- Email: [email protected]
Basic Mathematics for Biochemists
214
Book reviews / Biochemistry and Molecular Biology Education 29 (2001) 209–218
potassium acetate to the NaOH-SDS lysate. Occasionally, the authors’ oversimplification leads to either confusion or error. For instance, the formation of insoluble blue precipitate by BCIP-NBT is not correct as written. Also, the discussion of the role of dextrans (and related polymers) in nucleic acid hybridization becomes confused by oversimplification. Sloppy language also leads to errors. Agarose comes as a powder of beads, not crystals as stated in the text. Another example here is the statement that nylon binds DNA irreversibly, which it does not. The good news is that these examples were the only ones that I found. The discussion of the use of BLAST could be much better. There is no discussion of how to interpret Evalues in judging sequence similarity between the test sequence and the BLAST search output. I think students could benefit from a simple discussion of how this program works. In my experience, what is available at NCBI can be understood by only a small fraction of undergraduates. This text, written in 1997, has a couple of archaic procedures. Seal-O-Meal bags are messy when dealing with radioisotopes, such that other undergraduate-friendly containers are available. Filtration through activated charcoal filters is a safer and easier method for ethidium bromide disposal than what is described in this manual. While I appreciate the pedagogical intent of the last exercise (Independent Projects in Molecular Biology), it goes beyond what most lab courses can do in one semester. Given the time needed to complete the semester-long project of cloning and characterizing the lux genes, I cannot imagine there being enough time to do an independent project as the authors suggest. On the other hand, an advanced lab course could use the material in this text as a starting point for a variety of independent projects focusing on the lux genes. But these criticisms do not substantively diminish what I regard as fine undergraduate lab manual for molecular biology. For any instructor who likes teaching molecular biology techniques in the context of a semester-long biology project, this undergraduate lab manual may be the best of its kind. This paperback book has a sturdy binding with perforated pages, and it survives a fair amount of abuse so that at $51.00 this book is reasonably priced. A. Uzman Department of Natural Sciences, University of HoustonDowntown, Houston, TX 77002-1001, USA E-mail address: [email protected] PII: S 1 4 7 0 - 8 1 7 5 ( 0 1 ) 0 0 0 7 8 - 9
Basic Mathematics for Biochemists Athel Cornish-Bowden, Second edition, Oxford University Press, 1999, 221 pages, hardback ISBN 0-19-850217, d35, paperback ISBN 0.19-850216-8, d13.99
As we all know, maths is all too often viewed by trainee biochemists with horror, something to be avoided if possible. Nevertheless, much of biochemistry is quantitative and on the whole biochemists need to get to grips with the subject. This book aims to help them, and since it has gone to a second edition, it must have found favour with at least some of them. There is a serious effort to justify each of the mathematical topics chosen in terms of its relevance to biochemistry and the book is packed with discussions and examples involving real biochemistry. The great strength of the book is its singleminded approach. As the author points out in the introduction, it is maths for biochemists, not maths for scientists in general, or even maths for biologists. It presupposes some familiarity with biochemistry and a desire to get to grips with the basic biochemical concepts. The book begins with a useful review of the basic concepts of mathematics; manipulation of fractions, functions, plotting graphs etc. F the sort of things which science undergraduates could handle as a matter of course 15 years ago, but, which I am assured, even some mathematics students now find difficult because they have had so little practice at school. The remainder of the book is more or less A-level (high school) standard F sometimes a little higher. The major topics are exponents and logarithms, differentiation and integration, partial differentiation, equation solving (linear, simultaneous, quadratic and higher orders). A final chapter covers the basic concepts of statistics. In my opinion, the author has wisely avoided the ‘‘let’s do the maths first and then apply it to biochemistry at the end of the book’’ approach. We are into biochemical concepts from the start, with discussions of the Michaelis–Menten equation and the Henderson–Hasselbalch equations coming at an early stage. As one might expect, most of the examples given concern the areas where physical chemistry touches biochemistry F diffusion, equilibrium constants, pH, redox reactions, etc. F but there are plenty of unexpected exceptions. There is for example, an interesting discussion in the section on permutations, of the number of possible alternative sequences for the stages in glycolysis. This is the second edition of a widely used 20 year-old book. I share the opinion of the author that the reviewer of the first edition who commented that the book was written at too basic a level, must have been living on a different planet and I am sure it was the correct decision
Book reviews / Biochemistry and Molecular Biology Education 29 (2001) 209–218
