2
LIFE’S CHEMICAL BASIS
Chapter Outline
2.1 MERCURY RISING
2.2 START WITH ATOMS
Isotopes and Radioisotopes
2.3 WHY ELECTRONS MATTER
Energy Levels
2.5 WATER’S LIFE-GIVING PROPERTIES
Each Water Molecule is Polar
Water is an Excellent Solvent
Cohesion
Water Stabilizes Temperature
Swapping Electrons
2.6 ACIDS AND BASES
Sharing Electrons
MERCURY RISING (REVISITED)
2.4 WHY ATOMS INTERACT?
Ionic Bonds
SUMMARY
DATA ANALYSIS ACTIVITIES
Covalent Bonds
SELF-QUIZ
Hydrogen Bonds
CRITICAL THINKING
Objectives
1.
2.
3.
4.
5.
Understand how protons, electrons, and neutrons are arranged into atoms and ions.
Explain how the number and arrangement of electrons in an atom or ion determines the number
and kinds of chemical bonds that can be formed.
Know the various types of chemical bonds, how they form between atoms, and the relative
strengths of each type.
Understand the essential chemical properties of water that make life possible.
Understand the importance of pH and the relationships of acids and bases.
Key Terms
atoms
protons
neutrons
electrons
charge
nucleus
atomic number
elements
periodic table
isotopes
mass number
radioisotopes
radioactive decay
tracer
shell models
ion
electronegativity
chemical bond
molecule
compounds
mixture
ionic bond
covalent bond
polarity
hydrogen bond
solvent
solutes
salt
hydrophilic
hydrophobic
cohesion
evaporation
temperature
concentration
pH
acids
bases
buffer
Life’s Chemical Basis
9
Lecture Outline
2.1
Mercury Rising
A. Mercury is gradually being released to the atmosphere
1. This is due to both natural processes and human activities.
B. Mercury in the body can damage a variety of vital organs
2.2
Start With Atoms
A. Atoms are assembled from protons, neutrons and electrons.
1. Protons (positive) and electrons (negative) impact the charge of an atom.
2. Elements are pure substances, with all atoms have the same number of protons, and
therefore the same atomic number.
3. The periodic table arranges atoms in order of their atomic number and with regard to
their behavior.
B. Isotopes and Radioisotopes
1. Atoms with the same number of protons (for example, carbon with six) but a different
number of neutrons (carbon can have six, seven, or eight) are called isotopes ( 12C, 13C,
14C).
2. Radioisotopes spontaneously emit subatomic particles or energy when their nucleus
breaks down.
3. Decay occurs independent of external factors like temperature, pressure, or chemical
bonds with other atoms. This process occurs at a constant rate.
a. They can be used to date rocks and fossils.
b. Some can be used as tracers to follow the path of an atom in a series of reactions.
2.3
Why Electrons Matter
A. Energy Levels
1. Electrons are subatomic particles governed by different forces.
a. In general, atoms have the same number of electrons as protons.
b. Electrons travel in different orbitals, defined as volumes of space around the center
of the atom.
2. Orbitals can be thought of as occupying shells around the nucleus.
a. The shell closest to the nucleus has one orbital holding a maximum of two electrons.
Orbitals closest to the nucleus are lowest in energy level.
b. The next shell can have four orbitals with two electrons each for a total of eight
electrons. Orbitals further from the nucleus have successively higher energy levels.
3. A chemical bond is a union between the electron structures of atoms.
a. Atoms with “unfilled” orbitals in their outermost shell tend to be reactive with other
atoms.
b. The number or the distribution of its electrons changes when an atom gives up, gains,
or shares electrons.
B. Swapping Electrons
1. Ions are atoms that carry a charge—negative by acquiring electrons or positive by
donating electrons.
2. A measure of an atom’s ability to pull electrons away from another atom is called
electronegativity.
3. Electronegativity is dependent upon the atom’s size and electron vacancies. It is not a
measure of an atom’s charge.
