Fermentation (biochemistry)

# Overview
Fermentation is a process of energy production in a cell under anaerobic conditions (with no oxygen required). In common usage fermentation is a type of anaerobic respiration, however a more strict definition exists which defines fermentation as respiration under anaerobic conditions with no external electron acceptor. Fermentation does not necessarily have to be carried out in an anaerobic environment, however. For example, even in the presence of abundant oxygen, yeast cells greatly prefer fermentation to oxidative phosphorylation, as long as sugars are readily available for consumption .
Sugars are the common substrate of fermentation, and typical examples of fermentation products are ethanol, lactic acid, and hydrogen. However, more exotic compounds can be produced by fermentation, such as butyric acid and acetone. Yeast famously carries out fermentation in the production of ethanol in beers, wines and other alcoholic drinks, along with the production of large quantities of carbon dioxide. Anaerobic respiration in mammalian muscle under periods of intense exercise (which has no external electron acceptor) is, under the strict definition, a type of fermentation.

# History
French chemist Louis Pasteur was the first zymologist, when in 1857 he connected yeast to fermentation. Pasteur originally defined fermentation as respiration without air.
Pasteur performed careful research and concluded, "I am of the opinion that alcoholic fermentation never occurs without simultaneous organization, development and multiplication of cells.... If asked, in what consists the chemical act whereby the sugar is decomposed ... I am completely ignorant of it.".
The German Eduard Buchner, winner of the 1907 Nobel Prize in chemistry, later determined that fermentation was actually caused by a yeast secretion that he termed zymase.
The research efforts undertaken by the Danish Carlsberg scientists greatly accelerated the gain of knowledge about yeast and brewing. The Carlsberg scientists are generally acknowledged with jump-starting the entire field of molecular biology.

# Reaction
The reaction of fermentation differs according to the sugar being used and the product produced. Below the sugar will be glucose (C6H12O6) the simplest sugar, and the product will be ethanol (2C2H5OH). This is one of the fermentation reactions carried out by yeast, and which is used in food production.
Chemical equation
Word equation
The actual biochemical pathway the reaction takes varies depending on the sugars involved, but commonly involves part of the glycolysis pathway, which is shared with the early stages of aerobic respiration in most organisms. The later stages of the pathway vary considerably depending on the final product.

# Energy source in anaerobic conditions
Fermentation is thought to have been the primary means of energy production in earlier organisms before oxygen was at high concentration in the atmosphere and thus would represent a more ancient form of energy production in cells.
Fermentation products contain chemical energy (they are not fully oxidized) but are considered waste products since they cannot be metabolized further without the use of oxygen (or other more highly-oxidized electron acceptors). A consequence is that the production of ATP by fermentation is less efficient than oxidative phosphorylation, where pyruvate is fully oxidized to carbon dioxide. Fermentation produces 4 ATP molecules per molecule of glucose compared to 38 by aerobic respiration: 8 are produced from FADH2, and 30 are produced from NADH, for a total of 38. Since 2 ATP molecules are used in glycolysis, the net yield for fermentation is 2 ATP versus 36 ATP from aerobic respiration.
Aerobic glycolysis is a method employed by muscle cells for the production of lower-intensity energy over a longer period of time when oxygen is plentiful.  Under low-oxygen conditions, however, vertebrates use the less-efficient but faster anaerobic glycolysis to produce ATP.  The speed at which ATP is produced is about 100 times that of oxidative phosphorylation.  While fermentation is helpful during short, intense periods of exertion, it is not sustained over extended periods in complex aerobic organisms. In humans, for example, lactic acid fermentation provides energy for a period ranging from 30 seconds to 2 minutes.
The final step of fermentation, the conversion of pyruvate to fermentation end-products, does not produce energy. However, it is critical for an anaerobic cell since it regenerates nicotinamide adenine dinucleotide (NAD+), which is required for glycolysis. This is important for normal cellular function, as glycolysis is the only source of ATP in anaerobic conditions.

# Products
Products produced by fermentation are actually waste products produced during the reduction of pyruvate to regenerate NAD+ in the absence of oxygen. Bacteria generally produce acids. Vinegar (acetic acid) is the direct result of bacterial metabolism (Bacteria need oxygen to convert the alcohol to acetic acid). In milk, the acid coagulates the casein, producing curds. In pickling, the acid preserves the food from pathogenic and putrefactive bacteria.
When yeast ferments, it breaks down the glucose (C6H12O6) into exactly two molecules of ethanol (CH3CH2OH) and two molecules of carbon dioxide (CO2).
- Ethanol fermentation (performed by yeast and some types of bacteria) breaks the pyruvate down into ethanol and carbon dioxide. It is important in bread-making, brewing, and wine-making. When the ferment has a high concentration of pectin, minute quantities of methanol can be produced. Usually only one of the products is desired; in bread the alcohol is baked out, and in alcohol production the carbon dioxide is released into the atmosphere.
- Lactic acid fermentation breaks down the pyruvate into lactic acid. It occurs in the muscles of animals when they need energy faster than the blood can supply oxygen. It also occurs in some bacteria and some fungi. It is this type of bacteria that converts lactose into lactic acid in yogurt, giving it its sour taste.
In vertebrates, during intense exercise, cellular respiration will deplete oxygen in the muscles faster than it can be replenished. An associated burning sensation in muscles has been attributed lactic acid causing a decrease in the pH during a shift to anaerobic glycolysis. While this does partially explain acute muscle soreness, lactic acid may also help delay muscle fatigue, although, eventually the lower pH will inhibit enzymes involved in glycolysis. Contrary to currently popular belief, the lactic acid is not the primary causes for the drop in pH, but rather ATP-derived hydrogen ions.
Delayed onset muscle soreness cannot be attributed to the lactic acid and other waste products as they are quickly removed after exercise. It is actually due to microtrauma of the muscle fibres. Eventually the liver metabolizes the lactic acid back to pyruvate.
Hydrogen gas is produced in many types of fermentation (mixed acid fermentation, butyric acid fermentation, caproate fermentation, butyric acid fermentation, butanol fermentation, glyoxylate fermentation), as a way to regenerate NAD+ and FAD from NADH and FADH2. Electrons are transferred to ferredoxin, which in turn is oxidized by hydrogenase, producing H2. Hydrogen gas is a substrate for methanogens and sulphate reducers, who keep the concentration of hygdrogen sufficiently low to allow the production of such an energy-rich compound. 
Some anaerobic eukaryotic microorganisms also produce hydrogen gas, in their hydrogenosomes. The concentration of hydrogen gas is kept low by symbionts such as methanogens that reside in the cytosol of the eukaryot.

# Enzymology
Enzymology is the scientific term for yeast oriented fermentation. It deals with the biochemical processes involved in fermentation, with yeast selection and physiology, and with the practical issues of brewing. Enzymology is occasionally known as zymology or zymurgy.