Talk:Metabolism

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Contents

[edit] sources

am i the only one whos noticed all of this information is based on 1 source, if it isnt more needs to be added.

[edit] Image

What is the relevance of the picture?

It's a drawing of the original doctor to study metabolism. There may be something more relevant, like a fire or a stomach or a person in movement for example. Those would be good to add to or replace the current picture.

[edit] Fast metabolism

In layman's terms, when someone says "I have a fast metabolism", i.e. they can eat a lot and not put on weight, what does that mean?

It means that energy ingested (food) is not stored in the body as fat, but used in other ways or excreted. There is no difference in the "speed" of metabolism, but rather the relative amount and utilisation of metabolic products Onco p53 09:45, 19 Jun 2005 (UTC)
Well, they might still metabolize things faster. Tyciol 19:37, 26 March 2006 (UTC)

fast metabolism needs to be in the article

[edit] Metabolism as design

I know that metabolism is a biological term, but it is also used in defining post-modernism. I know it was a design strategy used in the 1960's, but is there any other information on it?

I haven't actually heard of that... if you do have knowledge of it, it would be a great thing to research to add. Tyciol 19:37, 26 March 2006 (UTC)

[edit] Citric acid cycle

Anyone object if I move it to the Catabolism section? --Arcadian 20:25, 27 November 2005 (UTC)

It seems like it has it's own article now, which is neat. Tyciol 19:37, 26 March 2006 (UTC)

[edit] Metabolism during Pregnancy

There is need to describe the metabolic changes that go on in the mother's body during pregnancy.

Belongs to pregnancy.   Andreas   (T) 23:27, 12 September 2006 (UTC)

[edit] Anabolism and catabolism

These are already mentioned in the box at the bottom of the page, so no more links are necessary.  Andreas  (T) 03:01, 21 November 2006 (UTC)

[edit] Alcohol tolerance

How does the metabolism affect alcohol tolerance? For example, will someone with a "fast" metabolism get drunk quicker, or recover quicker, or what? Some guy 09:10, 4 January 2007 (UTC)

[edit] General theory of metabolism

This edit by 66.215.123.233 looks like a general theory of metabolism. However, it is not backed by sources. The description of biological systems as Dissipative systems is important. The formulation by 66.215.123.233, although well-meant, looks like original research.  Andreas  (T) 23:02, 17 January 2007 (UTC)

[edit] Suggested merges

I propose merging both cell metabolism and total metabolism with this page and replacing these articles with redirects. TimVickers 23:38, 5 March 2007 (UTC)

[edit] Total metabolism

(also called metabolism) is all of a certain living organism's chemical processes. The organism's metabolism can be dichotomized into the synthesis of organic molecules (anabolism) and their breakdown (catabolism). This is to be distinguished from cell metabolism which is those processes of metabolism that occur within a single cell. The study of total metabolism is called metabolomics.

Some organisms can reduce their metabolism to almost zero for certain periods of time. Spores of fungi can survive thousands of years in that state. But every lifeform is bound to have metabolism at some point of its life cycle.

Human cells obtain most of their energy from chemical reactions involving oxygen. A starting point in measuring human metabolism is with basal metabolic rate. Some microbes metabolise the wrought iron on shipwrecks, forming structures known as rusticles with the waste compounds they produce.

[edit] Plan for expanded article

Proposed major sections in new version TimVickers 19:25, 6 March 2007 (UTC)

