PROTEINS Amino Acids

Amino Acid Molecular Structures
 Elmhurst College
Secondary Protein Structure Quaternary Protein Structure Denaturation  Chemistry Department
Tertiary Protein Structure Globular Proteins Minitopics  Virtual ChemBook

Secondary Protein - Structure


The secondary protein structure is the specific geometric shape caused by intramolecular and intermolecular hydrogen bonding of amide groups. The geometry assumed by the protein chain is directly related to molecular geometry concepts of hybridization theory. Experimental evidence shows that the amide unit is a rigid planar structure. This is derived from the planar triangle geometry of the carbonyl unit ( C = O ). See the graphic on the left.

The geometry around the nitrogen is derived from an unusual situation with a planar triangle geometry. Apparently, the double bond on oxygen can alternate to make a double bond between carbon and nitrogen. Rotation around bonds C-C and N-C does take place. The C=O and NH are always in a rigid plane. Notice that the carbonyl group and the hydrogen on nitrogen are almost always trans to each other. The result is that chains of amino acids as peptides with amide bonds reflect this geometry.

As a result of studying X-ray photographs and constructing molecular models, Linus Pauling and Robert Cory, in 1951, proposed that the protein structures were either in the form of an alpha helix or the beta pleated sheet.

Click for larger image 

Alpha Helix:

In the alpha helix, the polypeptide chain is coiled tightly in the fashion of a spring. The "backbone" of the peptide forms the inner part of the coil while the side chains extend outward from the coil. The helix is stabilized by hydrogen bonds between the >N-H of one amino acid and the >C=O on the 4th amino acid away from it.

One "turn" of the coil requires 3.6 amino acid units. The helix can be either right-handed or left-handed in the sense of threads on a screw. The naturally occurring alpha helixes found in proteins are all right-handed. Not all proteins have a helical structure, since some do not have it at all and are random.

Alpha Helix - Chime in new window

Main peptide in Chime is minus the hydrogens atoms. Also see "Different Protein" to see all hydrogen atoms present in a 10 alanine peptide.

Quiz:What are the atoms being represented around the outside of the helix?
What holds the protein in the alpha helical shape?  

Click for larger image 

 Structure of Silk:

The secondary structure of silk is an example of the beta pleated sheet. In this structure, individual protein chains are aligned side-by-side with every other protein chain aligned in an opposite direction. The protein chains are held together by intermolecular hydrogen bonding, that is hydrogen bonding between amide groups of two separate chains. This intermolecular hydrogen bonding in the beta-pleated sheet is in contrast to the intramolecular hydrogen bonding in the alpha-helix.

The hydrogen on the amide of one protein chain is hydrogen bonded to the amide oxygen of the neighboring protein chain. The pleated sheet effect arises form the fact that the amide structure is planar while the "bends" occur at the carbon containing the side chain.

See the graphic on the left.

Fortunately, the "side" chain R groups in silk are not very bulky. The basic primary structure of silk consists of a six amino acid unit that repeats itself. The sequence where every other unit is glycine in silk is: -gly-ala-gly-ala-gly-ala-. Although glycine and alanine make up 75-80% of the amino acids in silk, another 10-15% is serine and the final 10 % contain bulky side chains such as in tyr, arg, val, asp, and glu.

Silk - Chime in new window

These amino acids with bulky side chains disrupt the regular patterns set by the gly-ala-ser. Different species of silkworms produce different portions of ordered and disordered regions. The disordered regions provide a small amount of elasticity since the ordered beta-pleated sheet is already fully extended and cannot stretch further without breaking.

The beta pleated sheet motif is found in many proteins along with the alpha helix structure. The chains may run parallel (all N terminals on one end) or anti-parallel (N terminal and C terminal ends alternate). See small graphic on left.

Quiz: Explain the similarity in hydrogen bonding of the alpha-helix and the beta-pleated sheet secondary protein structure.
Explain the difference in hydrogen bonding of the alpha-helix and the beta-pleated sheet secondary protein structure.