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Quizzing the Anonymous - Why do we pee?
April 21st, 2008
01:47 am

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Why do we pee?
The textbook answer is that animals need to urinate in order to excrete extra salts and nitrogen metabolites from their blood. The ammonia in aquatic animals, insoluble uric acid in birds, diapsid reptiles, and insects, and soluble urea in amphibians and mammals are the means of disposing the N generated by transdeamination of unwanted amino acids. Terrestrial animals stay away from the ammonia as it takes a lot of water to dilute it to reduce toxicity. The familiar yellow color of urine is from a product of heme breakdown, urobilin, which is a minor component. This sounds reasonable, but urination is a deep mystery. The mystery is twofold: the physiology of peeing and the biochemistry of urea metabolism. The more one thinks about these matters, the stranger it looks. A visit to a restroom can and should be food for thought.



If the goal of peeing is disposing of waste, then having a separate urinary tract seems unnecessary. Most of animals do not have it. The vent in birds, the Malpighian tubules in insects, and the cloaca in reptiles, amphibians, marsupials, and monotremes combine all of the excretionary functions in one neat unit, and it works just fine. The turtles can even respire through their cloaca! It is not too obvious why the separate urinary tract exists in placental mammals and bony fish, and no other animal.

It makes even less sense, from the standpoint of waste management, to store the toxic waste in a bladder. Birds do not have a bladder and do very well without it. In mammals, the bladder seems to have little other use than storing urine for the purpose of marking territory. It goes without saying that one can find other ways of marking territory.

In our amphibian ancestors, the bladder was used to conserve fluids: when in water, the frog’s bladder rapidly fills up with urine. This water is reabsorbed into blood on dry land, to replace water that is lost by evaporation. Already in reptiles this function of the bladder has been lost. As the mammals branched off the reptile tree before the latter developed their efficient uric acid excretion (which requires very little water), we still possess the primitive and inefficient urea excretion metabolism of the amphibians. Actually, our (amphibian) way of producing the urea from ammonium and bicarbonate ions, by ornitine-urea cycle, is used by only one other living animal, the coelacanth. Most other vertebrate and invertebrate species make the urea from uric acid that is formed from purines, which is a much better way of disposing N. Biochemically, we are living fossils. We can make uric acid, but we do not rely on it. Some people can make more of it; those unlucky few develop gout.

The need of disposing of the ammonia is understandable, in view of its high toxicity, but the production of urea is not. The common way of disposing NH3 in Nature is converting it to nitrate (by aerobic nitrifying/NH3-oxidizing bacteria) which is converted to N2 by anaerobic denitrifying bacteria or directly converting it to N2 (by anaerobic anammox bacteria); there is a global operation of this sort by marine prokaryotes. Actually, most of the N2 we breathe has been made by the anammox bacteria. Getting rid of the gaseous N2 seems to be a much easier solution than production of urea and/or uric acid and the trouble of their disposal. Furthermore, the ammonia can be excreted by volatilization, and this is the main way of N excretion in snails, crabs, and isopods. The fish also flash most of their ammonia through their gills rather than kidneys; the latter serve mainly for regulation of the osmotic pressure. Livelock made a big deal out of urea/uric acid excretion by land animals: he made an elaborate argument that in this way N returns in a fixed form ready to be reabsorbed by plants. The urination proves that animals and plants form a harmonious union: peeing is ecologically responsible way of returning the surplus of N, as opposed to N2 evolution, which would be selfish and irresponsible. That may be so, but the bacteria do the “irresponsible” thing anyway, and animal urination has almost no effect on the global turnout of fixed N. I seriously doubt that we pee to restore harmony to Nature. Some ruminants, actually, behave rather “irresponsibly”: they convert ammonia to urea and leak the urea to their rumen, where it is degraded back to ammonia by symbiotic bacteria. This ammonia supports protein synthesis in these bacteria and also serves as the feed for nitrifiers present in the gut.

