Abiogenesis and the Origin of Life

• Topic 2a focuses on Abiogenesis and the ideas and concepts surrounding the origin of life.

Learning Objectives

• Determining if biomolecules can be generated in the absence of life, which relates to prebiotic chemistry.
• Discovering the origins of the building blocks of proteins, nucleic acids, lipids, and carbohydrates.
• Understanding that the formation of building blocks abiotiically and membranes is complex.

Abiogenesis

• Is the transformation of abiotic to biotic.
• Began with the Earth's formation around 4.55 billion years ago (By).
• Initially, the Earth surface cooled, leading to oceans, an outgassing atmosphere, and abiotic chemistry.
• Chemical evolution transitioned to biological evolution, taking over a billion years.
• Advanced forms of life, like microfossils, appear around 3.5 to 3.7 billion years ago (By).

Chemical Evolution

• Refers to molecular or biochemical origins of life.
• It describes the production of self-replicating systems from organic molecules and the RNA world.

Characteristics of Modern Life

• Life is cellular and contained within compartments.
• Life is based on aqueous solutions.
• Major atoms in life: C, N, H, O, P, S.
• Proteins are made of 20 amino acids.
• RNA (ribonucleotides) and DNA (deoxyribonucleotides) are key components.
• Carbohydrates are composed of a limited number of simple sugars.
• Phospholipids consist of a limited number of fatty acids.
• Energy flows through the formation and hydrolysis of phosphate bonds, such as ATP.
• An osmotically active barrier defines a cell.
• DNA or RNA stores information.
• Ribosomes are the sites of protein synthesis (translation).
• Chemical reactions inside cells use catalysts (enzymes).
• Reproduction in biological systems results in progeny similar but not necessarily identical, allowing for mutations.
• Life is a process that enables descent with modification via evolution.

Aspects of Biochemical Evolution

• Biochemical evolution has been very conservative.
• The translation mechanism (genetic code, ribosomes, DNA, RNA, transcription, DNA replication) is essentially universal.
• Life, from an origin view, is a process that can perpetuate and involves descent with modification.
• The "origin view of life" differs from the modern biological view of "life."

Key Questions and Concepts of Life

• What constitutes the simplest forms of life?
• The "old debate" asks what came first, metabolism vs. genetics.
• Replicators can exist if the environment provides metabolism and resources.
• There is a question whether viruses are alive, since they use a host cell to metabolize.
• Replicators can be abiotic, such as crystals or clay, or "simple" genetic replicators like nucleic acids.

Hypotheses of Abiogenesis

• Genetics-first: Simple molecules RNA Metabolic Cycles Life
• Metabolism-first: Simple molecules Metabolic Cycles RNA Life

Evidence for Early life

• Microfossils (~3.5-3.7 By old)
• Carbon deposits enriched in ¹²C compared to ¹³C signifying biological carbon assimilation.

Microfossils

• Resemble filamentous cyanobacteria and are of origin 3.0 to 3.7 By (Australia).
• Geological formations that resemble microfossils can be controversial.

Stromatolites

• Layered aggregations formed in shallow water
• Created via trapping, binding, and cementation of sedimentary materials by microbial communities such as cyanobacteria (blue-green algae).
• Rock-like buildups of microbial mats
• Living and "ancient" stromatolites are known, the most ancient fossils are 3.5 By old, potentially 3.7 By old.
• *In part due to "biological activities" such as microbial buildup.
• Stromatolites can thrive only in environments with lots of sun, yet not enough protozoans due to extra saline conditions, causing the species to colonise on the west coast of Australia.

Prebiotic Chemistry

• Focuses on the chemical evolution of biomolecules and the origins of building blocks for life.
• Involves various theories:
• Atmosphere and prebiotic soup in early shallow waters
• Thermal Vents
• Chemical evolution in sea ice
• Modern views involving the “puddle"
• Extraterrestrial impacts like meteorite impacts.

Abiotic Origin of Biomolecules

• Amino Acids (->peptides)
• Nucleic Acids (->RNA and DNA)

Life as Process

• Describing how can we achieve the conditions for life to perpetuate is key to the study, as we won't find it if we did it before, in these creatures.
• Identifing and understand "precursors" of life today because conditions were different, this may be not be possible

"Primordial Soup" Theory

• Postulates that a "primitive earth" with no free oxygen had conditions that favored the formation of oceans and biomolecules.
• Oparin & Haldane coined the term abiogenesis.
• In a time when the early earth was very hot with shallow seas, organic material accumulated a primordial soup.

Experiment of Oparin & Urey

• Aimed to simulate the early atmosphere.
• Assumed a reducing atmosphere without oxygen, comprising of Methane (CH₄), Water vapor (H₂O), Ammonia (NH₃) and Hydrogen (H₂).
• Others speculate that H₂O, H₂, N₂, CO, and CO₂ were present.
• The experiment cooled primitive earth slowly, which led to volatile gases that rained back down, forming early lakes.
• Major sources of energy were lightning, solar radiation, and cooling and heating.

