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Methodological developments in Biochemistry — Volume 4. Subcellular Studies
BIOCHEMICAL EDUCATION
January 1975 Vol. 3 No. l
The fourth section on Aromatic carbon metabolism disappointed me, perhaps because of the thirty years involvement with the subject and its explorers. Too many of them are absent from the record. Karstr~m's Enzymatische Adaptation bet Mikroorganismen would be too long for reproduction but not for substantial reference as in Knight's monograph on Bacterial Nutrition, (M.R.C. (Britain) Special reports 210, 1936). Stanier, who so outstandingly utilised Karstr6m's work and who himself made such a substantial contribution in his paper on simultaneous adaptations certainly summarises for us the main contributions made by Karstr6m but for me, he still remains inadequately recognised. The further development of Stanier's contribution with Hayaishi and later by Hayaishi and co-workers is complete but they too built on the work of others who find no mention; for example, Kilby's isolation of/3-ketoadipic acid on the pathway of phenol oxidation and subsequent metabolism was an elegant piece of work fully described in a paper of notable brevity and clarity and which incidentally acknowledged his own indebtedness to those who had preceded him. I miss, too, the complete absence of any reference to Butenandt and his colleagues. It is true that their work was a bye-product of genetic studies in
insect biochemistry but it did link together research on the structure of melanin with that of the ommochromes. The omission seems odd as the work is an excellent example of the unity of biochemistry which is stressed and utilized in other sections of the book. Some short papers of Mason and colleagues on oxygen transport and electron transfer are included as well as some of Gibson and Pittard's on the concept of the common pathway which links not only the oxidation and degradation of aromatic amino acids and hydrocarbons but also the biosynthesis of cellular materials. The final section on Anaerobic fermentation naturally includes Stickland's classical paper on the derivation of energy for bacterial growth from the simultaneous oxidation and reduction of a pair of compounds such as two amino acids. Sweck and Wood's discovery of transcarboxylation in propionibacteria is here together with other notable developments in the study of anaerobic fermentation. The last paper is Buchanan's Harvey lecture on the enzymic synthesis of purine nucleotides. I have enjoyed this book. It offers a valuable and important contribution by making accessible the evidence which we so often accept without having read it.
BOOK REVIEWS
15
I Methodological developments in BiochemistryVolume 4. Subcellular Studies.
A Computer-based Simulation Exercise in Biochemistry T e c h n i c a l R e p o r t No. 1 ( M a y 1974) of t h e C o m p u t e r s In E d u c a t i o n R e s e a r c h G r o u p , U n i v e r s i t y of M e l b o u r n e , P a r k v i l l e , V i c t o r i a , by A . M c D o u g a l l , W . H. Sawyer a n d V. C i e s i e l s k i . When an experimental situation can be summarised by one or more mathematical equations, the effect on the system of the variation in value of one of the controlling factors can best be seen by giving it a series of numerical values and doing some calculations. This is the simulation process, and in many cases only a computer can perform the calculations in a usefully short time. The report describes how students may investigate the effect on the oxygen-haemoglobin association of taking different values for the interaction constants in this 'aUosteric' situation. The values are used in the Adair equation to calculate the percentage of oxygen bound to haemoglobin as a function of the partial pressure of oxygen, and the results may be displayed graphically. A second situation is the reversible interaction of an enzyme with a single substrate to form a complex which irreversibly breaks down to give a single product and regenerate the enzyme. This situation is describable by a set of differential and other equations, whose explicit solution is impossible without the simplifying condition of having a very m u c h lower enzyme concentration than substrate concentration. With values of the three rate constants and of the total enzyme and initial substrate concentrations, the numerical Runge-Kutta technique is applied by the computer to solve the equations and produce values of the product concentration as a function of time. Students can therefore find for themselves the conditions under which the steady-state assumption is valid in enzyme kinetics. Tests showed that simulation programmes like these should not be presented as isolated computer-based exercises, but should be used to complement or extend material from the course as a whole, and in this way they were used in the second year Biochemistry course at the University of Melbourne. The programmes are listed at the end of the report and are designed for direct interaction between student and computer, via a remote terminal. This seems to the reviewer to be a very useful aid to teaching, and he has successfully established these exercises on the computer at his own university. D. G. Herries
E d i t e d by Eric R e i d . P p 438. L o n g m a n L o n d o n , 1974, p a p e r b a c k £ 5 . 2 5 .
