It is the oxygen deficiency that leads to a network of events ending in apoptosis: – slowing down of the transport of electrons along the respiratory chain; – a decrease in the electrochemical potential difference of hydrogen ions on the inner mitochondrial membrane; – swelling of mitochondria with disruption of the integrity of the outer mitochondrial membrane; – exit from the intermembrane space into the cytoplasm of cytochrome C, which leads to disconnection from the respiratory chain of cytochrome oxidase and to the termination of direct transfer of electrons to oxygen (disconnection of cytochrome oxidase from the respiratory chain is an elegant evolutionary device that excludes the possibility of senseless and therefore harmful “eating” oxygen that is already deficient under conditions of hypoxia); – activation of the reverse transfer of electrons (against the redox potential of the electron carriers of the respiratory chain) entering the respiratory chain from dehydrogenases of the second conjugation point; – increasing the concentration of the reaction product of one-electron reduction of Coenzyme Q; – chemical reaction of oxygen with the Coenzyme Q radical, leading to an increase in the concentration of free oxygen radicals.

1.2. The main results of the impact of free oxygen radicals generated by dying mitochondria. The most important result of the action of free oxygen radicals is the chemical modification of mitochondrial DNA, which is surrounded on all sides by outgrowths of the inner membrane (cristae), in which the enzymes of the respiratory chain are localized. The number of DNA copies in mitochondria reaches 10, and the number of mitochondrial DNA copies per cell is several tens of thousands due to the large number of mitochondria in it.

The main function of free oxygen radicals generated by the respiratory chain of mitochondria of cells that have entered apoptosis, which is positive for the body, is the covalent modification of mitochondrial DNA and mitochondrial enzymes of its duplication. The meaning of these processes is the inactivation or neutralization of mitochondrial DNA, which is in origin and structure (without introns and without histones) bacterial DNA, capable of integrating into cellular DNA and thereby facilitating cell transformation [20].

This does not mean that the appearance of free oxygen radicals (like many other, especially chemically active metabolites) in the wrong place and/or in unusually high concentrations exceeding the capabilities of antioxidant protection does not harm the cell and the body as a whole. This situation, apparently, is realized under conditions of intense radiation exposure.

The function of free oxygen radicals generated by NADPH oxidase of the plasma membrane of immunocompetent cells is also similar, the activity of which increases when they interact with bacteria and viruses. The meaning of the generation of free oxygen radicals, and in this case, lies in the covalent modification of foreign DNA. To destroy a bacterium or cell means, first of all, to damage its DNA.

The pathogenic function of an excess of antioxidants consumed by humans is to reduce the rate of mitochondrial DNA detoxification by free oxygen radicals, which, apparently, leads to an increase in the likelihood of oncological diseases [10].

1.3. Safety of free oxygen radicals generated by the mitochondria of a dying cell for neighboring cells. Due to the high chemical reactivity of free oxygen radicals and due to the small distances of their free path, neighboring cells with intact mitochondria are probably not susceptible to the pathogenic effects of these radicals.

First, in order to leave the mitochondria of a dying cell and get into a neighboring healthy cell, free radicals need to overcome many membranes with built-in densely packed proteins that contain a large number of potential targets for free radicals (unsaturated bonds in lipids and proteins; strong and numerous reducing agents in the form of natural antioxidants – vitamins, glutathione and thiol groups of proteins; as well as enzymes – catalase, peroxidase and superoxide dismutase, which neutralize radicals.

Secondly, even single free radicals that have reached the mitochondria of a neighboring healthy cell are able to engage in the normal functioning of their respiratory chains due to a chemical reaction with Coenzyme Q, a 50-fold excess of which in relation to other electron carriers (cytochromes, ferredoxins and dehydrogenases) is present in the inner membrane of mitochondria and diffuses freely in the membrane.

2. Activation of the disordered process of cell death – necrosis under conditions of deep or prolonged hypoxia, harmful to the surrounding tissues and to the organism as a whole. Disruption of apoptosis into necrosis is caused by a deficiency of oxygen and, consequently, a deficiency of free energy in the form of ATP and NAD(P)H, which are necessary to bring the energy-dependent process – apoptosis to the logical end.

3. Inflammation and autoimmune diseases. One of the last substrates inaccessible to proteases involved in apoptosis are transmembrane proteins of the plasma membrane. These proteins are present in apoptotic bodies, the end products of apoptosis, which are successfully captured by cells and digested by lysosomal enzymes of cells of the immune system. Interruption of this sequence of events under hypoxic conditions leads to the appearance of transmembrane proteins in the blood and to inflammation. The production of antibodies simultaneously against the external and intracellular epitopes of such proteins is likely to lead to autoimmune diseases accompanied by inflammation.