This blog post is a part of STEMTalksNC’s ever expanding General Biology Series. In the last post, we talked about lipids. In this post, we will examine how the structure of a protein fits its function.
Proteins are large 3 dimensional organic molecules with a structure that fits its function. These functions include structural support, storage, transport, cellular communication, movement, and defense against foreign substances. The table below highlights the types of protein and also the function of them.
A human has thousands of different proteins, each with a specific structure and function. Consistent with their diverse functions, they vary in structure and each type of protein has a unique three-dimensional shape.
Although proteins are diverse in their structure, they are all polymers made from the same 20 monomers. These 20 monomers of protein are called amino acids. All amino acids are composed of the same basic structure. At the center of the amino acid, there is an asymmetric carbon atom that we call the alpha (a) carbon. Its four different molecules that it binds to is an amino group, a carboxyl group, a hydrogen atom, and a variable group that is called a side chain (usually labeled R).
The side chain is different in each amino acid, and its physical and chemical properties determine the unique qualities of a particular amino acid. A group of amino acids are hydrophobic because their side chains are non-polar. Another group of amino acids are hydrophillic because their side chains are polar. Amino acids can also be electrically charged depending on whether their side chains are basic or acidic.
Amino Acid Polymers
Now that we have examined the monomer of proteins, let’s examine the polymers of amino acids. Many amino acids bonded together form a polypeptide. A protein consists of one or more polypeptides, each folded and coiled into a specific three-dimensional structure. Amino acids are joined together by a dehydration reaction. This dehydration reaction will take away a hydroxyl group from one amino acid and a hydrogen atom from another amino acid. A polypeptide chain will have an amino end (a free amino group called the N-Terminus end) and a carboxyl end (a free carboxyl group called the C-Terminus end). Each specific polypeptide has a unique sequence of amino acids and that creates a unique three-dimensional shaped protein.
The relation between protein function and structure
A protein’s specific structure determines how it works. In almost very case, the function of a protein depends on its ability to recognize and bind to some other molecule.
The Four Levels of Protein Structure
With the goal of understanding the function of a protein, learning about its structure is often essential. All proteins match three levels of structure, with the fourth level of structure arising when a protein has one or two polypeptides. A functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape. And it is the amino acid sequence of each polypeptide that determines what three-dimensional structure the protein will have.
The primary structure of a protein is the sequence of amino acids coded for by DNA. The precise primary structure of a protein is determined not by the random linking of amino acids, by inherited genetic information. Even a slight change in the primary structure can affect a protein’s conformation and ability to function.
The secondary structure is the shape caused by hydrogen bonding between adjacent amino acids and it involves interactions between the polypeptide backbone. It is the segments of the polypeptide chains repeatedly coiled or folded in patterns that contribute to the protein’s overall shape. One example of a secondary structure is the alpha helix, a delicate coil held together by hydrogen bonding between every fourth amino acid.
The other example of a secondary structure is the beta pleated sheet. In this structure, two or more regions of the polypeptide chain lying side by side are connected by hydrogen bonds between parts of the two parallel polypeptide backbones.
The tertiary structure is the folding of the polypeptide into 3-D shape. The tertiary structure is the result of the interactions between the side chains (R) groups in the amino acids. There is a hydrophobic interaction between side chain (R) groups. We know that hydrophobic molecules do not like water. As a polypeptide folds into its functional shape, amino acids with hydrophobic (non-polar side chains) usually end up in clusters at the core of the protein, out of contact with water. When they are clustered, the non-polar amino acid side chains are going to be held by Van Der Waals interactions. Meanwhile, there are hydrogen bonds between the polar amino acid side chains and ionic bonds between charged amino acid side chains. These are all weak interactions, but their combined effect helps give the protein a unique shape.
Quaternary Structure occurs when multiple polypeptides join to form a large protein. Hemoglobin, the oxygen-binding protein of red blood cells, is an example of a protein with Quaternary structure. It has four polypeptide sub-units, two alpha chains and two beta chains.
What determines protein structure?
The sequence of amino acids determines the protein’s shape- where an alpha helix can form, where beta pleated sheets can occur, etc. A polypeptide chain of a given amino acid sequence can spontaneously arrange itself into a three-dimensional shape determined and maintained by the interactions responsible for secondary and tertiary structure. However, protein structure also depends on the physical and chemical conditions of the protein’s environment. If the pH, salt concentration, temperature, or other aspects of its environment are altered, the protein may unravel and lose its native shape, a change called denaturation. Some, but not all, proteins can return to their functional shape after denaturation.
In the next post, we will talk about nucleic acids, its structure and the functions of the nucleic acids.
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