Group Limited,
This is the latest in a series of volumes of which the following titles have appeared. Vol 1 Separations with Zonal Rotors, Vol 2 Preparative Techniques, Vol 3 Advances with Zonal Rotors. Vol 1 was published by the University of Surrey at Guildford, and Vols 2 and 3 by the Longman Group. Vol 4 derives from a Symposium held at Guildford in July 1973. There are 38 contributions with a s u m m a r y of the discussion. The major theme running through the contributions is the determination of the constituents of subcellular organelles from a wide variety of tissues and the choice of 'marker constituents'. Since the centrifuge remains the most useful method of separating organelles a good deal of attention is given to the newer methodology in this field. The book should certainly prove useful for there is no doubt that a very high proportion of present day biochemical research centres around the isolation of subcellular constituents and not only from 'nice' tissue such as rat liver. W h e n a newly fledged biochemist is launched into a clinical or biochemical laboratory he is sure to be expected to be able to isolate anything from anything so he cannot be too experienced. The book starts well with a description by A. R. Poole from the Strangeways Laboratory at Cambridge of the use of immunological methods for the study of the cellular localization of proteins and their secretion. This leads into a series of papers on the methodology of density gradient centrifugation. R. Wattiaux from Belgium discusses the effect of centrifugation on subcellular structures and points out that one cannot centrifuge subcellular particles in a density gradient with impunity at any speed in any rotor, since the subcellular structures markedly deteriorate when the hydrostatic pressure they are exposed to in the centrifuge tube becomes too high. There follows studies on various particles from a large range of tissues, thyroid gland, rat liver, rabbit skeletal muscle, kidney, gastric cell membranes, pig blood platelets, cultured fibroblasts, yeasts, plants, lymphocytes and erythrocytes. The papers provide sufficient details to give one the impression that the method could be repeated. If, however, you should fail then the addresses of all authors are supplied and I am sure that the editor, Eric Reid, could help you out. He must by now have vast experience of the field if he is not too exhausted from the midnight oil that editing this book must have consumed. He must be congratulated on a useful product. P. N. Campbell
January 1975 Vol. 3 No. l
The fourth section on Aromatic carbon metabolism disappointed me, perhaps because of the thirty years involvement with the subject and its explorers. Too many of them are absent from the record. Karstr~m's Enzymatische Adaptation bet Mikroorganismen would be too long for reproduction but not for substantial reference as in Knight's monograph on Bacterial Nutrition, (M.R.C. (Britain) Special reports 210, 1936). Stanier, who so outstandingly utilised Karstr6m's work and who himself made such a substantial contribution in his paper on simultaneous adaptations certainly summarises for us the main contributions made by Karstr6m but for me, he still remains inadequately recognised. The further development of Stanier's contribution with Hayaishi and later by Hayaishi and co-workers is complete but they too built on the work of others who find no mention; for example, Kilby's isolation of/3-ketoadipic acid on the pathway of phenol oxidation and subsequent metabolism was an elegant piece of work fully described in a paper of notable brevity and clarity and which incidentally acknowledged his own indebtedness to those who had preceded him. I miss, too, the complete absence of any reference to Butenandt and his colleagues. It is true that their work was a bye-product of genetic studies in
insect biochemistry but it did link together research on the structure of melanin with that of the ommochromes. The omission seems odd as the work is an excellent example of the unity of biochemistry which is stressed and utilized in other sections of the book. Some short papers of Mason and colleagues on oxygen transport and electron transfer are included as well as some of Gibson and Pittard's on the concept of the common pathway which links not only the oxidation and degradation of aromatic amino acids and hydrocarbons but also the biosynthesis of cellular materials. The final section on Anaerobic fermentation naturally includes Stickland's classical paper on the derivation of energy for bacterial growth from the simultaneous oxidation and reduction of a pair of compounds such as two amino acids. Sweck and Wood's discovery of transcarboxylation in propionibacteria is here together with other notable developments in the study of anaerobic fermentation. The last paper is Buchanan's Harvey lecture on the enzymic synthesis of purine nucleotides. I have enjoyed this book. It offers a valuable and important contribution by making accessible the evidence which we so often accept without having read it.
