Many biologists regard proteins as being the fundamental compounds of living systems. Whether or not any one type of molecule may be singled out as "fundamental" is open to question, but proteins play many extremely important roles.
Although they are structurally and functionally diverse, they exhibit certain characteristics which enable us to make some generalizations about them. In terms of elementary chemical composition, proteins always contain carbon, hydrogen, oxygen, and nitrogen, and they usually contain sulfur as well.
The micro molecular units are called amino acids, and a given protein molecule may consist of several hundred or even thousands of these units. The feature shared by all amino acids is a carbon atom to which is attached a carboxyl group and an amino group. These compounds are called amino acids because of the amino and carboxyl groups.
A complete listing and illustration of their structure may be found in most textbooks concerned with organic chemistry. When amino acids link together, they do so in such a way that the acid group of one is attached to the amino group of another.
The bond thus formed between the carbon of the acid group and the nitrogen group if termed a Peptide Bond. This can be illustrated by showing how to amino acids are joined together. In this particular example, the two simplest amino acids, glycogen and almandine, are subjected to dehydration.
As shown, the carboxyl group of one molecule gives up its OH and the amino group of the other reacting molecule gives up one H. Water is thus formed, and the two molecules are linked from carbon to nitrogen.
By addition of any one of the twenty amino acids to this deceptive, a tripe tide would be formed. In similar fashion, continued addition to the chain would lead to the formation of a large polypeptide chain, or large protein molecule.
The specific amino acid sequence of any given protein molecule is called its primary structure. When we consider that there are twenty different amino acids which may be arranged in any order to form a sequence of hundreds of amino acids in the formation of a single protein molecule, it becomes apparent that a vast number of different protein molecules can exist.
This situation is analogous to having an alphabet of twenty letters with which to form words. If there is no prescribed sequence in which the letters must appear, then the number of words that can be formed becomes almost infinities.
As we shall see, this high degree of structural diversity if very important in the many and varied functional roles fulfilled by proteins in living systems. Physical studies have shown that few proteins exist a£ a straight-chain sequence of amino acids. For the most part, they are coiled or twisted in a number of ways, the most common of which is a spiral twisting called an alpha helix.
The geometry of an alpha helix can be visualized by letting a pipe cleaner of certain length represent a straight chain of amino acids. If the pipe cleaner is coiled around a pencil by proceeding from the tip of the pencil to the eraser in clockwise fashion; an alpha helix is formed. It shape can be seen more clearly if the pencil is then slipped out.
Experimental evidence indicates that this alpha helix is produced from a straight chain molecule whenever weak hydrogen bonds pull adjacent parts of the molecule into a helical form. Hydrogen bonding is thought to be an electrostatic attraction between the positively charged hydrogen end of polar molecule and an unshared electron pair of one atom of another molecule.
This situation if quite common in a chain of amino acids. The N - H structure of the peptide linkage presents a polar situation, while the C = O group of a peptide linkage in an advancement part of the chain. Hydrogen bonding to the present concept. Apparently, it is responsible for the formation of the alpha helix, which constitutes the secondary structure of a protein molecule.
The protein molecule owes its ultimate configuration to the diversity of exposed chemical groups comprising the amino acids which determine the primary structure of the molecule. Some of this diversity is illustrated, where the R groups may represent ring structures, acid groups, amino groups, or sulfhydryl groups.
This diversity makes it possible for a number of bonding situations to develop between adjacent groups. These interactions cause the molecule to fold upon it still further, producing what is termed the tertiary structure of the molecule.
This tertiary structure gives the molecule a final and specific surface configuration, leaving certain active groups exposed to react with other molecules, and also shielding certain groups from reaction with other molecules.
Although most of the active proteins within living systems exhibit the type of structure we have discussed, they may also assume a second type of configuration. Known as the beta configuration, it involves interaction or bonding between two or more polypeptide chains adjacent to each other.
The secondary structure and territory structure which are characteristic of the protein molecules we have discussed does not occur in those with a beta configuration. Instead, the molecules remain long and fibrous, and are therefore sometimes called fibrous proteins.
Biochemically, these proteins are generally far less active than the other type, which tend to be spherical or globular in form; rather type, which tend to be spherical or proteins in living systems. For example, they are the principal components of muscle, bone, and cartilage in the bodies of complex animals. Earlier, we discussed enzymes and the role they play as organic catalysts in living systems. You will recall that we defined them as proteins.
In the light of our discussion above regarding the structure of protein molecules, perhaps we are now in a better position to understand the specificity of enzymes as well as certain other aspects of their activity.
Enzymes belong to the group of globular or spherical proteins mentioned above, and each type of enzyme molecule has a very specific surface configuration due to its primary, secondary, and tertiary structure.
The specific surface configuration leaves certain chemical groups exposed which will react quite readily with certain stand that an almost infinite number of different and quite specific enzymes having certain active sites may exist. Perhaps our previous analogy of a lock and key type of relationship between an enzyme and substrate molecule is now clearer and more meaningful.