Biological complexity: 60 million proteins in a cell (Introduction)

by David Turell , Thursday, October 06, 2016, 02:32 (2971 days ago) @ David Turell

These molecules are polypeptides which are strings of amino acids, generally 200 or more, with folding that is required to be exact in 3-D form to be functional:-http://www.evolutionnews.org/2016/10/imagine_60_mill103182.html-"Here are some "wow" facts they share about the proteins in a tiny yeast cell:-"Collectively, proteins catalyse and control essentially all cellular processes. They form a highly structured entity known as the proteome, the constituent proteins of which carry out their functions at specific times and locations in the cell, in physical or functional association with other proteins or biomolecules. A proliferating Schizosaccharomyces pombe cell contains about 60 million protein molecules, which have abundances that range from a few copies to 1.1 million copies per expressed gene. Across the species, proteins constitute about 50% of the dry mass of a cell and reach a remarkable total concentration of 2-4 million proteins per cubic micrometre or 100-300 mg per ml. The extensive proteome network of the cell adapts dynamically to external or internal (that is, genetic) perturbations and thereby defines the cell's functional state and determines its phenotypes. Describing and understanding the complete and quantitative proteome as well as its structure, function and dynamics is a central and fundamental challenge of biology.-***-"All these millions of proteins cooperate to contribute to the life and health of the cell, responding dynamically to perturbations, each playing its role to provide energy from nutrients, deliver cargo, translate and maintain genetic information, remove waste, and replicate. -***
" Axe estimated the prevalence of sequences that could fold into a functional shape by random combinations. It was already known that the functional space was a small fraction of sequence space, but Axe put a number on it based on his experience with random changes to an enzyme. He estimated that one in 10^74 sequences of 150 amino acids could fold and thereby perform some function -- any function. -***-"It is useful to begin by considering the fraction of protein sequence space that is occupied by naturally occurring proteins. The number of distinct sequences that are possible for a protein of typical length is 20200 sequences (because each of the protein's 200 residues can be one of 20 amino acids), and the number of distinct proteins that are produced by extant organisms is on the order of 10^12. Evidently, evolution has explored only a tiny region of the sequence space that is accessible to proteins.-***-"Since 20^200 is about 10^260, and the space actually sampled by living organisms is 1012, the numbers differ by at least 240 orders of magnitude for proteins of length 200, or about 183 orders of magnitude the 150-amino-acid chains Axe used. No wonder the authors say that "the natural evolutionary process has sampled only an infinitesimal subset" of sequence space.-***-"Any random search has no possible chance, using all the atoms in the universe for the entire age of the universe, of finding a functional cluster in such a vast space. Dembski said that any search for a target that has less than 1 chance in 10^150 exceeds the universal probability bound; it will never happen anywhere in the entire history of the universe. (my bold)-***-"Functions that naturally occurring proteins mediate include: the use of solar energy to manufacture complex molecules; the ultrasensitive detection of small molecules (olfactory receptors) and of light (rhodopsin); the conversion of pH gradients into chemical bonds (ATP synthase); and the transformation of chemical energy into work (actin and myosin). Not only are these functions remarkable but they are encoded in sequences of amino acids with extreme economy. Such sequences specify the three-dimensional structure of the proteins, and the spontaneous folding of extended polypeptide chains into these structures is the simplest case of biological self-organization." (my bold)-Comment: This article once again shows that blind chance search of all available protein molecule sizes and shapes cannot create life. What has been created is too economical in function for a random process. Life comes from only 10^12 of the possibilities. How were they selected to efficiently run life? Not by chance!