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Do we have the complete metabolic map for humans? Do we know from the genome what enzimes are expressed and what each enzime does?

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closed as too broad by David, mdperry, The Last Word, kmm, AliceD Nov 21 '18 at 10:16

Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. Avoid asking multiple distinct questions at once. See the How to Ask page for help clarifying this question. If this question can be reworded to fit the rules in the help center, please edit the question.

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    $\begingroup$ Simple rule of thumb: If your question is about biology and contains the word "complete", the answer is "no". $\endgroup$ – Armatus Oct 28 '18 at 1:12
  • $\begingroup$ @Amatus. An exception, perhaps. Do we know the complete DNA sequence of any organism? Or the complete amino acid sequence of any protein? All great questions in their time. $\endgroup$ – user1136 Oct 28 '18 at 11:39
  • $\begingroup$ As regards the second part of your question, I think the answer in many, many cases is 'no'. What is the role of brain lactate dehydrogenase, for example? Exactly what reaction does it catalyze and when? What is the role of brain alcohol dehydrogenase (both ethanol dh and the so-called chi-adh)? What enzyme reduces succinic semialdehyde to gamma-hydroxybutyrate (the 'date-rape' drug G)? No shortage of candidates on the last one, but which one is it? $\endgroup$ – user1136 Oct 28 '18 at 11:45
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As Armatus notes, we don't know ALL human metabolites and the enzymes + metabolic reactions that produce them. Identifying small molecules is hard and metabolism is dynamic, it depends on what is being fed into the system.

The virtual metabolic human (VMH) is an attempt at compiling the information that we do know. You can read their paper here. The human build currently includes (and links together);

  • 13 543 metabolic reactions
  • 4138 metabolites
  • 3695 genes (enzymes)

It also attempts to compile all known metabolic reactions that result from the gut microbiome, nutritional metabolic pathways and genetic diseases that alter metabolism. Everything is linked via stable identifiers which is a real challenge.

The human metabolic database (HMDB) is also very good. It contains more metabolites than the VMH as it includes many partially or poorly characterised metabolites. The HMDB is really useful if you are working to identify metabolites while the VMH focuses on how they connect to one another.

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Roche has a pretty amazing map of metabolic pathways in the cell. You can find it here. During my Bachelor degree I contacted Roche and the mailed one to me for free (in a large poster format).

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    $\begingroup$ Amazing — Yes. Useful, other than wall decoration? The problem with such composite maps is that they don't distinguish between species — never mind tissues. And they mislead students into thinking that there is a mythical "cell" in which all the pathways are present. $\endgroup$ – David Oct 29 '18 at 8:37
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The answer is not yet. The sequencing of the human genome, considering its size (@ 3.2 bbp), and contrary to what's been hyped in media, is not the end of the quest for understanding the human body. On the contrary, it is only the first and the simplest step in the elucidation of the intricate workings of the human body. Even though a lot has been accomplished already, all of those tons of accomplishments still barely scratches the surface.

I can safely estimate that human genome sequencing represents less than 1% of the work that lies ahead, enormous work required to make sense of the whole base pair sequence. Each succeeding step multiplies the complexity exponentially, and so, even considering the exponential advancement in technology, it is again safe to say that at the rate things are going, the complete elucidation of the human metabolome and metabolic pathways cannot be accomplished within the next 50 years.

To get an idea of the complexities involved, one only has to consider the next step after genome sequencing; the next step is to identify all the human genes making up the coding sections of the genome, which account for less than about 2% of the human genome. Most genes do not transcribe into RNA in a straightforward manner; introns (which separate the exons that hold the coding sections), have to be spliced out; then the exons making up the code for the protein must be joined together. All of that accountws for less than 2 % of the human genome. The rest is non-coding DNA, the function of most of which hasn't yet been figured out.

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  • $\begingroup$ You don't appear to mention metabolism in your answer. I thought that was what the question was about. $\endgroup$ – David Nov 1 '18 at 18:42
  • $\begingroup$ I did mention it, albeit indirectly; i used the words 'metabolome' and 'metabolic pathways' instead, because that was the post was asking for, to wit: "Do we have the complete metabolic map for humans?". Oftentimes, an entire metabolic pathway has to be determined before the function of a single enzyme can be known with reasonable certainty. $\endgroup$ – lomdemanil Nov 4 '18 at 5:19

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