The Chemical Foundation of Life

At its most fundamental level, life is made up of matter. Matter is any substance that occupies space and has mass. Elements are unique forms of matter with specific chemical and physical properties that cannot be broken down into smaller substances by ordinary chemical reactions. Any pure element would be composed of one type of atom. The elements are shown below in the periodic table. The following are the six most abundant elements in life.

1. Carbon
2. Hydrogen
3. Oxygen
4. Nitrogen
5. Phosphorus
6. Sulfur

The periodic table shows the atomic mass and atomic number of each element. The atomic number appears above the symbol for the element and the approximate atomic mass appears below it.

An atom’s nucleus contains positively charged particles called protons and neutral, uncharged particles called neutrons. Surrounding the atomic nucleus is an area of electrons (negatively charged particles) that orbit. Protons and neutrons have approximately the same mass. Although similar in mass, protons and neutrons differ in their electric charge. A proton is positively charged whereas a neutron is uncharged. Therefore, the number of neutrons in an atom contributes significantly to its mass, but not to its charge. Electrons are much smaller in mass than protons, about 1/1800 of a proton. They do not contribute much to an element’s overall atomic mass. Atomic mass is based on the number of protons and neutrons alone. Electrons contribute greatly to the atom’s charge, as each electron has a negative charge equal to the positive charge of a proton. In uncharged, neutral atoms, the number of electrons orbiting the nucleus is equal to the number of protons inside the nucleus.

The number of protons determines an element’s atomic number and is used to distinguish one element from another. Uncharged atoms of each element contain an equal number of protons and electrons. An ion is an atom with unequal numbers of protons and electrons resulting in a charge. An isotope is an element with an unequal number of neutrons and protons.

Atoms naturally reach the most stable state possible. Many atoms become stable when they satisfy the octet rule, by having eight valence electrons. Electrons fill orbitals in a consistent order. First, the orbitals closest to the nucleus fill, then they continue to fill orbitals of increasing energy further from the nucleus. Electrons of the outermost energy level determine the energetic stability of the atom and its tendency to form chemical bonds with other atoms to form molecules. Under standard conditions, atoms fill the inner shells first, often resulting in a variable number of electrons in the outermost shell. The innermost shell has a maximum of two electrons but the next two electron shells can each have a maximum of eight electrons. This is known as the octet rule, which states, with the exception of the innermost shell, atoms are more stable energetically when they have eight electrons in their valence (outermost) shell. This principle drives atomic bonding. When atoms bond together, molecules are formed. When some elements form chemical bonds, the elements share, donate, or accept electrons so their valence shell contains eight electrons.

Ionic bonds are formed between ions with opposite charges and involve an atom that gains or loses an electron. For instance, positively charged sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride (table salt). These bonds form a crystalline molecule with zero net charge. Certain salts are referred to as electrolytes (including sodium, potassium, and calcium). These ions are necessary for nerve signals, muscle contraction and water balance.

Covalent bonds are stronger and much more common than ionic bonds in the molecules of living organisms. These bonds are the result of shared electrons. Sharing of electrons can be equally distant from both atoms nucleus (nonpolar covalent) or unequal (polar covalent). Oxygen and hydrogen are held by covalent bonds in water (H₂O).

Hydrogen bonds are the weak bonds, commonly found between individual water molecules. Although individual hydrogen bonds are weak and break easily, many of them together are strong enough for surface tension and adhesion. In water, each hydrogen has a slightly positive charge because hydrogen’s electron is pulled more strongly toward the other element and away from the hydrogen. Because the hydrogen is slightly positive, it will be attracted to neighboring negative charges. When this happens, a weak interaction occurs between the δ+ of the hydrogen from one molecule and the δ– charge on the more electronegative atoms of another molecule, usually oxygen or nitrogen, or within the same molecule. This type of bond is common and occurs regularly between water molecules.

Chemical reactions occur when chemical bonds between atoms are formed or broken. The substances that go into a chemical reaction are called the reactants, and the substances produced at the end of the reaction are known as the products. In a chemical equation, reactants usually appear on the far left followed by a directional arrow that points to the right. Products appear to the right of the arrow. The arrow indicates a reaction occurred.

The polarity of the water (H₂O) molecule and resulting hydrogen bonds make water a unique substance with special properties tied to the processes of life. Water is the universal solvent. The positively charged end of the water molecule attracts negatively charged particles. The negatively charged end of the water molecule attracts positively charged particles. These properties are vital to life as we know it on the surface of the earth.

Water has a high heat of vaporization, meaning water can turn into steam requiring a lot of energy to raise its temperature high enough for that to happen. Water has a high heat capacity, so it stores heat well. Water also has a crystalline lattice structure when frozen into ice, meaning the angles of its bonds form a lattice. This phenomena allows ice to be less dense than liquid water, so ice floats in water.

Water is attracted to other water molecules through the property of cohesion. This results in surface tension that allows some insects to cross water. Water molecules also display adhesion by attraction to other surfaces. The water droplets in an empty water bottle cling to the sides because of this property. The properties of adhesion and cohesion are vital to the energy cycle.

Many substances are hydrophilic or water loving. Others are hydrophobic and repel water. Oil is an example of a hydrophobic molecule.

Water has a neutral pH of 7 with more acidic pH numbers falling below 7 (smaller numbers) and basic pH numbers above 7 (higher numbers). The pH scale is logarithmic, so the difference between a 3 and a 4 is a change in the concentration of hydrogen ions [H+] times ten. Buffers are chemicals that act to minimize changes in pH.

Individual carbon atoms have an incomplete outermost electron shell. With an atomic number of 6, the first two electrons fill the inner shell, leaving four in the second shell. Therefore, carbon atoms can form up to four covalent bonds with other atoms to satisfy the octet rule. The methane molecule provides one example, as it has the chemical formula CH₄. Each of its four hydrogen atoms forms a single covalent bond with the carbon atom by sharing a pair of electrons. This results in a filled outermost shell. For this reason, methane is described as having tetrahedral geometry. Both of the images here represent methane.

As the backbone of the large molecules of living things, hydrocarbons may exist as linear carbon chains, carbon rings, or combinations of both. Structure determines function. Read more about the chemical properties of life here.