  • Introduction
  • Thermodynamics
  • Coenzymes as the critical intermediates in metabolism
  • Small molecules as group-transfer intermediates (NAD(P)H, SAM, AcetylCoA, folates)
  • Catabolism
  • Overview - general types of energy metabolism in animals, plants and microbes
  • Extracellular digestion
  • Intracellular catabolism of carbohydrates, lipids and proteins. Shared pathways to CoenzymeA.
  • Oxidative phosphorylation
  • Inorganic electron donors and acceptors in bacteria and archaea
  • Direct ATP generation by photophosphorylation
  • Nucleotide catabolism
  • Anabolism
  • Carbohydrates, lipids and proteins
  • Nucleotide synthesis and salvage
  • Photosynthesis in plants, bacteria and archaea
  • Xenobiotic metabolism and redox metabolism
  • Regulation
  • Intrinsic
  • Allosteric control, flux control coefficients
  • Post-translational modifications of enzymes
  • Compartmentalization
  • Extrinsic
  • Hormonal/nervous control
  • Evolution
  • Origin of metabolism and life
  • Evolution of novel pathways
  • Parasite metabolism and loss of functions
  • Investigation and manipulation
  • Biochemical techniques - nutritional studies, radioactive tracers, metabolite analysis, gene knockouts.
  • In silico models and metabolic networks
  • Metabolic engineering
  • History


That looks awesome!!!1!eleven When shall we start? - Zephyris Talk 23:46, 6 March 2007 (UTC)
The first section has been added, but to get this up to FA level this is going to take a long time. TimVickers 00:28, 7 March 2007 (UTC)
True, but it is a worthy goal for such a central article. - Zephyris Talk 08:03, 7 March 2007 (UTC)
I'm really glad someone else is interested in this article. I was upset by how weak it's been but felt overwhelmed by the thought of revamping the whole thing alone! Some comments:
  • There are a LOT of terrible 'daughter' articles that need work, especially the '..... metabolism' articles.
  • ATP deserves its own (sub)section, given how hugely important it is. Same with glucose, in my opinion.
  • I'm not sure about the regulation section.. How much can we really talk about this without describing how specific organisms regulate metabolism? It seems we should work on integration first, but don't let me stop you.
  • I'm not sure the strict division between catabolism and anabolism is helpful for all the classes of molecules... for example, protein catabolism is a function of digestion & ubiquitination, and serves primarily to provide amino acids for protein synthesis. On the other hand, amino acid catabolism often provides energy.
  • We need at least a brief introduction to the classes of biochemical molecules and the roles they play.
  • There are several well-wiki'd pathways such as Glycolysis, it would be nice to have prominent links to those instead of half-baked articles like carbohydrate catabolism.
  • There's a lot of mixing up between the metabolism of monomer subunits (e.g. glucose) and their polymeric storage forms (e.g. complex carbohydrates). These are very different processes, and mixing them together obscures the important idea that glucose is a central player in many, many pathways. Put another way: nucleotide metabolism and DNA synthesis are very, very different.
  • You're editing the page too fast for me to keep up! I'll help out when you take a break.
Robotsintrouble 01:35, 9 March 2007 (UTC)
Argh I thought you were done! Here's my revision of the new 'classes of molecules' section before your recent revisions:
<blockquote>===Amino acids, carbohydrates and lipids=== Most of the structures that make up animals, plants and microbes are made from three basic classes of molecule: [[amino acid]]s (which make up [[protein]]s), [[carbohydrate]]s and [[lipid]]s (often called [[fat]]s). From individual molecules are formed diverse biological [[macromolecules]] such as [[polysaccharide]]s from simple sugars and [[proteins]]s from amino acids; these macromolecules are essential parts of all living organisms and participate in every process within [[cell (biology)|cell]]s. Lipids are not typically polymerized as are carbohydrates and amino acids, instead their hydrophobic nature causes them to self-segregate in the formation of [[micelles]] and the [[plasma membrane]]. As these macromolecules are vital for life, metabolism encompasses numerous processes necessary to build and maintain them: synthesizing the individual "building blocks", linking these monomers into functional macromolecules in the construction of cells and tissues, transforming excess molecules into deficient nutrients, detoxification of waste and toxins, and extracting energy from food to drive all the above processes. ====Amino acids and proteins==== {{main|Protein}} '''Proteins''' are relatively large [[organic compound]]s made of [[amino acid]]s arranged in a linear chain and joined together by [[peptide bond]]s. Many proteins are [[enzyme]]s that [[catalysis|catalyze]] biochemical reactions, and are vital to [[metabolism]]. Other proteins have structural or mechanical functions, such as the proteins in the [[cytoskeleton]], which forms a system of [[scaffolding]] that maintains cell shape. Proteins are also important in [[cell signaling]], [[antibody|immune response]]s, [[cell adhesion]], and the [[cell cycle]]. Protein is also a necessary component in our diet, since animals cannot synthesise all the amino acids and must obtain [[essential amino acid]]s from food. Through the process of [[digestion]], animals break down ingested protein into free amino acids that can be used for [[protein biosynthesis|protein synthesis]]. [[Image:NADH-3D-vdW.png|thumb|right|170px|Space-filling model of the [[coenzyme]] [[nicotinamide adenine dinucleotide]].]]</blockquote>Robotsintrouble 05:25, 9 March 2007 (UTC)

