Origins of Biochemistry

Apart from its uses in the dispensary and Materia Medica, eighteenth-century medical chemistry was closely linked with animal and vegetable chemistry. In both, there were two main branches, one concerned with the composition of natural substances 

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Martin W, Russell MJ On the origin of biochemistry at an alkahne hydrothermal vent. Philos Trans R Soc Lond B Biol Sd 2007, 362(1486) 1887—1925. 

Morton, A., Baase, W. A., Matthews, B. W. Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry 34 (1995) 8564-8575. 

This chapter lists some representative examples of biochemicals and their origins, a brief indication of key techniques used in their purification, and literature references where further details may be found. Simpler low molecular weight compounds, particularly those that may have been prepared by chemical syntheses, e.g. acetic acid, glycine, will be found in Chapter 4. Only a small number of enzymes and proteins are included because of space limitations. The purification of some of the ones that have been included has been described only briefly. The reader is referred to comprehensive texts such as the Methods Enzymol (Academic Press) series which currently runs to more than 344 volumes and The Enzymes (3rd Edn, Academic Press) which runs to 22 volumes for methods of preparation and purification of proteins and enzymes. Leading referenees on proteins will be found in Advances in Protein Chemistry (59 volumes. Academic Press) and on enzymes will be found in Advances in Enzymology (72 volumes, then became Advances in Enzymology and Related Area of Molecular Biology, J Wiley Sons). The Annual Review of Biochemistry (Annual Review Inc. Patio Alto California) also is an excellent source of key references to the up-to-date information on known and new natural compounds, from small molecules, e.g. enzyme cofactors to proteins and nucleic acids. 

The deciding impulse which introduced biogenesis into scientific discussion came from Russia. After the upheavals of the civil war, that country was the subject of worried observation by the rest of the world. It was assumed that no great scientific achievements would be possible there. Then, in 1924, a book on the material basis of the origin of life on Earth appeared in Red Russia . Its author was Alexandr Ivanovich Oparin (1894-1980) from the Bakh Institute of Biochemistry in Moscow (Oparin, 1924). Basically, the Oparin hypothesis makes the following assumptions ... 

Looking back, I must thank my academic teachers, Gerhard Pfleiderer and Theodor Wieland, for introducing me to biochemistry and natural product chemistry, and thus to the phenomenon of life , the origins of which are still hidden in the darkness of the unknown. 

Wiberg, K.B. (2000). Origin of the amide rotational barrier. In The Amide Linkage. Structural Significance in Chemistry, Biochemistry and Materials Science, Greenberg, A., Breneman, C.M. and Liebman, J.F. (eds), p. 33. John Wiley Sons, Inc., New York... 

An Inquiry Into the Origins of Hybrid Sciences Astrophysics and Biochemistry. J. Chem. Educ., 46, 193-96 (1969). Dexter Award Address. 

Mancy, A., Dijols, S., Poli, S., Guengerich, P., and Mansuy, D. (1996) Interaction of sulfaphenazole derivatives with human liver cytochromes P450 2C molecular origin of the specific inhibitory effects of sulfaphenazole on CYP 2C9 and consequences for the substrate binding site topology of CYP 2C9. Biochemistry 35, 16,205-16,212. 

Clearly this means a complete rejection of the fundamental Darwinian principle of common descent. Also, he rejects mutation and natural selection as the mechanisms that produced species. Is this view also contrary to the universality of biochemistry, and in particular the monophyletic origin of life, to which most biochemists today would subscribe Probably yes but of course if one assumes an absolute determinism, then the laws of chemistry and physics would produce the same products at each different start. This goes against the notion of frozen accident and the unique origin of the genetic code. So, there was never a time on Earth with only one kind of species, and the development of species was parallel rather than sequential. Of course all these ideas are substantiated by arguments and data - for these, the reader should refer to the original sources. 

Since its foundation in 1956 the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) has continually revised and updated the list of enzymes. Entries for new enzymes have been added, others have been deleted completely, or transferred to another EC number in the original class or to different EC classes, catalyzing other types of chemical reactions. The old numbers have not been allotted to new enzymes instead the place has been left vacant or cross-references given to the changes in nomenclature. 

All information except the nomenclature of the enzymes (which is based on the recommendations of the Nomenclature Committee of lUBMB (International Union of Biochemistry and Molecular Biology) and lUPAC (International Union of Pure and Applied Chemistry) is extracted from original literature (or reviews for very well characterized enzymes). The quality and reliability of the data depends on the method of determination, and for older literature on the techniques available at that time. This is especially true for the fields Molecular Weight and Subunits. 

Warning Not everything in this book is true. Despite all efforts to get it right, there are unintentional errors and misinterpretations of experimental results. Indeed, the history of biochemistry is replete with accounts of experimental findings that were interpreted incorrectly. Yet, the ideas expressed often stimulated others to develop a more correct picture later. The same is true today. Students should be critical, should look at experimental details, and consult original literature as much as possible. 

The mechanical properties of many types of clots have been measured, but the origin of clot viscoelasticity is a mystery. Factor Xllla-induced crosslinking sites have been identified in the primary sequence, but the structure of the crosslinked C-terminal 7 chains is a matter of debate and that of the a chains is unknown. The biochemistry of fibrinolysis has been determined, but less is known of the physical mechanisms involved or of the interactions of regulatory systems. 

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