Laboratory 2: Atoms and Molecules
Background
The smallest of units of all matter, including living matter, are known as atoms. There are 92 different kinds of
atoms found in nature and several others that have been created in laboratories and quickly disintegrate. A kind
of matter that consists of exclusively of one kind of atom is known as an element. Atoms can be combined in
many ways to form countless different kinds of molecules. Each kind of molecule has a specific arrangement of
atoms within its structure. Kinds of matter that are composed of only one kind of molecule are called
compounds. Each kind of atom has a specific number and arrangement of parts that differs from the number
and arrangement of parts in other kinds of atoms. The specific structure of an atom determines the kinds of atoms
that it can bond with to form larger molecules. Each atom consists three types of subatomic particles: protons,
neutrons, and electrons. The positively charged protons and uncharged neutrons are located in a central area
called the nucleus and the negatively charged electrons move around outside the nucleus in specific regions
known as electron shells.
The periodic table of the elements (Click Here For Interactive
Periodic Table) arranges elements in order of increasing complexity and
according to how they react chemically. It identifies the number of
protons, neutrons and electrons in atoms of each element. Figure 1
demonstrates how to obtain this information about a carbon atom from
the periodic table. Each element has a one or two letter symbol;
Carbon’s is C, Sodium’s is Na, Chlorine’s is Cl, Gold’s is Au, etc.
Atomic Number: Determining the number of protons
and electrons
The number in each box that is a whole number (no decimal places) is
the atomic number. The atomic number tells us how many protons
(positively charged particles) there are in an atom’s nucleus. It is the identifying characteristic of an atom; it does not change.
Carbon, for example, will always be number 6 and will always, therefore, have 6 protons in its nucleus. Hydrogen (number 1)
has one proton—always. Helium always has two protons; its atomic number is two.
The number of protons in an atom affects the number of electrons exist in that atom’s outer orbitals because atoms are
neutral. The total number of positive particles (protons) must exactly match the number of negative ones (electrons).
Mass number: Determining the number of neutrons
To determine the number of neurons, the mass number—a.k.a. atomic mass—is used. Even though there are three
types of subatomic particles in an atom, electrons have almost no mass. The atomic mass, then, is essentially the mass of the
nucleus because the nucleus contains the particles that do have mass: the protons and neutrons. The mass of a proton and a
neutron are the same: 1 atomic mass unit (amu). The total atomic mass is the sum of the number of protons and neutrons in the
atom. You can determine the number of neutrons in a carbon atom, as an example, by subtracting the atomic number 6 from
the mass number 12 (rounded off); you will find that there are 6 neutrons in a carbon atom (12- 6 = 6). To determine the
number of protons, electrons, or neutrons in an atom, use the periodic table and the following equations:
1.
2.
3.
Atomic number = number of protons
Atomic number = number of electrons (in a neutrally charged atom)
Mass number (rounded off) – atomic number = number of neutrons (in a typical atom)
Ions
When the number of protons and electrons do not match, an ion is formed. Ions occur in nature or can be created during
chemical reactions. An ion is easy to distinguish from an atom. Ions always indicate whether they have too many or too few
electrons by showing a + or – sign next to the symbol. For example, a hydrogen ion would be shown as H+ , Magnesium ion
is Mg+, Silver ion is Ag -. A positive symbol indicates the atom has one or more too few electrons. The + sign does not
mean there is an extra proton (remember the number of protons in an atom does not ever change!); instead, the opposite is
true. Conversely, a negative sign means there is an extra electron.
Figure 1: Periodic table information for carbon
Atomic number
6
Symbol
C
12.01
(number of protons)
Mass Number
(the number of protons plus
neutrons--when rounded)
Electrons, Energy Levels and Orbitals
It is true that opposite charges attract and like charges repel; this very basic concept is what allows an atom to be configured
the way that it is. This is the reason negatively charged electrons (rotating around the nucleus) are held near the positively
charged center of the atom (full of protons: carrying a positive charge). Their movement prevents them from being pulled
into the nucleus. Considering electrons are negative, they will push away from each other. This is the reason electrons
move around the nucleus in specific regions called orbitals. Energy levels designate differences in an electron’s energy
and distance from the nucleus and increase in size as they move away from the nucleus (picture the layers of an onion: the
center is the nucleus and each layer gets bigger with distance from the center). The larger the layer (or energy level) the
more electrons can fit. Remember: electrons will move as far away from each other as possible; the more room available at
a particular level, the more orbitals and, therefore, electrons.
