Fermentation, Other Fuels and Metabolism in Society

Without oxygen to accept electrons at the end of the electron transport chain, the chain stops. NADH can no longer unload its electrons, so the cell's small supply of ${\text{NAD}}^{+}$ quickly gets used up. That is a crisis, because glycolysis needs ${\text{NAD}}^{+}$ to oxidize G3P; without it, even glycolysis (and its 2 ATP) would stop. Fermentation solves exactly this problem. It is glycolysis followed by one or two extra reactions that pass the electrons from NADH onto pyruvate (or a molecule made from it), regenerating ${\text{NAD}}^{+}$. Those extra reactions make no ATP; their only job is to recycle ${\text{NAD}}^{+}$ so that glycolysis can keep making its 2 ATP per glucose. In alcoholic fermentation (yeast and some bacteria), pyruvate first loses a carbon as ${\text{CO}}_2$ to become acetaldehyde, which is then reduced by NADH to ethanol. In lactic acid fermentation (animal muscle cells and bacteria such as Lactobacillus), pyruvate is reduced directly by NADH to lactate (lactic acid), with no ${\text{CO}}_2$ released.

Fermentation is fast but wasteful, so organisms use it when they must. After a sprint, you keep breathing hard: this oxygen debt, now called excess post-exercise oxygen consumption (EPOC), is the extra ${\text{O}}_2$ used to restore ATP and creatine phosphate stores, reload myoglobin and hemoglobin with oxygen, and deal with the lactate. Lactate is carried by the blood to the heart (which oxidizes it for energy) and the liver, which converts it back to pyruvate and then to glucose. (Lactate is not the main cause of the muscle soreness you feel a day or two later; that is mostly from tiny tears in muscle fibres.) Organisms differ in how they handle oxygen. Obligate aerobes (such as humans as whole organisms) need ${\text{O}}_2$ to survive. Facultative anaerobes (such as the yeast Saccharomyces cerevisiae and E. coli) respire aerobically when ${\text{O}}_2$ is present and ferment when it is not; they grow faster with oxygen because they get about 16 times more ATP per glucose. Obligate anaerobes (such as Clostridium botulinum and methane-producing archaea) cannot use oxygen and are often poisoned by it.

Respiration is not only about glucose. The pathways you have learned are a hub that other fuels plug into. Fats (triglycerides) are first split into glycerol and fatty acids. Glycerol is converted into a glycolysis intermediate (related to G3P) and enters glycolysis. Fatty acids are moved into the mitochondrial matrix and cut into 2-carbon pieces by beta-oxidation; each cut produces one acetyl-CoA, one NADH and one ${\text{FADH}}_2$, and every acetyl-CoA then enters the Krebs cycle. Fats are richer in C–H bonds than carbohydrates (they are more reduced), so they have more electrons to hand to ${\text{NAD}}^{+}$ and FAD: fat yields about $37\text{ kJ/g}$ versus about $17\text{ kJ/g}$ for carbohydrate or protein. Proteins are digested into amino acids, which are mainly used to build new proteins. When they are burned for energy, their amino group is first removed (deamination) as ammonia, which is toxic; the liver converts it into urea, which the kidneys excrete. The remaining carbon skeleton enters respiration as pyruvate, acetyl-CoA or a Krebs cycle intermediate, depending on the amino acid.

A cell does not make ATP at a fixed rate; it matches supply to demand by feedback inhibition. The main control point is phosphofructokinase (PFK), the enzyme that catalyzes the third step of glycolysis, the first step committed to breaking the sugar down. PFK is an allosteric enzyme: molecules binding at sites other than the active site change its shape and activity. ATP inhibits PFK (plenty of ATP means slow down), and so does citrate, a signal that the Krebs cycle is backed up. AMP and ADP activate PFK (low energy means speed up). Because PFK sits early in the pathway, controlling it adjusts the whole flow of fuel through respiration. Blocking the pathway at other points can be deadly, as the table shows.

• Food — Bread rises because yeast's alcoholic fermentation releases ${\text{CO}}_2$ bubbles (the ethanol evaporates in the oven). Beer and wine keep both the ethanol and, if sealed, the ${\text{CO}}_2$. In yogurt and cheese, lactic acid bacteria ferment milk sugar (lactose); the lactic acid lowers the pH, which thickens the milk proteins, adds tang and slows the growth of spoilage bacteria.
• Biofuels — Fermenting sugars from corn (widely grown in Ontario) or sugarcane produces ethanol that is blended into gasoline; most Canadian gasoline contains up to 10% ethanol. Supporters point to lower net carbon emissions and income for farmers; critics point to the land, water and fertilizer used, and the "food versus fuel" problem. Research on cellulosic ethanol aims to ferment inedible crop waste instead.
• Bioremediation of oil spills — Oil is made of reduced hydrocarbons, a rich fuel for certain bacteria that oxidize them to ${\text{CO}}_2$ and water by aerobic respiration. After the Exxon Valdez spill (Alaska, 1989), crews added nitrogen and phosphorus fertilizer to the shorelines (biostimulation) to speed up the native oil-eating microbes; after Deepwater Horizon (Gulf of Mexico, 2010), native deep-sea bacteria broke down much of the dispersed oil. Cold water, like that in Canada's Arctic, slows their enzymes and the clean-up.
• Wastewater treatment — Effluent from pulp and paper mills is loaded with dissolved organic matter from wood. Released raw into a river, it would feed bacteria that use up the dissolved oxygen (a high biochemical oxygen demand) and suffocate fish. Canadian mills therefore use secondary (biological) treatment: aerated lagoons or activated-sludge tanks where microbes respire the organic matter before the water is released. Leftover sludge can go to anaerobic digesters, where microbes produce methane biogas that can be burned for energy.
• Diet and exercise — Low-carbohydrate (ketogenic) diets force the body to rely on fat; the liver turns excess acetyl-CoA into ketone bodies that the brain and heart can burn. Weight change still depends on energy taken in versus energy spent, and many fad diets remove whole food groups without evidence of long-term benefit. Endurance training increases the number of mitochondria in muscle cells, raising aerobic capacity; sprint training improves the capacity for anaerobic ATP production.
• Mitochondrial disease — Mutations in mitochondrial DNA (inherited only from the mother) or in nuclear genes for mitochondrial proteins impair oxidative phosphorylation. Organs with the highest energy demand, such as the brain, muscles and heart, are affected most, causing weakness, seizures and developmental problems. Mitochondrial replacement therapy (using healthy mitochondria from a donor egg) is permitted under licence in the United Kingdom, but not in Canada, where heritable genetic changes to embryos are prohibited.