Pathways

[merah17]

Hi,

 

i am a newbie in Molecular Biology. I need help to differentiate between Energy Pathways, Detoxification pathways and degradation pathways. Which one is energy pathways, detoxification pathways or degradation pathways? How can i differentiate or identify them.

 

Any help on this is highly appreciated. Thanks

[ecoli]

Like Potter Stewart on Pornography, I know it when I see it.

[CharonY]

Pathways are pathways, i.e. a series of biochemical reaction. How we classify them depends a bit on context. The same pathway could be labeled energy metabolism, but also catabolic. Some names are more specific than others (e.g. catabolic and anabolic pathways can usually be labelled in a rather straightforward manner). In other words, looking at individual reactions alone will not tell it. How they act on the organism, i.e. their physiological role (and your viewpoint) will determine nomenclature.

[alpha2cen]

There are many pathway DB. How about this one?

http://www.genome.jp/kegg/pathway.html

http://web.expasy.org/pathways/

But actual situation, pathway , reaction and mass flux are important to know which mount molecules are in the cell or in the microorgamism product.

And, the reaction rates are differential equations. To solve this problem we have to use supercomputer. Simple 3 or 10 step reactions can solve by using desk top computer.

Edited August 26, 2012 by alpha2cen

[CharonY]

Off topic, but for most reactions we do not have actual in vivo rection rates. Those few that we have are normally based on in vivo assays which can be quite different in actual cells (due to e.g. crowding effects, changes in microenvironment etc.).

[alpha2cen]

But many enzyme reaction constants are known. The reaction in the cell is not simple as you said. It has stereotactic interference by other macromolecules. At the many reaction system calculation we use approximated 1st order reaction equation instead of Michaelis - Menten equation.

[CharonY]

That is my point. Modeling using multi-step reactions are notoriously inaccurate, except for a few very well known reactions (such as glycolysis, for example) for a number of well-characterized organisms. Those models tend not to be developed by using reaction constants, but rather empirical data (or if they do, it requires heavy tweaking). And again, for many we do not know. In fact, depending on organism, we do not even know the function for the majority of them.

[Jens]

Hi,

back to the original question.

I agree with the others it is somewhat arbitrary and might not make sense to differentiate. However if you still stick to differentiation I would try the following:

 

energy pathways: A pathway that finally leads to production of ATP out of ADP.

Examples:

- ATP production via light in purple bacteria

- most pathways in Eukarya which oxidize molecules to produce ATP (mostly via NADH)

 

detoxification pathways: A pathway that ensures removal of a molecule out of the cell without gaining energy out of it

 

degradation pathway: a pathway that makes smaller molecules out of bigger ones.

Examples:

- digestion in animals degrades nutrition without gaining energy, just for the purpose of producing the buidling block molecules which are than transported into the body.

- energy pathways of organisms that oxidize biomolecules (e.g. like fungis)

 

so the terms are not mutually exclusive.

 

Rule of thumb:

At least in Eukarya the usage of the NAD⁺/NADHsystemis a good hint for an energy pathway (a mainly catabolic pathway), while the usage of the NADP⁺/NADPH system is a good hint for an anabolic pathway. There is no miracle about it, this is simply to optimze reaction speed. The concentration of NAD⁺ is much higher than the concentration of NADH (a factor of 100 to 1000) and the concentration of NADP⁺ is lower than the concentration of NADPH (a factor of 0.1 to 0.01).

Edited September 2, 2012 by Jens

[CharonY]

energy pathways: A pathway that finally leads to production of ATP out of ADP.<br style="font-size: 12.727272033691406px; line-height: 16.363636016845703px; background-color: rgb(248, 250, 252); ">Examples:

 

 

Actually, I think this is a prime example of a nomenclature being arbitrary. For instance, Glycolysis could be seen as an energy pathways under this viewpoint (it generates ATP) but also as a simple catabolic pathways funneling carbon into the TCA cycle for other, anabolic processes.

The TCA cycle is not directly involved in ATP production, yet it produces reduction equivalents, which are crucial for oxidative phosphorylation . I am aware that this complicates matter, sometimes unnecessarily so. But it also highlights why biology is complicated: things are interconnected. A biochemical view tends to cut-off at a certain point in order to understand a certain sub-process (and I presume, to retain sanity). In order to understand physiological consequences of these elements their interactions and resulting emergent properties have to be understood (though we have preciously few tools and methodologies to achieve that).

[Jens]

Actually, I think this is a prime example of a nomenclature being arbitrary. For instance, Glycolysis could be seen as an energy pathways under this viewpoint (it generates ATP) but also as a simple catabolic pathways funneling carbon into the TCA cycle for other, anabolic processes.

 

Hi. I agree. This is exactly what I meant with that the terms are not mutually exclusive.

Personally, I do not like this nomenclature, since it produces artifical problems. I just wanted to help.

 

The TCA cycle is not directly involved in ATP production, yet it produces reduction equivalents, which are crucial for oxidative phosphorylation.

 

Hello CharonY. I know. This is why I have written "mostly via NADH".

 

 

[merah17]

hey guys,

 

Thanks so much for your responses and suggestions on this. i am looking into it now.

[Jens]

Hi CharonY,

 

Actually I think sometimes it is worth to distinguish catabolic from anabolic pathways (but not between degradation and energy pathways).

But not to make students crazy by asking it in a test.

 

I have already a few times seen artifical metabolic pathways in scientific literature which clearly look like laboratory artifacts by chaining single reactions together which are never active in a cell because they are not in the same compartiment or not active at the same time. (only to see a few years later somebody actually proving that this is not working like this in living plants / animals).

So beeing aware of the gradient between NAD and NADP helps in a way to be especially cautious if they are combined in the same pathway.

Of course metabolism is a network and there are no 100% design principles, since it is not designed.

 

And yes: Metabolism is a network.

 

Example:

As everybody in biosciences knows humans cannot synthesize the essential amino acids. However, the thing is much more interesting, if you look at the details: Actually if you go through all the synthesis pathways of the non-essential amino acids and remove all the enzymes which are anyhow already there, because they are needed for catabolism of the amino acids, you make a surprising (at least to me) finding: There is only one amino acid left. The only amino acid for which there are specific anabolic enzymes is Proline. Why did I personally found this interesting? Proline is extremely common in the protein collagen, which is the most common protein in animals and not needed in plants at all. So retaining (or gaining) the synthesis capability for Proline is especially important, since this is the only real issue, if you just eat plants. It is always amazing to see how optimized nature is. For all other non-essential amino acids you can say that humans can synthesize them just by chance.

 

Jens

Edited September 7, 2012 by Jens