quarta-feira, 24 de junho de 2015

Why RNA cannot come before DNA.

3 reasons : 

1. Ribonucleotide reductase (RNR) : 

Biosynthesis DNA is made from RNA. The deoxynucleotides are made from nucleotides with ribonucleotide reductases (RNR's), producing uracil-DNA or u-DNA. The uracil is then converted to thymine by adding a methyl group, making thymine-DNA or t-DNA, the kind that is actually used. 4) 

The reaction catalyzed by RNR is strictly conserved in all living organisms. Furthermore RNR plays a critical role in regulating the total rate of DNA synthesis so that DNA to cell mass is maintained at a constant ratio during cell division and DNA repair. A somewhat unusual feature of the RNR enzyme is that it catalyzes a reaction that proceeds via a free radical mechanism of action.The substrates for RNR are ADP, GDP, CDP and UDP. dTDP (deoxythymidine diphosphate) is synthesized by another enzyme (thymidylate kinase) from dTMP (deoxythymidine monophosphate). 1

The iron-dependent enzyme, ribonucleotide reductase (RNR), is essential for DNA synthesis.

The structures of a class III ribonucleotide reductase (RNR) and pyruvate formate lyase exhibit striking homology within their active site domains with respect to each other and to the previously published structure of a class I RNR. The common structures and the common complex-radical-based chemistry of these systems, as well as of the class II RNRs, suggest that RNRs evolved by divergent evolution and provide an essential link between the RNA and DNA world. 2

RNR is a complex of two dimeric proteins termed R1 and R2. 8

That brings us to the classic chicken and egg, catch22 situation. RNR enzymes are required to make DNA. DNA is however required to make RNR enzymes. What came first ?? We can conclude with high certainty that this enzyme buries any RNA world fantasies, and any possibility of transition from RNA to DNA world scenarios. 

and

2. Prebiotic thymine synthesis

Thymidylate synthases (Thy) are key enzymes in the synthesis of deoxythymidylate, 1 of the 4 building blocks of DNA. As such, they are essential for all DNA-based forms of life and therefore implicated in the hypothesized transition from RNA genomes to DNA genomes. Two unrelated Thy enzymes, ThyA and ThyX, are known to catalyze the same biochemical reaction. 7 

Thymidylate synthase (Thy) is a fundamental enzyme in DNA synthesis because it catalyzes the formation of deoxythymidine 5′-monophosphate (dTMP) from deoxyuridine 5′-monophosphate (dUMP). For decades, only one family of thymidylate synthase enzymes was known, and its presence was considered necessary to maintain all DNA-based forms of life. Then, a gene encoding an alternative enzyme was discovered and characterized (Dynes and Firtel 1989; Myllykallio et al. 2002), and the novel enzyme was named ThyX, whereas the other enzyme was renamed ThyA. Even though both reactions accomplish the same key step, the reaction mechanisms, or steps, catalyzed by the FDTS and TS enzymes are structurally different.The 2 enzymes, ThyA and ThyX, were found to have distinctly different sequences and structures, thus alluding to independent origins.

Thats interesting, as we find two distinct enzymes with two different sequences and structures synthesizing the same reaction, thus being a example of convergence right in the beginning. How remote was the chance for this to happen by natural means , considering, that convergence does not favour naturalistic explanations ? 

as Stephen J.Gould wrote: “…No finale can be specified at the start, none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages. Alter any early event, ever so slightly, and without apparent importance at the time, and evolution cascades into a radically different channel.1

Stephen J. Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York, NY: W.W. Norton & Company, 1989), 51.

By virtue of their function and phyletic distribution, Thys are ancient enzymes, implying 1) the likely participation of one or both enzymes during the transition from an RNA world to a DNA world (based on protein catalysts: Joyce 2002) and 2) the probable presence of a gene encoding Thy in the genome of the common ancestors of eukaryotes, bacteria, and archaea (Penny and Poole 1999; Woese 2002; Koonin 2003; Kurland et al. 2006). Thus, tracing back the pathway of genes encoding ThyA and ThyX may shed light on the actively debated wider issue regarding the origins of viral and cellular DNA 

This brings us to the same problem as with Ribonucleotide Reductase enzymes (RNR), which is the classic chicken and egg, catch22 situation. ThyA and ThyX enzymes are required to make DNA. DNA is however required to make these enzymes. What came first ?? We can conclude with high certainty that this enzyme buries any RNA world fantasies, and any possibility of transition from RNA to DNA world scenarios, since both had to come into existence at the same time. 

3. A new chicken-and-egg paradox relating to the origin of life

Cells could not have evolved without viruses, as they need reverse transcriptase (which is found only in viruses) in order to move from RNA to DNA.

In other words, instead of helping to solve the problem of the origin of life on Earth, recent research has only served to highlight one of its central paradoxes. And yet the science media reports the latest discoveries as if the solution is just around the corner. Don’t you find that just a little strange?

“In order to move from RNA to DNA, you need an enzyme called reverse transcriptase,” Dolja said. “It’s only found in viruses like HIV, not in cells. So how could cells begin to use DNA without the help of a virus?”

Creation of double-stranded DNA occurs in the cytosol as a series of these steps:

A specific cellular tRNA acts as a primer and hybridizes to a complementary part of the virus RNA genome called the primer binding site or PBS
Complementary DNA then binds to the U5 (non-coding region) and R region (a direct repeat found at both ends of the RNA molecule) of the viral RNA
A domain on the reverse transcriptase enzyme called RNAse H degrades the 5’ end of the RNA which removes the U5 and R region
The primer then ‘jumps’ to the 3’ end of the viral genome and the newly synthesised DNA strands hybridizes to the complementary R region on the RNA
The first strand of complementary DNA (cDNA) is extended and the majority of viral RNA is degraded by RNAse H
Once the strand is completed, second strand synthesis is initiated from the viral RNA
There is then another ‘jump’ where the PBS from the second strand hybridizes with the complementary PBS on the first strand

http://elshamah.heavenforum.org/t2028-origin-of-the-dna-double-helix#3436

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