Any substance that has mass and occupies space is defined as matter. All matter is composed of atoms. An atom consists of a nucleus of protons and neutrons surrounded by a cloud of electrons. Electrons are located in regions called orbitals. Atoms in which the number of electrons does not equal the number of protons are known as ions. An atom having more protons than electrons is called a cation. An atom having fewer protons than electrons is called an anion. Atoms with the same atomic number have the same number of protons and are said to be the same element. Atoms of a single element that possess a different numbers of neutrons are called isotopes of that element. The atomic mass of an element is equal to the sum of the masses of its protons and neutrons. An atom’s electrons determine its chemical behavior. Electrons have discrete energy levels. No orbital can contain more than two electrons, but each energy level consists of multiple orbitals. Electrons that are the same distance from the nucleus have the same energy, even if they occupy different orbitals. Electron orbitals are arranged so that as they are filled, this fills each energy level in successive order, and this is what is responsible for the chemical reactivity of elements. During some chemical reactions, electrons are transferred from one atom to another. In such reactions, the loss of an electron is called oxidation, and the gain of an electron is called reduction. Redox reactions occur when oxidation and reduction are coupled.
Valence electrons and their interactions are the basis for the differing chemical properties of elements. The octet rule states that atoms tend to establish completely full outer energy levels. Most chemical behavior can be predicted from this simple rule, combined with the tendency of atoms to balance positive and negative charges. Of the 94 naturally occurring elements, only 12 (in descending order of abundance: oxygen, carbon, hydrogen, nitrogen, sodium, chlorine, calcium, phosphorus, potassium, sulfur, iron, and magnesium) are found in living systems in more than trace amounts (0.01% or higher).
A group of atoms held together by energy in a stable association is called a molecule. When a molecule contains atoms of more than one element, it is called a compound. Ionic bonds form when atoms with opposite electrical charges (ions) attract. Covalent bonds form when two atoms share one or more pairs of valence electrons. Unlike ionic bonds, covalent bonds are formed between two individual atoms, giving rise to true, discrete molecules. An atom that requires two, three, or four additional electrons to fill its outer energy level completely may acquire them by sharing its electrons with two or more other atoms. Atoms differ in their affinity for electrons, a property called electronegativity. For bonds between identical atoms, the affinity for electrons is the same and the electrons are equally shared; such bonds are termed nonpolar. For atoms that differ greatly in electronegativity, electrons are not shared equally; such bonds are termed polar covalent bonds. The formation and breaking of chemical bonds is termed a chemical reaction. All chemical reactions involve the shifting of atoms from one molecule or ionic compound to another, without any change in the number or identity of the atoms. We refer to the original molecules before the reaction as reactants, and the molecules resulting from the chemical reaction as products. The extent to which chemical reactions occur is influenced by temperature, the concentration of reactants and products, and catalysts. Many reactions in nature are reversible.
Water consists of an oxygen atom bound to two hydrogen atoms by two single covalent bonds. The electronegativity of O is much greater than that of H, and so the bonds between these atoms are highly polar. The polarity of water underlies water’s chemistry and the chemistry of life. One of the most important chemical properties of water is its ability to form weak chemical associations, called hydrogen bonds. The polarity of water allows water molecules to be attracted to one another – that is, water is cohesive. Water’s cohesion is responsible for its being a liquid, not a gas, at room temperatures. The cohesion of water is also responsible for its surface tension. The polarity of water causes it to be attracted to other polar molecules as well. This attraction for other polar substances is called adhesion. Water adheres to any substance with which it can form hydrogen bonds. The attraction of water to substances that have electrical charges on their surface is responsible for capillary action.
Water has a high specific heat; a large input of thermal energy is required to break the many hydrogen bonds that keep individual water molecules from moving about. Water heats up more slowly than almost any other compound and holds its temperature longer. Because organisms have a high water content, water’s high specific heat allows them to maintain a relatively constant internal temperature. Water’s high heat of vaporization facilitates cooling by evaporation. Solid water is less dense than liquid water because the hydrogen bonds in ice space the water molecules farther apart. This is important ecologically because it means bodies of water freeze from the top down and not the bottom up. Polar molecules and ions are soluble in water. Water organizes nonpolar molecules; the tendency of nonpolar molecules to aggregate is known as hydrophobic exclusion, and can affect the structure of DNA, proteins, and biological membranes. Water dissociates to form ions (H+ and OH–).
The concentration of hydrogen ions, and concurrently of hydroxide ions, in a solution is described by the terms acidity and basicity, respectively. Pure water is considered to be neutral – neither acidic or basic. The pH scale measures hydrogen ion concentration. Any substance that dissociates in water to increase the [H+] (and lower the pH) is called an acid. A substance that combines with H+ when dissolved in water, and thus lowers the [H+], is called a base. The pH inside almost all living cells, and in the fluid surrounding cells in multicellular organisms, is fairly close to neutral. Most enzymes in living systems are extremely sensitive to pH; for this reason, it is important that a cell maintain a constant pH level. The pH level of an organism is kept at a relatively constant level by buffers, substances that resist changes in pH. Buffers act by releasing hydrogen ions when a base is added and absorbing hydrogen ions when acid is added, with the overall effect of keeping [H+] constant. The reaction of carbon dioxide and water to form carbonic acid is a crucial one because it permits carbon, essential to life, to enter water (e.g., the oceans) from the air.
—March 2021
—April 2023
Lance Jones 