DNA, RNA, chirality.

Biochemistry notes.

Slashdot discussion

Aside on optical microscopy

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"Eny fule no" that I've long been interested in OOL (Origin(s) Of Life). I think it even pre-dates the meeting I mentioned with Alan Cairns-Smith as a student, when he was promoting one of his books on his "clay life" hypothesis.

Well, I've just been having a conversation on Slashdot which has prompted me to improve my knowledge of biochemistry, because the question of chirality reared it's head again. (I hope any readers already know what chirality is, and why it is important in both biochemistry and discussions of OOL.)

This doesn't start at the beginning ; we'd been discussing, indirectly, OOL. See the discussion thread linked above. Slashdot has a fairly short window for discussion, before a thread is locked and archived. It also has a preview option (which too few people use, including me) because once you've posted, you can't edit or remove. (The admins can delete something, but very rarely do - it takes legal action.)

My comment to Immerman

I suspect that would be true even if the common ancestor was RNA-based.

Ummm, I think the UCGA bases in RNA are chiral - but I'd have to check. Hmmmm ...

The naturally occurring enantiomer of RNA is D-RNA composed of D-ribonucleotides. All chirality centers are located in the D-ribose. By the use of L-ribose or rather L-ribonucleotides, L-RNA can be synthesized.

Which rather implies that the bases themselves are not chiral. (I saw a mention that the purine group in RNA and DNA bases is made by metabolism of glycine - which itself is achiral.)

Adenine - achiral (just look at the structure of the molecule - no 4-radical carbons). I see an interesting note that "Both adenine and guanine are derived from the nucleotide inosine monophosphate (IMP), which in turn is synthesized from a pre-existing ribose phosphate through a complex pathway using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as the coenzyme tetrahydrofolate." ... so the atoms derived from glutamine and aspartic acid must be from parts of the achiral side chains, not including the chiral amino acid centre. I also note that the highest turnover molecule in metabolism, ATP, is derived from adenine, and so by extension is achiral.

Cytosine - again, achiral ; look at the structure. Which also means that other pyrimidine derivative are achiral (unless you put in a side chain which itself is chiral). So that disposes of uracil too (the two can interconvert by amination/ deamination). Again, from Wiki, When found third in a codon of RNA, cytosine is synonymous with uracil, as they are interchangeable as the third base. When found as the second base in a codon, the third is always interchangeable. For example, UCU, UCC, UCA and UCG are all serine, regardless of the third base. Which is another clue towards the proposal that the original form of the DNA/ RNA/ "Preceeding Genetic System" may have had two-base-pair long codons, which added a third codon to the coding system when more than 15 amino acids were required by the metabolism. Not a universally accepted idea in OOL, but suggestive.

Guanine - achiral. Useless, but interesting factoid : "In 1656 in Paris, a Mr. Jaquin extracted from the scales of the fish Alburnus alburnus so-called "pearl essence", which is crystalline guanine. In the cosmetics industry, crystalline guanine is used as an additive to various products (e.g., shampoos), where it provides a pearly iridescent effect. " (Going through the process of writing these things down helps me get them to stick in my mental piling system.) Isn't crystallised guanine a common competitor in "pretty PPL/ XPL microscopic images" competitions?

Uracil - achiral again. This is the base that is found in RNA, replacing thymine, but I didn't know until now that it is actively removed from DNA strands : " Uracil-DNA glycosylase excises uracil bases from double-stranded DNA." (How does uracil get into DNA? see the note above about the deamination of cytosine.) Ah, this is interesting too, and very relevant to my interests in OOL : This problem is believed to have been solved in terms of evolution, i.e. by "tagging" (methylating) uracil. Methylated uracil is identical to thymine. Hence the hypothesis that, over time, thymine became standard in DNA instead of uracil. This snippet is worth piling away as well : Uracil-containing DNA still exists, for example in

• DNA of several phages
• Endopterygote development
• Hypermutations during the synthesis of vertebrate antibodies.

. That's weird. as the saying goes, "who ordered that?".

Thymine - achiral. Nothing else particularly interesting, but a synthesis reaction described on Wiki leaves out a significant factor : "Patented 2013, the current method used for the manufacturing of thymine is done by dissolving the molecule Methyl methacrylate in a solvent of methanol." Odd capitalisation, but you probably have a few hundred grams of the compound around your house - it's the monomer of "Perspex" (under many names). Ye gods, it still shows that I spent 20 years living with a plastics chemist.

None of this is probably particularly interesting to you, but it has tickled some of my recurring interests in OOL matters. That chirality thing remains interesting. I'm probably going to have to read up on the chemistry of sugars, not just because of the thing about the spiral chirality of DNA being (by elimination) hosted in the deoxyribose backbone, not the bases. And as Molesworth and "eny fule no", biological sugars are as dedicatedly chiral as amino acids, but in the other sense (D- rather than L-). Which itself indicates that L-amino acids can produce enzymes that are perfectly happy to manipulate D- chiral molecules.

I'm going to file this post separately for my future reference.

- got hold of a biochemistry textbook . Revising my chemistry, with an emphasis on carbohydrates for the now, but I need to do some work on fats too. Noting that the "line" expression of carbohydrate structures (stretched along the carbon-carbon backbone) makes it easy to spot the chiral centres (the two off-backbone radicals are different ; this is a chiral centre [unless the two backbone segments are identical, which I don't think can happen in most sugars]).

Aside on optical microscopy.

I forgot to follow that thread (strand?) on PPL/ XPL. What do you call it when you illuminate a slide with PPL, but then insert the analyser parallel to the polarizer? You get a different set of interference colours (and not all petrological microscopes can do this), which are quite pretty. (I'm thinking of photos like this collection (of l-arginine crystals, particularly the contrasting nucleation rosettes and dendritic growths later in the article), but it seems my memory of particularly uracil and guanine being popular - lots of organic molecules are used.) Going back to the "polariser-parallel analyser" question, does it have a name? You're not looking at the ordinary vs extraordinary rays' path difference, but ... what? I really need to sit back at the microscope to work this out - probably with the plates to try some quantitative measurements.

next Article DNA/ RNA structure

https://en.wikipedia.org/wiki/A-DNA There are several different structures available to both DNA and double-strnaded RNA.

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