Genetics, self-replicating system

Animate objects are self-replicating systems containing a genetic code that undergoes mutation and whose variant individuals undergo natural selection. 

Some time after the evolution of this primitive protein-synthesizing system, there was a further development DNA molecules with sequences complementary to the self-replicating RNA molecules took over the function of conserving the genetic information, and RNA molecules evolved to play roles in protein synthesis. (We explain in Chapter 8 why DNA is a more stable molecule than RNA and thus a better repository of inheritable information.) Proteins proved to be versatile catalysts and, over time, took over that function. Lipidlike compounds in the primordial soup formed relatively impermeable layers around self-replicating collections of molecules. The concentration of proteins and nucleic acids within these lipid enclosures favored the molecular interactions required in self-replication. 

Many bacterial cells contain self-replicating, extrachromosomal DNA molecules called plasmids. This form of DNA is closed circular, double-stranded, and much smaller than chromosomal DNA its molecular weight ranges from 2 X 106 to 20 X 106, which corresponds to between 3000 and 30,000 base pairs. Bacterial plasmids normally contain genetic information for the translation of proteins that confer a specialized and sometimes protective characteristic (phenotype) on the organism. Examples of these characteristics are enzyme systems necessary for the production of antibiotics, enzymes that degrade antibiotics, and enzymes for the production of toxins. Plasmids are replicated in the cell by one of two possible modes. Stringent replicated plasmids are present in only a few copies and relaxed replicated plasmids are present in many copies, sometimes up to 200. In addition, some relaxed plasmids continue to be produced even after the antibiotic chloramphenicol is used to inhibit chromosomal DNA synthesis in the host cell. Under these conditions, many copies of the plasmid DNA may be produced (up to 2000 or 3000) and may accumulate to 30 to 40°/o of the total cellular DNA. 

The central component of this RNA World scenario is a replication system that can make copies of the genetic material to grow and produce progeny. The most basic scenario is a simple templated ligation of small oligomers in a cyclical replication scheme (13-16), but ultimately a catalytic entity responsible for this crucial function of replication would be necessary. The simplest example is a single self-replicating ribozyme that can copy itself. More elaborate scenarios for... 

Polypeptides would have played only a limited role early in the evolution of life because their structures are not suited to self-replication in the way that nucleic acid structures are. However, polypeptides could have been included in evolutionary processes indirectly. For example, if the properties of a particular polypeptide favored the survival and replication of a class of RNA molecules, then these RNA molecules could have evolved ribozyme activities that promoted the synthesis of that polypeptide. This method of producing polypeptides with specific amino acid sequences has several limitations. First, it seems likely that only relatively short specific polypeptides could have been produced in this manner. Second, it would have been difficult to accurately link the particular amino acids in the polypeptide in a reproducible manner. Finally, a different ribozyme would have been required for each polypeptide. A critical point in evolution was reached when an apparatus for polypeptide synthesis developed that allowed the sequence of bases in an RNA molecule to directly dictate the sequence of amino acids in a polypeptide. A code evolved that established a relation between a specific sequence of three bases in RNA and an amino acid. We now call this set of three-base combinations, each encoding an amino acid, the genetic code. A decoding, or translation, system exists today as the ribosome and associated factors that are responsible for essentially all polypeptide synthesis from RNA templates in modem organisms. The essence of this mode of polypeptide synthesis is illustrated in Figure 2.8. 

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