I've noticed the following errors in Bertini, Gray, Stiefel and Valentine's book. For my classes, and as a public service to others, I offer a compendium of the one's I've noticed or that students have brought to my attention.
pp 144 - 150) The ferritin chapter has a number of errors. In Figure VIII.2.1, F(ox) is an abbreviation for the ferroxidase site, so I don't know what the difference is between the two sites labelled Fe-1 and Fe-2. The figure caption for Fig. VIII.2.3 on page 146 does not correspond to the figure that is there. The figure that is there compares (a) the mechanism for oxidation of iron at the Fe(ox) site (equations 1 and 2 on p. 147) with (b) the mechanism for oxidation of methane by methane monooxygenase. Equations 1, 2 and 3 on p. 147 are misleading, because the oxidation of the iron and incorporation into the iron oxide mineral core occurs two iron atoms at a time, and not in a large scale sequential fashion (i.e., it is NOT TRUE that the ferritin molecule first synthesizes up to 1100 hydrated Fe-O-O-Fe centers, and then converts all 1100 of these into 2200 hydrated iron(3+) ions, and then converts these all at once into the mineral core). Furthermore, the equation 3 is unbalanced - it is not only missing water as a reactant, but the amount of H(+) produced should be twice as much as is indicated.
p. 178) There is an error in the structure of Succinate shown in Fig. IX.1.3. (There is no -OH group in succinate). Also, the bottom half of this figure shows a proposed mechanism for isocitrate dehydrogenase, which is an enzyme that is distinct from isocitrate lyase (notice that it catalyzes a redox reaction involving oxidation of the substrate by NAD+).
p. 179) There is an error in the structure of ATP shown in the upper left of Fig. IX.1.4. There is an extra oxygen atom shown between the two P atoms. The error can be fixed by erasing one atom and two bonds, and drawing in a new bond, as shown in at right (the new bond is shown in green):
p. 321) middle of page: the deltaG’s for reactions with O2 are not only in the archaic units of kcal/mol (to convert to kJ/mol, multiply by 4.2), but are also incorrect for the reactions as written; the values shown are for formation of one mole of the oxidized product.
p. 321) bottom of page: Footnote b is misleading and incorrect. It should be rewritten as follows: The standard state for O2 used here is gas phase at standard (1 bar) pressure. The alternative is to consider O2 in aqueous solution at standard (1 molal or approximately 1 mol/L) concentration; under these conditions the redox potentials increases by +0.17 V / n, where n is the number of electrons involved in the reduction. The distinction between these standard state choices is discussed further on p. 357.
p. 340) The two parenthetical references to reaction 12 in the paragraph in the middle of the page should be crossed out. (That figure shows inner and outer sphere mechanisms for the reduction of Ni(III) by superoxide, but in the middle paragraph of p. 340 the authors are discussing the other half of the dismutase reaction - the oxidation of Ni(II) by superoxide.
p. 340) The caption for Figure XI.2.7 switches the descriptions of (a) and (b). (a) is the Ni2+ and (b) is the Ni3+.
p. 348) In the hypothetical oxene intermediate at the bottom right of Fig. XI.3.8, erase the single dot (radical electron) that was placed on top of the oxygen bound to Fe(3+). Careful counting of electrons will show that this electron doesn't belong (all the other structures have an odd total number of electrons and the bottom right structure as drawn has an even number).
p. 356) The middle column is labeled "Active Site of Oxy" For both of the hemocyanins, this column should read CuII-O2-2-CuII to indicate a peroxide dianion bound between two copper(II) ions. The entry for hemerythrin should read FeIII...FeIII-O2(H)-1 to indicate a hydroxperoxide anion (OOH-1) bound to one of the iron(III) ions.
p. 362, line 13) change “Fig. XI.2.1b” to “Fig. XI.4.1b (p. 355)”.
pp. 536-537) the discussion of intramolecular electron transfer to the "Fe(III)Cyt c" heme center should say the "Fe(III) b5" heme center in each instance; cytochrome c is a separate molecule, so could not be part of intramolecular electron transfer.
p. 642) In the last sentence of the first complete paragraph on page 642, the terms "open" and "closed" should be switched, and change "apo-form" to "apo-like form". I.e., the sentence should read "the Ca1 form is found to be in equilibrium between two conformations, presumably a "closed" apo-like form and an "open" Ca1-form ...". An NMR study that showed this is described in Johan Evenas, Sture Forsen, Anders Malmendal and Mikael Akke, Backbone dynamics and energetics of a Calmodulin domain mutant exchanging between closed and open conformations, Journal of Molecular Biology, Volume 289, Issue 3, 11 June 1999, Pages 603-617. Unfortunately, the first sentence of the abstract of that article seems to makethe same confusing error in switching "open" and "closed", but the body of the article makes it clear in words and pictures that normally (in unmutated protein) the apo-form is in a closed conformation and the Ca2 form is in an open conformation.
January 15, 2012
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