Chapter 2: The

Chemistry of
Biology

2.1 Atoms: Fundamental Building

Blocks of All Matter in the Universe
Expected Learning Outcomes
1. Describe the properties of atoms and identify
the relationships of the particles they
contain.
2. Characterize elements and their isotopes.
3. Explain the differences between atomic
number, mass number, and atomic weight
4. List major elements associated with life.

5. Describe electron orbitals and energy shells and how they are
filled.
• The universe is composed of an infinite variety of substances
existing in gaseous, liquid, and solid states . All such tangible
materials that occupy space and have a mass are called matter.
• The organization of matter – whether air, rocks , or bacteria
begins with individual building blocks called Atoms.
• Atoms is defined as the smallest particle that cannot be
subdivided into smaller substances without losing its
properties.
• Although scientist have not directly observed the detailed
structure of an atom, the exact composition of atoms has
been well established by extensive physical and analysis
using sophisticated instruments.
• In general an atoms derives its properties from a combination
of subatomic particles called protons (p + ), which are
positively charged ; the neutrons (n 0), which have no charge
( are neutral) and electrons (e -), which are negatively
charged.
• Protons and neutrons are similar to one another in both
mass and volume while each is about 2,000 times as heavy
as an electron.
• The protons and neutrons make up a central core or atomic
nucleus that is surrounded by 1 or more electrons. The
nucleus makes up the larger mass (weight) of the atom ,
whereas the electron region, sometimes called the “electron
cloud” accounts for the greater volume.
• To get a perspective on proportions, consider this: if an atom
were the size of a football stadium , the nucleus would be
about the size of a marble.
• The stability of atomic structure is largely maintain by:
* the mutual attraction of the protons and
electrons ( opposite charges attracts each other)
* the exact balance of proton number and
electron number, which causes the opposing
charges to cancel each other out.
Different Types
of Atoms:
Elements and
Their Properties
• All atoms share the same fundamental structure. All protons
are identical, all neutrons are identical, and all electrons are
identical. But when this subatomic particles come together
in specific varied combinations, unique types of atoms called
elements result.

• Each element is a pure substance that has a

characteristic atomic structure and predictable
chemical behavior. To date 118 elements have been
described. Ninety- four of them are naturally
occurring, and the rest were artificially produced by
manipulating the particles in the nucleus. By
convention, an elements is assigned a distinctive
name with an abbreviated shorthand symbol.
In some forms or another, they make up matter of all
earth's organisms and viruses.
Microorganisms particularly important relationship
with the most of these elements. This is to the roles
microbes play in the cycling processes that maintain
the elements in forms of usable by other organisms.
Most life forms require only about 20 0f the 94
naturally occurring elements. The other 70 or so
elements are not critical to life, and several of them
such as arsenic and uranium, can be highly toxic to
cells.
Microbes have some incredible “survival skills” that enable them
to occupy extreme habitats containing large amounts of these
elements .
The word that describes such as microbe is
extremophile.
An extremophile is a microbe that can live in every
severe conditions that would be harmful to other
organisms.
The Major Elements of Life
and Their Primary
Characteristics
• The unique properties of each element result from the
number of protons ,neutrons , and electrons it contains, and
each element can be identified by certain physical
measurements.
• Each element is assigned an ATOMIC NUMBER (AN)
based on the number of protons it has. The atomic
number is valuable measurement because an
elements proton number does not vary , and knowing
it automatically tells you the usual number of
electrons ( recall that a neutral atom has an equal
number of protons and electrons).
• Another useful measurements is the mass number (MN),
equal to the number of protons and neutrons.

• If one knows the mass number of the atomic number,

it is possible to determine the number of neutrons by
subtraction. Hydrogen is a unique element because its
common form has only one proton, one electron, and
no neutron, making it the only element with the same
atomic and mass number.
• Isotopes are variant forms of the same element that
differ in the number of neutrons and thus have
different mass numbers .
• Carbon for example, exist primarily as carbon 12 with
neutrons (MN=12); but a small amount (1%) consist of
carbons 13 with 7 neutrons and carbon 14 with 8 neutrons.
• Although isotopes have virtually the same chemical
properties , some of them have unstable nuclei that
spontaneously release energy in the form of radiation.
• Such radioactive isotopes play a role in several
research and medical applications. Because they emit
detectable , energy they can be used to trace the
position of key atoms or molecules in chemical
reactions , they are tools in diagnosis and treatment ,
and they are even applied in sterilization procedures.

