code that links the amino acids to particular codons. However, is all this a “frozen accident” as Francis Crick once famously called it, or is there something more behind it? There are possible alternative bases that might be used in a genetic code. For example, the base pairs xanthosine with 2,4-diaminopyrimidine and isoguanine with isocytosine might offer alternative base structures. However, research work testing the base pairing of a range of other bases across a molecular landscape of possibilities found them to be limited. By making RNA molecules with alternative bases, base pairs can be tested for their efficacy. Some bases, such as the hexopyranoses, which have a six-carbon ring in them, instead of the familiar five carbon ring, are too large and do not allow binding. Other bases were found to allow for even stronger base pairing than our own RNA, but in these cases, the pairing may be too strong, failing to provide the flexibility needed. These experiments suggest that the bases used in DNA and RNA may not be a frozen accident, but may have been selected by evolution from a wide range of possibilities. Explore the literature on the incorporation of new bases into DNA and discuss whether you think the genetic bases are a matter of chance or a frozen accident, or whether they were selected specifically by the evolutionary process.
Eschenmoser, A. (1999). Chemical etiology of nucleic acid structure. Science 284: 2118–2124.
Hoshika, S., Leal, N.A., Kim, M-Y. et al. (2019). Hachimoji DNA and RNA: A genetic system with eight building blocks. Science 363: 884–887.
Malyshev, D.A., Dhami, K., Lavergne, T. et al. (2014). A semi-synthetic organism with an expanded genetic alphabet. Nature 509: 385–388.
Piccirilli, J.A., Benner, S.A., Krauch, T. et al. (1990). Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature 343: 33–37.
Focus: Astrobiologists: Nicol Caplin
Affiliation: European Space Research and Technology Centre (ESTEC), European Space Agency (ESA), The Netherlands
What was your first degree? Environmental Science at The University of the West of England, Bristol.
What do you study? I work as a science coordinator (Research Fellow) for the European Space Agency in the European Space Research and Technology Centre (ESTEC) in The Netherlands. My primary role is to support research scientists and ensure that requirements for carrying out biology experiments in space are defined, understood, and met by our engineering and operations teams.
What science questions do you address? The astrobiology experiments that I am involved in organizing address a range of physiological and morphological endpoints that can provide information about life in the universe, particularly the limits of life in extreme environments. All of the projects I am assigned to are run on the International Space Station. They can be divided into two main categories of exposure to space conditions, internal and external. The internal experiments predominantly address effects of weightlessness (microgravity) while external ones expose samples to full space conditions (albeit within Earth's magnetic field but outside of the atmosphere). Such work must be carried out in space, as many of the conditions (and a combination of them) cannot be replicated on Earth.
How did you get involved in astrobiology research? As part of my PhD in environmental radioactivity, I studied biological effects of low-dose ionizing radiation on Earth and later, in samples that had been in space. I chose to study the effects in a well-established plant model (Arabidopsis thaliana) and used analytical techniques such as morphometrics and physiological assays that can be applied to other organisms. When searching for a postdoctoral position, I focused on trying to find a job where specialist research knowledge could be useful in examining fundamental science questions relating to various organisms in space.
5.6.5 DNA Replication
One of the most crucial events in the cell is DNA replication during cell division. This event underpins what many consider to be at least one characteristic of life – reproduction. DNA replication proceeds in three coordinated steps: initiation, elongation, and termination. This process is worth examining because it illustrates that cells today are complex machines. The enzymes involved in DNA replication amount to a highly coordinated process that cannot have all come together at once. Questions that immediately arise from looking at DNA replication are: What is the minimum molecular requirement for replicating a strand of DNA? When did the parts of the DNA replication apparatus evolve? How did the earliest cells on Earth replicate their DNA? The answers to these questions are not precisely known, but it is instructive to investigate how DNA replication proceeds to understand what is involved in this process in present-day biology.
In a cell, DNA replication begins at specific locations on the DNA, or origins of replication. In bacteria, there is a single origin of replication on their circular genome or chromosome, whereas in eukaryotes, that have longer linear chromosomes, replication is initiated at multiple origins. The unwinding of DNA at these locations and the synthesis of new strands result in a replication fork (Figure 5.14). Let's examine this process in more detail.
Figure 5.14 The replication of DNA. The figure shows some of the diversity of machinery involved in the process.
An enzyme called a helicase is used to separate the two strands of DNA, essentially “unzipping” the hydrogen bonds. As the helicase separates the DNA at the replication fork, the DNA ahead of it is forced to rotate. This process results in a build-up of twists in the DNA, and a resistance becomes established, which, if not dealt with, would eventually halt the progress of the replication fork. A topoisomerase is an enzyme that temporarily breaks the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix.
The replication fork generates two single strands of DNA. Each of these strands (Figure 5.14) can then be used as a template to make the corresponding strand, resulting in two new double helices. This process is called semi-conservative replication because only one strand of the parent double helix is conserved in each new DNA molecule that is made.
The first important point to understand about this process of making two new double-stranded DNA molecules is that the process has directionality. The energy for making a new DNA strand is acquired by cleaving the 5′-triphosphate of the nucleotide that is added to the growing DNA chain. This means that DNA synthesis can only proceed from the 5′ to 3′ direction. On one of the strands, this means that the new complementary strand can be made by synthesizing DNA by following the replication fork as it moves forwards. This is called the “leading” strand. The synthesis of the new strand is accomplished by DNA polymerase. The DNA polymerase is an ancient multimeric enzyme that is responsible for assembling the nucleotides into the newly forming DNA strand.
However, on the other strand of DNA, the “lagging” strand, synthesis must always restart near the replication fork as the DNA unzips (Figure 5.14) and move back in the opposite direction to the replication fork because of the directionality of DNA synthesis. This results in the complication that the lagging strand must be synthesized in fragments. To accomplish this task, a small piece of RNA, an RNA primer, is synthesized and attached to the DNA by a primase enzyme (the primase enzyme is a type of RNA polymerase because it makes RNA). DNA synthesis then proceeds from the RNA primer, accomplished by DNA polymerase. The strands of DNA produced in this way are called “Okazaki” fragments. These fragments are finally stitched together with an enzyme called DNA ligase, generating the complete double strand.
There is one other problem during replication. Single-stranded DNA, produced after the helicase has separated the two DNA strands, tends to fold back on itself forming secondary structures. These structures