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Old 29 Oct 2017, 08:35 PM   #679062 / #1
lpetrich
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Default Was the Earth Once Purple?

When The Earth Was Purple - YouTube Host Kallie Moore mentions the speculation that our planet once had that color from the color of the dominant photosynthesizers back in the Archean, some 4 - 2.5 billion years ago.

Why is chlorophyll green? Why not some other color? The Sun's light is strongest in green, so why reflect it? To avoid an overdose?

DasSarma, Shiladitya | University of Maryland School of Medicine and others have proposed the (Wikipedia)Purple Earth hypothesis:
Early Earth Was Purple, Study Suggests Purple Signs of Life | News | Astrobiology
What purple can tell us about life on other planets - CNN

An important part of this hypothesis is the photosynthetic pigments of halobacteria (or haloarchaea; it's in Archaea rather than (Eu)bacteria). These organisms live in high salt concentrations, and they use a purplish pigment called retinal to collect light energy.

This hypothesis states that large populations of halobacterium-like organisms lived in the oceans and lakes and rivers of the Archean Earth, maybe enough to color the Earth purple.

In this hypothesis, chlorophyll users were latecomers, using light not used by these purple organisms. But when a chlorophyll user succeeded in cracking water and releasing oxygen, it was the beginning of the end for most of the purple organisms. They could not survive very well in oxygen, and the oxygen releasers eventually outperformed them.

-

Retinal is part of a protein complex called bacteriorhodopsin that resides in the organisms' cell membranes. When retinal absorbs a photon, it changes shape, and it pushes a hydrogen ion out of the cell. It eventually returns through an ATP synthase protein complex, where it helps assemble the energy intermediate ATP. This "chemiosmotic" energy metabolism is pretty much ubiquitous, though with different mechanisms to push the hydrogen ions outward.

That is rather limited photosynthesis compared to chlorophyll photosynthesis, it must be noted. Chlorophyll energizes electrons and sends them into an electron-transfer chain. The chain can extract energy from making the electrons loop around, or it can transfer the electrons to under-construction molecules as a part of biosynthesis. But leaving aside the chlorophyll antenna complexes, this electron-transfer chain is also pretty much ubiquitous.

I must note that many chlorophyll users also use other photosynthetic pigments, giving them a variety of colors, like yellow and brown and cyan and purple and red.

Retinal is a simpler molecule than chlorophyll. It is a terpene or isoprenoid composed of four isoprenes, which chlorophyll looks like a lollipop with a porphyrin-like ring of rings with a magnesium ion in its center and a 4-isoprene chain sticking out.

-

So the variety of photosynthesis colors means that there is no one "typical" such color.
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Old 30 Oct 2017, 03:01 PM   #679078 / #2
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I recall reading an sf story about a black photosynthetic molecule. It would seem that such a molecule would be the most efficient energy extractor, since it utilized all the light (at least all visible light) that struck it. But I don't know if that's a real thing, or not.

On the subject of photosynthesis, I'm curious if that process is more efficient than the best current photovoltaic systems. I wonder if some form of life might evolve to use metals or silicon, to extract energy from sunlight?
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Old 30 Oct 2017, 04:47 PM   #679087 / #3
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(Wikipedia)Photosynthetic efficiency -- for land plants, very low, around 1%. That's relative to all of incoming sunlight, and that's including the effects of such overhead as surviving nights and growing roots.

(Wikipedia)Solar cell efficiency -- a good present-day solar panel will have a nominal efficiency of 20%. But averaging over the Sun's different directions in the day may make it drop by a factor of 2, to about 10%.

So (PV cells) >> (plants)

Plants' energy capture levels off at about 10,000 lux or 100 W/m^2. (Wikipedia)Lux gives the illumination from different sources, with the Sun getting up to 100,000 lux.


(Wikipedia)Energy conversion efficiency has a big table of efficiency values.
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Old 30 Oct 2017, 05:41 PM   #679090 / #4
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As to organisms reducing metals, one can do a redox-potential calculation.

(Wikipedia)Standard electrode potential (data page), Oxidation-Reduction Potentials

As a rough guide, the more negative E0 is, the more to the left the reaction tends to go.

I'll use the second one to show how to use the tables. I'll do 2H2 + O2 -> 2H2O.

Here is the first half-reaction, for pH = 7 (neutrality)
2H+ + 2e- <-> H2 : -0.421

The standard reference is for pH = 0 (super acidity: lots of H+ ions)
2H+ + 2e- <-> H2 : 0
The reaction is forced rightward by all the H+'s.