C. Sharing Electrons
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Chapter Two
1.
2.
3.
4.
2.4
A molecules forms when two or more atoms of the same or different elements join in
chemical bonds.
A chemical bond is an attractive force between atoms resulting from the interaction of
their electrons.
A compound consists of two or more different elements, where the relative percentages
of the elements do not vary.
In a mixture, two or more elements intermingle, and their proportions may vary.
Why Atoms Interact
A. Ionic Bonds
1. When an atom loses or gains one or more electrons, it becomes positively or negatively
charged—an ion.
2. Two atoms with a large difference in electronegativity have a strong mutual attraction
and form an ionic bond.
B. Covalent Bonds
1. A covalent bond holds together two atoms that share one or more pairs of electrons.
2. Covalent bonds can be much stronger than ionic bonds, but not always.
3. In a nonpolar covalent bond, atoms share electrons equally.
4. In a polar covalent bond, atoms share the electron unequally, resulting in a slight
difference in charge between the two poles of the bond; water is an example.
C. Hydrogen Bonds
1. A hydrogen bond is an attraction between a hydrogen atom and an electronegative atom,
both of which are taking part in separate polar covalent bonds.
2. These are not chemical bonds; they do not form new molecules. They are weaker than
ionic or covalent bonds, easily forming and breaking.
3. These bonds are critical to life and impart structure to liquid water, and stabilize nucleic
acids and other large organic molecules.
2.5
Water’s Life-Giving Properties
A. Each Water Molecule is Polar
1. Water is a polar molecule due to the slight negative charge at the oxygen end and a slight
positive charge at the hydrogen end caused by the unequal sharing of electrons.
2. Water molecules often form hydrogen bonds with each other.
B. Water is an Excellent Solvent
1. The solvent properties of water are greatest with respect to polar molecules with which
they interact by pulling on ions or molecules, dispersing them.
2. Polar substances are hydrophilic (water loving); non-polar ones are hydrophobic (water
dreading, like oils) and are repelled by water.
C. Cohesion
1. Hydrogen bonding of water molecules provides cohesion, a property that helps the
molecules resist separating, which imparts surface tension.
2. In evaporative processes the input of heat energy increases molecular motion so that
hydrogen bonds are broken faster than they form and water molecules escape into the
air, thus cooling the surface..
3. Cohesion contributes to pulling water through plant tissues.
D. Water Stabilizes Temperature
1. Temperature is a way of measuring the energy of molecular motion.
2. Water’s hydrogen bonding slightly restricts molecular “jiggling,” absorbing some energy.
This property means that water acts as an energy reservoir, stabilizing surrounding air
temperatures.
Life’s Chemical Basis
11
3.
2.6
In freezing, the hydrogen bonds resist breaking and lock the water molecules in the
bonding patterns of ice.
Acids and Bases
A. The pH Scale
1. pH is a measure of the H+ concentration in a solution; the greater the H+ the
concentration the lower the pH scale.
2. The scale extends from 0 (acidic) to 7 (neutral) to 14 (basic).
3. Each one unit change reflects a 10-fold change in H+ concentration.
B. How Do Acids and Bases Differ?
1. A substance that releases hydrogen ions (H+) in solution is an acid—for example, HCl.
2. Substances that release ions such as (OH–) are called bases.
C. Buffers against Shifts in pH
1. Buffers are chemicals, often weak acids or bases and its salt, that help keep the pH of a
solution stable.
2. Buffer molecules act by combining with, or releasing, H+ to prevent changes in pH.
3. Bicarbonate is one of the body’s major buffers.
Suggestions for Presenting the Material

