CHAPTER 2

The Chemical Foundation

of Life

Figure 2.1 Atoms are the building blocks of molecules 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 in proportional
atomic size. The silver rods indicate chemical bonds. (credit: modification of work by Christian
Guthier)

INTRODUCTION Elements in various combinations comprise all matter, including living things. Some
of the most abundant elements in living organisms include carbon, hydrogen, nitrogen, oxygen, sulfur,
Chapter Outline
and phosphorus. These form the nucleic acids, proteins, carbohydrates, and lipids that are the
fundamental components of living matter. Biologists must understand these important building blocks 2.1 Atoms, Isotopes,
and the unique structures of the atoms that comprise molecules, allowing for cells, tissues, organ
Ions, and Molecules:
systems, and entire organisms to form.
The Building Blocks
All biological processes follow the laws of physics and chemistry, so in order to understand how
2.2 Water
biological systems work, it is important to understand the underlying physics and chemistry. For
example, the flow of blood within the circulatory system follows the laws of physics that regulate the 2.3 Carbon
modes of fluid flow. The breakdown of the large, complex molecules of food into smaller molecules—and
the conversion of these to release energy to be stored in adenosine triphosphate (ATP)—is a series of
chemical reactions that follow chemical laws. The properties of water and 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.
30 Chapter 2 • The Chemical Foundation of Life

2.1 Atoms, Isotopes, Ions, and Molecules: The

Building Blocks
By the end of this section, you will be able to do the following:
• Define matter and elements
• Describe the interrelationship between protons, neutrons, and electrons
• Compare the ways in which electrons can be donated or shared between atoms
• Explain the ways in which naturally occurring elements combine to create molecules, cells,
tissues, organ systems, and organisms

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 break
down into smaller substances by ordinary chemical reactions. There are 118 elements, but only 98 occur
naturally. The remaining elements are unstable and require scientists to synthesize them in laboratories.

Each element is designated by its chemical symbol, which is a single capital letter or, when the first letter is
already “taken” by another element, a combination of two letters. Some elements follow the English term for
the element, such as C for carbon and Ca for calcium. Other elements’ chemical symbols derive from their
Latin names. For example, the symbol for sodium is Na, referring to natrium, the Latin word for sodium.

The four elements common to all living organisms are oxygen (O), carbon (C), hydrogen (H), and nitrogen
(N). In the nonliving world, elements are found in different proportions, and some elements common to
living organisms are relatively rare on the earth as a whole, as Table 2.1 shows. For example, the atmosphere
is rich in nitrogen and oxygen but contains little carbon and hydrogen, while the earth’s crust, although it
contains oxygen and a small amount of hydrogen, has little nitrogen and carbon. In spite of their differences
in abundance, all elements and the chemical reactions between them obey the same chemical and physical
laws regardless of whether they are a part of the living or nonliving world.

Approximate Percentage of Elements in Living Organisms (Humans) Compared to the Nonliving World

Element Life (Humans) Atmosphere Earth’s Crust

Oxygen (O) 65% 21% 46%

Carbon (C) 18% trace trace

Hydrogen (H) 10% trace 0.1%

Nitrogen (N) 3% 78% trace

Table 2.1

The Structure of the Atom

To understand how elements come together, we must first discuss the element's smallest component or
building block, the atom. An atom is the smallest unit of matter that retains all of the element's chemical
properties. For example, one gold atom has all of the properties of gold in that it is a solid metal at room
temperature. A gold coin is simply a very large number of gold atoms molded into the shape of a coin and
contains small amounts of other elements known as impurities. We cannot break down gold atoms into
anything smaller while still retaining the properties of gold.

An atom is composed of two regions: the nucleus, which is in the atom's center and contains protons and
neutrons. The atom's outermost region holds its electrons in orbit around the nucleus, as Figure 2.2
illustrates. Atoms contain protons, electrons, and neutrons, among other subatomic particles. The only
exception is hydrogen (H), which is made of one proton and one electron with no neutrons.

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2.1 • Atoms, Isotopes, Ions, and Molecules: The Building Blocks 31

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 and neutrons have approximately the same mass, about 1.67 × 10-24 grams. Scientists arbitrarily define this amount of
mass as one atomic mass unit (amu) or one Dalton, as Table 2.2 shows. 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, weighing
only 9.11 × 10-28 grams, or about 1/1800 of an atomic mass unit. Hence, they do not contribute much to an element’s overall
atomic mass. Therefore, when considering atomic mass, it is customary to ignore the mass of any electrons and calculate the
atom’s mass based on the number of protons and neutrons alone. Although not significant contributors to mass, electrons do
contribute greatly to the atom’s charge, as each electron has a negative charge equal to the proton's positive charge. In
uncharged, neutral atoms, the number of electrons orbiting the nucleus is equal to the number of protons inside the nucleus. In
these atoms, the positive and negative charges cancel each other out, leading to an atom with no net charge.

Accounting for the sizes of protons, neutrons, and electrons, most of the atom's volume—greater than 99 percent—is empty
space. With all this empty space, one might ask why so-called solid objects do not just pass through one another. The reason they
do not is that the electrons that surround all atoms are negatively charged and negative charges repel each other.

Protons, Neutrons, and Electrons

Charge Mass (amu) Location

Proton +1 1 nucleus

Neutron 0 1 nucleus

Electron –1 0 orbitals

Table 2.2

Atomic Number and Mass

Atoms of each element contain a characteristic number of protons and electrons. The number of protons determines an
element’s atomic number, which scientists use to distinguish one element from another. The number of neutrons is variable,
resulting in isotopes, which are different forms of the same atom that vary only in the number of neutrons they possess.
Together, the number of protons and neutrons determine an element’s mass number, as Figure 2.3 illustrates. Note that we
disregard the small contribution of mass from electrons in calculating the mass number. We can use this approximation of mass
to easily calculate how many neutrons an element has by simply subtracting the number of protons from the mass number.
Since an element’s isotopes will have slightly different mass numbers, scientists also determine the atomic mass, which is the
calculated mean of the mass number for its naturally occurring isotopes. Often, the resulting number contains a fraction. For
example, the atomic mass of chlorine (Cl) is 35.45 because chlorine is composed of several isotopes, some (the majority) with
atomic mass 35 (17 protons and 18 neutrons) and some with atomic mass 37 (17 protons and 20 neutrons).
32 Chapter 2 • The Chemical Foundation of Life

VISUAL CONNECTION

Figure 2.3 Carbon has an atomic number of six, and two stable isotopes with mass numbers of twelve and thirteen, respectively. Its relative
atomic mass is 12.011

How many neutrons do carbon-12 and carbon-13 have, respectively?

Isotopes
Isotopes are different forms of an element that have the same number of protons but a different number of neutrons. Some
elements—such as carbon, potassium, and uranium—have naturally occurring isotopes. Carbon-12 contains six protons, six
neutrons, and six electrons; therefore, it has a mass number of 12 (six protons and six neutrons). Carbon-14 contains six protons,
eight neutrons, and six electrons; its atomic mass is 14 (six protons and eight neutrons). These two alternate forms of carbon are
isotopes. Some isotopes may emit neutrons, protons, and electrons, and attain a more stable atomic configuration (lower level
of potential energy); these are radioactive isotopes, or radioisotopes. Radioactive decay (carbon-14 decaying to eventually
become nitrogen-14) describes the energy loss that occurs when an unstable atom’s nucleus releases radiation.

EVOLUTION CONNECTION

Carbon Dating
Carbon is normally present in the atmosphere in the form of gaseous compounds like carbon dioxide and methane. Carbon-14
(14C) is a naturally occurring radioisotope that is created in the atmosphere from atmospheric 14N (nitrogen) by the addition of a
neutron and the loss of a proton because of cosmic rays. This is a continuous process, so more 14C is always being created. As a
living organism incorporates 14C initially as carbon dioxide fixed in the process of photosynthesis, the relative amount of 14C in
its body is equal to the concentration of 14C in the atmosphere. When an organism dies, it is no longer ingesting 14C, so the ratio
between 14C and 12C will decline as 14C decays gradually to 14N by a process called beta decay—electrons or positrons emission.
This decay emits energy in a slow process.

