The quantified cell.
Bottom Line: The microscopic world of a cell can be as alien to our human-centered intuition as the confinement of quarks within protons or the event horizon of a black hole.We are prone to thinking by analogy-Golgi cisternae stack like pancakes, red blood cells look like donuts-but very little in our human experience is truly comparable to the immensely crowded, membrane-subdivided interior of a eukaryotic cell or the intricately layered structures of a mammalian tissue.So in our daily efforts to understand how cells work, we are faced with a challenge: how do we develop intuition that works at the microscopic scale?
Affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720.Show MeSH
Mentions: Moving to the world of cell biology, we can test our intuition by asking, Which is heavier, a protein or the mRNA that codes for it? Even after years of studying and manipulating DNA, RNA, and protein in our labs, we may not be prepared for this question. Equipped with a few numbers, however, we can answer the question easily and begin to renovate our intuition. Natural amino acids vary somewhat in their molecular mass, but their average mass is ≈100 Da or about threefold less than a nucleotide (weighing ≈300 Da; for full reference to the primary literature Google “BNID 104886,” the BioNumbers ID for this particular quantity). Because the genetic code uses three nucleotides to encode each amino acid, we quickly conclude that an mRNA has a mass about ninefold greater than the protein it encodes (without even accounting for the mass of untranslated regions of mRNA). In contrast to the usual cartoon representations of the central dogma, which can obscure the relative sizes of molecular components, Figure 1 is drawn to scale. If more of our models and textbook figures respected quantitative properties like size and concentration, we might have developed a better intuitive grasp of these properties (for an example of a situation in which paying attention to the relative sizes of proteins was vital see Davis and van der Merwe, 2006; James and Vale, 2012).
Affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720.