The process from the biopolymers possessing self-replication and enzymelike activities to a real life is still unclear. 1
DNA/Protein World Dilemma
The RNA world claims that, in the beginning, phases of evolution, RNA behaved as both template and catalyst. All existing biological organisms exhibit the partition of tasks between template and catalyst. In existing biological systems, the partition of tasks is an elemental property: DNA stores genetic information whereas proteins function as catalysts. However, scientists are struggling to answer major questions such as: how did the DNA/Protein world come about, why would such partition of tasks evolve in the RNA world, and which came first, DNA or Protein? Again, we find the ‘chicken and egg’ problem.
Proteins may seem superficially better than RNA as chemical catalysts due to their larger range of chemical moieties and structural flexibility. On the contrary, due to the nonexistence of mechanisms for template-directed replication, proteins are greatly substandard to RNA for the storage of genetic information. Because of the absence of the 29-hydroxyl at its sugar moiety, as compared to RNA, DNA is usually not as much of a reactive molecule. Especially, DNA is significantly more resistant to hydrolysis than RNA, particularly in the presence of metal ions. For this reason, time and again it is recommended that DNA has an edge over RNA as a means of genetic information storage. Nevertheless, Forterre reported that the superior stability advantage of DNA could not account for the origin of DNA because the benefit of using DNA for information storage depends on the chance of evolving a longer genome, which in itself would not offer any direct selective advantage to the systems that included DNA. There is also no apparent experimental confirmation indicating that DNA is substandard to RNA as a chemical catalyst. The chemical properties of DNA do not inevitably support the conclusion that the function of DNA is limited to information storage. Takeuchi and his research group asked the question, “Given these considerations, we ask: What selective advantage could there be for an RNA-based evolving system to evolve an entity that is solely dedicated to the storage of genetic information, i.e., an entity that is functionally equivalent to DNA?”
The sequence of emergence of different types of biopolymers during primordial evolution is an extremely controversial issue. There is an impasse attached to both the cases: (1) proteins preceding RNA, and (2) RNA preceding proteins. In existing biological systems, DNA synthesis is fully reliant on RNA. For instance, the monomer units for DNA synthesis, 2’-deoxyribonucleotides, are produced by the alteration of ribonucleotides, and the primers utilized to start DNA polymerization are oligoribonucleotides. It is observed that the catalytic portion of the ribosome, which produces proteins, is made completely of RNA. This is the significant reason touted for proteins preceding RNA. If one accepts that RNA is an inferior and less flexible catalyst than proteins, then the immediate question would be: what is the selective pressure responsible for the evolution of RNA catalysts? Transitioning from RNA to DNA as the hereditary molecule significantly enhanced genomic steadiness. This is believed to improve the possibility that a given organism or molecule would be around long enough to reproduce. Transmission of the task of primary catalyst to proteins also presents major advantages. Both transitions provide understandable advantages to a ribo-organism, nonetheless in fundamentally different ways. Hence, both would manifest following different evolutionary pathways. If we presume RNA was the first of the three macromolecules, an unsolved dilemma is which came next, DNA or protein?
The transition from the RNA to the DNA world was a major event in the history of life. The invention of DNA required the appearance of enzymatic activities for both synthesis of DNA precursors, retro-transcription of RNA templates and replication of singleand double-stranded DNA molecules. Recent data from comparative genomics, structural biology and traditional biochemistry have revealed that several of these enzymatic activities have been invented independently more than once, indicating that the transition from RNA to DNA genomes was more complex than previously thought. The distribution of the different protein families corresponding to these activities in the three domains of life (Archaea, Eukarya, and Bacteria) is puzzling. In many cases, Archaea and Eukarya contain the same version of these proteins, whereas Bacteria contain another version. However, in other cases, such as thymidylate synthases or type II DNA topoisomerases, the phylogenetic distributions of these proteins do not follow this simple pattern. Several hypotheses have been proposed to explain these observations, including independent invention of DNA and DNA replication proteins, ancient gene transfer and gene loss, and/or nonorthologous replacement. We review all of them here, with more emphasis on recent proposals suggesting that viruses have played a major role in the origin and evolution of the DNA replication proteins and possibly of DNA itself. 2
Deoxyribonucleotides Are Synthesized by the Synthesis of Deoxynucleotides Reduction of Ribonucleotides Through a Radical Mechanism
We turn now to the synthesis of deoxyribonucleotides. These precursors of DNA are formed by the reduction of ribonucleotides; specifically, the 2' -hydroxyl group on the ribose moiety is replaced by a hydrogen atom. The
substrates are ribonucleoside diphosphates, and the ultimate reductant is NADPH. The enzyme ribonucleotide reductase a is responsible for the reduction reaction for all four ribonucleotides. The ribonucleotide reductases of
different organisms are a remarkably diverse set of enzymes. Yet detailed studies have revealed that they have a common reaction mechanism, and their three-dimensional structural features indicate that these enzymes are
a Ribonucleotide reductase (RNR), also known as ribonucleoside diphosphate reductase (rNDP), is an enzyme that catalyzes the formation of deoxyribonucleotides from ribonucleotides. It catalyzes this formation by removing the 2'-hydroxyl group of the ribose ring of nucleotide diphosphates. This reduction produces deoxyribonucleotides. Deoxyribonucleotides in turn are used in the synthesis of DNA. 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 3
1. GENESIS - IN THE BEGINNING, page 125
Last edited by Admin on Thu Mar 29, 2018 5:21 am; edited 4 times in total