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CHAPTER 2 FUNDAMENTAL
BUILDING BLOCKS:
Chemistry, Water, and pH
2.1 Chemistry’s Building Block: The Atom
2.2 Matter Is Transformed through Chemical Bonding
2.3 Some Qualities of Chemical Compounds
2.4 Water and Life
2.5 Acids and Bases Are Important to Life
Essays: Getting to Know Chemistry’s Symbols
Free Radicals
OBJECTIVES
Teaching Goals
Many nonscientists suffer from substantial “fear and loathing” of chemistry. The main goal of this
chapter is to make students see that they cannot achieve a true understanding about how life works if
they don’t understand the behavior of the chemicals that make up living organisms. For example, if
our cells are composed of water, does it make a difference whether a molecule likes water or is
repelled by water?
Convey the idea that chemicals are the physical material that makes up all biological life and
that an understanding of chemistry is critical to explaining the behavior of biological structures.
Put the students at ease about the concepts of atoms and how subatomic particles allow atoms to
interact to create compounds.
Relate the idea that there is a range of ways that molecules can form, that is, the three main
types of chemical bonds.
Student Goals
By the end of this lecture series, students should be able to do the following:
Explain the nature of matter and why different substances, such as gold and iron, are
fundamentally different.
Name the three subatomic particles. Which contribute weight? Charge? Which particles allow
atoms to interact with each other?
Be able to use the number of electrons in an element to determine whether an atom will react
and what kind of—and how many—chemical bonds it will normally make.
Full file at https://fratstock.eu12 Instructor Guide
Be able to describe the three types of chemical bonds, explaining their differences, and describe
the differences between nonpolar and polar molecules.
Explain what kinds of molecules go into solution in water and what kinds do not.
Define an acid and a base, and if given a pH reading, be able to understand what that means in
general and specifically for cells.
SCIENCE AND SOCIETY
This chapter provides the basis of all the biochemistry students will be asked to understand in the
following chapters on food, photosynthesis, DNA, and metabolism. If they don’t understand
chemical bonds, it will be difficult for them to understand why we eat, how we grow, how cells use
energy, and how food is created.
Basic chemistry also has a direct effect on students’ lives. For example, the public has been
increasingly expected to take a greater role in its own health care. Advertisements of prescription
drugs for conditions from baldness to allergies encourage patients to approach their doctors for more
information. It is now possible to buy prescription drugs over the Internet without seeing a doctor.
Indeed, many adults experiment with drugs for weight loss, for muscle gain, for cancer treatment, or
as “date-rape” drugs—without expert advice. All of these health care decisions make it increasingly
important for the public to understand some chemistry, at least to be able to understand the
information printed in the pamphlets they receive with a prescription or off the Internet.
As another example, many people are taking nutritional supplements. It is important to know
how these supplements function chemically, to understand that a lot of their function is due to their
three-dimensional shape and the placement of chemical bonds. Recently, media attention focused on
the death of 23-year-old baseball pitcher Steve Bechler due to use of a legal nutritional supplement,
Xenadrine RFA-1, which contains the active ingredient ephedra (ephedrine, currently used for
weight loss). Most students may be interested to know that ephedrine is used as the precursor for
illegal production of methamphetamines (speed) and that there is a great deal of chemical similarity
between ephedrine and amphetamines like those found in the common medication Adderall, used to
treat attention deficit disorder.
LECTURE OUTLINE
I. Introduction: Chemistry and Its Importance in Biology
A. Why do we need to study chemistry? Because you need to see what living organisms are
made of, from the small parts to the big parts, to understand how they function: Figure 2.1.
(City is composed of bricks and mortar.)
B. Also, the public is increasingly responsible for health care decisions that require knowledge
of chemistry (see “Science and Society”).
Interactive Activity 2.1
C. How do cells do anything? Chain of chemical reactions, latching on, reforming, depositing,
and breaking down.
D. Look at an object; what do you see? Matter: takes up space, has weight. Energy: types of
energy.
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II. Chemistry’s Building Block: The Atom (Section 2.1)
A. Subatomic particles: Figure 2.2.
1. Nucleus: very small size compared to the entire atom, composed of protons (positive
charge, mass) and neutrons (no charge, but mass).
