Earth’s crust and primordial ocean formed more than 4 billion years ago and life is believed to have originated on earth at least 3.6 billion years ago. This suggests that primitive cellular life must have evolved from non-living matter during that period of several hundred million years. To study the transition from chemistry to biology, a simple vesicular system called a protocell is an ideal model that is self-organized and contains informational or metabolic materials. This thesis starts by exploring the replication of a model genetic material under plausible prebiotic conditions. The non-enzymatic copying of RNA was found to be catalyzed by Fe2+, which used to be abundant in aqueous environments on the early anoxic earth. Fe2+ was found to be a better catalyst of non-enzymatic RNA copying and ligation in slightly acidic to neutral pH conditions than Mg2+, the divalent cation used to catalyze these reactions in previous studies. This finding suggests that ferrous iron could have facilitated the replication and evolution of RNA on the prebiotic earth. To gain a better understanding of the properties of protocell membranes, the impact of membrane composition and multi-bilayer structure on non-enzymatic and enzymatic biochemical reactions was studied. A fatty acid/phospholipid hybrid membrane system was proposed as a potential intermediate state in protocellular evolution. This membrane composition was investigated for its stability and permeability, two fundamental features of functional protocells. The system proved stable in the presence of divalent cations and retained permeability to small building block molecule. Vesicles with this composition were shown to host faster non-enzymatic RNA copying, and to enable enzymatic protein synthesis. To study the effects of multi-lamellarity, giant multilamellar vesicles (GMVs) were prepared by an extrusion-dialysis method. Compared with small unilamellar vesicles (SUVs), GMVs show slightly better ability to retain encapsulated RNA, while maintaining good permeability for small charged molecules. The multilamellar structure also promotes non-enzymatic RNA copying, providing preliminary evidence that membranes could also mediate catalytic functions as well as acting as a compartment. / 2020-07-02T00:00:00Z

The RNA world hypothesis posits that at some stage in the development of life, RNA functioned as both an informational polymer and a catalyst for important reactions. However, many questions remain as to how RNA molecules might have evolved into living organisms. This thesis uses computer simulations to model processes thought to be important to the development of an RNA world. First, a model is discussed which describes non-enzymatic polymerization of single-stranded RNA from different kinds of activated nucleotides, a necessary first step towards an RNA world. It was found that a system undergoing polymerization of RNA from 5′-activated triphosphates or imidazolides behaves differently from an equilibrium system undergoing reversible polymerization reactions from 2′,3′-cyclic monophosphates, for example. In the 5′-triphosphate case, the system is not in equilibrium but rather in a state of circular reaction flux that must be maintained by an external source of phosphates. This model is then adapted to investigate non-enzymatic template-directed replication of RNA strands. It is found that this process fulfills all the necessary requirements to function as a metabolism which maintains a difference between the outside non-living environment and the internal environment of the cell. Finally, byproducts arising from the template copying mechanism in this model are discussed, including the development of highly regular sequence patterns in the strand population due to selection for the ability to form duplexes with neighbouring strands. Altogether, this thesis illustrates new implications, potential pitfalls, and possibilities of the RNA world hypothesis for the origin of life. In particular, it emphasizes the fundamental link between the processes of replication and metabolism, both of which must have been crucial to the functioning of the earliest protocells. This link has been largely overlooked in scientific literature on the topic to date. / Thesis / Master of Science (MSc) / For millennia, humanity has told stories about the origin of life. Since the 1960s, scientists have hypothesized that RNA is a key player in this origin story. RNA can both hold information and catalyze chemical reactions, meaning only one molecule is needed for both these crucial functions. However, many questions remain about how this would work in practice. This project used computer simulations to model steps along the path from RNA to living organisms. First, a model was developed for the formation of single-stranded RNA from building block molecules. The model was then expanded to include copying of existing RNA strands, and it was found that this process constitutes a metabolism. Finally, it was discovered that over time the copying process produces simple patterns in the sequence of building blocks that make up the RNA strands. Altogether, these findings emphasize the link between replication and metabolism in early cells.