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Trying to deduce the topology of membrane proteins in a cell. I treated the outside of the cell with trypsin, and one protein (that I'm interested in) was partially digested and became smaller. What can be inferred from this?

1) The protein is located on the outer surface of the cell membrane
2) The protein is located on the inner surface of the cell membrane
3) The protein spans the entire cell membrane
4) The protein is not associated with the cell membrane

1 Answer

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Final answer:

The trypsin digestion indicates that the protein is either located on the outer surface or spans the entire cell membrane, as trypsin would not affect proteins solely on the inner surface or not associated with the membrane.

Step-by-step explanation:

Based on the trypsin digestion experiment described, it can be inferred that the membrane protein in question is either located on the outer surface of the cell membrane or spans the entire cell membrane. Trypsin is a protease that typically cannot cross the cell membrane to access the cytoplasmic side. Since the protein was partially digested and became smaller after treatment with trypsin which digests proteins accessible on the cell's exterior, this indicates that at least part of the protein is exposed on the outer surface of the cell membrane. If it were solely on the inner surface or not associated with the membrane at all, trypsin would not be able to access and digest the protein.

Additionally, transmembrane proteins often have segments that pass through the lipid bilayer, which can result in them having regions both inside and outside the cell. These regions are composed of hydrophobic amino acids that are compatible with the non-polar core of the lipid bilayer. If only part of the protein is digested, this suggests that not all regions of the protein were accessible to trypsin, consistent with a transmembrane topology where some segments are protected by the membrane itself.

Therefore, without further specific data (such as whether the protein's activity or cellular localization was affected), we can suggest two possibilities: the protein is located on the outer surface of the cell membrane (option 1), or the protein spans the entire cell membrane (option 3). For a definitive conclusion, additional experiments, such as protease protection assays with permeabilized cells or the use of other biochemical and biophysical techniques, would be required.

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