^† Be prepared to work a problem or answer an essay question for objectives indicated with this symbol.

Exam 1

1. What do ΔG° and K_eq tell us about a reaction?
2. What are the different weak interactions that are important in biochemistry?
^†3. What is pH? What is the pK_a of a weak acid? What is the Henderson-Hasselbalch equation?
4. What determines the net charge of an amino acid in solution?
5. How are amino acids bonded together to form peptides, and what type of bond is a peptide bond?
^†6. What are the structures, 3-letter abbreviations, and 1-letter abbreviations of the 20 amino acids commonly found in proteins?
7. What determines protein structure?
8. What are the types of regular secondary protein structure, and why are they important?
9. What levels of protein structure are involved in a protein's native conformation?
10. How can both the native conformation of a protein and denaturation be thermodynamically favorable?
^†11. What are the different levels of protein structure, and how is each structure stabilized?
12. What's the difference between an amino acid residue and a protein subunit?
13. What are motifs and domains, and how are they related to levels of protein structure?
^†14. What is K_d for a protein (P) that reversibly binds a ligand (L), and what does it indicate about the PL complex?
^†15. What is Θ, and what type of curve is produced by graphing Θ as a function of [L] for myoglobin?
^†16. What type of curve is produced by graphing Θ as a function of [L] for hemoglobin, and what causes the difference from myoglobin?
^†17. What part of hemoglobin (heme or globin) is affected by changing the concentration of CO₂, H⁺, or BPG (1,3-bis-phosphoglycerate)? How does the change affect O₂-binding?
18. What does carbonic anhydrase (in tissues and lungs) do that affects hemoglobin function?
^†19. How do the structure and function of hemoglobin resemble and differ from those of myoglobin? (That is, compare and contrast the two proteins.)
20. To what specific part of hemoglobin does CO₂ bind, and what change occurs as a result?
21. To what specific part of hemoglobin does H⁺ bind, and what change occurs as a result?
22. To what specific part of hemoglobin does BPG bind, and what change occurs as a result?

Exam 2

1. What interactions help to promote formation of an ES complex?
2. What are the different types of co-factors? What is a distinguishing feature of each type?
3. What are the different classes of enzymes, and how can you identify each type?
^†4. What is an active site, and what are active site characteristics?
^†5. What are the mechanisms by which enzymes catalyze reactions, and what is a distinguishing characteristic of each mechanism?
6. What observation led to derivation of the Michaelis-Menton equation as a description of enzyme behavior? What type of curve is described by the Michaelis-Menton equation?
7. What is the Michaelis-Menton equation, and what does each term in the equation mean?
8. Which enzyme characteristic–K_M and/or V_max–does each type of reversible inhibitor affect, and what is the effect?
9. How is K_M determined? How is V_max determined?
10. What is k_cat (how is it defined)?
11. Why is k_cat/K_M important?
^† 12. What are the different types of reversible enzyme inhibitors, and to what part of E or ES does each bind?
13. What is a serine protease, and what mechanism(s) does it use to catalyze proteolysis?
^†14. What is a kinase, and what mechanism(s) does hexokinase use to catalyze its reaction?
^†15. What reaction is catalyzed by carbonic anhydrase, and what co-factor(s) and active site residues are required?
^†16. How does enzyme regulation occur covalently? What are the advantages and disadvantages of using this method of regulation?
^†17. How does enzyme regulation occur allosterically? What are the advantages and disadvantages of using this method of regulation?
^†18. What two types of enzymes are needed for the most common type of covalent regulation? How do these enzymes recognize their protein substrates, and how does modification affect the substrates?
^†19. What are the characteristics of allosterically regulated enzymes?
20. What is amplification, and what is required for amplification to occur?
21. What are modulators, and how do they affect enzyme activity?
22. What is the characteristic structure of a carbohydrate? What is an anomeric carbon, and why is it important?
23. What are the major components of a nucleotide? How do nucleotides differ?
24. What is the important characteristic that defines a lipid? What are the different classes of lipids?
25. What are the characteristics of fatty acids? How is the structure of a triacylglycerol different from the structure of a phospholipid?

Exam 3

1. What type of molecule in the membrane structure creates the barrier? What type of molecule performs most of the membrane functions?
2. What factors must be considered in order to decide whether or not solute transport is favorable?
^†3. How are the proteins required for primary and secondary active transport alike, and how are they different?
^†4. What is the equation for ΔG of transport across the membrane? How does the concentration factor (R T ln [c₂/c₁]) change when the direction of transport across the membrane changes? How does the charge factor (Z F ΔV) change when the direction of transport across the membrane changes?
^†5. What are the characteristics of ion channels?
^†6. What are the characteristics of carriers?
7. For each biosignaling method we study, how does the receptor respond?
8. What makes a signal end? What is desensitization, and how does it occur?
^†9. How can biosignaling pathways differ from each other?
10. What are the domains of a receptor?
^†11. How does the nicotinic acetylcholine receptor function? What happens as a result?
How are the results reversed?
12. How does a 7tm receptor function?
^†13. What are the subunits of a G protein, and what does each do? How is a G protein activated, and how is it inactivated?
14. What reaction does adenylyl cyclase (AC) catalyze? How is its product removed from a cell?
^†15. What are the subunits of protein kinase A (PKA), and how is PKA activated?
16. What happens if a different G protein is activated?
17. What is the role of ATP in the cell? (Is it used for storing energy or for transferring energy?)
18. Why is ATP a "high energy" molecule? In general, what are the characteristics of high energy molecules?
19. What are the reactions catalyzed by nucleoside diphosphate kinase (NDP kinase) and by adenylate kinase? What reaction is catalyzed by pyrophosphatase?
20. What is the difference between H⁺, H, and H⁻? What is the half reaction to reduce NAD⁺?
^†21. Given two half reactions, how can you write a spontaneous whole reaction, and calculate ΔE°′ and ΔG°′ for the spontaneous reaction?
^†22. Which glycolysis reaction is the committed step, and what does "committed step" mean?
^†23. How is glyceraldehyde-3-phosphate changed during the reaction catalyzed by GAPDH? How is it changed, overall, during the reactions of the payoff phase of glycolysis?
^†24. What happens to pyruvate during fermentation? Why?
^†25. What is the overall reaction for glycolysis? What is the overall reaction for the preparation phase? For the payoff phase? What is the net energy yield per glucose from glycolysis?
26. What is the reaction catalyzed by hexokinase, and why is it important?
27. What is the reaction catalyzed by PFK-1, and why is it important? What does PFK-1 mean?
28. What is the reaction catalyzed by GAPDH, and why is it important?
29. What is the reaction catalyzed by pyruvate kinase?
30. What happens to pyruvate in anaerobic yeast cells? What enzymes are required, what is the intermediate, and what is the net energy yield per glucose as a result?
31. What happens to pyruvate in anaerobic skeletal muscle cells? What enzyme is required, and what is the net energy yield per glucose as a result?
^†32. What is gluconeogenesis, and why is it needed? As a pathway, does gluconeogenesis require energy or produce energy?
33. What type of enzyme is pyruvate carboxylase?
^†34. Which glycolysis enzymes catalyze irreversible reactions? Which gluconeogenesis enzymes are required to reverse the glycolysis reactions?

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