CHAPTER 2 FUNDAMENTAL BUILDING BLOCKS: Chemistry, … · Full file at 12 Instructor Guide Be able to describe the three types of chemical bonds, explaining their differences, and

Full file at https://fratstock.eu

11

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.

Full file at https://fratstock.euChapter 2 Fundamental Building Blocks: Chemistry, Water, And Ph 13

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).


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.


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.


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


hydrocarbon nonpolar covalent bond


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.


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:


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.



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.


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


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.


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.


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.

CHAPTER 2 FUNDAMENTAL BUILDING BLOCKS: Chemistry, … · Full file at 12 Instructor Guide Be able to describe the three types of chemical bonds, explaining their differences, and

Documents