Here is the second half-reaction:
1/2 O2 + 2H+ + 2e- <-> H2O : +0.816

To make water, we need
H2 -> 2H+ +2e- : +0.421
1/2 O2 + 2H+ + 2e- -> H2O : +0.816
H2 + (1/2) O2 -> H2O : +1.237

This number agrees with the number in (Wikipedia)Electrolysis of water: +1.23 volts
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Old 30 Oct 2017, 06:42 PM   #679091 / #5
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Now for what metals an organism can make. Making them involves doing (metal ions) + (electrons) -> (metal)

So we must look for a good chemical reducer, a good donor of electrons. The best is NADP at -0.324 volts, with close relative NAD at -0.320 volts. This is the form that organisms use niacin as, that B vitamin.

But after it is reduced, it must survive the presence of oxygen. It causes corrosion at +0.816 volts.

So we have these to conditions:
Can be reduced by NAD: E > -0.320 V
Can survive oxygen: E > +0.816 V

Let's now look at common metal ions and reduction to the metallic state:

K+ + e -> K : -2.931 V
Ca2+ + e -> Ca : −2.868 V
Na+ + e -> Na : -2.71 V
Mg2+ + 2e -> Mg : −2.372 V
Al3+ + 3e -> Al : −1.662 V
SiO2 + 4H+ + 4e -> Si + 2H2O : -0.91 V
Fe2+ + 2e -> Fe : −0.44 V
(NAD limit)
Sn2+ + 2e -> Sn : −0.13 V
Pb2+ + 2e -> Pb : −0.126 V
Fe3+ + 3e -> Fe : −0.04 V
Cu2+ + 2e -> Cu : +0.337 V
Cu+ + e -> Cu : +0.520 V
Ag+ + e -> Ag : +0.7996 V
(O2 limit)
Pt2+ + 2e -> Pt + +1.188 V
Au3+ + 3e -> Au : +1.52 V
Au+ + e -> Au : +1.83 V

So while organisms can make metallic iron and copper, those elements will nevertheless corrode.

Gold will not corrode, but it is most often in "native" form, as gold metal. It is present in teeny tiny quantity in our planet's oceans ((Wikipedia)Abundances of the elements (data page))

Silver does corrode, however.

Finally, I've found CorrosionPedia: The Online Hub for Corrosion Professionals
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Old 30 Oct 2017, 07:44 PM   #679093 / #6
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There must be a woprld out there somewhere, on which shirts like this would be good camouflage:

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Old 31 Oct 2017, 04:37 AM   #679104 / #7
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Cute. Such shirts would have made good camouflage if it was red algae rather than green algae that colonized land.
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Old 31 Oct 2017, 07:07 PM   #679133 / #8
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The purple went away with the British empire. Nice discussion.
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Old 07 Nov 2017, 02:54 PM   #679504 / #9
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Re metals, I was wondering if a living organism could even theoretically 'grow' its own photovoltaic cell, and thus outperform all other photosynthesizing life.

I understand that most (all?) of the iron ore bodies on Earth are the result of microorganisms concentrating it. But I still don't know if there's any evolutionary path that might lead to plants with their own photovoltaics.

Imagine how difficult that would make a herbivore's life. Munch, munch, ZAP!
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Old 09 Nov 2017, 03:25 AM   #679728 / #10
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Electric eels? They turn food into electric charge.

I'd have to look at the chemistry of photosynthesis to be sure that isn't what happens already. There is a lot of electron transfer in biochemistry. It's been almost 25 years since I got a degree in microbiology.
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Old 09 Nov 2017, 12:58 PM   #679753 / #11
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Quote:
Originally Posted by Jobar View Post
Re metals, I was wondering if a living organism could even theoretically 'grow' its own photovoltaic cell, and thus outperform all other photosynthesizing life.
A photovoltaic cell requires some semiconductor like silicon or germanium. Of the two, silicon is the more common one, by around a factor of 10^5. So we should expect silicon. For making into a PV cell, after it's been refined, it must be purified to some rather extreme purity, so that impurities don't affect its electronic properties. After that, it is "doped" with controlled amounts of impurities with suitable electronic properties.

Silicon is well above the NAD limit, so it can't be refined by organism electrochemistry, but germanium, with Ge4+ + 4e -> Ge at +0.12 V is well under that limit. However, it is above the oxygen limit, which makes it vulnerable to corrosion.

