The secondary structure of a protein describes certain repetitive, local conformations that are found in most peptide chains. The secondary structure does not describe the actual folding the protein in three dimensions, but instead illustrates the structure of small regions of the peptide. The actual secondary structure is very regular and common. There are two major forms of secondary structure that are found in almost all proteins, the alpha-helix and the beta-sheet (with the alpha-helix being most common). The following figure shows an alphahelix from a few different perspecitives. Figure A is a diagram of a helix from the end, with the long axis of the helix coming out of the page. Each amino acid is indicated with a different color. the red amino acid is closest to you and the blue is farthest away (into the page). From this view, you can tell tha the amino acids are 'curled' about a central space. Figure B shows the same helix from the side. It is difficult to see the helical aspect of the structure from this view, but it does demonstrate the length of the peptide. Figure C shows the same viewpoint as B, however, the 'backbone' of the peptide is shown in a ribbon configuation in which it is easy to see the helical structure.
What holds an apha-helix together? If you examine the figure of the peptide bond, notice that the bond is flanked by two electronegative (meaning electron loving) atoms, the N of the peptide bond itself and an O that is attached to the C of the bond. Thus the N-H bond and the C=O bond are polar bonds with the H having a positive dipole and the O having a negative dipole (remember that section?). These two atoms are capable of forming hydrogen bonds with one another. In actuality, adjacent H and O cannot get close enough to hydrogen bond, however, the chain itself can twist around so that a hydrogen bond can occur between an O and a H several amino acids away (usually 3). These bonds are shown in the followoing figure as the dotted lines beween red (oxygen) and white (hydrogen) atoms. Note that the hydrogens associated with the hydrogen bonds are connected to the blue (nitrogen) atoms.
Therefore, the chain of amino acids will continually twist around in a helical formation (something like the telephone cord) and stay twisted due to the presence of the hydrogen bonds. This helix is known as an alpha-helix. Every amino acid can form a peptide bond and therefore one might assume that every amino acid can form an apha-helix (note that R-groups are not involved in the hydrogen bonding that holds the helix together). In nature, however, several amino acids do not "fit" well into an due to either the size of the R- groups (large R-groups prevent the chain from twisting) or to the charge of the R-groups (charged R-groups want to form ionic bonds [which are stronger than hydrogen bonds] with other oppositely charged R-groups which pulls the chain away from the helix structure). This means that while some amino acids "like" to form helices, others don't. If one knows the primary sequence of a peptide chain, one could predict which areas of the chain would most likely form a helix and which areas don't based upon the amino acid sequence of those regions.
The beta-sheet likewise is held together by hydrogen bonds but generally only areas that contain large amounts of the amino acid glycine like to form these sheets. Nevertheless, it is still a common structure that is found in many different proteins.
Important things to remember concerning the secondary structure are:
