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Are the terms gene expression assays and protein expression assays used interchangeably in molecular biology? Or is it expected of you to differentiate between the two terms.

For example, if I replace the DNA sequence of a gene of interest with the GFP DNA; and then subsequently quantify the fluorescence levels, am I measuring the gene expression of the gene of interest OR the protein expression?

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Gene expression is the production of a functional gene product from a gene. So protein expression is a functional read-out of gene expression for gene loci that encode proteins.

However, gene expression is frequently, and erroneously, used to refer to measures of mRNA levels. The production of mRNA is a prerequisite step for the production of protein from a gene and it provides information about the transcriptional activity of a gene loci.

Translation of mRNA is a highly regulated process and global assays highlight that mRNA transcript levels explain less than half of the variation in protein concentrations.

For example, if I replace the DNA sequence of a gene of interest with the GFP DNA; and then subsequently quantify the fluorescence levels, am I measuring the gene expression of the gene of interest OR the protein expression?

You are measuring both gene expression and protein expression from the promoter + GFP gene loci. If you are interested in transcription from the promoter then measuring transcript would provide a more direct measure.

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Gene expression and protein expression are absolutely not the same thing. While counts of mRNA levels for a particular gene may give some indication of how much protein is present, many times it does not. Similarly, quantitating protein levels does not necessarily mean the relative levels of mRNA will be similar. There are many points for regulation between RNA polymerase rolling along the gene and creating the pre-mRNA and the protein coming out of the ribosome and being folded and transported to its correct place in the cell. mRNA can be silenced, degraded, or prevented from being translated by a number of mechanisms. Proteins themselves are subject to extensive regulation, with half-lives that can vary from seconds to weeks. Of course, genes are regulated in many different ways as well, from repressor proteins to methylated DNA to chemically-modified histones, and the number of polymerase complexes on the DNA and their relative transcription speed are also under regulatory control.

If I replace the DNA sequence of a gene of interest with the GFP DNA; and then subsequently quantify the fluorescence levels, am I measuring the gene expression of the gene of interest OR the protein expression?

You are quantifying the protein levels of GFP. mRNAs can be subject to sequence-specific regulation (such as siRNA), so you can't just say absolutely that GFP levels are equal to your gene product of interest. Many times they will be proportional, but some times they won't, so you'll need to do a number of other experiments to verify your results.

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