Chapter 2 | Basic Chemistry of Life

2 | Basic Chemistry of Life

Figure 2.1 Atoms are the building blocks of a l l t h e molecules found in the universe—air, soil, water, rocks . . . and also
the cells of all living organisms. In this model of an organic molecule, the atoms of carbon (black), hydrogen (white), nitrogen
(blue), oxygen (red), and sulfur (yellow) are shown in proportional atomic size. The silver rods indicate chemical bonds.
(credit: modification of work by Christian Guthier)

Chapter Outline

• Atoms, Isotopes, Ions, and Molecules

• Water
• The Energy of Life
• Carbon

Introduction
Elements in various combinations comprise all matter, including living things. The most abundant elements in living organisms
are carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Atoms of these elements form the nucleic acids, proteins,
carbohydrates, and lipids that are the fundamental components of living matter. Biologists must understand these important
building blocks and the unique structures of the atoms that make up molecules, allowing for the formation of cells, tissues,
organ systems, and entire organisms.
Biological processes follow the laws of physics and chemistry. For example, the flow of blood within the circulatory system
follows the laws of physics that regulate fluid flow. The breakdown of large, complex molecules of food into smaller molecules
to release energy to be stored in adenosine triphosphate (ATP) is a series of chemical reactions. The properties of water due to
the formation of hydrogen bonds are key to understanding living processes. Recognizing the properties of acids and bases is
important, for example, to our understanding of the digestive process. Therefore, the fundamentals of physics and chemistry
are important for gaining insight into biological processes.

Atoms, Isotopes, Ions, and Molecules

By the end of this section, you will be able to:
• Define matter and elements
• Describe the interrelationship between protons, neutrons, and electrons
• Explain the ways in which naturally occurring elements combine to create molecules
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At its most fundamental level, life is made up of matter: 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. There are more than 90 naturally occurring elements, plus other unstable ones that are synthesized in
laboratories. The four most common elements in living organisms are oxygen (O), carbon (C), hydrogen (H), and nitrogen (N).
These elements comprise 96% of living organisms.
Each element is designated by its chemical symbol, which is a single capital letter or a combination of two letters. Some
elements follow the English word for the element, such as C for carbon and Ca for calcium. Other elements derive their symbols
from their Latin names. For example, sodium is Na, because natrium is the Latin word for sodium.

The Structure of Atoms

An atom is the smallest unit of matter that retains all the chemical properties of an element. An atom is composed of two
regions: the nucleus, which is in the center of the atom and contains protons and neutrons, and the outer region of the atom,
which holds its electrons in orbit around the nucleus (Figure 2.2). Atoms contain subatomic particles, the largest of which
are protons, electrons, and neutrons.

Figure 2.2 Elements, such as helium, depicted

here, are made up of atoms. Atoms are made up
of protons and neutrons located within the nucleus,
with electrons in orbitals surrounding the nucleus.

Protons are positively charged, electrons are negatively charged, and neutrons are uncharged (Table 2.1). Each electron has
a negative charge equal to the positive charge of a proton. In neutral atoms, the number of electrons orbiting the nucleus equals
the number of protons in the nucleus. The positive and negative charges cancel, leading to an atom with no net charge.

Table 2.1. Properties of Subatomic Particles

Charge Mass (u) Location
Proton +1 1 nucleus
Neutron 0 1 nucleus
Electron –1 < 0.0006 orbitals

Atomic Number, Mass Number, and the Periodic Table

The number of protons in an atom, called the atomic number, determines which element that atom belongs to. For example,
carbon has atomic number 6, so all carbon atoms contain 6 protons. Neutral carbon atoms also contain 6 electrons. However,
the number of neutrons in the atoms of a given element is variable. Some carbon atoms have 6 neutrons, some have 7 neutrons,
and some have 8 neutrons. Together, the number of protons plus the number of neutrons determines an atom’s mass number.
Note that the small contribution of mass from electrons is disregarded when calculating the mass number.
The elements are organized in the periodic table in order of their atomic number. In the periodic table, shown in the elements
are arranged in rows and columns based on shared chemical and physical properties. Each square on the table gives the name,
chemical symbol, atomic weight, and relative atomic mass (atomic weight) for one element. For example, the first square
contains hydrogen, its symbol (H), its atomic number of (1), and its atomic mass (1.01). (Figure 2.3)
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Figure 2.3 The periodic table was devised by Russian

scientist Dmitri Medeleev in 1869. It shows the atomic
number, chemical symbol, and relative atomic mass of
each element.

Electron Shells and Orbitals

An early model of the atom was developed in 1913 by Danish scientist Niels Bohr (1885–1962). The Bohr model shows the
atom with electrons in circular electron shells at specific distances from the nucleus. The closer an energy shell is the nucleus,
the lower the energy of the electrons that occupy that shell. The first (1n) electron shell can hold two electrons, while the second
(2n) and third (3n) shells can hold eight electrons each (Figure 2.4).

