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Peptide bond formation via dehydration reaction. When two amino acids form a dipeptide through a peptide bond, [1] it is a type of condensation reaction. [2] In this kind of condensation, two amino acids approach each other, with the non-side chain (C1) carboxylic acid moiety of one coming near the non-side chain (N2) amino moiety of the other.
The peptide backbone dihedral angles (φ, ψ) are about (–140°, 135°) in antiparallel sheets. In this case, if two atoms C α i and C α j are adjacent in two hydrogen-bonded β-strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds.
The standard hydrogen-bond definition for secondary structure is that of DSSP, which is a purely electrostatic model. It assigns charges of ± q 1 ≈ 0.42 e to the carbonyl carbon and oxygen, respectively, and charges of ± q 2 ≈ 0.20 e to the amide hydrogen and nitrogen, respectively.
In organic chemistry, peptide synthesis is the production of peptides, compounds where multiple amino acids are linked via amide bonds, also known as peptide bonds. Peptides are chemically synthesized by the condensation reaction of the carboxyl group of one amino acid to the amino group of another.
Trigonal planar: Molecules with the trigonal planar shape are somewhat triangular and in one plane (flat). Consequently, the bond angles are set at 120°. For example, boron trifluoride. Angular: Angular molecules (also called bent or V-shaped) have a non-linear shape. For example, water (H 2 O), which has an angle of about 105°. A water ...
However, additional molecular interactions may render the amide form less stable; the amino group is expelled instead, resulting in an ester (Ser/Thr) or thioester (Cys) bond in place of the peptide bond. This chemical reaction is called an N-O acyl shift. The ester/thioester bond can be resolved in several ways:
In biochemistry, the Corey-Pauling rules are a set of three basic statements that govern the secondary nature of proteins, in particular, the CO-NH peptide link. They were originally proposed by Robert Corey and Linus Pauling. [1] The rules are as follows: The atoms in a peptide link all lie on the same plane.
In these cases, one is often interested in the half-planes defined by three consecutive points, and the dihedral angle between two consecutive such half-planes. If u 1, u 2 and u 3 are three consecutive bond vectors, the intersection of the half-planes is oriented, which allows defining a dihedral angle that belongs to the interval (− π, π].