Soft Machines

Biological macromolecules, such as DNA, RNA and protein, spend much of their time in the company of other macromolecules, rather than floating freely on their own. The resulting molecular behavior in a cell resembles the choreographed handoff of a product between machines in an assembly line, rather than the indiscriminate reactions of molecules in a chemistry-lab beaker. The intriguing twist is that the "machines" are themselves collections of biological macromolecules that can also come and go.

Specialized cellular structures, known as organelles, are basic to any introduction to cell biology. But the usual suspects, such as the nucleus, mitochondria, chloroplasts, the endoplasmic reticulum and golgi apparatus, and various vacuoles, are all delineated by membranes. The lipid molecules of the membrane are also free to come and go, of course, but this construction makes it easy to define the organelles.

Other structures, often not called organelles because they lack a membrane, are just as important. The best known examples are ribosomes, which are large enough (about 0.02 microns) to have been noticed in electron micrographs some fifty years ago. They are complexes of specialized RNA with specific proteins, together known as ribonucleoprotein, or RNP. The ribosomes translate the sequence of bases in a messenger RNA strand into a corresponding amino-acid sequence in a growing protein.

Another structure, found in the nucleus, is the spliceosome. This critical RNP complex processes pre-RNA that is directly transcribed from the DNA, cutting out some sections and splicing the rest back together to form a proper protein-coding sequence. The spliceosome frequently splices in different sections of the pre-RNA to specify different variants of the protein, depending on cellular conditions. Once the strand is equipped with a cap and a tail on opposite ends, it is a messenger RNA ready for export from the nucleus.

Back outside the nucleus, the messenger RNA may encounter two other types of RNP structures, known as processing bodies and stress granules (the latter appear only in stressed cells). Messenger RNA can be temporary stored in either of these complexes, delaying its translation into protein by the ribosomes. Processing bodies can also permanently degrade the RNA preventing it from being translated. In ways that are still being explored, this degradation is associated with the RNA interference, in which short regulatory RNAs work with proteins to target messenger RNA strands that have a mostly complementary sequence.

Experiments show that molecules are constantly entering and leaving these complexes (at least some of them), unimpeded by any membrane, so there may be no clear line between them and the transient association of a few macromolecules. These dynamic association are similar to the shifting alliances of politicians in congress, some formal and restrictive like a political party, some more of an informal hallway conversation, but each contributing to the political process. Molecular complexes in the cell, though not always recognized, are equally critical to its function.