Exam 1 Objectives |
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Introduction and pH
1. What do ΔG° and Keq tell us about a reaction?
2. How do water molecules relate to each other and to other molecules? How do these relationships affect cells and biochemical interactions within cells?
3. What happens to a weak acid in solution and to the pH of the solution when base is added?
4. What is the equation that relates ΔG, ΔG°, and Keq?
5. What are the different weak interactions that are important in biochemistry?
6. What is pH? What is the pKa of a weak acid? What is the Henderson-Hasselbalch equation?
Amino acids
1. What is the basic structure of an amino acid, and how are amino acids classified?
2. What determines the net charge of an amino acid in solution?
3. How are amino acids bonded together to form peptides, and what type of bond is a peptide bond?
4. What are the structures, 3-letter abbreviations, and 1-letter abbreviations of the 20 amino acids commonly found in proteins?
5. How do you calculate the pI of an amino acid or a peptide, given the relevant pKa's?
Protein structure
1. Why is protein structure important?
2. What determines protein structure?
3. What is the main advantage of Edman degradation?
4. What are the types of regular secondary protein structure, and why are they important?
5. What levels of protein structure are involved in a protein's native conformation?
6. How can both the native conformation of a protein and denaturation be thermodynamically favorable?
7. What are the different levels of protein structure, and how is each structure stabilized?
8. What's the difference between an amino acid residue and a protein subunit?
*9. What treatments are required prior to Edman degradation in order to sequence a large pure protein with no disulfide bonds? What is required for one with disulfide bonds?
10. What are the characteristics of an α-helix?
11. What are the characteristics of β-pleated sheets and β-bends?
12. What are motifs and domains, and how are they related to levels of protein structure?
13. What are the various denaturing agents, and how does each cause denaturation?
*14. Why is the ribonuclease renaturation experiment important, and why is it significant that ribonuclease was chosen rather than another enzyme?
*15. What are the functions of protein disulfide isomerase and protein chaperones?
Myoglobin and hemoglobin
1. What is Kd for a protein (P) that reversibly binds a ligand (L), and what does it indicate about the PL complex?
2. What is Θ, and what type of curve is produced by graphing Θ as a function of [L] for myoglobin?
3. What type of curve is produced by graphing Θ as a function of [L] for hemoglobin, and what causes the difference from myoglobin?
4. 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?
5. What does carbonic anhydrase (in tissues and lungs) do that affects hemoglobin function?
6. What is the function of myoglobin, and how are both heme and globin involved?
7. How do the structure and function of hemoglobin resemble and differ from those of myoglobin? (That is, compare and contrast the two proteins.)
8. To what specific part of hemoglobin does CO2 bind, and what change occurs as a result?
9. To what specific part of hemoglobin does H+ bind, and what change occurs as a result?
10. To what specific part of hemoglobin does BPG bind, and what change occurs as a result?
11. How is sickle cell Hb different from normal Hb, and how is that related to the disease?