Specificity and Editing Mechanisms

Figure 13.4 The double sieve analogy for the editing mechanism of the isoleucyl-tRNA synthetase. The active site for the formation of the aminoacyl adenylate can exclude amino acids that are larger than isoleucine but not those that are smaller. On the other hand, a hydrolytic site that is just large enough to bind valine can exclude isoleucine while accepting valine and all the smaller amino acids. (In some enzymes, the hydrolytic site offers specific chemical interactions that enable it to bind isosteres of the correct amino acid as well as smaller amino acids.)...

The first is that whereas each amino acid has its own activating enzyme precisely tailored to it, a single DNA polymerase with just one active site for synthesis has to cope with all four correct base-pair combinations. The specificity of the reaction is largely delegated to the specificity of the base pairing itself, with its inherent error rate of 1 in 104 to 105. An even higher accuracy would be obtained if there were four separate enzymes (or just four active sites), each precisely tailored for its own base pair of AT, TA> GC, or CG. But it has been found expedient in evolution for errors. to be corrected by editing mechanisms and for a common polymerase to be used. 

Both the language of valence bond theory and of molecular orbital theory are used in discussing structural effects on reactivity and mechanism. Our intent is to illustrate both approaches to interpretation. A decade has passed since the publication of the Third Edition. That decade has seen significant developments in areas covered by the text. Perhaps most noteworthy has been the application of computational methods to a much wider range of problems of structure and mechanism. We have updated the description of computational methods and have included examples throughout the text of application of computational methods to specific reactions. 

Because of the magnitude of the task of preparing the material for this new edition in proper detail, it has been necessary to omit several important topics that were covered in the previous edition. Topics such as corrosion and metallurgy, cost estimating, and economics are now left to the more specialized works of several fine authors. The topic of static electricity, however, is treated in the chapter on process safety, and the topic of mechanical drivers, which includes electric motors, is covered in a separate chapter because many specific items of process equipment require some type of electrical or mechanical driver. Even though some topics cannot be covered here, the author hopes that the designer will find design techniques adaptable to 75 percent to 85-1- percent of required applications and problems. 

As already noted, Newton replaced the concept of mechanical entanglement with the postulate of short-range interparticle forces of attraction and repulsion and applied this model in his Principia of 1687 to rationalize Boyle s law relating gas pressure and volume. However, it was not until the first decade of the 18th century that this new dynamic or force model was first specifically applied to chemical phenomena by the British chemists, John Freind and John Keill, and by Newton himself in the finalized version of the 31st query appended to the 1717 and later editions of his famous treatise on optics, where he succinctly summarized his new particulate program for chemistry ... 

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