Talk:Nitrogenase

Wiki Education Foundation-supported course assignment

This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Mlee17, Mgoetz2, Mlk803, Kjesse16. Peer reviewers: Vlisnyak, Lcaudrey, Rhli.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 01:39, 18 January 2022 (UTC)

Untitled

It is quite good to list all the relevant reactions and the information about enzyme generation. The wiki page is quite good organized and the information is well selected and aligned.

Figures about the structure of the enzyme and also the catalytic circle may be needed to have a more clear demonstration of the enzyme activity. And it may also to mention the structural interaction of the Fe and MoFe part which enables the electron transfer. Lcaudrey (talk) 04:20, 2 March 2017 (UTC)

Overall very good job, with a lot of details and sources. I would zoom in on both the pymol images and the cluster images. I would also suggest to delete either “Nitrogenase with active sites highlighted” or “Nitrogenase with Active Site Magnified”. The first sentence should be edited. Perhaps: “Nitrogenase is an enzyme responsible for catalyzing nitrogen fixation, which is the reduction of nitrogen (N2) to ammonia (NH3) and a process vital to sustaining life on Earth”. You link to nitrogen fixation more than once throughout the article, but it should only be done once (in your very first sentence). Vlisnyak (talk) 20:55, 4 March 2017 (UTC)

Wiki Education Foundation-supported course assignment

This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Aziz Hawsa.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 05:19, 17 January 2022 (UTC)

Source of the hydrogen

The article should explain the source of the hydrogen atoms in NH3.

Edits

Chemistry of Enzyme Catalysis: Evaluation Notes 1. There are types of nitrogenases that are not mentioned within the intro (eg vanadium nitrogenase) that should be incorporated either as a paragraph or with a link 2. The "Structure and Mechanism" section contains very little information on the mechanism. The two main pathways - distal and alternating - are not mentioned at all. 3. There are missing citations for the paragraphs written on enzyme structure. 4. There are no citations of Brian Hoffman's work on nitrogenase. 5. Graphics of the active site and of proposed mechanisms should be present. -Mlee17 (talk) 01:41, 22 February 2017 (UTC)

Largely have not changed the content, but have:

1. Broken up paragraphs. 2. Done wiki linking. As you can see, there are several terms that don't have articles, or at least, not in the form of the term used. 3. Elaborated somewhat more, taking things a bit more step by step. The original editor(s) clearly knew their biochemistry, but assumed, I think, a bit more expertise on the part of our readers than empirical experience indicates to be warranted. 4. Wrote a very high level outline of the process without all of the qualifications. If a lay reader comes away with the understanding that nitrogenase breaks three chemical bonds, one at a time, and the result is ammonia, we are in good shape.

Stirling Newberry 16:08, 2 January 2007 (UTC)

Kinetic stability of NH₃

I have corrected the line

"Since this reaction does not occur very often, and in fact goes the other way more easily, with ammonia breaking down into nitrogen and hydrogen, without nitrogenase, there would be much less life than presently exists."

As the formation of ammonia from 1/3H₂ and 1/2N₂ does in fact have a negative enthalpy of reaction. As Dr. Hoaglund notes, ammonia production is a problem of kinetic stability of the reactants. —Preceding unsigned comment added by Eutactic (talk • contribs) 06:25, 14 April 2008 (UTC)

The sentence as it now stands:

"Whilst the equilibrium formation of ammonia from molecular hydrogen and nitrogen has an overall negative enthalpy of reaction (ΔH0 = -45.2 kJ mol-1 NH3), the energy barrier to activation is generally insurmountable (EA = 420 kJ mol-1) without the assistance of catalysis"

definitely accomodates my previous correction. My only remaining comment is that the Gibbs free energy determines the spontaneity of the reaction, not the enthalpy. The Gibbs I've calculated for the reaction is ~ -15 kJ/mol NH3. The enthalpy reported in the sentence, ~ -45 kJ/mol NH3, is consistent with that Gibbs. Again, these values are for gaseous reactants and products and may be different for the most-likely aqueous phases involved in the biochemistry of nitrogenase. --Dr John Hoaglund, October 1, 2008 —Preceding unsigned comment added by 64.129.227.4 (talk) 18:07, 1 October 2008 (UTC)

Vanadium Nitrogenase reduces carbon monoxide to alkanes and alkenes - can't find it

as reported on science magazine in august or july, Vanadium Nitrogenase reduces Carbon monoxide (CO) to alkenes and alkanes C2H4,C2H6,C3H8. I read it on science, I can't find the link.. would someone add this fact to the main article with the appropriate reference ? --me. —Preceding unsigned comment added by 46.116.165.180 (talk) 21:59, 24 August 2010 (UTC) The Science citation is Lee, C.C., Hu, Y., and Ribbe, M.W. (2010) “Vanadium nitrogenase reduces CO.” Science 329 (5992), 642. [DOI:10.1126/science.1191455, PMID:20689010] I will edit this later when I correct the magnesium binding errors.john.garavelli 21:41, 5 September 2019 (UTC) — Preceding unsigned comment added by John.garavelli (talk • contribs)

