NADH and FADH₂ are electron carriers. They bring electrons from their production point (glycolysis or the Kreb's cycle) to the electron transport chain proteins. The electrons are then passed down the electron transport chain to generate energy.

ATP synthase, which is located on the inner mitochondrial membrane, requires a proton gradient in order to create ATP. This means that the protons need to be pumped across the inner mitochondrial membrane into the intermembrane space. This results in the intermembrane space having the lowest pH in the mitochondria, due to the high proton concentration.

The mitochondrial matrix is the interior of the inner mitochondrial membrane, while the cytosol is not a part of the mitochondria. Neither of these have particularly low pH values. Christae are the folds of the inner mitochondrial membrane that increase its surface area for the electron transport chain processes; though structurally useful in facilitating respiration, the pH of christae is roughly the same as that of the mitochondrial matrix.

After glycolysis is complete, we have generated pyruvate from glucose. We would then expect pyruvate decarboxylation to be the first step after glycolysis in aerobic respiration. When pyruvate is decarboxylated, we generate acetyl CoA, which fuels the Krebs cycle (aka TCA, and citric acid cycle). We would expect the next step after decarboxylation to be the citric acid cycle. In the citric acid cycle we generate FADH₂ and NADH, which release free energy in oxidative phosphorylation to generate the proton gradient across the mitochondrial membrane to fuel ATP synthase.

Oxidative phosphorylation is dependent on the functionality of the electron transport chain. In the electron transport chain, NADH and FADH₂ act as electron donors. The donated electrons are used by protein complexes along the inner mitochondrial membrane to establish the proton gradient in the intermembrane space. Once the electrons have passed through the complexes, they are donated to an oxygen molecule to create water. Oxygen is the final electron acceptor in the chain, and is essential for oxidative phosphorylation to occur.

NAD⁺ is the precursor of NADH, making it another crucial molecule for cell metabolism. NAD⁺ is converted to NADH during glycolysis and the Krebs cycle. A deficiency of NAD⁺ in the mitochondrial matrix will slow the Krebs cycle, which will turn slow oxidative phosphorylation.

Oxygen is necessary to be the last electron acceptor in the electron transport chain. This results in the formation of water.

Oxygen is not involved in glycolysis, which utilizes substrate-level phosphorylation, nor is it needed for the Krebs cycle. NAD⁺ is converted to NADH during glycolysis and the Krebs cycle without involving oxygen.

The two main classifications for transport are active transport and passive transport. Active transport requires the conversion of ATP to ADP, and generally involves pumping molecules against their concentration gradients. Passive transport, in contrast, does not require the use of cellular energy.

Any form of diffusion, either simple diffusion through a membrane or facilitated diffusion via a channel protein, qualifies as passive transport and does not require ATP mediation. Similarly, voltage-gated channels require a certain electrical environment to mediate their function, but do not require the presence of ATP. Proton pumps act to push protons against their concentration gradient, and require the input of cellular energy, thus qualifying as active transport.

ATP synthase is dependent on a proton gradient in the intermembrane space in order to produce ATP. As a result, the toxin will make it inactive. Oxidative phosphorylation would be inhibited in this case, as opposed to substrate-level phosphorylation.

Pyruvate is a product of glycolysis, and would not be affected by the toxin. NADH is key in the establishment of the proton gradient, so we would expect that it would be unable to be oxidized due to the toxin. Protons produced in the conversion of NADH to NAD⁺ (+H⁺) establish the proton gradient. If the gradient is absent, NADH is likely not be oxidized.

Bacteria are prokaryotes. Since prokaryotes do not have any membrane bound organelles, during respiration, protons are pumped from the cytoplasm to the extracellular region between the plasma membrane and the cell wall. This results in a gradient between those two regions, thus extracellular would have a lower pH.

The inhibition of cytochrome C means that the electron transport chain is no longer able to shuttle electrons from complex III to complex IV, which means it is no longer able to accept electrons from electron carriers. As a result, the citric acid cycle would slow down since there would be a build-up of NADH, which allosterically inhibits several enzymes in the citric acid cycle. 

Since the electron transport chain no longer functions properly, there wouldn't be as many  ions being pumped into the intermembrane space, which would increase the pH in the intermembrane space. Also, with the decline in the concentration, oxidative phosphorylation would no longer be efficient, and the cell would have to increase rate of fermentation to increase energy output.