First and foremost the instructor must consider that the abstract nature of Chemistry and the
associated terminology are tremendous obstacles to learning. This is highly intimidating—
especially to nonscience majors. While the chapter materials are considered elementary and
certainly critical to the topic of biology, care must be taken in developing a well grounded
presentation. As this topic most often comes early in the semester, take care to ensure students
are not overly discouraged if they struggle.

The extensive use of examples of common chemical compounds and their properties will help
provide context.

Use common examples and references highlighted throughout the text, for example: isotopes,
electron excitation, bonding, buffers, and water, to stress the importance of reading.

Use and have students reference in class the numerous diagrams and illustrations in the text.

Use of the ball-and-stick models (see the Enrichment section below) is very helpful. Larger
examples can be made using inexpensive materials like tennis balls and dowels. This is
especially effective when illustrating properties of polar molecules in a large lecture hall.

Stress the foundational nature of the material and its importance in biology.

Play the animation of Figure 2.11, which illustrates the ionic pull of polar water molecules as
an example of water’s solvent properties. Refer students back to this as a review tool.

Figure 2.14 provides an excellent reference for explaining acid, base, and pH scale. Note
particularly the pH values of common household products. Emphasize that acids and bases
are not necessarily terms that describe corrosive substances!

The properties of water are important to life on Earth. Describe the polarity of water
molecules; then proceed to the influence that water molecules have on cells and cellular
environments.

Common Student Misconceptions:
o
12
Students misunderstand and get confused when discussing atomic structures. Quiz
students on the basic terms to prod them to commit these to memory.
Chapter Two
Classroom and Laboratory Enrichment

Students are often intimidated by chemistry, especially if they lack sufficient high school
background in this area or if they have been out of school for several years. The more you
ground your presentations using everyday examples the more comfortable your students will
be. When possible, emphasize the biological significance of chemistry. Give students frequent
opportunities to use new terms. Use illustrations or diagrams, pause often, and interject
questions to gauge their level of understanding.

Most undergraduates have trouble visualizing abstract items such as atoms and molecules. To
help them visualize atoms and molecules, use ball-and-stick models that are very large and
easy to see. Models help students understand the size relationships among molecules.
Overhead transparencies of ball-and-stick models are especially useful when covering the
larger carbon compounds.

Reinforce chemical bonding patterns through the use of common examples. Present sketches
or illustrations of each type. Use a pair-share activity to have students identify chemical
bonding types with classmates.

Simple ball-and-stick models are also useful for demonstrating the hydrogen bonding that
occurs between water molecules and the latticework structure of ice.

Fill a large jar with water, then add salad oil. Shake the bottle, then allow it to sit on the front
desk. Ask students to explain what has happened. Add a few drops of methylene blue (a polar
dye) and sudan III fat stain (a nonpolar dye) to the jar and shake. Students will see that the
water layer is blue and the oil layer is red; ask them to speculate about how this occurs.

Draw a pH scale on the board (or use an overhead transparency of Figure 2.14), and discuss
pH values of familiar substances. Use examples of pH in nature, their own bodies, or food.

If your class is small, demonstrate the use of a pH meter. For larger groups or in lab, pH paper
can be used to give each student a chance to quickly determine the pH of sample solutions.

If you are teaching in a room with a periodic table of the elements hanging on the wall, point
out the major elements, or use an overhead transparency to show the same items. Relate
subatomic particles with the atomic number and mass.

Prepare a glass of iced tea (instant mix) with added sugar and lemon. Which ingredients are
compounds? What are the components of the mixture?

Bring a package of buffered and regular aspirin to class. Ask students to investigate the
difference(s) in ingredients.

Using the names of the active ingredients on an antacid package, explain how they act as
buffers to stomach acid.
Mercury Rising (revisited)

Have students estimate how much mercury they consume by analyzing their diet.

What body systems does mercury most impact?

Why is mercury so harmful to the developing brain?

Beyond Chinese coal-fired energy plants, investigate the other major contributors to mercury
emissions.

Are there other chemical substance that humans are responsible to releasing at high levels that
could be toxic? Have the students split into groups and investigate this.
Life’s Chemical Basis
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Additional Ideas for Classroom Discussion

Show diagrams of subatomic particles, atoms, and molecules to student groups. Have them
identify what they are and what their properties are.

Form small groups and have them discuss chemical bonding types. One at a time, call on
individual groups and have them explain one type to the whole class.

