Matter is made of atoms. There are around a hundred of different ones but only a handful are really important to understand fermentation. The word "element" is used to talk about the kind of atoms: there are billions atoms but only slightly more than a hundred elements. Every element is represented by one or two letters. For instance: hydrogen (H), oxygen (O), nitrogen (N), carbon (C), sulfur (S), sodium (Na). It is important that the second letter not be a capital (the first one is always a capital letter): CO is carbon monoxide (one atom of carbon C et one atom of oxygen O), colorless, tasteless and lethal gas, whereas Co is cobalt (metal).

Some molecules are useful in the following explanations but may be not linked to fermentation. The fact that a molecule appears in this text does not automatically imply it will necessarily be a part of fermentation.

Every atom has a nucleus made of protons and neutrons around which "rotate" electrons. The number of protons, which is equal to the number of electrons, is characteristic of the element and is called the atomic number. Its value is 1 in the case of hydrogen (H), 2 in helium (He), 82 for lead (Pb).

The periodic table

All elements are stored in a table called the periodic table of the elements (also known as Mendeleev table, figure 1.) They are sorted by increasing atomic number.

Electrons are organized in shells around the nucleus (somewhat like an onion). In the table, the row indicates the number of these electronic shells. The lighter atoms have few electrons (electrons are written e-, the - sign is to remind us that they are negatively charged) and therefore few shells: they are at the top of the table. Hydrogen and helium have only one shell, carbon, oxygen, nitrogen have two of them, etc. Electrons fill internal shells first. When an electronic shell is full, they go to the next. The first one can have 2 electrons and the second one can hold 8 e-.  Hydrogen has 1 e-, helium has 2. Lithium (Li), which has 3 electrons, needs a second shell to store its third electron, so we switch to the next row.

periodic table
Periodic chart (elements 58 through 71 and 90 through 103 are not shown)

In every row, elements are sorted by increasing number of electrons in the outer shell. Atoms like it when things are well organized, so they do not want electronic shells to be half empty. Therefore they will try to complete their outer shell (if only a few electrons are enough to fill it) or they will try and empty it if it contains only a few electrons. Elements from the same column all have the same number of electrons in their outer shell (called the valence shell). As this is the shell important to chemistry, elements from the same column have the same kind of behavior.


Some atoms prefer to stay alone (helium, neon, argon, etc.), they are called noble gases. They are the elements from the last column, their outer shell is full, so they do not feel they need to interact with other atoms, they are happy as they are. For this reason, they are not very reactive.

Elements from the first column (called alkalis) have one electron in their last shell, one says that their oxidation number is 1. Those of the column on the left of noble gases (they are called halogens) need one electron to complete their outer shell (oxidation number -1). Not surprisingly these atoms like each other. When they meet and form a molecule, their electron problem is solved. Molecules formed are for instance HCl (hydrochloric acid), NaCl (sea salt), etc.

For the same reason, atoms in the column left of halogens will meet atoms from the second column (alkaline earth metals) and form magnesia (MgO), lime  (CaO), etc. They can also form molecules with 2 atoms from the first column: H2O (water, figure 2), H2S, NaOH (caustic soda), etc. the index 2 in H2O indicates that the molecule is made of 2 hydrogen atoms and 1 oxygen atom.

   water molecule ethanol molecule
Water and ethanol [B1]

It can also happen that atoms form molecules with atoms of their own species: O2 (oxygen of air), O3 (ozone), N2 (nitrogen of air), etc. Or they associate with different atoms: CO2 (carbon dioxide), CH4 (methane), C2H5OH (ethanol, figure 2), etc. sharing their electrons. These electrons will be considered as belonging to both atoms. After the periodic table (figure 1), the atomic number of oxygen is 8, so there are 8 electrons total, the first shell is filled first using 2 electrons, there are six of them on the outer shell. Two oxygen atoms together have 12 e- in their outer shells. That is 4 each and 4 shared. The total is twelve and each atom feels that the 4 shared electrons belong to him so he has 4 + 4 = 8 electrons on his outer shell. Oxygen atoms are therefore happier in an O2 molecule than isolated.

When atoms form molecules to have an oxidation number of 0, one says the molecule is ionic. When they share one or more electrons, the molecule is called covalent.

Organic chemistry

It is the chemistry of carbon, because carbon is the main constituent of organic compounds. It is the chemistry of life because these molecules are produced and used by living beings. "Organic" in organic chemistry does not mean healthy food, no fertilizer, no preservatives...

acid, alcohol, aldehyde and ester molecules
Acid, alcohol, aldehyde, ester ('R' is a radical).

When oxygen atoms are added to carbon chains, one gets "functions" (acid, alcohol, etc.) which are characteristic of the molecule. Figure 3 shows the main functions. 'R' represents a radical (any carbon chain). All molecules with the same functions have something in common, they will have the same chemistry. There are differences (ethanol is the alcohol produced during fermentation, methanol -- another alcohol -- is toxic) but chemical reactions are more or less the same. The esterification reaction for instance can be written in the form:

R1-COOH  +  R2-OH -> R1-COO-R2  +  H2O

where the radicals R1 et R2 can be more or less any carbon chain, they will not modify the reaction.

An oxygen atom and a hydrogen atom at the end of the chain give an alcohol. Its name is obtained by adding the suffix -ol to the name of the carbon chain. Ethanol (figure 2), for instance, is ethane (C2H6) and an -OH group characteristic of alcohols.

A -COOH group is characteristic of organic acids (see tartaric and malic acids figure 7 and acetic acid figure 21). Names are of the form "xxxic acid". A very precise nomenclature based on their chemical formula is not used. Names come from where acid is found: formic acid is the acid produced by ants (formica in latin), citric acid is from citrus, etc.

As far as fermentation is concerned, the main aldehyde is acetaldehyde (CH3COH) that is made by yeasts during fermentation and that will eventually be turned into alcohol (figure 6). Therefore no or little acetaldehyde remains at the end of fermentation.

Esters are also naturally produced during fermentation. The higher the temperature the higher the production of esters.

One can find books or web sites entirely dedicated to organic chemistry. Formulas and names can get awfully huge, so be careful.


Atoms and molecules are electrically neutral, that is, they have as many electrons (negative) as protons (positive). When the are in aqueous solution (in water) they can give or take an electron, they are then called ions. Ions are not electrically neutral: they either have an excess of electrons (then they are negatively charged, and are called anions) or a deficit of electrons (positive charge, called cations).

If sea salt crystals are poured into water, salt will dissolve, which means there will not be salt on one side and water on the other side (which is what happens when flour is added to water: flour does not dissolve and remains solid). Sea salt (NaCl) will be splitted into Na+ and Cl- ions. We have already said that sodium (Na) is in the first column, so it tries to lose an electron whereas chlorine (Cl) is an halogen and tries to gain 1 e-.

The index (number at the bottom) indicates the number of atoms, the exponent (at the top) indicates the charge. Ca2+ means: a calcium atom with a double positive charge. Ca2+, which does not exist, would be 2 calcium atoms with a positive charge. So care must be taken to write everything properly, as slightly different writings can means completely different things.

May 29th 2002