Peptide bonds resulting from covalent

Figure 3. Structure of peptide and isopeptide bonds resulting from covalent attachment of amino acids to proteins by chemical methods. In isopeptide bond formation Rt = -CH2- or -CH2CH2- of aspartic or glutamic acid and R2 = -(CH2)n- of lysine.

Figure 16.3 Conceptual illustration of two peptides before (left) and after (right) a chemical reaction with formaldehyde. The amino acids are represented as circles. In this particular peptide, a tyrosine (Y) is located within the epitope (shaded circles). An arginine (R) is located elsewhere in the peptide. Formaldehyde results in the formation of a covalent bond between the two residues, due to a Mannich condensation reaction, as shown on the right. The new configuration prevents antibodies from binding to the epitope on the left. 

Protein catabolism begins with hydrolysis of the covalent peptide bonds that link successive amino acid residues in a polypeptide chain (fig. 22.3). This process is termed proteolysis, and the enzymes responsible for the action are called proteases. In humans and many other animals, proteolysis occurs in the gastrointestinal tract this type of proteolysis results from proteases secreted by the stomach, pancreas, and small intestine. 

CHAPTER 36, FIGURE 16 Proteinase inactivation by SERPINS. Proteinase inactivation occurs by reaction between proteinase and inhibitor, e.g., antithrombin. The proteinase is a stoichiometric reactant in this instance but is not a catalyst. This reaction results in the formation of a covalent bond between the reactive site residue of the inhibitor (Arg in antithrombin) and the active site residue (Ser in the proteinase). This complex formation prevents the proteinase from hydrolyzing any other peptide bond. Proteinases, thrombin, factor Xa, factor IXa, and, less effectively, factor Vila and factor XIa are all inactivated by the plasma protein inhibitor antithrombin (previously designated antithrombin III). The product AT is the cleaved form of antithrombin. It is formed in both the absence and presence of heparin, but more so in the presence. The proteinase is indicated is indicated by green, the inhibitor by red, and the inactivated proteinase by gray. Stripes on the inhibitor represent the helices (Figure 36-7). 

The primary structure of a protein is the amino acid sequence of the protein chain. It results from the covalent bonding between the amino acids in the chain (peptide bonds). The primary structures of proteins are translations of information contained in genes. Each protein has a different primary structure with different amino acids in different places along the chain. 

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. 

The sequence of amino acids dictates certain geometric constraints for the polypeptide. These constraints include maximum lengths between covalent bonds, limiting angles in which bonds can be bent, and van der Waals radii, which limit how tightly structures can be packed. These factors, mixed with forces that help preferentially stabilize structures, such as hydrogen bonds, ionic attractions/ repulsions, hydrophobic interactions, and others, ultimately determine the shape that a peptide has over a short distance. The structure resulting from all these interactions is called the secondary structure of the protein. 

The order or sequence of individual amino acid residues along the peptide chain defines the covalent structure of the molecule. It is also called primary structure in order to make a clear distinction from the three dimensional geometry in peptides and proteins. The latter is generated by non-covalent forces such as hydrogen bonds between amide groups secondary structure) and combination of polar and non-polar interactions and of disulfide bridges which result in chain folding tertiary structure). 

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