Elementary Idea of Polypeptides

Amino acids are connected by peptide bonds, which are covalent bonds that form between the amino acids. Many of these amino acids can be linked together in a straight line. A polypeptide is a long chain of amino acids. Two to three thousand amino acids make up a polypeptide in nature, small or large. It is the polypeptide chain that forms the fundamental structure, composed of a series of amino acids. It may be made up of one or more polypeptides.

Before we start with the polypeptide group, let’s get familiar with the basic terms used in the concept of polypeptide protein.

Amino Acids

Except that covalent bonds link them, polypeptides have the same structure as amino acid groups. The polypeptide group chain is built up of amino acids. There are twenty different amino acids, each having a unique structure. Building a protein is much easier if you know how amino acids will interact with one another and how they will link to one another.

Carboxyl Groups

There are carboxyl groups in every amino acid since they are composed of amino acids and a carboxyl group. A carboxyl group comprises a hydroxyl (OH) attached to a carbon and an oxygen double-bonded. It allows the covalent connection between the two atoms by forming the negative group. An amino group is joined to this group, resulting in new amino acids.

In transforming into proteins, polypeptides expand in complexity and variety. On the polypeptide’s one free end, the carboxyl group is known as the C-terminal. N-terminal, or amino-terminal, refers to the end of the peptide chain.

Anatomy of a Polypeptide

A biopolymer is a polymer made by an organism. Polysaccharides, polypeptides, polynucleotides, and fatty acids are the four major classes of biopolymers. Peptide bonds bind the amino acids in a polypeptide chain, forming a long, straight chain. 

Each amino acid’s carboxyl group is linked to the amine group of the following amino acid by a peptide bond, creating an amide. It is possible to name short polypeptides by the number of monomeric amino acids that make up their structure. Dipeptides have two amino acid subunits. Tripeptides have three, and tetrapeptides have four, making them all types of peptides found naturally.

Polypeptide Formation

The R-group side chain variation changes the amino acid molecule’s chemistry. Non-polar side chains are common in amino acids (do not have positive and negative poles). Some have charged side chains. Others have uncharged polar side chains. The side-chain chemistry influences how amino acids link together to make polypeptide protein.

Amino acids with charged side chains can form ionic bonds. They can form van der Waals interactions if they are hydrophobic. Polar amino acids form hydrogen bonds. These interactions govern how a protein folds together and where it folds. 

Note: Polypeptide proteins are classified into four structural levels: primary, secondary, tertiary, and quaternary.

Primary Structure

Primary structure, the most fundamental level of protein structure, is just the sequence of amino acids in a polypeptide chain. For example, the hormone insulin is composed of two polypeptide chains, Each chain contains its own set of amino acids assembled in a certain order. For example, the A chain sequence begins with glycine at the N-terminus and finishes with asparagine at the C-terminus, whereas the sequence of the B chain is the opposite of this.

Secondary Structure

The DNA of the gene that produces a protein is responsible for determining the sequence of a protein molecule (or encodes a portion of the protein for multi-subunit proteins). An alteration in the DNA sequence of a gene may result in an alteration in the amino acid sequence of the resulting protein. It is possible to alter the structure and function by altering the amino acid sequence by just one residue.

Local folded structures that arise inside a polypeptide due to interactions between atoms in the backbone are called secondary structures at the next structural level. (Since the backbone refers to the polypeptide chain itself, rather than the R groups, all we are saying is that secondary structure does not require R group atoms in this context.) The helix and the pleated sheet are two of the most prevalent forms of secondary structures. Hybrid bonds between the carbonyl O of one amino acid and the amino H of another hold the two structures together and keep them in shape.

α Helix

In α helix, one amino acid’s carbonyl (C=O) is hydrogen linked to an amino acid’s amino H (N-H). For example, make a hydrogen bond with the N-H of amino acid 5. To make a spiral ribbon-like structure out of the polypeptide chain, this bonding arrangement pulls it in three directions. They can interact because the R groups of amino acids stick out from the helix.

β Pleated Sheet

Each segment of a polypeptide chain aligns with another, generating a sheet-like structure bound together by hydrogen bonds. R groups extend above and below the plane of the sheet 33 cubed, forming hydrogen bonds between the carbonyl and amino backbone groups. If the N- and C-termini of the strands are aligned, the strands are parallel (meaning that the N-terminus of one strand is positioned next to the C-terminus of the other).

Tertiary Structure

The tertiary structure of a polypeptide is its overall three-dimensional structure. R groups of amino acids interact to form the protein’s tertiary structure.

There are a lot of non-covalent bonds that contribute to tertiary structure. Like-charged R groups repel each other, but opposite-charged R groups can form ionic bonds. Polar R groups can also generate hydrogen bonds and dipole-dipole interactions. To interact with water molecules, hydrophobic interactions are critical in tertiary structure.

Last but not least, a disulfide bond can contribute to tertiary structure. Other types of tertiary structure bonds, such as disulfide bonds, are weaker. In a sense, they operate as molecular “safety pins”, holding the polypeptide together.

Quaternary Structure

In many cases, a protein is composed of a single polypeptide chain and has just three levels of structure (the ones we’ve just examined). A few proteins, known as subunits, are composed of numerous polypeptide chains, which are themselves composed of polypeptide chains. This protein’s quaternary structure is formed due to the interaction of these subunits.

Conclusion

Peptides are amino acid molecules. An amino acid peptide bond links two amino acids together (in this case, two amino acids). An amino group combines with a carboxylic group on one molecule, connecting the two and releasing water.

To construct long-chain polypeptides, peptide bonds join numerous amino acids. To break an amide bond, you need to add a water molecule (amide hydrolysis). Biochemically, protein-peptide linkages are metastable, meaning they will spontaneously break. Enzymes that can build and break peptide bonds are found in all living creatures.