182 Chapter 6 cellular metabolism

FIG. 6-27 The Calvin, or carbon reduction, cycle is the main metabolic pathway used by autotrophs for the conversion of carbon dioxide to organic carbohydrates. The pathway, which is active in photoautotrophs and chemolithotrophs, requires the input of carbon dioxide, ATP (energy), and NADPH (reducing power).

neighboring pigment when the electron returns to a lower energy level. The high energy electron is trans­ferred to an electron acceptor. The capture of light en­ergy and the transfer of electrons and energy occurs via a system called a photosystem. These systems consist of pigment molecules that absorb light energy

and a series of molecules that alternately accept and donate electrons and protons to form a chain of oxi- dation-reduction reactions through which electrons and protons are passed. The transfers of protons es­tablishes a protonmotive force that is used for the chemiosmotic generation of ATP.

Nitrification

Nitrifying bacteria oxidize either ammonium or ni­trite ions. Bacteria, such as Nitrosomonas, oxidize ammonia to nitrite (FIG. 6-29). Other bacteria, such as Nitrobacter, oxidize nitrite to nitrate. Because the chemolithotrophic oxidation of reduced nitrogen compounds yields relatively little energy, chemo­lithotrophic bacteria carry out extensive transforma­tions of nitrogen in soil and aquatic habitats to syn­thesize their required ATP. The activities of these bacteria are important in soil because the altera­tion of the oxidation state radically changes the mobility of these nitrogen compounds in the soil col­umn. Nitrifying bacteria lead to decreased soil fertil­ity because positively charged ammonium ions bind to negatively charged soil clay particles, whereas the negatively charged nitrite and nitrate ions do not bind and are therefore leached from soils by rain­water.

Nitrogen Fixation

The evolution of a mechanism for converting atmos­pheric nitrogen into reduced nitrogen compounds such as ammonia was a major event in the progress and development of cellular metabolism. It is this process, called nitrogen fixation, that makes nitro­gen available for incorporation into proteins. This is critical because, while carbohydrates and lipids can be synthesized from photosynthetic products based on C0₂ fixation, proteins and nucleic acids cannot be synthesized, because they contain nitrogen. There­fore life could not have persisted and expanded in the early oceans unless a means of replacing organic nitrogen compounds evolved. The process of nitro-

FIG. 6-29 Nitrifying bacteria are chemolithotrophs that oxidize inorganic nitrogen com­pounds to generate ATP. Some, such as Nitrosomonas, oxidize ammonium ions (NH₄⁺) to ni­trite ions (N0₂~) (left); others, such as Nitrobacter, oxidize nitrite ions to nitrate ions (N0₃ ) (right). These reactions take place within specialized membranes that intrude within the cy­toplasm of nitrifying bacteria.

FIG. 6-28 The tube worms (Riftia pachyptila) that grow ex­tensively near deep sea thermal vents have no gut. They have extensive internal populations of sulfur-oxidizing chemolithotrophic bacteria that produce the nutrients used by these animals for sustenance. The red-brown color of the worms is due to a form of hemoglobin that supplies oxy­gen and hydrogen sulfide to the chemolithotrophic bacte­ria within the tissues of the tube worms. Microbial mats of Beggiatoa grow between strands of the tube worms at the Guaymas Basin vent site (Gulf of California) at a depth of 2,010 meters.

METABOLIC PATHWAYS 1 85

FIG. 6-31 Bacterial cells of Bradyrhizobium japonicum within a nodule of a soybean produce nitrogenase, which results in the conversion of molecular nitrogen to ammonia.

gen fixation, the incorporation of nitrogen atoms from N₂ gas into protein, requires the breaking of an N=N triple bond. This is a very strong bond that is extremely difficult to break.

In the biological fixation of nitrogen, the triple bond of molecular nitrogen is enzymatically broken by nitrogenase. This is a complex enzyme system. An iron-containing compound such as ferredoxin first obtains electrons from the breakdown of organic molecules or from photosynthetic light reactions and carries them to a protein, nitrogen reductase, which channels them to another protein, dinitrogenase. With the transfer of six electrons and the use of twelve ATP and four water molecules, nitrogenase converts ni­trogen gas into two molecules of ammonia.

Nitrogen-fixing bacteria, called Rhizobium and Bradyrhizobium, live mutualistically in the nodules on the roots of legume plants (FIG. 6-30). Within the nodule, leghemoglobin, a protein produced by the plant, provides controlled amounts of oxygen so that aerobic energy-yielding metabolism can be carried out without inactivating nitrogenase, which is sensi­tive to oxygen exposure. When growing alone, Rhizo­bium and Bradyrhizobium require oxygen for their me­tabolism and are unable to fix nitrogen. When they live within root nodules, Rhizobium and Bradyrhizo­bium survive in this oxygen-free environment by uti­lizing the metabolites of the plant.

Other nitrogen-fixing bacteria, such as Azotobacter and Beijerinckia, are free living. Nitrogen-fixing cyanobacteria have specialized cells, called hetero­cysts, that contain the nitrogenase (FIG. 6-31). The heterocyst provides protection for nitrogenase against molecular oxygen, which is produced photo- synthetically by cyanobacteria and which denatures nitrogenase.

Methanogenesis

Some archaebacteria are able to use hydrogen and carbon dioxide to generate the ATP and molecules that compose their cellular structures. The metabo­lism of these archaebacteria produces methane and they are therefore called methanogens (FIG. 6-32). Other methanogens use fatty acids instead of carbon dioxide for the production of methane. Hydrogen gas, carbon dioxide, and fatty acids were available at the time life evolved on Earth. The methanogenic ar-

FIG. 6-32 Colonized micrograph of Methanospirillum him- gatei cells within a sheath (orange). (84,000 X). The cells are separated by a cell spacer.

chaebacteria may have been among the first organ­isms to carry out cellular metabolism. The methano- genic archaebacteria are strict anaerobes. They not only do not use oxygen in their metabolism, they are killed by exposure to oxygen. Methanogens could have grown on the compounds available in the prim­itive atmosphere of the Earth. Descendants of these archaebacteria still carry out anaerobic methane pro­duction today.

The metabolism of methane-producing archaebac­teria involves a series of oxidation-reduction reac­tions. In these reactions, electrons and protons are transferred from one coenzyme to another (FIG. 6- 33). The oxidation-reduction reactions of the coen­zymes establish an electron chain through which the electrons move. This movement of electrons is cou­pled with the pumping of protons (hydrogen ions) across a membrane. The return flow of protons by diffusion across the membranes of these archaebacte- rial cells provides the energy needed to drive the syn­thesis of ATP by chemiosmosis. This process of chemiosmosis is able to drive the formation of ATP because when protons are pumped out of the cell, a low concentration of protons exists within the cell. This causes diffusion to force the flow of protons from outside the cell back in. The membrane is gen­erally impermeable to protons except that protons can pass through special proton-transporting chan­nels that cross the plasma membrane. The passage of protons through these channels releases energy that results in the synthesis of ATP from ADP and inor­ganic phosphate (Pj).

Anaerobic methane-producing archaebacteria (methanogens) use chemiosmosis, involving an elec­tron transport chain and proton movement across a membrane, to generate ATP.

FIG. 6-33 The production of methane by methanogens in­volves several unique coenzymes and oxidation-reduction reactions to establish a protonmotive force for chemios- motic ATP generation.