After approximately 5,730 years, half of the starting concentration of 14C will convert back to 14N. We call the time it takes for half
of the original concentration of an isotope to decay back to its more stable form its half-life. Because the half-life of 14C is long,
scientists use it to date formerly living objects such as old bones or wood. Comparing the ratio of the 14C concentration in an
object to the amount of 14C in the atmosphere, scientists can determine the amount of the isotope that has not yet decayed. On
the basis of this amount, Figure 2.4 shows that we can calculate the age of the material, such as the pygmy mammoth, with
accuracy if it is not much older than about 50,000 years. Other elements have isotopes with different half lives. For example, 40K
(potassium-40) has a half-life of 1.25 billion years, and 235U (Uranium 235) has a half-life of about 700 million years. Through the
use of radiometric dating, scientists can study the age of fossils or other remains of extinct organisms to understand how
organisms have evolved from earlier species.

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2.1 • Atoms, Isotopes, Ions, and Molecules: The Building Blocks 33

Figure 2.4 Scientists can determine the age of carbon-containing remains less than about 50,000 years old, such as this pygmy mammoth,
using carbon dating. (credit: Bill Faulkner, NPS)

LINK TO LEARNING
To learn more about atoms, isotopes, and how to tell one isotope from another, run the simulation.

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The Periodic Table

The periodic table organizes and displays different elements. Devised by Russian chemist Dmitri Mendeleev (1834–1907) in 1869,
the table groups elements that, although unique, share certain chemical properties with other elements. The properties of
elements are responsible for their physical state at room temperature: they may be gases, solids, or liquids. Elements also have
specific chemical reactivity, the ability to combine and to chemically bond with each other.

In the periodic table in Figure 2.5, the elements are organized and displayed according to their atomic number and are arranged
in a series of rows and columns based on shared chemical and physical properties. In addition to providing the atomic number
for each element, the periodic table also displays the element’s atomic mass. Looking at carbon, for example, its symbol (C) and
name appear, as well as its atomic number of six (in the upper left-hand corner) and its atomic mass of 12.01.
34 Chapter 2 • The Chemical Foundation of Life

Figure 2.5 The periodic table shows each element's atomic mass and atomic number. The atomic number appears above the symbol for the
element and the approximate atomic mass appears below it.

The periodic table groups elements according to chemical properties. Scientists base the differences in chemical reactivity
between the elements on the number and spatial distribution of an atom’s electrons. Atoms that chemically react and bond to
each other form molecules. Molecules are simply two or more atoms chemically bonded together. Logically, when two atoms
chemically bond to form a molecule, their electrons, which form the outermost region of each atom, come together first as the
atoms form a chemical bond.

Electron Shells and the Bohr Model

Note that there is a connection between the number of protons in an element, the atomic number that distinguishes one
element from another, and the number of electrons it has. In all electrically neutral atoms, the number of electrons is the same
as the number of protons. Thus, each element, at least when electrically neutral, has a characteristic number of electrons equal
to its atomic number.

In 1913, Danish scientist Niels Bohr (1885–1962) developed an early model of the atom. The Bohr model shows the atom as a
central nucleus containing protons and neutrons, with the electrons in circular orbitals at specific distances from the nucleus,
as Figure 2.6 illustrates. These orbits form electron shells or energy levels, which are a way of visualizing the number of electrons
in the outermost shells. These energy levels are designated by a number and the symbol “n.” For example, 1n represents the first
energy level located closest to the nucleus.

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2.1 • Atoms, Isotopes, Ions, and Molecules: The Building Blocks 35

Figure 2.6 In 1913, Niels Bohrs developed the Bohr model in which electrons exist within principal shells. An electron normally exists in
the lowest energy shell available, which is the one closest to the nucleus. Energy from a photon of light can bump it up to a higher energy
shell, but this situation is unstable, and the electron quickly decays back to the ground state. In the process, it releases a photon of light.

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, they fill with one electron in each
energy level before adding a second electron. The electrons of the outermost energy level determine the atom's energetic stability
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, that atoms are more stable
energetically when they have eight electrons in their valence shell, the outermost electron shell. Figure 2.7 shows examples of
some neutral atoms and their electron configurations. Notice that in Figure 2.7, helium has a complete outer electron shell, with
two electrons filling its first and only shell. Similarly, neon has a complete outer 2n shell containing eight electrons. In contrast,
chlorine and sodium have seven and one in their outer shells, respectively, but theoretically they would be more energetically
stable if they followed the octet rule and had eight.
36 Chapter 2 • The Chemical Foundation of Life

VISUAL CONNECTION

Figure 2.7 Bohr diagrams indicate how many electrons fill each principal shell. Group 18 elements (helium, neon, and argon) have a full
outer, or valence, shell. A full valence shell is the most stable electron configuration. Elements in other groups have partially filled valence
shells and gain or lose electrons to achieve a stable electron configuration.

An atom may give, take, or share electrons with another atom to achieve a full valence shell, the most stable electron
configuration. Looking at this figure, how many electrons do elements in group 1 need to lose in order to achieve a stable
electron configuration? How many electrons do elements in groups 14 and 17 need to gain to achieve a stable configuration?

Understanding that the periodic table's organization is based on the total number of protons (and electrons) helps us know how
electrons distribute themselves among the shells. The periodic table is arranged in columns and rows based on the number of
electrons and their location. Examine more closely some of the elements in the table’s far right column in Figure 2.5. The group
18 atoms helium (He), neon (Ne), and argon (Ar) all have filled outer electron shells, making it unnecessary for them to share
electrons with other atoms to attain stability. They are highly stable as single atoms. Because they are non reactive, scientists
coin them inert (or noble gases). Compare this to the group 1 elements in the left-hand column. These elements, including
hydrogen (H), lithium (Li), and sodium (Na), all have one electron in their outermost shells. That means that they can achieve a
stable configuration and a filled outer shell by donating or sharing one electron with another atom or a molecule such as water.
Hydrogen will donate or share its electron to achieve this configuration, while lithium and sodium will donate their electron to
become stable. As a result of losing a negatively charged electron, they become positively charged ions. Group 17 elements,
including fluorine and chlorine, have seven electrons in their outmost shells, so they tend to fill this shell with an electron from
other atoms or molecules, making them negatively charged ions. Group 14 elements, of which carbon is the most important to
living systems, have four electrons in their outer shell allowing them to make several covalent bonds (discussed below) with
other atoms. Thus, the periodic table's columns represent the potential shared state of these elements’ outer electron shells that
is responsible for their similar chemical characteristics.

Electron Orbitals
Although useful to explain the reactivity and chemical bonding of certain elements, the Bohr model does not accurately reflect
how electrons spatially distribute themselves around the nucleus. They do not circle the nucleus like the earth orbits the sun, but
we find them in electron orbitals. These relatively complex shapes result from the fact that electrons behave not just like
particles, but also like waves. Mathematical equations from quantum mechanics, which scientists call wave functions, can
predict within a certain level of probability where an electron might be at any given time. Scientists call the area where an
electron is most likely to be found its orbital.

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2.1 • Atoms, Isotopes, Ions, and Molecules: The Building Blocks 37

Recall that the Bohr model depicts an atom’s electron shell configuration. Within each electron shell are subshells, and each
subshell has a specified number of orbitals containing electrons. While it is impossible to calculate exactly an electron's location,
scientists know that it is most probably located within its orbital path. The letter s, p, d, and f designate the subshells. The s
subshell is spherical in shape and has one orbital. Principal shell 1n has only a single s orbital, which can hold two electrons.
Principal shell 2n has one s and one p subshell, and can hold a total of eight electrons. The p subshell has three dumbbell-shaped
orbitals, as Figure 2.8 illustrates. Subshells d and f have more complex shapes and contain five and seven orbitals, respectively.
We do not show these in the illustration. Principal shell 3n has s, p, and d subshells and can hold 18 electrons. Principal shell 4n
has s, p, d and f orbitals and can hold 32 electrons. Moving away from the nucleus, the number of electrons and orbitals in the
energy levels increases. Progressing from one atom to the next in the periodic table, we can determine the electron structure by
fitting an extra electron into the next available orbital.

Figure 2.8 The s subshells are shaped like spheres. Both the 1n and 2n principal shells have an s orbital, but the size of the sphere is larger
in the 2n orbital. Each sphere is a single orbital. Three dumbbell-shaped orbitals comprise p subshells. Principal shell 2n has a p subshell,
but shell 1 does not.

The closest orbital to the nucleus, the 1s orbital, can hold up to two electrons. This orbital is equivalent to the Bohr model's
innermost electron shell. Scientists call it the 1s orbital because it is spherical around the nucleus. The 1s orbital is the closest
orbital to the nucleus, and it is always filled first, before any other orbital fills. Hydrogen has one electron; therefore, it occupies
only one spot within the 1s orbital. We designate this as 1s1, where the superscripted 1 refers to the one electron within the 1s
orbital. Helium has two electrons; therefore, it can completely fill the 1s orbital with its two electrons. We designate this as 1s2,
referring to the two electrons of helium in the 1s orbital. On the periodic table Figure 2.5, hydrogen and helium are the only two
elements in the first row (period). This is because they only have electrons in their first shell, the 1s orbital. Hydrogen and helium
are the only two elements that have the 1s and no other electron orbitals in the electrically neutral state.

