Difference Between Polypeptide and Protein (With Table)

Organic compounds that comprise amine and carboxyl functional groups are called amino acids. Every amino acid has a specific side chain associated with it which makes it unique. The primary elements of any amino acid include carbon, oxygen, hydrogen, and nitrogen along with the elements found in the side chain of the particular amino acid.  

Polypeptides and proteins are two of the main Polymers of amino acids. Both polypeptides, as well as proteins, are present in biological systems. When several amino acids are linked together with the help of peptide bonds (Covalent bond created by condensation of two amino acids leaving out a water molecule), polymerization occurs to form polypeptides as well as proteins. 

Polypeptide vs Protein

The main difference between polypeptide and protein is that polypeptide comes into the picture from long amino acid chains. Proteins are formed from two or more polypeptide chains. Hence, it is easy to notice that polypeptides have a lower molecular weight as compared to proteins.

Comparison Table Between Polypeptide and Protein

Parameter of Comparison



Fundamental definition

A polypeptide is formed from several amino acids joined together with the help of peptide bonds to form a long unbranched chain.

A protein is a structure that is made when several polypeptides or a large number of amino acids.

Molecular weight

Polypeptides have a molecular weight lower than Proteins.

The molecular weight of a protein is higher than the polypeptide.

Structure Significance

It signifies the primary structure of the protein.

It can exist as secondary, tertiary, as well as quaternary structures.

Included Bonds

It contains peptide bonds.

Proteins are composed of peptide bonds, ionic bonds, disulfide bonds, and Van Der Waal attraction as well.


It acts as a building block for proteins.

Proteins participate in several important metabolic reactions due to the stable shape that makes them suitable for specific binding to a particular ligand.

What is Polypeptide?

Polypeptides are formed when peptide bonds are formed in order to form long chains of amino acids. A peptide bond is formed when two amino acids react together to condense one water molecule(H2O). Short and branched chains of amino acids are called peptides. These usually contain 20 to 30 amino acids. When the number of amino acids in the chain increases more than this, polypeptides are formed. Every polypeptide has a specific sequence of amino acids associated with it.

Polypeptides can contain up to 4000 amino acids in that chain. These are characterized by a polypeptide backbone which is formed by the continuous reputation of the sequence of atoms at the core of the chain. A specific side chain is included in the polypeptide backbone corresponding to the selected amino acids. The main function of the polypeptide is that they act as the building block for the formation of proteins. Hence, they are also referred to as the primary structure of the protein.

What is Protein?

Proteins have various functions in biological terms. These are functionally as well as structurally complex molecules created by a large number of amino acids coming together. Amino acids bind to form polypeptide chains which then combine themselves to form a protein.

The functions of proteins are mostly due to their structure and shape which makes them suitable to interact physically with various molecules. The involved interactions are highly selective and specific. Proteins bind with their ligand binding sites to very specific molecules associated with them called ligands. The binding site for the ligand is a particularly shaped cavity on the surface of protein which is formed due to the folding of various polypeptide chains. Every such cavity has a different ligand to interact with. Alteration in one amino acid can totally change its shape and can lead to disruptions in the function of that protein.

Proteins can be found with 4 different levels of structural organization:

  1. Primary structure: A simple long polypeptide chain is the primary structure of the protein.
  2. Secondary structure: it is also called the alpha helix structure and is spiral and well ordered in nature. Sometimes these are also found in the form of anti-parallel beta-pleated sheets.
  3. Tertiary structure: These are formed from reactions of polypeptide chains through disulfide bonds, Van Der Waal bonds, hydrogen bonds, and ionic bonds.
  4. Quaternary structure: It is composed of several polypeptides.

Main Differences Between Polypeptide and Protein

  • The fundamental difference between polypeptide and protein is that the polypeptide is formed from Sagar amino acids coming together through peptide bonds whereas a protein structure is made when many polypeptide chains come together.
  • Polypeptides have a molecular weight that is much lower than that of proteins. When polypeptides containing more than a hundred amino acids found, they are considered as proteins with a molecular mass of more than 10,000.
  • The structure of a polypeptide is basically an unbranched long chain of amino acids. On the other hand, proteins exist in secondary, tertiary, as well as quaternary structural organization.
  • The bond included in polypeptide chains is peptide bond whereas proteins are composed of various types of bonds like ionic bonds, disulfide bonds, peptide bonds, and Van Der Waal attractions.
  • The basic functionality of a polypeptide is that it acts as the building block for protein whereas proteins’ functionalities are very complex due to their stable shape and structure. Cavities found on the surface of the proteins due to the folding of polypeptide chains makes them suitable for various specific reactions with a specific ligand.


Polypeptides and proteins both are organic polymers with amino acids as their monomers. Both of them are naturally occurring organic compounds that are essential for a cell. The main difference between the both is that a polypeptide has a lower molecular weight as compared to that of a protein.


  1. https://patents.google.com/patent/US6194551B1/en
  2. https://www.sciencedirect.com/science/article/pii/096800049290005T