Furthermore, one may ask, how is it that we (the animals) need to get rid of N which is such a precious commodity? The problem is a major defect in our design: we can store the excess carbohydrates and lipids, but – unlike the plants - we cannot store the excess amino acids. So any excess of the latter has to be catabolysed to ammonia and/or glutamate. This is tremendous waste of a good thing, and the lack of such storing mechanism is evolutionary scandal. An idea that I have about this puzzling deficiency is that it would be very useful to symbiotic phototrophs, such as the zooxantellae in corals, as this inexplicable deficiency is precisely what forms the basis of mutualistic trade (N fertilizer exchanged for carbohydrates). If the animals began as symbionts with algae, as I argued elsewhere, the selfish storage of amino acids and/or the excretion of N2 would be penalized by their photosymbionts, so it is possible that we were forced to urinate by the selective pressure of such symbiosys. What Lovelock considers to be holistic unity of land animals and plants could be the consequence of mandatory co-operation between the proto-animals and their photosymbionts. Such symbiosys was the only realistic chance to survive the long periods of anoxia at the end of the Cryogenian. Perhaps we are peeing because such was our function back then, 600-700 Mya…

Said that, there are marine invertebrate animals that accumulate amino acids (glycine, alanine) in their intracellular compartments, although these amino acids are accumulated exclusively to… counterbalance the osmotic pressure of sea water (i.e., our core deficiency is still there). It turns out that our distant cousin the coelacanth uses the urea for the same purpose. So it appears that the urea metabolism originally served a different purpose than peeing: the osmoregulation. Then in some lobed fish that happened to be our ancestors it became also a way of ammonia disposal; though, it was not really a disposal, as they actually needed the urea. The amphibians that descended from these fish inherited their urea metabolism, although they had absolutely no need for osmoregulation. They compensated for the inherent deficiency of the urea excretion by using bladders for water retention. We inherited both this inferior metabolism and the useless organ from our dry land dwelling reptilian ancestors. As the rest of the tetrapods switched to a better way of dealing with the N waste, the mammals stubbornly stuck to the antique practice of urea peeing. At some point they began using pee for marking and signaling, and that transformed peeing into an art form. Having a full bladder of dilute urea solution became the necessity of social life.

Why do we pee?

PS: Further reading: http://jeb.biologists.org/cgi/reprint/198/2/273.pdf

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From:vdinets
Date:April 21st, 2008 05:06 pm (UTC)
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Very interesting!
Of course, desert mammals have been under intense pressure to produce more and more concentrated urine - and the result is that even a few drops of cat urine will give your carpet its smell forever...
But the purpose of bladder is pretty obvious. The alternative would be passing urine constantly - just laying a perfect scent trail for predators.
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From:shkrobius
Date:April 21st, 2008 05:18 pm (UTC)
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So that's why... It may be obvious to you, but it did not occur to me. I guess you are right, though it is not too clear to me, why mammalian predators would retain their bladders and how flightless birds go around this problem. On the other hand, that would explain why flying birds do not care. I still wonder if the function is mainly chemical communication. Amazingly, there is almost no literature on the evolution of urinary bladder - and there are thousands of papers on swim bladders and kidneys.

Do you know whether other animals than mammals use urine for (1) territory marking and (2) estrus communication? I cannot find anything, and this looks very odd. Are these unique mammalian traits?
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From:vdinets
Date:April 21st, 2008 06:31 pm (UTC)
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Mammalian predators start their lives as small and vulnerable. Besides, constant passing of urine, especially during sleep, would interfere with thermoregulation. Birds don't pass urine constantly, either. I wonder if u. bladders of whales show any sign of reduction (I should know that, but I don't).
I'm not aware of any other animals having estrus in mammalian sense, but I suspect terrestrial amphibians (lungless salamanders, poison-dart frogs etc.) could use urine for scent marking. No idea if they really do.
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From:shkrobius
Date:April 21st, 2008 07:23 pm (UTC)
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They do not. I got your point, but I am not sure about thermoregulation. I gotta check this out.
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From:vdinets
Date:April 21st, 2008 08:23 pm (UTC)
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Well, just imagine an Arctic fox sleeping in its snow den and constantly peeing...
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From:eta_ta
Date:April 21st, 2008 06:14 pm (UTC)

ot

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Need your assistance here.
I refuse to adhere to the author's view that development of morality is contradictory to theory of evolution; still, can't provide coherent reasoning. I think you wrote something on the subject in the past - or is it tooo broad for you?
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From:shkrobius
Date:April 21st, 2008 07:19 pm (UTC)