to put in more basic, explanatory material rather than extending the difficulty of the text. My impression is that many of the additions are the result of feedback from the chalkface. They answer points of confusion actually experienced by students, even down to irritating trivia like the different conventions for decimal points or multiplication signs. Of necessity, the book is inhomogeneous: any student who needs reminding that ( 4) = +4, is hardly likely to find the section on partial differentials very straightforward and some of the discussions rapidly get into deep water. For example, the dimensional analysis of an innocent-looking equation such as pH = log [H+] rapidly lands us in discussions of the role of standard states in physical chemistry. However, that is the nature of the subject. It is a fact that some of the most central concepts in biochemistry involve subtle physical chemistry, and there is no way to avoid it. In places, the book is refreshingly idiosyncratic. There is a delightful footnote to the section Having a rough idea of the answer, beginning; ‘‘If you really want to know whether 3000 lek would be enough to buy a house in Albaniay? The comments are all sensibly pragmatic (for example, why it is wise to write 5 l but 5 ml) and only a real biochemist could have pointed out that if a solution has a concentration >5 M it can be ‘‘nothing except urea, guanidine HCl and water’’. I especially like the couple of pages of comment on modern, commercial graph-drawing packages which ‘‘make it only too easy to produce perfectly horrible graphs exhibiting faults that no one would have thought of 20 years ago’’. In some circles it might not be considered appropriate to use a book intended for undergraduate use as a soapbox, but is certainly refreshing to read the occasional opinionated comment (especially when it coincides with one’s own prejudices). The author clearly does not like the concept of pH. (I would imagine that years of trying to help one generation of undergraduates after another to cope with the calculations involving pH in the HendersonHasselbalch equation must have brought him close to despair):
For the ludicrously trivial advantage of having a range of positive numbers around +7 rather than negative numbers around 7, chemists have paid the excessive price of discarding a scale of obvious meaning in favour of one that generates endless confusion. Other usages such as pKM are less common: I trust they will remain so. We are fortunate that at least some extensions of the pH idea such as the rH scale for application to redox potentials have virtually disappeared. (p. 73)
215
The book ends with a glossary. In general, I like glossaries. Short, to-the-point, stand-alone definitions and explanations are useful things to steal for lecture handouts and module manuals. Here the entries are mostly clear and valuable F but occasionally one gets the feeling that the author has run out of inspiration. I looked for the old favourite F ‘‘a parameter is a variable constant’’. It is not there (but the definition of a constant makes up for its absence) A constant: A number that does not change over the range of conditions being considered. Mathematically it is a number that does not change at all F but in scientific uses one cannot always be so rigid. You know what he means F but as definitions go, it is hardly stunning in its incisiveness F and not of much relevance either, if one is being pedantic, when talking about the variation of equilibrium constant with temperature for example. Similarly the definition of a differential: As an adjective this refers to the differential calculus, which is concerned with the limiting values of rates of change when the changes concerned are made indefinitely small. As a noun it refers to the limit of an actual change and is not the same as a derivative’’ [see Chapter 4, section 7.2]. F does not immediately ring bells in the grey matter, although, to be fair, the references to the text did eventually help to show what point the author is trying to make. Incidentally, this is the first book I have come across where a web site has been allocated to hold errata discovered after the book had been printed [http://ir21cb.cnrs-mrs.fr/Bathel/basmaths.htm]. This is obviously a sensible idea which I am sure will soon become standard procedure. When I checked, there was a handful of corrections (of errors which I had not noticed). I doubt whether there will be many more; this has the feel of a carefully edited book. To make a maths-for-biologists text appear interesting and relevant is an uphill task for any writer. How well this book succeeds depends, of course, on the criteria one adopts. This is scarcely likely to become anyone’s favourite textbook and I doubt whether it will inspire many students to desert biochemistry for mathematics. On the other hand, it is a reasonably priced, clear, earnest attempt to cover the maths essential for biochemists who want to understand their subject properly and I would consider that every part of the book will be useful at some point in most undergraduate biochemistry courses. There is just enough of the personality of the author showing to
216
Book reviews / Biochemistry and Molecular Biology Education 29 (2001) 209–218
add a personal touch, which makes the work readable. In the terms which it sets out for itself F this is a fine book. To echo the footnote about Albanian house prices F if you really want to know, here is an author who really wants to tell you.
