Structural Biochemistry/Organic Chemistry/Important Organic Reactions in Biochemistry/Peptide Bonding

Importance of Peptide Bonding
Peptide bonding (or amide bonding) is one of the most important reactions in biochemistry, as it is the bond used by amino acids to form proteins. Amino acids form peptide bonds with other amino acids when the amino group of the first amino acid bonds with the carboxyl group of the second amino acid. The dipeptide formed is followed by the loss of water. A chain of amino acids connected by peptide bonds is called a polypeptide chain, while each individual amino acid is referred to as a residue. These chains then fold due to various internal and external forces in order to become proteins.

Partial-Double Bond of Peptide Bond
The stability of the peptide bond is due to the resonance of amides. With resonance, the nitrogen is able to donate its lone pair of electrons to the carboxyl carbon and push electrons from the carboxyl double bond towards the oxygen, forming the oxygen anion. This resonance effect is very stabilizing because the electrons can be delocalized over multiple atoms, with one especially stable resonance structure containing the highly electronegative oxygen as an anion. The double bond character of the C-N bond results in a relatively short bond (1.32 angstroms vs. the normal length of a pure C-N bond, 1.47 angstroms). The double bond resonance form of the peptide bond helps to increase stability and decrease rotation about that bond. The partial double bond character is either strengthened or weakened depending upon the environment that it is in. An example would be a hydrophobic environment where the double-bond form would be highly discouraged since the double-bond form has a positive charge on the nitrogen and a negative charge on the oxygen.

The partial double bond results in the amide group being planar thus causing them to take either the cis or trans conformation. In the cis configuration, the two alpha carbon atoms fall on the same side of the peptide bond. In the trans configuration, these groups are on opposite sides of the peptide bond. While the proteins exist in their unfolded state, the peptide groups can isomerize at free will and thus often take the form of both conformations. This however, is not true in the folded state where with very rare exceptions, only one conformation is taken up at each position. In peptide bonds, the vast majority take the trans conformation with a cis:trans ratio of around 1:1000. There is preference for the trans configuration over the cis orientation because with trans there is less steric hindrance between groups attached to the alpha carbon atoms.

Unlike the rigid peptide bond, the bond linking the amino group to the alpha carbon atom and the bond linking the alpha carbon atom to the carbonyl carbon are single bonds. These two bonds are free to rotate about the amide bonds, allowing them to take on a variety of orientations. The enhanced freedom of rotation with regards to these two bonds allows proteins to fold in a variety of shapes. The degree of rotation of each of these bonds can be quantified by their torsion angle. A torsion angle is defined somewhere between -180 and +180. Torsion angles are also called dihedral angles. The angle of rotation in regards to the bond between the nitrogen and the alpha carbon is referred to as phi, while the angle of rotation between the alpha carbon and the carbonyl carbon is referred to as psi. Moving clockwise from the nitrogen atom towards the alpha carbon, or from the carbonyl carbon to the alpha carbon yields a positive value on the Ramachandran diagram. The Ramachandran diagram illustrates various orientations of polypeptides and shows specific orientations that are not possible due to steric hindrance based on phi and psi values. At certain phi and psi values some structures may not exist due to clashes between the atoms.

Overall Reaction
The overall reaction involves the reaction of two amino acids which is catalyzed by enzymes enzyme in the body to produce the two amino acids combined and a water molecule.

Reaction Mechanism
This reaction to form peptide bonds involves reacting the amine group of one amino acid (the N-terminal) to the carboxylgroup of another amino acid (the C-terminal). A peptide bond is a dehydration reaction, or condensation reaction, meaning it releases a molecule of water through the course of the reaction. The molecule formed by a peptide bond is called an amide.



In the presence of water, the peptide bond will break spontaneously; this is called amide hydrolysis. This occurs because the peptide reaction possesses an equilibrium that pushes the reaction towards hydrolysis (heading in the reverse direction), which means the reaction is endergonic, and requires energy to proceed. Although this reaction requires an input of energy, peptide bonds are still stable bonds as the rate of hydrolysis is incredibly slow. Enzymes facilitate the hydrolysis reaction of peptides to form proteins in living organisms.

The hydrolysis reaction is very slow because the bond between the amino group and carboxyl group is stable due to resonance. The lone pair from the nitrogen donates electrons to the carbonyl. The resonance decreases the electrophilicity, and stabilizes the carbonyl forming the peptide bond. Even though peptide bonds are stable, they can still react. The reactions of peptide bonds involve attack at the carbonyl carbon and the formation of a tetrahedral intermediate.

To form peptide bonds between specific amino acid residues, the functional groups of the amino acids must be protected. The amino end is usually blocked using a phenylmethoxycarbonyl group (or Cbz). The amino group is then restored by a hydrogenolysis reaction using the reagents H2 and Pd-C. Another amino protecting group used is 1,1-dimethylethoxycarbonyl (or tert-butoxycarbonyl, Boc). This can be removed under acidic conditions (for example, with HCl). On the other end, the carboxy terminus can be protected by the formation of an ester. Deprotection of the carboxy end can be achieved by treatment with base. Polypeptides can be synthesized by coupling an amino protected amino acid with another amino acid in which the carboxy end is protected with the help of dicyclohexylcarbodiimide (DCC).