Also, chlorophyll is part of a photovoltaic-cell-like system, something that I should explain in another post.

Quote:
I understand that most (all?) of the iron ore bodies on Earth are the result of microorganisms concentrating it. But I still don't know if there's any evolutionary path that might lead to plants with their own photovoltaics.
That's (Wikipedia)Banded iron formation (BIF), and BIF's are formed by microbes oxidizing iron from Fe++ to Fe+++, not from oxidizing iron metal.
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Old 09 Nov 2017, 01:36 PM   #679759 / #12
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I'll now explain the photosynthesis mechanisms in more detail, and describe the systems that they are parts of.

For retinal photosynthesis, I must describe chemiosmotic energy metabolism: (Wikipedia)Chemiosmosis

It is used by most prokaryotes, and also by mitochondria and chloroplasts, both "enslaved" prokaryotes. Mitochondria are descended from alpha-proteobacteria, and chloroplasts from cyanobacteria.

In it, various mechanisms pump hydrogen ions (protons, H+) out of the cell interior and into its exterior. These ions are then allowed to return through "ATP synthase" protein complexes. Their doing so makes them assemble ATP molecules, and these molecules supply energy for various chemical reactions, like biosynthesis.

Cyanobacteria and chloroplasts have a variant: thylakoids, small sacs that electrons get pumped into. But thylakoids' interiors are topologically equivalent to the cell exteriors.

Here is the structure of ATP and some chemical relatives of it.

Adenosine:
(adenine)-(ribose)

AMP, adenosine monophosphate:
(adenine)-(ribose)-(P)-(P)

ADP, adenosine tdphosphate:
(adenine)-(ribose)-(P)-(P)

ATP, adenosine triphosphate:
(adenine)-(ribose)-(P)-(P)-(P)

There's also something called cyclic AMP.

P is a phosphate ion, PO4---. AMP is a RNA nucleotide, with the others having its nucleobase, adenine, replaced by guanine, cytosine, and uracil. DNA is very similar, with deoxyribose instead of ribose, and thymine instead of uracil (thymine = uracil + methyl group at a spot in it).

So ATP synthase does the following:

AMP + (P) -> ADP
ADP + (P) -> ATP

where (P) or "Pi" is a phosphate ion in solution.

Here is a simple use of it:

(Molecule 1) + ATP -> (Molecule 1)-ADP + (P)
(Molecule 1)-ADP + (Molecule 2) -> (Molecule-1)-(Molecule-2) + ADP

Some reactions go from ATP straight to AMP, releasing (P)-(P): pyrophosphate.
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Old 09 Nov 2017, 01:47 PM   #679762 / #13
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Now for how retinal photosynthesis works. Each retinal molecule is attached to a protein called bacteriorhodopsin, and each of these proteins is embedded in the cell's membrane.

When a retinal molecule absorbs a sufficiently energetic photon, it changes shape, and a hydrogen ion at one end of it gets moved across the cell membrane from the interior to the exterior. After releasing the ion, the retinal molecule returns to its original shape. (Wikipedia)Bacteriorhodopsin
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Old 09 Nov 2017, 07:51 PM   #679794 / #14
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Quote:
Originally Posted by Jobar View Post
Re metals, I was wondering if a living organism could even theoretically 'grow' its own photovoltaic cell, and thus outperform all other photosynthesizing life.

I understand that most (all?) of the iron ore bodies on Earth are the result of microorganisms concentrating it. But I still don't know if there's any evolutionary path that might lead to plants with their own photovoltaics.

Imagine how difficult that would make a herbivore's life. Munch, munch, ZAP!
A 'photovoltaic cell' similar to human-built ones seems unlikely, but typical photosynthesis already generates electron flow. However this flow is very quickly used to drive the production of high-energy molecules that can power various processes in the cell. Even if the electric gradients were not so used, they are local (within a cell or a part of a cell, rather than across many cells). Thus you don't get a <zap>.

It is interesting to note that essentially all cells maintain an electric gradient across their plasma membrane, as well as across other membranes. In many cells (most obviously neurons and muscle fibres), this electric gradient can be rapidly altered (even reversed). In fact the electric organs of certain fish are made up of modified nerve and muscle tissue.

