Amino acids reactivity

The reactivity of amino acids within a protein actually can vary considerably with regard to their reactivity for labeling due to variations in the microenvironment of the residues. These differences in reactivity are related to a number of factors including proximity to hydrophobic sequences or bulky amino acids such as tryptophan. Accessibility to solvent also must be considered. The relative amino acid reactivity of amino adds toward labeling has not been investigated on mAbs because of their complexity. However, studies with smaller proteins and peptides have documented, for example, that the rate of iodination of tyrosine residues in these molecules can vary by factors of 50-100 (Dube et al. 1966 Seon et al. 1970). 

In contradiction to this, the protein biosynthesis proceeds via aminolysis of activated amino acids reactively bound to t-RNA, where the growing protein is liberated from the polymer RNA support (Fig. 3). This type of biosynthesis was imitated in the way of a drastically simplified model reaction, namely the peptide syntheses with solid phase bound activated amino acid esters [37, 38], which here are not the matter for discussion (Fig. 4). 

Luminescence has been used in conjunction with flow cells to detect electro-generated intennediates downstream of the electrode. The teclmique lends itself especially to the investigation of photoelectrochemical processes, since it can yield mfonnation about excited states of reactive species and their lifetimes. It has become an attractive detection method for various organic and inorganic compounds, and highly sensitive assays for several clinically important analytes such as oxalate, NADH, amino acids and various aliphatic and cyclic amines have been developed. It has also found use in microelectrode fundamental studies in low-dielectric-constant organic solvents. 

Short chains of amino acid residues are known as di-, tri-, tetrapeptide, and so on, but as the number of residues increases the general names oligopeptide and polypeptide are used. When the number of chains grow to hundreds, the name protein is used. There is no definite point at which the name polypeptide is dropped for protein. Twenty common amino acids appear regularly in peptides and proteins of all species. Each has a distinctive side chain (R in Figure 45.3) varying in size, charge, and chemical reactivity. 

Finally, in another study related to nutrition and the immune response in the aged, old mice were given oral doses of two amino acids (qv), lysine and arginine. The treated mice showed evidences of recovered mitogenic responsiveness, expression of T-ceU markers, and production of thymic semm factor (thymulin). The effect of the amino acid combination, sold commercially as Neoiodarsolo, seems to consist mainly of the reactivation of the... 

Much of protein engineering concerns attempts to explore the relationship between protein stmcture and function. Proteins are polymers of amino acids (qv), which have general stmcture +H3N—CHR—COO , where R, the amino acid side chain, determines the unique identity and hence the stmcture and reactivity of the amino acid (Fig. 1, Table 1). Formation of a polypeptide or protein from the constituent amino acids involves the condensation of the amino-nitrogen of one residue to the carboxylate-carbon of another residue to form an amide, also called peptide, bond and water. The linear order in which amino acids are linked in the protein is called the primary stmcture of the protein or, more commonly, the amino acid sequence. Only 20 amino acid stmctures are used commonly in the cellular biosynthesis of proteins (qv). 

The side groups of the amino acids vary markedly in size and chemical nature and play an important role in the chemical reactions of the fiber. For example, the basic groups (hisidine, arginine, and lysine) can attract acid (anionic) dyes, and in addition the side chains of lysine and hisidine are important sites for the attachment of reactive dyes. The sulfur-containing amino acid cysteine plays a very important role, because almost all of the cysteine residues in the fiber are linked in pairs to form cystine residues, which provide a disulfide bridge —S—S— between different polypeptide molecules or between segments of the same molecules as shown ... 

Antibiotic A201A. Antibiotic A201A (23), produced by S. capreolus is an /V -dimethyladenine nucleoside stmcturaHy similar to puromycin (19). Compound (23) which contains an aromatic acid and monosaccharide residues (1,4), inhibits the incorporation of amino acids into proteins but has no effect on RNA or DNA synthesis. Compound (23) does not accept polypeptides as does (19), and does appear to block formation of the initiation complex of the SOS subunit. It may block formation of a puromycin-reactive ribosome. 

