Chapter 2
The Chemical Basis of Life
Overview
In the previous chapter one of the definitions of life was that organisms must bring in raw materials from their
surroundings to grow, reproduce and respond to changes in their environment. In this chapter we will look at
the chemical basis of life, specifically elements and atoms. We will examine the structure of the atom, the role
of electrons, protons and neutrons and the types of chemical bonds that are possible between atoms.
The second half of the lecture will examine the role of hydrogen bonds in biological systems and the relationship
between hydrogen bonds and the properties of water. Finally, we will examine the pH system of measuring the
acid/base levels of a solution and the role of buffers in biology.
Assigned Reading
Text, Pages 17-29
PowerPoint Presentation
Chapter Review, Page 30
Testing Your Knowledge, Pages 30-31
Key Terms
 Electrons, protons, neutrons
 Valence shell, orbit, nucleus
 Matter, element, atom
 Atomic number
 Atomic mass
 Isotope, ion
 Covalent , ionic, hydrogen bonds
 Polar, nonpolar bonds
 pH scale, acid, base, buffer
 cohesion, adhesion
Introduction
For many people chemistry is a topic which they prefer to avoid completely. Yet in the previous chapter we
observed that in order to understand biological systems, we must understand the chemical building blocks from
which all living things are constructed. In this chapter we will be simply developing an overview of the principles
of chemistry so that we can start to build biologically important molecules in the next chapter. I would suggest
that you focus on the PowerPoint presentation for this chapter, as this should provide a good overview to keep
you focused on the chapter
Structure of the Atom
In Section 2.4 you need to focus on the general structure of the atom (see below) and what each subatomic
particle is. An important concept is that the number of protons determines the element (all carbon has 6
protons) and that the number of electrons = the number of protons. Is the number of neutrons variable?
The focus on the valance electrons, these give atoms their chemical reactivity. Valance electrons are those found
in the outermost orbit of the atom and thus would be the first to react with another atom in the vicinity. Look
at the diagrams in the PowerPoint presentation closely. We shall see that atoms prefer to have 8 electrons in
their valance shell (with a few exceptions). This is called the octet rule.
You need to spend some time learning what is meant by atomic mass (the weight of the atom) and atomic
number (# of protons). These terms are typically confused.
Isotopes
While the number of protons of an element is constant for an element, the number of neutrons is variable, and
thus so is the atomic mass of the atom (why?). When you vary the number of neutrons, the atom may become
unstable or radioactive. Radioactive atoms emit subatomic particles which may detected by special instruments
(Geiger counters, X-ray film, etc). The important thing to realize is that radioactive atoms have the same
number of protons as their non-radioactive counterparts, and thus behave chemically the same. From a
biological perspective, we could give an animal (or person) a radioactive element and then tract how it is
processed by the body, a useful diagnostic tool.
Chemical Bonds
This section can get complicated. In order to satisfy the octet rule, atoms like to have 8 electrons in the valance
shell (except Hydrogen and Helium which like 2). To do this they will either transfer electrons (ionic bonding) or
share electrons (covalent bonding). I will not ask you to predict which will occur, but you need to recognize the
difference between the two. Do not worry about the distribution of the electrons in the shells (orbitals) around
the atom. Just focus on valance electrons and the octet rule.
An ionic bond (see below) is formed when an atom transfers or receives electrons from another atom. When
this happens, the atom becomes electrically charged since the number of electrons no longer matches the
number of protons. These charged particles are called ions and ions of opposite charge attract one another to
form ionic bonds. Since the atom has altered the number of electrons, and electrons determine the chemical
reactivity of an atom, then the chemical properties of ions are not the same as the original atom. A good
example is of sodium chloride. Sodium is an explosive compound, but once ionic it is a useful ion (we shall see
this later). Chlorine is toxic as a gas, but once it is an ion it also becomes a useful ion to the body. Good thing
ions behave as they do, otherwise when you placed table salt into water there would be an explosion followed
by a release of toxic gas!
Ionic Bond Analogy—Two boys (atoms) are playing on a playground with toy cars (electrons). The first boy is a
bit of a bully and looks at the smaller boy’s cars and decides that he wants one. He reaches over and takes it,
putting it with his own cars. The second boy isn’t big enough or strong enough to take the car back, so it stays
permanently with the first boy. However, the second boy still wants the car, so whenever the first boy moves
around the playground, the second one follows him. In this way the two boys are “bonded”, because the car was
transferred from one to the other.
