Amino Acids & Polypeptide Chains — Structure & Synthesis

Polypeptides

Proteins are complex polymers that contain carbon, hydrogen, nitrogen, and oxygen. They are very large macromolecules made of amino acid monomers.

Amino acids are molecules with a carboxyl group (-$COOH$) and an amino group (-$NH_{2}$). The R group, or side chain, attached to the carbon atom is the identifier that lets us tell the difference between amino acids. Some R groups are polar, some are non-polar, some are huge ring structures, and others are tiny. There are more than 20 possible R groups and therefore there are more than 20 types of amino acids.

These amino acids are joined together by peptide bonds to form polypeptides. A peptide bond is a covalent bond between the amino group of one amino acid and the carboxyl group of a different amino acid. The formation of this bond releases a molecule of water.

Because peptide bonds only occur between the carboxyl and amino groups of amino acids, the R group does not influence the bond formation. This means that any amino acid can form a peptide bond with any other amino acid. The arrangement of amino acids in a polypeptide is dictated by DNA.

To really understand proteins, we need to look at the four levels of protein structure.

• A protein's primary structure is its sequence of amino acids.

• The secondary structure is the shape (coiling and bending) of the peptide chain.

• The tertiary structure is the 3D structure of the polypeptide chain.

• If a protein has multiple polypeptide chains, the way they are arranged with respect to each other is the quaternary structure.

Proteins are important in muscle contraction, transporting oxygen in the blood, and the immune system. Some proteins even regulate cell processes while others control the rate of reaction.

$$\color{#8925AE}{\text{Vocabulary Review:}}$$

$\color{#8925AE}{\text{Translation}}$ : The cell uses the information from RNA to make proteins

$\color{#8925AE}{\text{mRNA}}$ : Messenger RNA. mRNA nucleobases act as instructions for the cell to build polypeptides

$\color{#8925AE}{\text{tRNA}}$ : Transfer RNA. Carries a specific amino acid to the ribosomes to help build proteins

$\color{#8925AE}{\text{Codon}}$ : A group of three nucleobases that code for a specific amino acid

Amino Acids and Polypeptide Chains

Proteins are one of the essential macromolecules for life. To understand how they work in the bigger picture in the functioning of life, it's important to first understand what exactly a protein is and what it's made of.

Proteins can be broken down into smaller components called amino acids. In total there are 20 amino acids which are used in the vast majority of cases. Each amino acid shares a couple common characteristics:

• Each amino acid has an amine group with the chemical formula -$NH_{2}$.

• Each amino acid also has a carboxyl group with the chemical formula -$COOH$.

• Each amino acid also has a third component called the R group (also called a side chain). The R group is what differentiates one amino acid from another. Each R group gives the amino acid a specific quality which, when put into the structure of the overall protein, will help the protein function. Below is a diagram of the wide variety of R groups within amino acids:

Amino acids are joined together through a special type of chemical bond called a peptide bond. The carboxyl group of some amino acids will bond to the amine group of the next amino acid. This reaction requires a ribosome, and in this process a water molecule is created. Below is a good visual of what this reaction looks like:

A polypeptide chain is a term used when several amino acids are joined together by peptide bonds. A polypeptide chain is a long, continuous, and unbranched series of linked amino acids. A polypeptide chain is the basic structure of proteins. After a polypeptide chain is formed by the aid of ribosomes, the different R groups begin to interact with one another to form more and more complex structures. Different polypeptide chains can even come together to form a more functional protein overall. After a translation, polypeptide chains can be modified to make a final protein product in the rough ER and Golgi apparatus.

Below is an example of the four basic structures of protein using hemoglobin as an example. Hemoglobin is a protein in the blood which is used to carry oxygen to all the cells within the body.

(Video) Biochemistry: Polypeptides (Proteins)

by Mr Pollock

This video describes the structure of amino acids. It also shows how amino acids bond together to make polypeptide chains. These chains are folded and modified to make complete, functional proteins.