The second electron shell may contain eight electrons. This shell contains another spherical s orbital and three “dumbbell”
shaped p orbitals, each of which can hold two electrons, as Figure 2.8 shows. After the 1s orbital fills, the second electron shell
fills, first filling its 2s orbital and then its three p orbitals. When filling the p orbitals, each takes a single electron. Once each p
orbital has an electron, it may add a second. Lithium (Li) contains three electrons that occupy the first and second shells. Two
electrons fill the 1s orbital, and the third electron then fills the 2s orbital. Its electron configuration is 1s22s1. Neon (Ne),
alternatively, has a total of ten electrons: two are in its innermost 1s orbital and eight fill its second shell (two each in the 2s and
three p orbitals). Thus it is an inert gas and energetically stable as a single atom that will rarely form a chemical bond with other
atoms. Larger elements have additional orbitals, comprising the third electron shell. While the concepts of electron shells and
orbitals are closely related, orbitals provide a more accurate depiction of an atom's electron configuration because the orbital
38 Chapter 2 • The Chemical Foundation of Life

model specifies the different shapes and special orientations of all the places that electrons may occupy.

LINK TO LEARNING
Watch this visual animation to see the spatial arrangement of the p and s orbitals.

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Chemical Reactions and Molecules

All elements are most stable when their outermost shell is filled with electrons according to the octet rule. This is because it is
energetically favorable for atoms to be in that configuration and it makes them stable. However, since not all elements have
enough electrons to fill their outermost shells, atoms form chemical bonds with other atoms thereby obtaining the electrons
they need to attain a stable electron configuration. When two or more atoms chemically bond with each other, the resultant
chemical structure is a molecule. The familiar water molecule, H2O, consists of two hydrogen atoms and one oxygen atom. These
bond together to form water, as Figure 2.9 illustrates. Atoms can form molecules by donating, accepting, or sharing electrons to
fill their outer shells.

Figure 2.9 Two or more atoms may bond with each other to form a molecule. When two hydrogens and an oxygen share electrons via
covalent bonds it forms a water molecule.

Chemical reactions occur when two or more atoms bond together to form molecules or when bonded atoms break apart.
Scientists call the substances used in the beginning of a chemical reaction reactants (usually on the left side of a chemical
equation), and we call the substances at the end of the reaction products (usually on the right side of a chemical equation). We
typically draw an arrow between the reactants and products to indicate the chemical reaction's direction. This direction is not
always a “one-way street.” To create the water molecule above, the chemical equation would be:

An example of a simple chemical reaction is breaking down hydrogen peroxide molecules, each of which consists of two
hydrogen atoms bonded to two oxygen atoms (H2O2). The reactant hydrogen peroxide breaks down into water, containing one
oxygen atom bound to two hydrogen atoms (H2O), and oxygen, which consists of two bonded oxygen atoms (O2). In the
equation below, the reaction includes two hydrogen peroxide molecules and two water molecules. This is an example of a
balanced chemical equation, wherein each element's number of atoms is the same on each side of the equation. According to
the law of conservation of matter, the number of atoms before and after a chemical reaction should be equal, such that no atoms
are, under normal circumstances, created or destroyed.

Even though all of the reactants and products of this reaction are molecules (each atom remains bonded to at least one other
atom), in this reaction only hydrogen peroxide and water are representatives of compounds: they contain atoms of more than
one type of element. Molecular oxygen, alternatively, as Figure 2.10 shows, consists of two doubly bonded oxygen atoms and is
not classified as a compound but as a homonuclear molecule.

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2.1 • Atoms, Isotopes, Ions, and Molecules: The Building Blocks 39

Figure 2.10 A double bond joins the oxygen atoms in an O2 molecule.

Some chemical reactions, such as the one above, can proceed in one direction until they expend all the reactants. The equations
that describe these reactions contain a unidirectional arrow and are irreversible. Reversible reactions are those that can go in
either direction. In reversible reactions, reactants turn into products, but when the product's concentration goes beyond a
certain threshold (characteristic of the particular reaction), some of these products convert back into reactants. At this point,
product and reactant designations reverse. This back and forth continues until a certain relative balance between reactants and
products occurs—a state called equilibrium. A chemical equation with a double headed arrow pointing towards both the
reactants and products often denote these reversible reaction situations.

For example, in human blood, excess hydrogen ions (H+) bind to bicarbonate ions (HCO3-) forming an equilibrium state with
carbonic acid (H2CO3). If we added carbonic acid to this system, some of it would convert to bicarbonate and hydrogen ions.

However, biological reactions rarely obtain equilibrium because the concentrations of the reactants or products or both are
constantly changing, often with one reaction's product a reactant for another. To return to the example of excess hydrogen ions
in the blood, forming carbonic acid will be the reaction's major direction. However, the carbonic acid can also leave the body as
carbon dioxide gas (via exhalation) instead of converting back to bicarbonate ion, thus driving the reaction to the right by the
law of mass action. These reactions are important for maintaining homeostasis in our blood.

Ions and Ionic Bonds

Some atoms are more stable when they gain or lose an electron (or possibly two) and form ions. This fills their outermost
electron shell and makes them energetically more stable. Because the number of electrons does not equal the number of
protons, each ion has a net charge. Cations are positive ions that form by losing electrons. Negative ions form by gaining
electrons, which we call anions. We designate anions by their elemental name and change the ending to “-ide”, thus the anion of
chlorine is chloride, and the anion of sulfur is sulfide.

Scientists refer to this movement of electrons from one element to another as electron transfer. As Figure 2.11 illustrates,
sodium (Na) only has one electron in its outer electron shell. It takes less energy for sodium to donate that one electron than it
does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons, 11 neutrons, and
only 10 electrons, leaving it with an overall charge of +1. We now refer to it as a sodium ion. Chlorine (Cl) in its lowest energy
state (called the ground state) has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one
electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons, 17 neutrons, and 18 electrons,
giving it a net negative (–1) charge. We now refer to it as a chloride ion. In this example, sodium will donate its one electron to
empty its shell, and chlorine will accept that electron to fill its shell. Both ions now satisfy the octet rule and have complete
outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1
(sodium cation) or –1 (chloride anion) charge. Note that these transactions can normally only take place simultaneously: in order
for a sodium atom to lose an electron, it must be in the presence of a suitable recipient like a chlorine atom.

Figure 2.11 In the formation of an ionic compound, metals lose electrons and nonmetals gain electrons to achieve an octet.

Ionic bonds form between ions with opposite charges. For instance, 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
40 Chapter 2 • The Chemical Foundation of Life

charge.

Physiologists refer to certain salts as electrolytes (including sodium, potassium, and calcium), ions 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.

Covalent Bonds and Other Bonds and Interactions

Another way to satisfy the octet rule is by sharing electrons between atoms to form covalent bonds. These bonds are stronger
and much more common than ionic bonds in the molecules of living organisms. We commonly find covalent bonds in carbon-
based organic molecules, such as our DNA and proteins. We also find covalent bonds in inorganic molecules like H2O, CO2, and
O2. The bonds may share one, two, or three pairs of electrons, making single, double, and triple bonds, respectively. The more
covalent bonds between two atoms, the stronger their connection. Thus, triple bonds are the strongest.

The strength of different levels of covalent bonding is one of the main reasons living organisms have a difficult time in acquiring
nitrogen for use in constructing their molecules, even though molecular nitrogen, N2, is the most abundant gas in the
atmosphere. Molecular nitrogen consists of two nitrogen atoms triple bonded to each other and, as with all molecules, sharing
these three pairs of electrons between the two nitrogen atoms allows for filling their outer electron shells, making the molecule
more stable than the individual nitrogen atoms. This strong triple bond makes it difficult for living systems to break apart this
nitrogen in order to use it as constituents of proteins and DNA.

Forming water molecules provides an example of covalent bonding. Covalent bonds bind the hydrogen and oxygen atoms that
combine to form water molecules as Figure 2.9 shows. The electron from the hydrogen splits its time between the hydrogen
atoms' incomplete outer shell and the oxygen atoms' incomplete outer shell. To completely fill the oxygen's outer shell, which has
six electrons but which would be more stable with eight, two electrons (one from each hydrogen atom) are needed: hence, the
well-known formula H2O. The two elements share the electrons to fill the outer shell of each, making both elements more stable.

