Chains of amino acids often fold into spirals called alpha helices. In this lesson, we will discuss the structure and importance of an alpha helix, why we see so many alpha helices, and what happens when alpha helices fold incorrectly.
The Alpha Helix & Structures
The key to understanding alpha helices is the old saw about opposites attracting. If you’re a partially-positive hydrogen atom in an amino acid, you’ll be on the lookout for a partially-negative oxygen.
When you find a partially-negative oxygen, you’ll stick to it with a bond known as a hydrogen bond. Given enough amino acids, this will often make a long, twisted, rod-shaped alpha helix in what you might envision as an old-fashioned dance of amino acids. Just like attraction and dancing, there are things that we can easily predict, but there are some things that still remain a mystery.When we talk about alpha helices, we are talking about secondary structure. The primary structure of a protein is the order of amino acids that make it up. The secondary structure is the way in which these amino acids interact with each other to form regular shapes, usually alpha helices and beta pleated sheets. The many small secondary structures on a protein molecule interact to form a globular structure called a tertiary structure.
Several of these molecules may interact together to form a quaternary structure.
Amino Acid Structure
When we talk about our genetic code, what we mean is that genes code for different amino acids. Chains of amino acids then form proteins.
The shape and structure of these proteins determine their function in the body.Remembering amino acid structure will help us understand why an alpha helix forms the way it does. An amino acid always has a carbon in the middle, and as you may know, carbon forms four bonds. One of the carbon’s bonds is to a hydrogen atom.
Another bonds to an amino (-NH2) group and one to a carboxyl (-COOH) group. The last bond is to a side chain that is unique to each amino acid. Some of these side chains are relatively large, while some are small; some have charges, while others do not. These individual differences affect how amino acids interact to form proteins.
The Alpha Helix Structure
An alpha helix, sometimes called a Pauling-Corey-Branson alpha helix, is a coil of amino acid chain. It almost always coils in the right-handed direction. In an alpha helix, every partially-positive amino group sticks to the partially-negative oxygen in the carboxyl group of the amino acid four residues earlier on the chain. An alpha helix is tightly packed, and the end result of this twisting formation is that the amino acid chain will form a rod.The amino acids methionine, alanine, leucine, glutamate, and lysine are highly likely to form an alpha helix. The amino acids proline and glycine are unlikely to form an alpha helix.
Proline has a very large side chain, and it’s believed that prolines get in the way of alpha helix formation. On the other hand, glycine is small and flexible, so it does not tend to constrain itself in an alpha helix formation.
Why Alpha Helix?
The alpha helix is the most common secondary structure, with beta pleated sheets coming in a close second. Why?Alpha helices make the most efficient use of hydrogen-bonding, which is the stickiness between hydrogen in amino groups and oxygen in carboxyl groups. As discussed earlier, we can predict whether it is likely that an amino acid chain will form an alpha helix based on which amino acids are in the chain.
However, scientists aren’t able to predict precisely how a given amino acid chain will fold.Similar but rarer secondary structures include the pi-helix and 310 helix. The difference between an alpha helix and these other helices is how tightly they are wound. An alpha helix is wound just tightly enough that the atoms that are interacting form bonds at very stable, low-energy angles. Physicists have recently shown that alpha helices and beta pleated sheets appear to be the most stable secondary protein structures.
Are Alpha Helices Permanent?
Usually, amino acids will form the same secondary structure. However, they can be unfolded and refolded in different ways.
Bovine spongiform encephalopathy, or mad cow disease, happens when alpha helices incorrectly re-form into beta pleated sheets. The infectious agents of mad cow disease, prions, are wrongly-folded amino acid chains that cause neighboring alpha helices to fold into beta pleated sheets.Other diseases, such as Alzheimer’s, are suspected to involve the changing of alpha helices into beta pleated sheets.
The reverse, disease caused by beta sheets turning into alpha helices, is not generally observed. This may be because the helix is a simpler form and the beta sheet is more complex, but the reasons are yet unknown.
An alpha helix is a common shape that amino acid chains will form.
The alpha helix is characterized by a tight right-handed twist in the amino acid chain that causes it to form a rod shape. Hydrogen bonds between the hydrogen in an amino group and the oxygen in a carboxyl group on the amino acid cause this structure.A primary structure is the sequence of amino acids in an amino acid chain.
A secondary structure, of which alpha helices are a common example, is the small, regular shape that amino acids make when they interact. A tertiary structure is the collection of many secondary structures that make up a protein molecule, and a quaternary structure is what you see when several protein molecules interact.Amino acids make secondary structures by the way that their functional groups (amino groups and carboxyl groups) interact. Some amino acids are particularly likely to form an alpha helix, but some, like proline, are too large and get in the way. Alpha helices are low-energy and stable, which is why they are the most common secondary structure.
Alpha helices can sometimes be unfolded and refolded as beta pleated sheets. Mad cow disease is an example of a disease that occurs when alpha helices are refolded as beta pleated sheets. In mad cow disease, prions, which are misfolded proteins, cause neighboring proteins to unfold and re-fold the wrong way.