Fermentation Basic biochemistry

All living things require energy to continue living, and many different ways of obtaining that energy are found in nature. Plants convert the energy in sunlight into chemical energy their cells can use and store. Sugars, starches and fats are the most common energy storage products. Animals, fungi, and most bacteria break down the chemicals that are stored by plants to extract the energy they contain.

There are two fundamental methods of extracting this energy - with and without the assistance of oxygen. Energy production assisted by oxygen is six times more efficient than without it, so cells preferentially use oxidative metabolism whenever possible.

Fermentation is a method microorganisms use for extracting energy from food when oxygen is not available. In fermentation, complex molecules (like sugars) are partially broken down into simpler molecules, and the energy stored in the chemical bonds is released and captured by the cell.

There are many, many different kinds of fermentation, and most of them result in the production of organic acids (acetic acid, lactic acid, butyric acid, etc.). These fermentations are used to produce familiar food products such as sauerkraut, yogurt, many cheeses and black tea.

Some organisms, including many species of yeast, are capable of fermenting to produce an alcohol and carbon dioxide gas. Exploitation of these organisms is one of the oldest of human industries.

No natural organism does just one thing; as yeast grow and produce alcohol, they also produce acids via other types of fermentation. The enzymes that manage the reactions within the cell are also not perfect, and a percentage of the reactions in the cell produce a different result than expected. These mistakes become much more common when temperatures or chemical concentrations are high.

Enzymes are very large molecules with specially-shaped cavities in them. These cavities are just the right size and shape for a particular molecule (or group of molecules) to fit into, and when the molecules sit in the cavity just right, a chemical reaction happens. This process is driven by the energy present in all material - the constant collisions of molecules against one another, millions of times a second. The more concentrated a substance is, the more chances for it to collide with another molecule, whether in the correct position or not. The higher the temperature, the more forceful the collisions, which makes it more likely that an incorrect position (or an incorrect molecule) might lodge in the cavity, leading to an undesired reaction.

Another key point about biological (enzymatic) reactions is that they can run in both directions! An enzyme that makes a compound can also unmake it, and the end product of the reaction fits in the pocket in the side of the enzyme just as nicely as the starting compound. The reverse reaction is usually slower than the forward one though, which is why we can obtain an end product!

This means that these reactions slow down as their end products build up and the starting products are consumed - it becomes more likely that the enzyme that turns acetaldehyde into alcohol will encounter an alcohol molecule than one of acetaldehyde. In the same way, the acids produced by the yeast also build up, lowering the pH of the solution, which makes metabolism and growth more difficult. (This is the reason many preserved foods, like pickles and sauerkraut are acidic - bacteria have a very hard time at low pH).

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