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I'm not asking the question on a superficial level. Obviously, (most) transcription factors are not acting directly on a substrate to produce a chemical change. I pose the above question as more of a philosophical inquiry.

First, a definition: A catalyst is a substance that increases the rate of a chemical reaction and is not consumed in the reaction. As every biochemistry class emphasizes, catalysts do not change the equilibrium constant of a reaction, only the rate.

So for example, if we take the following example of transcribing a gene of length $n$ ($G$) into a transcript of length $n$ ($M$).

$$ \ce{RNAP + G + nNTP <=>> RNAP + G + M} \mbox{ (Reaction I)} $$

The hydrolysis of the NTP's bonds drives the reaction forward (source). The Gibbs free energy has decreased. Obviously, there is some probability that the NTPs in solution would spontaneously polymerize into the length-n transcript, this possibility is unfathomably infinitesimal though.

The RNA polymerase is acting as an enzyme here, since it's 1) increasing the rate of an otherwise slow reaction and 2) not being consumed in the reaction. Our nomenclature is consistent as we usually reserve "-ase" suffix reserved for enzymes.

Transcription factors bind elsewhere on the DNA and facilitate (or impede) the formation of RNA polymerase complex from its constituent subunits ($mS$). Assume we have an activating transcription factor $TF$. We can model this as:

$$\ce{TF + mS <=> TF + RNAP} \mbox{ (Reaction II)}$$

Putting these reactions $I$ and $II$ together, you might have:

$$\ce{TF + mS + nNTP <=> TF + RNAP + M}$$

From our understanding of activating transcription factors, we know that this will increase the rate of the transcription reaction. The TF is not being consumed in the reaction. So, what am I missing here? Why isn't this transcription factor considered a catalyst for helping to stabilize the initiation complex?

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  • $\begingroup$ TFs are a big group and at least some are considered catalysts - e.g. histone deactylases/acetylases. Because they aren't part of the reaction; your supposition about the reactions II and III are incorrect. In chemistry the TF would go over the arrows! $\endgroup$
    – bob1
    Commented Sep 16, 2022 at 1:02
  • $\begingroup$ If this is a question about philosophy you are on the wrong site. If you are using this as a platform to make an argument, you are misusing the site. If this is a question about historical linguistics, SE English Language and Usage might be more appropriate. And, paradoxically, your definition of an enzyme in naïve historical terms, although used in chemistry and taught to undergraduate biochemists, does not conform to what we know or think about enzymes. You must be aware that biochemists regard enzymes as macromolecules that participate in chemical reactions to increase their rate. $\endgroup$
    – David
    Commented Sep 16, 2022 at 13:49
  • $\begingroup$ I think the rewording of this question is devious. It sets up a straw horse because of the weakness of his original question. Biochemical classes talk about the properties of enzymes, not catalysts, and we do not talk about "factors and catalysts". If you want to ask a question about catalysts, ask it on SE Chemistry. It also suggests he is not interested in knowing why biochemists describe proteins the way the do, but is indulging in what our Help terms a "rant". Using the site as a soap box for his jesuitical casuistry. $\endgroup$
    – David
    Commented Sep 18, 2022 at 12:01
  • $\begingroup$ I’m voting to close this question because it is an attempt to start a discussion regarding a point of view rather than a question seeking an answer. $\endgroup$
    – David
    Commented Sep 18, 2022 at 12:02

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Because the TFs DO NOT PARTICIPATE in the catalyzing reaction themselves, and that reaction involves breaking of chemical bonds in the substance that's being catalyzed and forming temporary chemical bonds between it and the enzyme, which is not the case with the TFs.

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  • $\begingroup$ Your answer could be improved with additional supporting information. Please edit to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers in the help center. $\endgroup$
    – Community Bot
    Commented Sep 16, 2022 at 11:24
  • $\begingroup$ Do you mean TFs (transcription factors) instead of TTs? Please edit your post and clarify. $\endgroup$
    – MattDMo
    Commented Sep 16, 2022 at 14:16

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