Peptide Bonding between Amino Acids

Peptides are short chains of amino acids linked by peptide bonds. Most biologically active peptides contain two to ten amino acids. Peptide bonds are formed between the carboxyl carbon of one amino acid and the amino nitrogen of another. Since water is released, this is an example of dehydration synthesis. The bond forms as illustrated in Figure 16.7. 

Primary Structure The primary structure of the protein is the amino acid sequence of the protein. The primary structure results from the formation of covalent peptide bonds between amino acids. Peptide bonds are amide bonds formed between the a-carboxylate group of one amino acid and the a-amino group of another. 

Trypsin (Section 27 10) A digestive enzyme that catalyzes the hydrolysis of proteins Trypsin selectively catalyzes the cleavage of the peptide bond between the carboxyl group of lysine or arginine and some other amino acid... 

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. 

Mammals, fungi, and higher plants produce a family of proteolytic enzymes known as aspartic proteases. These enzymes are active at acidic (or sometimes neutral) pH, and each possesses two aspartic acid residues at the active site. Aspartic proteases carry out a variety of functions (Table 16.3), including digestion pepsin and ehymosin), lysosomal protein degradation eathepsin D and E), and regulation of blood pressure renin is an aspartic protease involved in the production of an otensin, a hormone that stimulates smooth muscle contraction and reduces excretion of salts and fluid). The aspartic proteases display a variety of substrate specificities, but normally they are most active in the cleavage of peptide bonds between two hydrophobic amino acid residues. The preferred substrates of pepsin, for example, contain aromatic residues on both sides of the peptide bond to be cleaved. 

Proteases (proteinases, peptidases, or proteolytic enzymes) are enzymes that break peptide bonds between amino acids of proteins. The process is called peptide cleavage, a common mechanism of activation or inactivation of enzymes. They use a molecule of water for this, and are thus classified as hydrolases. 

Neotame is an artificial sweetener designed to overcome some of the problems with aspartame. The dimethylbutyl part of the molecule was added to block the action of peptidases, enzymes that break the peptide bond between the two amino acids aspartic acid and phenylalanine. This reduces the availability of phenylalanine, eliminating the need for a warning on labels directed at people who cannot properly metabolize phenylalanine. 

Peptide A linear chain of a small number of amino acids linked by peptide bonds. The number of amino acids which differentiates between a protein and a peptide remains a matter for discussion. 

Nucleophilic attack by water generally results in the cleavage of the amide, glycoside, or ester bonds that hold biopolymers together. This process is termed hydrolysis. Conversely, when monomer units are joined together to form biopolymers such as proteins or glycogen, water is a product, as shown below for the formation of a peptide bond between two amino acids. 

There are two main classes of proteolytic digestive enzymes (proteases), with different specificities for the amino acids forming the peptide bond to be hydrolyzed. Endopeptidases hydrolyze peptide bonds between specific amino acids throughout the molecule. They are the first enzymes to act, yielding a larger number of smaller fragments, eg, pepsin in the gastric juice and trypsin, chymotrypsin, and elastase secreted into the small intestine by the pancreas. Exopeptidases catalyze the hydrolysis of peptide bonds, one at a time, fi"om the ends of polypeptides. Carboxypeptidases, secreted in the pancreatic juice, release amino acids from rhe free carboxyl terminal, and aminopeptidases, secreted by the intestinal mucosal cells, release amino acids from the amino terminal. Dipeptides, which are not substrates for exopeptidases, are hydrolyzed in the brush border of intestinal mucosal cells by dipeptidases. 

This enzyme (RNase A) is a single chain protein of 124 amino acid residues, cross-linked by four intrachain disulfide bonds. Limited proteolysis of the enzyme cuts a single peptide bond between residues 20 and 21 (Richards and Vithayathil, 1959). The derived protein, RNase S, retains enzymic activity although the N-terminal peptide of 20 amino acids (S-peptide) is no longer covalently attached to the balance of the molecule (S-protein). Removal of S-peptide from... 

Trypsin inhibitors in cucumber were first found in a study by Walker-Simmons et /. " after wounding of leaves and treatment with proteinase inhibitor-inducing factor (PIIF). The amino acid sequence of two inhibitors isolated from Cucurhita maxima (winter squash) were determined by Wilusz et at The peptides named ITD I and ITD 111 each comprised a 29-residue sequence with six cysteine residues. The only difference between the two peptides is in position 9, which is lysine in ITD I and glutamic acid in ITD III. The reactive site is located at the peptide bond between Arg5 and Ile6. Owing to their discovery and distribution in Cucurbitaceae the inhibitor family has been named squash inhibitors. Since the initial discoveries many other members of the squash family have been found. 

Protein synthesis occurs by peptide bond formation between successive amino acids whose order is specified by a gene and thus by an mRNA. The formation of a peptide bond between the carboxyl group on one amino acid and the amino group of another is illustrated in Figure 1-4-7. 

Several different proteases can attack a single protein at enzyme-selective amino-acid sequences. Proteases can be divided into two categories. Endopeptidases are enzymes that cleave peptide bonds between specific, nonterminal amino acids. There are endopeptidases specific for just about every amino acid. Exopeptidases are enzymes that cleave terminal peptide bonds at either the C-terminus or N-terminus. 

---