Miller-Urey Experiment

• Provided experimental evidence for the primordial soup concept (Oparin and Haldane).
• Used a reducing atmosphere.
• Molecules found in clouds of interstellar gas.
• Simulated primitive Earth conditions with high voltage to simulate lightning.
• Simulated rain to collect aqueous phase and conduct a chemical analysis

Miller's H₂S-rich Experiment

• A total of 23 amino acids and 4 amines, including 7 organosulfur compounds, were detected.
• The major amino acids with chiral centers were racemic, indicating no contamination during sample storage.
• Markes the first synthesis of sulfur amino acids from spark discharge experiments made to imitate primordial environments.
• Simulated primordial conditions similar to early volcanic plume chemistry in abiotic organic synthesis.
• Abundances of synthesized amino acids in the presence of H₂S were similar to those found in the carbonaceous meteorites, suggesting that H₂S played an important role in prebiotic reactions in early solar systems.

Orgel's Work

• Is on the origin of carbohydrates and nucleic acids.
• Orgel and coworkers (Oro, Ferris and Sanchez) found that in the presence of NH₃, HCN polymerizes to form purines.
• With Light and H₂O, HCN polymerizes into guanine.
• With urea and drying conditions, HCN creates pyrimidines that break and reform to become cytosine.

Prebiotic Synthesis of Sugars

• Formose reactions, with formaldehyde leading to various sugars.
• High temperatures and clay serve as a catalyst.
• ~40 sugars including glucose and Fructose, but Ribose is a rare.
• At best only generated in low amounts - so how to make Nucleosides?

Summary by Miller/Orgel

• Describes prebiotic chemistry as the synthesis of Amino acids, Carboxylic acids, Nucleic acid bases, and Sugar under prebiotic conditions.

Synthesis of Activated Pyrimidine

• Is based in prebiotically plausible conditions.
• Could form posphate and a nucleoside.

Powner et al. research

• Found that a single 2-amingoxazole intermediate could gave atoms to both sugar and the nucleobase portions of pyrimidine
• Resulting in less components forming individually.

Significance of Powner's work

• "Abiotic yields" of ribose are poor.
• Abiotic connecting of ribose to a purine/pyrimidine are difficult to envision
• New process is a solution to explain formation of nucleosideds/nucleotides in prebiotics

Formation of Polymers

• Requires concentration and condensation (abiotic).
• This done in repeated cycles of freezing and thawing, or cycles of evaporation and rehydration. heating or presence of condensing agents (H₂O "hungry" compounds
• Involves heating or the presence of condensing agents.
• Catalysts such as polyphosphate, zeolite, clays + Zn for short, straight nucleotides

The Role of Meteorites

• Inner source of organic, and molecules
• They have amino acids and other relevant molecules.
• Enriched the prebiotic soup with approximately between 1016 to 1018 organic materials.
• A source of triphosphates (found in NTPs)

Problem with Molecular Asymmetry

• Enantiomers (mirror images) are molecules that had a "scaffold" to favour the formation/accumulation on one or the other!
• In the context of homochirality, L-amino acids are used to make proteins, and D-sugars.
• Abiotic (non-biological) synthesis does not have a preference for one type of enantiomer over the other like biological systems do

Deep Sea Hydrothermal Vents

• Provide extreme suitable temperatures for organic compounds found in the last few Iroyos.
• Create Reducing environment, heat, pressure, where methane, NH₄, CO, CO₂, CN⁻, HS⁻, Fe⁺² etc can be found.
• They generate thermal/electrochemical gradients, versatile inorganic catalysts and support activities.
• Activities on the surface also give you activities, and heat. perfect for poreous mineral precipates in hydrothermal mounds

Iron-Sulfur World Theory

• Günter Wächtershäuser (2000)
• Theorizes Metabolism came first, and there are Hydrothermal origins of life through iron pyrites:
• Near hydrothermal vents chemical reactions can occur if there can be conditions.
• amino acids and peptides can be produced under these conditions, also acetic acid creates
• 'cells' with lipid bubbles extremely.

Electrochemical Diagrams

• They can map out deep sea vent biogeochemical cycles.

Hydrothenal Formose Reaction

• High temps and alkaline condtions are common here.

Theories from Researchers on Hydrothermal Vents

• Michael Russell and William Martin described vents as key locations the development of abiotic leading to RNA.
• E.V. Koonin theorized that a universal common ancestor was contained in the structures

The role of mineral pores

• Act as "Nature's test tubes" by protecting organic molecules from the ambient, and facilitating reactions.

"White Smokers"

• Are hydrothermal vents that generate acetyl thioesters in prebiotic events.

Common Origins, Cyanosulidic Protometabolism

• Meteorites, UV light, H2S, water, minerals and other ingredients can all come together to form amino acids, and lipids.

Abiotic Chemistry by Meteorite

• Can create components such rNA with Formamide

Summary of Prebiotic Chemistry

• The atmosphere and prebiotic is potentially responsible for providing the source material that resulted in a Thioester World by Christian de Duve