How does a ribosome find the exact one of the 20 different amino acids when synthesizing a protein? How fast could we synthesize proteins artificially, without the use of genes or chromosomes or DNA & RNA? I've heard that Solid Phase Protein Synthesis can assemble about 50 amino acids before the folding makes it impossible to attach more.
Last night I learned of the phrase "pulse-chase experiments" from Jeremiah Johnston of New Harvest Research. He led me to some wonderful links.
Treating both protein synthesis and DNA replication as chemical reactions, why does THESE specific chemical reactions "go to completion" instead of innumerably large other possible chemical reactions & rearrangements?
As usual, I want to model everything from the differential equations for the Schrodinger or Dirac wave equation for multiple particles on up.
The details of ribosomal protein synthesis and amino acid recognition by the ribosome through the tRNA are very well understood at the molecular level and can be found in any biochemistry textbook, as can the details of DNA synthesis.
Biosynthetic reactions such as protein synthesis, RNA synthesis, and DNA synthesis are driven forward by coupling them to exergonic reactions, namely phosphodiester bond hydrolysis, which is also explained in the textbooks.
These reactions are able to avoid by-products because they are catalyzed by macromolecular enzymes (also ribozymes in the case of ribosomal protein synthesis) that bind their substrates selectively, and enormously increase the reaction rate over the rate of spontaneous chemical reactions.
Good luck modeling complex biological phenomena with quantum mechanics!
As Adam B Shapiro says, the tRNA recognition mechanism is understood very well. What is not understood so well is the folding mechanism that occurs after/during the polypeptide synthesis. Some aspects are known, of course - e.g. the importance of the shape and size of the ribosome folding site, the necessity of chaperone proteins, etc. - but no one has a model that sufficiently predicts why proteins fold to their working conformations with the rapidity that they do (i.e. milliseconds). To get a scale of the problem, if you have a 100-residue peptide, and allow merely 3 conformations for the phi and psi bonds, and accept that perhaps 1,000,000 (the third power of 100) configurational state will wind up with the active version of your polypeptide, then the propability of that happening without a catalyst works out to 1 chance in 10^294 power. Essentially zero. That means that you need to have a catalyst in your model, and know how the catalyst is functioning. Otherwise, you will always calculate that it never realistically happens.
The "protein folding problem" is an active area of research, and has been for decades. Modern computing power has now reached a stage where small proteins can be folded in silico with a fair degree of agreement to the experimentally determined structures.
Relatively small proteins can be completely denatured with strong chaotropes, then refolded under experimentally determined conditions to the native state. This is how we know that the information for the 3-D structure of a protein is contained entirely within its amino acid sequence. In vivo, proteins fold while they are being synthesized by the ribosome. Chaperone proteins may be required to assist some proteins to fold properly by preventing aggregation.
Here is a nice Wikipedia article on protein folding:
https://en.wikipedia.org/wiki/Protein_folding#Computational_studies_of_protein_folding
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