Figure 2.

A. Nascent r-protein peptides cannot participate in translation before their own translation is completed. Sub-dividing the protein mass into more and smaller pieces reduces the inactive fraction, but also increases the number of translation initiations required. B. The penalty, due to finite number of r-proteins, that is incurred on the minimal time fraction (from Eq. 1) that ribosomes must spend on their own production. Penalty is plotted as a function of n for different values of τ/T_gen (1 Red, 1/2 Blue, 1/4 Yellow, 1/10 Magenta), and is calculated relative to τln(2)/T_gen which is the asymptotic value achieved at high n, possibly reducing the penalty as much as 1/ln(2)≃1.44 fold. C. The fraction of dedicated r-protein mass that is elongationally idle, due to nascent r-protein peptides and ribosomes occupied in initiation, is minimized for an optimal number of r-proteins, n_opt. D. The n_opt from Eq. (2) and panel C for E. coli (orange) and S. cerevisiae (blue), in the range of the expected ratios between initiation and elongation rates (see main text). The shaded area above the lines would be accessible if ribosome could produce slightly less of the larger sub-unit, which only enters at the last step of initiation (SI). E. Across organisms, average lengths of proteins in ribosomes are 2–3 times smaller than in genomes [22]. F. The average length (amino acids) of proteins in S. cerevisiae multi-protein complexes vs. the number of proteins in the complex. Each colored circle corresponds to a known complex [23] (area is proportional to total number of amino acids). Gray represents the predicted probability density when drawing random genes from the genome. Most of the 403 complexes fall within the expected 99 % confidence interval, except the ribosome (80S, including both subunits SSU and LSU independently), that falls ~7 standard deviations below.