2. Electrons: orbit the nucleus (negative charge, negligible mass).
3. Atoms are usually electrically neutral: Number of electrons = number of protons.
B. Elements: Figure 2.3. Gold—pure, cannot be reduced into a simpler component substance
through chemical processes.
1. Difference between iron and gold? Both are matter: Fe has 26 protons, and Au has
79 protons.
2. Atomic number = number of protons defines elements.
3. One element = one atomic number.
4. Elements are listed on periodic table by number of protons: H = 1, He = 2.
5. What kind of elements are we composed of? Dirt? Figure 2.4.
C. Atomic weight and isotopes.
1. Neutrons also contribute weight, but not identity, so different forms of the same element
may have different mass, called isotopes. Optional: Isotopes in health care or carbon
dating: Figure 2.6.
2. Mass number = number of protons + number of neutrons.
3. Atomic weight is the average mass number of isotopes for one element.
III. Matter Is Transformed through Chemical Bonding (Section 2.2)
A. Chemical bonding.
1. Electrons—the most important particles in allowing atoms to interact so they can attach.
2. Electrons are found in distinct energy levels (shells): Figure 2.7.
3. Atoms are driven to react by a “desire” to become more stable (like a rock perched on a
hill).
4. Stability—full outer electron shell (more energetically sound to have a full car when you
commute).
5. Nonreactive elements (inert gases such as argon) have full outer shells (cannot have any
more passengers, so will not react).
Interactive Activity 2.2
B. Covalent bonds: Atoms that don’t have full outer shells may want to share electrons so that
they can both have full outer shells.
1. Covalent bonds between two hydrogen atoms (each with one electron) and oxygen (with
eight) complete the shells of all three.
2. Law of conservation of mass—matter is neither created nor destroyed.
3. Molecules = two or more atoms combined.
a. Molecules have a three-dimensional shape. (Section 2.3)
4. Compound = defined number of atoms in a defined spatial relationship.
5. Nonpolar versus polar covalent bonds: Figure 2.9.
a. Nonpolar = H2. Like joint custody; equal electronegativity.
b Polar = H2O. Oxygen has greater electronegativity; listed under the resources for
Chapter 2 is a nice animation of formation of water.
c. Spectrum of electronegativity.
C. Ionic bonds—occur when one atom has a much greater electronegativity.
1. Formation of NaCl: Figure 2.10.
2. Ions = charged atoms after losing or gaining one electron.
3. Ionic compounds = ions’ electrostatic attraction to each other.
D. Hydrogen bonds.
1. Water in solution—polar covalent bonds in H2O generate partial negative and partial
positive charge on opposite sides.
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2. Partial negative end of one water attracted to partial positive end of another by a
hydrogen bond: Figure 2.11.
IV. Optional: Free Radicals (Essay: Free Radicals)
A. Atoms can come together but not share all the electrons. A free radical is one free, unpaired
electron.
B. Free radicals are unstable: Like a dancer without a partner, a free radical steals electrons
from others, breaking bonds.
C. Free radicals scar artery walls, damage DNA.
D. Free radicals are created in greater numbers by smoking, sunlight, and alcohol.
E. Free-radical scavengers = antioxidants (beta carotene, vitamins C and E).
V. The Importance of Water to Life (Section 2.4)
A. 71 percent of Earth’s surface, 66 percent of weight of human body.
B. Important properties of water.
1. Required/generated by many cellular reactions (breaking down food).
2. Important solvent—hydrogen bonds with polar or charged molecules (NaCl):
Figure 2.15. 3. Solid versus liquid densities, importance for marine organisms.
4. Specific heat (importance for insulating Earth and for cooling living organisms by
sweating).
5. Cohesion and surface tension.
6. Hydrophobic versus hydrophilic molecules.
7. Solubility.
Interactive Activity 2.3
VI. Acids and Bases Are Important to Life (Section 2.5)
A. Acids and bases.
1. Common acids (vinegar) and common bases (lye).
2. Definition of an acid—substance that yields hydrogen ions in solution (HCl):
Figure 2.18. 3. Definition of a base—substance that accepts hydrogen ions (NaOH): Figure 2.18.
4. pH scale (logarithmic, lower pH = more acidic; raise pH = less acidic, more basic, or
alkaline): Figure 2.19.