Covalent bonds involve a sharing of electrons, which is possible since electrons are traveling at close to the
speed of light! Covalent bonds still attempt to solve the octet rule, but the transferring of the electron between
the atoms makes the bond stronger, which is useful for biological organisms. An important concept of covalent
bonds is one of polarity. Large atoms have more protons and thus have a greater attraction for the shared
electrons. Since the electrons spend a little more time around the larger atom, the molecule has a positive and
negative end (don't get these confused with ionic!). This makes the molecule compatible with water and these
polar molecules are often called hydrophilic (water loving). Some molecules share the electrons evenly and thus
do not have positive and negative ends. These non-polar molecules do not interact well with water and are
often called hydrophobic (water-hating).
Covalent Bond Analogy—Two different boys (atoms) are playing on a playground with toy cars (electrons). Each
looks at the other’s cars, and decides that there are some that they want. But neither wants to completely get
rid of any of their cars. Instead of fighting about it, they decide to share. Sometimes these commonly desired
cars are with one boy and sometimes they are with the other. Since neither wants to be without any cars, they
stay together and follow each other around, staying “bonded”. They both get all of the cars they want without
having to give up any.
Polarity Analogy—When you’re young, you live with your parents. But you don’t spend all of your time there. In
fact, chances are that during a given day, you spend more of your time at your best friend’s house. Your friend’s
mom feeds you lunch, gives you snacks, and provides a place to hang out. You haven’t become that mom’s child,
and will eventually go back to your own home. You simply spend more time away from home than at it, but still
belong to your own parents. In a similar way, shared electrons can spend more time around one atom than
another without completely belonging to the atom it spends more time around.
Polar covalent compounds like water may be attracted to one another by weak electrical bonds called hydrogen
bonds. For water, these bonds occur between the hydrogen (+) of one water molecule and the oxygen (-) of
another water molecule. These bonds are very weak and are constantly being broken and reformed, but there
are typically so many of them that in mass they act as a significant chemical force for molecules. For example,
the double-strands of DNA are held together by hydrogen bonds, as are many large molecules. For us, hydrogen
bonds give water many of its properties which make it essential for life as we understand it.
Properties Of Water
This is a very important section and one which we will come back to often. As mentioned in the PowerPoint
presentation, the hydrogen bonds of water make this molecule unique. As water is heated, the molecules move
faster until the hydrogen bonds no longer form and the molecule escapes as a gas. Slow down the molecule
(lower the temperature) and the hydrogen bonds become fixed in place forming a solid. For us, focus on the
following important properties:
temperature stabilizing—a significant amount of energy is required to break all of the hydrogen bonds of
water, and thus water resists changes in temperature. Since our bodies are mostly water, this allows us to
stabilize our body temp at 37 C (98.6 F). Imagine how much energy you would have to expend if you were made
of aluminum!
Solvent—most compounds (except hydrophobic ones) dissolve readily in water. This is because the polar nature
of a water molecule interacts with the charges of many molecules to break them apart. However, if a molecule
is hydrophobic, then the molecule does not have a positive and negative pole (it is non-polar) and thus will not
interact with water. Fats are hydrophobic, and thus typically will not dissolve in water.
pH and Buffers
pH is defined as the -log [H+] concentration, but for use it is an indication of the acidity/alkalinity of a solution.
It is a logarithmic scale (see below), so a change from a pH of 3 to 2 represents a change by a power of 10. A pH
of 7.0 is considered neutral, but our bodies actually have a pH around 7.34 (slightly alkaline or basic). We will
not spend a tremendous amount of time discussing buffers and their action, but you should be familiar with the
term.
Concepts
 Name the four elements that make up the majority of living things.
 Understand the differences between atoms, molecules, and compounds.
 Understand the three particles that make up an atom, where they are found, and what their charge is.
 Understand the differences between atomic mass and atomic number.
 Understand how to determine the numbers of protons, electrons, and neutrons when given the atomic
number and atomic mass.
 Understand the octet rule.
 Understand and define isotopes and ions.
 Understand how the valence shell determines whether or not an atom is reactive.
 Understand the differences between ionic and covalent bonds.
 Understand the differences between polar and non-polar covalent bonds
 Understand the method of action and significance of hydrogen bonds.
 Understand the difference between hydrophobic and hydrophilic compounds.
 Understand the special biological properties of water related to cohesion, temperature regulation, and
solvency.
 Understand the differences between and characteristics of acids, bases, and buffers.
 Understand the pH scale, how it is determined, and where on the scale acids and bases will fall.
Links of Interest
Periodic Table of the Elements
ChemTutor - an online tutorial site providing assistance in basic and some advanced chemistry (maintained by
Dr. Harvey Moody). A link to many tutorials on atomic structure and general chemistry principles
Review Material
MyBiology.com—Study guides and resource for this text. Specifically look at MP3 Tutor and all Web Activities