Α-Helices Figure: Ball-and-stick model of the α helix. These structures are the first major steps in the folding of a polypeptide chain, and they establish important topological motifs that dictate subsequent tertiary structure and the ultimate function of the protein. The two most commonly encountered secondary structures of a polypeptide chain are α-helices and beta-pleated sheets. Secondary structure does not include bonding between the R-groups of amino acids, hydrophobic interactions, or other interactions associated with tertiary structure.

Secondary structure refers to the shape of a folding protein due exclusively to hydrogen bonding between its backbone amide and carbonyl groups. The hydrogen bonding pattern in a section of a beta-strand is shown below. Loops are relatively disordered segments of protein chain, but often assume a very ordered structure when in contact with a second protein or a smaller organic compound.īoth helix and the beta-sheet structures are held together by very specific hydrogen-bonding interactions between the amide nitrogen on one amino acid and the carbonyl oxygen on another. The figure below shows two different views of the same beta-sheet: in the left-side view, the two regions of protein chain are differentiated by color. In a beta-sheet (or beta-strand) structure, two sections of protein chain are aligned side-by-side in an extended conformation. In a helix, the main chain of the protein adopts the shape of a clockwise spiral staircase, and the side chains point out laterally. For the most part, there are three important elements of secondary structure: helices, beta-sheets, and loops. Secondary structure is three-dimensional, but is a local phenomenon, confined to a relatively short stretch of amino acids. Below is a Lewis structure of a short segment of a protein with the sequence CHEM (cysteine - histidine - glutamate - methionine) A protein’s primary structure is two-dimensional - simply the sequence of amino acids in the peptide chain. Protein structure can be discussed at four distinct levels.

Amide plane of peptide backbone