Show a copy of a soft drink ingredient label to the class. Have them explain why soft drinks
have such a low pH. What ingredient is responsible for this low pH?

What is acid precipitation? What chemical reaction is responsible for the mildly acidic pH of
normal rainwater? What chemicals are responsible for acid precipitation?

Discuss with the class why water is so critical to life. Assess student understanding of the
properties of water by using an open-ended question-and-answer format. Have students
explain what is meant by water being the “universal solvent” for Earth.

What would happen to fish and other aquatic organisms in temperate climates if water sank
when it froze instead of floated?

What is the difference between the composition of a molecule of a substance and an atom of
that substance?

If atoms are beyond the reach of visualization even by electron microscopes, how do we know
so much about their structure?

Some pain relievers are advertised as “tribuffered.” What is meant by this statement? Do you
think it is an important advantage or just a sales gimmick?

Television commercials portray the “acid stomach” as needing immediate R-O-L-A-I-D-S. Is
the stomach normally acidic? Have students find the pH of stomach acids (gastric fluids) on the
chart Figure 2.14. How do you know when there is too much acid down there?
How Would You Vote? Classroom Discussion Ideas

Monitor the voting for the online question. Ask students to justify their answer, considering
topics such as corporate responsibility, consumer education, and relative risk.

Have students investigate other chemical contaminants in food, and how these are handled by
different manufactures.
Term Paper Topics, Library Activities, and Special Projects
14

From the InfoTrac® College Edition site, have students search for and download an article on
elements (atoms) or biomolecules. Have them summarize the article and give a short
presentation in lab or prepare a short paper summarizing the information.

Have students investigate and prepare a short paper on common elements used in food
additives for humans, livestock, or plant fertilizers.

Why are the cells lining the stomach able to withstand pH ranges between one and three?

Have students investigate and explain the functional relationship between acids and bases.
What are the homeostatic mechanisms that help the human body regulate blood pH? Also,
how does the body measure blood pH?

Discuss strategies currently being considered by the United States and other nations to
remedy acid rain. What suggestions would you make to help solve this problem?
Chapter Two

Describe some of the roles played by ions in the human body.

Many elements have radioactive isotopes that are useful as tracers in biological systems. Show
how 14CO2 can be used to follow the fate of carbon as it is incorporated into carbohydrate.

The structure of atoms can be deduced using nuclear magnetic resonance (NMR) and mass
spectrometer machines. Have students prepare a short report on each of these instruments.

Using a pH meter or test paper, examine the degree of acidity/alkalinity of common
household products. If the substance is not a liquid, mix it with water according to package
directions before testing.

Most of the content of human blood is water. However, synthetic blood has been made and
tested. What is the base in this fluid? Is it a feasible substitute? Report on its advantages and
disadvantages.
Responses to Data Analysis Activities
1.
Approximately 2200 tons of mercury were released world-wide in 2006.
2.
Fossil fuel combustion was responsible for the largest fraction of mercury released. Artisanal
and small-scale gold production was second on the list.
3.
Asia emits the largest volume of mercury from producing cement.
4.
Gold production in South America released just over 100 tons of mercury.
Possible Responses to Critical Thinking Questions
1.
Medieval alchemists understood the transformative processes of heat and other simple chemical
reactions but lacked a fundamental understanding of matter at the atomic level. Specifically,
they were attempting to remove protons from lead (Pb) to create gold (Au), a process that would
be incredibly difficult and require massive quantities of energy as lead represents a particularly
stable element.
2.
The shell model for an uncharged nitrogen atom would have two electrons in the first orbital,
and five electrons in the second orbital.
3.
If 210Po emits an alpha particle, it is losing two protons. Given that Po contains 82 protons, and
investigation of the periodic table finds that the element with two less protons is Pb (lead).
4.
Lab workers are told to wipe off splashes with a towel before washing as in undiluted form, the
acid may not appreciable damage to the exposed surface. However, exposure to water can
increase the corrosive nature of the acid to the point where it will significantly degrade the
surface it is exposed to.
Life’s Chemical Basis
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