John Lydon Department of Biochemistry, University of Leeds, Leeds LS2 9JT, UK
PII: S 0 3 0 7 - 4 4 1 2 ( 0 0 ) 0 0 0 1 1 - X
Stereochemistry D. G. Morris; Royal Society of Chemistry Tutorial Chemistry Texts [www.rsc.org; [email protected]], Cambridge, UK, 2001, d9.95, 170 pp., ISBN 0-85404602-X (in US Springer Verlag NY Inc, PO. Box. 2485, Secaucus, NJ 07096-2485 [[email protected]]).
This is a short paperback mainly aimed at undergraduate chemistry students, but some parts would obviously be of interest to biochemistry undergraduates too. Each chapter starts with Aims (‘‘by the end of this chapter you should be able to...’’), and ends with a Summary of Key Points, some Problems (answers given at the end) and a few References. In additions there are some Worked problems, that students could work their way through at least partly unaided, although I have to say that stereochemistry is an area where the assistance of a teacher who can allow students to take things at their own pace, is often very helpful. The first chapter deals with the structures of simple molecules (Hybridization, Conformation and Configuration), and Chapter 2 deals with chirality. This is a fairly low level but sound treatment and includes Fischer projections with glyceraldehyde as an example, and the Cahn–Ingold–Prelog convention and rules. Chapter 3 is about molecules with two or more stereogenic centers and includes carbohydrates and also something about resolution of mixtures using enzymes. Chapter 4 deals with double bonds including amides (peptide bond), and Chapter 5 is about chirality without a stereogenic carbon atom, including inorganic compounds. Chapter 6 is on stereoisomerism in cyclic structures: sound but not much of interest to biochemists (an opportunity to discuss thalidomide missed?). Chapter 7 is on substitution reactions, and the last chapter is entitled ‘‘Prochirality, enantiotopic and
diastereotopic groups: use of NMR. This chapter deals with the addition of H+ to NAD+ catalysed by dehydrogenases but it might also have been nice to see something about citric acid (Ogston), and there is nothing about circular dichroism. My criticisms above are really from a biochemist’s point of view: chemists, for whom the book is intended, would likely have a different viewpoint. For biochemists and pharmacologists, chiral drugs and their manufacture are key topics, of course. Overall this is quite a nice text of handleable proportions that might be recommended to students interested in this area of chemistry or who are having difficulties with these topics in the heavier texts. E.J. Wood School of Biochemistry & Molecular Biology University of Leeds LS2 9JT, UK E-mail address: [email protected]
PII: S 1 4 7 0 - 8 1 7 5 ( 0 1 ) 0 0 0 6 8 - 6
Mitochondria, Immo E. Scheffler; Wiley-Liss, New York, 1999, 367 pages, ISBN 0-471-19422-0, $99
Mitochondria appear to be undergoing something of a renaissance. In addition to occupying their historic place at the centre of aerobic bioenergetics, they have lately attracted the interest of molecular biologists and students of evolution. Thus, the study of their genetic systems has shed light on their origins and biogenesis, as well as providing new insights into vertebrate evolution, human genetic diseases, ageing, and programmed cell death (apoptosis). The historic view of mitochondria as organelles committed to eukaryotic oxidative phosphorylation was perhaps most closely identified with Lehninger’s The Mitochondrion, first published in 1964. Now, Immo Scheffler has written a worthy contemporary successor, a broadly conceived and lively account of mitochondrial biology and biochemistry. The book begins with two short chapters which serve as appropriate introduction to the remainder. The first one describes the history of mitochondrial investigations, while the second addresses evolutionary origins, a topic that prepares the reader for later discussion of mitochondrial autonomy, genome organization, and the expression of individual genes. These are followed by chapters on mitochondrial structure, biogenesis, bioenergetics, metabolic pathways, diseases (including
Book reviews / Biochemistry and Molecular Biology Education 29 (2001) 209–218
potassium acetate to the NaOH-SDS lysate. Occasionally, the authors’ oversimplification leads to either confusion or error. For instance, the formation of insoluble blue precipitate by BCIP-NBT is not correct as written. Also, the discussion of the role of dextrans (and related polymers) in nucleic acid hybridization becomes confused by oversimplification. Sloppy language also leads to errors. Agarose comes as a powder of beads, not crystals as stated in the text. Another example here is the statement that nylon binds DNA irreversibly, which it does not. The good news is that these examples were the only ones that I found. The discussion of the use of BLAST could be much better. There is no discussion of how to interpret Evalues in judging sequence similarity between the test sequence and