[edit] Citric acid cycle "universal"?

"A striking feature of metabolism is the similarity of the basic metabolic pathways between even vastly different species. For example, the series of chemical steps in a pathway such as the citric acid cycle is universal among living cells as diverse as the unicellular bacteria Escherichia coli and huge multicellular organisms like elephants."

Maybe I'm nitpicking, but I'm not sure what is meant by "universal" here. Does it mean that the citric acid cycle is found in all organisms? Many bacteria appear to be missing several genes encoding the enzymes of the citric acid cycle. Several bacteria don't seem to encode any of these enzymes. NighthawkJ 03:09, 16 May 2007 (UTC)

re-reading the reference (it's free on-line) I've re-worded this to "For example, the set of chemical intermediates in the citric acid cycle are found universally, among living cells as diverse as the unicellular bacteria Escherichia coli and huge multicellular organisms like elephants." TimVickers 03:38, 16 May 2007 (UTC)

[edit] Group transfer reactions

The wikilinking of 'group transfer reactions' is incorrect. A wikilink must take you to an article expanding that term or containing its explanation. In this case it takes one to functional groups. If no wiki on group transfer reactions exists, it should be made. The functional groups wiki will naturally occur in the explanatory text of what the group transfer reactions are. Even a stub with a few lines is preferable to an inappropriate wikilink. Regards, AshLin 20:05, 21 July 2007 (UTC)

Good point, reworded to use the "functional groups" link correctly. Tim Vickers 20:35, 21 July 2007 (UTC)

[edit] only the cell?

This article is linked to the Swedish article "Metabolism". However, while this article defines metabolism as the processes in the cell, the Swedish word means processes in organisms, including multicellular organisms. I therefore ask whether the english word might also include processes outside the cell, for example trypsin digestion of proteins in the stomach? In that case the definition in the introduction needs to be changed slightly. Etxrge (talk) 19:34, 5 December 2007 (UTC)

I think the Swedish article is right, the OED defines metabolism as "The chemical processes that occur within a living organism in order to maintain life", I've re-jigged the lead a bit to fit this definition. Thanks for the correction! Tim Vickers (talk) 19:55, 5 December 2007 (UTC)

[edit] Photosynthesis is not catabolism

The kernel meaning of catabolism is that molecules are divided into smaller molecules. See the article, and e.g. [1]. As a consequence energy is (often) extracted. Photosynthesis provides energy but cannot reasonably be seen as dividing molecules. It rearranges atoms. The major end result is glucose, which is much bigger than the input molecules. photosynthesis is not a catabolism. --Etxrge (talk) 13:44, 15 December 2007 (UTC)

