is created by David Witten, a mathematics and computer science student at Vanderbilt University. For more information, see the "About" page.


What are proteins?

Proteins are polymers made up of amino acid monomers. Proteins perform most of the body's tasks, including moving muscles, transporting oxygen, and supporting hair. Enzymes, such as lactase (see the Carbohydrates post), are also considered proteins, and they affect the rate of a chemical reaction. 

Types of Proteins

There are four types of proteins:

Structural Protein

These proteins provide support, such as the proteins in hair and nails (called keratin). Although it doesn't make your hair move, it provides structural support.

Storage Protein

Storage proteins provide a source of amino acids for developing plants and animals. They can be found in seeds or eggs.

Contractile Protein

Contractile proteins are found in muscles, and their function is straightforward: they cause muscles to contract, causing movement.

Transport Protein

These proteins include hemoglobin, and transport proteins move things around in the body or in organs.

Monomer: Amino Acid

An amino acid consists of a central carbon atom linked to a hydrogen, an amino group (NH3), a carboxyl group (COOH), and a side group. 

There are twenty main amino acids, and the only thing that varies is the R group, which affects the amino acid A LOT. For example, the R group in Leucine makes it hydrophobic, whereas the R group in Serine is hydrophilic. 

Proteins as Polymers

Amino acids are linked by dehydration synthesis, just like carbohydrates. The resulting bond is called a peptide bond. So, there's a bond between the carbon in the 1st amino acid's carboxyl group and the nitrogen in the amino group in the 2nd amino acid. Proteins consist of over 100 amino acids, which creates a chain called a polypeptide chain. 

There are tens of thousands of proteins in our bodies while there are only twenty different amino acids. What this means is that the order of amino acids makes a big difference in the function of the protein. For example, in patients with Sickle-Cell Anemia, the amino acid in the 6th position is changed from Glutamic acid to Valine, and it causes their red blood cells to have a sickle shape.

Protein Shape

Polypeptide chains are not the same as proteins. The distinction is analogous to a strand of yarn to a wool sweater. The structure is very important. There are three (or four) layers of structure in a protein, they are primary, secondary, tertiary, and quaternary.

Primary Structure

A protein's primary structure is its sequence of amino acids (e.g. Val-Asp-Glu-Met).

Secondary Structure

A protein's secondary structure is the geometric structure of a specific stretch of the polypeptide chain (e.g. 10 amino acids in a 100-amino-acid polypeptide). There are two possible types of secondary structures:

Alpha Helix

This is shaped like a coil.

Pleated Sheet

This is shaped like an accordion paper fold.

Tertiary Structure

This is the overall geometric shape of a polypeptide. While the secondary structure only refers to a small section of the polypeptide, the tertiary structure refers to the entire polypeptide.

Quaternary Structure

This is only applicable to proteins with multiple polypeptide chains, and it refers to the arrangement of the polypeptide chains in the protein. This is the most complex structure, as it refers to the structure of the protein as a whole. 

What determines protein structure?

A protein's shape is sensitive to the surrounding environment. For example, an unfavorable change in pH, temperature, or another environmental quality may cause a protein to unravel and lose its normal shape. This is called denaturation. If you cook an egg, the transformation of the egg white from clear to white is caused by proteins in the egg white denaturing. They become insoluble in water and form a white solid. That's one of the reasons why extremely high fevers are dangerous- proteins may denature at 104*F. 

Given a suitable environment, the primary structure of a protein causes it to fold into its functional shape. Every sequence of amino acids has a specific primary structure. Every polypeptide chain has a sequence specified by an inherited gene. 

David Witten

Nucleic Acids