There are many animations of the ribosome in action, and all I have seen show the correct tRNA neatly entering the ribosome and its amino acid being added to the growing protein chain. My question is this: is it really possible that mere brownian motion and diffusion are responsible for getting the right tRNA out of 20 possible types to that point? Presumably that would require tRNAs of every type arriving and most being rejected until the right one meets its codon and is used. Not only that, you would expect orders of magnitude more tRNAs to be arriving at almost the right place but being the wrong way round or hitting the wrong place on the ribosome. Has anyone in the field ever done any calculations using dynamics equations, along with the known volume of cytoplasm and tRNAs to see if this is even feasible?
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$\begingroup$ I think it has something to do with the cytoskeleton. nature.com/articles/nrm2818 $\endgroup$– MesenterySep 10, 2019 at 16:18
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$\begingroup$ Forget any animations you have seen — they are irrelevant. But the fact is translation happens at a particular rate. That's chemistry. What else do you suggest? Magic? $\endgroup$– DavidSep 10, 2019 at 16:54
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1$\begingroup$ @user237650 — Certainly the cellular environment may increase the concentration of components, but the fact remains you can do it in the test tube with purified components. $\endgroup$– DavidSep 10, 2019 at 17:18
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$\begingroup$ Please look up the definition of Brownian (names after Brown) Motion. You will find it refers to macroscopic particles, not the molecules that cause it. $\endgroup$– DavidSep 10, 2019 at 19:04
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$\begingroup$ And why do you think it matters if there are 20 times as many collisions that cannot be productive as those that can? It would only matter if it competed with the potentionally productive collisions, which it is unlikely to do at the concentrations in the cell. The need for collision of molecules in the right orientation for reaction is a standard feature of chemistry. Catalytic or binding protein in biochemistry often work by facilitating the correct interaction by binding to others. Transfer RNA is brought to the proteins ribosome A-site by elongation factors. $\endgroup$– DavidSep 10, 2019 at 20:50
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The answer is simply due to the random walk of the amino acids. Over small volumes, this process is incredibly quick and is also responsible for nucleotide delivery to polymerases as well proteins searching for their substrates, in fact, only a few enzymes/proteins are limited by the rates of random walk motion. I'm sure there are lots of papers which discuss the rates of trna movement in the cell, but this is the first one that I found: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727733/ (You are completely right about competing tRNAs and the orientation of the tRNA entering the ribosome, all of these factors are taken into account in calculations. Ribosome animations are also a massive oversimplification, they illustrate certain points well but they are by no means accurate, they are useful for reaching purposes!)
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$\begingroup$ I have upvoted your answer as you provide a useful reference, but please edit it to remove the reference to diffusion. Diffusion is the movement of molecules down a concentration gradient. The motion of molecules in general (and in this context) is random (stochastic) motion resulting from their kinetic energy. Hence its temperature dependence. You might also mention the existence of elongation factors which have an affinity for the A-site on the ribosome. $\endgroup$– DavidSep 10, 2019 at 19:17
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$\begingroup$ Hi David, I think I would disagree with you on that, diffusion is a stochastic process and the paper both mentions this and states several times that the method of transport is diffusion. $\endgroup$ Sep 10, 2019 at 19:38
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$\begingroup$ I think you misunderstand my point. The basic movement of molecules that allows their collision and reaction is not due to diffusion but to their kinetic energy. The poster is asking a chemical question and seems not to understand that. Molecular diffusion can, of course, occur in addition to this when there is difference in concentration between the point at which there is an accumulation of molecules and that at which they react. The random component of this is in addition to the effect of concentration difference. $\endgroup$– DavidSep 10, 2019 at 20:44
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$\begingroup$ Thanks for the answers. I should say I am not a biologist or a chemist but a mechanical engineer by training but now I run an animation company. As per my original question I am somewhat frustrated by the way molecular biology animations always show proteins and other molecules involved in transcription/translation floating around as though they have agency and the ability to 'swim' where they are required. As the replies have asserted, this is not the way it works - I just wonder if there's a way of conveying something more accurate in an animation.. I will have to experiment $\endgroup$ Sep 11, 2019 at 16:50