BIBC 110 assignment wi06 - BIBC 110 Physical Biochemistry...

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BIBC 110 Physical Biochemistry WI06 TAKE HOME EXAM ASSIGNMENT – ANSWER GUIDE Friday March 3 rd 2006 Note that this is only an approximate guide to the answers for the take home exam. Calculations are shown as completely as possible. For questions that asked for short descriptions or interpretations, your score reflects how well you answered the question, both in accuracy and how well you justified your answer. For example, in some cases one or more answers are possible and sometimes I have shown some of the alternative answers. You may also have received credit for suggesting another alternative explanation that was deemed to partially or completely answer the question. Page 1 of 14
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Background to the investigation and the questions for the exam: The four questions below relate to aspects of an investigation by a biotechnology company. The company has developed a promising new drug, called X52, that has an effect on mouse heart muscle contraction and which may be effective in treating certain types of heart disease. The company is in the first stages of drug development and so the investigating scientists would like to know more about how the X52 drug works. As a first step in this process they use affinity chromatography to identify proteins in mouse heart cells that interact with the drug. As described below, their initial procedure identifies a small number of proteins that bind the drug. Interestingly, one protein is found only in cells that have been treated with the drug. It is not found in cells that have not been treated with drug. Since this protein seems to be made by the cells in response to the drug, the investigators decide it is a good candidate for mediating the effect of the drug and decide to characterize this protein, and its interaction with the drug, in more detail. The questions on the exam represent descriptions of different experiments performed by the investigators as they identify and characterize this protein. These can be summarized as follows: Question 1 (Experiment 1): The investigators use 2D-gel electrophoresis to characterize proteins isolated from mouse heart cells by affinity chromatography. They identify a protein that is found only in cells treated with drug and name it X52BP (for X52-binding protein). They use the observed behavior of the protein to deduce initial information about its amino acid composition and to choose a method to further purify the protein. Question 2 (Experiment 2): In the next step of the investigation, the investigators identify the X52BP protein (and the gene that encodes it) by determining its mass via mass spectrometry. They use the mass to identify the protein, and the gene, from the known sequence of the mouse genome. Now they have the sequence of the protein, so they can easily prepare the DNA that encodes it and use expression methods to make large quantities of X52BP for further analysis.
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