Chapter 2 – Orientation for the Bio-Curious  19

the DNA sequence that encodes for this structure). The general structure of a ribosome

consists of a large subunit and a small subunit, which are similar between prokaryotes and

eukaryotes. In fact, the DNA sequence that encodes part of the small subunit, which consists

of a type of nucleic acid (which we will discuss later called the “ribosomal RNA” (rRNA)—​in

prokaryotes, referred to as the 16S rRNA subunit, and in eukaryotes as the slightly larger

18S rRNA subunit), is often used by evolutionary biologists as a molecular chronometer

(or molecular clock) since changes to its sequences relate to abrupt evolutionary changes

of a species, and so these differences between different species can be used to generate an

evolutionary lineage between them (this general field is called “phylogenetics”), which can

be related to absolute time by using estimates of spontaneous mutation rates in the DNA

sequence.

The region of the nuclear material in the cell is far from a static environment and also

includes protein molecules that bind to specific regions of DNA, resulting in genes being

switched on or off. There are also protein-​based molecular machines that bind to the DNA

to replicate it, which is required prior to cell dividing, as well as molecular machines that

read out or transcribe the DNA genetic code into another type of molecular similar to DNA

called “ribonucleic acid” (RNA), plus a host of other proteins that bind to DNA to repair and

recombine faulty sections.

Other subcellular features in eukaryotes include the endoplasmic reticulum and Golgi

body that play important roles in the assembly or proteins and, if appropriate, how they are

packaged to facilitate their being exported from cells. There are also other smaller organelles

within eukaryotic cells, which appear to cater for a subset of specific biological functions,

including lysosomes (responsible for degrading old and/​or foreign material in cells), vacuoles

(present in plant cells, plus some fungi and unicellular organisms, which not only appear

to have a regulatory role in terms of cellular acidity/​pH but also may be involved in waste

removal of molecules), starch grains (present in plant cells of sugar-​based energy storage

molecules), storage capsules, and mitochondria (responsible for generating the bulk of a mol­

ecule called “adenosine triphosphate” [ATP], which is the universal cellular energy currency).

There are also invaginated cellular structures called “chloroplasts” in plants where light

energy is coupled into the chemical manufacturing of sugar molecules, a process known

as photosynthesis. Some less common prokaryotes do also have structured features inside

their cells. For example, cyanobacteria perform photosynthesis in organelle-​type structures

composed of protein walls called “carboxysomes” that are used in photosynthesis. There is

also a group of aquatic bacteria called “planctomycetes” that contain semicompartmentalized

cellular features that at least partially enclose the genetic DNA material into a nuclear

membrane–​type vesicle.

Almost all cells from the different domains of life contain a complex scaffold of protein fibers

called the “cytoskeleton,” consisting of microfilaments made from actin, microtubules made

from the protein tubulin, and intermediate filaments composed of several tens of different

types of protein. These perform a mechanical function of stabilizing the cell’s dynamic 3D

structure in addition to being involved in the transport of molecular material inside cells, cell

growth, and division as well as movement both on a whole cell motility level and on a more

local level involving specialized protuberances such as podosomes and lamellipodia.

2.2.5  CELL MEMBRANES AND WALLS

As we have seen, all cells are ultimately encapsulated in a thin film of a width of a few

nanometers of the cell membrane. This comprises a specialized structure called a “lipid

bilayer,” or more accurately a phospholipid bilayer, which functions as a sheet with a hydro­

phobic core enclosing the cell contents from the external environment, but in a more complex

fashion serves as a locus for diverse biological activity including attachments for molecular

detection, transport of molecules into and out of cells, the cytoskeleton, as well as performing

a vital role in unicellular organisms as a dielectric capacitor across which an electrical and

charge gradient can be established, which is ultimately utilized in generating the cellular fuel

of ATP. Even in relatively simple bacteria, the cell membrane can have significant complexity