Self-replication functions

Kemp s Acid Enzyme-Cleft and Self-Replication Models 347 5.2.1 Enzyme-Cleft Models with Convergent Functional Croups... 

Analytical chemistry having an interdisciplinary character cannot set aside the attractive power and advances of supramolecular chemistry - the chemistry beyond the molecule or the chemistry of molecular assemblies and of intermolecular bonds as defined by Jean-Marie Lehn, who won the Nobel Prize in 1987. Recognition, reactivity, and transport, as well as self-assembly, self-organization and self-replication are the basic functional features of supramolecular species and chemistry. 

In addition, the authors suggest that all such systems must have a semi-permeable active boundary (membrane), an energy transduction apparatus and (at least) two types of functionally interdependent macromolecular components (catalysts and records). Thus, the phenomenon of life requires not only individual self-replication and self-sustaining systems, but it also requires of such individual systems the ability to develop a characteristic, evolutionary dynamic and a historical collectivist organisation. 

The scientific world was amazed to hear that David Lee, from the laboratory of Reza Ghadiri (Scripps Research Institute, La Jolla, California), had found a self-replicating peptide (Lee et al., 1996) there are analogies to the experiments with oligonucleotides (see Sect. 6.4). Lee was able to show that a certain peptide, containing 32 amino acids, can both function as a matrix and also support its own synthesis autocatalytically. The information transfer is clearly more complex than that involved in nucleic acid replication. In the case of this particular peptide, both the... 

The term self-replication as used below involves two separate functions ... 

Fig. 6.6 Schematic representation of the first minimal self-replicating system. The hexameric product obtained from linking the two trideoxynucleotides can itself function as a matrix (von Kiedrowski et al., 1992)...

We can speak of self-replication only when these two functions occur together. 

More information on the square root law and on kinetic and thermodynamic aspects of the minimal replicator theory can be found in the literature (von Kiedrowski, 1999 and 1993). The square root law has its origin in the product inhibition involved in the mechanism of self-replication. The more C units are formed, the greater is the tendency of the molecules of C to dimerize to give C2 this species, however, cannot function as a catalyst. 

In a self-reproducing, catalytic hypercycle (second order, because of its double function of protein and RNA synthesis) the polynucleotides Ni contained not only the information necessary for their own autocatalytic self-replication but also that required for the synthesis of the proteins Ei. The hypercycle is closed only when the last enzyme in the cycle catalyses the formation of the first polynucleotide. Hypercycles can be described mathematically by a system of non-linear differential equations. In spite of all its scientific elegance and general acceptance (with certain limitations), the hypercycle does not seem to be relevant for the question of the origin of life, since there is no answer to the question how did the first hypercycle emerge in the first place (Lahav, 1999). 

The division of function between DNA (genetic information storage) and protein (catalysis) was, according to the RNA world hypothesis, a later development. New variants of self-replicating RNA molecules developed, with the additional ability to catalyze the condensation of amino acids into peptides. Occasionally, the peptide (s) thus formed would reinforce the self-replicating ability of the RNA, and the pair—RNA... 

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. 

A self-replicating polymer would quickly use up available supplies of precursors provided by the relatively slow processes of prebiotic chemistry. Thus, from an early stage in evolution, metabolic pathways would be required to generate precursors efficiently, with the synthesis of precursors presumably catalyzed by ri-bozymes. The extant ribozymes found in nature have a limited repertoire of catalytic functions, and of the ribozymes that may once have existed, no trace is left. To explore the RNA world hypothesis more deeply, we need to know whether RNA has the potential to catalyze the many different reactions needed in a primitive system of metabolic pathways. 

Difunctional binding and catalysis has been observed in functionalized cyclo-dextrins [5.66] and in a hydrogen bonding cleft [5.67], Functionalized crown ethers have been used as reagent for peptide synthesis [5.68]. Self-replication processes also involve bond formation reactions they will be discussed in Section 9.6. 

Dawkins concept of a gene as a piece of information passed down the generations is worth examining in somewhat greater detail as it has implications for both natural and unnatural self-replicating systems. A successful replicator requires several characteristics that allow it to function better than its competitors. It must be able to make copies of itself from available raw materials. One example of this is the passive... 

Copying is only part of the story. The process of replication is linear it merely produces more replicators. There needs to be another process that takes a functional property of the replicator, which may be derived from its self-replication motif, and translates it into other types of molecules. These other molecules should have some value to the replicator, for example if they either form a protective coat or help to collect and organize the subunits for subsequent incorporation. 

The autocatalytic hypothesis was backed by the reaction s pH sensitivity. Addition of CO2 to the micelles increased acidity resulting in vesicles as the pH dropped below 7. Overall the experiment showed that vesicles could form from a reaction that generates amphiphilic molecules that in turn form autocatalytic micelles. Upon addition of a gas, common in planetary atmospheres, the micelles form vesicles that could function as protocells. The protocells are self-replicating so this process can be considered to be autopoietic, from the Greek for self-forming, and therefore fulfils an essential step in the chemical evolution of life. 

Time sequenced, step growth of branch cells and dendrimer structure Self replication of branch cells throughout dendrimer construction Structural proliferation of dendrimers with exponential amplification of branch cells" and surface functionality as a function of generation... 

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