Protein Structure

What are Proteins Made Of?

All proteins are made up of alpha amino acids. A picture of an amino acid is shown below.

In this picture you have a carbon with an R group on it bonded to an amid and a caboxyl on each side. There are different R groups on the 20 common amino acids that are incorporated into proteins. These groups include some straight chains, aromatic groups, acids, and bases. Some of these groups bind quite well to water, these are the hydrophilic groups. Others do not bind at all to water, these are called hydrophobic groups. The stereochemistry of amino acids are important. All amino acids can exist in D and L forms. Amino acids incorporated into protein structures are of the L form.

How do These Amino Acids Bind Together?

Amino acids link together between the amide and carboxyl groups. Two amino acids bind together and eliminate water resulting in a peptide link. What is left is referred to as an amino acid residue. If this chain becomes very long, it is then called a polypeptide. All proteins are polypeptides of a defined sequence of amino acids.

Structures a Protein can Take

There are four different structures a protein can have. The first structure is primary structure. This is just a chain of amino acids linked together. Secondary structure results from hydrogen binding between the amide and the carboxyl of groups that are not very far apart on the backbone of the protein. This can make structures such as alpha helicies, beta sheets, and beta turns. Then there is tertiary structure. This is largely due to packing of the elements of secondary structure against one another. Here hydrophobic groups tend to stay close together. This is also true for hydrophilic groups. Usually hydrophobic groups pack closely in the center of the protein while the hydrophilic groups surround this hydrophobic center. This is because proteins are usually found in water. Finally, there is quaternary structure. This is where folded polypeptide chains interact with each other. All of the structures except primary structure depend on intermolecular forces.

Why is This so Important?

Not only the chemical structure is important, but its physical structure is just as important when you are determining the activity of the protein. This means that when you precipitate a protein, you can not do anything to change the physical structure. Examples of how a protein gets damaged or denatured are the addition of too much salt, or the pH of the solution becomes extremely acidic. Proteins are sensitive at low pH. This makes them more sensitive to anions in an acid or a salt in the solution.

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