Problem Set 1 PDF - Pharmaceutical Biochemistry PHM 381M

Pharmaceutical Biochemistry PHM 381M 1. Structure and Function of Proteins Problem Set #1 1. Identify the conjugate acids and bases in the following pairs of substances: (a) (CH3)3NH+ / (CH3)3N (b) H3N+_CH2COOH / H3N+_CH...

Pharmaceutical Biochemistry PHM 381M 1. Structure and Function of Proteins Problem Set #1 1. Identify the conjugate acids and bases in the following pairs of substances: (a) (CH3)3NH+ / (CH3)3N (b) H3N+_CH2COOH / H3N+_CH2COO- (c) H3N+_CH2COO- / H2N_CH2COO- (d) -OOC_CH2_COOH / -OOC_CH2_COO- (e) -OOC_CH2_COOH / HOOC_CH2_COOH 2. Identify conjugate acids and bases in the following pairs of substances: (a) (HOCH2)3 CNH3+ / (HOCH2)3 CNH2 TRIS (pKa 8.3) HOCH 2CH2 N N CH2CH2SO3- (b) HEPES HOCH 2CH2 N + N CH2CH2SO3- pK a 7.55 H -O + N CH2CH2SO3- 3SCH2CH 2 N (c) H PIPES -O pK a 6.8 3SCH2CH 2 N N CH2CH2SO3- 3. Aspirin is an acid with a pKa of 3.5; its structure includes a carboxyl group. To be absorbed into the bloodstream, it must pass through the membrane lining the stomach and the small intestine. Electrically neutral molecules can pass through a membrane more easily than can charged molecules. Would you expect more aspirin to be absorbed in the stomach, where the pH of gastric juice is about 1, or in the small intestine, where the pH is about 6? Explain your answer. 4. Why does the pH change by one unit if the hydrogen ion concentration changes by a factor of 10? 5. Calculate the hydrogen ion concentration [H+], for each of the following materials a. Blood plasma, pH 7.4 b. Orange juice, pH 3.5 c. Human urine, pH 6.2 d. Household ammonia, pH 11.5 e. Gastric juice, pH 1.8 6. List the criteria used to select a buffer for a biochemical reaction 7. What is the relationship between pKa and the useful range of a buffer? 8. What is the [CH3COO-]/[CH3COOH] ratio in an acetate buffer at pH 5.00? 9. What is the [CH3COO-]/[CH3COOH] ratio in an acetate buffer at pH 4.00? 10. What is the ratio of TRIS/TRIS-H+ in a TRIS buffer at pH 8.7? (see #2) 11. What is the ratio of HEPES/HEPES-H+ in a HEPES buffer at pH 7.9? (see #2) 12. You need to carry out an enzymatic reaction at pH 7.5. A friend suggests a weak acid with a pKa of 3.9 as the basis of a buffer. Will this substance and its conjugate base make a suitable buffer? Why or why not? 13. If the buffer suggested in question 12 were made, what would be the ratio of the conjugate base/conjugate acid? 14. Suggest a suitable buffer range for each of the following substances: a. Lactic acid (pKa = 3.86) and its sodium salt b. Acetic acid (pKa = 4.76) and its sodium salt c. TRIS (pKa = 8.3) in its protonated form and its free amine form d. HEPES (pKa = 7.55) in its zwitterionic form and is anionic form 15. Define buffering capacity. How do the following buffers differ in buffering capacity? How do they differ in pH? Buffer a: 0.01M Na2HPO4 and 0.01M NaH2PO4 Buffer b: 0.10M Na2HPO4 and 0.10M NaH2PO4 Buffer c: 1.0M Na2HPO4 and 1.0M NaH2PO4 16. A frequently recommended treatment for hiccups is to hold one’s breath. The resulting condition, hypoventilation, causes buildup of carbon dioxide in the lungs. Predict the effect on the pH of blood