Figure 2.4 In the Bohr model, developed by

Niels Bohrs in 1913, electrons exist in orbitals
within electron shells. The first shell contains
one orbital, which holds two electrons. The
second and third shells contain 4 orbitals and
hold eight electrons each.

Although useful to explain the reactivity and chemical bonding of certain elements, the Bohr model does not accurately
reflect how electrons are distributed. They do not circle the nucleus like the earth orbits the sun but are found in three-
dimensional electron orbitals. The area where an electron is most likely to be found is called its orbital. Each electron orbital
can hold only two electrons.
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Electrons fill orbitals in a consistent order: they first fill the orbitals closest to the nucleus, then they continue to fill orbitals of
increasing energy further from the nucleus. If there are multiple orbitals of equal energy, one electron will be added to each
orbital before a second electron is added to any of the orbitals. For example, the second energy level in the nitrogen atom shown
below has one electron in each of three orbitals and two electrons in the fourth orbital (Figure 2.5). Examples of some neutral
atoms and their electron configurations are shown below.

Figure 2.5 Bohr diagrams of elements common to living things show how many electrons are in each energy shell.
The octet rule states that atoms are most stable when their outermost energy shell, their valence shell, is full. In general, atoms
with 4-7 electrons in their valence shell will either gain electrons to become negatively charged ions or will share electrons
with other atoms to form covalently bonded molecules. Atoms with 1-3 electrons in their valence shell will tend to donate their
electrons to other atoms until they have a full outer shell. As a result of losing negatively charged electrons, they become
positively charged ions.

Concept Check  Draw Bohr’s diagrams for oxygen and magnesium atoms. How many electrons do
oxygen atoms need to gain in order to achieve a stable electron configuration? How
many electrons do magnesium atoms need to lose to achieve a stable configuration?

Chemical Reactions and Molecules

The octet rule drives the chemical behavior of atoms. Atoms will chemically react and bond to each other form molecules,
which are simply two or more atoms chemically bonded together. A compound is a type of molecule that contains two or
more different types of atoms. In short, atoms form chemical bonds with other atoms, thereby obtaining the electrons they
need to fill their valence shells. For example, the familiar water molecule, H2O, consists of two hydrogen atoms and one
oxygen atom covalently bonded together (Figure 2.6). Since all three atoms in water have full valence shells, water
is a stable molecule. Atoms can form molecules by donating, accepting, or sharing electrons to fill their valence shells.

Figure 2.6 Two or more atoms may

bond with each other to form a
molecule. When two hydrogens and
an oxygen share electrons via covalent
bonds, a water molecule is formed.

Chemical reactions occur when atoms bond together or when bonds between atoms are broken. The substances used in the
beginning of a chemical reaction are called the reactants and the substances found at the end of the reaction are known as
the products. An arrow is typically drawn between the reactants and products to indicate the direction of the chemical
reaction. Most chemical reactions can go in either direction. For the creation of the water molecule shown above, the chemical
equation would be:
2H2 + O2 2H2O
This is an example of a balanced chemical equation, where the number of atoms of each element is the same on each side.
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Ions and Ionic Bonds

The octet rule predicts that some atoms become more stable when they gain or lose electrons. Cations are positive ions that
are formed by losing negatively charged electrons. Anions are negative ions that are formed by gaining electrons.
Certain ions, such as sodium, potassium, and calcium, are referred to in physiology as electrolytes. These ions are necessary
for nerve impulse conduction, muscle contractions and water balance. Many sports drinks and dietary supplements provide
these ions to replace those lost from the body via sweating during exercise.
Transfer of electrons from one atom or molecule to another is referred to as a redox reaction. As Figure 2.7 illustrates, sodium
(Na) only has one electron in its outer electron shell. It will become stable by losing this electron and becoming a sodium cation
with a charge of +1. Chlorine (Cl) has seven electrons in its outer shell. It will become stable by gaining an electron and
becoming a chloride anion with a charge of -1. Both ions now satisfy the octet rule and have full valence shells.

Figure 2.7 In the formation of an ionic compound, an electron is transferred from one atom to another,
forming two oppositely charged ions, which are then attracted to each other.

An ionic bond is the electrical attraction that forms between ions with opposite charges. For example, positively charged
sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride, or table salt, creating a
crystalline molecule with zero net charge.

Covalent Bonds
Another way the octet rule can be satisfied is by the sharing of electrons between atoms to form covalent bonds. One, two, or
three pairs of electrons may be shared, making single, double, and triple bonds, respectively. The formation of water molecules
provides an example of covalent bonding (Figure 2.6). To completely fill the outer shell of oxygen, which has six electrons in
its outer shell, two electrons (one from each hydrogen atom) are needed. The electrons are shared between the two elements to
fill the outer shell of each, making both elements more stable.

