Talk:Michaelis–Menten kinetics/GA1

GA Review

Article (edit | visual edit | history) · Article talk (edit | history) · Watch

Reviewer: Sasata (talk) 20:58, 17 June 2011 (UTC)

Hi, I'll do this review. It may take me up to a week to put up some comments (I'll have to dig out some texts and compare notes, see if I remember anything from undergrad enzymology, get distracted by other stuff, etc.). Sasata (talk) 20:58, 17 June 2011 (UTC)

Thanks! I'm away until 4 July and probably won't be able to respond to any comments until then. U+003F? 10:39, 20 June 2011 (UTC)

Comments

• overall, I think the article currently needs a lot of work to bring it to GA-level. I think the average reader who came to this article trying to get a better understanding of the concept of M-M kinetics would leave in frustration. Consider the idea of writing a level down: if the expected audience is upper-year university students (e.g., taking intro biochem or intro enzymology), write it so a first year chem student would be able to understand it.
• more links needed throughout: substrate, reaction rate, enzyme-substrate complex, rate constant, antigen, antibody, DNA hybridization, adsorption
• "A model of one of the most basic enzymatic reactions was first proposed… " so what was the reaction? (I think it was sucrose -> glucose + fructose by invertase, IIRC)
• should explain somewhere that the arrows pointing both ways refers to chemical equilibrium
• please explain clearly what kcat means (a link to turnover number is insufficient)
• first section of derivation needs more explanation… please walk the reader through it. Define "t"

I'm averse to over-explaining here, for fear of the article becoming too text-booky. I suppose the rub is as to if the reader wants to know about the derivation or just be told the formula. U+003F? 16:43, 17 August 2011 (UTC)

• "… we find that …" sounds too much like a textbook, and is not encyclopedic language
• please add citations for the unreferenced paragraphs in the derivation section
• convert bulleted list in "Determination of constants" section into prose
• how about rate equations for the four types of enzyme inhibition (pure noncompetitive, pure competitive, anticompetitive, and mixed)?

I partially followed this suggestion. But I don't think this should be too heavily focussed on, as M-M refers to simple uninhibited kinetics. U+003F? 12:00, 8 August 2011 (UTC)

• to help illustrate the concept of steady state in enzyme kinetics, how about a graph showing how the concentrations of substrate, free enzyme, enzyme substrate complex, and product vary with time (this type of graph is common in undergrad textbooks)
• some examples/comparison of rate constants of various enzymes would help the reader grasp these theoretical concepts. For example, my textbook has a table with several enzymes (chymotrypsin, pepsin, tyrosyl-tRNA synthetase, ribonuclease, carbonic anhydrase, and fumarase) showing the reaction catalyzed, Km, cat, kcat/Km arranged in order of increasing efficiency.

What's the name of the textbook? Found it U+003F? 08:46, 26 July 2011 (UTC)

• the article would really benefit from an "Applications" section that would show several examples of how MM kinetics is used to describe and model various biochemical reactions and other natural phenomena. See the following reviews for ideas: Chen, W. W.; Niepel, M.; Sorger, P. K. (2010). "Classic and contemporary approaches to modeling biochemical reactions". Genes & Development. 24 (17): 1861–1875. doi:10.1101/gad.1945410. PMC 2932968. PMID 20810646.; Jones, A. W. (2010). "Evidence-based survey of the elimination rates of ethanol from blood with applications in forensic casework". Forensic Science International. 200 (1–3): 1–20. doi:10.1016/j.forsciint.2010.02.021. PMID 20304569. (elimination rates of ethanol from blood); Abedon, S. T. (2009). "Kinetics of Phage-Mediated Biocontrol of Bacteria". Foodborne Pathogens and Disease. 6 (7): 807–815. doi:10.1089/fpd.2008.0242. PMID 19459758. (kinetics of bacteriophage infection); JSTOR 3433577 (a model for pulmonary clearance); JSTOR 3547060 (modeling species richness). There are many more examples that may be found with a pubmed search.

No word from the nominator. I'll have to close this soon... Sasata (talk) 18:08, 22 July 2011 (UTC)

Many thanks for the review, and sorry for being silent for so long. I'll work through the comments this week and try and get my partners in crime to help out. U+003F? 22:49, 25 July 2011 (UTC)

Good to see the article is improving; I'll be outta town for a week or so starting tomorrow, so hopefully we can finish up the review when I get back. Sasata (talk) 16:03, 26 July 2011 (UTC)

The article's been under review for two months now; could this be wrapped up soon? Wizardman _{Operation Big Bear} 17:11, 15 August 2011 (UTC)

Back on track, sorry for the delay. Some more comments:

• The lead is rather short, and does not adequately summarize the contents of the article
• "In 1903, French physical chemist Victor Henri found that enzyme reactions were initiated by a bond between the enzyme and the substrate." I see this sentence is identical to one in the article Victor Henri, and in turn identical to the source. I think it needs some more explanation, check out the enzyme article for some more background.
• "… of the most basic enzymatic reactions, invertase" what does "most basic" mean? high pH? simple reaction mechanism? The source doesn't say it's basic.
• the double arrow should be fixed to an equilibrium arrow ("rightleftharpoons")
• "Change in concentrations over time" should indicate what S, P, E, and ES are
• The "Applications" section should really be longer than a single sentence. It would be good to have some more explanation about the the parameters are so different in the "Example parameter values" section. Perhaps these two sections could be combined somehow?
• why is Whonamedit? is reliable source?
• there is a translation of the 1913 Menten & Michaelis paper here
• please provide page references for the book sources (not the # of pages in the book). It will help me verify the citations. Sasata (talk) 20:20, 28 August 2011 (UTC)

• No response in over a week, so I'm going to close this review due to inactivity. Although there has been some improvement in the article, there still is some work to be done to bring it to GA standard. I hope to see the article at GAN again sometime after the above comments are addressed. Sasata (talk) 16:00, 6 September 2011 (UTC)