Peptide bonds chains

Proteins are large biomolecules made up of a-amino acid residues linked together by amide, or peptide, bonds. Chains with fewer than 50 amino acids are often called peptides, while the term protein is reserved for larger chains. Twenty amino acids are commonly found in proteins all are a-amino acids, and all except glycine have stereochemistry similar to that of l sugars. In neutral solution, amino acids exist as dipolar zwitterions. 

Polymer Polypeptide Polysaccharide Very long chains of like units, as in polythene . Chains of amino acids joined together with peptide bonds. Chains of sugar-like compounds as in cellulose (see monosaccharide). 

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. 

The geometry of the peptide bond is planar and the mam chain is arranged m an anti conformation (Section 27 7)... 

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... 

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... 

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). 

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.

Figure 11.4 Serine proteinases catalyze the hydrolysis of peptide bonds within a polypeptide chain. The bond that is cleaved is called the scissile bond. (Ra) and (Rb)j/ represent polypeptide chains of varying lengths.

The most important aspect of Table 27.1 is that the 20 anino acids that occur in proteins share the common feature of being a-anino acids, and the differences fflnong them are in their side chains. Peptide bonds linking carboxyl and a-anino groups characterize the structure of proteins, but it is the side chains that are mainly responsible for theh properties. The side chains of the 20 commonly occuning amino acids encompass both large and small differences. The major differences between amino acid side chains concern ... 

Peptide bond (Section 26.4) An amide bond in a peptide chain. 

Aspaityl proteinases are proteinases that utilize the terminal carboxyl moiety of the side chain of aspartic acid to effect peptide bond hydrolysis. 

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