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Biochemistry books and biochemistry courses plus teaching ppt files, mp3's (all free and online)

Go to the profile of Ferhan Sagin
Jul 04, 2018
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3 Comments

Go to the profile of Athel Cornish-Bowden
Athel Cornish-Bowden 4 months ago

This recommendation worries me, because the book revives some misconceptions that were found in most biochemistry textbooks when I first started teaching biochemistry, but which have gradually faded in the past half-century. For example, in the 4th edition of White, Handler and Smith (1968) the authors make it clear that they don't really believe in dipolar ions (zwitterions): they introduce amino acids with wrong (neutral) structures. After several pages of wrong structures they include a brief mention of dipolar ions, perhaps put in at the pedantic insistence of a physical chemist, and then return to wrong structures for the rest of the book. This was very common in 1970, but is relatively rare now, found only in the least satisfactory textbooks. Unfortunately the book recommended in the post perpetuates the misconception. Why does it matter? If students think of glycine, for example, as a molecule that combines the properties of acetic acid (a strongly smelling and reactive liquid) and ethylamine (a strongly smelling and reactive gas) how can they understand why it looks and behaves like a salt?

As a different example, in 1970 most textbooks showed the curve representing the rate of an enzyme-catalysed reaction obeying Michaelis-Menten kinetics as "reaching" the maximum velocity at about 5Km, though a simple calculation shows that 5/6 is much less than 1. Most authors have learned better since then, but the author this book is not one of them, and even shows the curve reaching saturation at about 3Km.

Go to the profile of Ferhan Sagin
Ferhan Sagin 4 months ago

In his criticism of the free online sources I suggested above (Biochemistry Free for All and related free sources by Kevin Ahern), Dr. Athel Cornish-Bowden has an interesting approach.
 
As Dr. Herraez well pointed out, Dr. Ahern’s book does not lead to misconceptions as it does not at all deny the presence of zwitterions but gives both the nonionic and zwitterionic (internal salt) forms of amino acids. By this way, the student can first learn the basic chemical and physical properties of amino acids which are crystalline solids with surprisingly high melting points (200 - 300°C). Here comes the questioning (that there must be stronger forces in play to cause such high melting points) in the student’s mind because for the size of these molecules, this is very high. The structure of zwitterions make sense in this regard (internal transfer of a proton from the –COOH group to the –NH2 group (the amino acid has both a negative charge at the carboxylate group and a positive charge at the ammonium group). 

The student then can comprehend the reason why the amino acids exist in zwitterionic forms even in the solid state. By this way, instead of the weaker hydrogen bonds and other intermolecular forces, there is actually much stronger ionic attractions between one ion and its neighbours which take more energy to break and so the amino acids have high melting points for the size of the molecules.

Personally, my primary aim in the biochemistry courses I give is to ensure that students learn the basic structures first and then to understand or predict how these basic structure behave in different environments such as neutral aqueous or acidic/basic solutions. I believe this is how we can help our students to see the fascinating world of biochemistry!  

The generalizing quote of Dr. Athel Cornish-Bowden; “ . . . found only in the least satisfactory textbooks” judges the entirety of these books on a very minor attribute of amino acids that he doesn’t agree with. How that would affect the rest of the content of these sources is beyond my comprehension.

Last but not least, these free online books have been downloaded over a quarter of a million times and in hundreds of reviews or comments from students and educators who use the books, I have not at all seen that these issues have ever been raised but I have noted many sincere thanks to the authors.

 

 

Go to the profile of Angel Herráez
Angel Herráez 4 months ago

I agree with Dr. Cornish-Bowden argument, as a desirable approach to address descriptions even from the introductory levels of biochemistry. I believe it is not uncommon to find these pitfalls in other sources, and a case might be made of tolerating such inaccuracies in favour of some simplification or when the stress is on some other aspects of the subject. It is, nonetheless, much better to provide in any case the most accurate representations, particularly to avoid misconceptions being seeded in the student brain.

However, I find the discredit not fair in this case. Checking the text, "Biochemistry Free For All", version 1.2 [1], the first introduction to "General amino acid structure" (Figure 2.1) does indeed present the carboxylic and amino groups uncharged (which may be claimed to be a better introductory illustration of the definition as amino+acid compound), but immediately in the next figures all the 20 amino acids are presented as zwitterionic structures (pages 59-61 , figures 2.3 to 2.7). And, subsequently, all the different equilibria and ionised forms for a single amino acid are shown along its titration curve (fig. 2-10). In the accompanying PowerPoint file [2], the structures are again first displayed uncharged but immediately as zwitterions.

Coming to the Michaelis & Menten curve, it is true that the drawing of the hyperbola in many places is often wrong in making the curve reach the asymptote at far too low concentrations of substrate. I remember myself fighting against these displays; fortunately, they are becoming less common now in highly accessed places like Wikipedia [3]. Once again, I do not see this is the case with Ahern's book. Some plots (fig. 4.18, p. 349) do not label the [S] axis with any values (as it also happens in other textbooks, e.g. Stryer [4]), while the one that quotes numeric values in the axes (fig.4.20, p.351 and slide 31 in ref.5) seems to be mathematically accurate, displaying 90% saturation at [S] = 9.75 times Km.


Cited references:

[1] http://biochem.science.oregonstate.edu/files/biochem/ahern/Biochemistry%20Free%20For%20All%201.1compressed.pdf

[2] http://biochem.science.oregonstate.edu/files/biochem/ahern/Teaching_Powerpoint/Amino%20Acids.pptx

[3] Confront, for example, https://es.wikipedia.org/wiki/Cinética_de_Michaelis-Menten with https://en.wikipedia.org/wiki/Michaelis–Menten_kinetics

[4] Berg JM, Tymoczko JL, Stryer L (2002) Biochemistry, 5th ed. https://www.ncbi.nlm.nih.gov/books/NBK22430/

[5] http://biochem.science.oregonstate.edu/files/biochem/ahern/Teaching_Powerpoint/Enzymes.pptx