Photosynthesis is tricky as it is divided into two major parts: the light reactions which are basically water-splitting and energy transduction (light => chemical energy); and the dark reactions which fix carbon into biomolecules. The dark reactions are very clearly anabolic and they're listed in that section. The light reaction splits water into oxygen and electrons with the help of light. Calling that catabolism seems a bit unusual since the term usually refers to the breakdown of biomolecules and the released energy coming from the molecular bonds whereas in this case it is provided by light to force the splitting of the water molecule which requires a lot of energy to do. So in a sense, the light reactions "catabolize" sunlight. The thing they have in common is the generation of energy and electrons in a chemical form that is useful for the cell (ATP, NADPH, NADH). This website also talks about the different ways to generate energy and reducing power (organotrophs, lithotrophs, chemotrophs, phototrophs) under the heading of catabolism. So I guess it is not uncommon to structure it that way.
Btw, glucose is not the end product of photosynthesis. The end product of carbon fixation is a 3-carbon sugar (PGAL) that is used to synthesize different kinds of compounds, including sugars, starch, amino acids, and fatty acids. Many textbooks oversimplify the reaction because it can be nicely balanced for glucose leading to the wrong impression that glucose is the end product, but it is only one of many products that can be made using the end product of photosynthesis. - tameeria (talk) 17:05, 15 December 2007 (UTC)
The article currently says Photosynthesis is the synthesis of glucose from sunlight. That should be changed. --Etxrge (talk) 15:44, 18 December 2007 (UTC)
I agree with all the factual content above, the view of what happens. Even, of course, that glucose is not THE end product of photosynthesis. But the object of this discussion is whether catabolism should be used about photosynthesis. My argument against is that photosynthesis does not divide molecules into smaller parts, which is the definition of catabolism. The referenced website is indeed a good counterargument. I think that web-site is wrong in this respect. Biochemistry, by Campbell and Farrel, 2006, says (p 417) "The breakdown of larger molecules to smaller ones is called catabolism. Small molecules are used as the starting points of a variety of reactions --- Cataboism is an oxidative process that releases energy;" In the gossary: "breakdown of nutrients to provide energy". Biology, by (another) Campbell, 1996, defines Catabolic pathway in the glossary as one "that releases energy by breaking down ..." on p 89 it says that they "release energy by breaking down complex molecules ...". For a process to qualify as catabolism there must be a relation such that the energy is generated by the breaking down of molecules. This is not happening in photosynthesis. Light is not a complex molecule that can be divided into smaller molecules. (Obviously). --Etxrge (talk) 10:40, 16 December 2007 (UTC)
Which chapters/headings is photosynthesis under in these books? I will also look at the textbooks I have at the office on Monday to see how they sort it. I think the term catabolism is tricky as it includes the breakdown of molecules as well as the release of energy. There is no question that the light reactions release energy for the cell to use. I find this definition interesting in this context: Catabolism is an oxidative process that releases energy. The light reaction actually is an oxidative process (water oxidation). But anyway, the article should probably go with whatever is most prevalent in textbooks in terms of sorting it, so let's find out. - tameeria (talk) 15:19, 16 December 2007 (UTC)
In Biology, photosynthesis is in Unit Two, The Cell. In Biochemistry (Campbell, Farrel) photosynthesis is a separate chapter under no other heading. So that gives no help. Here is one more citation: Biochemistry, Mathews, van Holde, 1990, "catabolism, the processes related to degradation of complex substances, with concomitant generation of energy.". Photosynthesis does not degrade complex substances. Neither is generation of energy following from such degradation, in photosynthesis. An easy and correct solution would be to just remove this classification from the article. It is in no way central or essential to the subject. --Etxrge (talk) 17:12, 16 December 2007 (UTC)
Catabolism is an oxidative process that releases energy. Does not seem to be a definition above. It comes a bit after the definition in that context. --Etxrge (talk) 17:10, 17 December 2007 (UTC)
Well, I'm afraid my textbooks aren't really helpful either. Most don't seem to even bother trying to fit photosynthesis in with the other metabolism in terms of catabolism/anabolism. Here's what I found:
  • Raven (Biology): Photosynthesis has its own chapter, following the chapter How Cells Harvest Energy which deals with respiration etc.
  • Starr/Taggert (Biology): Photosynthesis has its own chapter called How Cells Acquire Energy - interestingly, this chapter talks only about photosynthesis. It is preceded by a chapter called Ground Rules of Metabolism and followed by How Cells Release Stored Energy which basically talks about glycolysis and respiration.
  • Campbell/Reece (Biology): Photosynthesis has its own chapter under The Cell (and so do Metabolism and Cellular Respiration) - I think this is probably the same book that you have, just a later edition.
  • Freeman (Biological Science): Photosynthesis has its own chapter under Cell Structure and Function (and so does Cellular Respiration and Fermentation).
  • Brooker (Biology): Photosynthesis has its own chapter under Cell, following the chapter on Enzymes, Metabolism and Cellular Respiration.
  • Alberts (Molecular Biology of the Cell): This book takes a more cellular approach looking at organelle function and photosynthesis is dealt with in the chapter on Chloroplasts and Photosynthesis under Energy Conversions: Mitochondria and Chloroplasts.
The only reference I can find to photosynthesis as catabolism/anabolism is this page which talks about it under Phototrophic Metabolism: "Photosynthesis is a type of metabolism separable into a catabolic and anabolic component. The catabolic component of photosynthesis is the light reaction, wherein light energy is transformed into electrical energy, then chemical energy. The anabolic component involves the fixation of CO2 and its use as a carbon source for growth, usually called the dark reaction." That's the closest match I can find. I can look in more detail again at all those textbooks and see if they try to apply the terms catabolism/anabolism to photosynthesis, but I get a feeling that it might be somewhat of a futile exercise. - tameeria (talk) 21:50, 17 December 2007 (UTC)