LINK TO LEARNING
View this short video to see an animation of ionic and covalent bonding.

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Polar Covalent Bonds

There are two types of covalent bonds: polar and nonpolar. In a polar covalent bond, Figure 2.12 shows atoms unequally share
the electrons and are attracted more to one nucleus than the other. Because of the unequal electron distribution between the
atoms of different elements, a slightly positive (δ+) or slightly negative (δ–) charge develops. This partial charge is an important
property of water and accounts for many of its characteristics.

Water is a polar molecule, with the hydrogen atoms acquiring a partial positive charge and the oxygen a partial negative charge.
This occurs because the oxygen atom's nucleus is more attractive to the hydrogen atoms' electrons than the hydrogen nucleus is
to the oxygen’s electrons. Thus, oxygen has a higher electronegativity than hydrogen and the shared electrons spend more time
near the oxygen nucleus than the hydrogen atoms' nucleus, giving the oxygen and hydrogen atoms slightly negative and positive
charges, respectively. Another way of stating this is that the probability of finding a shared electron near an oxygen nucleus is
more likely than finding it near a hydrogen nucleus. Either way, the atom’s relative electronegativity contributes to developing
partial charges whenever one element is significantly more electronegative than the other, and the charges that these polar
bonds generate may then be used to form hydrogen bonds based on the attraction of opposite partial charges. (Hydrogen bonds,
which we discuss in detail below, are weak bonds between slightly positively charged hydrogen atoms to slightly negatively
charged atoms in other molecules.) Since macromolecules often have atoms within them that differ in electronegativity, polar
bonds are often present in organic molecules.

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 distribute equally between the two oxygen atoms.

Figure 2.12 also shows another example of a nonpolar covalent bond—methane (CH4). Carbon has four electrons in its
outermost shell and needs four more to fill it. It obtains these four from four hydrogen atoms, each atom providing one, making
a stable outer shell of eight electrons. Carbon and hydrogen do not have the same electronegativity but are similar; thus,

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2.1 • Atoms, Isotopes, Ions, and Molecules: The Building Blocks 41

nonpolar bonds form. The hydrogen atoms each need one electron for their outermost shell, which is filled when it contains two
electrons. These elements share the electrons equally among the carbons and the hydrogen atoms, creating a nonpolar covalent
molecule.

Figure 2.12 Whether a molecule is polar or nonpolar depends both on bond type 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 and Van Der Waals Interactions

Ionic and covalent bonds between elements require energy to break. Ionic bonds are not as strong as covalent, which determines
their behavior in biological systems. However, not all bonds are ionic or covalent bonds. Weaker bonds can also form between
molecules. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions. Without these two types
of bonds, life as we know it would not exist. Hydrogen bonds provide many of the critical, life-sustaining properties of water
and also stabilize the structures of proteins and DNA, the building block of cells.

When polar covalent bonds containing hydrogen form, the hydrogen in that bond 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
hydrogen's δ+ from one molecule and the molecule's δ– charge on another molecule with the more electronegative atoms,
usually oxygen. Scientists call this interaction a hydrogen bond. This type of bond is common and occurs regularly between
water molecules. Individual hydrogen bonds are weak and easily broken; however, they occur in very large numbers in water and
in organic polymers, creating a major force in combination. Hydrogen bonds are also responsible for zipping together the DNA
double helix.

Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. Van der Waals
attractions can occur between any two or more molecules and are dependent on slight fluctuations of the electron densities,
which are not always symmetrical around an atom. For these attractions to happen, the molecules need to be very close to one
another. These bonds—along with ionic, covalent, and hydrogen bonds—contribute to the proteins' three-dimensional structure
in our cells that is necessary for their proper function.

CAREER CONNECTION

Pharmaceutical Chemist
Pharmaceutical chemists are responsible for developing new drugs and trying to determine the mode of action of both old and
new drugs. They are involved in every step of the drug development process. We can find drugs in the natural environment or we
can synthesize them in the laboratory. In many cases, chemists chemically change potential drugs from nature chemically in the
laboratory to make them safer and more effective, and sometimes synthetic versions of drugs substitute for the version we find
42 Chapter 2 • The Chemical Foundation of Life

in nature.

After a drug's initial discovery or synthesis, the chemist then develops the drug, perhaps chemically altering it, testing it to see if
it is toxic, and then designing methods for efficient large-scale production. Then, the process of approving the drug for human
use begins. In the United States, the Food and Drug Administration (FDA) handles drug approval. This involves a series of large-
scale experiments using human subjects to ensure the drug is not harmful and effectively treats the condition for which it is
intended. This process often takes several years and requires the participation of physicians and scientists, in addition to
chemists, to complete testing and gain approval.

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, originally isolated from
willow tree bark. Finding drugs often means testing hundreds of samples of plants, fungi, and other forms of life to see if they
contain any biologically active compounds. Sometimes, traditional medicine can give modern medicine clues as to where to find
an active compound. For example, mankind has used willow bark to make medicine for thousands of years, dating back to
ancient Egypt. However, it was not until the late 1800s that scientists and pharmaceutical companies purified and marketed the
aspirin molecule, acetylsalicylic acid, for human use.

Occasionally, drugs developed for one use have unforeseen effects that allow usage in other, unrelated ways. For example,
scientists originally developed the drug minoxidil (Rogaine) to treat high blood pressure. When tested on humans, researchers
noticed that individuals taking the drug would grow new hair. Eventually the pharmaceutical company marketed the drug to
men and women with baldness to restore lost hair.

A pharmaceutical chemist's career may involve detective work, experimentation, and drug development, all with the goal of
making human beings healthier.

2.2 Water
By the end of this section, you will be able to do the following:
• Describe the properties of water that are critical to maintaining life
• Explain why water is an excellent solvent
• Provide examples of water’s cohesive and adhesive properties
• Discuss the role of acids, bases, and buffers in homeostasis

Why do scientists spend time looking for water on other planets? Why is water so important? It is because water is essential to
life as we know it. Water is one of the more abundant molecules and the one most critical to life on Earth. Water comprises
approximately 60–70 percent of the human body. Without it, life as we know it simply would not exist.

The polarity of the water molecule and its resulting hydrogen bonding make water a unique substance with special properties
that are intimately tied to the processes of life. Life originally evolved in a watery environment, and most of an organism’s
cellular chemistry and metabolism occur inside the watery contents of the cell’s cytoplasm. Special properties of water are its
high heat capacity and heat of vaporization, its ability to dissolve polar molecules, its cohesive and adhesive properties, and its
dissociation into ions that leads to generating pH. Understanding these characteristics of water helps to elucidate its
importance in maintaining life.

Water’s Polarity
One of water’s important properties is that it is composed of polar molecules: the hydrogen and oxygen within water molecules
(H2O) form polar covalent bonds. While there is no net charge to a water molecule, water's polarity creates a slightly positive
charge on hydrogen and a slightly negative charge on oxygen, contributing to water’s properties of attraction. Water generates
charges because oxygen is more electronegative than hydrogen, making it more likely that a shared electron would be near the
oxygen nucleus than the hydrogen nucleus, thus generating the partial negative charge near the oxygen.

As a result of water’s polarity, each water molecule attracts other water molecules because of the opposite charges between
water molecules, forming hydrogen bonds. Water also attracts or is attracted to other polar molecules and ions. We call a polar
substance that interacts readily with or dissolves in water hydrophilic (hydro- = “water”; -philic = “loving”). In contrast, nonpolar
molecules such as oils and fats do not interact well with water, as Figure 2.13 shows. A good example of this is vinegar and oil
salad dressing (an acidic water solution). We call such nonpolar compounds hydrophobic (hydro- = “water”; -phobic = “fearing”).

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2.2 • Water 43

Figure 2.13 Oil and water do not mix. As this macro image of oil and water shows, oil does not dissolve in water but forms droplets instead.
This is because it is a nonpolar compound. (credit: Gautam Dogra).

Water’s States: Gas, Liquid, and Solid

The formation of hydrogen bonds is an important quality of the liquid water that is crucial to life as we know it. As water
molecules make hydrogen bonds with each other, water takes on some unique chemical characteristics compared to other
liquids and, since living things have a high water content, understanding these chemical features is key to understanding life. In
liquid water, hydrogen bonds constantly form and break as the water molecules slide past each other. The water molecules'
motion (kinetic energy) causes the bonds to break due to the heat contained in the system. When the heat rises as water boils,
the water molecules' higher kinetic energy causes the hydrogen bonds to break completely and allows water molecules to escape
into the air as gas (steam or water vapor). Alternatively, when water temperature reduces and water freezes, the water molecules
form a crystalline structure maintained by hydrogen bonding (there is not enough energy to break the hydrogen bonds) that
makes ice less dense than liquid water, a phenomenon that we do not see when other liquids solidify.

