Each week, I will hand out a study guide to alert you to important activities and study questions to help as you read the text. Study guides will be posted on the course website – if you miss the class in which they are handed out, it is your responsibility to download a copy. The instructor does not bring copies of past handouts to later classes.

Our goal for the first 7 weeks of this course is to understand cells. Cells are chemical machines. Everything a cell does involves the manipulation of chemicals. For example, in order to contract a muscle, a Calcium channel in the muscle membrane must open to allow Ca⁺⁺ ions to rush into the cell in order to trigger a protein rearrangement. It is necessary to use a chemical vocabulary in describing cells, and our first week will be spent developing this vocabulary. By the end of this week, you should be familiar with terms such as: ion, covalent bonds, hydrogen bonds, buffers, molarity, and much more.

This chemical review has a practical side as well. Much of what happens in many biology labs involves preparing and using solutions with precisely known ingredients. Go to work in any laboratory and your first assignment is likely to be something like “Prepare 500 ml. of a 0.2 M solution of MgSO₄ and make sure the pH is adjusted to 7.5”. Our first labs will reinforce chemical concepts and develop your skill in working with basic laboratory techniques, such as pipetting, that you will need for any work in a biology or medical laboratory.

Note that outlined lecture notes are available online. These should help you focus on the major points covered, and direct your attention to ideas the instructor considers important. The actual content of lectures will necessarily include some materials not in these notes, and you are strongly encouraged to print notes ahead of time, bring them to lecture, and add your own annotations during the lecture.

For Dr. Terry’s lectures, each set of lecture notes includes some practice questions as an online self-quiz. These questions will give you some idea of how well you can apply ideas from text and lecture. Don’t wait until a couple of days before an exam to find out what you don’t know – make a habit of taking the online quiz with each day’s lecture.

Your purchase of a new copy of Cambell’s Biology, 6^th Ed., includes a free subscription to the text website: http://www.campbellbiology.com/. The first page of your textbook includes an access code and full information about website access and the CD-ROM that accompanies your textbook. Both are valuable resources, and will help increase your familiarity with the material.
Among the most useful online resources are a series of activities developed for each chapter. These make excellent use of graphic media, including animations and interactive exercises that will you’re your learning more exciting and more involving. I have reviewed these activities carefully, and selected those that are especially relevant to our learning goals.

Once you are logged in to the textbook website, choose the appropriate chapter from the popup menu near the top. Then click the “Activities” link on the left column, and select activities listed below. Note that many activities include several pages – always look at the buttons above the text to see how many pages are included, and use the “previous | replay | next” buttons to navigate within the activity.

Note: Many of the online activities involve interactive graphics that require a Shockwave plugin to be viewed on your computer. Plugins are free bundles of software that add extra capabilities to an internet browser such as Internet Explorer or Netcape Communicator. Plugins are always installed in a “Plugins” folder (directory) for the browser you use, and must be up-to-date. If you have any difficulty viewing the graphics, or receive a message that your Shockwave plugin needs updating or is not present, you will need to install a new version. The process is highly automated, and only requires you to click occasional buttons to allow installation, and to register your name and note whether you want to receive e-mailings of future update (recommended). For links to all plugins needed for this course, see the plugin information page on our class website.

Ch. 2:

Activity 2C: Electron arrangement. (Note that there are 2 pages to this activity – use the “next” button above the text to advance)

Activity 2D: Build and atom. (1 page) At the very least, build a Carbon atom. I strongly recommend trying at least 3 of the CHNOPS atoms to make sure you are familiar with atomic structure.

Activity 2E: Covalent bonds. (4 pages).

Activity 2F: Nonpolar and Polar covalent bonds (2 pages).

Activity 2G: Ionic bonds (1 page).

Ch. 3

Activity 3A: Polarity of water (4 pages).

Activity 3C: Dissociation of water molecules (2 pages).

Activity 3D: Acids, Bases, and pH (3 pages).

E. Consult the study questions below as you read the text.

Chapter 1. Read through the chapter to get a good overview of major themes in biology. Be able to answer the following questions.

1. Arrange the following terms in sequence from smallest to largest: organism, molecule, organelle, tissue, community, atom, cell.

2. What is "reductionism?" If you wish to explain how a cell is capable of motility by a reductionistic explanation, what kinds of data would you need? Can you think of other ways of explaining cell motility that are not reductionistic?

3. What are "emergent properties?" Identify 3 properties of a cell that are not present in cell molecules. Identify 3 properties of a human being that are not present in cells alone.

4. All living systems, be they as diverse as bacterial cells, mushrooms, or termites, share certain properties in common. Identify at least 5 of these properties (Hint: see how many you can enumerate before you look in your text!)

5. Cells are the units from which all living organisms are made. What two kinds of cells have been discovered? How do they differ? In what ways are they alike?

6. All cells use DNA. Why is DNA so important?

7. It is convenient to group organisms into different categories (domains, kingdoms, etc.) for effective study. The broadest category recognized today is the domain. How many domains are there, and what organisms belong in each domain?

8. Prof. T. Dobzhansky, a famous biologist of the 20th century, observed that "nothing in biology makes sense without the theory of evolution." Suggest at least 3 ways in which evolutionary ideas explain things that would otherwise be inexplicable.

9. What are the characteristics of "science" that distinguish it from other ways of knowing? This is not a simple question -- scholars continue to debate this issue. Still, there are some basic ideas that are characteristic of most scientific work. Review the discussion on pp 13-18 carefully. Note the interplay of hypothesis, prediction, and experiment. What is meant by the "hypothetico-deductive" method? Is it theoretically possible to prove any hypothesis with absolute certainty?

