The Basics of Protein Structure Part 1: The Levels of Structure

In a previous post, we had explored the characteristics of the 20 amino acids that make up proteins.  These amino acids make up a diverse collection of molecules that can be strung together, making up proteins that have a multitude of functions within the cell.

Amino acids form a protein through the action of the ribosome, which we will discuss in a future post.  At this time, suffice it to say that the ribosome uses an elegant mechanism to read mRNA and translate it into the protein encoded by the mRNA by adding amino acids in a string.  As this string of amino acids is created, it begins to form a structure that will have functions within the cell.

Four levels of protein structure exist:

Primary (1^o) structure:  The order of the amino acids is the primary structure.  Think of the primary structure as the alphabet of the amino acids: MGRYNVPL, for example.  The primary structure describes what order amino acids are in, and even though it might not seem like very much information, even the primary structure of a protein can provide a great deal of information in terms of its function and its potential 3-dimensional shape.

Secondary (2^o) structure:  When amino acids are polymerized, they form local structures, which make up the secondary structure.  Think of secondary structure as the shape of a group of amino acids.  Two primary forms of secondary structure exist:  alpha helices and beta sheets.  Alpha helices result from the coiling of the amino acid string turning about itself.  In contrast, beta sheets are flatter and lack coiling.  There are several types of alpha helices and beta sheets, which we will save for a future post, and these different types of structures have important implications for overall shape of a protein.

Tertiary (3^o) structure:  Protein structure gets exciting when you talk about tertiary structure, which can be described as the overall three-dimensional shape of a protein.  In general, the tertiary structure is the “final” form of a protein, although modifications on the protein, as well as interactions with other proteins can affect this structure.

Quaternary (4^o) structure:  When proteins interact with each other, they can form complexes, which is the quaternary structure of these proteins.  You can think of this structure as the way proteins contact each other.  The bundling of proteins together can be between proteins of the same type (such as is the case with hemoglobin) or other types of proteins.

The drawing attempts to illustrate the concept of the different levels of protein structure.  Again, think of the primary structure as the order; the secondary structure as the local shape; the tertiary structure as the overall shape; and the quaternary structure as the way this tertiary structure of the protein interacts with other proteins.

How protein structure is established is a fascinating question and a field that is actively studied by prominent labs around the world.  Protein folding is the process of a chain of amino acids curling into its final shape, and how this process occurs is complex and not completely understood.  In general proteins fold depending on their environment (exposed to water or not, for example) and with the help of other proteins, called chaperones.  Protein chaperones help to establish a protein’s structure as well as maintain it during times of stress.  Further, modifications on proteins can change their structures, such as when p53, a protein that is involved in regulating many processes within the cell, is phosphorylated – its structure and, consequently, its function is altered slightly. 

The structure of proteins has fascinated scientists since we first learned about proteins.  Thousands of scientists around the world are still working to discover new structures and to learn how proteins fold.  The science behind protein folding has important implications in diseases such as Alzheimer’s, cancers, and infectious diseases.