Re: OOL VIII - The Last Major Morphological Transition

> From: "Perplexed in Peoria" <jimmenegay@xxxxxxxxxxxxx>
> I should probably clarify that there is no particular reason to refer
> to quasi-cells (aka liposomes) before RNA as "inside-out". At that
> point in time, there was no biochemistry taking place in the aquaeous
> phase either inside or outside.

I decided to look up the definition before responding:

Linkname: liposome. The Columbia Encyclopedia, Sixth Edition. 2001
URL: http://www.bartleby.com/65/li/liposome.html
(A technological method, typically used for delivering medicines,
optionally forcing chemical reactions in the confined environment
inside the liposome just prior to delivery. Seems to be nothing related
to abiogenesis. Is that the correct definition?)
It seems unlikely that liposomes would spontaneously appear in the
prebiotic environment.

But:
Linkname: A Central Dogma Molecular Biology Glossary
URL: http://fig.cox.miami.edu/~cmallery/150/gene/CMBglossary.htm
Liposomes behave dynamically by engulfing
smaller liposomes then splitting
into two smaller liposomes. Combining Liposomes and
Enzymes: creates the ability for the
liposome to absorb a substrate and "spit out" a
transformed product acted upon by the
enzymes in the lipid bilayer.
Do I understand that, if 5-7 is the optimal size range, and there are
liposomes of sizes 1,2,3,5, the size-5 liposome will absorb the 1 2 and
3 liposomes, producing a size-11 liposome, which will then split into
size-5 plus size-6 or somesuch? This doesn't seem like "quasi-cells" at
all, unless you posit some magic genie which generates unlimited
quantities of size 1,2,3 liposomes which the normal-size-5 liposomes
can use as "food".

> I believe that there is good fossil evidence that the proton-motive
> force is an earlier "energy currency" in life than is ATP.

I agree. A few months ago I read some description of the two major
kinds of photosynthis or respiration, I forget which, one of which took
ADP + PO4 and generated ATP while the other generated a proton
potential across a membrane by forcing protons from one side to the
other. I got a general impression the proton-imbalance method was more
primitive.

A few minutes ago, as I was starting to write this reply, I got an idea
for an evolutionary path from proton-imbalance to ATP: Suppose the
proton imbalance had a problem, that the energy production method was
runaway, didn't have good regulation tended to over-charge the proton
capacitator causing destructive sudden discharge. There as selective
advantage to solving this problem. One solution was to attach something
that would drain away any charge greater than a particular potential.
The obvious way to do this was to catalyze some chemical reaction that
consumed some specific amount of energy, whereby if the charge
difference across the membrane wasn't sufficient the reaction wouldn't
occur, while if the charge difference *was* sufficient then one unit of
catalyzed reaction would drain away a single proton of that particular
potential difference (or slightly greater) and use most of the energy
to drive the energy-consuming reaction. Several different such
specific-energy-draining reactions were discovered by evolution. These
were all very simple reactions, because the simpler they are the more
likely they are for some randomly-evolved enzyme to catalyze the
reaction. So most of these reactions were just shoving two molecules
together that would rather be apart but where the combination is
meta-stable, or ripping some side-chain off some organic molecule and
allowing H and OH respectively (from ambient water) to connect to the
loose ends thereby produced. Each of these emergency-discharge methods
had a different activation energy. Those too high didn't protect
against accidental discharge well enough. Those too low left too little
potential difference across the barrier so not enough chemical
reactions could continue to work using that potential. Only those with
approximately "just right" discharge threshold would be favored by
natural selection. ADP + PO4 -> ATP was one of those with near optimum
discharge threshold which was retained by natural selection.

What then happened was the ATP or other meta-stable molecule would
simply float around the cell until it accidently got discharged. The
result was a large number of ATP discharges resulting in a tiny surge
of heat randomly distributed around the cytoplasm, nothing horrible at
all, nothing like a catastrophic collapse of an entire membrane
capacitor which not only punctures the membrane possibly destroying it
but also totally deprives the cell of all the energy that had been
stored to that point. So draining off surplus energy and safely wasting
it as heat was a definite improvement, a solution to the original
problem.