the BLAST search output. I think students could benefit from a simple discussion of how this program works. In my experience, what is available at NCBI can be understood by only a small fraction of undergraduates. This text, written in 1997, has a couple of archaic procedures. Seal-O-Meal bags are messy when dealing with radioisotopes, such that other undergraduate-friendly containers are available. Filtration through activated charcoal filters is a safer and easier method for ethidium bromide disposal than what is described in this manual. While I appreciate the pedagogical intent of the last exercise (Independent Projects in Molecular Biology), it goes beyond what most lab courses can do in one semester. Given the time needed to complete the semester-long project of cloning and characterizing the lux genes, I cannot imagine there being enough time to do an independent project as the authors suggest. On the other hand, an advanced lab course could use the material in this text as a starting point for a variety of independent projects focusing on the lux genes. But these criticisms do not substantively diminish what I regard as fine undergraduate lab manual for molecular biology. For any instructor who likes teaching molecular biology techniques in the context of a semester-long biology project, this undergraduate lab manual may be the best of its kind. This paperback book has a sturdy binding with perforated pages, and it survives a fair amount of abuse so that at $51.00 this book is reasonably priced. A. Uzman Department of Natural Sciences, University of HoustonDowntown, Houston, TX 77002-1001, USA E-mail address: [email protected] PII: S 1 4 7 0 - 8 1 7 5 ( 0 1 ) 0 0 0 7 8 - 9
Basic Mathematics for Biochemists Athel Cornish-Bowden, Second edition, Oxford University Press, 1999, 221 pages, hardback ISBN 0-19-850217, d35, paperback ISBN 0.19-850216-8, d13.99
As we all know, maths is all too often viewed by trainee biochemists with horror, something to be avoided if possible. Nevertheless, much of biochemistry is quantitative and on the whole biochemists need to get to grips with the subject. This book aims to help them, and since it has gone to a second edition, it must have found favour with at least some of them. There is a serious effort to justify each of the mathematical topics chosen in terms of its relevance to biochemistry and the book is packed with discussions and examples involving real biochemistry. The great strength of the book is its singleminded approach. As the author points out in the introduction, it is maths for biochemists, not maths for scientists in general, or even maths for biologists. It presupposes some familiarity with biochemistry and a desire to get to grips with the basic biochemical concepts. The book begins with a useful review of the basic concepts of mathematics; manipulation of fractions, functions, plotting graphs etc. F the sort of things which science undergraduates could handle as a matter of course 15 years ago, but, which I am assured, even some mathematics students now find difficult because they have had so little practice at school. The remainder of the book is more or less A-level (high school) standard F sometimes a little higher. The major topics are exponents and logarithms, differentiation and integration, partial differentiation, equation solving (linear, simultaneous, quadratic and higher orders). A final chapter covers the basic concepts of statistics. In my opinion, the author has wisely avoided the ‘‘let’s do the maths first and then apply it to biochemistry at the end of the book’’ approach. We are into biochemical concepts from the start, with discussions of the Michaelis–Menten equation and the Henderson–Hasselbalch equations coming at an early stage. As one might expect, most of the examples given concern the areas where physical chemistry touches biochemistry F diffusion, equilibrium constants, pH, redox reactions, etc. F but there are plenty of unexpected exceptions. There is for example, an interesting discussion in the section on permutations, of the number of possible alternative sequences for the stages in glycolysis. This is the second edition of a widely used 20 year-old book. I share the opinion of the author that the reviewer of the first edition who commented that the book was written at too basic a level, must have been living on a different planet and I am sure it was the correct decision
Book reviews / Biochemistry and Molecular Biology Education 29 (2001) 209–218
