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jubei33
14th June 09, 08:46 AM
Prologue


I also heard a theory that much of the hydrogen and oxygen in our atmosphere is a side product of nuclear reactions at our earths core where heavier densers atoms are being continually split.


really? I heard a large portion of the oxygen came from certain kinds of bacteria as a byproduct of their respiration.


You're both wrong. Hydrogen is just *there*, like Cullion said. It was the main product of the Big Bang and that's what everything else starts from. You need to fuse the hydrogen into higher elements, such as helium, lithium, etc. and that's only possible in a star... pretty much by definition.

What you are thinking of, jubei, is that our atmosphere was CO2 at first and then bacteria converted it to regular old oxygen. This is true, but the oxygen was there anyway.
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La Carne
We had this discussion earlier and I wanted to give it an appropriate answer, but time is short and I had to settle for a half-assed answer hoping another would add to such an interesting topic. 'It was there' is an unsatisfactory answer in the same tone of some brimstone spouting minister. Saying it was just a product of the big bang, though fundamentally correct, is unsatisfactory because it doesn’t answer the fundamental question. One could easily arrive at a similar conclusion if he’d said God put it there.

The answer, at least the non-half-assed one, lies with the evolution of metabolism on earth, a theory (a collection rather) of how microscopic organisms developed the ability to harvest energy from chemical bonds and put it to use. The first organisms were thought to have survived by breaking the bonds in naturally formed organic molecules. Studies have shown that in a mix of basic gaseous ingredients like methane (CH4), ammonia (NH3), water and hydrogen as well as a source of energy (think lightening), more complex molecules like amino acids and basic sugars will eventually form on their own. A re-evaluation of the classic Urey-Miller experiment (http://en.wikipedia.org/wiki/Miller_urey) data in 2008 showed that 22 amino acids were formed and “10-15% of the carbon in the system in the form of organic compounds.” They used more sensitive methods and found even more compounds than they originally published. Furthermore, William MacNevin’s(1) unpublished research showed that 100,000 volt sparks passed through methane and water vapor produced “resinous solids too complex for analysis.” (3)

The first major breakthrough in an efficient metabolism was the use of ATP as an energy storage molecule. ATP is used by all organisms today for their energy needs. This allowed early organisms easy access to energy and a reliable method to direct this energy toward other processes like growth and development and most importantly forcing reactions that require an energy input to take place (known as an ‘endergonic reaction’). ATP allowed early organisms to have a relatively stable, easy to manipulate molecule for their energy needs. It can be directed for use in other processes and controlled without having undesirable reactions taking place.

The second major event was glycolysis, the harnessing of energy from the chemical bonds in glucose, a simple six carbon sugar. In this pathway, glucose is progressively broken down into smaller molecules and the chemical energy contained in its bonds put to producing ATP molecules. One glucose molecule will eventually produce a net two ATP molecules. All living organisms have also retained this pathway, indicating its ancient evolutionary heritage. It is thought to have not changed significantly in well over 3 billion years. The usefulness of gycolysis was that is required no special organelles and occurred in the cytoplasm with the help of a few enzymes. These mediated the process giving the organisms a little control over when and how much ATP the produced. It also gave them a reliable means of manufacturing ATP as long as glucose was available.

Anerobic photosynthesis is the process of using light to produce ATP rather than stumbling upon and breaking down glucose. Earth’s early atmosphere is known to have lacked oxygen, showing that photosynthesis probably evolved without it. Cellular respiration (not the lungs kind) requires a source of hydrogen as an electron donor at the end of the chain and where it comes from is the interesting part. (4) These early organisms used the energy contained in photons to pump protons out of their cells creating a diffusion gradient, which is a fancy way of saying the concentration of protons inside their bodies is lower than the concentration outside. They then used the net flow inside them to power ATP synthesis through specialized mechanisms. They used H2S dissolved in the sea as a source of hydrogen atoms and the resulting reaction left elemental sulfur as a byproduct. They used the energy they gained to produce large, biologically useful organic molecules. Purple sulfur bacteria (http://en.wikipedia.org/wiki/Purple_sulfur_bacteria) are a good example of these critters and they still exist today.