Later some branches of life developed regulation mechanisms for the
process that charged the capacitor in the first place, so they no
longer needed the emergency discharge mechanism, so the emergency
discharge disappeared due to neutral drift. But other branches of life
accidently evolved some catalyst that could discharge the ATP in a way
that actually used that energy to drive another useful chemical
reaction instead of just wasting it as heat. This was a great
advantage, so the ones that wasted ATP energy all went extinct.

So now there were two distinct branches of metabolism, the one that
safely charged the capacitor so had no need for emergency discharge so
it'd never evolve ATP, and the ones that already used ATP and were
locked into using it for essential chemical reactions so they couldn't
abandon ATP.

Now on the branch that used proton gradient which got converted to ATP,
a shortcut was discovered whereby the reaction that charged the
capacitor and the reaction that discharged it to make ATP were put
right next to each other, so the capacitor wasn't really needed in a
global sense, and over time the linked reactions broke away from the
membrane totally. When all the charge-discharge pairs were standalone,
the membrane was no longer needed at all for separating proton charge,
so neutral mutations eventually caused it to be no longer formed.

So now the two branches used two totally different methods to couple
energy-production to energy-consumption, the maker->charge->user
method, and the maker->ATP->user method. Later symbiosis or horizontal
gene transfer etc. resulted in *some* branches of life that had *both*
mechanisms used for different sources of energy and correspondingly
different users of that energy.

How's that for a brand-new "just-so" story? Any Sahara-snowball chance
of it being reasonable, or did I just tell a whopper of a tall tale?

Back to your original topic: Is it believed that originally the
proton-gradient-across-membrane method for storing energy originally
developed as a way to store surplus energy from some form of
respiration in undersea-vent environments, possibly as a way to
detoxify something like hydrogen sulfide or cyanide or pure H2 gas
dissolved in the water, whereby just reacting the noxious chemical
warmed the catalyst too much due to excess thermal energy released so
locally, but using some of the excess energy to shove a proton across a
slight gradient left a smaller amount of energy as heat thereby
allowing the catalyst to be heated-to-destruction less often?
(Hmm, is this looking like another of my "just so" stories?)
The original detoxifying catalyst might have merely shoved a proton
across itself and allowed it to spontaneously return back to its
starting point, effectively "electrocuting" the catalyst, but any
catalyst that tended to stick to a membrane in an appropriate
configuration would instead shove the proton across the membrane where
it'd have a hard time getting back where it came from, and many times
it'd go off a different direction instead, discharge harmlessly
somewhere else along the membrane instead of right at the catalyst. At
that point the membrane was very leaky with respect to proton gradient.
It'd hold a proton on the wrong side long enough for it to get away
from the catalyst must of the time, but then discharge it shortly
after. So anyway, the actual charge across the membrane was very tiny,
because the membrane was so proton-leaky, which had two consequences,
only a small amount of the excess energy was consumed by shoving the
proton across, just enough to avoid overheating the catalyst, and if
any catalyst was going to make actual use of that protein gradient,
it'd have to work from just a tiny unit of energy. Well, as it turns
out (in my just-so story), along came at least one catalyst that could
use that little bit extra energy, so the capacitor started to actually
be used as an energy storage source instead of just a way to protect
the proton-pushing enzyme. Over time, with somebody actually using that
electric charge, it became advantageous for the membrane to become less
leaky, which increased the charge on it, which increased its usefulness
for avoiding excessive heating of the proton-pushing enzyme, and also
allowed other catalysts which needed a larger unit of energy to draw
off the membrane potential, and opened a new ecolotical niche for other
proton-pushing enzymes that needed a large unit of energy drainage to
avoid overheating. This "arms race" in proton-pushing enzymes able to
push protons up higher gradients thus charge the capacitor more, and
the membrane becoming less leaky hence able to hold a larger charge,
and the occurrance of potential-consuming enzymes able to make
effective use of this larger potential, finally stablized at a point
when spontaneous discharge of even a single proton would often cause
some local damage of the membrane allowing a catastrophic
chain-reaction of several nearby protons discharging through the
weakened spot causing further damage until a total rupture allows all
the remaining protons to escape at the same time, or alternately one of
the original enzymes consuming a tiny unit of charge but now getting a
very large unit of charge and thereby overheating.

