The peptide bond

The bond between the carbon atom of the carbonyl group and the amide nitrogen has partial double bond character that can be attributed to resonance  

The partial double bond character of each third bond in the peptide backbone would cause some limitation in the possible geometries of the chain but this in itself is certainly not sufficient to determine a preferred conformation. A well defined architecture requires further limiting factors and such can be found in the restricted rotation around the N —Q and the Q—C bonds. Negative (repulsive) interaction between side chains of neighboring amino acid residues hinders free rotation around these bonds and the dihedral angles 0 and W, corresponding to rotation out of the plane around the N —Q and Q—C bonds respectively 

Which groups on amino acids react to form a peptide bond  

This structural feature has important implications for the three-dimensional conformations of peptides and proteins. There is free rotation around the bonds between the a-carbon of a given amino acid residue and the amino nitrogen and carbonyl carbon of that residue, but there is no significant rotation around the peptide bond. This stereochemical constraint plays an important role in determining how the protein backbone can fold. 

When the carboxyl group of one amino acid reacts with the amino group of another to give an amide linkage and eliminate water, a peptide bond is formed. In a protein, upward of a hundred amino acids are so joined to form a polypeptide chain. 

The peptide group is planar as a result of resonance stabilization. This stereochemical feature determines a number of features of the three-dimensional structure of proteins. 

In protein molecules, a-amino adds are linked in a linear sequence. The a-carboxyl group of one amino acid is linked to the a-amino group of the next through a special amide bond known as 

Note that the acidic and basic character of the carboxyl and amino groups taking part in forming the bond are lost after condensation. The hydrolysis of the peptide bond to free amino acids is a spontaneous process, but is normally very slow in neutral solution. 

In naming peptides, we start with the amino acid that has the free cr-NH3 (the N terminal) and replace the -ine endings (except the last one) with the ending -yl. The amino acids in the peptide are called residues, since they are the residues left after the removal of water during peptide bond formation. 

We start naming a peptide from the amino terminus thus, glycylalanine has a free a-amino group on the glycine residue, while the free carboxyl group is that of the alanine residue. 

Glycylalanine and alanylglycine are examples of sequence isomers they are composed of the same amino acids, but they are combined in different sequences. 

Cowgill pointed out that there are essentially two distinct quenching processes of tyrosine fluorescence resulting from association with the peptide bond.(3) Tyrosines affected by these mechanisms are classified in Table 1.3 as 

II Exposed and quenched by a hydrated peptide carbonyl group 

V Buried and hydrogen bonded to a peptide carbonyl group 

Organism Classification size3 (Mb) Organism Classification size3 (Mb) 

Aeropyrum pernix Archaea 1.67 Treponema pallidum Eubacteria 1.14 

Pyrococcus furiosus Archaea 2.10 Candida albicans Fungi 15.0 

Bacillus anthracis Eubacteria 4.50 parvum Leishmania major Protozoa 33.6 

Bordetella pertussis Eubacteria 3.88 Arabidopsis thaliana Plant 70.0 

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Where helical secondaiy structures are represented by the cylinder model, the /i-strand. structures are visualized by the ribbon model (see the ribbons in Figure 2-124c). The broader side of these ribbons is oriented parallel to the peptide bond. Other representations replace the flat ribbons with flat arrows to visualize the sequence of the primary structure. 

To direct the synthesis so that only Phe Gly is formed the ammo group of phe nylalanme and the carboxyl group of glycine must be protected so that they cannot react under the conditions of peptide bond formation We can represent the peptide bond for matron step by the following equation where X and Y are amine and carboxyl protecting groups respectively... 

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... 

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... 

The bond highlighted m yellow is the peptide bond ) Pencyclic reaction (Section 10 12) A reaction that proceeds through a cyclic transition state Period (Section 1 1) A honzontal row of the penodic table Peroxide (Section 6 8) A compound of the type ROOR Peroxide effect (Section 6 8) Reversal of regioselectivity oh served m the addition of hydrogen bromide to alkenes brought about by the presence of peroxides m the reaction mixture... 

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. 

Now, it is seen that polar groups dominate the molecular structure, resulting from hydroxyl groups from the two serine and threonine fragments in addition to the peptide bonds themselves. Only weak dispersive interactions will be contributed by glycine fragments (CH2 groups). 

The Peptide Bond Has Partial Double Bond Character... 

Peptide bond resonance has several important consequences. First, it restricts free rotation around the peptide bond and leaves the peptide backbone with only two degrees of freedom per amino acid group rotation around... 

FIGURE 5.2 The peptide bond is shown in its usnal trans conformation of carbonyl O and amide H. The atoms are the oi-carbons of two adjacent amino acids joined in peptide linkage. The dimensions and angles are the average valnes observed by crystallographic analysis of amino acids and small peptides. The peptide bond is the light gray bond between C and N. (Adapted from Ramachandran, G. A., ct ai, 1974. Biochimica Biophysica Acta 359 298-302.)... 

Parallel /3-sheets tend to be more regular than antiparallel /3-sheets. The range of (f) and i/t angles for the peptide bonds in parallel sheets is much smaller than that for antiparallel sheets. Parallel sheets are typically large structures those composed of less than five strands are rare. Antiparallel sheets, however, may consist of as few as two strands. Parallel sheets characteristically distribute... 

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