This article throws light upon the two ways used for the formations of ATP in organisms. The ways are: 1. Substrate-Level Phosphorylation 2. Electron Transport Phosphorylation
Way # 1. Substrate-Level Phosphorylation:
Substrate-level phsophorylation is most significant in anaerobes, and yields of ATP are low. Consequently production of biomass is low and the production of fermentation intermediates for downstream metabolism by other microbes is high. Oxidation of organic molecules (removal of e– and H+) allows incorporation of inorganic phosphate and formation of a phosphorylated intermediate.
Examples of such intermediates include 1, 3- bisphosphoglycerate and phosphoenolpyruvate, both in the Embden-Myerhof-Parnas pathway, plus acetyl phosphate, in anaerobes that form acetate.
Hydrolysis of the phosphoryl group of these intermediates releases enough energy to form ATP when they are coupled with ADP and Pi. Acetate kinase catalyzes the transfer of a phosphoryl groups from acetyl phosphate to ADP â†’ ATP.
Way # 2. Electron Transport Phosphorylation:
Electron transport phosphorylation is more important than substrate level phosphorylation in phototrophs and aerobic and facultatively anaerobic chemotrophs. It occurs during respiration and photosynthesis. During C metabolism by chemo-organotrophs. NADH and FADH are produced from oxidation of organic substrates, for example in the TCA cycle.
Electron transport phosphorylation entails transfer of electrons from donors such as NADH (or FADH) with a negative redox potential to acceptors such as O2 with a less negative of positive redox potential. The associated energy change is coupled to the phosphorylation of ADP + Piâ†’ ATP. Electron transport phosphorylation is associated with membranes.
Given that ATP is used to energize soil microbial biomass formation, how much ATP is produced during oxidation of a fixed amount of substrate? Understanding the relationship between substrate oxidized, O2 consumed or electrons (e–) transferred, and ATP formed helps us understand carbon utilization efficiency (CUE; ratio of C consumed/C converted to biomass) on one hand or quantities of alternate electron acceptors needed on the other.
The CUE in turn helps regulate elemental dynamics; for example, N mineralization increases and N immobilization decreases as CUE decreases. Similarly, as the amount of ATP produced per mole of e– decreases, there is an associated increase in the number of moles of O2 needed to generate a fixed amount of ATP, or alternate electron acceptor (e.g., NO3–), needed in the absence of O2.
Under aerobic conditions, each mole of NADH or FADH carries 2e– and each 2e– reduce one atom of O. Therefore under aerobic conditions ATP production from electron transport phosphorylation with O2 as the electron acceptor can be equated to electrons released or atoms of O consumed.
If O is not the terminal electron acceptor, then ATP production from electron transport phosphorylation can be equated only to electrons released. The ratio of ATP production to e– released or atoms of O consumed may be designated the P/O or P/2e– ratio, under aerobic conditions, or P/2e– ratio when O2 is not the terminal electron acceptor.
The P/O or P/2e– ratio may be estimated using either a general rule or slightly more detailed calculations. Generally the oxidation of 1 mol or NADH is considered to generate 3 mol of ATP, and oxidation of 1 mol of FADH generates 2 mol of ATP. Expressed as a ratio of ATP/NADH or ATP/FADH one gets.
3ATP/NADH and 2ATP/FADH
Expressed as P/O ratio the above ratios become:
P/O = 3 for NADH + H+ oxidized by O2 and
P/O = 2 for FADH + H+ oxidized by O2.
Consider the TCA cycle, which generates 3 NADH + H+, 1 FADH + H+ and 1 ATP. According to the general rule the expected ATP production in the TCA cycle becomes:
From NADH + H+: 3 Ã— 3 = 9 mol ATP
From FADH + H+: 1 Ã— 2 = 2 mol ATP
Substrate-level phosphorylation: 1 = 1 mol ATP
Total: 12 mol ATP per turn of the cycle
Each turn of the cycle releases 2 mol of CO2, consumes 2 mol of O2 or 4 atoms of O, and releases 8 electrons. Given the classical concept that each turn of the cycle produces 12 mol of ATP as above, the classical P/O ratio for the entire TCA cycle becomes.
