Talk:Metabolic pathway

Untitled

the first external link (dmoz.org) isn't functioning. does someone know where that page has been moved to?

Wiki Education Foundation-supported course assignment

This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Sazhnyev. Peer reviewers: Lisa96liu.

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Some Questions

Is it really necessary to have such a large space between the image and the next section "Cellular respiration". According to whoever added those spaces it was done for a 17" screen. I have a wide-screen computer, does this huge space still exist for anyone else?

Also, what exactly the point of the "Cellular respiration" section, if it is even that. As of now it's just a bolded title. Does the title and text following it refer to 'Metabolic Pathways and Cellular Respiration'? It's tite should be more specific. I'm also not sure that all of the text following the title actually belongs there, considering the fact that Photosynthesis and Chemosynthesis are certainly not processes of Cellular respiration. Does that make them part of a whole new section? Could someone who knows about this topic help figure this out as I am certainly no expert. --France3470 06:16, 7 May 2007 (UTC)

I have removed the huge space.It is not necessary. Shrimp wong (talk) 04:47, 14 February 2008 (UTC)

Reversibility

If "all reactions are chemically reversible," why do charts of metabolic pathways often display arrows that aren't double-ended? I think "all" should be changed to "most." Unfree (talk) 01:12, 30 November 2008 (UTC)

All chemical reactions are reversible but to varying degrees. The threshold where one decides that a reaction is considered irreversible is arbitrary. It might be better to simply say that "all reactions are chemically reversible to varying degrees". --Rhodydog (talk) 19:38, 6 January 2009 (UTC)

Flux Generating Step

I noticed the phrase "flux generating step" near the start of the article, what exactly is a flux generating step? I think such terms should be defined, unfortunately I've no idea what it is so I can't help. --Rhodydog (talk) 19:39, 6 January 2009 (UTC)

definitions

Should there be definitions to distiguish the words pathway, superpathway and map? The word superpathway which features heavily in metacyc and all those who cite it is quite handwaving, hence the question. --Squidonius (talk) 02:21, 29 May 2011 (UTC)

Biochemical pathway

See my comment in the talk of metabolic network. The two articles are basically overlapping and both slightly wrong. This article does not restrict itself to metabolism, and does not talk only of pathways, a notion that is now attached to directionality. Nowadays, one would talk about metabolic networks and signaling pathways. Sometimes of biochemical pathways/networks. But metabolic pathways is a notion that is fading rapidly because imprecise and slightly wrong (because of directionality). Nicolas Le Novere (talk) 13:16, 16 November 2011 (UTC)

Flux Generating Step

Top of page: "To initiate another metabolic pathway, called a flux generating step" - There is not such thing as a flux generating step, see Kacser and Burns, 1973 on Control of Flux. Rhodydog (talk) 18:46, 14 May 2014 (UTC)

Plan for editing the page

I am currently planning to edit this page, so I compiled a list of references I plan to use. Any feedback is greatly appreciated.

Bibliography of References

1. Fundamentals of Biochemistry.
2. Major Metabolic Pathways and Hormone Production in Unstimulated Monolayer Cultures of the Rate Anterior Rituitary.
3. Metabolic Pathways of Glycerol Dissimilation.
4. The Quarterly Review of Biology.
5. Molecular Biology: Principles and Practice.
6. Life: The Science of Biology.
7. Organic Chemistry.

References

Sazhnyev (talk) 05:45, 28 April 2016 (UTC)

@Sazhnyev: All good sources. I also suggest online version of MBOC4 and Biochemistry5 as useful general references. They're often useful because they're fully available online. T.Shafee(Evo﹠Evo)^talk 11:04, 28 April 2016 (UTC)

@Evolution and evolvability and T.Shafee(Evo﹠Evo): Thank you for your suggestions. Those are helpful resources. Sazhnyev (talk) 11:46, 5 May 2016 (UTC)

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Outline for Editing the Article

I propose the following strategy for organizing this page and incorporating new material: I will add new sections and categorize them based on the classes and subclasses of metabolic pathways. It is important to expand on the topic by promulgating on the different types of pathways that occur in eukaryotes and prokaryotes. Furthermore, I will specify and briefly describe several important metabolic pathways and the roles they each play in the cell.

In addition, the provided information about metabolic pathways in this article lacks proper structure in order to be efficient in conveying that information; hence, I will rearrange some of the already mentioned material to allow for comfortable reading and a better conceptual understanding.

Finally, I intend to add proper citations for the information provided to allow for a smoother verification of the stated facts.

Any feedback on my proposition is greatly appreciated.

Sazhnyev (talk) 12:36, 5 May 2016 (UTC)

New map of Metabolic Pathways

I've replaced the map of metabolic pathways to a new one. Feel free to comment here or at Wikipedia_talk:WikiProject_Molecular_and_Cell_Biology. Chakazul (talk) 17:43, 10 June 2016 (UTC)

For reference, the old interactive image was {{Metabolic pathways}}, and the updated one is {{Metabolic metro}}. T.Shafee(Evo﹠Evo)^talk 10:23, 11 June 2016 (UTC)

I am impressed by the level of detail of the new infographic. Additionally, I've placed the old map at the end of the section titled External Links, for it provides further visual elaboration of the metabolic pathways. Sazhnyev (talk) 05:42, 12 June 2016 (UTC)

Glucuronate metabolism Pentose interconversion Inositol metabolism Cellulose and sucrose metabolism Starch and glycogen metabolism Other sugar metabolism Pentose phosphate pathway Glycolysis and Gluconeogenesis Amino sugars metabolism Small amino acid synthesis Branched amino acid synthesis Purine biosynthesis Histidine metabolism Aromatic amino acid synthesis Pyruvate decarboxylation Fermentation Fatty acid metabolism Urea cycle Aspartate amino acid group synthesis Porphyrins and corrinoids metabolism Citric acid cycle Glutamate amino acid group synthesis Pyrimidine biosynthesis All pathway labels on this image are links, simply click to access the article. A high resolution labeled version of this image is available here.

