Proteomics is a fancy term that has been used for the past several years. You talk about the expression of mRNA and of protein. When you say that a molecule modulates a protein it involves both of these. Expression of functional protein confirms the statement concerning this modulation. A diseased state is a remodeling of the cell environment wherein aberrations in proteins may occur. Proteins define the molecular architecture of of cells in eukaryotes. Study of the expression of proteins give clues to potential underlying molecular mechanisms of proteins in normal and altered states. One example is collagen. In diseased state its expression may be modified. Observations of altered proteins (example hemoglobin variants) in individuals with modified health status have provided crucial information on the role of functional proteins in health.
The levels of mRNA not always give a good representation of the final level of the protein is codes for, due to post-transcriptional regulation. Therefore, when studying protein coding genes, the best and more significant way it is to look directly at the protein level, instead of stopping at the mRNA.
Yes.
mRNA expression gives an idea of what cellular changes are elicited at transcription level. This, of course needs to be corroborated, by elucidating the expression of the protein in question. A good example is cellular (receptor) protein tyrosine kinase (PTK), which is intricately involved in cell signaling. Evaluation of the expression of tyrosine kinase mRNA on exposure to a certain molecule furnishes an initial clue that the modulation of this enzymic activity (here at mRNA level; transcription) might be implicated. Final confirmation of such a modifying effect is obtained by assessing TPK protein expression (translational level).
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