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Appendix B
Basic Chemistry for the Biology Student

Elements
All things, living and nonliving, are composed of chemical substances that can-
not be broken down, called elements. Each element has its own name, sym-
bol, and properties. Of the approximately 100 known elements, 25 are essential
for living organisms. Four of these—hydrogen (H), oxygen (O), nitrogen (N),
and carbon (C)—are by far the most common in living organisms. The period-
ic table is a chart found in every chemistry text and classroom. It lists the ele-
ments, including their name, symbol, and mass number (discussed below).
Figure B.1 shows the first three rows of the periodic table.

Figure B.1
1 4 The first three rows of the periodic table.
1 H 2 He Highlighted elements are most commonly
found in organisms.
7 9 11 12 14 16 19 20
3 Li 4 Be 5 B 6 C 7 N 8 O 9 F 10 Ne
23
11 Na 2412 Mg 2713 Al 28
14 Si 31
15 P 32
16 S 35
17 Cl 40
18 Ar

The Structure of Atoms

Atoms are composed of protons, neutrons, and electrons. Together, protons and
neutrons make up the nucleus. Protons are positively charged, and neutrons are
electrically neutral and thus have no charge. Electrons are found outside the nu-
cleus in the electron cloud. Electrons, symbolized e–, have a negative charge. Elec-
trons are attracted to the positively charged nucleus. Atoms are electrically neutral
and therefore have the same number of electrons as protons (Figure B.2).

– Electron Figure B.2

The carbon atom, showing pro-
– tons and neutrons in the nucleus
– Electron cloud
and electrons orbiting the nucleus.
+
+ + Proton
+ +
+
– Neutron
–
–

Nucleus

The hydrogen atom (Figure B.3) has the least complex structure of any atom.
Its nucleus has only one proton. Balancing the positive charge of the nucleus is
one negatively charged electron.

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430 Appendix B

Figure B.3
The hydrogen atom. –

Hydrogen

The number of protons in the nucleus of an atom is called the atomic num-
ber. Look back at the abbreviated periodic table. The atomic number is written
as a subscript to the left of the abbreviation for the element. Since the number
of protons in the nucleus equals the number of electrons in the electron cloud,
the atomic number also indicates the number of electrons.
It is possible to deduce the number of neutrons from the mass number, which
is the sum of the protons and the neutrons in the nucleus of an atom. This num-
ber is written as a superscript to the left of the symbol for the element. Hydrogen,
which has no neutrons, can be symbolized as in Figure B.4. Note that hydrogen
has no neutrons, because its mass number is the same as its atomic number.

Figure B.4 Mass number

Representation of (number of protons 1
the hydrogen atom. + neutrons) 1 H
Atomic number
(number of protons)

Electrons have almost no mass, so the mass of the atom does not take into
account the contributions of the electron cloud. Subtracting the atomic number
(the number of protons) from the mass number (number of protons and neu-
trons) indicates the number of neutrons.
Sometimes two atoms have different mass numbers and the same atomic
number. These are called isotopes. For example, carbon (C) has 6 protons. 12C
has an atomic number of 6 and a mass number of 12. Its nucleus is composed
of 6 protons and 6 neutrons. It has 6 electrons in its electron cloud. An isotope
of carbon, 13C, has a nucleus composed of 6 protons and 7 neutrons. There are
6 electrons in its electron cloud. Both of these isotopes have 6 protons; otherwise
they would not be carbon, because it is the number of protons that determines
the identity of an atom. Both of these isotopes are stable, meaning that they do
not have a tendency to lose particles. Radioisotopes are isotopes that are not
stable; they give off particles and energy.

Electrons and Energy

The electrons in the electron cloud that surrounds the nucleus have different en-
ergy levels based on their distance from the nucleus. The first energy level,
sometimes called a shell, is the closest to the nucleus and the electrons located
there have the lowest energy. The second energy level is a little farther away and
the electrons located in the second shell have a little more energy. The third en-
ergy level is even farther away and electrons located in the third shell have
even more energy and so on. The periodic table gets its name because the ele-
ments are arranged in rows, or periods, that correspond to the number of elec-
tron shells each atom of an element contains.
Each energy level can hold a maximum number of electrons. The first shell
holds 2 electrons, and the second shell holds a maximum of eight. This is called
the octet rule. Electrons fill the lowest energy shell before advancing to fill a
higher-energy-level shell. Atoms with the same number of electrons in their
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Appendix B 431

outermost, valence shell exhibit similar chemical behaviors. When the valence
shell is full of electrons, the atom is unreactive. Figure B.5 shows some exam-
ples, the electron configurations of hydrogen, carbon, nitrogen, and oxygen.

Hydrogen Carbon Nitrogen Oxygen

1 H 6 C 7 N 8 O
Figure B.5
Sample electron configurations.

Molecules
Atoms combine to form molecules. Molecules consist of 2 or more atoms of the
same or different elements. For example, oxygen (O2) consists of 2 atoms of
oxygen while carbon dioxide (CO2) consists on 1 atom of carbon and 2 of oxy-
gen. One molecule of glucose (C6H12O6) contains 6 atoms of carbon, 12 of hy-
drogen and 6 of oxygen. If you have more than 1 molecule, the number of
molecules is written to the left of the molecule. For example, 6 water molecules
is written 6 H2O. This means that there are actually 12 hydrogens and 6 oxygens
in these 6 molecules combined.