5. pH and health; asthma, cardiac arrest, vomiting as result of acidosis.
6. pH and the environment—acid rain.
KEY TERMS
acid hydrogen bond nucleus
acid rain hydrophilic pH scale
alkaline hydrophobic polar covalent bond
atomic number hydroxide ion polarity
ball-and-stick model ion product
base ionic bonding proton
buffering system ionic compound reactant
chemical bonding isotope specific heat
covalent bond law of conservation of mass solute
electron mass solution
electronegativity molecular formula solvent
element molecule space-filling model
free radical neutron structural formula
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hydrocarbon nonpolar covalent bond
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INTERACTIVE ACTIVITIES
Interactive Activity 2.1—Chemistry in the News
Introduction: The purpose of this activity is to demonstrate to students that there is a lot of
chemistry that affects their day-to-day lives. Stories in newspapers and magazines that they may (or
may not) have been ignoring (because, “Yuck, it’s chemistry!”) may actually be quite interesting. A
secondary purpose is to encourage students to form a group that meets outside of class—studies
have shown that forming student study groups is linked with success.
Estimated time to complete: Although students may need a rather variable amount of time at home
or in the library outside of class, the activity should take about 25 minutes of class time to complete.
Materials needed: This activity relies mostly on the handout provided in this guide, the textbook
(as a reference), and after class access to newspapers and/or news magazines (or Internet news sites
as a last resort).
Procedures
Part 1: About 10 minutes before the end of class, ask students to form groups of three to four and
discuss chemistry-related topics that they may have heard or read about recently. After about 5
minutes of discussion, direct each group to select one to two topics they find most interesting and/or
believe they can realistically find current information about. Sources may not always need to be very
recent, as long as the information is still accurate and relevant. You may then visit each group to
provide the handout and approve/disapprove their topic choice(s). Some students are more in tune
with news and current events than others, so the handout provides them with backup support. Tip:
Visit first the groups you have observed to be struggling a bit. Showing them the list of suggested
topics in the handout can help minimize their frustration. This also gives other groups a little more
time to select a topic of their own. At your discretion, you may or may not wish to allow them the
flexibility to switch to a different topic, based on availability of information.
Part 2: Reconvene the student groups the next class meeting so that they may finalize and present
their brief oral report. The handout provides organizational guidance.
Assessment suggestions: A brief oral report to the class is the quickest method of assessment and
allows prompt feedback. Alternatively, you may wish to collect the handout and return it with
comments.
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Name: ________________________________ Date: ___________________
Instructor: _____________________________ Course Section: ___________
Interactive Activity 2.1 Handout—Chemistry in the News
Introduction: The purpose of this activity is to explore the impact of chemistry on society. You will
be asked to discuss chemistry-related topics that you may have heard or read about recently. You
will then be asked to choose one of these topics to explore further.
Instructions Write your selected topic: ____________________________________________________
If you had difficulty with selecting a topic, perhaps you can choose one from this list:
Acid rain Ethanol in gasoline Solar energy chemistry
Biofuels Gamma hydroxy butyrate (GHB) Steroid abuse
Ephedrine Ozone layer and CFCs Toxic waste
Title of article:
Source:
Summary:
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Interactive Activity 2.2—Electrons Ride the Bus!
Introduction: The purpose of this activity is to demonstrate the process by which electron shells are
filled. You will simulate filling electron slots in shells using the “bus analogy.”
Estimated time to complete: Although students may need a rather variable amount of time at home
or the library outside of class, the activity should take about 25 to 30 minutes of class time to
complete.
Materials: This activity relies mostly on the textbook (as a reference), and, after class, access to
newspapers and/or news magazines (or Internet news sites as a last resort).
Procedure: Perform a classroom demonstration showing how creating covalent bonds is simply like
“carpooling” in a shuttle bus. It is energetically favorable for people to use public transportation, so
why not for atoms? Set up 10 chairs at the front of the classroom, representing the 10 spaces in the
first two atomic orbitals:
Tell the students that the chairs are spaces for electrons to sit, like spaces on a school bus. Then,
role-play. Ask for a student volunteer to be the electron of hydrogen. Ask him or her to choose a
seat. The electron of hydrogen is in the first orbital, the one closest to the bus driver. Why does it
want to sit there? The bus driver is like the nucleus full of protons, very desirable, just as the front of
the bus is superior to the rear because it’s a shorter walk and easier to exit. Have this student get up
and remain on “standby” on the side of the room.
