We have already learned that proteins are made up of a chain of amino acids linked by peptide bonds. But what exactly is an amino acid? There are three main parts to each amino acid. The first part is the carboxylic acid group, typically written as “COOH” because it is made of one carbon (C) atom, two oxygen (O) atoms, and one hydrogen (H) atom. The second part is the amine group and is typically written “NH2” because it is made of one nitrogen (N) atom bound to two hydrogen atoms. These two groups are identical in all twenty amino acids, but it is the third group that is different in each one. This group is called the “R” group, where R stands for one of twenty possibilities of side chains. The different side chains are what give the amino acids different properties. For example, a side chain could be positively or negatively charged or attracted to or repelled by water. Amino acids that are attracted to water are called hydrophilic, or water loving, while amino acids that are repelled by water are called hydrophobic, or water fearing. The different properties of each side chain determine how the amino acids will interact with each other and with the surrounding environment. The carboxylic acid, the amine, the R group, and a single hydrogen atom are all bound to a central carbon atom to make an amino acid.
When two amino acids are linked together, the carboxylic acid group (COOH) of one amino acid connects to the amine group (NH2) of another amino acid. The new bond that is formed is called a peptide bond.
Now that we know more about the basic subunits of protein, we can learn more about their overall form. Proteins have four increasingly complex levels of structure. The first level, primary structure, describes the specific order, or sequence, of the amino acids. Remember that the order of amino acids comes directly from the DNA sequence from which it was transcribed. This chain of amino acids is basically what we are left with immediately following translation. Recall that the 4 letters of the DNA alphabet have been translated into the 20 letters of the protein alphabet. The primary structure also holds all of the information needed for forming the other three levels of structure.
A straight chain of amino acids is not the final form of the protein. In fact, proteins can have very complex shapes, and the final form of the protein is essential to its intended function. Perhaps you have heard of protein “folding.” Folding is the word used to describe the process by which the chain of amino acids is modified to reach its final form. After primary structure, the next level of complexity is called secondary structure. Secondary structure describes common folding patterns (often called “motifs”) seen in proteins. One type of secondary structure is the alpha helix. An alpha helix looks like a coil.
Another type of secondary structure is the beta sheet. A beta sheet looks kind of like a pleated skirt, or a piece of paper folded back and forth like a fan.
The reason why proteins fold in these characteristic ways has to do with the order of different types of amino acids. Remember how some amino acids are hydrophilic while others are hydrophobic? Well, depending on the type of environment where the protein ends up, it will fold so that its hydrophobic parts are hidden from water and its hydrophilic parts are facing water. In a watery environment, the hydrophilic amino acids will face out, while the hydrophobic amino acids will face inside the coil away from the water. Sometimes several secondary structure motifs will come together to form one bigger structure; this is called supersecondary structure. An example of supersecondary structure is when a bunch of alpha helices or beta sheets form a ring, called a barrel. Barrels are often found in the cell membrane and act as pores.
To review the secondary structure motifs, click on the buttons below to highlight alpha helices and beta sheets.
The next level of complexity is called tertiary structure. Tertiary structure describes the overall three-dimensional structure of a single folded amino acid chain. This level includes the different kinds of bonds that hold the protein in its three-dimensional shape. Sometimes, tertiary structure is the highest level of complexity seen in a protein. However, often a fourth level is needed to describe the final protein’s structure; this level is called quaternary structure. When a protein is made up of more than one polypeptide chain, the complete protein with all of the subunits together makes up the quaternary structure. The subunits can all be copies of the same polypeptide, or they can be different polypeptides linked together.
Last Modified: 02/12/2006
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