Polar Covalent Bonds

Although atoms share electrons in covalent bonds, they do not always share
the electrons equally. Atoms have different electronegativities, or attraction
for electrons (Figure 2.8). When a covalent bond is formed between two
atoms with different electronegativities, the shared electrons will spend more
time around the nucleus of the atom with the higher electronegativity and less
time around the nucleus with lower electronegativity. Since electrons are
negatively charged, the atom that gets more time with the electron acquires a
slightly negative charge (δ–). The atom with lower electronegativity gets less
time with the electron and acquires a slightly positive charge (δ+). Figure 2.8 Electronegativity values for
The type of covalent bond that forms between two atoms with different selected elements.
electronegativities is called a polar covalent bond. Molecules with polar
covalent bonds are called polar molecules, due to the separation of charges across the molecule. For example, water is a polar
molecule, since oxygen has an electronegativity of 3.5 and hydrogen has an electronegativity of 2.1. The oxygen atom in a
water molecule attracts the shared electrons more and acquires a partial negative charge, while the hydrogen atoms attract the
shared electrons less and acquire a partial positive charge (Figure 2.9). Many of the important properties of water result from
its polarity.
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Nonpolar Covalent Bonds

Nonpolar covalent bonds form between two atoms of the same element or between different elements that share electrons
equally. For example, molecular oxygen (O2) is nonpolar because the electrons will be equally distributed between the two
oxygen atoms. Another example of a nonpolar covalent bond is methane (CH4), also shown in Figure 2.9. Carbon and hydrogen
have similar electronegativity values. Therefore, these elements share electrons equally, creating a nonpolar covalent molecule.
Some molecules are nonpolar due to symmetry, as seen in the carbon dioxide molecule in Figure 2.9.

Figure 2.9 Whether a molecule

is polar or nonpolar depends
both on electronegativity values
and molecular shape. Both
water and carbon dioxide
have polar covalent bonds,
but carbon dioxide is linear, so
the partial charges on the
molecule cancel each other out.

Hydrogen Bonds
As described above, covalent and ionic bonds occur between atoms to form molecules. Other types of interactions occur
between molecules. Two examples of weak bonds that occur frequently between molecules are hydrogen bonds and van der
Waals interactions. Without these two types of bonds, life as we know it would not exist.
Hydrogen bonds are weak interactions between two polar molecules. The δ+ of the hydrogen from one molecule is attracted
to the δ– charge of a more electronegative atom (usually oxygen or nitrogen) of another molecule. Individual hydrogen bonds
are weak and easily broken; however, a large number of them can be collectively very strong. Hydrogen bonds between water
molecules (Figure 2.10) provide many of the critical, life-sustaining properties of water, and hydrogen bonds also stabilize the
structures of proteins and DNA.

Figure 2.10 Since water is a polar molecule,

hydrogen bonds form between the partially
negative oxygen atom of one molecule and the
partially positive hydrogen atom of another
molecule. These hydrogen bonds give water
many special properties.
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Pharmaceutical Chemist
Pharmaceutical chemists are responsible for developing new drugs and f o r trying to determine the mode
of action of drugs. Drugs can be found in nature or can be synthesized in the laboratory. In many cases,
potential drugs found in nature are changed chemically in the laboratory to make them safer and more
effective.
After the initial discovery or synthesis of a drug, the chemist develops the drug, perhaps by chemically
altering it, testing to see if it is toxic, and designing methods for large-scale production. Next, the process of
getting the drug approved for human use by the Food and Drug Administration (FDA) begins. This involves a
series of large-scale experiments using human subjects to make sure the drug is safe and effective. Approval
often takes several years and requires the participation of physicians and chemists.
An example of a drug that was originally discovered in a living organism is Paclitaxel (Taxol), an anti-cancer
drug used to treat breast cancer. This drug was discovered in the bark of the pacific yew tree. Another
example is aspirin, which was originally isolated from willow tree bark. Both of these drugs are now
produced synthetically. Finding drugs often means testing hundreds of samples of plants, fungi, and other
forms of life to see if any biologically active compounds are found within them. Sometimes, traditional
medicine can give modern medicine clues to where an active compound can be found. For example, the
use of willow bark to make medicine has been known for thousands of years, dating back to ancient Egypt.
It was not until the late 1800s, however, that the aspirin molecule, known as acetylsalicylic acid, was purified
and marketed for human use.
Occasionally, drugs developed for one use are found to have unforeseen effects that allow these drugs to
be used in other, unrelated ways. For example, the drug minoxidil (Rogaine) was originally developed to
treat high blood pressure. When tested on humans, it was noticed that individuals taking the drug would
grow new hair. Eventually the drug was marketed to men and women with baldness to restore lost hair.
The career of the pharmaceutical chemist may involve detective work, experimentation, and drug
development, all with the goal of making human beings healthier.