to put in more basic, explanatory material rather than extending the difficulty of the text. My impression is that many of the additions are the result of feedback from the chalkface. They answer points of confusion actually experienced by students, even down to irritating trivia like the different conventions for decimal points or multiplication signs. Of necessity, the book is inhomogeneous: any student who needs reminding that ( 4) = +4, is hardly likely to find the section on partial differentials very straightforward and some of the discussions rapidly get into deep water. For example, the dimensional analysis of an innocent-looking equation such as pH = log [H+] rapidly lands us in discussions of the role of standard states in physical chemistry. However, that is the nature of the subject. It is a fact that some of the most central concepts in biochemistry involve subtle physical chemistry, and there is no way to avoid it. In places, the book is refreshingly idiosyncratic. There is a delightful footnote to the section Having a rough idea of the answer, beginning; ‘‘If you really want to know whether 3000 lek would be enough to buy a house in Albaniay? The comments are all sensibly pragmatic (for example, why it is wise to write 5 l but 5 ml) and only a real biochemist could have pointed out that if a solution has a concentration >5 M it can be ‘‘nothing except urea, guanidine HCl and water’’. I especially like the couple of pages of comment on modern, commercial graph-drawing packages which ‘‘make it only too easy to produce perfectly horrible graphs exhibiting faults that no one would have thought of 20 years ago’’. In some circles it might not be considered appropriate to use a book intended for undergraduate use as a soapbox, but is certainly refreshing to read the occasional opinionated comment (especially when it coincides with one’s own prejudices). The author clearly does not like the concept of pH. (I would imagine that years of trying to help one generation of undergraduates after another to cope with the calculations involving pH in the HendersonHasselbalch equation must have brought him close to despair):
For the ludicrously trivial advantage of having a range of positive numbers around +7 rather than negative numbers around 7, chemists have paid the excessive price of discarding a scale of obvious meaning in favour of one that generates endless confusion. Other usages such as pKM are less common: I trust they will remain so. We are fortunate that at least some extensions of the pH idea such as the rH scale for application to redox potentials have virtually disappeared. (p. 73)
215
The book ends with a glossary. In general, I like glossaries. Short, to-the-point, stand-alone definitions and explanations are useful things to steal for lecture handouts and module manuals. Here the entries are mostly clear and valuable F but occasionally one gets the feeling that the author has run out of inspiration. I looked for the old favourite F ‘‘a parameter is a variable constant’’. It is not there (but the definition of a constant makes up for its absence) A constant: A number that does not change over the range of conditions being considered. Mathematically it is a number that does not change at all F but in scientific uses one cannot always be so rigid. You know what he means F but as definitions go, it is hardly stunning in its incisiveness F and not of much relevance either, if one is being pedantic, when talking about the variation of equilibrium constant with temperature for example. Similarly the definition of a differential: As an adjective this refers to the differential calculus, which is concerned with the limiting values of rates of change when the changes concerned are made indefinitely small. As a noun it refers to the limit of an actual change and is not the same as a derivative’’ [see Chapter 4, section 7.2]. F does not immediately ring bells in the grey matter, although, to be fair, the references to the text did eventually help to show what point the author is trying to make. Incidentally, this is the first book I have come across where a web site has been allocated to hold errata discovered after the book had been printed [http://ir21cb.cnrs-mrs.fr/Bathel/basmaths.htm]. This is obviously a sensible idea which I am sure will soon become standard procedure. When I checked, there was a handful of corrections (of errors which I had not noticed). I doubt whether there will be many more; this has the feel of a carefully edited book. To make a maths-for-biologists text appear interesting and relevant is an uphill task for any writer. How well this book succeeds depends, of course, on the criteria one adopts. This is scarcely likely to become anyone’s favourite textbook and I doubt whether it will inspire many students to desert biochemistry for mathematics. On the other hand, it is a reasonably priced, clear, earnest attempt to cover the maths essential for biochemists who want to understand their subject properly and I would consider that every part of the book will be useful at some point in most undergraduate biochemistry courses. There is just enough of the personality of the author showing to
216
Book reviews / Biochemistry and Molecular Biology Education 29 (2001) 209–218
add a personal touch, which makes the work readable. In the terms which it sets out for itself F this is a fine book. To echo the footnote about Albanian house prices F if you really want to know, here is an author who really wants to tell you.
