CHEMISTRY I: ATOMS AND MOLECULES

Atoms
Most of the Universe consists of matter and energy. Energy is the capacity to do work.
Matter has mass and occupies space. All matter is composed of basic elements that
cannot be broken down to substances with different chemical or physical
properties. Elements are substances consisting of one type of atom, for example
Carbon atoms make up diamond, and also graphite. Pure (24K) gold is composed of
only one type of atom, gold atoms. Atoms are the smallest particle into which an
element can be divided. The ancient Greek philosophers developed the concept of the
atom, although they considered it the fundamental particle that could not be broken
down. Since the work of Enrico Fermi and his colleagues, we now know that the
atom is divisible, often releasing tremendous energies as in nuclear explosions or (in a
controlled fashion in) thermonuclear power plants.

Subatomic particles were discovered during the 1800s. For our purposes we will
concentrate only on three of them, summarized in Table 1. The proton is located in the
center (or nucleus) of an atom, each atom has at least one proton. Protons have a
charge of +1, and a mass of approximately 1 atomic mass unit (amu). Elements differ
from each other in the number of protons they have, e.g. Hydrogen has 1 proton;
Helium has 2.

The neutron also is located in the atomic nucleus (except in Hydrogen). The neutron
has no charge, and a mass of slightly over 1 amu. Some scientists propose the neutron
is made up of a proton and electron-like particle.

The electron is a very small particle located outside the nucleus. Because they move at
speeds near the speed of light the precise location of electrons is hard to pin down.
Electrons occupy orbitals, or areas where they have a high statistical probability of
occurring. The charge on an electron is -1. Its mass is negligible (approximately 1800
electrons are needed to equal the mass of one proton).

Table 1. Subatomic particles of use in biology.

Name Charge Location Mass

-27
Proton +1 atomic nucleus 1.6726 X 10 kg
Neutron 0 atomic nucleus 1.6750 X 10-27 kg
Electron -1 electron orbital 9.1095 X 10-31 kg
The atomic number is the number of protons an atom has. It is characteristic and
unique for each element. The atomic mass (also referred to as the atomic weight) is
the number of protons and neutrons in an atom. Atoms of an element that have
differing numbers of neutrons (but a constant atomic number) are termed isotopes.
Isotopes, shown in Figure 1 and Figure 2, can be used to determine the diet of ancient
peoples by determining proportions of isotopes in mummified or fossilized human
tissues. Biochemical pathways can be deciphered by using isotopic tracers. The age of
fossils and artifacts can be determined by using radioactive isotopes, either directly on
the fossil (if it is young enough) or on the rocks that surround the fossil (for older
fossils like dinosaurs). Isotopes are also the source of radiation used in medical
diagnostic and treatment procedures.

Figure 1. Note that each of these isotopes of hydrogen has only one proton. Isotopes
differ from each other in the number of neutrons, not in the number of protons.

Some isotopes are radioisotopes, which spontaneously decay, releasing radioactivity.

Other isotopes are stable. Examples of radioisotopes are Carbon-14 (symbol 14C), and
deuterium (also known as Hydrogen-2; 2H). Stable isotopes are 12C and 1H.

Figure 2. Carbon has three isotopes, of which carbon-12 and carbon-14 are the most
well known.
Figure 3. The Periodic Table of the Elements. Each Roman numeraled column on the
label (at least the ones ending in A) tells us how many electrons are in the outer shell
of the atom. Each numbered row on the table tells us how many electron shells an
atom has. Thus, Hydrogen, in column IA, row 1 has one electron in one shell.
Phosphorous in column VA, row 3 has 5 electrons in its outer shell, and has three
shells in total.

Electrons and energy

Electrons, because they move so fast (approximately at the speed of light), seem to
straddle the fence separating energy from matter. Albert Einstein developed his
famous E=mc2 equation relating matter and energy over a century ago. Because of his
(and others) work, we think of electrons both as particles of matter (having mass is a
property of matter) and as units (or quanta) of energy. When subjected to energy,
electrons will acquire some of that energy, as shown in Figure 4.

Figure 4. Excitation of an electron by energy, causing the electron to "jump" to another

electron (energy) level known as the excited state.

An orbital is also an area of space in which an electron will be found 90% of the time.
Orbitals have a variety of shapes. Each orbital has a characteristic energy state and a
characteristic shape. The s orbital is spherical. Since each orbital can hold a maximum
of two electrons, atomic numbers above 2 must fill the other orbitals. The px, py,
and pz orbitals are dumbbell shaped, along the x, y, and z axes respectively. These
orbital shapes are shown in Figure 5.

