Chapter2fundamentalbuilding BLOCKS:Chemistry, Water, and Ph

Chapter 2 Fundamental Building Blocks: Chemistry, Water, And Ph 1

Chapter2FUNDAMENTALBUILDING BLOCKS:Chemistry, Water, and pH

2.1Chemistry’s Building Block: The Atom

2.2Matter Is Transformed through Chemical Bonding

2.3Some Qualities of Chemical Compounds

2.4Water and Life

2.5Acids 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.

• 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.

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.

bPolar = 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. Afree 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):Figure2.15.

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 bondnucleus

acid rainhydrophilicpH scale

alkalinehydrophobicpolar covalent bond

atomic numberhydroxide ionpolarity

ball-and-stick modelionproduct

baseionic bondingproton

buffering systemionic compoundreactant

chemical bondingisotopespecific heat

covalent bondlaw of conservation of masssolute

electronmasssolution

electronegativitymolecular formulasolvent

elementmoleculespace-filling model

free radicalneutronstructural formula

hydrocarbonnonpolar 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.

Chapter 2 Fundamental Building Blocks: Chemistry, Water, And Ph 17

Name: ______Date: ______

Instructor: ______Course Section: ______

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 rainEthanol in gasolineSolar energy chemistry

BiofuelsGamma hydroxy butyrate (GHB)Steroid abuse

EphedrineOzone layer and CFCsToxic 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.

Chapter 2 FundamentalBuilding Blocks 17

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.