de-regulation of protein kinase cascades and kinases Homework Help

de-regulation of protein kinase cascades and kinases

1) Cancer is largely driven by the de-regulation of protein kinase cascades and kinases are both drug targets and biomarkers of cancer. In a genetic screen you identify a protein tyrosine phosphatase as a tumour suppressor. Describe approaches to identify possible targets of the phosphatase within the phosphoproteome. Give the general work-flow and emphasize the important aspects of the experimental design. Discuss the relative advantages and disadvantages of the strategies you consider useful (20 marks). What resources are available that would allow you to sort quickly through the data to identify potentially important targets of the phosphatase (5 marks)?
(2) From your analysis you identify a protein “X” of unknown function. However, you note that analysis of a wide range of tumours show it to be down-regulated. What methods could be used to characterize experimentally the “interactome” of protein X (i.e. proteins that interact with X)? Include a description of the approaches that you would use to substantiate and verify your findings. As above, emphasize the important aspects of the experimental design within a general description of the work-flow. Compare and contrast the approaches you propose, discussing their merits and disadvantages. Also, avoid any unnecessary direct repetition of any technique/methodology you have already discussed in part (1) above (25 marks).
(3) One protein “Y” that interacts with “X” is always identified using different screening approaches. It shows homology with zinc dependent proteases and your preliminary cell biology experiments with a GFP (green fluorescent protein) fusion protein (Y-GFP) demonstrate localization on the cell surface. What role do you suspect this protein to have in tumorigenesis? Describe experimental strategies to test your hypothesis, with an appraisal of each on its ability to substantiate your hypothesis (25 marks).
(4) In your answers above you would have given consideration to various “omic” (e.g. proteomic, transcriptomic, interactomic) approaches to characterizing biological processes that, in the research laboratory, have led to the identification of many proteins with potential roles in carcinogenesis. Describe and critique antibody-based techniques that could be implemented in personalized cancer therapeutic regimes (25 Marks).
Maximum 2500 words for the complete answer (questions 1-4). In all cases you should justify clearly your response and cite relevant material where appropriate. Citations (20 max; not included in the word count) should not be a substitute for including key information in your answers; they should indicate the extent of your reading and ability to identify key information. The use of diagrams is encouraged (maximum one original, clearly legible, half-page per question), but the figure legend is included in the word count.