Biology 200

Sample Midterm Exam

Question 1. ( /5 marks)

The following microscopy images (a) and (b) show two adjacent cells. The scale bar in both images represents 10µm.

A. What type of microscopy technique was used to produce image (a)? How do you know? (2 marks)

B. What type of microscopy technique was used to produce image (b)? How do you know? (2 marks)

C. What is one benefit of using the technique in (b)? Be specific (1 mark).

Question 2 ( /8 marks)

For the following statements, indicate if they are true or false and provide a short rationale for your answer. (2 marks each)

A. In order to remain fluid at a lower temperature, a cell membrane will be composed of phospholipids with a greater degree of unsaturation of their hydrocarbon tails.

B. Only proteins can have a nuclear localization sequence.

C. Core histone proteins have an abundance of negatively charged amino acids that form. ionic bonds with the DNA backbone.

D. The hydrophilic pore within the interior of a single a-helix allows the passage of small molecules.

Question 3 ( /7 marks)

One of the primary characteristics of cancer cells is their ability to become mobile and move away from their site of origin. This characteristic (known as metastasis) allows cancer cells to develop into tumours at new sites in the body. There is a strong positive correlation between a cancer cell’s ability to move around and the fluidity of its membranes.

Researchers at the University of Texas were trying to find ways to inhibit metastasis by changing the properties of the membranes of mammalian cancer cells. They tested a drug called Haloperidol, suggested to affect membrane fluidity as a potential inhibitor of metastasis. To this end they carried out a fluorescence recovery after photobleaching (FRAP) experiment using a fluorescent dye that binds to plasma membrane lipids in metastatic breast cancer cells. The results are shown in the graph above.

A. Which treatment would be considered to be the experimental control? Explain your reasoning (1 mark)

B. Describe the change in fluorescence recovery of cells in the presence and absence of Haloperidol and explain how it relates to the fluidity of the cell’s membrane in each case. (2 marks)

C. Based on the data here, is Haloperidol a good candidate for inhibiting metastasis? Explain your logic. (2 marks)

D. ABCA1 is a protein that has been shown to be involved in regulation of cholesterol levels. ABCA1 has also been shown to expressed in higher amounts in breast cancer cells that are undergoing metastasis. How might ABCA1 be promoting metastasis? Explain. (2 marks)

Question 4 ( / 9 marks)

The clcn5 gene encodes for a membrane protein that forms a chloride-proton channel in the kidney epithelium. Tanaka et.al. (2010) studied how the clcn5 gene is regulated by analyzing the transcription activity of different segments of DNA upstream of the clcn5 gene in the presence or absence of a transcription factor HNF-1a. Below is a schematic of the gene and DNA regions they analyzed:

A. What is the control in this experiment? Explain why it is used. (1 mark)

B. Describe what the data show for each DNA segment and explain based on this data how HNF-1a impacts the expression of the ccln5 gene. (4 marks)

C. Consider if the first 3 base pairs at the 5’ end of segment 1 were mutated from TCT to AAA. Predict how this mutation could affect transcriptional activity of ccln5 in the above experiment. Justify your predicted experimental outcome. (2 marks)

D. You are working in a lab and you decide to try and repeat the experiment from A and B. However your data do not agree with the published results (see your data below). Your supervisor points out that you were accidentally using cells that lack enzymes that modify core histone proteins by adding acetyl groups. Explain why this omission could explain your result. (2 marks)

Question 5 ( / 8 marks)

Wodrich et al. (2006) looked at the number of nuclear localization signals (NLS) and their locations within Adenovirus protein pVII. This is one of their experiments:

▪ Full length and deletion mutants of pVII were fused to GFP (green fluorescent protein) and injected into the cytoplasm of cells.

▪ Injected cells were viewed using fluorescence microscopy.

a: Full length pVII (amino acids 1 to 198)

b: Amino acids 1 to 81 (of primary sequence)

c: Amino acids 82 to 198 (of primary sequence)

d: Amino acids 82 to 114 (of primary sequence)

e: Amino acids 115 to 169 (of primary sequence)

f: Amino acids 170 to 198 (of primary sequence)

A. Identify the cellular location of the fluorescence in each panel (a through f). (3 marks)

B. What can you conclude from this experiment? Explain. (2 marks)

C. Does this experiment tell you how many NLS there are in pVII? Explain your answer. (2 marks)

Question 6 ( /9 marks)

The CFTR protein is an integral membrane protein containing a single polypeptide chain that forms a channel that transports chloride ions across the plasma membrane. Cystic Fibrosis results from a mutation in this protein that causes it to mis-fold.

Describe the importance of the amino acids found within CFTR’s primary sequence, and explain how the non-covalent interactions they make (with each other and with molecules in their environment) determine the folding of this structure, its location within the cell, and the function of this protein.

Your answers should include aspects of how the properties of the amino acids and their non-covalent interactions with each other (intramolecular interactions) and intermolecular interactions with their environment, where these amino acids would be within the protein structure, and how these noncovalent interactions determine the overall function of the protein.