Primary Structure

Protein Structure Tutorials

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Primary Structure

Protein Structure Tutorials

Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure

Proteins are Important to All Life

Take a deep breath. When you take air into your lungs the oxygen binds to a protein called hemoglobin, which carries the normally reactive oxygen safely through the blood and on to all 100 trillion cells in your body.

Take a bite of an apple. When you eat sugars, your body senses the hightened glucose levels in your blood and releases a protein called Insulin, which helps cells absorb the sugar from the blood.

Visit Friday Harbour in the Pacific northwest on a warm summer evening, and experience the green shimmer in the water as jellyfish rise to the surface. The green color is generated by the Green Fluorescent Protein(GFP) produced by the jellyfish

Proteins Have Complex 3-dimensional Shapes

Click on the images to display the 3-dimensional shape of the three common proteins proteins that were introduced above. Note that the display is fully interactive and can be rotated by clicking and dragging with your mouse!

Hemoglobin Proteins safely carry oxygen in the blood.

Insulin Proteins help regulate sugar in the bloodstream.

Green Fluorescent Proteins create bioluminescence in animals like jellyfish.

Proteins are incredibly complex molecules. They come in an almost endless array of shapes and types, acting like molecular machines that perform countless microscopic tasks. Because of their complex and variable structures, scientists break down their overall shapes using four layers of "protein structure":

Primary Structure: Amino Acids are the Building Blocks of Proteins

All proteins are composed of small subunits called amino acids that are joined together like links in a chain to make large complex protein structures. There are twenty different types of amino acids that can be linked together in various orders and frequencies. Every type of protein is made of a different and unique sequence of amino acids.

Protein Chain

The Molecular Shape of Amino Acids

There are twenty different types of amino acids used to make proteins. The chemical structure of each of the twenty types of amino acids are identical in some ways, but unique in others.

  • Identical Backbone - the backbone region of each of the twenty different amino acids is identical. The backbone is composed of an amino group, a central alpha carbon and a carboxylic acid group.
  • Unique R-Group - attached to this backbone is a group called the R-group, or the sidechain. The chemical composition of this R-group is different for each of the twenty amino acids and gives each different type of amino acid its unique attributes. The twenty different R-groups are discussed in more detail in the next section.

Shown below is the chemical structure of a single amino acid (left), a physical model of a single amino acid (right) and an interactive 3-dimensional structure of a single amino acid (far right). Use the buttons below to highlight the different parts of a single amino acid.

A Closer Look at the R-Group or Sidechain

Let's take a closer look at the part of the 20 different amino acids that makes them each unique - the R-group, also called the Sidechain. The R-group is considered the functional group of each amino acid, meaning that it gives each amino acid its unique attributes.

The 20 amino acids are often sorted into five catagories based on the unique attributes the R-groups create:

Hydrophobic - water-hating amino acids with a lot of hydrophobic carbon atoms in their R-group.
Hydrophillic - water-loving amino acids with a lot of hydrophillic oxygen and nitrogen atoms in their R-group.
Positively Charged - water-loving amino acids that have a net positive charge (+) due to an abundance of nitrogen atoms in their R-group.
Negatively Charged - water-loving amino acids that have a net negetive charge (-) due to an abundance of oxygen atoms in their R-group.
Cysteine - a unique amino acids that have can form strong bonds called disulfide bonds with other cysteine amino acids.

Click on the table below to explore the shapes of all twenty amino acids and their R-groups. Click Here to download a chart summarizing all 20 amino acids and their R-group shapes.

Alanine Arginine Asparagine Aspartic Acid Cysteine
Glutamine Glutamic Acid Glycine Histidine Isoleucine
Leucine Lysine Methionine Phenylalanine Proline
Serine Threonine Tryptophan Tyrosine Valine

Creating a Protein Chain

Amino acids are chemically linked together to make long amino acid chains through a condensation reaction (sometimes called dehydration synthesis). This chemical reaction will form a bond linking two amino acids together. This type of bond between two amino acids is called a peptide bond.

This reaction also creates a molecule of water as a byproduct. One oxygen atom and one hydrogen atom come from the carboxylic acid group of the first amino acid and join with another hydrogen atom from the amino group of the second amino acid.

Click Here to display a dipeptide connected by a peptide bond (show in yellow) in the interactive display to the right.


A chain of many amino acids linked together by peptide bonds is called a polypeptide. The specific sequence of amino acids in a polypeptide is known as the protein's primary structure. The twenty types of amino acids can be joined together in any order or frequency, allowing for an astronomical variety of potential primary structures.

Each type of protein in our body has a unique primary structure. This specific order of amino acids determines the protein's final 3-dimensional shape and function.

Move on to Secondary Structure