When you shine the UV light on the gel while the native proteins are separating, the proteins are still in their native structure. There will be no clear visible protein bands on the gel.
How proteins are visualized on gel by UV illumination?
First denaturation of protein is done by SDS and the protein is converted into its primary structure.
Proteins are visualized on gel by staining the gel in trichloroacetic acid and followed by illumination under UV light.
The UV- light driven reaction of tryptophan in the presence of trichloroacetic acid yields products that emit sufficiently in the visible region to identify the location of protein bands on the gel.
How the gel will differ from denatured one?
Since protein is in native structure during UV illumination, tryptophan is not available to yield product in visible region.
Hence clear protein bands will not be visible compare to the denatured protein lane.
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