Peptide Bond~ Definition of Peptide Bond~ formation & mechanism of peptide bond

Peptide Bond~ Definition of Peptide Bond~ formation & mechanism of peptide bond

See This Vedio

A peptide bond (amide bond) is a covalent chemical bond formed between twomolecules when the carboxyl group of one molecule reacts with the amino groupof the other molecule, causing the release of a molecule of water (H₂O), hence the process is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acids. The resulting C(O)NH bond is called a peptide bond, and the resulting molecule is an amide. The four-atom functional group -C(=O)NH- is called a peptide link. Polypeptides and proteinsare chains of amino acids held together by peptide bonds, as is the backbone ofPNA.

Figure 1: Dehydration synthesis (condensation) reaction forming an amide

A peptide bond can be broken by amide hydrolysis (the adding of water). The peptide bonds in proteins are metastable, meaning that in the presence of water they will break spontaneously, releasing 2-4 kcal/mol ^[1] of free energy, but this process is extremely slow. In living organisms, the process is facilitated by enzymes. Living organisms also employ enzymes to form peptide bonds; this process requires free energy. The wavelength of absorbance for a peptide bond is 190-230 nm

The Peptide Bond

A peptide bond (sometimes mistakenly called amino bond) is a covalent bond that is formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the another molecule, releasing a molecule of water. This is a a condensation reaction and usually occurs between amino acids. The resulting CO-NH bond is called a peptide bond, and the resulting molecule is an amide.

Formation of the peptide bond

The molecules must be orientated so that the carboxylic acid group of one can react with the amine group of the other. For example, two amino acids (glycine) combining through the formation of a peptide bond to form a dipeptide.

Any number of amino acids can be joined together in chains of 50 amino acids called peptides, 50-100 amino acids called polypeptides, and over 100 amino acids called proteins. A number of hormones, antibiotics, antitumor agents and neurotransmitters are peptides (proteins).

A peptide bond can be broken down by hydrolysis (the adding of water). The peptide bonds that are formed within proteins have a tendency to break spontaneously when subjected to the presence of water (metastable bonds) releasing about 10 kJ/mol of free energy. This process, however, is very slow. Living organisms use enzymes to broken down or to form peptide bonds. The wavelength of absorbance for a peptide bond is 190-230 nm.

Structure of the Peptide Bond

X-ray diffraction studies of crystals of small peptides by Linus Pauling and R. B. Corey indicated that the peptide bond is rigid, and planer. Pauling pointed out that this is largely a consequence of the resonance interaction of the amide, or the ability of the amide nitrogen to delocalize its lone pair of electrons onto the carbonyl oxygen.

Because of this resonance, the C=O bond is actually longer than normal carbonyl bonds, and the N–C bond of the peptide bond is shorter than the N–Cα bond. Notice that the carbonyl oxygen and amide hydrogen are in a trans configuration, as opposed to a cis configuration. This configuration is energetically more favorable because of possible steric interactions in the other.

The Polarity of the Peptide Bond

The peptide bond is usually portrayed as a single bond between the carbonyl carbon and the amide nitrogen. Normally, this should allow free rotation about than bond. However, notice that the nitrogen has a lone pair of electrons, which are adjacent to a carbon-oxygen bond. Therefore, a reasonable resonance structure can be draw with a double bond linking the carbon and nitrogen, and which result in a negative charge on the oxygen and a positive charge on the nitrogen.

The resonance structure prevents rotation around the peptide bond. The real structure of course is a weighted hybrid of these two structures. Therefore, the question is how significant is the resonance structure in depicting the true electron distribution. It is know that the peptide bond has approximately 40% double-bond character and therefore it is rigid.

Charges give the peptide bond a permanent dipole. Because of the resonance, the oxygen has a -0.28 charge, while the nitrogen bears a +0.28 charge.

Amino Acid Peptide Bonds Peptide Bond Formaion or Amide Synthesis: The formation of peptides is nothing more than the application of theamide synthesis reaction. By convention, the amide bond in the peptides should be made in the order that the amino acids are written. The amine end (N terminal) of an amino acid is always on the left, while the acid end (C terminal) is on the right. The reaction of glycine with alanine to form the dipeptide glyclalanine is written as shown in the graphic on the left. Oxygen (red) from the acid and hydrogens (red) on the amine form a water molecule. The carboxyl oxygen (green) and the amine nitrogen (green) join to form the amide bond. If the order of listing the amino acids is reversed, a different dipeptide is formed such as alaninylglycine. QUES. Write the reactions for: a) ala + gly ---> Answer graphic b) phe + ser ----> Answer graphic Salt Formation Contrast: The salt formation reaction is simply the transfer of the -H (positive ion) from the acid to the amine and the attraction of the positive and negative chagres. The acid group becomes negative, and the amine nitrogen becomes positive because of the positive hydrogen ion. No water is formed and there is only one product, the salt.
Click for larger image	Backbone Peptide or Protein Structure: The structure of a peptide can be written fairly easily without showing the complete amide synthesis reaction by learning the structure of the "backbone" for peptides and proteins. The peptide backbone consists of repeating units of "N-H 2, CH, C double bond O; N-H 2, CH, C double bond O; etc. See the graphic on the left . After the backbone is written, go back and write the specific structure for the side chains as represented by the "R" as gly-ala-leu for this example. The amine end (N terminal) of an amino acid is always on the left (gly), while the acid end (C terminal) is on the right (leu). gly-ala-leu - Chime in new window Example: Write the tripeptide structure for val-ser-cys. First write the "backbone" and then add the specific side chains. Answer graphic QUES. Write the structure for the tripeptide: a ) glu-cys-gly ---> Answer graphic b) phe-tyr-asn ---> Answer graphic
	Glutathione: Glutathione is an important tripeptide present in significant concentrations in all tissues. It contains glutamic acid, cysteine, and glycine. What is unusual about the structure of glutathione (bottom figure in the left graphic? Compare it to a "normal" tri peptide of glu-cys-gly (top graphic). Instead of the usual backbone, the carboxyl acid "side chain" is part of the backbone peptide structure. The normal carboxyl group is the so called side chain in this case. The function of glutathione is to protect cells from oxidizing agents which might otherwise damage them. The oxidizing agents react with the -SH group of cysteine of the glutathione instead of doing damage elsewhere. Many foreign chemicals get attached to glutathione, which is really acting as a detoxifying agent.