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In our discussion so far we have concentrated mainly on carbohydrate metabolism. We have not yet considered the metabolism of nitrogen or sulfur. These two elements are constituents of proteins and nucleic acids, which are the two most important classes of macromolecules in the cell and make up approximately two-thirds of its dry weight. Atoms of nitrogen and sulfur pass from compound to compound and between organisms and their environment in a series of reversible cycles.
Although molecular nitrogen is abundant in the earth's atmosphere, nitrogen is chemically unreactive as a gas. Only a few living species are able to incorporate it into organic molecules, a process called nitrogen fixation. Nitrogen fixation occurs in certain microorganisms and by some geophysical processes, such as lightning discharge. It is essential to the biosphere as a whole, for without it life would not exist on this planet. Only a small fraction of the nitrogenous compounds in today's organisms, however, represents fresh products of nitrogen fixation from the atmosphere. Most organic nitrogen has been in circulation for some time, passing from one living organism to another. Thus present-day nitrogen-fixing reactions can be said to perform a "topping-up" function for the total nitrogen supply.
Vertebrates receive virtually all of their nitrogen in their dietary intake of proteins and nucleic acids. In the body these macromolecules are broken down to component amino acids and nucleotides, which are then repolymerized into new proteins and nucleic acids or utilized to make other molecules. About half of the 20 amino acids found in proteins are essential amino acids (Figure 2-27) for vertebrates, which means that they cannot be synthesized from other ingredients of the diet. The others can be so synthesized, using a variety of raw materials, including intermediates of the citric acid cycle. The essential amino acids are made by nonvertebrate organisms, usually by long and energetically expensive pathways that have been lost in the course of vertebrate evolution.
The nucleotides needed to make RNA and DNA can be synthesized using specialized biosynthetic pathways: there are no "essential nucleotides" that must be provided in the diet. All of the nitrogens in the purine and pyrimidine bases (as well as some of the carbons) are derived from the plentiful amino acids glutamine, aspartic acid, and glycine, whereas the ribose and deoxyribose sugars are derived from glucose.
Amino acids that are not utilized in biosynthesis can be oxidized to generate metabolic energy. Most of their carbon and hydrogen atoms eventually form CO2 or H2O, whereas their nitrogen atoms are shuttled through various forms and eventually appear as urea, which is excreted. Each amino acid is processed differently, and a whole constellation of enzymatic reactions exists for their catabolism.