Re: ot

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It is a bit too broad, but I can suggest you a book where you will find the arguments you need to strengthen your case. It is "The origin of virtue" by M. Ridley
http://www.amazon.com/Origin-Virtue-Matt-Ridley/dp/0670863572
Ridley reviews various evolutionary theories of altruism, co-operation, and conformism. I think you will enjoy this book; it is exceptionally well written and goes over a lot of different theories; it is also thin and it has no technical slang in it. The "burning house" situation is explicitly examined there. Perhaps your opponent might be interested in reading it, too.
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From:eta_ta
Date:April 21st, 2008 07:29 pm (UTC)

Re: ot

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many thanks
From:(Anonymous)
Date:April 21st, 2008 08:53 pm (UTC)

Re: ot

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'eta-ta', not quite as pretty as your other name, but anyway, you might also like to try Ridley's "The Red Queen: Sex and the Evolution of Human Nature". A fascinating book which I will now have to re-read so that I am ready for your criticisms. However, I should warn you that the neo-Darwinist arguments used to explain altruism are almost painful to behold in their extreme contortions! Anyway, if Richard Dawkins says that morality does not exist in a Darwinian world, who am I to argue?

"Be warned that if you wish, as I do, to build a society in which individuals cooperate generously and unselfishly towards a common good, you can expect little help from biological nature. Let us try to *teach* generosity and altruism, because we are born selfish." 'The Selfish Gene', ch.1, p.3.

David Duff - http://duffandnonsense.typepad.com
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From:eta_ta
Date:April 21st, 2008 09:01 pm (UTC)

Re: ot

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David, it's not as pretty only because you don't know Russian (hint: it's a pun: a nod to a line from our famous poet + my nickname + a letter from my last name)
Anyway,
I appreciate the reading sugestion.

Have to tell you, though - you might decide never talk to me again when you learn that I consider altruism, as a guiding principle, appaling and people who constantly demand others to be altruistic - suspect. What's more, I'm a prime example of what's called a "Randoid". My apologies.
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From:shkrobius
Date:April 22nd, 2008 12:23 am (UTC)

Re: ot

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If you liked the Red Queen, "The Origin of Virtue" is a better book and it has a broader scope. BTW, I do not see why is it totally impossible to explain morality, altruism, unselfshness, cooperation, conformism, etc. using the existing evolutionary theories. Your own body is "a society in which individuals cooperate generously and unselfishly towards a common good." If it troubles you that these individuals are genetic clones, consider Myxomycete slime molds. Genetically varied individuals get together on their own accord, form a slug, move out, form a fruiting body, and multiply. Ca. 10-30% of these individuals selflessly die in the process. Why isn't this "a society in which individuals cooperate generously and unselfishly towards a common good?" Dawkins may believe that morality cannot emerge in a Darwinian world; he is entitled to his opinion. If morality does not emerge in his version of the Darwinian world, this only means that we do not live in such a world, and better theories of evolutionary transitions are required. Claiming that no such theories are possible is arrogant nonsense.
From:(Anonymous)
Date:April 22nd, 2008 02:16 pm (UTC)
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eta-ta: I share your suspicion of anyone who urges *others* to indulge in altruism, but the word covers a huge variety of actions and no doubt some of them prove beneficial, others not. However, the point is that altruism exists, and thus requires an explanation..

Shkrobius: I have a sinking feeling that you are much more informed on the details of biology than me. Even so, I suggest, gently, that you may be using words in the wrong context. Microbe 'A' does, blindly and unknowingly, whatever microbe 'A' is supposed to do. Likewise, microbe 'B' does what it is supposed to do. Their combined efforts may (or may not) provide a slight advantage to organism 'X'. To suggest that either 'A' or 'B' is altruistic (or even "selfish", as Dawkins calls it) or to suppose that they are co-operating, is to imply a degree of self-knowledge by microbes that is unwarranted. It is true (I believe) that some insects (bees? ants?) apparently(!) sacrifice themselves in order to protect others of their kind, but the word "sacrifice" is not appropriate. They just do what they do and I suspect that in the unlikely event of them being given a choice, they would not do it!

