Note: there is one more thing I need to tell you about the Ras-Sos homework, you need to know that the number of Ras molecules per cell is 10,000.

Chem 532 Prof. Gelb Chemical Cell Biology Homework Problem

1. In class we spoke about mRNAs that code for proteins that have an N-terminal signal peptide that binds to the SRP on the ER membrane and allows the protein to be imported into the ER. The signal peptide is eventually clipped off by a signal peptides that is inside the ER. There are two possibilities with respect to the timing of the signal peptidase action: 1) The signal peptide is removed only after the protein has been fully synthesized on the ribosome bound to the SRP; 2) The signal peptide is removed soon after it appears in the ER and before the full length protein is synthesized.

Devise an experimental strategy to distinguish between these 2 possibilities.

2. One approach for the treatment of cancer is to discover a protein that is selectively expressed on the extracellular membrane surface of cancer cells but not on non-cancer cells and to design an immunotoxin for this cancer cell specific protein, that is an antibody that binds only to this cell surface protein and is covalently tethered to a toxic molecule that kills the cancer cell when tethered to the cell surface. So the game is to discover a protein that has the following properties:

1) It is expressed only in cancer cells

2) It is an integral plasma membrane protein (i.e. it has a at least one segment that passes through the plasma membrane) with at least a portion of the protein not in the membrane but on the extraceullar face of the cell.

3) Or instead of property 2 above, it is a peripheral plasma membrane protein that does not pass through the plasma membrane but rather is completely on the extracellular face of the cell but tightly bound to the extracellular face of the plasma membrane.

The idea is to selectively purify only those cellular proteins that satisfy properties 2 or 3 above from both cancer cells and from non-cancer cells, to use mass spectrometric proteomic techniques to identify these two sets of proteins and then to decide which proteins are found in cancer cells but not in non-cancer cells.

Come up with a reasonable scheme for selectively purifying only those proteins that satisfy properties 2 or 3. Your scheme can make use of specially designed chemical reagents, if so describe the design of such reagents and how they would be used to accomplished the desired task.