The Basics – Proteins

Most people know of proteins in the nutritional sense. When the word protein is used, often a mental image of joint of roast beef or a full cheese board springs to mind. However, for scientists that study proteins, they think of something much less appetising, this is what they see…

Protein Function

Proteins are everywhere in your body. Right this very moment they are being used for countless tasks from long distance signalling, movement, and some are even busy in the ribosome helping make new proteins. Proteins have an intimate connection between their structure and their function. This is a mantra you will keep reading when it comes to proteins, structure equals function.

An easy example for how a protein’s structure is related to its function are enzymes. Enzymes are crucial to the functioning of the metabolism; their role is to ensure reactions take place. An obstacle to any organism is the need for reactions to occur that would either not normally occur or occur too slowly. Enzymes place stress on target molecules thereby increasing the reaction rate.

The analogy for this enzyme and target molecule relationship is the lock and key analogy. Enzymes have a particular structural feature, an active site, which is the lock, while their target is the key. Just like locks and keys, one size does not fit all and the targets for an enzyme are specific. Only certain targets will fit into the enzymes lock. Once bound the enzyme is able to exert stress on the target molecule making the desired reaction more likely to happen. Now if there is a change in the structure of the protein then it may not be able to bind the target molecule or exert the same pressures, therefore and the reaction may not happen or will happen too slowly.

This is just one example to illustrate how proteins are dependent on their structure. Proteins that have lost their function are the cause of many different conditions. This loss of function is normally due to mutation causing a disruption to the normal primary sequence although the protein could also fold incorrectly.

Protein Structure

A protein is made up of one or more chains of polypeptides which, in turn, are made from amino acids linked together. The complex interactions that take place along a polypeptide are described in terms of four levels of structure, primary, secondary, tertiary and quaternary.

Primary Structure

The primary structure is the most fundamental level. It is the order of the amino acids in the polypeptide chain. The amino acid order is dictated by the gene in the DNA that encodes for the protein. There are 20 different amino acids, which all have an amino group and a carboxyl group but they each have a different R group. The amino group of one amino acid reacts with the carboxyl group of the other to from the backbone of the protein, while the different qualities that R groups carry confer different properties on the protein, influencing the folding of the protein.

Secondary Structure

The R-group properties that influence folding are first witnessed in the formation of secondary structures. There are two secondary structures, alpha helices or beta sheets. R-groups contain several different properties that affect if either of these structures are adopted including whether they are polar or non-polar group. This is because non-polar R-groups prefer in non-polar conditions and associate with similar non-polar R-groups, and the same is true for polar R-groups.

Tertiary Structure

The tertiary structure describes how the secondary structures fold. It is the shape of the polypeptide as a whole. R-groups from further away in the polypeptide can form hydrogen or disulphide bonds that folds the polypeptide into a particular shape.

Quaternary Structure

Up until now each structure has described the interactions within a single polypeptide chain however proteins can be made up of more than one chain and this is where the quaternary structure comes in. This structure describes how different polypeptide chains combine to form a protein.

Summary

Proteins have many different roles within the body and in order to be able to function properly, they rely on their structure. They are made from long chains amino acids and are described by four different levels of structure. The primary structure is the order of amino acids, while secondary structure is the interaction between the R groups of the amino acids. The tertiary structure is how the protein folds based on the interactions between the R groups of the secondary structures. Finally, the quaternary structure describes how the chain interacts with other polypeptide chains forming the protein. Each layer is important because changes to any of these layers of structure, from the amino acid order to mis-folding, can result in a protein that is unable to function.

Further Reading

News Medical Life Sciences – Protein Structure and Function

Describing with pictures the four levels of structure found in proteins.

Scitable by Nature Education – Protein Structure

Outlining proteins and their structure in more detail.

Learn More from The Basics series

DNA

If the order of amino acids is so important to the functioning of a protein how and where is this information stored?

Coming soon in The Basics series

From DNA to proteins

An overview of the transcription and translation processes. How the information stored in the DNA in converted into the amino acid sequence of a protein