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I approved an edit on this question where the tag was added. I am not 100% sure that I would agree that the essence of the question is about metabolism, but I did not disagree strongly enough to reject the edit either.

That then raised the question of what the appropriate use of the tag is. The tag description states:

The set of chemical reactions that happen in the cells of living organisms to sustain life.

Technically any question related to a cellular process could be classified as cell metabolism, but metabolism may not be at the heart of the question. Nature's Scitable gives the following definition:

Cell Metabolism

A cell's daily operations are accomplished through the biochemical reactions that take place within the cell. Reactions are turned on and off or sped up and slowed down according to the cell's immediate needs and overall functions. At any given time, the numerous pathways involved in building up and breaking down cellular components must be monitored and balanced in a coordinated fashion. To achieve this goal, cells organize reactions into various enzyme-powered pathways.

So my question is when is it appropriate to tag a question as being a question about metabolism and when should the question not be tagged with the metabolism tag?

Would we want to reserve the tag for only those questions that dealt with cellular processes such as Glycolysis, The Citric Acid Cycle, Oxidative Phosphorylation, etc. or is any question about cell function fair game for the tag?

A secondary question would be is the question that I linked above an example of a question that would warrant the tag.

Thank you in advance.

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  • $\begingroup$ thanks for posting @AMR - I'm a metabolic physiologist by training so I see the world through that lens... I think you could take a strict "biochemical" definition of "metabolism" but since cell signaling cascades and regulation of metabolic enzymes (i.e. glycolytic, gluconeogenic enzymes) are an integral part of metabolic regulation (i.e. second messengers, reversible phosphorylation) I consider that part of intermediary metabolism as well. I'm curious to hear others' thoughts $\endgroup$ – Vance L Albaugh Dec 2 '15 at 18:05
  • $\begingroup$ @VanceLAlbaugh You should add an answer as well as your thoughts are equally relevant. $\endgroup$ – AMR Dec 7 '15 at 0:12
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    $\begingroup$ At undergrad I presented a poster for a module. The posters were chosen at random from a list. My topic was "metabolomics". One of my examiners couldn't wrap their heads around the vast-ness of metabolomics and they thought it was a redundant word for biochemistry and molecular biology. Due to the complexity of biology almost anything from DNA to copper arguably is a metabolite. This potentially is a massive tag, but I'm sure we can find a place for it! $\endgroup$ – James Dec 11 '15 at 3:52
  • $\begingroup$ Any one of you (AMR, Vance, Roland) can improve the tag-wiki for metabolism. $\endgroup$ – WYSIWYG Dec 14 '15 at 9:58
  • $\begingroup$ @WYSIWYG we understand; the discussion is more to get a consensus on the scope of the definition. I would have liked for there to be more input on how to proceed, as there can be a narrow definition or a broader one that could encompass almost any question on cellular process. I really don't have a horse in this race, I was only interested in gaining guidance for how to proceed. $\endgroup$ – AMR Dec 14 '15 at 13:35
  • $\begingroup$ @WYSIWYG I tried to improve (i.e. broaden) the metabolism tag - would be interested in what you and others think - appreciate your feedback. $\endgroup$ – Vance L Albaugh Dec 29 '15 at 17:38
  • $\begingroup$ @Roland I tried to improve (i.e. broaden) the metabolism tag - would be interested in what you and others think - appreciate your feedback. $\endgroup$ – Vance L Albaugh Dec 29 '15 at 17:38
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Good question. I agree the formulation "The set of chemical reactions that happen in the cells of living organisms to sustain life" for this tag is way too broad. Pretty much all of biology is chemical reactions that happens in cells!

I would define metabolism as the collection of chemical processes whose main purpose is to synthesize biomass or extract energy for cellular work. This includes breakdown of fat, protein and carbohydrates derived from the diet / environment, and synthesis of other compounds required to build cellular structures, as well as energy metabolism. These are "physical" processes that provide matter and energy.

Many enzymatic reactions (and other chemical processes) do not provide matter or energy and should not be considered as "metabolism" in my view. For example, protein kinases that transmit signals to regulate other proteins, or synthesis and release of neurotransmitters and hormones. These processes may be catalyzed by enzymes, and they may involve small molecules that we might call "metabolites", but their purpose is to send or receive information (signals); they do not by themselves produce biomatter or energy, and therefore I would not consider them as truly metabolic processes.

This is a bit subjective of course, and there certainly are gray zones. For example, phosphatidylinositol metabolism is mainly involved in cell signalling, but many would include it in lipid metabolism. But generally I think the dividing line is whether a process actually provides matter or energy, or merely information.

That would be my definition of metabolism itself. I would agree with Vance though that questions about regulation of metabolic processes is also relevant for the "metabolism" tag. This includes effects of metabolic hormones on metabolism of various cell types, and regulatory enzymes such as pyruvate dehydrogenase kinase or fructose-2,6-biphosphatase, for example. But I would not include questions about "pure" signalling processes such as the MAPK cascade or PI3 kinase, unless it immediately relates to their effects on a metabolic process.