I can see the logic of this article and I think it is a good way to present it. Clearly the light reaction have more in common with the catabolic electron transport in mitochondria than anything. On the other hand carbon fixation is clearly anabolic (essentially the reverse of glycolysis) . I prefer to think of photosynthesis as two processes, light reaction and light independent reaction, as it make the whole of photosynthesis more logical. On the other hand I can understand that the overall process of photosynthesis could be regarded as anabolic. i.e. the simplistic notion that photosynthesis is carbon dioxide + water + light energy → glucose + oxygen + water. The problem I have with the latter presentation is it is not really accurate to consider it as one process and can lead to misconceptions like the oxygen is released from the carbon dioxide rather than from water during carbon fixation. David D. (Talk) 23:06, 17 December 2007 (UTC)

Catabolism is a word with a particular meaning, division of complex molecules into smaller molecules. Photosynthesis therefore is not a catabolism. We cannot say it is catabolic because we think it groups well with the reactions that are. It seems the previous editors thought that catabolism means energy production. But it doesn't. All catabolic reactions produce energy. Not all energy-producing reactions are catabolic. --Etxrge (talk) 15:44, 18 December 2007 (UTC)
Good point and as a whole it is certainly anabolic. We could just remove the light reactions altogether. David D. (Talk) 15:50, 18 December 2007 (UTC)
If we do it this way, oxidative phosphorylation is not catabolism either and should be a subsection of non-catabolic energy production. Also, I would still keep that section between catabolism and anabolism rather than moving it below. It makes for a nice logical connection between catabolism and anabolism. - tameeria (talk) 15:59, 18 December 2007 (UTC)
Sounds good. Why don't you test it out to see how it looks? David D. (Talk) 16:09, 18 December 2007 (UTC)
That was quick. I think that new section could do with a short intro to put the subsections into perspective. David D. (Talk) 16:14, 18 December 2007 (UTC)
Good idea. The intro to the catabolism section would need to be rewritten as well to make sense with the new structure. - tameeria (talk) 19:09, 18 December 2007 (UTC)

[edit] Endocrine system?

I was astonished to discover that there is not a single reference anywhere in the article to the role of the Endocrine system in regulating the metabolism. I realize that not all organisms have an endocrine system -- but this is still a major oversight, imo. Surely there should be a section addressing this issue. Cgingold (talk) 13:26, 24 March 2008 (UTC)

There is a brief summary of extrinsic regulation in the second paragraph of the section on "Regulation and control" and insulin is discussed as an example in the third paragraph. Tim Vickers (talk) 16:00, 24 March 2008 (UTC)