The fourth major event was Nitrogen fixation (http://en.wikipedia.org/wiki/Nitrogen_fixation). This refers to the ability to take atmospheric nitrogen gas and use it to make ammonia NH3 and then other nitrogen containing compounds like nucleic acids and proteins. <nucleic acids picture> Nitrogen gas is readily available, but the problem is its fairly inert, because it contains a high energy triple bond <look for shape gif> This bond requires 226 kcal per mol to break it, making it one of the strongest bonds found in nature. Organisms (http://en.wikipedia.org/wiki/Nitrogen_fixing_bacteria) today accomplish this feat by way of specially tailored enzymes, which grasp, bend and then break the bond. Virtually all of these enzymes contain transition metals which are used to grasp the molecule on both ends in a ‘bridge-like’ fashion and snap it like a match. The pieces are supplied with hydrogen to make the more usable and reactive ammonia product by this reaction:.
N2 + 8H+ + 8e− + 16 ATP → 2NH3 + H2 + 16ADP + 16 Pi
The development of this process led to the means of producing specialized nitrogen containing compounds. These compounds are ubiquitous throughout all life on earth and a relatively easy method to produce them led to the development of even more complex systems. Exemplary of the cyclical nature and inter-relatedness of life, all of it relies on the organisms that produce them. A correlation in a human perspective can be seen by the dietary idea of ‘essential nutrients (http://en.wikipedia.org/wiki/Essential_nutrients)’.

The final part of this long story comes to oxygen forming photosynthesis. This was an improvement upon the previous anaerobic photosynthesis, typified by the substitution of an even more ubiquitous molecule, water, in the process. Instead of using H2S, these organisms used H2O as source of hydrogens and electrons. Before the byproduct was elemental sulfur, but with this innovation oxygen gas was released. Currently our atmosphere is around 20% oxygen and nearly every molecule of it was produced by this kind of photosynthetic reaction. Cyanobacteria (http://en.wikipedia.org/wiki/Cyanobacteria) were thought to be among the first to develop this. They were dominant around 2 billion years ago and their respiration byproducts slowly accumulated, greatly changing earth’s atmosphere.

Aerobic respiration evolved sometime later and it uses the same kind of proton pumps as photosynthesis. This is seen in the mitochondria (with the electron transport chain) in our cells, which are thought to have descended from early photosynthesizers. This is an interesting topic, but for now I'll leave it at this.



(1) He’s from the Ohio State University, a shameless alma mater plug. I had to listen to this story for like 4 years and now so will you.
(3) On a side note this is a method of producing fullerenes (http://en.wikipedia.org/wiki/Fullerines), an interesting group of chemicals named after the famed architect Buckminster Fuller (http://en.wikipedia.org/wiki/Buckminster_Fuller). Buckyballs and Carbon nanotubes are a few of these, which are finding new uses in industry and materials manufacturing, because of their interesting properties.
(4) Aerobic respiration in Eukaryotic cells, by contrast, uses oxygen in the air you breathe as the electron acceptor at the end. Certain yeasts use organic molecules as the electron acceptor at the end of the chain, which is called fermentation.

http://en.wikipedia.org/wiki/Haber-Bosch_Process

Chemical process that revolutionized farming with the cheap, easy production of chemical fertilizer. It has a natural analogue as well.

Ajamil
16th June 09, 01:21 AM
Thank you for this. My understanding was the the set-up for the Urey-Miller experiment was incorrect. Was the 2008 re-evaluation to show that organic molecules can come from inorganic sources, or was it to re-create the early atmosphere. If the latter, then what did they do to change the mixture and make it a better representative of current knowledge?

jubei33
16th June 09, 04:09 AM
Its not so much that it was incorrect as much as it was just a guess based on certain known facts and data among many guesses. Their atmosphere was meant to be a general or like an average atmosphere at the time. There have been many experiments along the same lines of thought and many have designed slightly different conditions in which these chemicals form. It was meant to show that given those prebiotic conditions, basic molecules can form on their own.

the 2008 re-evaluation was a retest of the same solutions originally taken from the mixture using better techniques than they had when they first tested. since them spectroscopy has grown by leaps and bounds. Before in the 70's parts per billion was high tech, the very limit of detectability, but now we're testing Ion trap mass spectrometers which easily reach part per trillion in analysis.

Incidentally, this leaves quite a conundrum with the law and the legal limits of certain chemicals. most of these laws were written in the 70's and are kind of inadequate given what we know. Asbestos and lead are two strong examples of this imo.

bob
16th June 09, 04:44 AM
Help a brother out with a crossword clue?


"Final product of the glycolysis?"

- - - - - - - - c - d

Arhetton
16th June 09, 06:23 AM
nucleic acid?

jubei33
16th June 09, 07:26 AM
Help a brother out with a crossword clue?


"Final product of the glycolysis?"

- - - - - - - - c - d
pyruvic acid.

I mention it as 'pyruvate' in the article, b/c it refers to it in solution as an ion.

bob
16th June 09, 07:58 AM
doh, of course. Thanks.