Origin of Life Chemistry?

An interesting review was published in the Chem. Rev. ASAPs a few weeks ago (doi: 10.1021/cr078240l) concerning some of the possible chemistry at the beginning of life.  We all know life is sustained and perpetuated through the DNA/protein world which exists today.  An RNA world is thought to have pre-dated this DNA/protein world.  And the authors of this review contend that a carbohydrate polymer world probably existed before modulating into the RNA world which eventually gave way to today’s DNA world.

I rather like reading and pondering about life’s origins.  It’s really interesting to me as a synthetic organic chemist to consider how the complex array of life came to exist from simple building blocks, and how the building blocks we have today arose from the generally-accepted conditions of early Earth at the time life began.  Perhaps we’ve all heard of the famous Miller-Urey experiment which attempted to recreate those conditions.  Methane, ammonia and hydrogen were circulated over boiling water.  Electrodes were introduced to mimic lightning.  After a time, the composition of the mixture was analyzed, and a number of amino acids were detected.

But did that really recreate the conditions of early Earth?

This paper includes some interesting conditions I hadn’t really thought about.  Consider: it is generally accepted that the reducing conditions of early Earth did not include significant amounts of oxygen.  But no oxygen means no ozone.  No ozone means no protection from high energy UV light.  This UV light perhaps provided a significant amount of energy to drive the early reactions.

Also consider: even as more (and more complex) molecules were created, the concentration of these molecules remained small – even if you allow that all of these molecules might be dissolved in the early oceans.  For these molecules to randomly collide and ultimately react to form polymers would be unlikely.  But the authors contend that perhaps, over time, those early molecules adhered to mineral-rich clay particles in the water.  The clay would serve to concentrate reagents, and the minerals (aluminum, iron, magnesium, calcium, sodium, and potassium being the most abundant) would serve to catalyze the early reactions.   Eventually, more complex molecules were synthesized.  The authors postulate that saccharides were among the first complex molecules to form in significant amounts.  But how?

Given that only the simplest molecules were present on early Earth, it is likely that formaldehyde was one of them present in non-trivial amounts.  Perhaps formaldehyde self-polymerizes on these clay surfaces to form small saccharides, which eventually undergo aldol condensation to more advanced hexoses and pentoses.  The authors argue this pathway for the formation of a number of monosaccharides on early Earth.  Note that in the cyclic isomer of glucose – β-D-glucopyranose (left) – all 5 substituents on the pyran ring are in the low-energy equatorial position (actually, the lowest-energy conformation of glucose is α-D-glucopyranose, where one of the -OH substituents is in the axial position. It is stabilized by what is known as the anomeric effect).  Perhaps it is not surprising that glucose is the most abundant organic compound on Earth today.

Additionally, assume the authors are correct that a carbohydrate polymer world existed as a precursor to the RNA and DNA/protein world.  This propensity for the newly-forming carbohydrates to favor stereoisomers which existed in low-energy cyclic forms could produce disproportionate amounts of glucose and other low-energy carbohydrates.  If these carbohydrates somehow formed the scaffold involved in the template for the mass production of the known amino acids, might it not be so coincidental that L-amino acids were created with near exclusivity?

It might also not be difficult to see how the carbohydrate polymers world gave way to an RNA world.  The authors suspect carbohydrates polymerized along with abundant phosphates to form longer chain polymers.  There are several possible polymers that can form, but one of them might have looked like RNA without the base pairs: a series of ribofuranose units linked together by phosphate groups (right, click for larger).  The highly oxidized purine and pyrimidine bases probably came about later than sugars.  When they did arrive, only a substitution was needed to create the first strands of RNA (below).

The authors continue to discuss how the first cells may have come to be and how the first unicellular organisms might have appeared, but I’ll let the curious reader find that out by reading the paper.  One issue that often comes up in talks of this nature is the creation/evolution issue (am I really going there in only my second post?) (Yes).  I’ll refrain from offering my take on that issue (maybe after we get to know each other a bit better…), but I will say that it is interesting that people often talk about the two issues as if they were two mutually exclusive options.  Are they?  Does the acceptance of one theory necessarily preclude the option of the other theory?  Discuss.

15 Comments

  1. I’ve been following this recent development for the past 2 months or so. I find it amazing that the samples from the original experiments have survived over 50 years. I make a new organic compound and (sometimes) I’m lucky if it’ll survive a week at -5 C.

