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In this video, I explain the details of the alpha helix (alpha helices).
The alpha helix is an important type of secondary protein structure. The alpha helix is, specifically, a right handed helix held together by hydrogen bonds (H-bonds) between the carbonyl oxygen and amide hydrogen of the polypeptide backbone. These hydrogen bonds are parallel to the axis of the helix, and they exist between every 4th amino acid of the backbone. The side chains of the amino acids (R-groups) extend out of the helix, running perpendicular to the axis of the helix. The alpha helix is often thought of as having polarity, with the N-terminus (amino terminus) having a partial positive charge, while the C-terminus (carboxy terminus) carries a partial negative charge.
There are a few things that can disrupt or damage and alpha helix:
1. Proline – Proline’s side chain is wrapped around and connected to its alpha amino group. This restricts rotation that is necessary to form the particular structure of the alpha helix. Also, when proline’s amino group is part of a peptide bond, it has no hydrogen on it that can hydrogen bond. In short, substituting a proline in for an amino acid that is part of an alpha helix will ruin the alpha helix’s structure.
2. Electrostatic Repulsions between Side Chains with Like Charges – If the R groups of the amino acids that extend outward from the alpha helix happen to be next to each other with like charges, they can repel each other and bend the helix in a way that compromises its structure. For instance, if two negatively charged aspartate side chains are next to each other, they will repel. Likewise, this could occur with two positively charged arginine side chains.
3. Steric Hindrance – The alpha helix is a fairly tightly packed helix, and amino acids with bulky side chains can disrupt its structure by taking up too much space being next to each in the peptide chain that makes up the helix. For example, two phenylalanine side chains next to each other means two aromatic rings (bulky) next to each other. This could disrupt the alpha helix.
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