Lecture 15. Prebiotic Chemistry, Pyrite, Clays, RNA World, Transition from Abiotic to Biotic World

1. Lecture 15. Prebiotic Chemistry, Pyrite, Clays, RNA World, Transition from Abiotic to Biotic World reading: Chapter 5

2. Prebiotic Chemistry 1. Taking natural geochemicals, reacting them together, eventually producing an early cell. 2. Darwinian Evolution. 3. Last common ancestor that gives rise to all known Earth life. Prebiotic chemistry likely produced amino acids, nucleic acids, and lipids. Assembled to make early cells.

3. Concept of the Prebiotic Soup Organic compounds dissolved in the oceans. A dilute ‘soup’. Organic compounds react when they encounter each other. Earliest types of organisms would have consumed the organic compounds in the soup as C and energy source. Heterotrophs - use organic carbon as a carbon source. Eventually soup would have been exhausted, leading to a crisis. Heterotrophs would have had to evolve into autotrophs - can use CO2 as a carbon source.

4. Problems with the Prebiotic Soup • Major Problem with the Soup: • Soup is dilute. • Dilute solutions favor molecules breaking apart, not forming. • One Possible Solution: • Evaporation could increase the concentration. • Then they could react together to form more complex molecules. • To make sugar ribose: formose reaction • Need to polymerize formaldehyde in strong base • high concentration of formaldehyde • formaldehyde with react with other stuff • will generate hundreds of sugars, only one is ribose

5. Problems with the Prebiotic Soup, cont. To make bases found in nucleic acids (RNA, DNA): Oró-reaction using HCN -need high concentration of HCN -yields are low -products degrade under polymerization conditions To form a nucleotide: have to hook up D-ribose, base, and phosphate. To form a strand of DNA: have to polymerize nucleotides. No way nucleotides would form spontaneously! Amino acids would have formed more easily. Adenine

6. Surfaces • Act as catalysts and help facilitate chemical reactions. • bind reactants - concentrate them so that they can react many surfaces will have a net charge • orient the reactants - can react faster surfaces act as catalysts • chemistry of the surface different than in bulk solution • surfaces can contain mineral catalysts “Good” Surfaces: Would have been present and abundant on the early Earth. Those that bind and facilitate reactions with organic compounds.

7. Pyrite • FeS2 • “fool’s gold” • common mineral in • magmatic rocks • -also common in • sedimentary rocks Gunter Wachtershauser patent lawyer in 1988 suggested that pyrite could have acted as a a catalyst proposed an early “Iron Sulfur World” organic compounds bound to (+)-charged pyrite reacted together to create more sophisticated molecules eventually encased the surface with lipids then evolved into cellular life

8. Why Pyrite? Cells use FeS clusters in metabolic proteins. Many organisms make pyrite as a product of metabolism. Pyrite can be readily oxidized - is reactive. The formation of pyrite generates energy that can be coupled to the formation of organic compounds.

9. Catalytic Cycles Reactions occur on the surface start forming catalytic cycles. Cycles become more complicated with time.

10. Catalytic Cycles, cont. • Catalytic cycles eventually become similar to the chemical • reactions seen in cells. • Generate amino acids and nucleic acids. • Lipids form to create a boundary with the environment. • Eventually formed a cell. • Power of this approach: • Can have an autotrophic origin of life (ancient form of metabolism) • Weakness: • Don’t know if pyrite would catalyze the host of prebiotic reactions.

11. Clays Are also abundant, but in sedimentary rocks. Clays formed when igneous rocks react with water. Layered structures. Layers can bind a number of substances. - ions (K, Na) - water - organic compounds Wide variety of clay minerals.

12. Clays are Natural Catalysts Add amino acids, subject to heating and/or drying cycles. Amino acids will polymerize into peptides. Will also catalyze polymerization of modified RNA monomers. Binding can solve problem of chirality.

13. Lipid World Organic solvent extracts of Murchison meteorite Produces lipid compounds Molecules are not as large as lipids found in cells. Could have formed early lipid barriers for primitive organisms.

14. RNA World First Proposed by Walter Gilbert in 1988. (Nobel Prize winner 1980 - method for sequencing DNA) Prebiotic chemistry produced the building blocks of RNA. RNA molecules reacted together and replicated each other. RNA world an intermediate stage in the origin of life.

15. Why RNA? DNA: Bases adenosine (A), guanine (G), thymine (T), cytosine (C). Is an information carrier - genetic material of the cell. One strand is a template for the other strand. Very stable, linear molecule.

16. Why RNA?, cont. RNA: DNA ---> RNA ----> Protein (The Central Dogma) More complex roles: -makes temporary copies of genes (mRNA) -adaptor molecules in protein synthesis (tRNA) -catalytic role in protein synthesis (rRNA) Most roles are in protein synthesis. ATP is energy currency of the cell. Many protein enzymes use RNA-like catalysts. Very unstable, reactive molecule. Simpler (single-stranded). Not a linear molecule - highly folded. Reactive molecule - ribozymes. Nobel Prize - 1989. Can act as a template. RNA viruses have genomes made of RNA instead of DNA. RNA genomes used to both carry genetic information and to synthesize proteins.

17. RNA World • catalytic - react with one another • templating - copy each other RNA viruses have RNA genomes have very high mutation rates rapid rates of change use nucleotides from the “soup” (??)

18. Problems with The RNA World 1. RNA is not very stable -breaks down with heat (>50˚C) -breaks down in the presence of Mg2+, Ca2+, Mn2+, Fe2+ The reactions RNA can catalyze are limited. Has to be some external source of nucleotides (the soup??) RNA world would have eventually given rise to The DNA/Protein world. DNA is much stabler. -less sensitive to heat -stable in the presence of Mg2+, Ca2+, Mn2+, Fe2+ Proteins with 20 amino acids can catalyze a much larger variety of chemical reactions. The RNA world hypothesis calls for a temporary phase in the origin of life.

19. Lecture 16. Prokaryotes, Eukaryotes, and the Tree of Life, rRNA, Constructing Trees. reading: Chapters 3, 5

20. Mystery of Enceladus Cassini Spacecraft found older terrains and major fractures on moon Enceladus Course crystalline ice which will degrade over time. Must be < 1000 years old! Organic compounds found in the fractures. Must be heated - required T > 100K (-173˚C) Erupting jets of water observed. Cause of eruptions not known….