  2. If you are liberal with your belief system than I doubt Creation and Evolution would preclude each other.

  3. Very interesting stuff! I really like this question as well. From a research perspective, it’s a fascinating overlap of so many traditional fields (synthetic chemistry, mineralogy, biochemistry, etc). One minor clarification that I’m sure goes without saying: clays *are* minerals–the aluminum, iron, magnesium, calcium, sodium, and potassium are just the elements that give them a specific identity (and impart a certain reactivity) that may allow them to catalyze certain reactions. It’s actually a surface science problem (yet another field brought into the mix).

    Keep up the good work on the blog! I enjoy reading it.

  4. One minor clarification that I’m sure goes without saying: clays *are* minerals

    I did know this. I played with the wording of that sentence for a while, and decided that was the easiest way to get my point across.

    http://en.wikipedia.org/wiki/Clay

  5. I think you mean preclude, Mitch. Athough, one being a prelude to the other would be an interesting twist.

    But which is a prelude to which?

  6. Unfortunately I’m going to have to preclude my prelude teaser. Comment above edited. 😉

  7. Another interesting issue that is related to the origin of life is the origin of chirality. How come that (almost) all amino acids found on earth are the L-isomer? The same holds for nucleic acids. You would think that structures that had formed accidentally would be racemic as neither enantiomer is energetically more favourable…

    Imagine a scenario like this: By pure chance, some homochiral nucleic acids form a structure that starts to self-replicate. All the replica structures would then be of the same chirality as the original one. If this initial self-replicating structure is formed only once, all nucleic acids generated in this way would be homochiral, and the symmetry would be broken!

  8. The origin of chirality is another one of my favorite concepts to ponder. It was actually kind of cute: the other day I was sitting in an undergrad first-semester organic class, and the professor brought up that all amino acids (except glycine) are L-amino acids and mentioned that that was one of the big mysteries still out there in chemistry. One of the students piped up, “is it really that unclear? Couldn’t proteins have just made one enantiomer over the other?”

    The first-one-to-self-replicate theory is a good one. It assumes a singular point origin of chirality. If there were two ‘first molecules’ that began replicating at opposite ends of the Earth, they’d have to have been the same chirality to begin with. I’ve heard several other theories as to the origin of chirality. The spiral nature of our galaxy perhaps imparted some preference for one over the other… Circular polarized light affected the early reactions to be enantioselective…

    The authors of the above paper don’t really go into it, but if their carbohydrate world theory holds true, maybe the early sugars were the template upon which homochiral amino acids/nucleic acids were formed, as I talked about above? If glucose was synthesized preferentially through thermodynamic preference for the equatorial position of the hydroxyl groups, maybe that enantioselectivity was the basis for the enantioselectivity of future amino acids or nucleic acids?

    Some references I found just now by Googling…
    http://www-geology.ucdavis.edu/~cowen/HistoryofLife/chirality.html
    http://www.ifa.hawaii.edu/~meech/bioast/program/OTHER.7.41.pdf
    http://courses.washington.edu/bangblue/L4a5FA08_2.pdf
    http://www.zoology.ufl.edu/Evolution/Lecture%20Notes/Lecture%2017%20-%20Origin%20of%20Life%20on%20Earth.pdf

  9. Another theory is that it is due to the Weak Interaction (http://en.wikipedia.org/wiki/Weak_interaction), which violates parity symmetry. I.e. it only acts on left-handed particles. Please ask no further.

  10. Maybe this girl can write a rap about it and explain it to me.

  11. In regards to the anomeric effect, no one else finds it strange that when there is no good stereoelectronic effect explanation all of a sudden hyperconjugation is the key?

  12. Very Interesting. Randy Wysong’s newest book, “Living Life,” has also answered a lot of my questions concerning the philosophy of the origin of life.

  13. From Becky’s link:

    If you tire of the insanity in our world, want to be a better and healthier person, feel despair, suspect that there is more to this drama called life than the mere interaction of atoms, are confused by notions of creation, evolution, religion, atheism, and immortality, and would like rational answers that accord with reality and satisfy your intellect and intuition—WELCOME!

    Sound like quackery. What’s more important than the interaction of atoms at a Chemistry Blog?

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