What a fantastic question! This is what I spend most of my time working on…
The main way we study what proteins look like in cells interestingly is by taking them out of the cell so we can study them without all the other proteins in a cell complicating the picture! We can then take pictures of the protein using the electron microscope, and work out what they look like down to the very building blocks, amino acids, that make the proteins.
If we are looking for an individual protein in a cell, it is far too crowded to be able to spot an individual protein. But we can use special tags to make this possible! One very clever one involves adding a short bit of code onto the end of the gene for our protein. When this gene is turned into a message (called messenger RNA), which is then used to make the protein (a special machine called a ribosome does this), the protein we are interested on has an extra section on the end the ‘tag’. If we then put gold particles onto the cells, these stick to the special ‘tag’ and let us find the protein!
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