Macromolecular sequences

Volume 266. Computer Methods for Macromolecular Sequence Analysis... 

Felsenstein, J. (1996). Inferring phylogenies from protein sequences by parsimony, distance and Likelihood methods. In Computer Methods for Macromolecular Sequence Analysis (Doolittle, R. F., ed.), Methods Enzymol. 266, 418-427. 

There are numerous computer software programs that permit one to investigate sequence ahgnment and phylogenetic relationships among (a) various proteins, domains, motifs, modules, etc., and (b) nucleic acid sequences in DNA and RNA. In addition to those presented below, various Internet-based algorithms afford rapid and convenient analysis of macromolecular sequences. 

MACROMOLECULAR SEQUENCE ANALYSIS (Computer Methods) MACROSCOPIC CONSTANTS MICROSCOPIC CONSTANTS ZWITTERION... 

Having highlighted some of the data and issues about the prebiotic chemistry of low-molecular-weight compounds, let s now turn to the functional long chains -mostly proteins and nucleic acids. The first part of this chapter is devoted to the prehiotic chemistry of hiopolymers, the second part, which will necessarily be more speculative, to ideas of conceiving the very origin of macromolecular sequences. 

Let us go back to the problem of the formation of specific macromolecular sequences. The core of the problem lies in the fact that the synthesis of such copoly-meric sequences, like lysozyme or t-RNAP, is not under thermodynamic control. How can we then conceive their formation under prebiotic conditions, i.e., in a time where only spontaneous reactions were possible ... 

Every one of us working in the held has some bias or other. One of mine concerns the question of macromolecular sequences. The bias is, that the bottom-up approach to the origin of life will never be close to a solution - both conceptually and experimentally - unhl the problem of the onset of macromolecular sequences is clarihed. Obviously the origin of the specihc macromolecular sequences (as opposed to simple polymerizahon) is not an easy queshon to answer, as it is linked to the general problem of structure regulahon. 

Tbe answer to the question of the aetiology of macromolecular sequences is elusive as is the emergence of homochirality in the biopolymer chains. Have chains emerged when on Earth there was already an established homochirality of the biomonomers, or was the formation of long chains the cause of the emergence of homochirality ... 

The bottle neck macromolecular sequences Questions for the reader... 

Would you encourage experiments according to the scheme developed in this chapter for explaining the emergence of macromolecular sequences If not, what would you add/modify ... 

Are you in favor of a double origin of macromolecular sequences (one for proteins, one for nucleic acids) or do you believe that one derives from the other in a causal way (genetic code or something similar in primordial time) ... 

As already mentioned, self-organizahon processes give a kind of free ticket to move upwards in the ladder of complexity. However, is this really enough to reach the point of building macromolecular sequences and the hrst self-reproducing protocells ... 

This question is linked to that asked in the previous chapter, relative to the onset of products under kinetic control, such as ATP and, at another level, specihc macromolecular sequences. In fact, the critical point in the origin-of-life scenario is the emergence of kinetic control in chemical reactions. Can this property emerge spontaneously from a scenario of reactions under thermodynamic control Or is it too much to expect from emergence ... 

The bottle neck of the bottom-up approach is the difficulty of reproducing on paper and/or in the laboratory those processes which have been moulded by contingency - such as the synthesis of specific macromolecular sequences. 

Schlesinger, D. H., ed. (1988) Macromolecular Sequencing and Synthesis, Liss, New York... 

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