RPE65 is a major protein of unknown function found associate…
RPE65 is a major protein of unknown function found associated with the human eye that is associated with a number of different eye diseases. One hypothesis is that RPE65 is an enzyme involved in the chemical synthesis of the pigment that makes the human eye light sensitive. In a search as to which pathway intermediate RPE65 acts on, the following dissociation constants were measured (Table 1). They were compared to BSA, which stands for bovine serum albumin and is found in large concentrations in cow milk. Table 1: Binding Constants of Various Retinoids with RPE65 and BSA in pM (10^-12 M). The numbers in brackets ( ) indicate the errors of the binding constant determination. Ligands RPE65 (pM) BSA (pM) A: all-trans-retinyl palmitate 20 (6) 2143 (790) B: 11-cis-retinyl palmitate 14224 (3006) 2310 (611) C: all-trans-retinol 1078 (144) 2316 (1216) D: 11-cis-retinol 3811 (100) 2143 (800) Part A. 4 points What is the purpose of comparing the dissociation constants of 4 different ligands with two different proteins, RPE65 and BSA? Part B. 5 points What is the association constant for 11-cis-retinol binding to RPE65? Part C. 5 points What is the difference in standard binding free energy between ligand A binding to RPE65 as compared to BSA. Part D. 4 points Which is the best (highest affinity) ligand for RPE65? Justify your choice. Part E. 4 points Would you say that RPE65 binding to any of the ligands is specific? Justify your answer. Part F. 10 points If you add a 10 nanomolar concentration of ligand A to a solution containing RPE65, what percent of ligand A is bound to RPE65? Part G. 10 points If you repeat the same experiment as in part F with BSA, i.e. if you add a 10 nanomolar concentration of ligand A to a solution containing BSA, what percent of ligand A is bound to BSA? Solve this problem on paper, document your approach and provide intermediate results. Report the final answers with 3 significant figures. Scan the pages(s) and upload them for grading. Answer all parts A to G.
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PART 2: Written Response Questions Write down your written responses for Questions 18-20 with pen and paper (or on a tablet computer with an electronic pen) and keep the exam and RPNow running. Once you are done or once the time limit is up, you have 20 minutes to scan your written responses to Questions 23-25 and upload them as a single PDF file in the following assignment section in the Midterm 1 Module on Canvas. We can only accept PDF documents. Try to limit the size of your files to less than 5 MB and make sure that your answers are complete and legible. PDF files > 5 MB will be automatically compressed before grading, which may negatively affect readability. If you are using a phone or digital camera to take pictures of your written work and don’t use a scanner app, a popular way to convert your files into a single PDF is to import your pictures into a MS Word document (other word processing software should work, too) and export it into a PDF file. In order to receive full points, the first 3 significant figures of your numerical answers must be correct.
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