Ions
Ions are charged atoms. A positively charged atom arises when an electron is
lost from a neutral atom. If an atom gains an electron, it becomes negatively
charged. When a hydrogen atom loses an electron it becomes a hydrogen ion,
H+, due to the loss of its electron from the electron cloud. A hydrogen ion is
also called a proton.
The sodium atom (Na) has 1 electron in its valence shell (Figure B.6).

Figure B.6
Sodium atom.

Na

Sodium atom
11 protons
12 neutrons
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432 Appendix B

When the sodium atom gives up the electron in the outer shell, it becomes
stable, because its valence shell is filled with electrons. In doing so, it becomes
a positively charged ion, Na+. Likewise, a chlorine atom that gains an electron
becomes a chloride ion, Cl–. The chlorine atom (Figure B.7) can gain an electron
because its valence shell needs 1 electron for the atom to become stable.

Figure B.7
Chlorine atom.

Cl

Chlorine atom
17 protons
18 neutrons

The chlorine atom gains an electron when some other atom loses an electron.
Oppositely charged ions form bonds with each other called ionic bonds. When
a sodium ion loses an electron and a chloride ion gains an electron, the two ions
make an ionic bond to form NaCl (sodium chloride, or table salt) (Figure B.8).

Figure B.8
Sodium chloride (NaCl).

Na+ Cl-

Sodium ion (Na+) Chlorine ion (Cl-)

When sodium chloride is placed in water, the ionic bonds are weakened,
and the two ions can dissociate, or separate, from each other.
Ions dissolve in water easily because water can dissociate also. Water dis-
sociates to produce H+ + OH–. These ions are very reactive and form chemical
bonds with many different ions.

Chemical Bonds
Atoms with one or two electrons in the valence shell tend to lose electrons while
atoms with six or seven electrons in the valence shell tend to gain electrons. Atoms
with four or five electrons in the valence shell tend to share electrons to complete
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their valence shells. When atoms share electrons, a type of bond called a covalent
bond is formed. Carbon atoms are often involved in covalent bonding.
Sharing electrons is different from gaining and losing electrons. Gain or loss
of electrons produces ions. Sharing electrons does not produce ions. The carbon
atom, atomic number 6, has four electrons in its valence shell. According to the
octet rule, it needs four more electrons to complete its valence shell and be-
come stable. Most atoms that are involved in electron-sharing covalent bonds
reach a stable configuration by having eight electrons in the valence shell. How-
ever, this is not the case for hydrogen, which is stable when it has two electrons
in its valence shell; it only has electrons in the first shell and the first shell holds
only two electrons. Carbon can form four bonds with hydrogen because carbon
needs four electrons to complete its valence shell (producing CH4, or methane,
Figure B.9).

Figure B.9
Covalent bonding in the
H
methane molecule.

H C H

H
CH4 Methane

Note that in methane there are a total of eight electrons around the valence
shell of the carbon atom and two electrons around each hydrogen atom. Thus,
both C and H have filled their valence shells. Thus, both carbon and hydrogen
have their valence shells filled by sharing electrons.
Covalent bonds are symbolized by a short line indicating a shared pair of
electrons.

H C H

When carbon enters into bonds involving two pairs of shared electrons, this
is called a double bond. A carbon-to-carbon double bond is symbolized as follows:

C C

Carbon can make four bonds to fill its valence shell. Note that even though the
molecule below has double bonds, each carbon atom is still involved in four
chemical bonds total, since a double bond counts as two bonds.

H H H H

H C C C C H

Atoms have characteristic levels of attraction to electrons. Atoms with high

levels of attraction to electrons have a high electronegativity. When two atoms
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434 Appendix B

have the same electronegativity, electrons are shared equally between them,
that is, the electrons are not pulled more toward one atom than another. When
electrons involved in a covalent bond are shared equally, the bond is consid-
ered to be a nonpolar covalent bond. When electrons are not shared equally,
that is, when they are pulled more toward the more electronegative atom, the
bond is said to be a polar covalent bond. Water (H2O) consists of hydrogen and
oxygen atoms. The oxygen atom is more electronegative than most other
atoms, including hydrogen. This means that the electrons shared in the cova-
lent bonds of water are shifted toward the oxygen atoms. When shared elec-
trons are closer to one atom than another, the atom to which they are the closest
will have a partial negative charge, symbolized by the Greek delta, δ–. The
atom from which the electrons are pulled away will have a partial positive
charge, symbolized δ+ (Figure B.10).

Figure B.10 Electrons are δ–

Polarity in the water molecule. pulled toward
oxygen
O

H H
δ+ δ+

One other type of chemical bond is the hydrogen bond. Hydrogen bonding
is a type of weak chemical bond that forms between hydrogen and another
atom. This bonding is based on the attraction of partial charges for each other.
Figure B.11 shows hydrogen bonding that occurs in water molecules. Hydro-
gen bonds are represented by dashed lines.

Figure B.11 (a)

Hydrogen bonds in the water molecule.
(a) Bond between two water molecules.
(b) Bonds among many water molecules.
δ– δ+

(b)