Some Issues with Voet/Voet/Pratt Textbook.
1) The sample pH calculation on page 34 is wrong. The calculation assumes that acetic
acid is a strong acid and that it is fully dissociated in water. That is not correct.
2) On page 48 the text book states that tautomers are 'easily converted isomers'.
The relevant tautomeric forms are shown in Figure 3-7. This may be of
historical interest because apparently Watson and Crick were initially confused about
the tautomer forms. In fact the keto forms are
MUCH more stable that the enol forms, to the extent that there is
no convincing evidence that the enol forms exist to any appreciable extent. Since the
equilibrium lies so far to one side, it is not correct to say that the tautomeric states
are easily converted. It is also possible to draw weird tautomeric forms of amino acids and
peptides. But since they are irrelevant to biology, we don't do it. The same standard should apply
to nucleic acids.
3) Table 4-1, page 80. This table contains pKs of the (-COOH) acids and bases (-NH2) of each amino acid monomer.
That information is not very interesting or relevant. For this course you could ever need to know is that the
carboxylic acid is deprotonated (anionic) and the
base (the amino group) is protonated (cationic). There is no utility in knowing these pKa's, which vary only
slightly among the amino acids, and are not generally relevant in biological systems. However the Pka's of the side
chains are a different matter altogether. Those are important. For this course I suggest you ignore
Table 4-1 and use my table, which
has some important
information, like some of the structural and catalytic roles of each amino acid, and omits the irrelevant part.
4) More on Table 4-1, page 80. The astrixes on isoleucine and threonine are not explained in the table legend,
but are probably intended to indicate that the beta-carbons of those residues are chiral.
5) More on Table 4-1, page 80. The atoms of tryptophan are not numbered correctly. That atoms of phenylalanine and
tyrosine are not numbered at all.
But those atom numbers are not significant for the purposes of this course, so never mind.
6) Skip chapter 5. It seems a little obsolete and out of date. In the first place,
mass spectrometry, not mentioned in the chapter, has replaced many of the analytical
techniques described there. In addition, protein purification is rarely conducted in the ways described in the text.
Proteins are almost always purified by the attachment (at the DNA level) of affinity tags, such
as hexahistidine (binds to Ni or Cu), maltose binding protein, chiton binding protein, etc. Finally, no one sequences
proteins (or DNA) in their own lab anymore. We always send them out sequencing services. So there is not much gain
in learning the chemistry of that.
7) Protein Electrophoresis. Page 104. The first paragraph of the section in polyacrylamide electrophoresis
is sort of incoherent. It is not correct to say that, "Molecular separations are based on sieving effects as
well as electrophoretic mobiility", because sieving effects are an intrinsic part of electrophoretic mobility.
Size, shape, charge, and matrix (agarose, acrylamide, etc)
effect electrophoretic mobility. Also, the direction of protein migration depends on pH and on the pI.
Finally, electrophoresis cannot be converted to a verb, so don't say "I am electrophoresing this protein".
8) On page 153, section 4C. An n-residue protein does not have 2^n (2 raised to the n) torsion angles.
An n-residue protein has 2xn (2 times n) torsion angles.
9) Myoglobin/Hemoglobin. Page 164. Just before equation 7-3 is the phrase , "Since O2 is a gas...". When thinking about Mb,
it is not reasonable to think that it is contact with gaseous O2. In cells O2 is in solution,
it is a solute. But it is, in priniple (but not really), in equalibrium with O2 in the gas phase. Therefore it is common to substitute
the partial pressure for the concentration.
10) Myoglobin/Hemoglobin. Page 168. In the equation for binding of Hb and nO2, the arrow should be replaced by the standard
double arrow, indicating reversible chemical equation.
10a) On page 168 the graph of oxygen binding to Hb and Mb is very confusing. The S-shaped curve, which is the Hb curve, is not clearly
labeled as such. Maybe that is what "hemoglobin in whole blood" is supposed to indicate, but that is a strange label for it.
11) Carbohydrates. Figure 8-2. The labels (Ketotriose, Ketotetrose, etc) have been omitted.
12) Carbohydrates. Page 203-204, figures showing lactose, cellulose, chiten, etc. For these structures, VVP have
represented a bond with an acutely bent line. In all other situations it would be correct for a student to assume that a
joint like that would indicate a carbon atom. But here it is used so that some lazy artist did not have to flip one
of the sugars over. One result is that the molecular interactions shown in Figure 8-9 (3D model of cellulose), are not
apparent from the chemical structure of cellulose. Figure 8-12 contains a lot of these wierd chemical structures. Simpler,
more intuitive, and chemically correct representations are shown here
13) Biological Membranes. There is something really wrong with figure 10-35 (page 269). The glucose molecule, is not red, as
stated in the legend. The red dots on the glucose molecule do not, as far as I can tell, coorespond to the sites of chemical
modification stated in the text. So who knows what they are?
14) Chapter 11, Section 3-3. The section on General Catalytic Mechanisms (3-3) is sort of indecipherable,
because it is written as if those catagories are separate and independent when in reality they are overlapping and redundant.
Those are not mechanisms, they are features of mechanisms. Any given mechanism can use one of more of those features.
15) Chapter 11. The reaction schemes on page 290, 291, 293, should use reversible arrows of chemical reactions.
16) Figure 11-24. That figure is confusing because Gly 193, Asp 194, and Ile 16 are basically irrelevant, and should be omitted.
17) Electron Transport. One page 497, for the half reactions, there should be no deltas before the epsilons.
17a) From a student: There is a typo on page 217 in the student companion. #21 b should read 117,000, but it reads 11,700.
17c) Figure 17-8 shows that Q pumps the protons but the text on page 506 says that Complex III pumps the protons.
18) Photosynthesis. For question 4a) the answer is correct but the solution is not set up correctly (the O2 half reaction must be divided by 2.
19) Chapter 23. Nucleic Acid Structure. Page 740. "Watson-Crick geometry is the most stable mode of base pairing..." That
statement is incorrect. It was shown by David Wilson that G-G mismatches (when tandem) are more stable than WC base pairs.
20) Chapter 23, section D. Ionic Interactions. This section is not correct. The shielding of DNA charges by ions is relatively constant over a large
range of ion concentration. The salt dependence of DNA melting comes from entropic effects. Ions are released into bulk upon melting.
The entropy gain for that depends on ion concentration. See Tom Record.