Answer to Bioenergetics Question B-03
Answering this kind of questions is very easy. It just requires recalling the composition and organization of the Respiratory Chain:
NADH.H+ is accumulated. Observe that reductions equivalents (Hydrogens) from NADH.H+ enter the electron transport chain through Complex I (NADH dehydrogenase). It means that Complex I is not working properly.
Hydrogens from FAD can not enter the electron transport chain either. It means that Complex II (succinate dehydrogenase) and other enzymes related to the Electron Transport Chain hat use FAD as cofactor can not be dehydrogenated.
Coenzyme Q (Ubiquinone) is also accumulated in a reduced form.
Which compound is in an oxidized state? Cytochrome c.
It is obvious then that there is a problem between CoQ, that remains reduced, and Cytochrome c, that remains oxidized. (Of course, since Coenzyme Q remains reduced, it can not accept more electrons from FADH2 or from NADH.H+ and these cofactors remain in the reduced state.)
Observing the organization of the electron transport chain, we can say that this new inhibitor probably is affecting Complex III.
Antimycin A is known to block the transfer of electrons between two components of Complex III, (Cytocrom b and c1), so its effect would be very similar to the effects described in the question for the new inhibitor.
Answer to Bioenergetics Question B-04:
Once again, observe the organization of the respiratory chain.
X represents Complex III
Answer to Bioenergetics Question B-05:
ATP synthase is called Complex V of the Respiratory chain (observe the position in the graphic).
During the spontaneous flow of electrons through the ETC (from the component with the most negative to the component with the most positive redox potential), energy is released. This energy is used to pump protons from the mitochondrial matrix to the intermembrane space.
This accumulation of protons in the intermembrane space creates an electrical potential (positive in the outside of the internal membrane) and a pH gradient (outside the internal membrane is more acid, since there are more free H+).
These protons tend to return spontaneously to the matrix, driven by the electrical and the chemical gradient that have been created through their pumping across the membrane.
ATP synthase synthesize ATP from ADP and (P) using the energy released from the spontaneous return of protons from the intermembrane space to the matrix.
That is why it is said that the energetic coupling between the ETC and the Oxidative Phosphorylation is indirect.
Sometimes the terms Electron Transport chain and Respiratory chain are use indistinctly. However, a more strictly use restricts the term Electron Transport Chain to the components of the Respiratory chain responsible of the transport of reduction equivalents from reduced cofactors to Oxygen, forming water, and releasing energy in the process.
Oxidative Phosphorylation is the process of biosynthesis of ATP using the energy that is released in the respiratory chain. (This energetic coupling is indirect, as described before)
The concept of Respiratory chain then would include the concepts of Electron Transport Chain and Oxidative Phosphorylation, and should be described as the set of reactions through which reduction equivalents are transferred from reduced cofactors to Oxygen releasing energy that is used for the biosynthesis of ATP.
The integration between the Electron Transport Chain and the Oxidative phosphorylation, forming the Respiratory chain, is clearly seen in this short movie
This animation also illustrates this relationship:
Voet, Voet, Pratt: Fundamentals of Biochemistry
The coupling of Electron Transport chain and ATP Synthesis