10. What does the term "theory" mean in science? How does this differ from everyday usage of this term?

Chapter 2. Once you start looking inside a cell, everything is chemistry. This chapter and the accompanying lecture review basic chemical concepts from which to build an understanding of biochemistry, the "molecules of life". This will be review for most of you, so shake the cobwebs off your brain cells and make sure these terms and ideas are comfortable and familiar.

1. Terms. Be able to recognize and correctly apply the following terms:

Element

Trace element

Neutron

Proton

Electron

Atomic number

Atomic weight

Isotope

Electron shell

Valence electrons

Covalent bond

Double bond

Triple bond

Nopolar bond

Polar bond

Ionic bond

Hydrogen bond

Van der Waals bond

Electronegativity

2. What does a dalton (a.m.u) measure? What is the approximate weight of a proton in daltons? A neutron? An electron?

3. Explain why the chemical properties of an element are defined by the number of protons, using the concept of electron shells.

4. Would knowing that an atom had a certain # of electrons allow you to tell what kind of element it was? Why or why not? Would knowing the number of protons tell you what kind of element it was?

5. Which of the following are elements? Water, Sodium, Carbon dioxide, Sugar, Oxygen, Carbon.

6. How does the abundance of elements in the earth’s crust compare with the abundance of elements in living tissue? Of the 6 major elements of life, which are also very abundant in the earth’s crust?

7. What 6 elements are required in largest quantity by all life? What additional element is required in large quantity by vertebrate animals, but not by invertebrates?

8. Animals with nervous systems require substantial concentrations of two elements that are used to create electrical charges across membranes. What are these two elements?

9. Most trace elements are (choose one): __ metals __ salts __ gases __ noble gases

10. What is an isotope? Are all isotopes radioactive? The substances 2H and ³H differ in that ³H has one more ____________ than ²H

11. Compared to normal ¹²C, how does the radioactive isotope ¹⁴C differ?

12. Note the discussion of electron orbitals and shells on pp. 32-33. The correct description of electron geometry is based on orbitals. The concept of electron shells is an oversimplification that works only as a first approximation. However, for purposes of Biology 107, we will ignore the actual orbitals and use the concept of outer electron shells to predict valences and chemical bonding. Be aware that this is somewhat of a fiction, which your chemistry teachers will undoubtedly clear up in some detail.

13. What are the valences of each of the CHNOPS elements?

14.  What is a covalent bond? How does it differ from an ionic bond? A hydrogen bond? A Van der Waals bond?

15. Which of the following structural formulas has incorrect valences? (more than one may be incorrect)

(a) NH₃ (b) H=C=H (c) SH₃ (d) O=C=O

16. How many errors can you find in the following structural formula? Circle them. (Hint: look at each element to see if its valence is properly matched with the number of bonds shown)

17. The concept of "polarity" is very important, so be sure you understand this. Note that, in most chemical bonds between different elements, electrons are shared unevenly, resulting in polarity. What are some examples of chemical bonds that are nonpolar?

18. What is the difference between a polar and a nonpolar bond? Which of the following covalent bonds is not polar (note: not all bonds have been filled in)? More than one answer may apply.

(a) — C—O— (b) —C—H (c) —C=O (d) —O—H (e) O=O

19. Why are ionic bonds weaker in aqueous solutions than in a crystal?

20. Why are weak chemical bonds important for living systems?

21. Is the shape of a molecule important in understanding its chemistry? Why or why not?

Chapter 3. This short chapter deals with properties of water, including the concept of dissociation, acids and bases, pH, buffers, and molarity.

1. Terms. Be able to recognize and correctly apply the following terms:

Adhesion

Cohesion

Surface tension

Specific heat

Solvent

Solute

Hydrophilic

Hydrophobic

Molecular weight (Formula weight)

Mole

Hydrogen ion (H⁺)

Hydroxyl ion (OH^-)

Acid

Base

pH

Buffer

Weak (partial) dissociation

Strong (full) dissociation

2. Water is very polar. One result of this is that water interacts with itself to form extensive weakly-bonded structures. What type of bond is involved?

3. What's the difference between adhesion and cohesion?

4. Compare the specific heat of water with that of other liquids such as alcohol. Is it higher, the same, or lower? Why?

5. Relative to the previous question, imagine an organism whose interior liquid was 70% alcohol instead of water. What effect would this difference have on the organisms ability to dissipate heat generated during metabolism or activity?

6. Identify four properties of water that are of significance to life.

7. How is pH defined? How is a mole defined?

8. What is the pH of pure water? What is the concentration of H⁺? Of OH^–?

9. Is a pH of 6 more acid or less acid than a pH of 7? How many more H⁺ ions are present at pH 3 than at pH 7? What is the concentration of H⁺ in a pH 3 solution?

10. The atomic weights of several elements are: C = 12 daltons; O =16 daltons, H =1 dalton. How many grams of pure acid (CH₃COOH) are needed to make 1 liter of solution 1 molar in acetic acid? How many grams of pure acid (CH₃COOH) are needed to make 1 liter of solution 0.2 molar in acetic acid?

11. How does a strong acid differ from a weak acid? How does a base differ from an acid? Give an example of each.

12. If the (H⁺) concentration of a neutral, buffered solution were suddenly made 10^-8 M, what would be the result (choose one)?

(a) there would be more H⁺ than at neutral pH;

(b) the buffer would dissociate to release more H⁺;

(c) the buffer would soak up more H⁺