Water’s lower density in its solid form is due to the way hydrogen bonds orient as they freeze: the water molecules push farther
apart compared to liquid water. With most other liquids, solidification when the temperature drops includes lowering kinetic
energy between molecules, allowing them to pack even more tightly than in liquid form and giving the solid a greater density
than the liquid.

The lower density of ice, as Figure 2.14 depicts, an anomaly causes it to float at the surface of liquid water, such as in an iceberg
or ice cubes in a glass of water. In lakes and ponds, ice will form on the water's surface creating an insulating barrier that
protects the animals and plant life in the pond from freezing. Without this insulating ice layer, plants and animals living in the
pond would freeze in the solid block of ice and could not survive. The expansion of ice relative to liquid water causes the
detrimental effect of freezing on living organisms. The ice crystals that form upon freezing rupture the delicate membranes
essential for living cells to function, irreversibly damaging them. Cells can only survive freezing if another liquid like glycerol
temporarily replaces the water in them.
44 Chapter 2 • The Chemical Foundation of Life

Figure 2.14 Hydrogen bonding makes ice less dense than liquid water. The (a) lattice structure of ice makes it less dense than the liquid
water's freely flowing molecules, enabling it to (b) float on water. (credit a: modification of work by Jane Whitney, image created using
Visual Molecular Dynamics (VMD) software1; credit b: modification of work by Carlos Ponte)

LINK TO LEARNING
Click here (http://openstax.org/l/ice_lattice2) to see a 3-D animation of an ice lattice structure.

Water’s High Heat Capacity

Water’s high heat capacity is a property that hydrogen bonding among water molecules causes. Water has the highest specific
heat capacity of any liquids. We define specific heat as the amount of heat one gram of a substance must absorb or lose to
change its temperature by one degree Celsius. For water, this amount is one calorie. It therefore takes water a long time to heat
and a long time to cool. In fact, water's specific heat capacity is about five times more than that of sand. This explains why the
land cools faster than the sea. Due to its high heat capacity, warm blooded animals use water to more evenly disperse heat in
their bodies: it acts in a similar manner to a car’s cooling system, transporting heat from warm places to cool places, causing the
body to maintain a more even temperature.

Water’s Heat of Vaporization

Water also has a high heat of vaporization, the amount of energy required to change one gram of a liquid substance to a gas. A
considerable amount of heat energy (586 cal) is required to accomplish this change in water. This process occurs on the water's
surface. As liquid water heats up, hydrogen bonding makes it difficult to separate the liquid water molecules from each other,
which is required for it to enter its gaseous phase (steam). As a result, water acts as a heat sink or heat reservoir and requires
much more heat to boil than does a liquid such as ethanol (grain alcohol), whose hydrogen bonding with other ethanol
molecules is weaker than water’s hydrogen bonding. Eventually, as water reaches its boiling point of 100° Celsius (212°
Fahrenheit), the heat is able to break the hydrogen bonds between the water molecules, and the kinetic energy (motion) between
the water molecules allows them to escape from the liquid as a gas. Even when below its boiling point, water’s individual
molecules acquire enough energy from other water molecules such that some surface water molecules can escape and vaporize:
we call this process evaporation.

The fact that hydrogen bonds need to be broken for water to evaporate means that bonds use a substantial amount of energy in
the process. As the water evaporates, energy is taken up by the process, cooling the environment where the evaporation is taking
place. In many living organisms, including in humans, the evaporation of sweat, which is 90 percent water, allows the organism
to cool so that it can maintain homeostasis of body temperature.

Water’s Solvent Properties

Since water is a polar molecule with slightly positive and slightly negative charges, ions and polar molecules can readily dissolve
in it. Therefore, we refer to water as a solvent, a substance capable of dissolving other polar molecules and ionic compounds. The
charges associated with these molecules will form hydrogen bonds with water, surrounding the particle with water molecules.
We refer to this as a sphere of hydration, or a hydration shell, as Figure 2.15 illustrates and serves to keep the particles separated
or dispersed in the water.
1W. Humphrey W., A. Dalke, and K. Schulten, “VMD—Visual Molecular Dynamics,” Journal of Molecular Graphics 14 (1996): 33-38.

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2.2 • Water 45

When we add ionic compounds to water, the individual ions react with the water molecules' polar regions and their ionic bonds
are disrupted in the process of dissociation. Dissociation occurs when atoms or groups of atoms break off from molecules and
form ions. Consider table salt (NaCl, or sodium chloride): when we add NaCl crystals to water, the NaCl molecules dissociate
into Na+ and Cl– ions, and spheres of hydration form around the ions, as Figure 2.15 illustrates. The partially negative charge of
the water molecule’s oxygen surrounds the positively charged sodium ion. The hydrogen's partially positive charge on the water
molecule surrounds the negatively charged chloride ion.

Figure 2.15 When we mix table salt (NaCl) in water, it forms spheres of hydration around the ions.

Water’s Cohesive and Adhesive Properties

Have you ever filled a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water forms
a dome-like shape above the rim of the glass. This water can stay above the glass because of the property of cohesion. In
cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together at the
liquid-gas (water-air) interface, although there is no more room in the glass.

Cohesion allows for surface tension, the capacity of a substance to withstand rupturing when placed under tension or stress.
This is also why water forms droplets when on a dry surface rather than flattening by gravity. When we place a small scrap of
paper onto a water droplet, the paper floats on top even though paper is denser (heavier) than the water. Cohesion and surface
tension keep the water molecules' hydrogen bonds intact and support the item floating on the top. It’s even possible to “float” a
needle on top of a glass of water if you place it gently without breaking the surface tension, as Figure 2.16 shows.

Figure 2.16 A needle's weight pulls the surface downward. At the same time, the surface tension pulls it up, suspending it on the water's
surface preventing it from sinking. Notice the indentation in the water around the needle. (credit: Cory Zanker)

These cohesive forces are related to water’s property of adhesion, or the attraction between water molecules and other
molecules. This attraction is sometimes stronger than water’s cohesive forces, especially when the water is exposed to charged
surfaces such as those on the inside of thin glass tubes known as capillary tubes. We observe adhesion when water “climbs” up
the tube placed in a glass of water: notice that the water appears to be higher on the tube's sides than in the middle. This is
because the water molecules are attracted to the capillary's charged glass walls more than they are to each other and therefore
adhere to it. We call this type of adhesion capillary action, as Figure 2.17 illustrates.
46 Chapter 2 • The Chemical Foundation of Life

Figure 2.17 The adhesive forces exerted by the glass' internal surface exceeding the cohesive forces between the water molecules
themselves causes capillary action in a glass tube. (credit: modification of work by Pearson-Scott Foresman, donated to the Wikimedia
Foundation)

Why are cohesive and adhesive forces important for life? Cohesive and adhesive forces are important for transporting water
from the roots to the leaves in plants. These forces create a “pull” on the water column. This pull results from the tendency of
water molecules evaporating on the plant's surface to stay connected to water molecules below them, and so they are pulled
along. Plants use this natural phenomenon to help transport water from their roots to their leaves. Without these properties of
water, plants would be unable to receive the water and the dissolved minerals they require. In another example, insects such as
the water strider, as Figure 2.18 shows, use the water's surface tension to stay afloat on the water's surface layer and even mate
there.

Figure 2.18 Water’s cohesive and adhesive properties allow this water strider (Gerris sp.) to stay afloat. (credit: Tim Vickers)

pH, Buffers, Acids, and Bases

The pH of a solution indicates its acidity or basicity.

You may have used litmus or pH paper, filter paper treated with a natural water-soluble dye for use as a pH indicator, tests how
much acid (acidity) or base (basicity) exists in a solution. You might have even used some to test whether the water in a
swimming pool is properly treated. In both cases, the pH test measures hydrogen ions' concentration in a given solution.

Hydrogen ions spontaneously generate in pure water by the dissociation (ionization) of a small percentage of water molecules

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2.2 • Water 47

into equal numbers of hydrogen (H+) ions and hydroxide (OH-) ions. While the hydroxide ions are kept in solution by their
hydrogen bonding with other water molecules, the hydrogen ions, consisting of naked protons, immediately attract to un-
ionized water molecules, forming hydronium ions (H3O+). Still, by convention, scientists refer to hydrogen ions and their
concentration as if they were free in this state in liquid water.

