Protein world

In today s discussion of the origin of life, the RNA World (Chapter 6) is seen as much more important, and is much better publicized, than the protein world . However, nucleic acids and proteins are of equal importance for the vital metabolic functions in today s life forms. Peptides and proteins are constructed from the same building blocks (monomers), the aminocarboxylic acids (generally known simply as amino acids). The way in which the monomers are linked, the peptide bond, is the same in peptides and proteins. While peptides consist of only a few amino acids (or to be more exact, amino acid residues), proteins can contain many hundreds. The term protein (after the Greek proteuein, to be the first) was coined by Berzelius in 1838. 

What is the importance of this enzyme family for the biogenesis problem These enzymes form the link between the protein world and the nucleic acid world . They catalyse the reaction between amino acids and transfer RNA molecules, which includes an activation step involving ATR The formation of the peptide bond, i.e., the actual polycondensation reaction, takes place at the ribosome and involves mRNA participation and process control via codon-anticodon interaction. 

V. Swiss-prot + TrEMBL A Complete and Nonredundant View on Protein World... 

M9. Meuwissen, J., Heirwegh, K., and De Groote, J., Intracellular bilirubin binding to proteins. World Congr. Gastroenterol. [Proc.], 3rd, Tokyo, 1966 4, 85-86 (1967). 

Figure 8.4 The autopoietic cycle extended to the DNA/RNA/protein world. This is the autopoietic representation of coded life.

The notion that RNA existed prior to enzymes and that RNA molecules can be catalytically active is by now well accepted. Indeed, RNA molecules have been observed to catalyze phophodiester bond breaking and synthesis (as occurs during replication and splicing) but also reactions more distant to its stmcture, such as amide bond formation (Wiegand, 1997). RNA thus provided the means to assemble peptides which may have led to the protein world of today (Zhang and Cech, 1998). Reactions catalyzed by RNA molecules have thus far not been employed in biocatalysis and it is unlikely that... 

How might a self-replicating polymer come to be How might it maintain itself in an environment where the precursors for polymer synthesis are scarce How could evolution progress from such a polymer to the modern DNA-protein world These difficult questions can be addressed by careful experimentation, providing clues about how life on Earth began and evolved. 

Phillips, D C. Protein Engineering/ Review (Umv. of Wales), 46 (March 1987). Richards, F.M. The Protein Folding Problem, ScL Amer., 54 (January 1991). Radousky, H.B., G. Hammond, Z. Xu, et al. Gene Families Studies of DNA, RNA, Enzymes and Proteins, World Scientific Publishing Company. Inc., River Edge, NJ, 2001. 

The first hypothesis is that RNAs have used available amino acids to evolve from an RNA only world towards a nucleic acid-protein world. This hypothesis is in agreement with the role of RNA in the translation machinery, as for example the fact that the peptidyl transferase activity of the ribosome has been associated with the nucleic acid moiety and not the protein moiety [16,17]. The driving force that guided the evolution from the RNA world towards the emergence of the translation machinery might have been that amino acids played a role of ribozyme cofactors [6,7]. 

Let us assume for now that an exponentially growing protocell with an enclosed autocatalytic metabolism could form and eventually evolve RNA enzymes. RNA enzymes would have co-evolved with the original metabolic pathways. After the evolution of protein enzymes, further takeover and transformation of pathways would have occurred. Pohorille and New [138] observed since there is no relationship between the RNA catalytic power of a given RNA and the protein for which that RNA can code, there is no clear path from the RNA world to the protein world. Therefore, protein cladis-tics can only make conclusions about metabolism after protein enzymes have... 

All this tells us that the evolution of primitive ribosoids into protoribomes and ribogenomes could have produced - at equal thermodynamic conditions - a countless number of other protein worlds, and therefore countless other forms of life. In the course of precellular evolution, therefore, two distinct processes went on in parallel the development of metabolic structures, and the development of a particular genetic code that gave life the familiar forms of our world, and not those of countless other possible worlds. 

Before describing the protein world, let us reflect on motion and time scales in general. When we consider human life on Earth, we observe a very wide range of different motions, naturally distinct from—but not completely dissimilar to—... 

Figure 2.8. Linking the RNA and Protein Worlds. Polypeptide synthesis is directed by an RNA template. Adaptor RNA molecules, with amino acids attached, sequentially bind to the template RNA to facilitate the formation of a peptide bond between two amino acids. The growing polypeptide chain remains attached to an adaptor RNA until the completion of synthesis.

In the protein world structural conservatism and diversity are combined on two different levels conservatism in the more macroscopic, that is, the structural level and diversity on the microscopic level, that is, the individual amino acid sequence. The fold defines the scaffold of the protein, that is, the 3D structure of the amino acid backbone, as well as the shape and size of the active site and the spatial orientation of the catalytic residues. The individual amino acid side chains forming the active site and its catalytic residues determine the molecular interactions between the protein and the ligand. The same fold can be assembled by amino acid sequences with only as little as a few percent sequence similarity. Thus both, fold and sequence, determine together the binding properties of any protein and enable the vast number of specific functions to be carried out by a limited number of fold types. ... 

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