• Another important measurement of an element is its

atomic mass or atomic weight. This is given as the
average mass numbers of all isotopic forms. You will
notice that this number may not come even, because
most elements have several isotopes and differing
proportions of them.
Electron and Orbital Shells
• The structure of an atom can be envisioned as a
central nucleus surrounded by a cloud of electrons
that constantly spin at exceedingly high speed within
confined pathways surrounding the nucleus.
• The pathways taken by electrons are called orbitals,
which are not actual objects are exact locations but
represent volumes of three dimensional space in
which an electron is likely to be found.
• The position of an electron at any one instant is dictated by
its energy level or shell, proceeding from the lower- level
energy electrons nearest the nucleus to the higher-energy
electrons in the outer shells.
Electron fill the orbitals and shells in pairs, starting the
shell nearest the nucleus.
• The first shell contains one orbital and a maximum of
2 electrons.
• The second shell has four orbitals and up to 8
electron.
• The third shell with nine orbitals can hold up to 18
electrons
• The fourth shell with 16 orbitals contains up to 32
electrons.
The number of orbitals and shells and how completely they
are filled on the number of electrons, so that each element
will have a unique pattern. For example
• Helium (AN=2) has only a filled first shell of 2 electrons
• Oxygen (AN= 8) has a filled first shell and a partially filled
second shell of 6 electrons.
• Magnesium (AN=12) has a filled first shell, a filled second
shell, a third shell that has only one orbital, so is nearly
empty.
As we will see, the chemical properties of an element are
controlled mainly by the distribution of electron in the
outermost shell.
2.2 Bonds and Molecules

Expected Learning Outcomes

6. Explain how elements make chemical bonds to form
molecules and compounds.
7. State the relationship among an atom, a molecules,
and a compound.
8. Identify the differences between covalent, ionic , and
hydrogen bonds
9. Summarize the concepts of valence, polarity, and
diatomic elements.
10. Describe ionization and distinguish between anions
and cations.
11. Compare oxidation and reduction and their effects.
• Most elements do not exist naturally in pure, uncombined
form but are bound together as molecules and compounds.

• A molecule is a distinct chemical substance that

results from the combination of two or more atoms. A
few of them such as oxygen consist of the same
element. But most molecule for example, carbon
dioxide and water contain two or more different
elements and are more appropriately termed
compounds. So compounds are some major type of
molecule. Other examples of compounds are
biological molecules such as protein sugar and fats.
The Nature of Diatomic Elements
• You will notice that hydrogen , oxygen , nitrogen ,
chlorine , and iodine are often shown in notation with
a subscript 2-H2 or O2 . These elements are diatomic
(two atoms), meaning that in their pure elemental
state, they exist in pairs, rather than as a single atom.
In heavy case, these elements are more stable as a
pair of atoms joined by a covalent bond than as a
single atom. The reason in this phenomenon can be
explained by their valences.
The electrons in the outer shell are configured so as to
complete a full outer shell for both atoms when they bind.