David Duff http://duffandnonsense.typepad.com/
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From:shkrobius
Date:April 22nd, 2008 02:52 pm (UTC)
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David, the problem with this argument is that I can furnish exactly the same kind of reasoning about humans, e.g. you. I'd argue that you do what you do and your actions have little to do with what you call your self-knowledge, and that the latter, including morality, is ad hoc rationalization of what you are doing anyway that is supplied by your cortex. Prove me wrong. As for the "microbes," the amoebas that form the fruiting body of the slime mold have their choice of joining the others or not; it is free choice, and many decide not to join and try their own luck. You deny them self-awareness, but I do not know on which grounds. Their genomes are 5-10 times larger than ours; we simply do know what are they capable of, and in some ways they are more complex than us. They can recognize each other, they can communicate with each other, so they de-facto behave as if they have the concept of the self. I can be no more certain about them having no self-awareness as about you. It is not written on your forehead that you are self-aware; it is my conjecture based on the hypothesis that you are just like me. Well, in many regards these "microbes" are like me, too. Why should I deny them self-awareness and intelligence? There is, actually, lively debate on this topic. I once had a post on the intelligence of molds. Look at the references given therein
http://shkrobius.livejournal.com/34729.html
They do mazes no worse than mice.

Ants and bees do sacrifice themselves for the benefit of their colony and I do not see in which way the use of this word is inappropriate. I mean, suppose you are a Martian observing a city defending itself. You look at the action and take field notes. Then you look at the anthill and take notes again. The notes would be pretty much the same. What would be the conclusion of the Martian?
From:(Anonymous)
Date:April 22nd, 2008 03:40 pm (UTC)
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shkrobius: Oh dear! It's difficult enough arguing the pros and cons of human 'free will' without worrying about amoebas!

However, my proposition is that in a Darwinian world altruism/morality cannot exist. If I read you correctly you are suggesting that it does exist in amoebas and ants, etc. For an act to be altruistic it is absolutely necessary that the 'thing' being altruistic has a choice, that is, an awareness that it need not take the altruistic action. Also, it must be aware that the action it is taking is a danger to itself, and the only likely result is a benefit to another creature. Can you say that of an amoeba? I think not.

Now, I admit that I am no biologist but I always understood that that level of 'sophisticated' thinking requires a large brain, certainly larger than that of an amoeba or an ant. Even so, to test your hypothesis let us consider the animals who do possess larger brains and I see no signs of altruism in their behaviour except that a parent will attempt to deflect a threat to its young - but hardly ever giving up its own life in the effort.

Are you sure that the scientists observing the amoebas are not simply placing *their* human values on *their* interpretations of the organisms' behaviour?

David Duff http://duffandnonsense.typepad.com/
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From:shkrobius
Date:April 22nd, 2008 04:23 pm (UTC)
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Not only I cannot say it about amoeba, I cannot say it about you. Moreover, I cannot say it about the hero who saved a child from a burning house. It is not difficult to represent this act as yet another instance of reciprocal altruism, kin selection, groupishness, status enhancement, etc. Morality does not belong to a Darwinian world only in a sense that it does not belong to the world, period. It exists in our heads and serves as rationalization of our altruistic acts. What causes these acts may not have anything to do with their rationalizations. The hero might be convinced that he had freely chosen the right thing to do, but he would be utterly unable to explain, clearly and logically, why is it the right thing to do. The more you ask, the more declarative answers you'll hear. Our self-awareness is shallow and it does not go to the core issue of why people behave altrustically. The fact is that they do act this way, and so an explanation is due. If evolutionary theory explains it that's fine; if not, we still need a theory to explain it. Claiming that no such explanation is possible is big talk.

I do not see why it takes sophisticated brain to make the kind of deductions you suggest. In economics games, 10 lines of code represent free agents that are capable of making exactly such decisions.

