Chemistry, protein peptide bonds

Schemes are available, however, that start from the free carboxylic acid, plus an activator . Dicyclohexylcarbodiimide, DCC, has been extensively employed as a promoter in esterification reactions, and in protein chemistry for peptide bond formation [187]. Although the reagent is toxic, and a stoichiometric concentration or more is necessary, this procedure is very useful, especially when a new derivative is targeted. The reaction usually proceeds at room temperature, is not subject to steric hindrance, and the conditions are mild, so that several types of functional groups can be employed, including acid-sensitive unsaturated acyl groups. In combination with 4-pyrrolidinonepyridine, this reagent has been employed for the preparation of long-chain fatty esters of cellulose from carboxylic acids, as depicted in Fig. 5 [166,185,188] ...

An important element in the three-dimensional structure of a protein is the secondary structure. The secondary structure results from the formation of hydrogen bonds between the—N—H groups and the carbonyl (C O) groups of the peptide bonds —N—H 0=C. There are two basic ways to do this. We can form a helix or we can form a sheet. The great American chemist Linus Pauling won the Nobel Prize in Chemistry in 1954 for the elucidation of these structures. 

There are many instances where a problem in protein chemistry or biology can be studied efficiently and effectively by semisynthesis. For this section, semisynthesis means the combination of a synthetic peptide with a large protein segment derived from natural sources. The combination can be by a covalent peptide bond or, in certain cases, by a specific... 

Corresponding improvements in the semisynthesis of proteins have been developed (see Section 5.1.11). They, too, have involved intermolecular and intramolecular reactions to form normal peptide bonds between small synthetic peptides and large protein components derived from natural sources or produced by recombinant techniques. In this case, there is the potential to produce derivatives of much larger proteins than can currently be prepared by total chemical synthesis. The total synthesis and semisynthesis approaches are useful for somewhat different purposes, but can be considered complementary together, they greatly broaden the field of protein chemistry and biology. 

In the paragraph on organic chemistry in chapter 3 a protein molecule was described as a polymer of amino acids which are linked by means of peptide bonds (not included in figure 5.6). The molecule can possess additional acid carboxyl (COOH) and alkaline amino (NH2) groups. When dissolved in a polar environment like e.g. water... 

What helped next in case of proteins is that the quasi-rigid subunits (peptide bonds) are all the same, though perturbed by the presence of twenty possible side chains (which were treated almost case by case using also the pseudoatom concept). This approach may also help in other domains of chemistry. 

Biuret Reaction. The particular capabilities of the stop-ped-flow vidicon system have been used to help explain some unusual behavior in the biuret reaction. The biuret reaction is the basis for the standard clinical chemistry technique for determining the total protein content of human blood serum (23). It involves a complexation reaction, in alkaline solution, between the cupric ion (Cu2+) and the peptide bonds of the protein. In the standard biuret technique, the reaction is allowed to go to completion and then the absorbance of the copper-protein complex is measured at 55 nm. This technique tends to be rather slow since the reaction, although very rapid over the first few seconds, does not go to completion for at least 20 to 30 minutes. 

The enzymes used for this type of digestion in Analytical Chemistry are mainly hydrolytic enzymes, the catalytic effect of which is based on the insertion of water at a specific bond of the substrate. The hydrolytic enzymes used in analytical applications include lipases (which hydrolyse fats into long-chain fatty acids and glycerol) amylases (which hydrolyse starch and glycogen to maltose and to residual polysaccharides) and proteases (which attack the peptide bonds of proteins and peptides themselves). 

Where peptide chemistry can make a contribution toward the proof of protein structure is in the application and continued formulation of degrada-tive techniques. Since fragmentation of the protein molecule to smaller peptides is probably the key reaction in degradative processes, the search for specific reagents for the selective cleavage of various peptide bonds and the standardization of existing techniques is of prime importance (Katsoyannis, 1961). 

Fig. 19. Topography of the NBS cleavage of the six tyrosyl peptide links of native and

All amino acids share two chemically functional groups, the carboxyl group and the amino group. Thus, they will share the chemical reactions of these groups familiar from organic chemistry. Many of these reactions are exploited in the laboratory manipulation of amino acids, peptides, and proteins. Note that these reactions are also common to the side chains of asp, glu (-COOH), and lys (-NH2). Another side-chain with important chemistry is cys (-SH). Biologically the most important reactions are those required for protein formation, particularly the peptide bond. 

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