• When atoms bind together in molecules , they lose

their properties of the atom and take on the
properties of the combined substance. In the same
way that an atom has an atomic weight, a molecule
has a formula mass or molecular weight (MW) , which
is calculated from the sum of all of the atomic masses
of the atoms it contains.
• Chemical bonds of molecules are created when two or
more atoms share, donate (lose) , or accept (gain)
electrons.
• This capacity of making bonds termed valence, is
determined by the number of electrons that an atom
has to lose or share with other atoms during bond
formation. The valence electrons determine the
degree of reactivity and the types of bonds an
element can make. Elements with a filled outer orbital
are relatively nonreactive because they have no extra
electrons to share with or donate to other atoms.
• For example , helium has one filled shell, with no tendency
either to give up electrons or to take them from other
elements , making it stable, inert 9nonreactive) gas.
Elements with partially filled outer orbitals are less
stable and are more apt to form some sort of bond.
• Many chemical reactions are based on the tendency
of atoms with unfilled outer shells to gain greater
stability by achieving , or at least approximating, a
filled outer shell. For example, an atom (such as
oxygen ) that can accept two additional electrons will
bond readily with atoms( such as hydrogen) that can
share or donate electrons.
• In addition to reactivity, the number of electrons in the
outer shell also dictates the number of chemical bonds an
atom can make. For instance hydrogen can bind with one
other atom , oxygen can bind with up two or other atoms , and carbon
can bind with four.
Covalent Bonds: Molecules with Shared
Electrons
• Covalent (cooperative valence) bonds form between
atoms with valences that suit them to sharing
electrons rather than to donating or receiving them. A
simple example is hydrogen gas which consist of two
hydrogen atoms. A hydrogen atom has only one
electron, but when two of them combine, each will
bring its electron to orbit about both nuclei, thereby
approaching a filled orbital for atoms and thus
creating a single covalent bond.
• Covalent bonding also occurs in oxygen but with a
difference. Because each atom has 2 electrons to share in
this molecule, the combination creates two pairs of shared
electrons , also known as a double covalent bond.
The majority of the molecules associated with living
things are composed of single and double covalent
bonds between the most common biological elements
(carbon , hydrogen , oxygen, nitrogen , sulfur, and
phosphorus)
Polarity in Molecules
• Electronegativity refers to the tendency of an atom or
molecule to attract electrons. When atoms of
different electronegativity form covalent bonds, the
electrons will not be shared equally and will be pulled
toward the more electronegative atom. This force
causes one end of a molecule to assume a partial
negative charge and the other end to assume a partial
positive charge.
A molecule with such an unequal distribution of charges is
termed polar and shows polarity meaning it has positive and
negative poles.
• Observe the water molecules and note that because
the oxygen atom is larger and has more protons that
the hydrogen atoms, it will have a stronger attraction
for the shared electrons that the hydrogen atoms
have. Because the electrons will spend more time
near the oxygen , it will express a partial negative
charge. The electrons are less attracted to the
hydrogen orbitals, causing the positive charge of a
hydrogens single proton to dominate.
The polar nature of water plays an important role in a number
of biological reactions. Polarity is a significant property of many
large molecules in living systems and greatly influences both
their structure.
• When covalent bonds are formed between atoms that
have the same or similar electronegativity, the
electrons are shared equally between the two atoms.
Because of this balanced distribution, no part of the
molecule has a greater attraction for the electrons.
This sort of electrically neutral molecule is termed
nonpolar.
• Examples of a nonpolar molecules are oxygen,
methane, and lipids.

Ionic Bonds: Electron Transfer Among Atoms

• In reactions that form ionic bonds, electrons are
transferred completely from one atom to another and
are not shared. These reactions invariably occur
between atoms with complementary valences. This
means that one atom has an unfilled outer shell that
can readily accept electrons and the other atom has
an unfilled outer shell that will readily give up electrons.

• A striking example is the reaction that occurs between

sodium (Na) and chlorine (Cl). Elemental sodium is a
soft, lustrous metal so reactive that it can burn flesh,
and molecular chlorine is a very poisonous yellow gas.
But when the two are combined, they form sodium
chloride (NaCl)- the familiar nontoxic table salt- a
compound with properties quite different from either
parent element.
How this transformation occur?