The placement of an electron in an atom (close to or far from the
nucleus) is related to how much energy that electron
represents. The relationship is simple: an increase in distance from the
nucleus signifies an increase in energy for that electron. In other words,
electrons with the greatest energy are found in the orbitals farthest
from the nucleus. The reason this is important for biology is that it is
only these outermost electrons that are involved in the chemical
bonding between two or more atoms. When two or more atoms bond
together, the result is a molecule.
Why Do We Need Chemistry to Understand Biology?
As you are surely aware, biology is the study of living things, organisms. When we deduce life to its most basic foundation,
we are looking at cells. When we dare to look a little further, we soon see
that a cell is made of tiny bits of matter. The cell membrane, the part of a cell
that contains it and regulates what enters and what leaves, is made of only a
handful of types of atoms, bonded together into larger molecules. Membranes
are made of millions of lipid molecules (a type of fat) that are comprised of
carbon, hydrogen, and oxygen atoms bound to a group of other atoms that
happen to include a phosphate atom, as well as a few hydrogen and oxygen
atoms.
That we have at least a working understanding of some chemistry basics is as critical
to our knowledge of biology as knowing that cells are the basic building block of life
or that animals breathe oxygen, or that the sun’s energy is used by plants to make
food. Chemistry is the foundation for life and living things. It is the interaction
between and among atoms that make up the chemical reactions we call life.
Click here to see some biologically important molecules. To the left is a single
strand of DNA, the genetic blueprint for life.
Molecular Structure
As we discussed earlier, a group of atoms bonded together is called a
molecule. To what extent atoms are able to react in such a way as to create a
bond is dependent upon the chemistry of the atoms. The number of electrons
that exist in the outermost orbital, the size of the atom, and other factors
determine which atoms will bond to which others and what type of bond they
will form. There are two types of bonds that we will explore: ionic and
covalent.
Ionic Bonds
Some kinds of atoms have such a strong attraction for electrons that they steal electrons from other atoms that have loosely
held electrons. When this happens, the atom with the stronger pull is able to “coax” an electron from the atom that has the
weaker hold on its electrons. The atom who “steals” the electron has, then, gained one—it now is a negatively charged ion
because it has an extra electron (recall that an ion is formed when the number of protons and electrons do not match). The
atom that has given up an electron is now a positive ion; it has one more proton than it has electrons. The formation of
oppositely charged ions means that they will now have an electrochemical attraction and they will develop an ionic bond.
The old statement is true: opposites do attract, especially in chemistry. Like charges (two of the same, ++ or - -) will repel
each other.
Covalent Bonds
A second kind of bond that holds atoms together to form molecules is known as a covalent bond. In covalent bonds, the
electrons are not actually transferred from one atom to another as in the formation of ions and ionic bonds, but are shared
by two or more atoms. Each pair of electrons that is shared is the equivalent of one covalent bond. Chemists typically
diagram molecules by using a line between atoms to represent a single covalent bond.
pH: The Power of Hydrogen
Understanding how molecules react in the presence of solutions (like water) tells us a great deal about their properties.
Determining if a substance is acidic or basic gives us some insight into how it will react in general, in living systems and with
other molecules. Something is considered acidic if it easily releases its hydrogen ions (H+) when placed in water.
Remember, an ion is an atom that does not have the same number of protons as it has electrons. A basic molecule is one
that removes hydrogen ions from solution by bonding to them or by releasing hydroxide ions (OH-). If a solution has the
same number of these ions (hydrogen and hydroxide) the solution is said to be neutral. Water, for example, is neutral
because it has exactly the same proportion of each of these ions.
H+
+
OH-
H2O
If it has more hydrogen ions
than hydroxide, it is acidic.
A solution with more
hydroxide ions than
hydrogen ions is said to be
basic (alkaline). See the
pH scale.
For your Lab Assignment, open “Lab2AnswerSheet” Under the Laboratory link on BlackBoard.