What is a peptide?
A peptide is a short-chain made up of amino acids that, together with other peptides, forms a protein.
The number of amino acids in a peptide can range from two amino acids to fifty amino acids.
Depending on the number of amino acids present in the peptide, the peptides are of many types; peptides with ten or fewer amino acids are called oligopeptides, and peptides with more than ten amino acids are called polypeptides.
Polypeptides with around 100 amino acids are considered proteins.
Peptide bond definition
- A peptide bond is a special type of amide bond formed between two molecules where one α-carboxyl group in one molecule reacts with the α-amino group in another molecule, releasing one molecule of water.
- The peptide bond is also known as the isopeptide bond where the amide bond is formed between the carboxyl group of one amino acid and the amino group of another amino acid at positions other than alpha.
- The peptide bond formation process is an example of a condensation reaction that results in dehydration (removal of water).
- Peptide bonds are covalent bonds that exist between any two amino acids that result in a peptide chain.
- There is a partial double bond between the carbon and the nitrogen in the amide bond that stabilizes the peptide bond.
- The nitrogen involved in the bond donates its solitary pair to the carbonyl group, which produces a resonance effect.
- The resonance is highly stabilizing since the electrons can be delocalized on multiple atoms resulting in a resonance structure.
- Therefore, the resonance structure stabilizes the bond but also limits rotation around the amide bond due to the partial double bond.
- Peptide bonds have a flat configuration that suffers very little movement around the C-N bond, but the other individual bonds on either side of the C-N bond exhibit a high degree of rotational motion.
Peptide bond formation mechanism
- The mechanism of peptide bond formation is a dehydration synthesis process.
- During the formation of a peptide bond, the carboxyl group of one amino acid moves to the amino group of another amino acid.
- Subsequently, a hydrogen atom and an oxygen atom of the carboxyl group (COOH) of the first amino acid are lost. In contrast, one hydrogen is lost from the amino group (NH2) of the other amino acid.
- This results in the release of a water molecule (H2O) along with the formation of an amide bond (C-N) between the two amino acids.
- The process of forming a peptide bond between two amino acids results in a dipeptide molecule.
- Therefore, a peptide bond is formed when the carboxyl group of one amino acid is condensed with the amino group of another amino acid that is released in a water molecule.
- The formation of peptide bonds is an endergonic reaction that requires energy, which is obtained from ATP in living beings.
- Because this reaction involves the removal of a molecule of water, it is called a dehydration synthesis reaction.
Peptide bond degradation mechanism
- The degradation of the peptide bond takes place through hydrolysis, therefore it requires the presence of water molecules.
- The degradation reaction is very slow since the amide bond between the amino acids is stabilized by the partial double bond.
- Due to the partial double bond between the carbon and nitrogen molecules, the carbon atom generates a slight positive charge.
- In the presence of water, the OH– ions in the water attack the carbon atom, resulting in the degradation of the peptide bond.
- The remaining hydrogen ion in the water attacks the nitrogen atom that results in the amino group.
- As a result of this, the peptide molecule is divided into two units; one unit with the carboxyl group and one with the amino group.
- Peptide degradation is an exergonic reaction that releases approximately 8-16 Kjol / mol of energy.
- Because protein degradation reactions are very slow, they are generally catalyzed by proteolytic enzymes such as proteases and peptidases.
Peptide bond hydrolysis
- Hydrolysis of the peptide bond is the main step in all protein hydrolysis reactions.
- The most common method of protein degradation is acid-catalyzed hydrolysis of the peptide bond.
- Peptide hydrolysis is also essential in some synthetic reactions in which amino acids in one peptide are cleaved and transferred to another peptide, resulting in separate peptide synthesis.
- Similarly, different peptides and proteins accumulate in cells resulting in toxicity. Hydrolysis of the peptide bond is also essential in the elimination of these toxins.
- The hydrolysis of the peptide bond is also an important step in protein digestion in living beings.
- The hydrolysis of the peptide bond occurs in the presence of water and is catalyzed by the presence of acid.
