Protein Structure
Home Up Peptides Primary Structure Secondary Structure Tertiary Structure Quaternary Structure Protein Structure


Protein Structure

So you can see that proteins have structure at several different levels.

The primary structure of a protein consists of the order in which amino acids are bonded to one another by peptide bonds.

The secondary structure of a protein involves the way that that chain of amino acids either twists or folds back upon itself to form either alpha helical, beta sheet or a variety of other possible arrangements.

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That secondary structure in turn folds back and twists and bonds to itself in a three-dimensional manner, it is referred to as the tertiary structure.

And, if a protein consists of more than one chain, the shape in which those separate chains bond together is referred to as the quaternary structure.

The combined shape of the secondary and tertiary structure and the quaternary structure, if there is one, is referred to as the conformation of the protein.

Structure and Function

The proper functioning of a protein requires that certain functional groups be in certain locations which requires the proper conformation for that particular protein, which in turn depends on perhaps the quaternary but certainly the tertiary and secondary structure of the protein being the way it should be which in turn depends on the side groups of particular amino acids being in a certain location with respect to one another which is the amino acid sequence that we call the primary structure and that primary structure is determined genetically by a method that we will discuss when we talk about nucleic acids.

Because the proper conformation of a protein is dependent on the secondary and tertiary structure which in turn is dependent on the van der Waals, hydrogen, ionic and covalent bonds, it's possible to view the protein as being essentially folded in place and then pinned together with van der Waals, hydrogen, ionic and covalent bonding, primarily the first three.

Denaturing a Protein

It's possible to change the shape and alter the conformation of a protein by changing the environment of the protein. By putting it in an environment which will change the ability of the van der Waals, hydrogen, ionic and covalent bonds to hold that molecule together in its particular conformation, it's possible to cause the molecule to unfold by breaking those bonds. That can be done by changing the pH, or heating it. A variety of other methods can also be used.

When a protein is caused to be unfolded in this way, it is referred to a having been denatured. The denaturation process can be irreversible but it can also be reversed if the change in conditions are not drastic and they are returned to the proper conditions (pH, temperature, et cetera) gradually. Remember that the primary structure, the sequence of amino acids, is what dictates that a certain secondary, tertiary and so forth structure will occur. Given the time and the proper conditions, a protein which has retained its primary structure can regenerate its secondary and tertiary structure, and thus its conformation and become a viable working protein again.

Prosthetic Groups

In addition to all of the amino acids which are bonded together, some proteins will have additional molecular units attached to them. These are generally called prosthetic groups and they are usually quite important in carrying out the function of the particular protein.

Fibrous and Globular Proteins

In general, we can use the conformation of a protein to classify it into one of two very broad categories. One of those is fibrous, the other is globular. The fibrous proteins are generally long and insoluble in water. The globular proteins are tightly folded and most of them are soluble in water. Some proteins combine the properties of both fibrous and globular within the same protein.

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