Chemistry Tutor for Biology Students
Part 1
Why Chemistry? Why Now?
You, your friends, and all other things in the world
are made of chemicals. You are made up of many
different combinations of a fairly small number of
basic building blocks. How these building blocks
combine with one another and how they work
together to make you a living , breathing person is
part of what we call chemistry. An important part
of understanding biology is understanding some of
these basic structures and how they interact with
one another. So, as you begin to study living
things it is important for you to have a background
in basic chemistry.
These are some of the things chemistry can tell
you: the basic building blocks of matter and some
of their characteristics; how the building blocks
combine to make larger, more complicated
structures; how these structures combine with one
another; how to predict the chemical nature of
things based on their structure;
the major groups of chemicals that make up living
things; how the structure of chemicals relates to
their function in living things
Lesson One: The Basic Building Blocks of
Matter
It has been about 100 years since scientists
demonstrated that matter is composed of
extremely small particles that we call atoms.
Every atom has a small, dense region called the
nucleus. The nucleus has nearly all the mass of an
atom. There are two types of particles found in the
nucleus of nearly every atom – positively charged
protons and neutrally charged neutrons.
Around the nucleus is a region containing small,
rapidly moving, negatively charged particles
called electrons.
A substance that consists of the same type of atom
is called an element. There are just over 100
elements – about 90 of them occur naturally on
Earth.
The thing that is most important about an atom is
the number of protons and electrons the atom has.
In all atoms the number of protons is equal to the
number of electrons. If something has a different
number of protons than electrons, then it has an
electric charge and is called an ion.
There are some other important terms related to
atoms and elements. Each element has its own
atomic number; this is simply the number of
protons in the nucleus (which, of course, is also
the number of electrons).
Each type of atom has a mass number (atomic
weight). This is the number of protons plus the
number of neutrons. [Electrons are not added in
because they are so much less massive than
protons and neutrons. A proton is nearly 2,000
times more massive than an electron. The mass of
a neutron is about the same as that of a proton plus
an electron, thus, for general purposes, it is given
the same value as that of a proton.]
Some elements have more than one type of atom.
All atoms of an element have the same atomic
number; however, they can have different
numbers of neutrons in the nucleus. This means
they have different mass numbers. Atoms of one
element having different mass numbers are called
isotopes.
Here are some examples of isotopes: hydrogen
normally has one proton (and one electron); its
mass number is one. [Remember: you do not
count electrons in finding mass number.] There
are two other isotopes: hydrogen with one proton
and one neutron. This has a mass number of two
and is called deuterium. Hydrogen with two
neutrons has a mass number of three and is called
tritium. You probably have heard of “carbon 14;”
it is an isotope of carbon that has 6 protons and 8
neutrons; its mass number is 14. The most
common form of carbon has 6 protons and 6
neutrons and thus has a mass number of 12.
An interesting result of having extra neutrons in
the nucleus is that some of these isotopes are not
stable and will break apart. This gives off energy
that we call radioactivity. For example, both
tritium and carbon 14 are radioactive atoms.
Electrons are the most important part of an atom
in terms of how the atom interacts with other
atoms. You can see why this is true by knowing
the structure of an atom – the outermost part of the
atom is the cloud of electrons surrounding the
nucleus, and thus it will be the part of the atom
that interacts directly with other atoms.
Electrons have certain amounts of energy
associated with them, and this determines the
region they will occupy around a nucleus. Each
level of energy is associated with what we call an
electron shell.
Electron shells all have a maximum number of
electrons that fit in them. The lowest level or first
shell can have only two electrons in it. All other
outer shells can have only eight electrons. [There
is one confusing point here; in some electron
shells there can be more than eight electrons;
however, when this occurs, these shells are not the
outer shells. The outermost shell of an atom can
have only eight electrons.]
Lesson Two: The Periodic Table of the
Elements
One of the greatest intellectual achievements in
the history of science has been the creation of a
systematic organization of the elements that make
up all matter. The Russian chemist Mendeleev was
among the first to organize elements in a way that
showed a repeating pattern of characteristics.
[When something repeats in a regular manner, it is
said to have a periodic nature. This is how the
table of elements gets its name.]
It would be a good idea to have a copy of a
periodic table to look at as we discuss various
things about chemical properties of the elements.
Your textbook has a periodic table.
We can see various trends both across the table
and vertically up and down columns in the table.
Elements that are in the same vertical column have
similar chemical properties.