The concentration of hydrogen ions dissociating from pure water is 1 × 10-7 moles H+ ions per liter of water. Moles (mol) are a
way to express the amount of a substance (which can be atoms, molecules, ions, etc.). One mole represents the atomic weight of
a substance, expressed in grams, which equals the amount of the substance containing as many units as there are atoms in 12
grams of 12C. Mathematically, one mole is equal to 6.02 × 1023 particles of the substance. Therefore, 1 mole of water is equal to
6.02 × 1023 water molecules. We calculate the pH as the negative of the base 10 logarithm of this concentration. The log10 of 1 ×
10-7 is -7.0, and the negative of this number (indicated by the “p” of “pH”) yields a pH of 7.0, which is also a neutral pH. The pH
inside of human cells and blood are examples of two body areas where near-neutral pH is maintained.

Non-neutral pH readings result from dissolving acids or bases in water. Using the negative logarithm to generate positive
integers, high concentrations of hydrogen ions yield a low pH number; whereas, low levels of hydrogen ions result in a high pH.
An acid is a substance that increases hydrogen ions' (H+) concentration in a solution, usually by having one of its hydrogen
atoms dissociate. A base provides either hydroxide ions (OH–) or other negatively charged ions that combine with hydrogen
ions, reducing their concentration in the solution and thereby raising the pH. In cases where the base releases hydroxide ions,
these ions bind to free hydrogen ions, generating new water molecules.

The stronger the acid, the more readily it donates H+. For example, hydrochloric acid (HCl) completely dissociates into hydrogen
and chloride ions and is highly acidic; whereas the acids in tomato juice or vinegar do not completely dissociate and are weak
acids. Conversely, strong bases are those substances that readily donate OH– or take up hydrogen ions. Sodium hydroxide
(NaOH) and many household cleaners are highly alkaline and give up OH– rapidly when we place them in water, thereby raising
the pH. An example of a weak basic solution is seawater, which has a pH near 8.0 This is close enough to a neutral pH that
marine organisms have adapted in order to live and thrive in a saline environment.

The pH scale is, as we previously mentioned, an inverse logarithm and ranges from 0 to 14 (Figure 2.19). Anything below 7.0
(ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. Extremes in pH in either direction from
7.0 are usually inhospitable to life. The pH inside cells (6.8) and the pH in the blood (7.4) are both very close to neutral. However,
the environment in the stomach is highly acidic, with a pH of 1 to 2. As a result, how do stomach cells survive in such an acidic
environment? How do they homeostatically maintain the near neutral pH inside them? The answer is that they cannot do it and
are constantly dying. The stomach constantly produces new cells to replace dead ones, which stomach acids digest. Scientists
estimate that the human body completely replaces the stomach lining every seven to ten days.
48 Chapter 2 • The Chemical Foundation of Life

Figure 2.19 The pH scale measures hydrogen ions' (H+) concentration in a solution. (credit: modification of work by Edward Stevens)

LINK TO LEARNING
Watch this video for a straightforward explanation of pH and its logarithmic scale.

Click to view content (https://www.openstax.org/l/pH_scale)

How can organisms whose bodies require a near-neutral pH ingest acidic and basic substances (a human drinking orange juice,
for example) and survive? Buffers are the key. Buffers readily absorb excess H+ or OH–, keeping the body's pH carefully
maintained in the narrow range required for survival. Maintaining a constant blood pH is critical to a person’s well-being. The
buffer maintaining the pH of human blood involves carbonic acid (H2CO3), bicarbonate ion (HCO3–), and carbon dioxide (CO2).
When bicarbonate ions combine with free hydrogen ions and become carbonic acid, it removes hydrogen ions and moderates
pH changes. Similarly, as Figure 2.20 shows, excess carbonic acid can convert to carbon dioxide gas which we exhale through the
lungs. This prevents too many free hydrogen ions from building up in the blood and dangerously reducing the blood’s pH.
Likewise, if too much OH– enters into the system, carbonic acid will combine with it to create bicarbonate, lowering the pH.
Without this buffer system, the body’s pH would fluctuate enough to put survival in jeopardy.

Figure 2.20 This diagram shows the body’s buffering of blood pH levels. The blue arrows show the process of raising pH as more CO2 is
made. The purple arrows indicate the reverse process: the lowering of pH as more bicarbonate is created.

Other examples of buffers are antacids that some people use to combat excess stomach acid. Many of these over-the-counter
medications work in the same way as blood buffers, usually with at least one ion capable of absorbing hydrogen and moderating
pH, bringing relief to those who suffer “heartburn” after eating. Water's unique properties that contribute to this capacity to
balance pH—as well as water’s other characteristics—are essential to sustaining life on Earth.

LINK TO LEARNING
To learn more about water, visit the U.S. Geological Survey Water Science for Schools (http://openstax.org/l/all_about_water) All
About Water! website.

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2.3 • Carbon 49

2.3 Carbon
By the end of this section, you will be able to do the following:
• Explain why carbon is important for life
• Describe the role of functional groups in biological molecules

Many complex molecules called macromolecules, such as proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids
comprise cells. The macromolecules are a subset of organic molecules (any carbon-containing liquid, solid, or gas) that are
especially important for life. The fundamental component for all of these macromolecules is carbon. The carbon atom has
unique properties that allow it to form covalent bonds to as many as four different atoms, making this versatile element ideal to
serve as the basic structural component, or “backbone,” of the macromolecules.

Individual carbon atoms have an incomplete outermost electron shell. With an atomic number of 6 (six electrons and six
protons), 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 an example: 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.

Hydrocarbons
Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane (CH4) described above. We
often use hydrocarbons in our daily lives as fuels—like the propane in a gas grill or the butane in a lighter. The many covalent
bonds between the atoms in hydrocarbons store a great amount of energy, which releases when these molecules burn (oxidize).
Methane, an excellent fuel, is the simplest hydrocarbon molecule, with a central carbon atom bonded to four different hydrogen
atoms, as Figure 2.21 illustrates. The shape of its electron orbitals determines the shape of the methane molecule's geometry,
where the atoms reside in three dimensions. The carbons and the four hydrogen atoms form a tetrahedron, with four triangular
faces. For this reason, we describe methane as having tetrahedral geometry.

Figure 2.21 Methane has a tetrahedral geometry, with each of the four hydrogen atoms spaced 109.5° apart.

As the backbone of the large molecules of living things, hydrocarbons may exist as linear carbon chains, carbon rings, or
combinations of both. Furthermore, individual carbon-to-carbon bonds may be single, double, or triple covalent bonds, and
each type of bond affects the molecule's geometry in a specific way. This three-dimensional shape or conformation of the large
molecules of life (macromolecules) is critical to how they function.

Hydrocarbon Chains
Successive bonds between carbon atoms form hydrocarbon chains. These may be branched or unbranched. Furthermore, a
molecule's different geometries of single, double, and triple covalent bonds alter the overall molecule's geometry as Figure 2.22
illustrates. The hydrocarbons ethane, ethene, and ethyne serve as examples of how different carbon-to-carbon bonds affect the
molecule's geometry. The names of all three molecules start with the prefix “eth-,” which is the prefix for two carbon
hydrocarbons. The suffixes “-ane,” “-ene,” and “-yne” refer to the presence of single, double, or triple carbon-carbon bonds,
respectively. Thus, propane, propene, and propyne follow the same pattern with three carbon molecules, butane, butene, and
butyne for four carbon molecules, and so on. Double and triple bonds change the molecule's geometry: single bonds allow
rotation along the bond's axis; whereas, double bonds lead to a planar configuration and triple bonds to a linear one. These
50 Chapter 2 • The Chemical Foundation of Life

geometries have a significant impact on the shape a particular molecule can assume.

Figure 2.22 When carbon forms single bonds with other atoms, the shape is tetrahedral. When two carbon atoms form a double bond, the
shape is planar, or flat. Single bonds, like those in ethane, are able to rotate. Double bonds, like those in ethene, cannot rotate, so the atoms
on either side are locked in place.

Hydrocarbon Rings
So far, the hydrocarbons we have discussed have been aliphatic hydrocarbons, which consist of linear chains of carbon atoms.
Another type of hydrocarbon, aromatic hydrocarbons, consists of closed rings of carbon atoms with alternating single and
double bonds. We find ring structures in aliphatic hydrocarbons, sometimes with the presence of double bonds, which we can
see by comparing cyclohexane's structure to benzene in Figure 2.23. Examples of biological molecules that incorporate the
benzene ring include some amino acids and cholesterol and its derivatives, including the hormones estrogen and testosterone.
We also find the benzene ring in the herbicide 2,4-D. Benzene is a natural component of crude oil and has been classified as a
carcinogen. Some hydrocarbons have both aliphatic and aromatic portions. Beta-carotene is an example of such a hydrocarbon.

