Most proteins in a cell are synthesized in close proximity to the nucleus through a process known as ‘translation,’ in which ribosomes translate mRNA into protein following its export from the nucleus. Proteins that will be secreted or integrated into membranes must be processed within the endoplasmic reticulum (ER). This requires a signal sequence that enables the docking of the ribosome to the ER. During translation, the protein is moved into the lumen of the ER, where it will be processed. Other mRNAs are targeted for transport to selected regions of the cytoplasm or for sequestration until proper signals are received. The number of proteins synthesized from a single mRNA is highly variable, but is usually in the range of 100–1000 copies. The subsequent lifetime of the protein depends largely upon whether it is properly synthesized. Defective, misfolded proteins, or proteins that are no longer required, will be actively removed from the cytoplasm. This is achieved through a process of ubiquitinylation, which flags the protein for degradation by a proteasome. This process is dependent upon the activation of ubiquitin ligases that are downstream in a number of signaling pathways. Both localized protein synthesis and targeted degradation can facilitate cellular functions by dramatically altering the concentrations of proteins at critical times.

Protein production is truly the hallmark of life as we know it, as proteins form the machinery that performs most cellular functions. As such, the translation of mRNA into protein is an extremely sophisticated process and one can imagine that virtually every mutation of the proteins in the ribosome and in the ribosomal RNA have been tested by cells or organisms. Any improvements would be shared with other organisms and, thus, the current ribosomes should be viewed as particularly robust. In this chapter, we will first discuss the actual process of protein production and the sophisticated adaptations for larger eukaryotes, including localized synthesis, protein folding, and processing. Protein degradation is the balance to synthesis and is used to rapidly block functions as well as to remove denatured proteins or recycle proteins in starvation conditions. Assuming proper nutrient levels, the goal of protein production and turnover is to provide the cell with the tools needed to perform the differentiated cell functions as well as face many environmental challenges from hyperthermia and trauma to various bacterial and viral challenges.