As we look at how the elements are arranged we
see that they increase by adding one proton to the
nucleus and one electron to an electron shell. [For
our purposes we can ignore the neutrons, since
they do not have much effect on the chemical
properties.] Since the electron shells represent
different energy levels and since each outer shell
can have only a certain number of electrons, as the
atomic number changes the kinds of interactions
that an atom can have with other atoms changes. It
turns out that if an outer shell is nearly empty,
such atoms have a strong tendency to lose
electrons to produce positive ions ( called
cations). On the right-hand side of the table we
see the opposite tendency; these atoms have outer
shells that are nearly full, and therefore they tend
to gain electrons to form negative ions (called
anions).
There is an important exception that must be noted
about the right-hand side of the table. The column
on the far right has a completely full outer shell,
and therefore has almost no tendency to gain or
lose electrons; these atoms are almost completely
inert – meaning they do not react chemically with
any other elements (under normal conditions).
They are called the inert gases, or the noble gases.
As we move across the table from left to right
(horizontal rows are periods) we see an increase in
the tendency for an atom combined with other
atoms to attract electrons towards itself. This
tendency is called electronegativity.
Electronegativity also decreases as we move down
in a column on the table (vertical columns are
groups). Thus, we expect the most electronegative
element to be in the upper right hand corner (when
we exclude the inert gases). And this is exactly
what we find – fluorine is the most electronegative
element. Its neighbor, oxygen, is right behind it. In
biological systems oxygen is the most
electronegative element that is normally
encountered. What this means in studying
biological chemicals is that electrons will tend to
spend most of their time near oxygen and less time
around other elements (such as carbon or
hydrogen). This will be discussed in more detail in
a later lesson.
Most of the elements on the periodic table have a
significant tendency to give up electrons easily
(ones on the left side). These elements are called
metals. Only a fairly small number of elements on
the right side fit into the category of non-metals.
Many periodic tables show a line separating the
metals and non-metals; this line consists of a few
elements that have properties intermediate
between metals and non-metals. These are
sometimes called metalloids.
There are other trends one can see on the periodic
table – such as the size of the atoms [The atomic
radii decrease moving left to right across a period
and increase moving down in a group.]. However,
for our purposes in beginning biology, these things
are not important enough to go into.
Lesson Three : Atoms and Energy
As mentioned in Lesson One electrons are found
in different regions associated with different
amounts of energy. Energy is a critical concept in
all sciences. Nothing changes without energy to
make it happen. Despite the importance of energy,
it is one of the most puzzling concepts we have to
deal with. In fact, it is probably impossible to say
exactly what energy is. However, we can say that
it is the ability to perform work. All things (atoms)
are constantly moving due to what we call kinetic
energy (kinetic simply means movement). Some
energy is not actually doing anything at a given
time – it is available to do something and is
therefore called potential energy.
Another way to look at energy is to say that it
exists in various forms: light is a form of energy;
heat is energy; chemicals can store and release
energy; this is chemical energy. Objects that are
moving or can move are said to have mechanical
energy. All of these are important in biology.
So, let us look at an atom in terms of energy. The
nucleus is a collection of protons and neutrons.
The protons have a positive charge. You may
already be aware that objects with the same charge
have a strong tendency to repel one another. How
do protons stay together in a nucleus? There is an
extremely strong force and a somewhat weaker
force involved. Most of the time there is not
enough energy to overcome these forces, and the
nuclei remain stable regardless of chemical
changes. [It is only in radioactive decay and
nuclear bombs that such forces affect biology.]
Since the nucleus has a positive charge, electrons
naturally tend to be attracted to it; however, the
electrons are moving about in a very rapid and
somewhat unpredictable manner. [Some people
like to compare them to a swarm of gnats buzzing
about.] The electrons are kept near the nucleus
most of the time, but they do not actually contact
it. To make an electron move farther away from
the nucleus, energy has to be added. As it turns out
the energy has to be in a packet of exactly a
certain amount. This is because electrons exist at
different levels of energy and there are no in
between levels. [A packet of energy at a certain
level is called a quantum , plural is quanta.]
This movement of electrons has been observed by
scientists. When they give energy to an atom (as
by shining light on it or passing an electric current
through it), if the light consists of quanta that are
just the right amount to make an electron move to
a higher level, the electron will jump to the new
level. Then, when the electron drops back down to
the lower level, energy is given off – typically as
visible light. [This is the basis on which
fluorescent lights work. Incandescent lamps work
by having a current pass through a substance that
heats up greatly, giving off light as a result of the
enormous amount of heat energy.]
