Now folks, if we look at the same Figure 3.24 in Devlin, we note that the peptide bond itself is rigid.That is, it does not rotate, any more than the double or triple bond between two carbons can rotate.H
owever, if you look carefully at the figure, there are respective and bonds on either side of the
peptide bond. These can and in fact do rotate.
So why am I making a point about this?Well, these rotations allow configuration (3-D) changes in the way a polypeptide chain can in factconfigure. It also causes some 3-D or conformational constraints, known as steric hindrance, when, for example, two hydrogens are rotated too close to one another. Their respective electrons will repel.What does all this boil down to? Well, it provides for many permutations/combinations of where the R groups of each amino acid will be positioned with respect to one another. This, in turn, will affect possible interactions between R groups, which in turn exert a tremendous affect upon higher order protein structure and thus its function. (Remember lecture one, structure/function relationships????)Before we investigate how interactions between amino acids (known also as amino acid residues) of a polypeptide determine the protein’s three-dimensional structure, (as well as its functional role andrelationship to other proteins), let us define polypeptides that have similar amino acid sequences andfunctions as
This is significant, because sequence comparisons among homologous polypeptides have been used to evaluate genetic relationships of different species. For example, acomparison of the mitochondrial oxidation/reduction protein, cytochrome C, among different speciesreveals a significant amount of sequence conservation. Further, those amino acids within a given protein which do not differ from species to species are referred to as invariant and are believed to beessential for the function of that protein. This is why, for example, there are invariant similarities andsome variant differences in the structure of human vs. that of porcine vs. that bovine insulin. It is theseinvariant amino acids that allow porcine insulin to be substituted for that of human insulin in somecases. I wouldn’t be surprised if the variant differences, however, could contribute to immunologicalreactions by a human against say porcine insulin. Thus, the use of genetically-engineered humaninsulin produced from bacteria.There are many other examples. Later, when we study energy transformation in the mitochondria, weshall see that the invariant amino acid residues in cytochrome C are essential for interaction with theimportant heme group.One other point: Some amino acid substitutions do not affect the function of the protein. They arereferred to as conservative substitutions, whereas those amino acid substitutions which result in adefective protein are known as non-conservative substitutions. Now we can state the bottom line of primary structure. It is whatever amino acids are bonded together via peptide bonds in whatever order they appear. This primary amino acid sequence forms the basis for all higher order protein structure – various types of folding through bonding interactions.When we consider the
structure of a protein, we need to realize that a polypeptide chainconsists of a regularly repeating structure, called the backbone, and a variable component comprisingdistinct R side chains of their respective amino acids. The polypeptide is very rich in potentialhydrogen bonds, because each amino acid residue contains a carbonyl group (a good hydrogen bondacceptor – except for proline) and an amine group (a good hydrogen bond donor). This is the basis of secondary structure, which assumes one of two likely configurations. The first is the alpha
α(right-handed) helix, and second is the beta-pleated sheet. Your text shows the
Figures 3.25 and