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Author Topic:   Targets of prebiotic syntheses
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11-22-2003 5:27 PM

Many of us know a thing or two about biology: there's something called RNA and it contains stuff like ribose that is bonded with other things somehow. But is simply "ribose" the best target we can come up with for OOL experiments? Or is that not specific enough? To better understand at least some of the specific targets of OOL research - as dictated by the commonality displayed by all extant life forms - we have to examine ribose and RNA a little more deeply.

What is ribose?

The first question is, is ribose an organic or an inorganic compound? Since it consists of a carbon chain with hydrogen and oxygen atoms attached, it is an organic molecule. Organic compounds ending in the suffix “ose” are sugars (some common examples being glucose, sucrose, fructose, lactose, galactose, and maltose). So ribose is some form of sugar. Ribose is a single unit: for example, it exists either as a single, independent open chain or as a single, independent closed ring. Thus we can be more precise and say that ribose is a simple sugar: a monosaccharide. Monosaccharides typically have 3 to 7 carbon atoms linked in series forming the molecule’s backbone or carbon chain. If a monosaccharide has 3 carbons it’s a triose. 4 carbons makes a monosaccharide a tetrose; pentoses have 5 carbons, and so on. Ribose is a pentose. So we can be even more precise and say that ribose is a monosaccharide (simple sugar) that has a 5-carbon backbone. A characteristic of sugars is that they have a carbonyl group (-C=O): if the carbonyl group is terminal (the carbon is attached to only one alkyl group…the other bond is to just a hydrogen atom) the sugar is an aldose; if the carbonyl group is interior (the carbon is attached to two alkyl groups) the sugar is a ketose. Ribose has a terminal carbonyl group making it an aldose. Thus we be even more precise and say that ribose is a 5-carbon monosaccharide with the carbonyl group on the terminal carbon (C1). While that statement describes ribose pretty well it still doesn’t properly define it because arabinose, xylose, and lyxose are also 5-carbon monosaccharides with a terminal carbonyl group. The following definition may be “clunky”, but it does seem to properly delineate ribose from all other chemical compounds: ribose is an aldopentose (5-carbon monosaccharide with a terminal carbonyl group) that has, in a Fischer projection, the hydroxyl groups on carbons 2, 3, and 4 all on the same side.

However, life doesn’t use just “any old” ribose…it uses a particular type. Thus, for origin of life experiments, the target, determined by biology, is not just ribose, but B-D-ribofuranose specifically. What exactly is that?

First, let’s consider the furanose part of B-D-ribofuranose. Pentoses can exist as open chains or as closed rings. When forming a ring, the two ends of the open chain approach each other and an existing oxygen atom forms a covalent link between the two ends, thereby closing the loop. Thus one oxygen atom is a member of the ring backbone. Two common types of rings are pyranose and furanose rings. A pyranose ring has six members (5 carbons and 1 oxygen) while a furanose ring has only five members (4 carbons and 1 oxygen). So ribofuranose is the 5-membered ring form of ribose.

Second, let’s consider the D part of B-D-ribofuranose. Since a furanose ring has only 5 members, one of which is an oxygen atom, it has only four members that are carbon atoms. But ribose is a pentose, so one of its carbon atoms cannot be a member of the ring. C5 is the outcast: it lies outside of the ring and is bonded to only one ring member, C4. A furanose ring is considered to be flat and C5 - actually, the bulkier group CH2OH that it is the center of - lies either above or below the ring, connected to C4. Which is it, above or below? In a standard Hawthorn projection of a furanose ring (oxygen atom in the back, C1 to the far right), the line connecting C5 to the ring projects up from C4 for the D enantiomer and projects down from C4 for the L enantiomer. Thus the D in B-D-ribofuranose tells us that the terminal (C5) CH2OH group projects up from C4 of the furanose ring.

Third, let’s consider what the B part of B-D-ribofuranose means. When the open chain transforms into a ring, C1 changes from being achiral to being chiral. In the open chain, C1 is attached to only three substituents (double-bonded to an oxygen atom, and single-bonded to a hydrogen atom and also to another carbon of the backbone). But in the ring it no longer has any double bonds and thus has four substituents, and they all differ: a hydroxyl group, a hydrogen atom, and two connections to the ring which differ depending upon which direction it is traversed. Thus, it becomes an asymmetric carbon atom. There are two possibilities for C1: considering a Hawthorn projection again, either the hydroxyl group can be up (with the hydrogen being down) or the hydroxyl group can be down (with the hydrogen atom up). If the hydroxyl group is down then it is trans to the terminal CH2OH group (which projects up in D-ribofuranose), making it the [alpha] form; if the hydroxyl group is up then it is cis to the terminal CH2OH group, making the molecule the beta (B) form.

Thus B-D-ribofuranose is ribose (a specific aldopentose) as it exists in a 5-membered ring with the terminal (C5) CH2OH group up and the C1 hydroxyl group cis to it.

Since B-D-ribofuranose is the sugar moiety of RNA nucleotides, it, specifically, is the target of prebiotic experiments. Getting “any old” sugar doesn’t cut it, and neither does getting generic aldoses or even pentoses. In fact, neither does getting just some kind of ribose.

What is RNA?

In simplest terms, RNA is a linear polymer of ribonucleotides. When found in RNA, B-D-ribofuranose is modified by having a monocyclic or bicyclic nitrogenous base attached to C1 (the base - adenine, guanine, cytosine, or uracil - replaces the C1 hydroxyl group during the formation of the glycosidic bond) and one phosphate group attached to C5 (actually, once the base is added, the carbons on the sugar start being labeled with prime symbols to distinguish them from the carbons in the nitrogenous base: so the phosphate group is actually attached to C5’). These alterations form a ribonucleoside monophosphate, which can also be called a ribonucleotide (and is frequently just called a nucleotide). In all biological systems studied, it is ribonucleoside triphosphates that serve as the individual monomers – the building blocks – that are strung together in a specific manner to form an RNA polymer. The 3’ hydroxyl group of one ribonucleotide combines with the 5’ phosphate group of another nucleotide to form a R-C-O-P-O-C-R linkage called a 5’,3’-phosphodiester bond (the energy needed to drive this reaction is provided by enzymatic hydrolysis of the terminal two phosphates, thus converting a nucleoside triphosphate into a nucleoside monophosphate).

The exact mechanism behind polymerizing ribonucleotides into polymers is not important in a prebiotic context: except that it must be prebiotically plausible, of course. For example, nothing says the nucleotides must exist as triphosphates before incorporation, nor does any rule state that it must be the hydrolysis of attached phosphates that drives the reaction. But the final product has to be an RNA polymer consisting of ribonucleoside monophosphates (see below). That is, the target is important, not how it is hit (as long as "cheating" is not involved).

Ribose and RNA: More-Exact Targets for OOL Experiments

Thus the two targets of interest, which are specified by biology and must be hit using only prebiotically plausible conditions, are as follows:

(1) B-D-ribofuranose (ribose - a specific aldopentose - as it exists in a 5-membered ring with the terminal (C5) CH2OH group up and the C1 hydroxyl group cis to it)


(2) Linear, unbranched RNA polymers consisting of 5’,3’-phosphodiester-linked ribonucleoside monophosphates (of course, the B-D-ribofuranoside kind)

PS: The purpose of the above was to more tightly constrain what counts as success in OOL experiments, not to define the absolute definitive targets. I don’t claim to have considered all possible constraints and so “reserve the right" to refine the targets in the future.

[This message has been edited by DNAunion, 11-22-2003]

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