Cellular respiration divided into three steps: glycolysis, citric acid cycle (also known as the Krebs or TCA cycle), and the electron transport chain (also known as oxidative phosphorylation). While glycolysis takes place in the cytosol, the other two steps occur in the mitochondria.

The major processes that occur in mitochondria are the citric acid cycle and the electron transport chain. The citric acid cycle forms electron carries  that are used in the electron transport chain to reduce oxygen to water and produce ATP.

ATP Synthase work by converting the energy in the protons electrochemical gradient into production of ATP. This gradient is oriented across in the inner mitochondrial membrane so that protons is at a higher concentration in the intermembrane space than the matrix, and thus will flow from the intermembrane space to the matrix. This gradient is produced by the electron transport chain pumping protons from the matrix across the inner membrane to the intermembrane space.

During the reduction of oxygen to water, reactive oxygen species such as superoxide or hydrogen peroxide can be produced. These molecules are highly reactive and such can react with proteins or DNA to cause cellular damage or mutations. 

 produced by glycolysis and the citric acid cycle and  produced by the citric acid cycle as electron carries. These molecules "drop off" electrons to the complexes in the electron transport chain.  is also an electron carrier, however is main role is during the Calvin cycle of photosynthesis. 

The electron transport chain (ETC) is responsible for oxidative phosphorylation, resulting in the production of ATP. The ATP is produced by a proton gradient made as electrons are transported throughout the chain. Inhibition of this process by "Substance Y" will block the formation of a proton gradient. Blocking the proton gradient will not allow for oxidative phosphorylation to occur, thus greatly decreasing the amount of ATP produced.

The correct answer to this question is oxygen.

Oxygen is the final electron acceptor of electrons as they are passed down the electron chain. The electrons move and combine with oxygen to produce . Water and hydrogen are just byproducts of the acceptance of the electron, not the acceptor. The electrons are actually brought to the electron transport chain by carries like  and .

This is because glucose can net 36 ATP, NADH actually nets 3, FADH2 can net 2, and pyruvate can net 15. This answer involves a careful examination of respiration processes.

FADH2 is directly attached onto the second protein of the electron transport chain and therefore the electrons of FADH2 (electron carrier) are dropped off at the second protein not the first. As a result, the electrons from FADH2 do not pump as much electrons across the membrane as NADH. This results in a lower proton gradient created from FADH2 then NADH and therefore less ATP production from FADH2. 

Remember that NADH and FADH2 are electron carriers and do not directly create any energy. The movement of the electrons through the electron transport chain also does not create energy directly, but does create a proton gradient that is later used to create energy. The movement of protons down its proton gradient through ATP synthase does, however, generate energy. It actually generates around 30 ATP molecules per one glucose.