Carbon (C), hydrogen (H), nitrogen (N), and oxygen (O) make up 96.5% of an organism's weight. However, only a very small percentage of the 92 naturally occurring elements may be found in living creatures. In order to form molecules, the atoms of these elements must first form covalent bonds with one another. Because they are one hundred times more powerful than the thermal energy that is contained within a cell, covalent bonds frequently resist being pulled apart by thermal motions. Furthermore, covalent bonds are typically only broken through certain chemical reactions with other atoms and molecules. It is possible for two separate molecules to be held together by noncovalent bonds, which are substantially weaker than covalent ones.

The cellular functions that occur on the inside of a cell are carried out in an aqueous environment. The conditions that existed in that primordial home, the ocean, which is where life first emerged on Earth, left an indelible mark on the chemistry of living things.

In each molecule of water, the two hydrogen atoms and the oxygen atom are connected to one another by covalent bonds (H2O). Both of these bonds are highly polar because of the strong electron attraction that the oxygen has in contrast to the weak attraction that the hydrogen has. As a consequence of this, the two hydrogen atoms in a water molecule have a disproportionately high level of positive charge, whereas the oxygen atom has a disproportionately high level of negative charge. This leads to an imbalanced distribution of electrons within the water molecule. The electrical attraction that exists between two water molecules can lead to the formation of hydrogen bonds. This occurs when the positively charged H atom of one water molecule approaches the negatively charged O atom of another water molecule. These bonds are far less stable when compared to covalent connections, and they are easily broken by the random thermal motions that are caused by the heat energy that is radiated off of the molecules. As a result, every connection is temporary. However, the combined effect of a large number of weak links could have a considerable influence. For example, because each water molecule has two H atoms, it is possible for it to build hydrogen connections with two other water molecules. This results in the formation of a network in which hydrogen bonds are constantly forming and breaking. Because of the hydrogen bonds that bind its molecules together, water is a liquid at room temperature even though its boiling point is high and its surface tension is high. This is the only reason for these properties.

Alcohols and other compounds with polar bonds that are able to dissolve easily in water are those that have the potential to establish hydrogen bonds with the water. Ion-carrying molecules, which are also known as charged molecules, get along swimmingly with water. These molecules are known as being hydrophilic, which is a fancy term that says they are drawn to the presence of water. In the aquatic environment of a cell, this category naturally contains a variety of chemicals, including sugars, DNA, RNA, and the vast majority of proteins. To give just a few examples: sugars, DNA, and RNA. Hydrophobic molecules, on the other hand, are uncharged and produce very few or no hydrogen bonds, which prevents them from dissolving in water. Hydrophobic molecules are also known as water-hating molecules. An excellent example of this would be hydrocarbons. Because each of the hydrogen atoms in these molecules is covalently attached to the carbon atoms through a bond that is predominately nonpolar, it is impossible for these molecules to successfully form hydrogen bonds with the molecules of other substances.

Ionic bonds, hydrogen bonds, van der Waals attractions, and a fourth force that can push molecules together known as the hydrophobic force all play key parts in the specific binding of different molecules that takes place during the course of a living organism's existence. Even though the strength of a single noncovalent interaction between two molecules would be far too weak to be effective in the face of thermal movements, the sum of the energies of these interactions can provide a significant force between the molecules. This is true despite the fact that each interaction, on its own, would provide far too little force. Because of this, the complimentary surfaces of two macromolecules can commonly keep those two macromolecules together due to different sets of noncovalent attractions.

One of the most fundamental kinds of chemical reactions takes place when a molecule that has a strongly polar covalent connection between a hydrogen and another atom dissolves in water. This form of reaction has substantial consequences on the cells that it occurs in. The positively charged nucleus of hydrogen, denoted by the symbol "H+," is produced when a hydrogen atom in a molecule gives up almost all of its electrons to its partner atom. This process results in the formation of a proton. When the polar molecule is surrounded by water molecules, the proton will be pulled to the partial negative charge on the O atom of an adjacent water molecule. This will occur because water molecules have partial negative charges. This proton can readily detach from its original companion and join the oxygen atom of the water molecule in order to produce a hydronium ion, which is denoted by the symbol H3O+.

Acids are chemicals that, when dissolved in water, give out protons, which ultimately leads to the creation of the anion H3O+. When there is a higher concentration of H3O+ in the solution, the acidity of the solution will increase. Because protons move from one water molecule to another, H3O+ can be found in pure water at a concentration of 10-7 M. This is because H3O+ is produced when water molecules exchange protons. It is usual practice to refer to the concentration of H3O+ as the H+ concentration, despite the fact that the vast majority of protons found in an aqueous solution are H3O+.

The concentration of H3O+ is expressed on a logarithmic scale, also known as the pH scale, in order to avoid the use of extremely high numbers. The pH of pure water is 7.0, which classifies it as neutral and indicates that it does not have an acidic (pH 7) or basic (pH > 7) charge.

The ease with which an acid can give up its proton to water determines whether or not it is considered to be a strong or weak acid. The proton content of hydrochloric acid (HCl), one of the more powerful acids, is quickly depleted. Acetic acid, on the other hand, is considered to be a weak acid due to the fact that, when dissolved in water, it holds onto its proton more tenaciously. The majority of the important acids that can be found in cells are of the weak acid variety. These include molecules that include a carboxyl (COOH) group.

Due to the fact that many distinct classes of molecules found within cells are able to readily accept the proton of a hydronium ion and undergo a transformation as a result, the concentration of H3O+ that is found within a cell (its acidity) needs to be carefully managed. When there is a low concentration of H3O+ in solution, acids, particularly weak acids, have a tendency to lose their protons more easily. On the other hand, acids have a tendency to regain their protons when there is a large quantity of H3O+ in solution.

A base is the opposite of what an acid is. Any molecule that is capable of accepting a proton from a water molecule is considered to be a base. Basic sodium hydroxide, denoted by the chemical formula NaOH, quickly dissociates into the ions Na+ and OH- when dissolved in water (the term "alkaline" is also used). Due to the presence of this quality, NaOH is a powerful base. On the other hand, weak bases, which are defined as those that have a low tendency to reversibly receive a proton from water, are far more important in living cells. An amino (NH2) group is present in a significant amount of biologically important substances. Because this group is capable of producing OH- by removing a proton from water, we can classify it as a weak base: –NH2 + H2O → –NH3 + + OH–

Because an OH- ion and an H3O+ ion must combine in order to produce two water molecules, an increase in the concentration of OH- results in a decrease in the concentration of H3O+, and vice versa. A solution made of pure water has an identical concentration (10-7 M) of both types of ions, which gives it a neutral charge. The presence of buffers, which are weak acids and bases that can either release or take up protons at a pH of 7, also keeps the interior of a cell close to neutrality, thereby maintaining an environment that is essentially consistent despite the presence of a wide variety of different environmental factors.