Of course some enzymes could avoid overheating merely by adding lots of
bulk mass, such as polypeptides simply adding a lot of inert amino
acids. But wasting a lot of energy in that way wouldn't be as good as
finding a way to save some of the extra energy for use in a second
reaction, or evolving a totally different biochemical pathway whereby
each reaction uses almost exactly the same unit of energy.

Question: In cells that have both an ATP mechanism and a
proton-imbalance mechanism, is the energy unit different for these two
mechanisms, with a particular catalyst using one or the other to best
match its energy-unit needs?

Another question: Given that two different size molecules, each with a
single electric charge on it, the smaller molecule will on the average
have the larger charge gradient around its periphery, right? So could
co-enzymes that directly carry a charge be size-optimized so their
charge gradient is "just right" for the particular reactions they
catalyze, with different reactions using different-sized charge-carrier
co-enzymes according to their particular charge-gradient need?

> Coupling of two processes in biochemistry can be direct or indirect.
> Modern coupling between H+ transport and the formation of high-energy
> phosphate bonds may be somewhat indirect, but there is no reason why
> it could not have been direct originally. After all, the very mechanism
> of joining two phosphates with release of water demands that an H+
> be delivered to the proper location so that it can remove an OH- from
> one of the phosphates as water.

Indeed, evolution could proceed in either direction, more closely
coupling two processes to eliminate an intermediate, for more
efficiency, or decoupling two processes, introducing an intermediate,
for the extra flexibility of using that intermediate to attach
additional half-reactions on either side.

> In future postings, I will offer some hypotheses as to how the
> lipo-organism created and maintained an H+ trans-membrane potential,

It seems to me you need to explain where all the lipids come from, to
make lipid-bubbles (liposomes) which don't have any other chemistry
attached to them nor within them, no RNA attached on the outside yet.
Are you proposing that some random replicator just happened to produce
large amounts of lipids as a waste product, just dump it into the giant
ocean-sewer, and nobody (except geothermal vents and UV) ever destroyed
it, so the over time the quantity built up to such a high level that
lipid molecules started bumping into each other and sticking together
to form bubbles, and eventually the ocean was virtually full of such
lipid bubbles, crowding the available ocean space so much that it
became inevitable that RNA already present in freefloating form would
chance into colliding with such a bubble in a way that made it attach,
like even if RNA doesn't normally stick to a lipid bubble, if it
collides a thousand times with different configurations it would
eventually chance upon a configuration where it gets wedged into a
crevice or somesuch and thereby sticks?

By the way, random bumping and occasional sticking also would explain
why adetoxifying proton-pushing enzyme got started sticking to some
membrane within the cell: Some random enzyme might have produced some
lipid as a waste product, which formed liposomes within the cell, which
eventually merged with the cell membrane and evacuated to the outside.
But in the crowded cell, occasionally an enzyme would stick to such a
membrane for a short time. There was variation in the exact shape of
any given enzyme, even if the active sites were forced to all be just
about the same, due to selection pressure, the inactive parts could be
just about any random shape, due to neutral mutations. So some genomes
would generate more sticking than others, and some would generate
sticking at different parts of the enzyme than others. If a particular
form of sticking allowed discharge of the proton across the membrane,
and that was advantageous, then there's be selection pressure toward
such sticking and against not-sticking or other-way-sticking.

.

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