Polypeptide Chain: Definition, Structure & Synthesis

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Jennifer Gilley
Expert Contributor
Elaine Chan

Dr. Chan has taught computer and college level physics, chemistry, and math for over eight years. Dr. Chan has a Ph.D. in Chemistry from U. C. Berkeley, an M.S. Physics plus 19 graduate Applied Math credits from UW, and an A.B. with honors from U.C .Berkeley in Physics.

A polypeptide chain is comprised of amino acids that are linked together to form the building blocks of proteins. Learn the definition of a polypeptide chain, study amino acid structure, and explore the synthesis of polypeptide chains. Updated: 10/11/2021

What Are Proteins?

Your cells use various types of molecules in order to perform their daily functions. One of the most important classes of molecules are called proteins. Proteins are molecules that have several different functions within the cell. Such functions include transporting things in and out of the cell, speeding up chemical reactions, and helping cells recognize and join to one another. Therefore, proteins are really versatile molecules that can be used for multiple purposes. Just like a Swiss army knife has multiple tools that can be used in different ways, proteins have different structures that specify their particular function.

Proteins consist of one or more polypeptide chains. Each polypeptide chain consists of smaller sub-units or amino acids that are linked together. Amino acids serve as the building blocks of polypeptides, and polypeptides serve as the building blocks of proteins. Think of an individual amino acid as a paper clip. When you link several paper clips together, you make a paper clip chain. Joining dozens of amino acids together makes a polypeptide chain. A polypeptide chain can serve as a protein on its own. However, lots of proteins are made up of several polypeptide chains.

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  • 0:00 What Are Proteins?
  • 1:19 Amino Acid Structure
  • 2:25 Making a Polypeptide Chain
  • 3:36 Lesson Summary
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Amino Acid Structure

There are 20 naturally-occurring amino acids, and each one is a little different. All amino acids have the same basic structure; however, something called an R group distinguishes one amino acid from another. Here, you can see the chemical structures of all 20 amino acids.

Although the black parts of each amino acid are the same, the R groups (shown in brown) are all different from one another. The differences in these R groups are what help give a polypeptide chain its structure and, ultimately, its function.

The order and arrangement of these amino acids in a polypeptide chain will produce different chemical structures. A protein's structure is essential to its function. So, multiple amino acids can be strung together to make a particular polypeptide chain with a specified function. Similarly, letters of the alphabet can be rearranged to make different words, each with its own meaning. This image is a simple representation of a polypeptide chain made of several different amino acids. Each pattern represents a different amino acid.

Making a Polypeptide Chain

You know now that a polypeptide chain consists of a bunch of different amino acids linked together. But, how are these amino acids linked together? Actually, the process called dehydration synthesis is not that difficult to understand.

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Additional Activities


Given an unknown polypeptide, you might want to find out its sequence using chemical reactions to break the molecule into smaller pieces. The N-terminal residue (the first amino acid in the sequence) can react with phenylisothiocyanate to form a compound that can be analyzed to determine what that residue was. The rest of the original sequence is usually left intact. The process can be repeated many times to get the identity of the next amino acid. This is called the Edman degradation.

Certain chemicals react with specific amino acids of the chain. Trypsin (Tryp) breaks the peptide bonds on the carboxyl side of lysine and arginine. Chymotrypsin breaks the peptide bonds on the carboxyl side of phenylalanine, tyrosine, and tryptophan. Cyanogen bromide (CNBr) cleaves the peptide bond on the carboxyl side of methionine.

Question 1:

A peptide was broken into two smaller peptides by CNBr and into two different peptides by Tryp. The sequences are as follows:

CNBr 1: Gly-Thr-Lys-Ala-Glu

CNBr 2: Ser-Met

Trp 1: Ser-Met-Gly-The-Lys

Trp2: Ala-Glu

What was the sequence of the parent polypeptide?

Answer 1:

By arranging the four sequences in an overlapping set, we can read off the parent. The dots in the sequences below are only intended to provide spacing, so as to line things up.

CNBr2: Ser-Met

Trp 1: .. Ser-Met-Gly-Thr-Lys

CNBr 1: ............. Gly-Thr-Lys-Ala-Glu

Trp2: ...................................... Ala-Glu

Parent: Ser-Met-Gly-Thr-Lys-Ala-Glu

Question 2:

What peptides would be released by trypsin treatment of the peptide?


Answer 2:

Trypsin breaks the bond at the carboxyl side of lysine and arginine residues. It will produce Ala-Ser-Thr-Lys and Gly-Arg and Ser-Gly

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