Now we get to the part that is most important in
biology – how this affects the way atoms interact
with one another. The outermost electron shell or
energy level is the part of the atom that interacts
with other atoms. Electrons can move from one
atom to another or they can be shared by
atoms. In all cases the energy involved is what we
called electromagnetic energy. Electromagnetic
energy is what is involved in light, magnetism,
and all chemical interactions. This type of energy
is, as far as we can tell, never great enough to
affect the nuclei of atoms.
[Visible light is simply a narrow band within a
much wider spectrum of energy levels (quanta).
Other kinds of electromagnetic energy include:
gamma rays, X-rays, ultraviolet light, infrared
light, microwaves, and radio waves. Each of these
consists of quanta (called photons) that have a
specific range of energy levels. You may have
heard about a characteristic of light called its
wavelength. Each energy level has one specific
wavelength. The more energy a quantum has the
shorter is its wavelength.]
Atoms seek to have the most stable configuration
for their electrons. What makes them “happiest” is
to have an outer shell that is exactly full. This is
important in understanding how atoms interact
with one another – all atoms will tend to interact
with other atoms in a way that makes (or
maintains) full outer shells. In all atoms except
hydrogen and helium (whose outer shells can hold
only 2 electrons) the outer shell is full with 8
electrons.
The way atoms connect to each other involves
electromagnetic energy and is called bonding.
There are two main types of bonding based on
how electron shells interact with one another.
When atoms of different elements are bonded
together, we have chemical compounds.
Ionic bonding: in some cases electrons will
actually leave an atom, making a positive ion; in
other cases electrons may be added to an empty
outer shell, making a negative ion. Positive and
negative ions are attracted to one another by their
opposite charges due to electromagnetic energy.
This attraction is called ionic bonding. Example:
sodium metal on the left side of the periodic table
tends to lose an electron; chlorine gas tends to
accept an electron. Sodium ions and chloride ions
will form solid crystals held together by ionic
bonds. We call these crystals table salt. Ionic
bonding takes place between elements that are far
apart on the periodic table and therefore have very
different values for electronegativity (tendency to
attract electrons).
Covalent bonding: in many cases the elements
involved have somewhat similar values of
electronegativity. These elements do not tend to
give up or accept electrons from one another.
Instead, they tend to share electrons. Sharing
electrons is covalent bonding. Atoms that are held
together by covalent bonding are called
molecules. The sharing of electrons usually forms
very stable electron configurations that take a lot
of energy to break.
Comparing ionic bonds and covalent bonds:
covalent bonding is quite strong compared to ionic
bonding. Most biological molecules are made of
atoms held together by covalent bonds. Ionic
bonds are rather weak. When an ionic substance
(such as a salt) is placed in water, the forces
created by the kinetic energy and electrostatic
attractions of the water molecules will cause these
bonds to fail. The salt components dissociate (the
salt dissolves) in the water. [If we were made of
things held together by ionic bonds, we would
wash down the drain when we took a shower.]
Footnote on chemical reactions
When/if you take chemistry, you will spend a great
deal of time learning about how various ionic
substances (usually) interact with each other,
exchanging parts that create more stable electron
configurations. Rearrangements of chemical
compounds are called chemical reactions. When
we write out that happens in a chemical reaction,
we use chemical equations. Since this tutorial is
for biology students, we will not spend very much
time on chemical equations. But, there is one
really important thing to keep in mind about this
topic. A chemical equation is like a mathematical
equation; what is on one side has to be the same
as what is on the other – just in different
arrangements. Also, in chemical equations there
are no equality signs; we use arrows.
So, in a chemical equation the number and kind of
each type of atom must be the same on both sides
of the arrow. For example, here is the chemical
equation that summarizes what happens in
photosynthesis when water and carbon dioxide
combine to produce glucose (sugar) and oxygen.
6CO2 + 6H2O  C6H12O6 + 6O2
There are a few things you should notice about
how this is written. The chemical compounds are
shown written together with the symbols for each
type of atom having a subscript after it that shows
how many of that type of atom there are. If there is
no subscript, the number is 1. The numbers written
before a compound show how many units of that
entire compound there are. So, in 6CO2 there are
6 atoms of carbon and 12 atoms of oxygen. Count
up the number of each type of atom on each side;
is this a balanced chemical equation? [Yes; each
side has 6 carbon, 12 hydrogen, and 18 oxygen
atoms.]