Energy levels (also referred to as electron shells) are located a certain "distance" from
the nucleus. The major energy levels into which electrons fit, are (from the nucleus
outward) K, L, M, and N. Sometimes these are numbered, with electron
configurations being: 1s22s22p1, (where the first shell K is indicated with the number
1, the second shell L with the number 2, etc.). This nomenclature tells us that for the
atom mentioned in this paragraph, the first energy level (shell) has two electrons in
its s orbital (the only orbital it can have), and second energy level has a maximum of
two electrons in its s orbital, plus one electron in its p orbital.

Figure 5. Geometry of orbitals. S-orbitals are spherical, p-orbitals are shaped like a
dumbbell or figure 8.
Chemical Bonding | Back to Top
During the nineteenth century, chemists arranged the then-known elements according
to chemical bonding, recognizing that one group (the furthermost right column on the
Periodic Table, referred to as the Inert Gases or Noble Gases) tended to occur in
elemental form (in other words, not in a molecule with other elements). It was later
determined that this group had outer electron shells containing two (as in the case of
Helium) or eight (Neon, Xenon, Radon, Krypton, etc.) electrons.

As a general rule, for the atoms we are likely to encounter in biological systems,
atoms tend to gain or lose their outer electrons to achieve a Noble Gas outer electron
shell configuration of two or eight electrons. The number of electrons that are gained
or lost is characteristic for each element, and ultimately determines the number and
types of chemical bonds atoms of that element can form. Atomic diagrams for several
atoms are shown in Figure 6.

Figure 6. Atomic diagrams illustrating the filling of the outer electron shells
Ionic bonds are formed when atoms become ions by gaining or losing electrons.
Chlorine is in a group of elements having seven electrons in their outer shells (see
Figure 6). Members of this group tend to gain one electron, acquiring a charge of -1.
Sodium is in another group with elements having one electron in their outer shells.
Members of this group tend to lose that outer electron, acquiring a charge of +1.
Oppositely charged ions are attracted to each other, thus Cl- (the symbolic
representation of the chloride ion) and Na+ (the symbol for the sodium ion, using the
Greek word natrium) form an ionic bond, becoming the molecule sodium chloride,
shown in Figure 7. Ionic bonds generally form between elements in Group I (having
one electron in their outer shell) and Group VIIa (having seven electrons in their outer
shell). Such bonds are relatively weak, and tend to disassociate in water, producing
solutions that have both Na and Cl ions.

Figure 7. TOP: Formation of a crystal of sodium chloride. Each positively charged

sodium ion is surropunded by six negatively charged chloride ions; likewise each
negatively charged chloride ion is surrounded by six positively charged sodium ions.
The overall effect is electrical neutrality.
Covalent bonds form when atoms share electrons. Since electrons move very fast they
can be shared, effectively filling or emptying the outer shells of the atoms involved in
the bond. Such bonds are referred to as electron-sharing bonds. An analogy can be
made to child custody: the children are like electrons, and tend to spend some time
with one parent and the rest of their time with the other parent. In a covalent bond, the
electron clouds surrounding the atomic nuclei overlap, as shown in Figure 8.

Figure 8. Formation of a covalent bond between two Hydrogen atoims.

Carbon (C) is in Group IVa, meaning it has four electrons in its outer shell. Thus to
become a "happy atom", Carbon can either gain or lose four electrons. By sharing the
electrons with other atoms, Carbon can become a happy atom,. alternately filling and
emptying its outer shell, as with the four hydrogens shown in Figure 9.

Figure 9. Formation of covalent bonds in methane. Carbon needs to share four

electrons, in effect it has four slots. Each hydrogen provides an electron to each of
these slots. At the same time each hydrogen needs to fill one slot, which is done by
sharing an electron with the carbon.

The molecule methane (chemical formula CH4) has four covalent bonds, one between
Carbon and each of the four Hydrogens. Carbon contributes an electron, and
Hydrogen contributes an electron. The sharing of a single electron pair is termed a
single bond. When two pairs of electrons are shared, a double bond results, as in
carbon dioxide. Triple bonds are known, wherein three pairs (six electrons total) are
shared as in acetylene gas or nitrogen gas. The types of covalent bonds are shown in
Figure 10.

Figure 10. Ways of representing covalent bonds.

Sometimes electrons tend to spend more time with one atom in the bond than with the
other. In such cases a polar covalent bond develops. Water (H2O) is an example. Since
the electrons spend so much time with the oxygen (oxygen having a greater
electronegativity, or electron affinity) that end of the molecule acquires a slightly
negative charge. Conversely, the loss of the electrons from the hydrogen end leaves a
slightly positive charge. The water molecule is thus polar, having positive and
negative sides.