Merger proposal

I propose that Nitrogenase (flavodoxin) be merged to this page as it is essentially not a duplication. The information in that article could easily be accommodated here. Rainbowwrasse (talk) 20:57, 18 October 2011 (UTC)

NO₂

See also Nitrite, a new substrate for nitrogenase — Preceding unsigned comment added by 50.243.27.154 (talk) 13:10, 13 August 2014 (UTC)

References

Oxygen tolerant nitrogenase

The oxygen-tolerant nitrogenase of Streptomyces thermoautotrophicus has been discredited in the literature. See this paper

http://www.nature.com/articles/srep20086 (doi:10.1038/srep20086)

and this comment on the original paper describing the oxygen-tolerant nitrogenase, citing sources.

http://www.ncbi.nlm.nih.gov/pubmed/9334244#cm9334244_14110

would be nice if the article on nitrogenase could be updated to reflect this. — Preceding unsigned comment added by Jwmurray1 (talk • contribs) 18:43, 19 February 2016 (UTC)

Educational Assignment

Hi, I'm a final year student at Imperial and am planning to edit this page as coursework for a science communication course.

Aeb221267 (talk) 12:55, 9 March 2016 (UTC)

Assessment comment

The comment(s) below were originally left at Talk:Nitrogenase/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.

Comment(s)

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The article is extremely important, the reaction is perhaps the 2nd most fundamental bio-reaction after photosynthesis. I don't want to grade this, but I do believe there is an error here. I am not [yet?] a registered wikian, so someone else may want to make this change. I will, however, freely identify myself: John R. Hoaglund, III, Ph.D. Senior hydrogeologist Geotrans Inc. [formerly with Penn State University] Irvine, CA 92614 My edit [ this same edit may apply to http://wiki.riteme.site/wiki/Nitrogen_fixation ]: In this sentence: "Since this reaction does not occur very often, and in fact goes the other way more easily, with ammonia breaking down into nitrogen and hydrogen, without nitrogenase, there would be much less life than presently exists." the clause: "..., and in fact goes the other way more easily, ..." is in error. The thermodynamics of the reaction: N2(g) + 3H2(g) → 2NH3(g) has a Gibbs Free energy of -33.3 kJ/mol, and thus runs most favorably in the direction written. Though the article lists the reaction as N2 + 6H + energy → 2NH3, the full reaction that occurs is what I list above. The reaction written in the article with "6H" should at least be written as "6H+" (perhaps the H+ is provided by an acid...otherwise hydrogen occurs diatomically as H2). It is possible that the reaction N2 + 6H+ + energy → 2NH3 is correctly asserted as energetically favorable in the other direction [I haven't checked the thermo on that]. It may also be possible that the reaction I've written would be energetically favorable in the other direction if the phases were aqueous (i.e. dissolved), written as (aq), rather than gases, written as (g). Again, I haven't checked the thermo on that either. However, the net reaction is what I have written. The reaction is important enough to include the phases and the correct associated thermodynamics. The main issue / problem with the reaction is not the thermodynamics, but rather that the kinetics are extremely slow at room temperature. Thus, very large activation energies are required to get the reaction started. Thus the reaction only runs in the presence of certain enzymes (biological catalysts) biologically [namely nitrogenase], or in the presence of catalysts [usually Fe ] + high temperature + high pressure industrially (The Haber-Bosch process). Please add this reference when editing: Alberty*,Robert A., 2005. Thermodynamics of the mechanism of the nitrogenase reaction. Biophysical Chemistry, Volume 114, Issues 2-3, Pages 115-120. Date of publication: April 22, 2005 Dept. of Chemistry, MIT Abstract The fixation of molecular nitrogen by nitrogenase requires a lot of energy because 16 mol of ATP are hydrolyzed per mole of nitrogen converted to ammonia. Kim and Dees determined the crystallograpic structure of nitrogenase and this has led to a three-step mechanism that involves Feprotein and MoFeprotein in addition to ferredoxin. Each of these steps can be interpreted in terms of two half reactions that are connected through their transfer of electrons. Estimates can be made of the standard apparent reduction potentials of these three steps and their dependencies on pH and ionic strength. This mechanism is compared with the same type of analysis of an alternative three-step mechanism in which the hydrolysis of ATP is coupled with the reduction of molecular nitrogen, rather than the reduction of Feprotein. The problem with the first mechanism is that the second step produces 12 mol of hydrogen ions per mole of nitrogen fixed and the third step consumes 10 mol of hydrogen ions per mole of nitrogen fixed. The alternative mechanism does not have this problem.

Last edited at 18:01, 14 February 2008 (UTC). Substituted at 01:20, 30 April 2016 (UTC)