As for parents giving life for their children, how about bugs? It is not uncommon that one of the parents is used to lay eggs inside its body and then left as the food supply for their young. You may say that it is instinct rather than altruism. Perhaps. But I can say exactly the same about humans; that altruism is instinctual and hard-wired. And even that would be debatable. Only the tiniest fraction of the tiniest fraction of human parents gave up their lives for the lives of their children. With the mortality rate of 80%, such heroics made very little sense. We call heroes heroes not because they are norm but because they are exceptions. We selfishly want other people behave altruistically, but behaving altruistically towards other people has always been a struggle.
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From:eta_ta
Date:April 22nd, 2008 05:43 pm (UTC)
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Heh. Is all I'll say.
From:(Anonymous)
Date:April 22nd, 2008 06:43 pm (UTC)
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No time this evening but I hope to return to this fascinating conversation tomorrow.

Eta_ta: "Heh"? I wish all women could be as brief as that! :)

David
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From:eta_ta
Date:April 22nd, 2008 06:46 pm (UTC)
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shshsh! You're lucky that Memsahib isn't listening.
From:(Anonymous)
Date:April 24th, 2008 08:17 pm (UTC)
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Sorry for the delay.

I agree with you on the difficulty of pinpointing exactly the causes of any action in either the physical world, or the world of living things. Perhaps I haven't made myself clear, so let me restate my opinon.

I have *no* doubts concerning Darwin's theory as to why there are variations *within* species. (One thinks of the finches on the Galapagos.)

I have severe doubts that his theory provides the correct explanation for the origin of new species/phylum. (Although I do believe that all living things share an ancestry. I know of another explanation which seems to me, a complete non-expert, more peruasive than Darwin, but that need not detain us today.)

Neither of those two concern our current conversation, however, in addition ...

I do think that there are some fundamental differences between the behaviour of humans and other living things. These differences appear to cast even more doubts on that part of Darwin's theory summed as as 'survival of the fittest'. These differences in behaviour come under the following headings:

Altruism
Chastity
Homosexuality

It is not strange that these characteristics arose because we are all subject to mutations in our DNA. However, what absolutely flies in the face of Darwin's theory is that *they still exist*! According to his theory, in which only those characteristics will continue to exist which permit the owner to live longer and procreate more often thus ensuring the passage of his DNA into more copies than a conspecific who is less 'fitted to survive', these characteristics should have died out almost before they began. Any human who subscribes to the behaviours described above could not be 'less-fitted' to pass on their genes!

I suggest that we need not waste our time in considering the psychology of causation, it is sufficient that 'zillions' of people throughout the ages have subscribed to these practices and continue to do so. Thus, in my opinion, there is something about the very nature of human beings that is fundamentally different from animals. How or why these differences arose, I do not know, but I think an explanation is needed - and Darwin certainly doesn't offer one.
From:(Anonymous)
Date:April 24th, 2008 08:18 pm (UTC)
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Sorry, that was from me, if you hadn't guessed!

David Duff http://duffandnonsense.typepad.com/
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From:shkrobius
Date:April 24th, 2008 09:51 pm (UTC)
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Here is your problem: you start from the assumption that altruism, chastity, and homosexualism cannot be compatible with fitness and reproductive success of individuals. If you measure this success in the fraction of the genome that is passed to the progeny and the quantity of offspring, it begins to make much sense. We've discussed altruism already; in a group that practices reciprocal altruism, being altrustic makes perfect sense in terms of fitness and reproductive success of each individual.

Now, consider chastity. Worker ants are more than chaste - they are sterile. The same goes for mole rat ants. The sterility makes sense if one's genes will be transferred by someone who shares a large chunk of your genome and to whom you consigned your reproductive rights. Then you do not have to worry about wasting time and energy for sex. Back to humans. Chastity makes Darwinian sense if the probability of childbirth fatality is very high. Then you would have higher probability of passing your genes delegating the childbirth to your blood relative and helping this kin to look after his or her children - than doing it all yourself, facing colossal odds. Actually, in rare cases natural selection can and will favor sterility. You can read about it here http://shkrobius.livejournal.com/96646.html

The genetics of homosexualism is poorly known, but consider the following scenario: suppose a gene that makes males homosexual when coupled to another gene makes them more fertile when it is coupled to a different gene. Or, alternatively, it makes their mothers more fertile. Then it makes perfect sense that a fraction of homosexual males will appear in each generation, because it bestows reproductive advantage over the rest of the population, including the parents of these males. That's hypothetical, but homosexuality is too common among animals
http://en.wikipedia.org/wiki/Homosexuality_in_animals
to strongly suspect that it has genetic basis.