Carbon fixation Photo- respiration Pentose phosphate pathway Citric acid cycle Glyoxylate cycle Urea cycle Fatty acid synthesis Fatty acid elongation Beta oxidation Peroxisomal beta oxidation Glyco- genolysis Glyco- genesis Glyco- lysis Gluconeo- genesis Pyruvate decarb- oxylation Fermentation Keto- lysis Keto- genesis feeders to gluconeo- genesis Direct / C4 / CAM carbon intake Light reaction Oxidative phosphorylation Amino acid deamination Citrate shuttle Lipogenesis Lipolysis Steroidogenesis MVA pathway MEP pathway Shikimate pathway Transcription & replication Translation Proteolysis Glycosyl- ation Sugar acids Double/multiple sugars & glycans Simple sugars Inositol-P Amino sugars & sialic acids Nucleotide sugars Hexose-P Triose-P Glycerol P-glycerates Pentose-P Tetrose-P Propionyl -CoA Succinate Acetyl -CoA Pentose-P P-glycerates Glyoxylate Photosystems Pyruvate Lactate Acetyl -CoA Citrate Oxalo- acetate Malate Succinyl -CoA α-Keto- glutarate Ketone bodies Respiratory chain Serine group Alanine Branched-chain amino acids Aspartate group Homoserine group & lysine Glutamate group & proline Arginine Creatine & polyamines Ketogenic & glucogenic amino acids Amino acids Shikimate Aromatic amino acids & histidine Ascorbate (vitamin C) δ-ALA Bile pigments Hemes Cobalamins (vitamin B12) Various vitamin Bs Calciferols (vitamin D) Retinoids (vitamin A) Quinones (vitamin K) & tocopherols (vitamin E) Cofactors Vitamins & minerals Antioxidants PRPP Nucleotides Nucleic acids Proteins Glycoproteins & proteoglycans Chlorophylls MEP MVA Acetyl -CoA Polyketides Terpenoid backbones Terpenoids & carotenoids (vitamin A) Cholesterol Bile acids Glycero- phospholipids Glycerolipids Acyl-CoA Fatty acids Glyco- sphingolipids Sphingolipids Waxes Polyunsaturated fatty acids Neurotransmitters & thyroid hormones Steroids Endo- cannabinoids Eicosanoids Major metabolic pathways in metro-style map. Click any text (name of pathway or metabolites) to link to the corresponding article. Single lines: pathways common to most lifeforms. Double lines: pathways not in humans (occurs in e.g. plants, fungi, prokaryotes). Orange nodes: carbohydrate metabolism. Violet nodes: photosynthesis. Red nodes: cellular respiration. Pink nodes: cell signaling. Blue nodes: amino acid metabolism. Grey nodes: vitamin and cofactor metabolism. Brown nodes: nucleotide and protein metabolism. Green nodes: lipid metabolism.

More Citations Needed

There are a lot of claims in the Overview section that are most likely true, but are not properly cited. For instance, the article claims that "Glycolysis was the first metabolic pathway discovered," but it does not provide a source. Avevanduz (talk) 22:30, 19 March 2017 (UTC)

General Comments

The last paragraph of the first section of this article(Metabolic pathway) is missing a word and does not make sense as it stands: "The end product of a pathway may be used immediately, initiate another metabolic pathway or be stored for later use." In addition to this minor grammatical issue, as noted by other users, this article is missing proper citation in some areas. Over all this article could be expanded to discuss more aspects of the full chart for metabolic pathways. Wasso392 (talk) 13:06, 21 March 2017 (UTC)

Number of metabolic pathways?

How many metabolic pathways are know? a) Completely? b) Partial?

How many metabolic pathways are there, that are unknown - estimation?

What is the number of metabolic pathways in the brains vs. number of metabolic pathways in the rest of the body? — Preceding unsigned comment added by 92.192.14.162 (talk) 08:29, 15 July 2017 (UTC)

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1 st Para. Do these sentences make sense ?

1. "In most cases a metabolic pathway, the product of one enzyme acts as the substrate for the next."

Should it not be "In most cases of a metabolic pathway"

2. "However, set products are considered waste and removed from the cell."

    What are set products ? Should it not be "some products"  — Preceding unsigned comment added by Ruskin (talk • contribs) 08:57, 10 March 2018 (UTC) 

There is no formal definition of a metabolic pathway on the page

At present, it says: "In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell.", but it's more than that. A pathway is a linked series of reactions that can sustain a steady state. See "A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks", Schuster and Fell and Dandekar, Nature Biotech, 2000, 18, 326-332. These authors define pathways in terms of elementary modes which is a nice formal way of defining what exactly a metabolic pathway is. Rhodydog (talk) 22:15, 16 April 2018 (UTC)