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Author Topic:   Transition from chemistry to biology
Quetzal
Member (Idle past 5146 days)
Posts: 3228
Joined: 01-09-2002


Message 27 of 415 (77713)
01-11-2004 8:41 AM
Reply to: Message 25 by sidelined
01-10-2004 12:37 AM


Side:

I more or less agree with DNAunion that the particular research cited in the essay is somewhat overblown. Or at least, doesn't go into enough detail on what the problems are with proteinoid microspheres being the LUCA precursor. One of the key problems is that there has been little or no evidence produced that these microspheres self-replicate. Although there have been a wide variety of different kinds of microsphere produced, there's no indication that they reproduce themselves - one of the critical capabilities that the first "critter" had to have.

Note, however, that Fox's proteinoids (or more acurately thermal proteins) very likely could have formed the first protocell - and may have served as a template or "home" for the self assembly of more complex polypeptides.

Anyway, for a look at what these things are, you can get no better than the source, Fox himself.

Przybylski AT, Fox SW, 1984 "Excitable artificial cells of proteinoid", Appl Biochem Biotechnol 10:301-7

quote:
The proteinoid cells are assembled of thermal polymers of amino acids. Typically, an appropriate mixture of amino acids containing aspartic or glutamic acid is heated at 190 degrees C for 6 h, stirred with water for 2 h, dialyzed during 2 d, and lyophilized. Spheroidal cells are made from such polymer by dissolving it in the water by boiling, and then cooling. Many of them can be made by sonication at room temperature. These artificial cells, ranging from microns to tens of microns in diameter (depending on composition and preparation), have double membranes and various internal compositions. The spherules can microencapsulate dyes, oxidant-reductant compounds or acceptor-donor substances, and can be packed together. Such spherules display electrical polarization and electrical discharges and respond to intra- and extracellular ionic and electric influence upon membrane and action potential. These properties arise from the double membrane structure, asymmetric membrane permeability, and channeling phenomena. Such features as exponential dependence of the steady-state conductance and capacitance as well as negative resistance of the membrane seem to be responsible for the flip-flop alternations of the membrane polarization, rhythmic electric oscillations, and all-or-none action potentials. The presence of such chromophores as pteridine and flavin in polymers constituting these cells is responsible for their photosensitivity.

Fox's original paper isn't on line, but if anyone wants a reference:

Fox SW, Jungck JR, Nakashima T 1974, "From proteinoid microsphere to contemporary cell: formation of internucleotide and peptide bonds by proteinoid particles", Orig Life 5:227-37.

I still prefer an RNA or pRNA or PNA First scenario for abiogenesis, probably at a submarine thermal vent or cracking front, but Fox's microspheres could be the first cells.


This message is a reply to:
 Message 25 by sidelined, posted 01-10-2004 12:37 AM sidelined has taken no action

Replies to this message:
 Message 28 by DNAunion, posted 01-11-2004 10:53 AM Quetzal has taken no action

Quetzal
Member (Idle past 5146 days)
Posts: 3228
Joined: 01-09-2002


Message 33 of 415 (77948)
01-12-2004 8:36 AM
Reply to: Message 31 by sidelined
01-11-2004 4:51 PM


Side,

I concur with DNAunion in both post 30 and 32. I'd like to add that all of the current abiogenesis hypotheses have weakenesses, so like he says, we haven't (yet?) been able to cover the last couple of gaps. Also, as he noted, there are rather significant problems with assuming full-blown RNA is the "first" replicator. Simpler, more stable molecules would appear to me to be more likely. There are two that I can think of (although others have been proposed) - peptide RNA aka pRNA or peptide nucleic acid aka PNA. PNA especially is quite stable, doesn't require the complex ribose sugars (which are problematic to synthesize in adequate quantities under most of the plausible pre-biotic conditions).

In addition, DNAunion mentioned the possibility that other molecules or substances could have assisted the formation of complex polymers. Cairns-Smith is the person credited with coming up with the idea that clays - because of their catalytic properties - may have provided a template or even catalyzed the formation of early complex polymers. Of course, this has problems as well - for instance clays don't necessarily form a lattice or matrix that is ideally designed for the assembly of biologically significant macromolecules.

Anyway, one of the bigger problems with abiogensis research up to now is that most researchers have concentrated on one hypothesis pretty much to the exclusion of everybody else's ideas. My "gut feeling" is that the final solution is going to be a synthesis of several different approaches.

A few references, of the hundreds on the subject:

Lazcano A, Miller SL, 1996 “The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World, and Time” Cell vol 85:793-798

Martin W, Russell MJ, 2002 "On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells" The Royal Society: Philosophical Transactions: Biological Sciences 358:59-85

In addition, further to what DNAunion mentioned about RNA autocatalysis, one relevant reference is:

Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP 2001, "RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension", Science, 292:1319-25

quote:
The RNA world hypothesis regarding the early evolution of life relies on the premise that some RNA sequences can catalyze RNA replication. In support of this conjecture, we describe here an RNA molecule that catalyzes the type of polymerization needed for RNA replication. The ribozyme uses nucleoside triphosphates and the coding information of an RNA template to extend an RNA primer by the successive addition of up to 14 nucleotides-more than a complete turn of an RNA helix. Its polymerization activity is general in terms of the sequence and the length of the primer and template RNAs, provided that the 3' terminus of the primer pairs with the template. Its polymerization is also quite accurate: when primers extended by 11 nucleotides were cloned and sequenced, 1088 of 1100 sequenced nucleotides matched the template.

And a final ref on my favorite PNA:

Lee DH, Granja JR, Martinez JA, Severin K, and Ghadri MR, 1996 "A self-replicating peptide" Nature, 382:525-8

quote:
The production of amino acids and their condensation to polypeptides under plausibly prebiotic conditions have long been known. But despite the central importance of molecular self-replication in the origin of life, the feasibility of peptide self-replication has not been established experimentally. Here we report an example of a self-replicating peptide. We show that a 32-residue alpha-helical peptide based on the leucine-zipper domain of the yeast transcription factor GCN4 can act autocatalytically in templating its own synthesis by accelerating the thioester-promoted amide-bond condensation of 15- and 17-residue fragments in neutral, dilute aqueous solutions. The self-replication process displays parabolic growth pattern with the initial rates of product formation correlating with the square-foot of initial template concentration.

This message is a reply to:
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Replies to this message:
 Message 34 by DNAunion, posted 01-13-2004 9:32 PM Quetzal has replied

Quetzal
Member (Idle past 5146 days)
Posts: 3228
Joined: 01-09-2002


Message 35 of 415 (78352)
01-14-2004 7:13 AM
Reply to: Message 34 by DNAunion
01-13-2004 9:32 PM


Thanks for the corrections. Type in haste... Anyway, as my daughter always says, "I knew that..."

This message is a reply to:
 Message 34 by DNAunion, posted 01-13-2004 9:32 PM DNAunion has taken no action

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