Proteins

The secondary structure of proteins is due to foldings that occur within their structure. These foldings are either in a helical shape, called the "alpha-helix" (which was first proposed by Linus Pauling), or a beta-pleated sheet shaped similar to the zig-zag foldings of an accordion. The turns of the alpha-helix are stabilized by hydrogen bonding between every fourth amino acid in the chain. The alpha-helix can cover specific regions of the protein or it may involve the entire protein, as in the alpha-keratin found in claws and horns. The two sides of the alpha-helix may differ in polarity, with hydrophilic R groups projecting to the lining of the channel, while hydrophobic R groups project to the outside of the channel, where they embed in the hydrophobic membrane. This structure is exemplified in membrane channel proteins, proteins that channel ions across from one surface to another. The beta-pleated sheet is formed by folding successive planes. Each plane is five to eight amino acids long. The folds are stabilized by hydrogen bonding. The strength observed in silk fibers is due to their stacks of beta-pleated sheets.

Combinations of secondary structure form "motifs." A coiled-coil motif is common among proteins that associate with the DNA helix. The helix-loop-helix motif is a knobby structure, and the zinc finger projects outward like its name. These last two motifs allow associations between RNA and proteins that form the basis of their interactions.