Then ask for volunteers to be the electrons of oxygen. How many are there? And where will they
sit? Coach the students to first fill “unpaired” seats to show how electron orbitals really do fill up.
Ask, how many empty seats does oxygen have? Then ask students this question: if they were
striving for efficient transportation, wouldn’t it be a waste for two hydrogen atoms to drive
separately when the oxygen “bus” has two empty seats? Yes, so they want to hitch a ride. It is
energetically favorable. That explains why oxygen makes two bonds, but not three, and carbon
makes four bonds, not three. Use any of the elements students will be studying in biology—C, S, or
N. Explain to them how easy it is to visualize this way.
Assessment suggestions: Before repeating the above procedure with carbon, sulfur, or nitrogen, ask
students to predict how the electrons would be distributed and how many empty seats will be
available. Ask how many hydrogen atoms would normally bond with each of these atoms, too.
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Interactive Activity 2.3—Water: Love It or Leave It!
Introduction: The purpose of this activity is to demonstrate that students already know a fair
amount about water’s properties as a solvent, as well as the properties of substances that do or don’t
dissolve in water. This will also build confidence that they can apply this “common sense” to the
course if they keep simple rules of solvency in mind. This also teaches students how to reason their
way through some of the questions about the properties of things we deal with in a biology course.
And, of course, the title is a playful pun on the hydrophilic/hydrophobic properties we focus on.
Estimated time to complete: This activity should take about 15 to 20 minutes of class time to
complete.
Materials needed: This activity relies mostly on the handout provided in this guide, the textbook
(as a reference), and the students’ recall.
Procedure: Ask students to form groups of three to four and to fill out the list provided in the
handout asking them to identify common things around the house (or garage) that do dissolve in
water and that do not. Advise them not to include obviously insoluble things such as rocks and
metals, but rather to focus on things that are not large solid objects at room temperature (the handout
advises this, as well). Although they are working as group, each student should fill out his or her
own handout.
After about 10 minutes, students should have a list of several items on each side. Stop to remind
them (the handout does this, too) that things that do not dissolve in water are most often nonpolar
molecules or are made of large atoms, such as the larger metals; things that do dissolve in water are
typically made of ionically bonded or polar covalently bonded molecules. Instruct them to guess
whether any or all of their insoluble items are made of nonpolar molecules or are simply large
molecules. Have them write “NP” or “L” next to any molecules they might confidently guess about.
Then, instruct them to guess whether any or all of their soluble items are made of polar or ionically
bonded molecules. You might give them the hint that molecules made of atoms on opposite sides of
the periodic table are a bit more likely to bond via ionic bonding. Visit each group, and coach them a
little if necessary (see handout—you have the flexibility to offer as much or as little help as you
consider appropriate for your class).
After about 5 minutes, have each group choose a few of their soluble and insoluble items and report
to the class. Give feedback about their accuracy trying to be as positive as possible.
Assessment suggestions: The interactive oral report recommended in the procedure can be the best
assessment tool, giving immediate feedback. If time does not permit a thorough interaction at the
end, collecting and returning the handouts with comments is suitable for giving and receiving
feedback.
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Name: __________________________ Date: ____________________
Instructor: _______________________ Course Section: ___________
Interactive Activity 2.3 Handout—Water: Love It or Leave It!
Introduction: In this activity, you will explore water’s properties as a solvent by examining the
substances that do and do not dissolve in water. This should also prepare you to reason your way
through some of the questions about the properties of things we deal with in a biology course.
Instructions: Write things one might find around the house (or garage) that do or do not dissolve in
water (soluble items and insoluble items) in the appropriate part of the chart provided below. Do not
include obviously insoluble things such as rocks or metals, but rather focus on things that are not
large solid objects at room temperature. Although you are working as group, each member of the
group should fill out his or her own handout. Ignore the smaller columns for now.
