An enzyme is made of another substance called protein. Enzymes are very big and complicated, and each one is different, each being built to control a certain special reaction. The names of the enzymes are written in Fig. 3–1 at each reaction. (Sometimes the same enzyme may control two reactions.) We emphasize that the enzymes themselves are not involved in the reaction directly. They do not change; they merely let an atom go from one place to another. Having done so, the enzyme is ready to do it to the next molecule, like a machine in a factory. Of course, there must be a supply of certain atoms and a way of disposing of other atoms. Take hydrogen, for example: there are enzymes which have special units on them which carry the hydrogen for all chemical reactions. For example, there are three or four hydrogen-reducing enzymes which are used all over our cycle in different places. It is interesting that the machinery which liberates some hydrogen at one place will take that hydrogen and use it somewhere else.
The most important feature of the cycle of Fig. 3–1 is the transformation from GDP to GTP (guanosine-di-phosphate to guanosine-tri-phosphate) because the one substance has much more energy in it than the other. Just as there is a “box” in certain enzymes for carrying hydrogen atoms around, there are special energy-carrying “boxes” which involve the triphosphate group. So, GTP has more energy than GDP and if the cycle is going one way, we are producing molecules which have extra energy and which can go drive some other cycle which requires energy, for example the contraction of muscle. The muscle will not contract unless there is GTP. We can take muscle fiber, put it in water, and add GTP, and the fibers contract, changing GTP to GDP if the right enzymes are present. So the real system is in the GDP-GTP transformation; in the dark the GTP which has been stored up during the day is used to run the whole cycle around the other way. An enzyme, you see, does not care in which direction the reaction goes, for if it did it would violate one of the laws of physics.
Physics is of great importance in biology and other sciences for still another reason, that has to do with experimental techniques. In fact, if it were not for the great development of experimental physics, these biochemistry charts would not be known today. The reason is that the most useful tool of all for analyzing this fantastically complex system is to label the atoms which are used in the reactions. Thus, if we could introduce into the cycle some carbon dioxide which has a “green mark” on it, and then measure after three seconds where the green mark is, and again measure after ten seconds, etc., we could trace out the course of the reactions. What are the “green marks”? They are different isotopes. We recall that the chemical properties of atoms are determined by the number of electrons, not by the mass of the nucleus. But there can be, for example in carbon, six neutrons or seven neutrons, together with the six protons which all carbon nuclei have. Chemically, the two atoms C12 and C13 are the same, but they differ in weight and they have different nuclear properties, and so they are distinguishable. By using these isotopes of different weights, or even radioactive isotopes like C14, which provide a more sensitive means for tracing very small quantities, it is possible to trace the reactions.
Now, we return to the description of enzymes and proteins. All proteins are not enzymes, but all enzymes are proteins. There are many proteins, such as the proteins in muscle, the structural proteins which are, for example, in cartilage and hair, skin, etc., that are not themselves enzymes. However, proteins are a very characteristic substance of life: first of all they make up all the enzymes, and second, they make up much of the rest of living material. Proteins have a very interesting and simple structure. They are a series, or chain, of different amino acids. There are twenty different amino acids, and they all can combine with each other to form chains in which the backbone is CO-NH, etc. Proteins are nothing but chains of various ones of these twenty amino acids. Each of the amino acids probably serves some special purpose. Some, for example, have a sulfur atom at a certain place; when two sulfur atoms are in the same protein, they form a bond, that is, they tie the chain together at two points and form a loop. Another has extra oxygen atoms which make it an acidic substance; another has a basic characteristic. Some of them have big groups hanging out to one side, so that they take up a lot of space. One of the amino acids, called proline, is not really an amino acid, but imino acid. There is a slight difference, with the result that when proline is in the chain, there is a kink in the chain. If we wished to manufacture a particular protein, we would give these instructions: put one of those sulfur hooks here; next, add something to take up space; then attach something to put a kink in the chain. In this way, we will get a complicated-looking chain, hooked together and having some complex structure; this is presumably just the manner in which all the various enzymes are made. One of the great triumphs in recent times (since 1960) was at last to discover the exact spatial atomic arrangement of certain proteins, which involve some fifty-six or sixty amino acids in a row. Over a thousand atoms (more nearly two thousand, if we count the hydrogen atoms) have been located in a complex pattern in two proteins. The first was hemoglobin. One of the sad aspects of this discovery is that we cannot see anything from the pattern; we do not understand why it works the way it does. Of course, that is the next problem to be attacked.
Another problem is how do the enzymes know what to be? A red-eyed fly makes a red-eyed fly baby, and so the information for the whole pattern of enzymes to make red pigment must be passed from one fly to the next. This is done by a substance in the nucleus of the cell, not a protein, called DNA (short for deoxyribonucleic acid). This is the key substance which is passed from one cell to another (for instance, sperm cells consist mostly of DNA) and carries the information as to how to make the enzymes. DNA is the “blueprint.” What does the blueprint look like and how does it work? First, the blueprint must be able to reproduce itself. Secondly, it must be able to instruct the protein. Concerning the reproduction, we might think that this proceeds like cell reproduction. Cells simply grow bigger and then divide in half. Must it be thus with DNA molecules, then, that they too grow bigger and divide in half? Every atom certainly does not grow bigger and divide in half! No, it is impossible to reproduce a molecule except by some more clever way.