John Lydon Department of Biochemistry, University of Leeds, Leeds LS2 9JT, UK
PII: S 0 3 0 7 - 4 4 1 2 ( 0 0 ) 0 0 0 1 1 - X
Stereochemistry D. G. Morris; Royal Society of Chemistry Tutorial Chemistry Texts [www.rsc.org; [email protected]], Cambridge, UK, 2001, d9.95, 170 pp., ISBN 0-85404602-X (in US Springer Verlag NY Inc, PO. Box. 2485, Secaucus, NJ 07096-2485 [[email protected]]).
This is a short paperback mainly aimed at undergraduate chemistry students, but some parts would obviously be of interest to biochemistry undergraduates too. Each chapter starts with Aims (‘‘by the end of this chapter you should be able to...’’), and ends with a Summary of Key Points, some Problems (answers given at the end) and a few References. In additions there are some Worked problems, that students could work their way through at least partly unaided, although I have to say that stereochemistry is an area where the assistance of a teacher who can allow students to take things at their own pace, is often very helpful. The first chapter deals with the structures of simple molecules (Hybridization, Conformation and Configuration), and Chapter 2 deals with chirality. This is a fairly low level but sound treatment and includes Fischer projections with glyceraldehyde as an example, and the Cahn–Ingold–Prelog convention and rules. Chapter 3 is about molecules with two or more stereogenic centers and includes carbohydrates and also something about resolution of mixtures using enzymes. Chapter 4 deals with double bonds including amides (peptide bond), and Chapter 5 is about chirality without a stereogenic carbon atom, including inorganic compounds. Chapter 6 is on stereoisomerism in cyclic structures: sound but not much of interest to biochemists (an opportunity to discuss thalidomide missed?). Chapter 7 is on substitution reactions, and the last chapter is entitled ‘‘Prochirality, enantiotopic and
diastereotopic groups: use of NMR. This chapter deals with the addition of H+ to NAD+ catalysed by dehydrogenases but it might also have been nice to see something about citric acid (Ogston), and there is nothing about circular dichroism. My criticisms above are really from a biochemist’s point of view: chemists, for whom the book is intended, would likely have a different viewpoint. For biochemists and pharmacologists, chiral drugs and their manufacture are key topics, of course. Overall this is quite a nice text of handleable proportions that might be recommended to students interested in this area of chemistry or who are having difficulties with these topics in the heavier texts. E.J. Wood School of Biochemistry & Molecular Biology University of Leeds LS2 9JT, UK E-mail address: [email protected]
PII: S 1 4 7 0 - 8 1 7 5 ( 0 1 ) 0 0 0 6 8 - 6
Mitochondria, Immo E. Scheffler; Wiley-Liss, New York, 1999, 367 pages, ISBN 0-471-19422-0, $99
Mitochondria appear to be undergoing something of a renaissance. In addition to occupying their historic place at the centre of aerobic bioenergetics, they have lately attracted the interest of molecular biologists and students of evolution. Thus, the study of their genetic systems has shed light on their origins and biogenesis, as well as providing new insights into vertebrate evolution, human genetic diseases, ageing, and programmed cell death (apoptosis). The historic view of mitochondria as organelles committed to eukaryotic oxidative phosphorylation was perhaps most closely identified with Lehninger’s The Mitochondrion, first published in 1964. Now, Immo Scheffler has written a worthy contemporary successor, a broadly conceived and lively account of mitochondrial biology and biochemistry. The book begins with two short chapters which serve as appropriate introduction to the remainder. The first one describes the history of mitochondrial investigations, while the second addresses evolutionary origins, a topic that prepares the reader for later discussion of mitochondrial autonomy, genome organization, and the expression of individual genes. These are followed by chapters on mitochondrial structure, biogenesis, bioenergetics, metabolic pathways, diseases (including