BOOK REVIEWS
15
I Methodological developments in BiochemistryVolume 4. Subcellular Studies.
A Computer-based Simulation Exercise in Biochemistry T e c h n i c a l R e p o r t No. 1 ( M a y 1974) of t h e C o m p u t e r s In E d u c a t i o n R e s e a r c h G r o u p , U n i v e r s i t y of M e l b o u r n e , P a r k v i l l e , V i c t o r i a , by A . M c D o u g a l l , W . H. Sawyer a n d V. C i e s i e l s k i . When an experimental situation can be summarised by one or more mathematical equations, the effect on the system of the variation in value of one of the controlling factors can best be seen by giving it a series of numerical values and doing some calculations. This is the simulation process, and in many cases only a computer can perform the calculations in a usefully short time. The report describes how students may investigate the effect on the oxygen-haemoglobin association of taking different values for the interaction constants in this 'aUosteric' situation. The values are used in the Adair equation to calculate the percentage of oxygen bound to haemoglobin as a function of the partial pressure of oxygen, and the results may be displayed graphically. A second situation is the reversible interaction of an enzyme with a single substrate to form a complex which irreversibly breaks down to give a single product and regenerate the enzyme. This situation is describable by a set of differential and other equations, whose explicit solution is impossible without the simplifying condition of having a very m u c h lower enzyme concentration than substrate concentration. With values of the three rate constants and of the total enzyme and initial substrate concentrations, the numerical Runge-Kutta technique is applied by the computer to solve the equations and produce values of the product concentration as a function of time. Students can therefore find for themselves the conditions under which the steady-state assumption is valid in enzyme kinetics. Tests showed that simulation programmes like these should not be presented as isolated computer-based exercises, but should be used to complement or extend material from the course as a whole, and in this way they were used in the second year Biochemistry course at the University of Melbourne. The programmes are listed at the end of the report and are designed for direct interaction between student and computer, via a remote terminal. This seems to the reviewer to be a very useful aid to teaching, and he has successfully established these exercises on the computer at his own university. D. G. Herries
E d i t e d by Eric R e i d . P p 438. L o n g m a n L o n d o n , 1974, p a p e r b a c k £ 5 . 2 5 .
Group Limited,
This is the latest in a series of volumes of which the following titles have appeared. Vol 1 Separations with Zonal Rotors, Vol 2 Preparative Techniques, Vol 3 Advances with Zonal Rotors. Vol 1 was published by the University of Surrey at Guildford, and Vols 2 and 3 by the Longman Group. Vol 4 derives from a Symposium held at Guildford in July 1973. There are 38 contributions with a s u m m a r y of the discussion. The major theme running through the contributions is the determination of the constituents of subcellular organelles from a wide variety of tissues and the choice of 'marker constituents'. Since the centrifuge remains the most useful method of separating organelles a good deal of attention is given to the newer methodology in this field. The book should certainly prove useful for there is no doubt that a very high proportion of present day biochemical research centres around the isolation of subcellular constituents and not only from 'nice' tissue such as rat liver. W h e n a newly fledged biochemist is launched into a clinical or biochemical laboratory he is sure to be expected to be able to isolate anything from anything so he cannot be too experienced. The book starts well with a description by A. R. Poole from the Strangeways Laboratory at Cambridge of the use of immunological methods for the study of the cellular localization of proteins and their secretion. This leads into a series of papers on the methodology of density gradient centrifugation. R. Wattiaux from Belgium discusses the effect of centrifugation on subcellular structures and points out that one cannot centrifuge subcellular particles in a density gradient with impunity at any speed in any rotor, since the subcellular structures markedly deteriorate when the hydrostatic pressure they are exposed to in the centrifuge tube becomes too high. There follows studies on various particles from a large range of tissues, thyroid gland, rat liver, rabbit skeletal muscle, kidney, gastric cell membranes, pig blood platelets, cultured fibroblasts, yeasts, plants, lymphocytes and erythrocytes. The papers provide sufficient details to give one the impression that the method could be repeated. If, however, you should fail then the addresses of all authors are supplied and I am sure that the editor, Eric Reid, could help you out. He must by now have vast experience of the field if he is not too exhausted from the midnight oil that editing this book must have consumed. He must be congratulated on a useful product. P. N. Campbell