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Secondary Structure of Proteins
Once the primary structure of proteins is formed, the linear polypeptide begins to twist in regular patterns that make up the secondary structure. These patterns include alpha helices, beta-pleated sheets, beta turns and omega loops. All these patterns arise from the ability of the polypeptide to rotate some of its bonds. The final secondary structure is stabilized by the formation of hydrogen bonds between different amino acids on the polypeptide chain. In the alpha helix secondary structure, the polypeptide resembles a rod-like structure that contains the backbone on the inside and the side chains protruding to the outside. The hydrogen bonds are formed between the NH group of one amino acid and the C=O group of an amino acid that is four units ahead of it. The screw sense of the alpha helix describes the direction in which the polypeptide rotates about the axis of rotation. The more stable right-handed helix, which rotates in the clockwise direction, is much more common than the less stable left-handed helix, which rotates in the counterclockwise direction. Unlike the alpha helix, the beta pleated sheet structure consists of linear polypeptide regions that are stacked on top of one another. The antiparallel beta sheet contains two or more beta strands that are running in opposite directions with respect to one another. In this arrangement, the amino acids are all lined up so that the amino acid on one strand forms two hydrogen bonds with the amino acid on the opposite strand. In the parallel beta sheet, two or more beta strands run in the same direction. In this case, the amino acids do not line up exactly and the hydrogen bonding is slightly different. Beta turns are sharp turns that arise in the polypeptide chain; these usually allow the polypeptide to get into its compact and tight structure. Just like the other secondary structures, beta turns arise from rotations in single bonds on the polypeptide chain and are stabilized by hydrogen bonds.
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