plants and animals. This is a very tiny mechanism but multiplied on a large scale it is of critical importance in allowing plant growth and food production on our planet to continue.
One thing is certain—that matter obeying existing laws of chemistry could not have created, on its own, such a masterpiece of chemical engineering.
Substantial energy input is needed to overcome this large activation energy and break the N=N triple bond. In this biological system, the energy is provided by ATP.
The nitrogenase complex requires three metal clusters as co-factors. They demonstrate the amazing catalytic ability of iron-sulfur clusters in biological systems. The biosynthesis of one of the three co-factors, the MoFe, is extremely complex.Biosynthesis of the Cofactors of Nitrogenase https://reasonandscience.catsboard.com/t2429-biosynthesis-of-the-cofactors-of-nitrogenase
It must be assembled in a multistep process. That begins with the recruiting of Sulfur, Iron, and molybdenum to the assembly site. Sulfur must be obtained in the right form. Six different enzymes are needed in the sulfur synthesis pathway. Biosynthesis of Iron-sulfur clusters, basic building blocks for life https://reasonandscience.catsboard.com/t2285-iron-sulfur-clusters-basic-building-blocks-for-life
Sulfur must be imported by specialized membrane protein channels, called sulfate transporters.
Iron mobilization and uptake is a far more complex process. It requires the transformation of iron in the environment into siderophores, an iron form that organisms can uptake, and import into the cell. Three major sets of components are involved in iron uptake in Gram-negative bacteria. First non-ribosomal peptide synthetases.
The second component required for proper iron uptake is the export system for siderophores are essential, because they produce the siderophores needed to chelate iron in the extracellular space. ABC transporters have the job of uptake of the productAmazing molecular assembly lines and non-ribosomal amino-acid chain formation pathways come to lighthttps://reasonandscience.catsboard.com/t2445-new-amazing-molecular-assembly-lines-and-non-ribosomal-amino-acid-chain-formation-pathways-come-to-lightThe short-range of the strong nuclear force is strong, extending no farther than atomic nuclei. But despite its short range, changing the strong nuclear force would have many wide-ranging consequences, most of them detrimental to life. The periodic table of the elements would look different with a changed strong nuclear force. If it were weaker, there would be fewer stable chemical elements. The more complex organisms require about twenty-seven chemical elements. Instead of ninety-two naturally occurring elements, a universe with a strong force weaker by 50 percent would have contained only about twenty to thirty. That would eliminate Iron and molybdenum, which are life-essential elements, used in many co-factors required in life-essential proteins. Iron Uptake and Homeostasis in Cells https://reasonandscience.catsboard.com/t2443-iron-uptake-and-homeostasis-in-prokaryotic-microorganisms
Maintaining adequate intracellular levels of transition metals is fundamental to the survival of all organisms. While all transition metals are toxic at elevated intracellular concentrations, metals such as iron, zinc, copper, and manganese are essential to many cellular functions. In prokaryotes, the concerted action of a battery of membrane-embedded transport proteins controls a delicate balance between sufficient acquisition and overload.
Once, the basic materials have been imported, the assembly of of co-factors can begin. https://reasonandscience.catsboard.com/t2429-biosynthesis-of-the-cofactors-of-nitrogenase#5924Biosynthesis of FeMoco is a complicated process that requires several Nif gene products, specifically those of nifS, nifQ, nifB, nifE, nifN, nifV, nifH, nifD, and nifK . Assembly of nitrogenase FeMo-co is a considerable chemical feat because of its complexity and intricacy.
Once the co-factors are synthesized, they can be incorporated in the assembly of the nitrogenase enzyme. That is not a simple feat either. Metallocluster carrier proteins escort FeMo-co biosynthetic intermediates in their transit between scaffolds. The insertion of FeMo-co into apo-NifDK generates a mature, functional holoenzyme
Following we summarize what we know of the biosynthetic processes that lead to the formation of active MoFe protein.
1. Molybdate enters the cell and is processed by NifQ, or possibly just cystine, to form a putative Mo-S containing species.
2. Iron (possibly from NifU) and sulfur (from NifS activity) are combined by NifB to form NifBco.
3. NifBco binds to NifN2E2 .
4. The next events are still obscure, but it is widely assumed that NifN2E2 acts as a scaffold for the combination of NifBco with the putative MoS species to form FeMoco.
5. In the final stage of activation, FeMoco is bound to the ‘‘apo- MoFe protein.’’ The ‘‘apo-MoFe proteins’’ must be bound to NifY or . NifY or dissociate after the activation of the MoFe protein by FeMoco. The role
of (NifY) may be to hold the ‘‘apo-MoFe protein’’ in an open conformation that will allow access of FeMoco to its binding site.
By evolution, or design ?