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To the Origin of Life - the Early Evolution of Biosynthesis and Energy Metabolism


Jul 28, 2000
Eugene, OR
Basic Beliefs
I'll be posting on some stuff I'd collected some years ago -- stuff that I'll be wanting to update wherever possible.

Did DNA replication evolve twice independently? [Nucleic Acids Res. 1999] - PubMed - NCBI In Bacteria and Archaea (or Eubacteria and Archaebacteria) separately, with eukaryotes inheriting their DNA-replication system from Archaea.

Modern mRNA proofreading and repair: clues that the last universal common ancestor possessed an RNA genome? [Mol Biol Evol. 2005] - PubMed - NCBI

I've seen the theory that the LUCA (Last Universal Common Ancestor) had a heteroduplex genome, with DNA and RNA strands bound to each other. But the LUCA did have DNA, meaning that DNA had a pre-LUCA origin. DNA building blocks are built from RNA ones, first by chemically reducing the ribose parts to deoxyribose, then by adding a methyl group to uracil, making thymine. DNA without the second step is uracil-DNA.

Also pre-LUCA is the protein-synthesis apparatus. It involves transcription from genomic DNA to messenger RNA, and translation from mRNA to proteins. This translation is done with the help of RNA-protein complexes called ribosomes, and the RNA in them seems to be their most essential part. The translation involves transfer RNA's, snippets of RNA where one end fits the mRNA, and the other end has an amino acid attached. Amino acids are the building blocks of proteins. Transfer RNA's are notable for having nucleobases that were modified after being transcribed from the genome, postttranscriptional modification. Some of these modified nucleobases make their tRNA's capable of matching onto more than one mRNA nucleobase, enabling one tRNA to match onto several different three-nucleotide "codons".

So we see so far RNA, RNA, RNA, and more RNA. RNA can act as an enzyme, and some enzyme cofactors contain bits of RNA: Coenzymes as coribozymes. [Biochimie. 2002] - PubMed - NCBI, Modern metabolism as a palimpsest of the RNA world. [Proc Natl Acad Sci U S A. 1989] - PubMed - NCBI mention B vitamins B1 (thiamine), B2 (riboflavin), B3 (niacin), B5 (pantothenate), B6 (pyridoxal).

The remaining B vitamins are B7 (biotin), B9 (folate), and B12 (cobalamin). Biotin likely emerged after proteins did, not in the RNA world. B12 has a porphyrin ring, and porphyrins likely date back to the RNA world, if not farther.

Niacin's more formal name is nicotinic acid, and it occurs as nicotinamide adenine dinucleotide (NAD), a length-2 RNA snippet. The nicotinamide part looks suspiciously like some modified nucleobase.

Another cofactor is ATP, adenosine triphosphate: (adenine) - (ribose) - (P) - (P) - (P) where the (P) is a phosphate ion. It is often used as an energy intermediate, and that energy resides in its phosphate-phosphate bonds. When used in that fashion, it gets reduced to adenosine diphosphate (2 phospates) or adenosine monophosphate (1 phosphate), and it gets rebuilt by adding phosphates to make ATP again.

More and more and more RNA.

Because of all that RNA, the RNA world has become a very widely accepted hypothesis.

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