Hydrogen bonds, as shown in Figure 11, result from the weak electrical attraction
between the positive end of one molecule and the negative end of another.
Individually these bonds are very weak, although taken in a large enough quantity, the
result is strong enough to hold molecules together or in a three-dimensional shape.

Figure 11. TOP: Formation of a hydrogen bond between the hydrogen side of one
water molecule and the oxygen side of another water molecule. BOTTOM: The
presence of polar areas in the amino acids that makeup a protein allows for hydrogen
bonds to form, giving the molecule a three-dimensional shape that is often vital to that
protein's proper functioning.
Chemical reactions and molecules
Molecules are compounds in which the elements are in definite, fixed ratios, as seen
in above. Those atoms are held together usually by one of the three types of chemical
bonds discussed above. For example: water, glucose, ATP. Mixtures are compounds
with variable formulas/ratios of their components. For example: soil. Molecular
formulas are an expression in the simplest whole-number terms of the composition of
a substance. For example, the sugar glucose has 6 Carbons, 12 hydrogens, and 6
oxygens per repeating structural unit. The formula is written C6H12O6.
Chemical reactions occur in nature, and some also can be performed in a laboratory
setting. One such reaction is diagrammed in Figure 13. Chemical equations are linear
representations of how these reactions occur. Combination reactions occur when two
separate reactants are bonded together, e.g. A + B -----> AB. Disassociation reactions
occur when a compound is broken into two products, e.g. AB -----> A + B.

Biological systems, while unique to each species, are based on the chemical bonding
properties of carbon. Major organic chemicals (those associated with or formed by the
actions of living things) usually include some ratios of the following elements: C, H,
N, O, P, S.
Learning Objectives
 All forms of matter are composed of one or more elements. Be able to list the
major elements in living things.
 Describe how protons, electrons, and neutrons are arranged into atoms and
ions.
 Define the terms atomic number and atomic mass and be able to describe their
sugnificance.
 Atoms with the same atomic number but a different mass number are isotopes.
List the isotopes of hydrogen and of carbon.
 Be able to describe radioisotopes and list three ways they are used in biology.
 The union between the electron structures of atoms is known as the chemical
bond. Be able to list and describe the three types of chemical bonds found in
living things.
 Be able to describe the distribution of electrons in the space around the nucleus
of an atom.
 An atom tends to react with other atoms when its outermost shell is only partly
filled with electrons. Be able to discuss why this happens.
 Be able to define the two types of ions and describe thow ionic bonds form
between positive and negative ions.
 In a covalent bond, atoms share electrons. List several elements that tend to
form covalent bonds.
 Distinguish between a nonpolar covalent bond and a polar covalent bond and
give an example of each.
 Define hydrogen bond and describe conditions under which hydrogen bonds
form and cite one example.
 Explain what is meant by the polarity of the water molecule, and how the
polarity of water molecules allows them to interact with one another.

Review Questions
1. Which of these is not a subatomic particle? a) proton; b) ion; c) neutron; d)
electron
2. The outermost electron shell of every Noble Gas element (except Helium) has
___ electrons. a) 1; b) 2; c) 4; d) 6; e) 8
3. An organic molecule is likely to contain all of these elements except ___. a) C;
b) H; c) O; d) Ne; e) N
4. The chemical bond between water molecules is a ___ bond. a) ionic; b) polar
covalent; c) nonpolar covalent; d) hydrogen
5. A solution with a pH of 7 has ___ times more H ions than a solutrion of pH 9.
a) 2; b) 100; c) 1000; d) 9; e) 90
6. The type of chemical bond formed when electrons are shared between atoms is
a ___ bond. a) ionic; b) covalent; c) hydrogen
7. The type of chemical bond formed when oppositely charged particles are
attrached to each other is a ___ bond. a) ionic; b) covalent; c) hydrogen
8. Electrons occupy volumes of space known as ___. a) nuclei; b) periods; c)
wavelengths; d) orbitals
9. Carbon has an atomic number of 6. This means it has ___. a) six protons; b) six
neutrons; c) six protons plus six neutrons; d) six neuitrons and six electrons
10.Each of the isotopes of hydrogen has ___ proton(s). a) 3; b) 1; c) 2; d) 92; e)
1/2
11.A molecule is ___. a) a mixture of various components that can vary; b) a
combination of many atoms that will have different ratios; c) a combination of
one or more atoms that will have a fixed ratio of its components; d) more
important in a chemistry class than in a biology class