Tuesday, 7 January 2020

metabolism - Breakdown of energy expenditure at the level of a single cell


The metabolic rate measures how much energy an organism expends over a unit of time. Its breakdown for the human body in terms of its functions is well documented : so much for the heart, for the brain, etc.


In West et al, 2002 I have found an estimate for the metabolic rate of a single cell. But how does this breakdown in terms of elementary functions in the cell?



E.g., how much of the energy made available from nutrients is used in the process of replicating genome, of expressing proteins, of trafficking...?


Following Jeremy Kemball's link suggestions, I find in this paper the fraction of ATP consumption for the following processes:


Protein synthesis    0.34
Na+/K+ ATPase 0.16
Ca2+ ATPase 0.17
RNA/DNA synthesis 0.25
Unidentified 0.09

(which adds up to 1.01 rather than 1 for spurious reasons). Their measurement is indirect, based on $O_2$ consumption for an assumed steady-state regeneration of ATP. I wonder how GTP-based processes are accounted for? Or are they negligible compared to ATP ones?


This is for a specific cell type, rat thymocyte, is there a reason to expect that this will be hugely different for say a fibroblast? Also, they stimulate their thymocyte with concanavalin A. I understood they are not getting RNA/DNA consumption signal without Con-A, but didn't get why it would be so.



Finally, what would be in the remaining 9% ? One candidate for ATP consumption suggested by Jeremy Kemball is actin turnover, I guess it fits only in the "unidentified" line. Tubulin turnover is a GTP process, not sure about intermediate filaments (do they turnover?). All ATP-molecular motors (myosin, kinesin, dynein at least?) have to be there too. What else?


I am particularly interested in the total amount of ATP energy that goes to myosin.



Answer



I was musing on this and did some strange googling, and have some ballpark figures for a bunch of different organisms. It's far from a complete answer but it's at least a start, and all this won't fit in a comment.


DNA replication, I assumed, was a huge metabolic drain on the cell. Turns out that is far from the case. Many helicases are passive, requiring no ATP, and the amount of ATP-equivalent triphosphates to synthesize the entire genome is pretty small compared to the amount that gets used and recycled every day.


According to these guys humans go through their bodyweight in ATP every day, about 50% of which is actin turnover, and 30% is synthesis (60% or more in rapid bacteria). Proteins cost about 4-5 ATP per AA to break down and rebuild.


You're not going to get a really good general breakdown, I don't think, but in crop plants or E. coli there are numbers for this, sort of. A lot of them are based on indirect measurements of protein uptake/turnover and ATP cost per AA or BP. They're fascinating but insane and often contradictory.


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