Soluble Items Polar/Ionic Insoluble Items NP/L
Salt (NaCl)
Ionic Olive oil NP
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Things that do not dissolve in water are most often nonpolar molecules or are made of large atoms,
such as the larger metals; things that do dissolve in water are typically made of ionically bonded or
polar covalently bonded molecules. See if you can guess whether any of your listed insoluble items
are made of nonpolar (NP) molecules or are simply large (L) molecules. Do this by writing write
“NP” or “L” next to any molecules you feel you might confidently guess about. Try to guess
whether any of your listed insoluble items are made of polar or ionically bonded molecules.
Do this by writing write “Polar” or “Ionic” next to any molecules you feel you might confidently
guess about.
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ANSWER KEY CHAPTER 2
The answers for the So Far and Brief Review questions are also printed in the student text. Answers
to the Applying Your Knowledge questions appear only in the Instructor Guide.
Answers to So Far Questions
Page 23
1. proton; neutron; electron
2. element; protons; nuclei
3. neutrons; nuclei
Page 29
1. filled; eight; electrons; two; electrons
2. covalent
3. polar covalent; electrical charge
Page 31
1. loses; electrons; charges
2. hydrogen atom; electronegative; hydrogen; oxygen; nitrogen
3. bind
Page 25
1. solute; solvent; solution
2. hydrogen bonds; cohesion; specific heat; energy
3. hydrophobic; hydrophilic
Page 37
1. yields; ions; accepts
2. 7; 0; 14
3. neutral (7)
Answers to Brief Review Questions
1. The forms are called isotopes. Isotopes of an element differ from one another in accordance
with the number of neutrons they have. A regular carbon atom has six neutrons in its nucleus,
while a carbon-14 atom has eight neutrons.
2. An atom’s electrons move through volumes of space outside the atom’s nucleus. An entire
atom is about 100,000 times larger than its nucleus. Thus, most of an atom is the space
through which electrons move.
3.
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4. When its valence (outer) shell is filled, an atom is at a lower, more stable energy state.
5. Water absorbs tremendous amounts of heat from the sun and releases this heat slowly with the
onset of night’s colder temperature. The perspiration human beings throw off carries with it a
great deal of heat, which has been absorbed by the water.
6. Living things must control their internal pH, keeping it in most instances near the neutral point
of 7, because an extreme pH can begin to interfere with such critical structures as membranes
and such critical processes as the work of enzymes. Put another way, the normal structures
and operations of organisms can begin to break down if pH is allowed to fluctuate very far
from near-neutral levels.
Answers to Applying Your Knowledge Questions
1. One way to approach this question would be to make sure that the alchemist had heard of
Democritus. Tell him that basically Democritus was right, that there are pure substances; but
that he was wrong about what these were. Teach the alchemist that iron and gold are pure
substances. They are elements that cannot be reduced further and changed into anything else.
One would have to be able to change the number of protons in the nucleus of all the iron
atoms to turn it into something else—something that cannot be done by ordinary (or even
extraordinary) chemistry. Nuclear physics technology, which we currently possess only to a
limited degree, and an enormous input of energy would be required to change the atomic
nature of elements.
2. Atoms with complete outer shells are stable, and those with incomplete outer shells are
reactive. Helium already has a full outer shell of electrons, which makes it very stable and safe
to use in balloons (even those handed to children at birthday parties!). Hydrogen’s outer shell
is not complete, and it is a reactive atom. It is so reactive that it will react with oxygen to
“burn” and create water and other chemicals under the right conditions. The famous
Hindenburg disaster, in which a hydrogen-filled Zeppelin burst into flames and crashed in
Lakehurst, New Jersey, in 1937, is a graphic example.
3. Most living things have a relatively narrow pH range that is at least fairly close to neutral
(pH = 7). This is partly a function of organisms being composed of so much water that acids
and bases would be greatly diluted, and is partly due to the potentially harmful reactive nature
of acidic and basic solutions. Aquatic organisms are often a product of their environment—
that is, their internal pH somewhat reflects the pH of the water surrounding them. Similarly,
terrestrial organisms reflect the watery environment of their evolutionary past.
In most cases, the properties of water (e.g., powerful solvent, heat capacity) would not be
greatly affected by pH slightly above and below neutral. However, as you will learn in the next
chapter, some of the molecules essential for life may be adversely affected by high or low pH.