- Hydrolysis of the peptide bond is one of the degradation mechanisms of the peptide bond where polypeptides break down into smaller peptides or smaller peptides break down into separate amino acids.
Examples of Peptide Bond
The peptide bond is present in all the proteins that bind the amino acid in the chain.
Monopeptide: having one amino acid
Dipeptide: having two amino acids
Tripeptide: having three amino acids
Tetrapeptide: having four amino acids
Pentapeptide: having five amino acids
Hexapeptide: having six amino acids
Heptapeptide: having seven amino acids
Octapeptide: having eight amino acids
Formation of Peptide Bond
- At the molecular level, a peptide bond is formed through a dehydration reaction. As seen in the image below, two amino acids can bind when two hydrogens and oxygen are removed from the molecules. An amino acid presents a carboxyl group to the reaction and loses a hydroxyl group in the reaction (C binds to O in duplicate). The amino group of the other amino acid loses hydrogen. The nitrogen is then replaced in place of the hydroxyl group, forming a peptide bond. This is the reason why peptide bonds are also known as substituted amide bonds. The two amino acids are now known as residues since they have lost several atoms and are now covalently linked together.
- The carbon to nitrogen bond formed in a peptide bond is different from the carbon-nitrogen bonds in other parts of the molecule. Oxygen on the carboxyl side of the bond has a slightly negative charge. Nitrogen retains a slightly positive charge. This interaction causes carbon and nitrogen to share more electors than they normally would, and an electrical dipole is established. The additional electrons cause the bond to act as a double bond, which is rigid and cannot rotate. This 6-molecule unit is known as a peptide group and is often represented as a ball or plane. The carbons at the centers of each amino acid have 4 equal bonds and can rotate freely. Therefore, when many amino acids are linked, they form rigid plane chains of atoms around the peptide bond, connected by flexible carbon bonds. This allows a peptide chain to twist and bend, leading to advanced formations that can catalyze reactions.
- While scientists have figured out how to connect a chain of various amino acids, a typical protein has thousands of residues connected in series. Furthermore, the reaction favors the individual amino acids and requires a lot of activation energy. Therefore, creating proteins without enzymes is not easy. To do this efficiently, cells have developed an efficient mechanism to build new proteins. In the genome of each organism, there are codons that describe different amino acids. The genome carries the exact sequence of these amino acids, which together will produce a functional protein. First, the information must be copied into a messenger RNA (mRNA) molecule. Then the transfer RNAs (tRNAs) bind to specific amino acids. These tRNAs correspond to different codons of mRNA, which in turn correspond to different DNA codons. The actual peptide bond is formed in a special protein macrostructure known as a ribosome, shown below.
- The ribosome is a very large and complex cell structure consisting of proteins, RNA, and other components that help catalyze the formation of a peptide bond. This is known as the lengthening stage of protein synthesis. The ribosome helps to match the tRNA with the corresponding mRNA. In turn, the RNA changes slightly in shape, catalyzing the reaction between two amino acids and expelling a molecule of water. The chain that forms leaves the ribosome. The ribosome, being a large protein in itself, changes shape after the reaction has taken place and moves further down the mRNA chain, starting the process all over again. Finally, a codon is found that signals the end of the protein, allowing the ribosome to know that all of the protein has been created. At this point, the mRNA and the new protein will be expelled, and a new mRNA will be collected, creating a completely different protein
- All life is based on links between approximately 20 different amino acids, which all organisms use and modify for their own purpose. The number of different combinations is unlimited, while the peptide groups in the proteins form peptide backbones in all the proteins. The different groups attached to each amino acid cause the molecule to fold and fold into complicated structures, due to the weak interactions between the molecules of the different groups. Therefore, across the many millions of proteins created by different species, there are several very similar structures that correspond to similar amino acid sequences. Because amino acids are connected in a series with a similar direction, scientists generally draw and identify proteins from the amino or nitrogen side, and pass through the carboxyl terminus as an endpoint.