Figure 2.23 Carbon can form five- and six-membered rings. Single or double bonds may connect the carbons in the ring, and nitrogen may
be substituted for carbon.

Isomers
The three-dimensional placement of atoms and chemical bonds within organic molecules is central to understanding their
chemistry. We call molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or
chemical bonds isomers. Structural isomers (like butane and isobutane in Figure 2.24a) differ in the placement of their covalent
bonds: both molecules have four carbons and ten hydrogens (C4H10), but the different atom arrangement within the molecules
leads to differences in their chemical properties. For example, butane is suited for use as a fuel for cigarette lighters and torches;
whereas, isobutane is suited for use as a refrigerant and a propellant in spray cans.

Geometric isomers, alternatively have similar placements of their covalent bonds but differ in how these bonds are made to the
surrounding atoms, especially in carbon-to-carbon double bonds. In the simple molecule butene (C4H8), the two methyl groups
(CH3) can be on either side of the double covalent bond central to the molecule, as Figure 2.24b illustrates. When the carbons are
bound on the same side of the double bond, this is the cis configuration. If they are on opposite sides of the double bond, it is a
trans configuration. In the trans configuration, the carbons form a more or less linear structure; whereas, the carbons in the cis
configuration make a bend (change in direction) of the carbon backbone.

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2.3 • Carbon 51

VISUAL CONNECTION

Figure 2.24 We call molecules that have the same number and type of atoms arranged differently isomers. (a) Structural isomers have a
different covalent arrangement of atoms. (b) Geometric isomers have a different arrangement of atoms around a double bond. (c)
Enantiomers are mirror images of each other.

Which of the following statements is false?

a. Molecules with the formulas CH3CH2COOH and C3H6O2 could be structural isomers.
b. Molecules must have a double bond to be cis-trans isomers.
c. To be enantiomers, a molecule must have at least three different atoms or groups connected to a central carbon.
d. To be enantiomers, a molecule must have at least four different atoms or groups connected to a central carbon.

In triglycerides (fats and oils), long carbon chains known as fatty acids may contain double bonds, which can be in either the cis
or trans configuration, as Figure 2.25 illustrates. Fats with at least one double bond between carbon atoms are unsaturated fats.
When some of these bonds are in the cis configuration, the resulting bend in the chain's carbon backbone means that
triglyceride molecules cannot pack tightly, so they remain liquid (oil) at room temperature. Alternatively, triglycerides with trans
double bonds (popularly called trans fats), have relatively linear fatty acids that are able to pack tightly together at room
temperature and form solid fats. In the human diet, trans fats are linked to an increased risk of cardiovascular disease, so many
food manufacturers have reduced or eliminated their use in recent years. In contrast to unsaturated fats, we call triglycerides
52 Chapter 2 • The Chemical Foundation of Life

without double bonds between carbon atoms saturated fats, meaning that they contain all the hydrogen atoms available.
Saturated fats are a solid at room temperature and usually of animal origin.

Figure 2.25 These space-filling models show a cis (oleic acid) and a trans (eliadic acid) fatty acid. Notice the bend in the molecule caused
by the cis configuration.

Enantiomers
Enantiomers are molecules that share the same chemical structure and chemical bonds but differ in the three-dimensional
placement of atoms so that they are non-superimposable mirror images. Figure 2.26 shows an amino acid alanine example,
where the two structures are nonsuperimposable. In nature, the L-forms of amino acids are predominant in proteins. Some D
forms of amino acids are seen in the cell walls of bacteria and polypeptides in other organisms. Similarly, the D-form of glucose
is the main product of photosynthesis and we rarely see the molecule's L-form in nature.

Figure 2.26 D-alanine and L-alanine are examples of enantiomers or mirror images. L-forms of amino acids are predominant in proteins.

Functional Groups
Functional groups are groups of atoms that occur within molecules and confer specific chemical properties to those molecules.
We find them along the “carbon backbone” of macromolecules. Chains and/or rings of carbon atoms with the occasional
substitution of an element such as nitrogen or oxygen form this carbon backbone. Molecules with other elements in their carbon
backbone are substituted hydrocarbons.

The functional groups in a macromolecule are usually attached to the carbon backbone at one or several different places along its
chain and/or ring structure. Each of the four types of macromolecules—proteins, lipids, carbohydrates, and nucleic acids—has
its own characteristic set of functional groups that contributes greatly to its differing chemical properties and its function in
living organisms.

A functional group can participate in specific chemical reactions. Figure 2.27 shows some of the important functional groups in

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2.3 • Carbon 53

biological molecules. They include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl. These groups play an
important role in forming molecules like DNA, proteins, carbohydrates, and lipids. We usually classify functional groups as
hydrophobic or hydrophilic depending on their charge or polarity characteristics. An example of a hydrophobic group is the
nonpolar methyl molecule. Among the hydrophilic functional groups is the carboxyl group in amino acids, some amino acid side
chains, and the fatty acids that form triglycerides and phospholipids. This carboxyl group ionizes to release hydrogen ions (H+)
from the COOH group resulting in the negatively charged COO- group. This contributes to the hydrophilic nature of whatever
molecule on which it is found. Other functional groups, such as the carbonyl group, have a partially negatively charged oxygen
atom that may form hydrogen bonds with water molecules, again making the molecule more hydrophilic.

Figure 2.27 These functional groups are in many different biological molecules. R, also known as R-group, is an abbreviation for any group
in which a carbon or hydrogen atom is attached to the rest of the molecule.

Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the
function of many macromolecules and help them to fold properly into and maintain the appropriate shape for functioning.
Hydrogen bonds are also involved in various recognition processes, such as DNA complementary base pairing and the binding
of an enzyme to its substrate, as Figure 2.28 illustrates.
54 Chapter 2 • The Chemical Foundation of Life

Figure 2.28 Hydrogen bonds connect two strands of DNA together to create the double-helix structure.

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Chapter 2 • Key Terms 55

KEY TERMS
acid molecule that donates hydrogen ions and increases the outside of the nucleus in the electron orbital; lacks
concentration of hydrogen ions in a solution functional mass and has a negative charge of –1 unit
adhesion attraction between water molecules and other electron configuration arrangement of electrons in an
molecules atom’s electron shell (for example, 1s22s22p6)
aliphatic hydrocarbon hydrocarbon consisting of a linear electron orbital how electrons are spatially distributed
chain of carbon atoms surrounding the nucleus; the area where we are most
anion negative ion that is formed by an atom gaining one likely to find an electron
or more electrons electron transfer movement of electrons from one element
aromatic hydrocarbon hydrocarbon consisting of closed to another; important in creating ionic bonds
rings of carbon atoms electronegativity ability of some elements to attract
atom the smallest unit of matter that retains all of the electrons (often of hydrogen atoms), acquiring partial
chemical properties of an element negative charges in molecules and creating partial
atomic mass calculated mean of the mass number for an positive charges on the hydrogen atoms
element’s isotopes element one of 118 unique substances that cannot break
atomic number total number of protons in an atom down into smaller substances; each element has unique
balanced chemical equation statement of a chemical properties and a specified number of protons
reaction with the number of each type of atom equalized enantiomers molecules that share overall structure and
for both the products and reactants bonding patterns, but differ in how the atoms are three
base molecule that donates hydroxide ions or otherwise dimensionally placed such that they are mirror images of
binds excess hydrogen ions and decreases the hydrogen each other
ions' concentration in a solution equilibrium steady state of relative reactant and product
buffer substance that resists a change in pH by absorbing concentration in reversible chemical reactions in a closed
or releasing hydrogen or hydroxide ions system
calorie amount of heat required to change the temperature evaporation change from liquid to gaseous state at a body
of one gram of water by one degree Celsius of water's surface, plant leaves, or an organism's skin
capillary action occurs because water molecules are functional group group of atoms that provides or imparts a
attracted to charges on the inner surfaces of narrow specific function to a carbon skeleton
tubular structures such as glass tubes, drawing the water geometric isomer isomer with similar bonding patterns
molecules to the tubes' sides differing in the placement of atoms alongside a double
cation positive ion that is formed by an atom losing one or covalent bond
more electrons heat of vaporization of water high amount of energy
chemical bond interaction between two or more of the required for liquid water to turn into water vapor
same or different atoms that results in forming molecules hydrocarbon molecule that consists only of carbon and
chemical reaction process leading to rearranging atoms in hydrogen
molecules hydrogen bond weak bond between slightly positively
chemical reactivity the ability to combine and to charged hydrogen atoms and slightly negatively charged
chemically bond with each other atoms in other molecules
cohesion intermolecular forces between water molecules hydrophilic describes ions or polar molecules that interact
caused by the polar nature of water; responsible for well with other polar molecules such as water
surface tension hydrophobic describes uncharged nonpolar molecules that
compound substance composed of molecules consisting of do not interact well with polar molecules such as water
atoms of at least two different elements inert gas (also, noble gas) element with filled outer electron
covalent bond type of strong bond formed between two shell that is unreactive with other atoms
atoms of the same or different elements; forms when ion atom or chemical group that does not contain equal
electrons are shared between atoms numbers of protons and electrons
dissociation release of an ion from a molecule such that the ionic bond chemical bond that forms between ions with
original molecule now consists of an ion and the charged opposite charges (cations and anions)
remains of the original, such as when water dissociates irreversible chemical reaction chemical reaction where
into H+ and OH- reactants proceed unidirectionally to form products
electrolyte ion necessary for nerve impulse conduction, isomers molecules that differ from one another even
muscle contractions, and water balance though they share the same chemical formula
electron negatively charged subatomic particle that resides isotope one or more forms of an element that have
56 Chapter 2 • Chapter Summary

