C2006

C2006/F2402 '02 -- Review Questions for Exam #2 -- Last Update: 03/08/02 11:07 AM

These questions = relevant questions from exams 2 & 3 of last year. (Order of topics was different in '01.) For most of questions 1-4, each answer = 2 pts; each explanation = 2. Breakdown for question 5 is given below.

1. Protein A is made in muscle cells. Protein B is not. The two proteins are unrelated and are encoded by different genes.
A. Consider genes A and B in a muscle cell. In this cell, which gene(s) should have enhancers? (Gene A) (gene B) (both) (neither) (one or the other but can’t predict which), AND If any enhancers are present, they should be located (downstream from the start of transcription) (upstream) (either way). Explain briefly.

B. In a muscle cell, hypersensitive site(s) should be associated with (gene A) (gene B) (both) (neither) (one or the other), AND relative to purified, protein-free DNA, the hypersensitive site(s) should be (more sensitive to DNase digestion) (less sensitive) (about the same) (can't predict). Explain briefly.

C. Consider the region(s) of the genes downstream from the start of transcription. In a muscle cell, in these downstream regions, which gene(s) should be associated with more molecules of H2A (per 1000 base pairs)? (gene A) (gene B) (both should be about the same) (can’t predict) AND during mitosis there should be about _________ molecules of H2A per 1000 bases of gene A. Explain briefly.

2. Consider proteins F, G, & H. All are encoded in the nucleus. Protein F is RNA polymerase I (responsible for making rRNA for cytoplasmic ribosomes). Mature protein G is found in cytoplasmic ribosomes and mature protein H is found in mitochondrial ribosomes (in the mitochondrial matrix).

A. Where would you expect to find protein F? It should be primarily associated with the (nuclear pores) (heterochromatin) (nucleolus) (IFs) (MTs) (MFs) (nuclear envelope) (soluble cytoplasm) (plasma membrane) (nucleoplasm). Explain briefly.

For the rest of this question, circle all correct answers to each part and explain for each part of C how the protein gets to its final destination.
B. Which protein(s) should be made on free cytoplasmic ribosomes? (protein F) (protein G) (protein H) (none of these).

C-1. Newly made protein F should have a (transit peptide) (signal peptide) (NLS) (peroxisomal localization signal) (site for mannose-6-P attachment) (none of these) AND the localization signals in mature protein F are likely to be (the same) (different) (either way).

C-2. Newly made protein G should have a (transit peptide) (signal peptide) (NLS) (peroxisomal localization signal) (site for mannose-6-P attachment) (none of these) AND the localization signals in mature protein G are likely to be (the same) (different) (either way).

C-3. Newly made protein H should have a (transit peptide) (signal peptide) (NLS) (peroxisomal localization signal) (site for mannose-6-P attachment) (none of these) AND the localization signals in mature protein H are likely to be (the same) (different) (either way).

3. There are multiple trimeric G proteins. Consider two of them, say G₁ and G₂. They have the same gamma and beta subunits but the alpha subunits are different. Both G proteins affect adenylyl cyclase (AC), but G₁ inhibits AC and G₂ activates it. The inhibition by G₁ lasts longer than the activation by G₂ (given the same concentrations, conditions, etc.)
A. G₁ probably inhibits adenylyl cyclase by interfering with (binding of GTP) (hydrolysis of GTP) (phosphorylation of GDP) (binding of ATP) (hydrolysis of cAMP) (binding of cAMP) (hydrolysis of ATP to ADP), AND A-2. You would expect that adenylyl cyclase binds to (alpha) (beta) (gamma) (beta + gamma) (alpha or beta+gamma) (a trimer) (an octamer) (depends which G protein it is). Explain both choices briefly.

B. G₂ should be activated by (binding of GTP) (hydrolysis of GTP) (phosphorylation of GDP) (binding of ATP) (hydrolysis of cAMP) (binding of cAMP) (hydrolysis of ATP to ADP), AND The two G proteins probably differ from each other in ________________________ (same choices). Explain both choices briefly.

4. Suppose ligand L activates G₂, and enzyme Z is a substrate of protein kinase A. Phosphorylated enzyme Z is inactive.
A. When you add ligand L to cells in vitro, you expect a change in (# of protein kinase A molecules) (activity of individual protein kinase A molecules) (# of cAMP molecules) (activity of individual cAMP molecules) (# of IP3 molecules) (activity of individual IP3 molecules) (cytoplasmic Ca⁺⁺ levels) (none of these). Circle one or more answers and show how binding of ligand L should lead to changes in enzyme Z. (A clear and well labeled diagram is sufficient.)

B. Ca⁺⁺ is known to activate phosphodiesterase. Compared to ligand L alone, ligand L plus Ca⁺⁺ should give levels of enzyme Z activity that are (higher) (lower) (same as with L alone) (can’t predict) AND the activity of protein kinase A with L plus Ca⁺⁺ should be (higher) (lower) (same as with L alone) (can’t predict). Explain both choices briefly.

5. In 1985, a cluster of people in South Dakota complained of symptoms that seemed like hyperthyroidism. The mystery of this sudden onset of disease was solved when one family was found where everyone had these symptoms…except for the 12-year old vegetarian son. After visiting the local slaughterhouse, researchers learned that the ground beef produced there consisted of more than the usual skeletal muscle – other parts of the animal were ground up and added to the mixture.

Could something in the meat have led to these symptoms? To answer this, the researchers fed a volunteer a hamburger containing thyroid gland at time 0, and measured hormones in the blood for several hours afterwards. The results are graphed in Figure 3. The researchers knew that there are enzymes in the lumen of the intestines that can break down proteins into their constitutive amino acids.

A. These symptoms showed by the affected people were most likely to be (sweating and weight loss) (feeling chilly and weight gain). (1)

B. Describe the path by which thyroxine got into the blood of the volunteer. (4)

C. Is it likely that TSH could enter the blood if it were ingested as part of hamburger? Why or why not? (4)

D. Suggest two mechanisms that could possibly account for the decrease in blood levels of thyroxine that occurred in Figure 3. (4)

E. Explain what caused the TSH to decrease over the same time period. (4)