The complexity of Gram-positive and -negative membranes should leave you in no doubt that the commonly held idea that prokaryotes are “simple” or “primitive” is likely to be misleading. Clearly, the first cells to have emerged on Earth could not have had the complexity of the modern cell membrane. The question arises – how far away, biochemically, are the most “ancient” prokaryotes on Earth today from the first cells to emerge on Earth? As this chapter progresses, you might like to consider this question. As we discuss microbial motility, the complexity of the genetic machinery, the replication of DNA, and other facets of cells, you will see the exquisite complexity of a whole range of biochemical functions represented in modern prokaryotes. Other questions emerge from this picture: Can we reconstruct the biochemistry of the earliest cells on Earth using modern-day cells, or have they advanced too far for us to truly know the biochemistry of the first living things? What is the minimum set of biochemical machinery needed to build a replicating, evolving cell? Has the evolution of the major fundamental capabilities of prokaryotes finished, or could even more complex machinery and capabilities naturally evolve in future prokaryotes?
The bacterial cell wall is often surrounded by a further layer called the glycocalyx. The glycocalyx is a network of polysaccharides. A distinct, gelatinous glycocalyx is called a capsule, whereas an irregular, diffuse layer is called a slime layer. Sugars attached to the outside of cells are sometimes called extracellular polysaccharide (EPS). The EPS acts as a protective layer of sugars that mediates interactions with surfaces. EPS allows cells to bind minerals and form biofilms. It is the substance that bonds minerals and bacteria together into macroscopic stromatolites or domes of microorganisms. Cyanobacteria are particularly prolific producers of EPS.
5.5.2 Archaeal Membranes
A fascinating difference in cell membranes is to be found in the archaea (Figure 5.8). This domain of microorganisms is discussed in more detail in the chapters on life in extreme environments (Chapter 7) and phylogenetic trees (Chapter 8). In the archaea, the lipids that make up the membranes are different from those of the bacteria and eukaryotes, one of the characteristics that put them into a separate domain of life. Instead of ester groups within the hydrophilic head of their lipids, they have ether groups, which are more resistant to a variety of chemicals and could play a role in their resistance to extreme environments. The long tails of the lipids are also different. They are called terpenoids (or isoprenoids) and have methyl side groups, in contrast to bacteria where the lipid tails are long and simple (fatty acids). These side groups might make the membranes less leaky and more resistant to extreme conditions. Even more strangely, in some archaea the bilayer is replaced by a monolayer where the tails from two lipids are fused together (Figure 5.8). This is the case in Ferroplasma, an archaeon (member of the archaea) that lives in acidic environments. It is thought that this adaptation might make the membranes more resistant to extreme conditions, preventing the membranes from falling apart.
Figure 5.8 The structure of archaeal cell membrane lipids compared to bacterial lipids. The lower diagram also shows how, in some organisms, archaeal lipids can be joined in the middle.
These membrane differences between archaea and bacteria have astrobiological significance. Preserved membrane lipids can be used to tell the identity of long-dead organisms. For example, archaea are often the dominant microorganisms in salty environments. Membrane isoprenoids preserved in salts are diagnostic of archaea and can be used to infer information on the microbial communities that once lived in the salts. Different membrane lipids preserve differently. In other words, their taphonomic potential is different. To be able to interpret which organisms lived in ancient environments, preserved in salt or rock, we need to know about cell membrane components, their ability to be preserved, and which ones might be more quickly degraded, leaving no trace.
5.6 The Information Storage System of Life
We now have a membrane containing the molecule of life. But obvious questions arise: How is the biochemistry of life controlled? What is the way in which instructions are read and directed to make molecules required for the cell to function and eventually to reproduce itself? The key information storage molecule of life is deoxyribonucleic acid, DNA. We briefly explored the structure of this molecule in the previous chapter. We learned about the four bases, guanine, adenine, cytosine, and thymine, which comprise the information code within the DNA, the bases strung together in a long sequence of different combinations. Here, we investigate how the code is turned into useful proteins.
The information storage system is crucial to the cell, since from this information, all cell instructions and coordinated biological patterns emerge. Instructions for the cell to replicate itself and interact with its environment are provided. Within complex multicellular organisms, this information coordinates cells, allowing them to communicate with each other and create differentiated cell structures, with each cell playing a dedicated role in the whole.
5.6.1 Transcription – DNA to RNA
The question arises: How do we go from the DNA information storage system to making proteins and other molecules needed by the cell for growth and reproduction?
This extraordinary transformation is accomplished in two stages. First, DNA is used to make a similar molecule called ribonucleic acid, RNA, the structure of which was described in the last chapter. This process is called transcription. RNA is similar to DNA except for three features: (i) the thymine base is replaced by uracil (U), (ii) it has a ribose sugar with a hydroxyl group (–OH) in the 2′ position, which is not present in DNA (DNA is deoxy-ribose), (iii) it generally (but not always) is single-stranded. DNA and RNA are similar in that they both contain a base, sugar, and phosphate in each structural unit.
The first step in reading the DNA is to make a copy of the sequences of the bases, or a “complementary” copy of the DNA. This copy is made out of RNA. The DNA molecule unwinds along a small part of its length (about 15 base pairs long) called the transcription bubble (Figure 5.9). At this point on the DNA, an RNA polymerase binds. RNA polymerase is a protein with five subunits and a sigma factor, a small specialized protein that recognizes particular promoters on the DNA. Promoters are sequences of DNA that correspond to the beginning of the sequences of DNA that are to be decoded. In colloquial language, the promoters tell the RNA polymerase: “Start decoding the DNA into an RNA strand here.” The RNA polymerase reads along the DNA strand, generating an RNA molecule, called messenger ribonucleic acid or mRNA. This mRNA molecule is sometimes called the mRNA transcript or primary transcript. The production of the mRNA strand occurs from the 3′ to the 5′ end of the DNA strand.
Figure 5.9 The transcription of DNA into mRNA.
In prokaryotes, this process occurs in the cytoplasm of the cell. In eukaryotes, it occurs in the cell nucleus. In eukaryotic cells, the RNA transcript must be transported out of the cell nucleus into the cytoplasm. The mRNA strand so produced can then act as the template for protein synthesis.
5.6.2
