Biochemistry 2 (CHM161)

Take Home Exam

1. In eukaryotes, the 20S proteasome in conjunction with the 19S component degrades ubiquitinated proteins with the
hydrolysis of a molecule of ATP. Archaea lack ubiquitin and the 26S proteasome but do contain a 20S proteasome. Some
archaea also contain an ATPase that is homologous to the ATPases of the eukaryotic 19S component. This archaeal
ATPase activity was isolated as a 650-kd complex (called PAN) from the archaeon Thermoplasma, and experiments were
performed to determine if PAN could enhance the activity of the 20S proteasome from Thermoplasma as well as other
20S proteasomes. Protein degradation was measured as a function of time and in the presence of various combinations of
components. Graph A shows the results.

(a) What is the effect of PAN on archaeal proteasome activity in the absence of nucleotides?
(b) What is the nucleotide requirement for protein digestion?
(c) What evidence suggests that ATP hydrolysis, and not just the presence of ATP, is required for digestion?

A similar experiment was performed with a small peptide as a substrate for the proteasome instead of a protein. The results
obtained are shown in graph B.

(d) How do the requirements for peptide digestion differ from those of protein
digestion?
(e) Suggest some reasons for the difference.

2. Allopurinol, an inhibitor of xanthine oxidase, is used to treat chronic gout. Explain the biochemical basis for this
treatment. Patients treated with allopurinol sometimes develop xanthine stones in the kidneys, although the incidence of
kidney damage is much lower than in untreated gout. Explain this observation in the light of the following solubilities in
urine: uric acid, 0.15 g/L; xanthine, 0.05 g/L; and hypoxanthine, 1.4 g/L.

3. Folic acid deficiency, believed to be the most common vitamin deficiency, causes a type of anemia in which hemoglobin
synthesis is impaired and erythrocytes do not mature properly. Explain the biochemical basis in the metabolic
relationship between hemoglobin synthesis and folic acid deficiency?

4. Explain how caloric restriction can potentially lead to longevity. What are the possible effects of mutations in the SIRT1
gene in humans. Explain your answer in terms of the metabolic role of SIRT1 gene and the role of SIR2 gene, an
ortholog in yeast.

5. Explain how the brain can utilize ketone bodies as metabolic fuel during prolonged starvation. If a person has a b-
ketoacyl-CoA transferase deficiency, how long will he/she can survive if the glucose supply was already depleted.
Explain the biochemical basis of your answer.