As for the specific question you mentioned, I would probably not tag it "metabolism", because it relates mainly to how cAMP signalling achieves specificity. It does fit endocrinology though.

Sorry for the long post :) Anyway, I would suggest revising the "metabolism" tag description to something like "Biochemical processes whose main purpose is to synthesize biomass or extract energy, and their regulation".

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  • $\begingroup$ thanks! I'll keep that metabolism definition in mind. $\endgroup$ – Vance L Albaugh Dec 6 '15 at 17:34
  • $\begingroup$ Hi Roland. Thank you for the response. I agree with your answer, but as I would like to generate more thoughts on the issue I am going to leave this question open and not mark as the accepted answer, though I appreciate your input. I think that to come to some consensus, we will need broader discussion. $\endgroup$ – AMR Dec 6 '15 at 23:55
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Great question and thanks for posting!

My perspective is that of a physiologist who studies metabolism in general. I tagged the question specifically with the metabolism tag and didn't think twice about doing so. From my perspective, I consider "metabolism" to include not only the strict biochemical reactions (e.g. Glycolysis, Krebs Cycle, Glycogenolysis, Gluconeogenesis, Cori Cycle, etc), but also the regulation of those metabolic enzymes and pathways. This regulation includes not only the classical allosteric effects and feedback/product inhibition that is taught in basic biochemistry courses, but also includes the hormonal and organ-to-organ communication that is emphasized in graduate level biochemistry and integrative physiology courses.

If you study metabolism in a vacuum (i.e. just the strict biochemistry reactions) you easily miss the complex regulation, subcellular sequestration, and organ-to-organ communication that is vital to having a thorough understanding of intermediary metabolism. For example, the organ-to-organ flux of citrulline between the intestinal-kidney-liver axis is a vital part of whole body citrullin/arginine/glutamine metabolism and nitrogen balance. No biochemist would argue that those processes are somehow separate from "metabolism" - they are an important part of the reactions that control whole-body nitrogen balance.

As for the question that sparked this discussion, it was asking about a fundamental concept of metabolic regulation - that is, how hormones like insulin, glucose and epinephrine signal through second messengers with specificity.

I thought the question was excellent! This is one of those questions that is fundamental to graduate study in physiology. It is those second messenger processes that can have very different effects depending on the tissue type and receptor expression. The concept of second messengers actually grew out of studies from biochemists like Earl Sutherland and others at Vanderbilt University, Washington University in St. Louis, Case Western Reserve (and others). These scientists were trying to understand the hormonal regulation of metabolic enzymes in tissues like liver, skeletal muscle, adipose tissue, etc.

Also, note that the definition above is for cell metabolism, however, I would argue that metabolism is much more than the metabolism of an individual cell - which is what I have tried to emphasize in my answer above.

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  • $\begingroup$ What would your thoughts be about Homeostasis as the catchall term/tag and reserve Metabolism for the narrower, more basic definition? I do however see your points and I think both perspectives are valid. It may end up being a community choice as to what people are more comfortable with. I would like the see what some of the High Reputation and Moderator Users think on the topic. $\endgroup$ – AMR Dec 7 '15 at 5:03
  • $\begingroup$ I completely agree that regulatory mechanisms should be included in the "metabolism" tag. But to define the scope, I think it is helpful to first define metabolic processes (as I tried to do), and then state that regulation relevant to these processes are also included. Otherwise the scope can easily grow too broad. I also agree the tag should in no way be restricted to the cellular level, but I think the definition for an organ or a whole individual is similar, it's still about processes that supply matter or energy. $\endgroup$ – Roland Dec 7 '15 at 6:35
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    $\begingroup$ @AMR my thoughts on homeostasis... I think that homeostasis is more of a endocrinology-type term and not as much a biochemical one. When I think of homeostasis I think of "maintenance of a constant internal environment" - like salt/water balance, temperature regulation, thirst/hunger mechanisms, blood pH/buffering - if you look at Walter Cannon's original text where he describes homeostasis ("The Wisdom of the Body"), the book reads much more like an endocrine physiology text than a biochemistry/metabolism text - - - thus, I don't think homeostasis would work very well as a catch-all $\endgroup$ – Vance L Albaugh Dec 7 '15 at 14:50
  • $\begingroup$ I agree with this answer, both as a (former) molecular biologist (concerned mostly with the subcellular level) and a physician (concerned mostly with the whole organism.) $\endgroup$ – anongoodnurse Dec 27 '15 at 21:03
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I think these two definitions deserve a mention - Catabolism and Anabolism. The two components of meta-bolism are cata-bolism and ana-bolism. Roughly, catabolism is the process of 'breaking down' and anabolism is the process of 'building up'. Here are more formal definitions for your reference.

Anabolism https://en.wikipedia.org/wiki/Anabolism

Catabolism https://en.wikipedia.org/wiki/Catabolism

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