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Old 10 Nov 2017, 12:43 AM   #679817 / #15
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Now for chlorophyll photosynthesis. But I must first explain electron-transfer energy metabolism: (Wikipedia)Electron transport chain. Like chemiosmotic energy metabolism, it also is used by many prokaryotes and also by the "enslaved" ones: mitochondria and chloroplasts. In fact, electron-transfer metabolism feeds hydrogen ions into chemiosmotic metabolism.

In mitochondria, it has this form:

Electron donors -> NAD (electron carrier) -> Complex I (H+ pump) -> Ubiquinone (electron carrier)
Electron donors -> Complex II -> Ubiquinone
Ubiquinone -> Complex III (H+ pump) -> Cytochrome c (electron carrier)
Cytochrome c -> Complex IV (H+ pump) -> (O2 + 4e + 4H+ -> 2H2O in exterior)

The electron donors all release H+'s in the interior. Combined with oxygen-to-water, that effective pumps H+'s outward.

This is the general form of it in prokaryotes, though they can add and remove electrons at several places with a wide variety of electron donors and acceptors. They also have varying numbers of proton pumps: 1, 2, and 3, but always at least 1. The counterparts of Complex IV can use electron acceptors other than oxygen, like nitrate ions.

Electron donors -> Dehydrogenase -> Quinone
Electron donors -> Quinone -> Oxidase/reductase -> Electron acceptors
Quinone -> bc1 -> Cytochrome
Electron donors -> Cytochrome -> Oxidase/reductase -> Electron acceptors
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Old 10 Nov 2017, 01:20 AM   #679822 / #16
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Now to chlorophyll photosynthesis itself.

First, what cyanobacteria and chloroplasts do. Their photon-absorbing parts of their photosynthesis is called the light reactions, from being powered by visible-light photons. These reactions take place on the membranes of thylakoids, pumping H+ ions inward and letting them return outward -- the thylakoid interiors or lumens are topologically equivalent to cell exteriors. The main body of cytoplasm is called the stroma, and it is topologically interior.

(2H2O -> O2 + 4e + 4H+ in thylakoid) -> Water-splitting complex -> Photosystem II -> (H+'s from stroma) -> plastoquinone -> (H+'s into thylakoid) -> cytochrome b6f -> plastocyanin -> Photosystem I -> ferredoxin -> (H+'s from stroma) -> NADP (close relative of NAD)

Electrons can go in a loop, from Photosystem I to plastoquinone. This is useful for getting energy.

Photosystems I and II are antenna complexes, containing chlorophylls and various other photosynthetic pigments, like carotenoids. They capture photons and energize electrons, much like photovoltaic cells.

Cyanobacteria can also do
NAD -> Dehydrogenase -> Plastoquinone -> Cytochrome bc6 - Cytochrome aa3 -> (Oxygen -> water)

like some aerobic bacteria, including the ancestors of mitochondria.

-

Various other prokaryotes also have chlorophyll photosynthesis. They only have one of photosystems I and II, and those with only II can also run electrons in a loop, using plastoquinone and cytochrome bc6. None of them use water as an electron source, using a variety of other electron donors.
  • Purple bacteria, both sulfur and nonsulfur (in Proteobacteria): PS II
  • Green sulfur bacteria (Chlorobium): PS I
  • Green nonsulfur bacteria (Chloroflexus): PS II
  • Heliobacteria: PS I

This produces a conundrum in eubacterium evolution: how did chlorophyll photosynthesis evolve? Did some ancestor have both photosystems I and II? Only one of them? Neither of them? In the latter two cases, one or both of PS I and PS II must have been transferred by lateral gene transfer.
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Old 10 Nov 2017, 07:01 AM   #679840 / #17
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Originally Posted by Aupmanyav View Post
The purple went away with the British empire. Nice discussion.
And ushered in the Phaeophytin. Y'all need something like this.
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Old 10 Nov 2017, 11:21 AM   #679855 / #18
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I wouldn't be surprised when considering the bashing that homo sapiens has foisted on it in a relatively short time.
And yes I do recall when the map of the world was mostly pink...appealing to a 10 year old.
Since every country is set on annihilating its neighbour and since all colours mixed together make the colour black..We--ell chi sas?
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Old 10 Nov 2017, 12:54 PM   #679862 / #19
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Rie, this was long before humanity existed. LONG LONG LONG before humanity existed. In fact, our ancestors back then were microbes.

As to a lot of pink on maps, that was a cartographical convention, not anything real. The purple here was something physically real, like the green of land plants.
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