User:WeepingBritney/Enzyme prof review

For the purposes of students learning something for the first time...

Breadth
•	Does the article cover its field completely?

•	Are all the common terms of the field defined?

•	Are all the basic concepts of the field described?

•	Were important topics missed?

Overall, I was very pleased with the breadth of the article. There are no glaring gaps in coverage, though some topics require discussion in greater depth (see below). Most of the terms were explained, with only a few exceptions [e.g., stereospecificity, regiospecificity, and chemoselectivity were not defined in the Specificity section (though links were provided); ΔH╪ was not defined in the Mechanisms section; kinase and phosphatase—for addition and removal of phosphate groups—was not defined in the Biological Function section; and the important terms general acid/general base were missing].

Depth
•	Amount of detail appropriate for topic

•	History given?

The depth seems to be gauged well in general, but I would have liked to have seen more description of how enzymes actually function. For example, I think it appropriate to include a specific example (and figure!) of a reaction involving general acid/general base catalysis (important terms that were not included). The figure could show how the substrate is bound and how specific groups are positioned to accelerate catalysis—a point made in the “structures and mechanisms” section, but not clearly shown. To provide more appreciation of enzyme catalysis, the article could have included a discussion of biomimetic studies (non-enzyme models that accelerate reactions by placing catalytic groups on cyclodextrin or another scaffold—demonstrating that enzymes do more that simply position these groups appropriately). Also, studies of catalytic antibodies and the engineering of a protein to generate enzyme activity (e.g., creating triose phosphate isomerase activity in the ribose binding protein) would be useful additions. A nice section is included on the history of enzymes. Of interest, the work of Sumner on urease was mentioned as showing the enzyme was a pure protein; however, urease was later shown to possess nickel as a cofactor so it is not a pure protein. A minor quibble about this section is the ending that stated the “structure of lysozyme marked the beginning of the field of structural biology”—this ignores the earlier crystallography work of Perutz on hemoglobin (not an enzyme).

Readability/Writing
•	Is the writing clear?

•	Is the writing interesting?

•	Is the writing organized, good flow?

•	Architecture to the article (beginning, middle, end)?

•	Is the writing redundant?

I found the writing to be very clear, with a logical flow and negligible redundancy. I would have re-written the line about “unique…sequence…, unique structure, …unique properties” in Structures and Mechanisms. Also, in Kinetics I would change “This is shown … shown on the right.”

Learnability
•	Is the level of explanation good for undergraduate students? Not too simple or complex?

•	Is the teaching well-organized, clear progression of topics?

Well done!

Figures
•	Are there Figures at all?

•	Are the Figures clear?

•	Are the Figures three-dimensional?

•	Are the Figures consistent with each other?

The figures were a major disappointment to me, since several had no clear purpose other than to provide splashes of color. Why not use the space to provide clarification of the text? One example is mentioned above, where the interactions of substrate and enzyme could be depicted along with the positions of general acid/general base groups that affect catalysis. The first figure in the article shows TIM (not defined as triose phosphate isomerase) with no indication of what the colors represent and only a link to see what the ribbon diagram means. Perhaps this figure would be more useful if a stick representation of the substrate was included so as to contrast the large size of the enzyme versus the tiny substrate. The figure illustrating the structure of carbonic anhydrase shows the zinc suspended in a vacuum—a totally wrong impression to leave with students. By including the side chain imidazoles, the figure could have highlighted the point about how the enzyme achieves tight binding of the cofactor (and mention should be made that other side chains are not depicted). The cartoon figure related to induced fit is OK, but this could be accompanied by actual side chain and backbone motions in an enzyme example. The model of NADH seems to serve no purpose. A reader can’t even distinguish the site of the hydride that is mentioned. The reaction profile figure gives the unfortunate impression that the reaction proceeds unidirectionally to the right. For a general enzyme example, this is not the case. For reversible enzymes, the activation energy proceeding left to right will differ from that proceeding from right to left; thus, complicating the diagram. The legend includes the term “niveau” rather than a more common and understandable word. The rate versus [S] diagram should be replaced by authentic hyperbolic data. The rate is shown reaching Vmax at the 200 (units?) point (~ 5-fold the Km), which does not reflect reality. The cartoon depicting competitive inhibition is OK, but the comparison of folate and methotrexate is worrisome. A reader might mistakenly think the near mirror symmetry is the key point; the two molecules should be shown from the same perspective. The red, blue, and white colors should be explained. The depiction of phenylalanine hydroxylase is another use of gratuitous color. The stick diagram of bound folate is not even mentioned. Perhaps the mutated side chain associated with phenylketonuria could be highlighted?

Quality
•	How up-to-date is the article? When would this article have last been an up-to-date review of the field?

•	Glaring errors, minor errors, and misleading statements?

•	How precise and quantitative is the article?

This article is quite up to date. Here are some more points of concern:

•	The second sentence in the article states that enzymes convert substrates into products; this statement could give the incorrect impression that enzymes catalyze unidirectional reactions.

•	In Structures and Mechanisms the mention of “small molecules” would be clarified by saying “small molecule effectors” (as used in the section on Allosteric Modulation).

•	The discussion of Organic Cofactors would have been clearer without mentioning coenzymes—they are described in the next section.

•	Also in the Cofactors section, the article is wrong when stating that thiamine pyrophosphate is covalently bound to pyruvate dehydrogenase (lipoic acid would be correct for this enzyme, or biotin could be used for other enzymes).

•	The Kinetics section suggests that “orotidine 5'-phosphate decarboxylase will consume half of its substrate in 78 million years if no enzyme is present. However, when the decarboxylase is added, the same process takes just 25 milliseconds.” This is nonsense (how can an enzyme do anything if it is not present) and needs significant improvement. It would be correct to state that it takes 78 million years for ½ of orotidine 5’-phosphate to spontaneously decarboxylate. I haven’t gone to the primary literature to see what is appropriate for describing the situation for the enzyme, but clearly the amount of enzyme added will be important!

•	Also in this section, the Km is incorrectly described as showing how tight the binding of the substrate is to the enzyme—that phrase describes Kd (the dissociation constant), the Km is distinct.

•	Near the end of this section quantum tunneling is said to occur in tryptamine; this is incorrect. The quantum tunneling occurs in aromatic amine dehydrogenase which uses tryptamine as a substrate.

•	The section on Competitive Inhibitors would be improved by mention of “slow-binding” inhibitors. Many of these compounds have found utility in the pharmaceutical industry. Of note, characterization of the inhibition mechanism of these compounds cannot be done by simple Michaelis-Menton kinetic approaches.

•	The next section on non-competitive inhibitors says that inhibitor binding “stops the active site (from?) binding substrate”; this is not necessarily the case.

•	The section on Irreversible Inhibitors includes the unfortunate phrase “suicide inhibitors”, which is still used by some scientists but should be abolished. An enzyme cannot make a conscious decision to kill itself; thus, the preferred term for this process is “mechanism-based inhibitors”.

•	In Uses of Inhibitors, aspirin “irreversibly” inhibits COX-1 and -2 (this word should be inserted) and cyanide binds tightly but not irreversibly to cytochrome c oxidase.

•	With regard to ruminants (next section), “a” should be deleted from “which have a herbivorous diets” and “gut” should be replaced by “rumen” (gut is inappropriate).

•	I wonder why the British spelling of “mould” is used in the section on Dairy industry?

•	For the starch industry, “amyloglucosidases” has an extra “e”.