Amino acids representative examples

Amino acid separations represent another specific application of the technology. Amino acids are important synthesis precursors - in particular for pharmaceuticals -such as, for example, D-phenylglycine or D-parahydroxyphenylglycine in the preparation of semisynthetic penicillins. They are also used for other chiral fine chemicals and for incorporation into modified biologically active peptides. Since the unnatural amino acids cannot be obtained by fermentation or from natural sources, they must be prepared by conventional synthesis followed by racemate resolution, by asymmetric synthesis, or by biotransformation of chiral or prochiral precursors. Thus, amino acids represent an important class of compounds that can benefit from more efficient separations technology. 

However, they have not yet found many applications in asymmetric Ugi reactions [41-43], and this is probably due to the fact that diastereomeric excesses are often only moderate and strongly influenced by the structure of the side chain of the a-amino acid. A thorough study was carried out by Yamada et al. [42], who observed that the configuration of the newly generated stereocenter of the major diastereoisomer is always opposite to that of the amino ester. Representative examples are shown in Scheme 1.15. Although Yamada often also used chiral protected aminoacids as the carboxylic component, they were proved to have a negligible influence on the stereoselectivity. 

Several studies have suggested that the extent of organic matter degradation may be imprinted on the relative distribution of amino acids. For example, the depth-dependant relative enrichment of certain amino acids in POM has been interpreted as enhanced preservation of particular proteins. Hecky et al. (1973) showed that diatom cell wall proteins were relatively enriched in serine and glycine Cowie and Hedges (1992) found that these amino acids were relatively unreactive in sinking POM and concluded that the observed pattern represented selective preservation of diatom cell wall material within POM. Glycine is enhanced in HMWDOM relative... 

By 1961, it was clear that the sequence of bases in DNA serves to direct the synthesis of mRNA, and that the sequence of bases in mRNA corresponds to the order of amino acids in a particular protein. However, the genetic code, the exact relationship between mRNA sequences and amino acids, was unknown. At least 20 mRNA words are needed to represent uniquely each of the 20 amino acids found in proteins. If the mRNA words consisted of a single letter represented by a base (A, C, G, or U), only four amino acids could be uniquely represented. Thus, it was proposed that it is not one mRNA base but a combination of bases that codes for each amino acid. For example, if a code word consists of a sequence of two mRNA bases, there are 4 = 16 possible combinations, so 16 amino acids could be represented uniquely. This is a more extensive code, but it still contains too few words to do the job for 20 amino acids. If the code consists of a sequence of three bases, there are 4 64 possible combinations, more than enough to specify uniquely each amino... 

Amino squaric acids 186 and 188, the relatives of natural amino acids, represent an intuitive example of bioisostere, although the heterocycle is absent in these molecules. These were obtained by radical reaction of 2-stannylcyclobutenedione [133] and carbanion addition to squarate ester [134,135] (Scheme 33). 

Amino acids are carboxylic acids that contain an amino (—NH2) group attached to C-2 (the alpha carbon) and are thus called a-amino acids. They also contain another variable group, R. The R group represents any of the various groups that make up the specific amino acids. For example, when R is H—, the amino acid is glycine when R is CH3—, the amino acid is alanine when R is CH3SCH2CH2—, the amino acid is methionine. 

Figure 17 (a) Helical net cartoon of Zwit-IF with amino acids represented by single-letter codes. For example, stands for... 

The first number represents the number of carbon atoms of diamine, and the second number indicates the number of carbon atoms of dicarboxylic acid. If only a single-digit number is used, it indicates the number of carbon atoms in the lactam or amino acids. For example, nylon-66 is a poly(hexamethylene adipamide) compound synthesized from hexamethylenediamine and adipic acid. Nylon-1010 is poly(decamethylene sebacamide) synthesized by decamethylenediamine and sebacic acid. 

Fig. 3. Some representative pair potentials Uy(r), sealed to move their interesting range to [0,5]. The numbers above each potential denote the class label 7 and the iiinnber of data points available for the fit. (For example, elass 63 gives distanee 3 potentials for the amino acid pairs Lys-Asp, Arg-Lys and Glu-Tyr.) The spectrum below each potential consists of 50 lines pieked uniformly from the data.

The presence of certain substituents e.g., the amino group) may markedly affect the solubibty and other properties of the sulphonic acid or carboxylic acid. Thus such sulphonic acids as the aminobenzenesul-phonic acids, pyridine- and quinoline-sulphonic acids exist in the form of inner salts or zwitter-ions that result from the interaction of the basic amino group and the acidic sulphonic acid. Sulphanilic acid, for example, is more accurately represented by formula (I) than by formula (II) ... 

Example Crippen and Snow reported their success in developing a simplified potential for protein folding. In their model, single points represent amino acids. For the avian pancreatic polypeptide, the native structure is not at a potential minimum. However, a global search found that the most stable potential minimum had only a 1.8 Angstrom root-mean-square deviation from the native structure. 

There is some confusion in using Bayes rule on what are sometimes called explanatory variables. As an example, we can try to use Bayesian statistics to derive the probabilities of each secondary structure type for each amino acid type, that is p( x r), where J. is a, P, or Y (for coil) secondary strucmres and r is one of the 20 amino acids. It is tempting to writep( x r) = p(r x)p( x)lp(r) using Bayes rule. This expression is, of course, correct and can be used on PDB data to relate these probabilities. But this is not Bayesian statistics, which relate parameters that represent underlying properties with (limited) data that are manifestations of those parameters in some way. In this case, the parameters we are after are 0 i(r) = p( x r). The data from the PDB are in the form of counts for y i(r), the number of amino acids of type r in the PDB that have secondary structure J.. There are 60 such numbers (20 amino acid types X 3 secondary structure types). We then have for each amino acid type a Bayesian expression for the posterior distribution for the values of xiiry. 

FIGURE 15.2 Enzymes regulated by covalent modification are called interconvertible enzymes. The enzymes protein kinase and protein phosphatase, in the example shown here) catalyzing the conversion of the interconvertible enzyme between its two forms are called converter enzymes. In this example, the free enzyme form is catalytically active, whereas the phosphoryl-enzyme form represents an inactive state. The —OH on the interconvertible enzyme represents an —OH group on a specific amino acid side chain in the protein (for example, a particular Ser residue) capable of accepting the phosphoryl group. 

Biochemists represent each amino acid with a three-letter abbreviation. These abbreviations appear under the names of the amino acids in Figure 13-32. For example, the abbreviation for glycine is Gly. 

Chapter 9 shows the importance of PLC in the critical field of medical research, with representative examples of the applications to amino acids, carbohydrates, lipids, and pharmacokinetic studies. 

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