1. I will arise and go now, for always night and day

2. I hear lake water lapping with low sounds by the shore;

3. While I stand on the roadway, or on the pavements gray,

4. I hear it in the deep heart’s core.

5. (William Butler Yeats, The Lake of Innisfree, 1888)

GENERAL IDEA

Here we venture beneath the surface of the cell membrane to explore some of the key biological processes that occur in the core of cells, which have been investigated using single-molecule biophysics techniques either in living samples or in physiologically relevant settings in the test tube.

Introduction

As we saw in the previous chapter, the cell membrane, with its various associated integrated protein complexes, is a key structure being the first point of contact for the cell with the outside world. However, the meat of the cellular machinery for metabolizing nutrients, manufacturing new molecular material, responding to signals detected at the cell membrane surface and for storing its genetic code are all located in the innards of the cell, either occurring in the cytoplasm often associated with a variety of cellular sub-structures or, in the case of eukaryotic cells, in specialized membrane-bound organelles. Previously, we discussed some details of two such organelles in the context of membrane-localized processes, the chloroplasts that perform photosynthesis in plant cells and mitochondria that generate the universal cellular fuel of ATP. Here, we will also extend the discussion to processes occurring in the cell nucleus, how the genetic code is packaged and ultimately replicated, and the means by which this code is converted into molecules of protein. But we will begin the chapter outside the nucleus and discuss the biophysical properties of the cytoplasm, and the mechanisms by which molecular cargo is controllably trafficked and sorted inside the cell.