• Sodium has 11 electrons ( 2 in shell one, 8 in shell

two, and only 1 in shell three) so it is 7 short of having
a complete outer shell. When these two atoms come
together, the sodium atom will readily donate its
single valence electron and the chlorine atom will
avidly receive it. The reaction is slightly more involved
than a single sodium atoms combining with single
chloride atom, but the details do not negate the
fundamental reaction.
The outcome of this reaction is a solid crystal complex
that interlinks millions of sodium and chloride atoms.
• The binding of Na+ and Cl- exists in three dimensions.
Each Na is surrounded by 6 Cls and vice versa. The
charges balance out, and no single molecule of NaCl is
present.
Ionization: Formation of Charged Particles
• Compounds with intact ionic bonds are electrically
neutral, but they can produce charged particles when
dissolved in a liquid called a solvent. This
phenomenon, called ionization, occurs when the ionic
bond is broken and the atoms dissociate (separate)
into unattached, charged particles called ions.
• When a sodium atom reacts with chlorine and loses 1
electron, the sodium is left with 1 more proton than
electrons.
• This imbalance produces a positively charged sodium
ion (Na+).
• Chlorine on the other hand, has gained 1 electron and
now has 1 more electron than protons, producing a
negatively charged ion (Cl-). Positively charged ions
are termed cations, and negatively charged ions are
termed anions. Substances such as salts, acids, and
bases that release ions when dissolved in water are
term electrolytes because their charges enable them
to conduct electrical current.
• Owing to the general rule that particles of like charge repel
each other and those of opposite charge attract each other,
we can expect ions to interact electrostatically with other
ions and polar molecules. Such interactions are
important in many cellular chemical reactions, in
formation of solutions, and in the reactions
microorganisms have with dyes.
Hydrogen Bonding
• Some types of bonding do not involved sharing,
losing, or gaining electrons but instead are due to
attractive forces between nearby molecules or atoms.
One such bond is a hydrogen bond, a weak
electrostatic forms between a hydrogen covalently
bonded to one molecule and an oxygen or nitrogen
atom on the same molecule or on different molecule.
• This phenomenon occurs because a hydrogen atom
in a covalent bond tends to be positively charged.

• Thus, it can attract a nearby negatively charged atom

and form an easily disrupted bridges with it. This type
of bonding is usually represented in molecular models
with a dotted line. A simple example of hydrogen
bonding occurs between water molecules.
• More extensive hydrogen bonding is partly
responsible for the structure and stability of proteins
and nuclei acids.
• Weak molecular interactions similar to hydrogen bonds that
play major roles in the shape and function of biological
molecules are van der Waals forces.
• The basis for these interactions is also an attraction of
two regions on atoms or molecules that are opposite
in charge but van der Waals forces can occur between
nearly a types of molecule and not just those
containing hydrogen, oxygen, and nitrogen.
• These forces come into a play whenever the electrons
in molecules move about their orbits and become
unevenly distributed.
• This unevenness leads to short-term “steaky spots” in the
molecule- some positively charged and others negatively
charged.
• When such regions are located close together, their
opposite charges pull them together. These forces can
hold even large molecules together because of the
cumulative effects of numerous sites of interaction.
• They only function with between molecules but may
occur within different regions of the same large
molecules. Van der Waals forces are a significant
factor in protein folding and stability.
Electron Transfer and Oxidation-Reduction
Reactions
• The metabolic work of cells ,such as synthesis,
movement, digestion, revolves around energy
exchanges and transfers. The management of energy
in cells is almost exclusively dependent on chemical
rather than physical reactions, because most cells are
far too delicate to operate with heat, radiation, and
other more potent forms of energy.
• The outer-shell electrons are readily portable and
easily manipulated sources of energy.
• It is in fact the movement of electrons from molecule to
molecule that accounts for most energy exchanges in cells.

• Fundamentally, then cells must have a supply of atoms

that can gain or lose electrons if they are to carry out
life processes.
• The phenomenon in which electrons are transferred
from one atom or molecule to another is termed an
oxidation-reduction (shortened to redox) reaction.
• The term oxidation was originally adopted from
reactions involving the addition of oxygen, but this is
no longer the case.
• In current usage, oxidation includes any reactions occur in
pairs it follows that reduction is the result of a different
atom gaining the same electrons.
• Keep in mind that because electrons are being added
during reduction, the atom that receives them will
become more negative; and that is the meaning of
reduction. It does not imply an atom is getting smaller.
In fact reduction often results in a greater complexity
of the molecule.
• When these two atoms, called the redox pair, react to
from a sodium chloride, a sodium atom gives up an
electron to a chlorine atom.
• During this reaction, sodium is oxidized because it loses an
electron , and chlorine is reduced because it gains an
electrons.
• With this system, an atom such as sodium that can
donate electrons and thereby reduce another atom is
a reducing agent. An atom that can receive extra
electrons and thereby oxidize another molecule is an
oxidizing agent. You my find this concept easier to
keep straight if you think of redox agents as partners:
The reducing partner gives its electrons away and is
oxidized; the oxidizing partner receives the electrons
and is reduced.
• In cellular metabolism, electrons are frequently
transferred from one molecule to another.
• In other reactions oxidation and reduction occur with
the transfer of a hydrogen atom ( a proton and
electron) from one compound to another.