Amino Acids. Chloroformates play a most important role for the protection of the amino group of amino acids (qv) during peptide synthesis (32). The protective carbamate formed by the reaction of benzyl chloroformate and amino acid (33) can be cleaved by hydrogenolysis to free the amine after the carboxyl group has reacted further. The selectivity of the amino groups toward chloroformates results in amino-protected amino acids with the other reactive groups unprotected (34,35). Methods for the preparation of protected amino acids on an industrial scale have been developed (36,37). A wide variety of chloroformates have been used that give various carbamates that are stable or cleaved under different conditions. 

Usually, a rapid binding step of the inhibitor I to the enzyme E leads to the formation of the initial noncovalent enzyme-inhibitor complex E-I. This is usually followed by a rate determining catalytic step, leading to the formation of a highly reactive species [E—I ]. This species can either undergo reaction with an active site amino acid residue of the enzyme to form the covalent enzyme-inhibitor adduct E—I", or be released into the medium to form product P and free active enzyme E. 

A significant difference between pseudoirreversible inhibitors and mechanism-based inactivators is the reversibiUty of the inactivation. A complete evaluation of the mechanism involved would require evidence not only for the covalent enzyme-inhibitor complex, but also for its decomposition products and its rate of reactivation. It is often difficult to identify the active site amino acid residue covalently linked to the inhibitor because of the instabiUty of the complex. 

Me3SiNEt2- Trimethylsilyldiethylamine selectively silylates equatorial hydroxyl groups in quantitative yield (4-10 h, 25°). The report indicated no reaction at axial hydroxyl groups. In the prostaglandin series the order of reactivity of trimethylsilyldiethylamine is Cii > Ci5 C9 (no reaction). These trimethylsilyl ethers are readily hydrolyzed in aqueous methanol containing a trace of acetic acid. The reagent is also useful for the silylation of amino-acids. ... 

The enzyme provides a general base, a His residue, that can accept the proton from the hydroxyl group of the reactive Ser thus facilitating formation of the covalent tetrahedral transition state. This His residue is part of a catalytic triad consisting of three side chains from Asp, His, and Ser, tvhich are close to each other in the active site, although they are far apart in the amino acid sequence of the polypeptide chain (Figure 11.6). 

Tnflrc anhydride is a useful reagent for the preparation of covalent triflate esters from alcohols, ketones, and other organic substrates [66] In many cases, very reactive triflates can be generated m situ and subjected to subsequent transformation without isolation [94, 95, 96, 97] Typical examples are cyclization of amides into dihydroisoqumolines (equation 45) and synthesis of Al-hydroxy-a-amino acid denvatives (equation 46) via the intermediate covalent triflates... 

Nucleophilic substitution by ammonia on a-halo acids (Section 19.16) The a-halo acids obtained by halogenation of carboxylic acids under conditions of the Hell-Volhard-Zelinsky reaction are reactive substrates in nucleophilic substitution processes. A standard method for the preparation of a-amino acids is displacement of halide from a-halo acids by nucleophilic substitution using excess aqueous ammonia. 

To fonn a peptide bond between two suitably protected amino acids, the free carboxyl group of one of them must be activated so that it is a reactive acylating agent. The most ffflniliar- acylating agents are acyl chlorides, and they were once extensively used to couple fflnino acids. Certain drawbacks to this approach, however, led chemists to seek alternative methods. 

In the second major method of peptide synthesis the carboxyl group is activated by converting it to an active ester, usually a p-nitrophenyl ester. Recall from Section 20.12 that esters react with ammonia and amines to give fflnides. p-Nitrophenyl esters are much more reactive than methyl and ethyl esters in these reactions because p-nitrophenoxide is a better (less basic) leaving group than methoxide and ethoxide. Simply allowing the active ester and a C-protected amino acid to stand in a suitable solvent is sufficient to bring about peptide bond formation by nucleophilic acyl substitution. 

The chemical properties of peptides and proteins are most easily considered in terms of the chemistry of their component functional groups. That is, they possess reactive amino and carboxyl termini and they display reactions characteristic of the chemistry of the R groups of their component amino acids. These reactions are familiar to us from Chapter 4 and from the study of organic chemistry and need not be repeated here. 

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