P/O = 12ATP/4O= 3
According to chemiosmotic theory, electrons are passed from donors such as NADH to redox receptors in respiratory complex within the inner membrane or mitochondria or the plasma membrane of bacterial cells. The redox receptors are connected in a series of couples within up to four of these complexes. Reduction of some redox receptors draws an H+ ion from the cytoplasm (n phase of the membrane).
As if flips to the reduced state, the H+ is extruded to periplasmic space (p phase), thereby increasing the H+ concentration in the periplasm. As this process continues a gradient of H+ develops across the membrane with a high concentration in the p phase compared to the n phase.
Consequently an electrical potential, or proton motive force (AP), is developed to drive H+ from the p to the n phase through the ATP synthase complex. The energy released in this process is used to form ATP from ADP.
Consequently the production of ATP per mole of O2 consumed or per 2e– released in determined first by the number of redox couples in the membrane, which determines the moles of H+ extruded to the p phase, and second by the number of moles of H+ that must be driven from the p to the n phase through the ATP synthase complex to produce a mole of ATP.
The product of these two ratios determines the actual P/O ratio:
P/O = H+/2e Ã— ATP/H+(1)
The electron transport chain contains up to four complexes involved in H+ extrusion and electron transport. The number of such complexes through which the electrons flow for a particular electron source determines the value of the H+/2e– ratio as schematically represented in Fig. 18.49.
The H+/2e– ratio appears to vary from 10 for NADH oxidized by O2 to 6 for FADH oxidized by O2. We can calculate the P/O ratio using Eq. (1). Consequently the P/O ratio may be:
P/O = H+/2e Ã— ATP/H+ = 10 Ã— 1/4 = 2.5 for NADH + H+oxidized by O2
and P/O = H+/2e Ã— ATP/H+ = 6 Ã— 1/4 = 1.5 for FADH + H+oxidized by O2.
The ATP produced per turn of the TCA cycle can now be calculated using these values derived from the more mechanistic chemiosmotic theory. Specifically we now get 3 Ã— 2.5 = 7.5 mol of ATP from NADH + H+, 1 Ã— 1.5 = 1.5 mol ATP from FADH + H+, and 1 mol of ATP from substrate-level phosphorylation.
Given the values above from the chemiosmotic theory each turn of the cycle produces 7.5 + 1.5 + 1 = 10 mol of ATP per turn of the TCA cycle. The more detailed P/O ratio for the entire TCA cycle now becomes:
P/O = H+/2e Ã— ATP/H+ = 6 Ã—1/4 = 1.5
Photosynthesis is the ultimate source of energy to allow soil organisms to work. Photosynthesis requires no oxygen (although it may partially cycle O2) and may or may not generate O2. If photosynthesis uses HOH as an electron donor, as it does for photo aquatrophs, then it generates O2 and is called oxygenic photosynthesis (Table 18.11 Eq. ).
Photosynthesis that uses a reduced mineral such as H2S as electron donor, as is the case with photolithotrophs, produces SÂ° (Eq. ) (or SO42-; Eq. ), which is called anoxygenic photosynthesis.
All anoxygenic photosynthetic organisms can use H2 as H donor; in addition the purple non-sulfur bacteria (Rhodospirillaceae) and the green gliding bacteria (Chloroflexaceae) can use organic substrates, and the green sulfur bacteria (Chromatiaceae) can use H2S and organic substrates, the purple sulfur bacteria (Chlorobiaceae) can use H2S, and but not organic substrates.
Photon activation of electron in the photosynthesis reaction site (PS Rxn) generates cyclic transfer of electrons through a series of redox couples, resulting in formation of ATP, and eventually the electron returns to its ground state and to the PS Rxn site. NAD+ is reduced using reverse electron transfer driven by AP generated from photosynthesis.
Subsequent trans-hydrogenation allow NADH to reduce NADP+ to NADPH, which is used to reduce C in the Calvin cycle. In the Chlorobiaceae CO2 is reduced by reversal of the TCA cycle, all other anoxygenic photosynthetic organism’s use the Calvin cycle. NADH is used to reduce CO2, so the electron and H transfer to CO2 in anoxygenic phototrophic bacteria can be summarized by Eq.  in Table 18.12.
In oxygenic photosynthesis (Table 18.11, Eq. ) ATP is synthesized during e–transfer from HOH to NADP+, and pseudo cyclic e– transfer without formation of NADPH meets additional ATP needs. The reducing equivalents (NADPH + H+) are used in the Calvin cycle for reduction of C.