Finally, with our chemical background behind us, we’re moving into cell biology! First we must review notions of energy in order to understand the extraordinary properties of enzymes, without which life as we know it would not be possible. Then we will look in some detail at various features of cells. A question you should keep in mind throughout this material is: “How is form related to function?” Every structure we find in a cell has some very important role to play – our task is to correlate these structures with their functions.

See links at bottom of lecture note web pages.

Ch. 6:

Activity 6A: Energy Transformations (Note that there are 3 pages to this activity – use the “next” button above the text to advance). Be sure to click the archer’s arm in screen 3.

Activity 6B: The Structure of ATP (2 pages)

Activity 6C: Chemical Reactions and ATP (4 pages)

Activity 6D: How Enzymes work (4 pages)

Ch. 7

Activity 7B: Prokaryotic cell (2 pages)

Activity 7D: Build a plant cell and an animal cell (1 page)

Activity 7E: Role of the nucleus and ribosomes (3 pages). Label components in screen 3.

Activity 7F: Endomembrane system (5 pages)

Activity 7H: Cilia and flagella (1 page)

Chapter 6.

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

Enzyme

Substrate

Induced fit

Active site

2. What is meant by the term "metabolism"? How do catabolic and anabolic metabolism differ?

3. State the 1st and 2nd laws of thermodynamics. How does each apply to biological systems?

4. How is free energy defined? Why is free energy rather than heat energy used to measure changes in chemical reactions?

5. Informational note: the free energy change, ΔG, of any chemical reaction will vary depending on concentrations of the reactants and temperature. Biochemists often refer to the “standard free energy change” of a reaction, ΔGo’, which is a constant for any given reaction, and which can be used to predict something about the amount of energy liberated (or taken up) by the reaction. For example, the ΔGo’ for ATP hydrolysis is –7.3 kcal/mole. However, in actual cells, the amount of energy liberated is somewhat higher (because concentrations are different from standard conditions), around –10 to –12 kcal/mole.

6. One use of the ΔG notation is in predicting direction and amount of energy involved. All spontaneously occurring reactions have negative ΔG values. The larger the value, the more energy is released. A reaction with ΔGo’ = –1.5 kcal/mole will release a little energy, but not enough to do useful cell work. A reaction with a ΔGo’ = –688 kcal/mole will release lots of energy. Such reactions are the primary source of metabolic energy for most cells.

7. What is an enzyme? What do enzymes do? Pay special attention to Fig. 6.14 and 6.15.

8. Do enzymes affect the ΔGo’ of a reaction (e.g., can an enzyme make a reaction that would normally have a + value into a spontaneous reactions with a – value?)

9. How big is the catalytic site of an enzyme, relative to the number of amino acids in an enzyme? (See Fig. 6.14 if you're stumped). What is meant by “induced fit”?

10. How and why do the following factors affect enzyme activity: temperature, pH, salt, denaturation, inhibitors, cofactors.

11. What is an allosteric enzyme? How does it differ from a normal enzyme? Which reaction in a pathway A — (E1) → B — (E2) → C — (E3) → D — (E4) → E would you expect to be an allosteric enzyme? [Note: the notation employed here means that E1 is the enzyme catalyzing the reaction A → B, etc.] Why?

Chapter 7.

1. Terms. Be able to recognize and correctly apply the following terms. Note: other terms not listed here are found throughout the following questions.

Chromatin

Chromosome

Nucleolus

Ribosome

Lysosome

Phagocytosis

Mitochondria

Chloroplast

2. Study Fig. 7.1. How big are the smallest cells? How big are most bacteria? How big are most plant and animal cells? Can cells be seen with the unaided human eye? Can viruses be seen with the light microscope? What are the smallest biological objects that can bee seen with the light microscope?

3. What is meant by cell "fractionation"? What laboratory instruments are typically used to fractionate cells?

4. What is the surface-to-volume ratio of a cubic cell 1 mm in length? 10 mm in length? Based on this analysis, how would you predict that cells of these two sizes would differ?

5. What is a "plasma membrane" (aka cell membrane)? Where is it found? What does it do? Could a cell survive without one?

6. What is resolving power? What are the resolving powers of the following optical instruments: (a) human eye, (b) light microscope, (c) electron microscope?

7. The following list jumbles biological objects without reference to size. Sort this list into a sequence from smallest to largest:

Nucleus, Protein molecule, Plant cell, Glucose molecule, Ribosome, Mitochondrion

9. How could you distinguish a transmission electron micrograph from a scanning electron micrograph? (Note: a “micrograph” is a picture taken through a microscope).

10. Distinguish prokaryotes from eukaryotes. Which of the following are found in a bacterial cell? In a plant cell? In an animal cell?

nucleus:

70S ribosome:

80S ribosome:

DNA:

cytoplasmic membrane:

cell wall:

11. Cell sizes are typically measured in micrometers (mm). If you were shown an electron micrograph of a bacterium, how big would you expect it to be (ball park estimate)? How big might a “typical” animal cell (there ain’t no such thing, but indulge the fantasy momentarily) be?

12. Why are rER, sER, lysosomes, plasma membrane, and Golgi bodies all considered parts of the endomembrane system, but mitochondria are not?

13. What is a lysosome? What is phagocytosis? How are lysosomes involved in phagocytosis?

14. What is the signal hypothesis? What does it explain?

15. Which of the following structures is bounded by a double membrane system?

mitochondrion

rough ER

smooth ER

Golgi body

cytoplasm

nucleus

16. What is the difference between a vacuole and a vesicle? How does the role of vacuoles differ in animal (especially single-celled protists) and plant cells?

17. In what ways are mitochondria and chloroplasts similar? In what ways are they different?

18. What is a peroxisome? What does it do?

19. How could you distinguish a microtubule from a microfilament? Describe common functions of each.

20. Scientists have been able to identify the organization of cytoskeletal fibers much more easily using light microscope techniques rather than electron microscope techniques, even though the individual fibers are too small to be seen by light microscopes. What special technique has made light microscopy so useful in this case?

21. Identify three cell structures in which you could find microtubules.

22. Identify a specific activity in which the proteins kinesin and dynein are involved. Note that these are important as "motor molecules". See Fig. 7.21 and 7.25 especially.

23. Be able to identify major functions for each of the cell components listed in the Key List below (flashcards work well for this sort of exercise).

24. Match descriptions on the left with items in the Key List. (Note: Key List items may be used more than once, or not at all.)

Nucleus

Nucleolus

Nuclear membrane

rER

sER

Golgi complex

cytoplasm

lysosome

plasma membrane

mitochondrion

chloroplast

vacuole

microtubule

microfilament (actin)

ribosome

peroxisome