A Quick Guide on Writing of The Peptide Bond Structure

Some different nutrients and molecules contribute to the health of a living organism. As a macromolecular class, proteins are essential for several biological reactions inside the body. Every organism has one or multiple protein types that all perform different functions. 

Whether they help build a part of the overall molecular structure of different parts like keratin in hair or work as a catalyst in biochemical processes, proteins are important. One thing that maintains the structure of protein is the amino acid linkages or peptide bonds. So, it is important to know about peptide bonds properly first. 

What is the Peptide Bond?

In the structure of a protein, carboxylic and amino acid functional groups within amino acid molecules combine to create amine bonds. This is what forms the peptide bond. In most sequences, the amino acid component with a free amine group is added to the peptide chain’s N-terminus, present at the left end. 

On the other hand, the amino acid with a free carboxylic acid is written on the C-terminus on the ride side. The free carboxylic acid and amino acid functions within the peptide chain get a zwitterionic structure at the isoelectric pH level. 

The peptide bond plays a major role in proteins performing their main functions in living organisms. For example, proteins are important for proper energy usage and muscle contraction. Additionally, Peptide bond formation enzymes are also noticeable in the stomach, and they are biological catalysts that improve digestion.

Writing Protein and Peptide Sequences

Writing the primary peptide structure or sequence starts with putting the amino terminus on the left-hand side. From there, the sequence goes right to the carboxy terminus. Sometimes the full sequence cannot fit into one line. Then, it is possible to go to the second line, as long as the left-to-right sequence is still maintained for the amino-to-carboxyl terminus. 

Additionally, it is possible to write the amino acid structure of protein in a one-letter code or three-letter code. For different applications, the sequence formatting can change. Generally, the single-letter codes are written in capitalized format. 

Here are some of the amino acid codes. 

Structures Common in Protein 

When discussing the structure of protein, it is important to mention that there are four levels available. 

Primary Level 

The primary type of protein structure involves amino acid residues within the polypeptide chain. They are written from the N- to C- terminus in a left-to-right sequence. 

Secondary Level 

These ordered structures occur within the internal hydrogen bonding that exists between two amino acid residues. Generally, this involves the β-strand, the α-helix, turns, and loops. Examples include α-helices, β-sheets, and subsets like Parallel β-sheets and anti- Parallel β-sheets. 

Tertiary Level 

This three-dimensional conformation creates independently folded, and distinct regions called domains. 

Quaternary Level 

The quaternary structure of protein relates to complex proteins that hold more than a single polypeptide chain. Each polypeptide is known as a subunit. 

Formation of Peptide Bond 

The main reaction that causes peptide bonds is dehydration synthesis or condensation in the molecular sense. First, one oxygen atom and two hydrogen atoms are removed from the amino acids. Then, one amino acid enters a carboxyl group within the reaction. 

After that, that causes the loss of the hydroxyl group, i.e., the C-O double bond. The hydrogen in another amine group within an amino acid gets removed. After that, the nitrogen atom takes the hydroxyl group’s vacant place. That creates the peptide bond. 

Since all of the atoms in the amino acids are not in place, they are called residues. The atoms get covalently bonded. 

Notably, the C-N bond in the structure of a protein is not the same as the C-N bonds within the molecule. The oxygen atom in the carboxyl group of the amino acid within the bond has a negative charge, while the nitrogen holds a positive change. After that, the nitrogen and carbon share extra electrons, which results in an electric dipole. With the excess electrons, the bond works as a double bond. This makes it rigid and stops rotation. 

A unit with 6 molecules forms a peptide group and appears in a flat plane or ball. Typically, there are 4 equal bonds in the core of every amino acid, which rotates without blockage. So, many of the connected amino acids become atom chains in a rigid plan around the formed peptide bond, linked with flexible carbon bonds. 

Thus, the structure of protein or peptide chains can bend and rotate freely. This results in advanced formations that work as catalysts in natural biological reactions. 

Conclusion 

The structure of protein or peptide bonds involves different amino acid molecules joined together. Therefore, there are different visible types of structures, keeping with the number of polypeptides and sequence of the amino acid residues. 

It is possible to write the sequences or structure in an N terminus to C terminus direction, putting the right codes for the amino acid sequence. It is important to know the main formation and sequence to understand how peptide bonds in proteins affect their stability and nature.