You say there is a fundamental difference between people and the rest of the Creation. I agree, but the same can be said about any species, they are all unique. However, chastity, altruism, and homosexuality all have precedents in Nature. This is not what makes us unique. The many instances suggest that there is common mechanism by which such traits occur time and time again. Darwinian theory suggests such a mechanism. It falters in other respects, but it works pretty well regarding the concerns that preoccupy you.
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From:live4him4eva
Date:November 20th, 2008 11:13 pm (UTC)
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I only read a little because I gotta get to work on a paper, but my best guess is because the colon absorbs water. Therefore, if we had urine pass through the colon, it's possible the toxins would be absorbed. I'm not sure though.

But you need to keep in mind that all animals have different organs and systems, so it's no surprise if we need different systems for different things. (I'm sure you probably covered that, but I didn't get to read it all.)
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From:shkrobius
Date:November 21st, 2008 02:36 am (UTC)
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Amphibians have been damping liquid urine through their cloaca since the Devonian, without any major complaint. Urine is not really toxic, and you can drink it by a gallon, especially if it is your own. The danger is from salts rather than some dangerous "toxins," and the colon does not absorb these salts.
http://en.wikipedia.org/wiki/Urophagia
http://en.wikipedia.org/wiki/Urine_therapy
The toxins in urine are blood toxins. Once out of the bloodstream, these are not particularly toxic, especially at such great dilution.
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From:live4him4eva
Date:November 21st, 2008 04:01 am (UTC)
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Okay, I guess that makes sense. I don't know the Urinary system as well as I could, being a Health Science student. But now that I think of it, your explanation about the blood toxins makes sense.
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From:freedom_of_sea
Date:October 20th, 2009 09:30 am (UTC)

почему нельзя запасать аминокислоты в белках?

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я бы не отказался иметь классные мышцы вместо того чтобы писать
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From:shkrobius
Date:October 20th, 2009 02:25 pm (UTC)

Re: почему нельзя запасать аминокислоты в белках?

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I gave a possible answer: if animals started as N-supplying symbionts with algae (a bit like corals) then peeing is what you are for, this is your main function in life. Those retaining N have been penalized by their symbionts. The tradeoff was photosynthetic carbohydrates for N, and both sides were penalized for not keeping their end of the deal. The rationale for this form of symbiosis is the hypoxia and global glaciation at the end of the Cryogenian, when fully modern animals have appeared. The symbiosis with algae helped to survive the hypoxia, providing oxygen. But it was not for free. Quite a few things in animals derive from dinoglagellate algae, like the opsins in your eyes. We then parted our ways, but the genetic baggage needed for storage of N has been irretrievably lost. It is not as bad as you think: most animals can afford being wasteful. The carnivores simply do not have such a problem; it is the problem of obligatory herbivores, and the solution is eating more!
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From:freedom_of_sea
Date:October 21st, 2009 06:10 am (UTC)

Re: почему нельзя запасать аминокислоты в белках?

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в это трудно поверить, что за миллиарды лет не появилась функция синтезировать белок про запас.

В симбиозе тоже непонятно, какова функция животных симбионтов? Фиксация азота из атмосферы?

Я полагаю что осколки азота, которые выводятся, просто не могут быть использованы для синтеза белка, возможно это "стружка" аминокислот пошедших на строительство белка.

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From:shkrobius
Date:October 21st, 2009 04:19 pm (UTC)

Re: почему нельзя запасать аминокислоты в белках?

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(1) This is not billions of years, but 500-600 Myr. You may be surprised to learn that the basic biochemistry of the eukaryotes has not changed in 900 Myr. In the fundamentals, there was no innovation whatsoever, just occasional acquisition of bacterial genomes at the beginning. In particular, urea cycle is not an animal invention, it occurs in halobacteria, such as H. pylori.

