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Tag words: bacteriology, bacteria, microbiology, microbe, metabolism, energy generation, autotroph, heterotroph, lithotroph, phototroph, chemoautotroph, lithoautotroph, photoheterotroph, archaea, carboxydobacteria, nitrifying bacteria, iron bacteria, thermophile, hyperthermophile, anabolism, catabolism, nicotinamide adenine dinuclotide, NAD, NADH, adenosine triphosphate, ATP, proton motive force, pmf, electron transport system, fermentation, alcohol fermentation, lactic acid fermentation, mixed acid fermentation, butanediol fermentation, butanol fermentation, pyruvate, acetyl CoA, respiration, aerobic respiration, anaerobic respiration, denitrification, sulfate reduction, methanogenesis, photosynthesis, oxygenic, anoxygenic photosynthesis, bacterial photosynthesis, light reactions, dark reactions, CO2 fixation, RUBP carboxylase, ribulose bisphosphate carboxylase, RUBP, Calvin cycle, glycolysis, Embden Meyerhof pathway, Entner Doudoroff pathway, phosphoketolase pathway, homolactic, heterolactic, KDPG aldolase, tricarboxylic acid cycle, TCA, reverse TCA, citric acid cycle, Kreb's cycle, CODH pathway, ATP synthesis, substrate level phosphorylation, electron transport phosphorylation, oxidative phosphorylation, photophosphorylation, cytochrome system, chlorophyll a, bacterial chlorophyll, carotenoid, ferredoxin, biosynthesis.

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Diversity of Metabolism in Procaryotes (page 7)

(This chapter has 8 pages)

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Autotrophic CO2 fixation

The use of RUBP carboxylase and the Calvin cycle is the most common mechanism for CO2 fixation among autotrophs. Indeed, RUBP carboxylase is said to be the most abundant enzyme on the planet (nitrogenase, which fixes N2 is second most abundant). This is the only mechanism of autotrophic CO2 fixation among eucaryotes, and it is used, as well, by all cyanobacteria and purple bacteria. Lithoautotrophic bacteria also use this pathway. But the green bacteria and the methanogens, as well as a few isolated groups of procaryotes, have alternative mechanisms of autotrophic CO2 fixation and do not possess RUBP carboxylase.

RUBP carboxylase (ribulose bisphosphate carboxylase) uses ribulose bisphosphate (RUBP) and CO2 as co-substrates. In a complicated reaction the CO2 is "fixed" by addition to the RUBP, which is immediately cleaved into two molecules of 3-phosphoglyceric acid (PGA). The fixed CO2 winds up in the -COO group of one of the PGA molecules. Actually, this is the reaction which initiates the Calvin cycle (Figure 22 below).

The Calvin cycle is concerned with the conversion of PGA to intermediates in glycolysis that can be used for biosynthesis, and with the regeneration of RUBP, the substrate that drives the cycle. After the initial fixation of CO2, 2 PGA are reduced and combined to form hexose-phosphate by reactions which are essentially the reverse of the oxidative Embden-Meyerhof pathway. (Now is a good time to go back to Figure 8 and look at the E-M pathway for the location of PGA and glucose-phosphate). The hexose phosphate is converted to pentose-phosphate, which is phosphorylated to regenerate RUBP. An important function of the Calvin cycle is to provide the organic precursors for the biosynthesis of cell material. Intermediates must be constantly withdrawn from the Calvin cycle in order to make cell material. In this regard, the Calvin cycle is an anabolic pathway. The fixation of CO2 to the level of glucose (C6H12O6) requires 18 ATP and 12 NADPH2.

Figure 22. The Calvin cycle and its relationship to the synthesis of cell materials.

The methanogens, a very abundant group of procaryotes, use CO2 as a source of carbon for growth, and as a final electron acceptor in an energy-producing process that produces methane. If a methanogen is fed labeled CO2 as a sole form of carbon, 95 percent of the label winds up in methane and 5 percent winds up in cell material. The methanogens fix CO2 by means of the enzyme CODH (carbon monoxide dehydrogenase) and the Acetyl CoA pathway (Figure 23 below).

The pathway of methanogenesis steadily reduces CO2 to the methyl (CH3) level, mediated by the coenzyme methanopterin (MP), related to folic acid. MP-CH3 may be reduced to methane (not shown) or the MP may be replaced by a vitamin B12-like molecule to enter the pathway of CO2 fixation. The "B12"-CH3 is substrate for CO fixation mediated by the CODH. CODH reduces CO2 to CO and adds the CO to "B12"-CH3 to form acetyl-[CODH]. Coenzyme A (CoA) then replaces the CODH, resulting in the formation of Acetyl CoA, which is in the heart of biosynthetic metabolism. The net effect is the reduction of 2 CO2 to Acetyl CoA.

Figure 23. The CODH or acetyl CoA pathway of CO2 fixation in the methanogens. See text for explanation.

Finally, in the photosynthetic Green Bacteria, the pathway of autotrophic CO2 fixation involves the reversal of familiar decarboxylation reactions in and around the TCA cycle. The two primary reactions utilized by the Green Bacteria are  two Ferredoxin (FD)-mediated reactions, the reduction of Acetyl CoA to pyruvate, and the reduction of succinyl CoA to alpha-ketoglutarate This is referred to as the reverse TCA cycle for CO2 uptake.

Figure 24. The two ferredoxin (FD)-mediated reactions used for CO2 uptake in the green bacteria are a reversal of the oxidation of keto acids mediated by NAD and CoA (c.f. Figure 4).

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