Proteins may be represented in several ways. Below you can choose from two views of insulin.
The space-filling representation shows the actual size and location of each atom. The color code is the CPK scheme. Note the types of atoms present. What is the importance of the sulfur atoms in insulin, which consists of two polypeptide chains?
The secondary structure is emphasized in this representation. The polypeptide chain is shown as a ribbon to reveal the locations of alpha-helices and beta-sheets. (But only alpha-helices are present here.)
(Optional: If your computer has Java, you can get a better view of the above by clicking here.)
The primary structure of a protein is its linear sequence of specific amino acids. A single amino acid is shown to the right. The "side chain" is the portion that is different in each of the 20 different amino acids.
Peptide bonds hold the adjacent amino acids together in the polypeptide chain. The figure to the right shows two amino acids held together by a peptide bond (in red). Note the polar nature of the region around the peptide bond.
A local region of the polypeptide chain may fold into either an alpha-helix or a beta sheet. These special structures comprise the secondary structure.
The secondary structure of some proteins is essentially all alpha-helices.
Myoglobin is good example of this type. This second view of myoglobin shows the hydrogen bonds that hold the alpha helices together.
QUESTION: Do you know why hydrogen bonds tend to form so frequently in a polypeptide chain?
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Some proteins are largely formed from beta-sheets. Antibodies and T cell receptors fall in this category. Shown here are the constant and variable domains of one polypeptide chain of a T cell receptor. (The membrane and intracellular portions are not shown.)
Alpha-helix and Beta-sheet Proteins
Many proteins have both alpha-helices and beta-sheets. The large domain of hexokinase, which phosphorylates glucose, is an alpha/beta structure. Glucose is shown at the center of the enzyme.
The tertiary structure of a protein refers to the actual three dimensional structure of the polypeptide chain. A number of forces act to hold the polypeptide chain in this final configuration:
Polar/Nonpolar Interactions. A polypeptide chain folds so that nonpolar, hydrophobic amino acids tend to point inward, where they are shielded from the water, and polar, hydrophilic amino acids tend to point outward, where they interact with the water. Indeed, this is one of the most important factors determining the tertiary structure of most proteins. In this view of myoglobin the amino acids with hydrophobic side chains are colored blue, while those with hydrophilic side chains are colored red.
In the previous two dimensional view, it can be a little difficult to see that the hydrophobic amino acids point inward. It is much easier to see if you view myoglobin three dimensionally. If your computer has Java, click here.
Van der Waals Forces. These become significant when many atoms can line up closely, and tend to most important in the case of nonpolar amino acids.
Ionic Interactions. Certain amino acids, such as glutamate, have a side chain that normally is in ionic form.
Disulfide Bonds. These are found in secreted proteins only. The reducing environment inside cells readily disrupts these bonds.
Some proteins have a quaternary structure; that is, they are comprised of two or more polypeptide chains. Each polypeptide chain in such a protein is called a subunit. Hemoglobin is one example. Each of the four polypeptide chains is similar to myoglobin. Note the presence of the oxygen binding heme groups, which are discussed below.
Collagen is a widespread connective tissue protein, which consists of three polypeptide chains. Only a short segment in the middle of this large, fibrous extracellular molecule is shown.
Myoglobin is a protein with a prosthetic group called a heme. It contains an iron ion that binds oxygen. You may look at the space-filling representation or further type of representation in which bonds are shown as sticks