Replication autocatalysis

New developments in chemistry can arise from the planning and testing of new synthetic methods. In contemporary chemistry, we can see developments whose roots can be found in biological processes, as the terms signal recognition , replication , autocatalysis or self-replication indicate. Modern ideas in these areas can be found in laboratories where work on peptide chemistry is being carried out. 

Nevertheless, the RNA World hypothesis would seem to answer most of the questions raised above how can an essentially linear molecule be autocatalytic, how can it synthesize proteins, and how can it replicate Autocatalysis can occur because RNA can adopt a wide range of secondary and tertiary structures that position RNA monomers into a preorganized sequence and link them together, it can apply the same flexibility to bind other small molecules and catalyse their polymerization, and it could form weakly interacting sense and antisense duplexes. The main problem is... 

Rebek and his co-workers have shown that replication - autocatalysis based on molecular recognition - best accommodates the facts observed in the reaction of 42 with 43, and that under the published conditions 44 is responsible for the autocatalysis. The results indicated template-catalyzed replication as the source of autocatalysis, where recognition surfaces and functional groups interact to form a productive termolecular complex. The mechanism demands that catalysis would be absent with esters that lack hydrogen-bonding sites. One complication of this system is that the initial product of this bimolecular preassociative mechanism is postulated to be a cw-amide, which isomerized to the frani-amide, the active form of template. This appears to be one major background reaction for product formation (Scheme 14). 

Autocatalysis, although not rare, is not common either. A study of this phenomenon is crucial for the treatment of oscillating reactions, which are presented in Section 8.8. If the data give an indication of autocatalytic behavior, one quick laboratory test is to use the leftover solution from a completed reaction as the solvent for the next. If the replicate is faster than the first trial, autocatalysis is suggested. 

Winter, A. E. (1996), Autocatalysis and the generation of self-replicating systems , Acta Chem. Scand., 50, 469-485... 

In accordance with the autocatalytic process, matrices are again formed. It is surprising that the autocatalysis decreases when only 1 of the 15 building blocks of the peptide has the opposite handedness, e.g., when the N-peptide fragment contains one D-amino acid as well as the 14 L-amino acids. These experimental results show that such a system is able to form homochiral products via self-replication. It can be assumed that similar mechanisms influenced the origin of homochirality on Earth (Saghatelian et al., 2001 Siegel, 2001). 

The initial rate at which the matrix C is formed in these matrix-dependent experiments is related to the initial concentration c by a square-root dependence. This square root law of autocatalysis is found in most self-replicating systems ... 

We still need to clear up one or two points of nomenclature in normal replication of nucleic acids, the matrix (the + strand) and the newly formed daughter strand (- strand) are held together by Watson-Crick hydrogen bonding. This process is also referred to as cross-catalytic . Normal autocatalysis is different it leads to a product which corresponds in structure to the matrix, so that there is no difference between the + and - strands. Such self-complementary sequences are called palindromes. 

This dilemma could be overcome by the hypercycle model hypercycles are in fact not theoretical concepts, but can be observed (in a simple form) in today s organisms, where an RNA virus transfers the information for an enzyme in the host cell, which is able to carry out the preferred synthesis of new virus RNA. This RNA synthesis is supported by host factors, and an RNA minus-strand is formed. The following RNA replication affords a plus-strand. The process corresponds to a double feedback loop and involves the enzyme coded by the RNA matrix and the information present in the matrix in the form of a nucleotide sequence. Both factors contribute to the replication of the matrix, so that there is second-order autocatalysis (Eigen et al., 1982). 

The relation between self-organization and autocatalysis is discussed in some detail by Burmeister (Burmeister, 1998), and that between chirality and self-organization/self-replication in biopolymers is considered from the theoretical point of view by Avetisov and Goldanski (1991). 

Burmeister, J. (1998). Self-replication and autocatalysis. In The Molecular Origin of Life, ed. A. Brack. Cambridge University Press, pp. 295-310. 

In earlier publications we have shown that the principle of selection can be deduced from the premises of a self-replicating system as an extremum principle. It states that inherent linear autocatalysis causes the relative population numbers to take on values that correspond to the highest reproductive efficiency of the system as a whole. The distribution of relative concentrations in the stationary population is, after a short induction period, independent of changes of the system as a whole. The population consists of a uniquely defined wild-type (or several equivalent,... 

Self-replication takes place when a molecule catalyses its own formation by acting as template for the constituents, which react to generate a copy of the template. Such systems display autocatalysis and may be termed informational or non-infor-mational depending on whether or not replication involves the conservation of a sequence of information [9.196]. A problem is the occurrence of product inhibition when the dimer of the template, formed after the first condensation round, is too stable to be easily dissociated by the incoming components for a new cycle. 

In self-replicating systems employing three starting constituents competition between constituents can occur [9.205]. Such processes are on the way to systems displaying information transfer, whereas the two-components ones are non-infor-mational. A shift from parabolic kinetics to exponential growth of the template concentration is required for a selection process to take place [9.197]. The evidence for self-replication on the basis of template-directed autocatalysis as in 184 requires detailed mechanistic investigation on the origin of the catalytic effects observed [9.206]. 

Life is a chemical system capable to replicate itself by autocatalysis and to make errors which gradually increase the efficiency of autocatalysis. 

Autocatalysis in self-complementary systems is generally due to an efficient reaction within the complex T-A-B. If the reaction has no intermediate, or formation of an intermediate is rate limiting, rate enhancement is derived from the reduction in entropy caused by bringing together the reagents on a template. If breakdown of an intermediate is rate limiting (as in the case with our amide-forming replicators), rate enhancement is derived from template stabilization of an intermediate A-B such that product formation is favored over reversion to substrates. 

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