different numbers of neutrons result of unequal electron sharing, resulting in creating

law of mass action chemical law stating that the rate of a slightly positive and negative charged molecule regions
reaction is proportional to the concentration of the product molecule that is result of chemical reaction
reacting substances proton positively charged particle that resides in the atom's
litmus paper (also, pH paper) filter paper treated with a nucleus; has a mass of one amu and a charge of +1
natural water-soluble dye that changes its color as the pH radioisotope isotope that emits radiation comprised of
of the environment changes in order to use it as a pH subatomic particles to form more stable elements
indicator reactant molecule that takes part in a chemical reaction
mass number total number of protons and neutrons in an reversible chemical reaction chemical reaction that
atom functions bidirectionally, where products may turn into
matter anything that has mass and occupies space reactants if their concentration is great enough
molecule two or more atoms chemically bonded together solvent substance capable of dissolving another substance
neutron uncharged particle that resides in an atom's specific heat capacity the amount of heat one gram of a
nucleus; has a mass of one amu substance must absorb or lose to change its temperature
noble gas see inert gas by one degree Celsius
nonpolar covalent bond type of covalent bond that forms sphere of hydration when a polar water molecule
between atoms when electrons are shared equally surrounds charged or polar molecules thus keeping them
between them dissolved and in solution
nucleus core of an atom; contains protons and neutrons structural isomers molecules that share a chemical
octet rule rule that atoms are most stable when they hold formula but differ in the placement of their chemical
eight electrons in their outermost shells bonds
orbital region surrounding the nucleus; contains electrons substituted hydrocarbon hydrocarbon chain or ring
organic molecule any molecule containing carbon (except containing an atom of another element in place of one of
carbon dioxide) the backbone carbons
periodic table organizational chart of elements indicating surface tension tension at the surface of a body of liquid
each element's atomic number and atomic mass; provides that prevents the molecules from separating; created by
key information about the elements' properties the attractive cohesive forces between the liquid's
pH paper see litmus paper molecules
pH scale scale ranging from zero to 14 that is inversely valence shell outermost shell of an atom
proportional to the hydrogen ions' concentration in a van der Waals interaction very weak interaction between
solution molecules due to temporary charges attracting atoms
polar covalent bond type of covalent bond that forms as a that are very close together

CHAPTER SUMMARY
2.1 Atoms, Isotopes, Ions, and to dissolve in water. Therefore, water is an excellent solvent.
Molecules: The Building Blocks The hydrogen bonds between water molecules cause the
water to have a high heat capacity, meaning it takes
Matter is anything that occupies space and has mass. It is considerable added heat to raise its temperature. As the
comprised of elements. All of the 98 elements that occur temperature rises, the hydrogen bonds between water
naturally have unique qualities that allow them to combine continually break and form anew. This allows for the overall
in various ways to create molecules, which in turn combine temperature to remain stable, although energy is added to
to form cells, tissues, organ systems, and organisms. Atoms, the system. Water also exhibits a high heat of vaporization,
which consist of protons, neutrons, and electrons, are the which is key to how organisms cool themselves by
smallest units of an element that retain all of the properties evaporating sweat. Water’s cohesive forces allow for the
of that element. Electrons can transfer, share, or cause property of surface tension; whereas, we see its adhesive
charge disparities between atoms to create bonds, including properties as water rises inside capillary tubes. The pH value
ionic, covalent, and hydrogen bonds, as well as van der Waals is a measure of hydrogen ion concentration in a solution and
interactions. is one of many chemical characteristics that is highly
2.2 Water regulated in living organisms through homeostasis. Acids
and bases can change pH values, but buffers tend to
Water has many properties that are critical to maintaining moderate the changes they cause. These properties of water
life. It is a polar molecule, allowing for forming hydrogen are intimately connected to the biochemical and physical
bonds. Hydrogen bonds allow ions and other polar molecules processes performed by living organisms, and life would be

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Chapter 2 • Visual Connection Questions 57

very different if these properties were altered, if it could exist for cellular function. Carbon has four electrons in its
at all. outermost shell and can form four bonds. Carbon and
hydrogen can form hydrocarbon chains or rings. Functional
2.3 Carbon groups are groups of atoms that confer specific properties to
The unique properties of carbon make it a central part of hydrocarbon (or substituted hydrocarbon) chains or rings
biological molecules. Carbon binds to oxygen, hydrogen, and that define their overall chemical characteristics and
nitrogen covalently to form the many molecules important function.

VISUAL CONNECTION QUESTIONS

1. Figure 2.3 How many neutrons do carbon-12 and 3. Figure 2.24 Which of the following statements is false?
carbon-13 have, respectively? a. Molecules with the formulas CH3CH2COOH and
2. Figure 2.7 An atom may give, take, or share electrons C3H6O2 could be structural isomers.
with another atom to achieve a full valence shell, the b. Molecules must have a double bond to be cis-trans
most stable electron configuration. Looking at this isomers.
figure, how many electrons do elements in group 1 need c. To be enantiomers, a molecule must have at least
to lose in order to achieve a stable electron configuration? three different atoms or groups connected to a
How many electrons do elements in groups 14 and 17 central carbon.
need to gain to achieve a stable configuration? d. To be enantiomers, a molecule must have at least
four different atoms or groups connected to a
central carbon.

REVIEW QUESTIONS
4. If xenon has an atomic number of 54 and a mass number 8. Which of the following statements is not true?
of 108, how many neutrons does it have? a. Water is polar.
a. 54 b. Water stabilizes temperature.
b. 27 c. Water is essential for life.
c. 100 d. Water is the most abundant molecule in the Earth’s
d. 108 atmosphere.

5. Atoms that vary in the number of neutrons found in their 9. When acids are added to a solution, the pH should
nuclei are called ________. ________.
a. ions a. decrease
b. neutrons b. increase
c. neutral atoms c. stay the same
d. isotopes d. cannot tell without testing

6. Potassium has an atomic number of 19. What is its 10. We call a molecule that binds up excess hydrogen ions in
electron configuration? a solution a(n) ________.
a. shells 1 and 2 are full, and shell 3 has nine electrons a. acid
b. shells 1, 2 and 3 are full and shell 4 has three b. isotope
electrons c. base
c. shells 1, 2 and 3 are full and shell 4 has one electron d. donator
d. shells 1, 2 and 3 are full and no other electrons are
11. Which of the following statements is true?
present
a. Acids and bases cannot mix together.
7. Which type of bond represents a weak chemical bond? b. Acids and bases will neutralize each other.
a. hydrogen bond c. Acids, but not bases, can change the pH of a
b. atomic bond solution.
c. covalent bond d. Acids donate hydroxide ions (OH–); bases donate
d. nonpolar covalent bond hydrogen ions (H+).
58 Chapter 2 • Critical Thinking Questions

12. Each carbon molecule can bond with as many 13. Which of the following is not a functional group that can
as________ other atom(s) or molecule(s). bond with carbon?
a. one a. sodium
b. two b. hydroxyl
c. six c. phosphate
d. four d. carbonyl

CRITICAL THINKING QUESTIONS

14. What makes ionic bonds different from covalent bonds? 18. What property of carbon makes it essential for organic
15. Why are hydrogen bonds and van der Waals interactions life?
necessary for cells? 19. Compare and contrast saturated and unsaturated
triglycerides.
16. Discuss how buffers help prevent drastic swings in pH.
17. Why can some insects walk on water?

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