Polypeptide Chains

Submitted by ChemPRIME Staff on Thu, 12/16/2010 - 16:23

The backbone of any proteinA biological polymer of amino acids joined by peptide bonds. moleculeA set of atoms joined by covalent bonds and having no net charge. is a polypeptideA polymer of many amino acids joined by amide linkages or "peptide bonds." chain obtained by the condensationThe process in which a liquid forms from gas or vapor of the same substance. A chemical reaction in which two molecules combine to form a very small molecule and a larger molecule than either of the two reactants. of a large number of amino acids with the elimination of water. You will recall that the amino acids are bifunctional organic nitrogen compounds containing an acid groupThose elements that comprise a single column of the periodic table. Also called family., —COOH, and an amineAn organic compound formally derived from ammonia by the replacement of one or more hydrogen atoms by alkyl groups. Examples are primary amine: RNH2; secondary amine: R2NH; tertiary amine: R3N. group, —NH2. The amine group is attached to the carbon atom adjacent to the —COOH (the α carbon atom). The three simplest amino acids are



File:Structures of Three Amino Acids.jpg
Rotatable Jmol representations for three amino acids.

In practice, though, these acids are usually in the form of their zwitterions, and we should write them


File:Zwitterionic Forms of Three Amino Acids .jpg
Zwitterionic forms of 3 amino acids.

If these three amino acids are now condensed, water is eliminated and a simple polypeptide contaning three amino acids is obtained:

      (1)

The two CO—NH bonds produced by this reaction are called peptide bonds. Notice that the peptide bond is an amide linkageA chemical bond linkage formed when a carboxylic acid reacts with an amine, often found in polymers such as nylon and proteins; in proteins also called a peptide bond.. An important feature of such a peptide bond is that it is planar. This is because of the existence of two resonance structures

Image:Resonance Structures of a Peptide Bond .jpg

In the second of these structures, there is a double bondAttraction between two atoms (nuclei and core electrons) that results from sharing two pairs of electrons between the atoms; a bond with bond order = 2. between the carbon and the nitrogen atomsThe smallest particle of an element that can be involved in chemical combination with another element; an atom consists of protons and neutrons in a tiny, very dense nucleus, surrounded by electrons, which occupy most of its volume. but no lone pairs around either atom. This insures that all the bonds involving the C and N atoms must lie in the same plane. The planarity of the peptide bond places considerable constraint on the conformations available to a polypeptide chain. Rotation can only occur around the single bonds involving the α carbon atoms. That is, the gray shaded areas in the polypeptide chain of Eq. (1) can twist relative to one another, but they must remain planar. This limitation offers important constraints which can greatly aid analysis of protein structure and of the conformations available for different polypeptide chains.

Another important aspect of the peptide bond is the opportunity it provides for hydrogen bonding. The oxygen on theImage:Carbonyl Group.jpg carbonyl group can bond to the hydrogen on an Image:amino group.jpg group further along the chain:

Image:H bonding.jpg

Such a bond is somewhat stronger than a normal hydrogen bond because of the partially negative character of the oxygen atom and the partially positive character of the nitrogen atom conferred by resonance structure II.