At this point, let us consider a number of interesting behaviors associated with translation. First, the onset of translation begins with the small ribosomal subunit interacting with the 5’ end of the mRNA.; the assembly of this initial complex involves the a number of components, and takes time to occur, but once formed can persist. While this complex exists (that is, before it dissociates) multiple ribosomes can interact with the mRNA, each synthesizing a polypeptide. This leads to a behavior known as translational bursting, in which multiple polypeptides a synthesized in a short period of time from a single RNA. Once the translation initiation complex dissociates, it takes time (more time than just colliding with another small ribosome subunit) before it forms again. This leads to bursts of new polypeptide synthesis followed by periods when no new polypeptides are made. A similar process, transcriptional bursting, is observed with the synthesis of mRNAs. Since the number of mRNA molecules encoding a particularly polypeptide can be small (less than 10 per cell in some cases), the combination of transcriptional and translational bursting can lead to noisy protein synthesis.
The translation system is dynamic and a major consumer of energy within the cell240. When a cell, particularly a bacterial cell, is starving, it does not have the energy to generated amino acid charged tRNAs. The result is that uncharged tRNAs accumulate. Since uncharged tRNAs fit into the amino-acyl-tRNA binding sites on the ribosome, their presence increases the probability of unproductive tRNA interactions with the mRNA-ribosome complex. When this occursthe stalled ribosome generates a signal (see241) that can lead to adaptive changes in the cell that enable it to survive for long periods in a “dormant” state242.
Another response that can occur is a more social one. Some cells in the population can “sacrifice” themselves for their (generally closely related) neighbors (remember kin selection and inclusive fitness.) This mechanism is based on the fact that proteins, like nucleic acids, differ in the rates that they are degraded within the cell. Just as ribonucleases can degrade mRNAs, proteases degrade proteins and polypeptides. How stable a protein/polypeptide is depends upon its structure, which we will be turning to soon.
A common system within bacterial cells is known as an addiction module. It consists of two genes, encoding two distinct polypeptides. One forms a toxin molecule which when active can kill the cell. The second is an anti-toxin, which binds to and renders to toxin molecule inactive. The key feature of the toxin-anti-toxin system is that the toxin molecule is stable, it is has a long-half life. The half-life of a molecule is the time it takes for 50% of the molecules present within a population at a particular time to be degraded (or to otherwise disappear from the system.) In contrast, the anti-toxin molecule’s half-life is short. The result is that if protein synthesis slows or stops, the level of the toxin will remain high, while the level of the anti-toxin will drop rapidly, which leads to loss of inhibition of the toxin and the death of the cell. Death leads to the release of the cell’s nutrients, nutrients that can be used by its neighbors. A similar process can occur if a virus infects a cell. If an infected cell kills itself before the virus can replicate, the virus is destroyed and the cell’s neighbors (who are likely to be its relatives) survive.
Questions to answer & to ponder:
•What are the “natural” limits to the structure of an R-group in a polypeptide?
•How would a condensation reaction be effected by the removal of water from a system?
•Why do we think that the use of a common set of amino acids is a homologous trait?
•What factors can you imagine influenced the set of amino acids used in organisms?
•Why so many tRNA genes?
•Why does the ribosome tunnel inhibit the folding of the newly synthesized polypeptide?
•What types of molecules does DNA directly encode? How about indirectly?
•How might a DNA molecule encode the structure of a lipid?
•How, in the most basic terms, do different tRNAs differ from one another?
•What is the minimal number of different tRNA-amino acid synthetases in a cell?
•What could happen if a ribosome started translating an mRNA at the "wrong" place?
•Why don’t release factors cause the premature termination of translation at non-stop codons?
•What does it mean to say that the genetic code is an algorithm?
•What is meant when people call the genetic code a "frozen accident"?
•What is (seriously) unrealistic about this tutorial [http://youtu.be/TfYf_rPWUdY]?
•Design a process (and explain the steps) by which you might reengineer an organism to use a new (non-biological) type of amino acid in its proteins.
240 Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources: http://www.ncbi.nlm.nih.gov/pubmed/24766808
242 Characterization of the Starvation-Survival Response of Staphylococcus aureus: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC107086/