Why we can't store amino acid N like plants? You need special storage proteins and polymers, organs storing these proteins, special proteolytic enzymes, transporters, etc. Plants and algae store their storage proteins in chloroplasts which were derived from endosymbiotic cyanobacteria that invented this type of metabolism and relied on storage granules. Only some bacteria do it, because the function of the bacteria is not to store its N but use it as soon as possible for protein synthesis and multiplication. There is little point in storing, by definition, unless in special situations (see below). Obtaining the right kind of endosymbiont was astronomically rare events, it happened only few times, and it was mainly luck. Phototrophic eukaryotes were lucky to get the cyanopbacteria that (apart from the photosynthesis) were also capable of N storage. They still do, storing N in a polymer cyanophycin. Only cyanobacteria and a handful of other bacteria do it.
http://en.wikipedia.org/wiki/Cyanophycin
It is not known why they are doing it in general, but some cyanobacteria are N-fixing and they need a dynamic buffer (sink) to store N that they fix, so that their nitrogenases would keep working. It is a means for a completely different problem than food storage.

The others were less lucky. Animals are descendants of eukaryotes that did not undergo this endosymbiosis and we do not have biochemical machinery for plastid storage of N. In N storage organs in plants, it is also plastids. So the difference is that the ancestors of animals have either been missing amino-acid storing plastids (never acquiring the right kind of endosymbiont) or lost them. You should keep in mind who our probable ancestors were. Our closest relatives are mesomycetozoea
http://en.wikipedia.org/wiki/Mesomycetozoea
which are almost all parasitic. One branch removed are fungi. These live by degrading live and/or dead tissues that are rich in N. Storage of N, quite simply, was not needed, as it is an adaptation of free-living species.

(2) the function of the animal symbiont was predation on zoo- and phyto- plankton obtaining their N.

(3) No, most of N is removed via urea cycle of breaking the amino acids. This is done on purpose; it is not a side metabolite if that is what you mean. See
http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/amino.htm
http://themedicalbiochemistrypage.org/nitrogen-metabolism.html
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From:freedom_of_sea
Date:October 22nd, 2009 06:21 am (UTC)

Re: почему нельзя запасать аминокислоты в белках?

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Большое спасибо.
Почему для хранения N используются спецорганеллы, почему нельзя хранить белки например в мышцах или других богатых белком клетках?

И еще новые вопросы:
Почему захват эндосимбионтов астрономически редок? Теория (игр) учит, что любой паразит старается быть симбионтом, а паразитов уж точно полно, есть и множество экзосимбионтов типа лишайников. Процесс ассимиляции симбионтов и обмена генами должен происходить непрерывно, возможно мы очень редко его замечаем. Симбиотический характер митохондрий и хлоропластов был открыт по-моему недавно.

Еще, если захваченные растениями цианобактерии азотфиксирующие, почему так мало растений это умеют, при том что они отчаянно нуждаются в нитратах?
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From:shkrobius
Date:October 22nd, 2009 07:36 am (UTC)

Re: почему нельзя запасать аминокислоты в белках?

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(1) I have to read about it or ask someone; I do not know much about plant storage proteins. With the cyanobacteria, the problem is low solubility of the polymer (it is not even a protein), it is granulated. I do not know why it MUST be granulated in this case, but bacteria generally granulate metabolites they store, from elemental sulfur to sugars. The idea is to have as low concentration in the cytoplasm as possible, so the equilibria are driven towards the insolubles, providing free energy gradient for the reactions to occur.

In animal cells that are not rigidified by cellulose, these granules and fibriles would wreck the cell. I'll return later, this is part of biochemistry I poorly know, as it is peculiar to plants only.

About the endosymbionts: this is a long story, I cannot possibly fit it into a comment. The short answer is metabolical incompatibility and extreme rarity of bacterial endosymbiosis in general. You are quite right that it has been accepted quite recently (about 30 years ago), but it was first proposed almost 100 years ago.

