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 could not exist on this planet. Only a small fraction of the nitrogenous compounds in today’s organisms, however, is due to 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 from their dietary intake of proteins and nucleic acids. In the body, these macromolecules are broken down to amino acids and the components of nucleotides, and the nitrogen they contain is used to produce new proteins and nucleic acids—or other molecules. About half of the 20 amino acids found in proteins are essential amino acids for vertebrates (Figure 2–62), which means that they cannot be synthesized from other ingredients of the diet. The other amino acids can be so synthesized, using a variety of raw materials, including intermediates of the citric acid cycle. The essential amino acids are made by plants and other 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. 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. There are no “essential nucleotides” that must be provided in the diet.
Amino acids not used 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.
Sulfur is abundant on Earth in its most oxidized form, sulfate (SO42–). To be useful for life, sulfate must be reduced to sulfide (S2–), the oxidation state of sulfur required for the synthesis of essential biological molecules, including the amino acids methionine and cysteine, coenzyme A (see Figure 2–39), and the iron-sulfur centers essential for electron transport (see Figure 14–16). The sulfur-reduction process begins in bacteria, fungi, and plants, where a special group of enzymes use ATP and reducing power to create a sulfate assimilation pathway. Humans and other animals cannot reduce sulfate and must therefore acquire the sulfur they need for their metabolism in the food that they eat.
Figure 2–60 The generation of an H+ gradient across a membrane by electron-transport reactions. an electron held in a high-energy state (derived, for example, from the oxidation of a metabolite) is passed sequentially by carriers a, B, and C to a lower energy state. in this diagram, carrier B is arranged in the membrane in such a way that it takes up h+ from one side and releases it to the other as the electron passes. The result is an h+ gradient. as discussed in Chapter 14, this gradient is an important form of energy that is harnessed by other membrane proteins to drive the formation of aTp (for an actual example, see figure 14–21).