cytoplasm. Additional membranes are found in photosynthetic organisms, in particular the thylakoid membrane, which is the site of photosynthesis in chloroplasts and cyanobacteria.
Membranes also contain proteins, either integral membrane proteins, which span the lipid bilayer, or peripheral membrane proteins, which are associated with one or other side of the membrane but do not cross the bilayer. Many of the proteins essential for photosynthesis are membrane proteins. All cells also contain a variety of carbohydrates, or sugars, as well as many other small molecules essential for proper cellular function. When viewed in this way, the similarities among the various classes of life far outweigh the differences.
Despite the fundamental similarities just pointed out, life nevertheless comes in a remarkable variety of shapes and sizes. These differences form the basis of our mechanisms of classification of living things.
2.2 Classification of life
There are many ways to organize and classify life. No one method is inherently superior to any other, as all such systematic organizations are ultimately only for our benefit. Classification methods are usually structured to accomplish a desired goal, such as rapid identification of organisms in the field or the laboratory. One of the most informative ways to classify organisms is based on evolutionary relationships. This evolutionary, or phylogenetic, approach has led to the recognition that there are three fundamental domains of living organisms: bacteria, archaea (formerly called archaebacteria), and eukarya. This division of the tree of life into the three domains is based on a classification of organisms according to the small subunit rRNA method introduced by Carl Woese (Fig. 2.1). This method relies on comparisons of the sequences of RNA molecules that are part of the ribosome, the protein‐synthesizing particle. For bacteria and archaea, the RNA molecule that is used is known as 16S rRNA, while for eukaryotes it is a related molecule known as 18S rRNA. The S stands for Svedberg units, which derive from early methods of molecular weight determination using ultracentrifuges. The basis of this molecular evolution method is the fact that the positional order, or sequence, of building blocks of a biological macromolecule retains information about the evolutionary history of the organism. Two organisms that are closely related will have macromolecules (DNA, RNA, or proteins) whose sequences are highly similar, while distantly related organisms will have sequences that have diverged in the long time interval since their common ancestor. The selection of the rRNA molecule as the molecular chronometer is based on the fact that this molecule is universally present in all organisms, has the same function in all organisms, and has an excellent dynamic range. Parts of the molecule change slowly and are therefore useful for establishing distant evolutionary relationships, while other parts change more rapidly and are therefore more useful for fine distinctions among more closely related organisms.
The rRNA molecules are thought to be a proxy for the evolutionary relationships of the entire organisms that are being compared. This view is something of an oversimplification, because the method actually establishes only the evolutionary relationships of the rRNA molecule, which is part of the protein synthesis machinery of the cell. However, the rRNA molecules appear to be only very rarely transferred from one cell type to another, a process known as horizontal gene transfer. All these reasons make the rRNA molecules a good proxy for the evolutionary history of the organism as a whole. A tree of organismal evolutionary relationships is often called a species tree.
Figure 2.1 Small subunit rRNA phylogenetic tree of Life, with division into the three domains of bacteria, archaea, and eukarya. The highlighted taxa contain photosynthetic organisms. The color coding represents the type of reaction center complex found in the organism, with purple indicating Type II reaction centers and green indicating Type I reaction centers. The red arrow indicates the endosymbiotic origin of chloroplasts from cyanobacteria.
Source: Blankenship (2010) (p. 435)/The American Society of Plant Biologists.
It is clear from analysis of complete genome sequences for many organisms that there has been significant horizontal transfer of genetic information among various bacteria and even between bacteria and eukaryotes (Soucy et al., 2015). Therefore, the image of a single, branching evolutionary tree that applies to all organisms is increasingly being replaced by a more complex netlike arrangement, in which some parts of an organism bear different evolutionary relationships to other organisms (Doolittle, 1999). However, the process of horizontal gene transfer has apparently not been so extensive as to blur the essential distinctions among the different groups of organisms, as the groupings according to more traditional classification methods are reasonably consistent with those predicted by the RNA analysis, at least in broad outline.
The evolutionary history of any gene or gene family reflects the development of that gene, regardless of what organism has been its host during the course of evolution. An evolutionary tree of a particular gene is therefore called a gene tree and may be very different from the species tree of organisms. The origin and early evolution of life with special emphasis on photosynthesis are discussed in more detail in Chapter 12.
2.2.1 Nomenclature
Living organisms are classified according to the binomial nomenclature method, introduced by Linnaeus in the 1700s. The first name (always capitalized) is the genus name (plural, genera), while the second name (never capitalized) is the species name. Both names are italicized. The grouping of organisms into species, genera, and higher order taxa is based on a number of characteristics and represents a useful, but ultimately arbitrary, decision as to where to place the divisions along the continuous variations among related organisms. A genus is a group of organisms that share many but not all characteristics. Higher‐order classifications that are intermediate between the genus and phylum, such as family and order, serve to classify groups of organisms into broader categories.
2.3 Prokaryotes and eukaryotes
An older, but still very useful, concept to distinguish among living things is the division into prokaryote and eukaryote. Prokaryotes are the structurally simplest life forms, including bacteria and Archaea. No Archaea that carry out chlorophyll‐based photosynthesis have yet been found, so our discussion of them will be limited. Both these groups of organisms are nearly always single‐celled and have a relatively simple cellular organization without a nucleus or other subcellular organelles. A bilayer lipid cytoplasmic membrane surrounds the cell and serves as the main permeability barrier. In Gram‐negative bacteria, including most types of phototrophic bacteria, a second, more permeable, outer membrane is present, as well as a tough cell wall that provides mechanical stability (Madigan et al., 2017). The space between the outer surface of the cytoplasmic membrane and the inner surface of the cell wall is called the periplasm. This region contains a number of soluble proteins, including some cytochromes and chemosensory binding proteins. These proteins are actually topologically outside the cell, but are prevented from being lost by the cell wall. The cell wall has several layers and a complex chemical structure consisting of lipids, proteins, and polysaccharides. Nutrients pass into the periplasm from outside the cell through pores, which are made of proteins called porins. A porin is an integral membrane protein that forms a small hole in the outer membrane. Ions and small molecules, such as sugars and amino acids, can easily pass through the pore, but larger molecules cannot. Bacteria are almost always submicroscopic cells, with typical dimensions on the order of one to a few micrometers. They