I wish I can answer your question because it is a $1b question. Modern plants rely on N-fixing rhizobia bacteria in root nodules. These bacteria are anaerobes, whereas the plants are aerobes. There is metabolical incompatibility, because the nitrogenazes (all but in one thermophylic bacterium) are inhibited by oxygen. To go around, the plants use leghemoglobin to remove oxygen from these nodules. I wrote about those a while ago
http://shkrobius.livejournal.com/36903.html
there is more detail there.
How isolated aerobic N-fixing bacteria, including the cyanobacteria go around this problem is not known, to my knowledge. In filamentous cyanobacteria the cells differentiate and N2 fixation occurs only in heterocysts while the photosynthesis occurs in vegetative cells, The fixation is very expensive; if it can be avoided, it is better be avoided. Hence the possible devilry with exploiting animal symbionts. The eukaryote acquiring the N-fixating cyanobacterium almost certainly would not be able to capitalize on it, because the nitrogenase would be inactivated by oxygen in the O2-respiring host. This is a solvable problem but the nitrogenase will be lost in the genetic drift faster then the system for deoxygenation will be evolved and implemented. Another problem is that the nitrogenases are using Mo. Bacteria have learned how to collect Mo, but eukaryote host would not not know how to do it. If the bacterium finds itself inside the eukaryote host, it would not get Mo to make the nitrogenase. So the logic of the transitional period at the outset of endosymbiosis suggests that the nitrogenases would be lost. If it is not O2 deactivation, it is Mo starvation. Also, O2 binding by hemoglobin-like proteins needed to keep N2 fixation going is not practiced by the cyanobacteria or single-cell eukaryotes. It is the adaptation of yet another class of bacteria that use it for NO detoxification under hypoxic stress. You can see even from this one example the biochemical difficulty of blending two different metabolical pathways. That it has worked out at all is a miracle of miracles, and it happened just a few times in 3.5 Gyr. The barriers are very formidable. We are extremely lucky that it happened at all.

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From:shkrobius
Date:October 22nd, 2009 03:30 pm (UTC)

Re: почему нельзя запасать аминокислоты в белках?

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I have to apologize for misleading you. I've asked around, and I was not correct about N storage in higher plants. It is true that the majority of plants store secreted proteins in their plastids (such as leucoplasts in the roots). However, protein-rich seeds contain storage proteins in endoplasmic reticulum (ER) in the endosperm. Here is how it looks
http://en.wikipedia.org/wiki/Endoplasmic_reticulum
ER is a crumped membrane inside the cell with the protein-making ribosomes located right there. The storage proteins, except for albumins, are long and insoluble and these are extruded by the ribosomes into the ER membrane, post-assemble (several units combine) there and stay there in the ER. So these storage proteins (globulin-family legumins in soybeans, and prolamin-family zein, in maize) are not necessarily in the plastids, as I thought, but also in the ER. In fact, there are similarities between some of these storage proteins in plants and animal proteins, not in the sequence, but in the overall structure and the way these assemble; we also use our ER and cisternae for some of our problematic proteins.
http://www.biologie.uni-hamburg.de/b-online/e17/17i.htm
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC160892/pdf/070945.pdf
I do not recall structural or N-rich proteins residing there in animals (eg, our keratin filaments are right in the cytoplasm) but these seeds contain up to 40% protein, so it has to be packed properly. It is clear that different superfamilies of these proteins (prolamins, albumins and globulins) are independent inventions, as they related to different ancestral proteins.

Back to your question. My plastid rationale explains why animals are lacking plastid storage proteins and I stand on it. ER storage proteins seem to be unrelated to those, these have been evolved separately, possibly recently. I see no reason why this type of ER storage proteins couldnt've evolved in animals, except for one consideration. Synthesis of such proteins is cheap, but you need to cut it into amino acids for it to be useful. In animals, peptidases that do it are in lysosomes that operate at high acidity. There is no clear way how the insoluble storage protein from the ER can be delivered into the lysosome to be degraded there. The plants do not do it. The peptidases are right there, in the protein bodies, so when the seed germinates, these can degrade the storage proteins. There is analogy with animal eggs: the albumin is degraded to supply the embryo with N for biosynthesis, so there is perfect analogy and the plants did not best us there, we can do it to, but we do not rely on insoluble large proteins, which is another way of doing it. But that's for embryos/seeds. In the plant tissues, it is plastids. I guess tissue cells cannot function properly (mechanically) with the stiffened ER, so the granulation is the only way of doing it, and animals do not have and perhaps never had the plastids for such granulation.
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