Protein peptide bond

The pyrophosphate thus produced is often degraded by a ubiquitous enzyme, pyrophosphatase, to inorganic phosphate, thus pushing the reaction ever further toward completion. Another process that requires energy input is the formation of peptide bonds, which hold amino acids together in proteins. Peptide bonds cannot form spontaneously, and their biosynthesis requires at least four ATP equivalents, amounting to some 33,600 cal. The whole point of ATP hydrolysis in biologic systems is thus to drive forward those reactions that would otherwise not occur because of unfavorable AG. ... 

Endopeptidases Cleave protein/peptide bonds other than terminal ones ... 

Trypsin, chymotrypsin, and elastase are members of a large group of endopeptidases known collectively as serine proteases. (Recall that an endopeptidase cleaves a peptide bond that is not at the end of a peptide chain see Section 22.13). They are called proteases because they catalyze the hydrolysis of protein peptide bonds. They are called serine proteases because each one has a serine side chain at the active site that participates in the catalysis. 

Serine proteases, which consist of trypsin, chymotrypsin, and elastase, catalyze the hydrolysis of protein peptide bonds. The net reaction for the enzyme (Enz)-catalyzed hydrolysis of peptide bond (i.e., amide bond) may be expressed as... 

If the enzyme-catalyzed hydrolysis of peptide bond involves a simple reversible reaction as shown by Equation 2.5 then, indeed, the enzyme must catalyze the rate of formation of peptide bond from amino acids (i.e., lq,-step), provided the amino acids do not react irreversibly with the enzyme. Incidentally, if the function of serine proteases is to catalyze both the rate of hydrolytic cleavage and the rate of formation of protein peptide bond, then, probably, these enzymes cannot digest the proteins that we eat and, consequently, the results would have been disastrous for all protein-eating creatures — which certainly Nature will never allow. Although the mechanisms of most of the enzyme-catalyzed reactions are unknown, even at a very rudimentary level, the mechanism of a-chymotrypsin-catalyzed hydrolysis of peptide bond has been relatively well understood. The reaction has been almost ascertained to involve acylation and deacylation of enzyme as shown by Equation 2.6. Widely accepted mechanisms for acylation and deacylation steps are shown in Scheme 2.6 and Scheme 2.7. ... 

Most reactions in cells are carried out by enzymes [1], In many instances the rates of enzyme-catalysed reactions are enhanced by a factor of a million. A significantly large fraction of all known enzymes are proteins which are made from twenty naturally occurring amino acids. The amino acids are linked by peptide bonds to fonn polypeptide chains. The primary sequence of a protein specifies the linear order in which the amino acids are linked. To carry out the catalytic activity the linear sequence has to fold to a well defined tliree-dimensional (3D) stmcture. In cells only a relatively small fraction of proteins require assistance from chaperones (helper proteins) [2]. Even in the complicated cellular environment most proteins fold spontaneously upon synthesis. The detennination of the 3D folded stmcture from the one-dimensional primary sequence is the most popular protein folding problem. 

A dipeptide is a molecule consisting of two ammo acids joined by a peptide bond A tnpeptide has three ammo acids joined by two peptide bonds a tetrapeptide has four ammo acids and so on Peptides with more than 30-50 ammo acids are polypeptides Proteins are polypeptides that have some biological function... 

A key biochemical reaction of ammo acids is their conversion to peptides polypeptides and proteins In all these substances ammo acids are linked together by amide bonds The amide bond between the ammo group of one ammo acid and the carboxyl of another IS called a peptide bond Alanylglycme is a representative dipeptide... 

Knowing how the protein chain is folded is a key ingredient m understanding the mechanism by which an enzyme catalyzes a reaction Take carboxypeptidase A for exam pie This enzyme catalyzes the hydrolysis of the peptide bond at the C terminus It is... 

Chymotrypsin (Section 27 10) A digestive enzyme that cat alyzes the hydrolysis of proteins Chymotrypsin selectively catalyzes the cleavage of the peptide bond between the car boxyl group of phenylalanine tyrosine or tryptophan and some other ammo acid... 

Critical micelle concentration (Section 19 5) Concentration above which substances such as salts of fatty acids aggre gate to form micelles in aqueous solution Crown ether (Section 16 4) A cyclic polyether that via lon-dipole attractive forces forms stable complexes with metal 10ns Such complexes along with their accompany mg anion are soluble in nonpolar solvents C terminus (Section 27 7) The amino acid at the end of a pep tide or protein chain that has its carboxyl group intact—that IS in which the carboxyl group is not part of a peptide bond Cumulated diene (Section 10 5) Diene of the type C=C=C in which a single carbon atom participates in double bonds with two others... 

N terminus (Section 27 7) The amino acid at the end of a pep tide or protein chain that has its a ammo group intact that IS the a ammo group is not part of a peptide bond... 

Hydrolyzed Vegetable Protein. To modify functional properties, vegetable proteins such as those derived from soybean and other oil seeds can be hydrolyzed by acids or enzymes to yield hydrolyzed vegetable proteins (HVP). Hydrolysis of peptide bonds by acids or proteolytic enzymes yields lower molecular weight products useful as food flavorings. However, the protein functionaHties of these hydrolysates may be reduced over those of untreated protein. 

Deamidation of soy and other seed meal proteins by hydrolysis of the amide bond, and minimization of the hydrolysis of peptide bonds, improves functional properties of these products. For example, treatment of soy protein with dilute (0.05 A/) HCl, with or without a cation-exchange resin (Dowex 50) as a catalyst (133), with anions such as bicarbonate, phosphate, or chloride at pH 8.0 (134), or with peptide glutaminase at pH 7.0 (135), improved solubiHty, whipabiHty, water binding, and emulsifying properties. 

The mechanism of the tarmage is accepted to be largely one of replacement of the bound water molecules by the phenoHc groups of the tannin and subsequent formation of hydrogen bonds with the peptide bonds of the protein. The effect of this bonding is to make the leather almost completely biorefractive. 

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 amide linkage between monomer units in a protein is called a peptide bond. Peptides and polypeptides, which often exhibit biological activity (see Antibiotics, peptides Neuroregulators), are smaller than proteins. Although the differentiation between polypeptide and protein is somewhat arbitrary, the usual distinction is drawn around 100 monomer units. Proteins are also characterized by higher levels of stmcture resulting from internal interactions. 

Figure 1.2 Proteins are built up by amino acids that are linked by peptide bonds to form a polypeptide chain, (a) Schematic diagram of an amino acid. Illustrating the nomenclature used in this book. A central carbon atom (Ca) is attached to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom (H), and a side chain (R). (b) In a polypeptide chain the carboxyl group of amino acid n has formed a peptide bond, C-N, to the amino group of amino acid + 1. One water molecule is eliminated in this process. The repeating units, which are called residues, are divided into main-chain atoms and side chains. The main-chain part, which is identical in all residues, contains a central Ca atom attached to an NH group, a C =0 group, and an H atom. The side chain R, which is different for different residues, is bound to the Ca atom.

All protein molecules are polymers built up from 20 different amino acids linked end-to-end by peptide bonds. The function of every protein molecule depends on its three-dimensional structure, which in turn is determined by its amino acid sequence, which in turn is determined by the nucleotide sequence of the structural gene. 

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