Lecture 12: Origin of Life & Course Logistics – Comprehensive Bullet-Point Notes

Big-Picture Taxonomy Recap

Cellular microbes: Bacteria, Archaea, single-celled Eukaryotes, and some tiny animals.
Acellular entities: Viruses.
Note: The boundaries between these groups are human-made; focus on understanding the concepts.

Key Questions About Life’s Origin

Pasteur disproved spontaneous life in sterile media using a swan-neck flask.
Darwinian evolution suggests all life came from one original form.
Conflict: How did the first cell appear if life can't spontaneously generate now?
Three main questions for today:
- WHEN did life begin?
- HOW can we find evidence of it from long ago?
- WHERE on Earth might it have started?

Geological & Fossil Evidence

Earth's age: $4.5\times10^9\;\text{years}$ .
First prokaryotic fossils (stromatolites): $3.7\text{–}3.5\;\text{billion years ago}$ .
First eukaryotic fossils: $\,\approx\, 1.5\;\text{billion years ago}$ .
First multicellular life (Cambrian explosion): $\,\approx\, 0.5\;\text{billion years ago}$ .
Stromatolites:
- Layered mats of microbes, still found in shallow seas today.
- They give us the oldest clear cell fossils, but even these were already complex.
Scarcity of older rocks:
- Plate tectonics recycles the Earth's crust, erasing the earliest records.
- The oldest Earth rocks found so far are not on Earth, but on the Moon, ejected there by impacts.
Biosignature techniques (how we detect ancient life):
- Microfossils: Cell-like shapes with preserved organic carbon; highly debated.
- Raman spectroscopy: Detects organic carbon in old sediments.
- Isotopic fractionation: Living things prefer storing lighter carbon ( $^{12}C$ ) over heavier carbon ( $^{13}C$ ); unusual ratios of these isotopes point to past life.
- Redox fingerprints: Banded iron formations (BIFs) show times when oxygen was released.

Molecular Phylogeny & The Tree of Life

Carl Woese used the $16S\;\text{rRNA}$ gene to create the three-domain tree of life: Bacteria, Archaea, and Eukarya.
Different ways to root the tree exist, but all include LUCA (Last Universal Common Ancestor).
The diagram shows Eukarya formed from an archaeal host merging with a bacterial symbiont.

Deeply Branching Lineages & Insight into LUCA

The oldest living groups known are strict anaerobic chemoautotrophs (organisms that create their own food using chemical energy without oxygen).
Two key chemical reactions:
1. Methanogenesis (Archaea): CO2+4H2→CH4+2H2O
2. Acetogenesis (Bacteria):
  2CO2+4H2→CH3COOH+2H2O
Gene-comparative reconstruction (what we think LUCA was like):
- Had RNA polymerase and the universal genetic code.
- Was chemoautotrophic, likely producing methane.
- Was a strict anaerobe (lived before Earth had much oxygen).
- Already used a proton/ion gradient and F1F0 ATP synthase to make ATP (energy molecule).
- Its DNA replication machinery is NOT the same as modern bacteria or archaea.

From Prebiotic Chemistry to Protocells

Requirements for "life functions":
1. A way to copy genetic information (replication).
2. Metabolism and energy control to fuel replication.
3. A boundary membrane for a separate inside (compartmentalisation).
4. Homeostasis (keeping a stable internal environment).
Prebiotic synthesis experiments:
- Oparin–Haldane's "primordial soup" idea (early Earth had a reducing atmosphere and energy) led to Miller–Urey's 1953 experiment, which produced amino acids and simple organic molecules.
- Newer experiments create nucleotides, lipids, and sugars under both reducing and carbon dioxide-rich conditions.
Key understanding: Just a mix of polymers isn't life (like an "E. coli smoothie"). Life needs functional parts working together.

Competing Origin Models

“Information-First” / RNA-World

The discovery of ribozymes (by Cech & Altman) showed RNA can both store information AND act as an enzyme.
Hypothesis: Self-replicating RNA molecules came before DNA and proteins.
Challenges & controversies:
- RNA is chemically unstable.
- No RNA in labs has been evolved to fully copy itself.
- Modern life uses DNA (more stable) and protein enzymes—why and how did this change happen?
- Homochirality puzzle: Why does life only use right-handed DNA?

“Metabolism-First” / Autocatalytic Networks

Hypothesis: Life began as self-sustaining chemical cycles (early metabolism) contained within compartments ("protobionts").
"Protobionts" have been created in labs: lipid bubbles that contain reaction networks, grow, and divide.
Strength: This idea links growth to replication-like behavior without needing genes.
Obstacles: Explaining how encoded heredity (genes) appeared and why nucleic acids later took over this role.

Candidate Birthplaces of Life

Criteria: Liquid water, an energy source, a way to concentrate materials, and good chemical/physical gradients.
Environments considered:
1. Terrestrial shallow ponds: Energy from UV light/lightning and concentration by evaporation, but likely limited energy.
2. Deep-sea hydrothermal vents (like Lost City, Mid-Atlantic): Most favored.
  - Alkaline hot fluids rich in hydrogen (H2), methane (CH4), ammonia (NH3), and metal sulfides, plus lots of carbon dioxide (CO2).
  - The porous structure of the chimney provides:
    - Natural tiny compartments (mineral cells).
    - Semi-permeable walls that create pH, redox, and temperature differences (proto-chemiosmosis).
    - A constant supply of chemicals and removal of waste.
  - Modern microbes found at vents are hyperthermophilic chemoautotrophs, similar to what early life might have been like.

Post-Origin Evolutionary Timeline (Ga = billion years ago)

$4.54\;\text{Ga}$ : Earth forms.
$\sim 4.0\;\text{Ga}$ : Earth's crust solidifies; potential time for life to start (abiogenesis).
$3.7\;\text{Ga}$ : Fossil stromatolites; Bacteria and Archaea split apart.
$3.4\;\text{Ga}$ : Anoxygenic photosynthesis (without producing oxygen) evolves.
$2.9\text{–}2.5\;\text{Ga}$ : Oxygenic photosynthesis (produces oxygen, by cyanobacteria) leads to the Great Oxidation Event (GOE); oxygen levels rise to about $0.1\%\;\text{of modern levels}$ .
- Geological sign: banded iron formations (layers of $Fe^{2+}$ and $Fe^{3+}$ ).
$2.1\;\text{Ga}$ : Ozone layer forms, protecting living things from harmful UV radiation.
$1.8\text{–}1.3\;\text{Ga}$ : First eukaryotes appear; this period is called the "boring billion" because complex cell structures were developing.
$0.54\;\text{Ga}$ : Cambrian explosion: Rapid increase in diverse multicellular animals.
$0.2\;\text{Ga}$ : Mammals emerge; dinosaurs disappear around $\sim 0.065\;\text{Ga}$ .
$\sim 0.0002\;\text{Ga}$ : Homo sapiens (humans) appear ("just a second ago" in geological time).

Oxygen & Metabolic Shifts

All oxygen in the atmosphere started from biological processes.
Oxygen allowed for aerobic respiration, which is the most energy-efficient way to break down food (produces the most $ATP$ per substrate).
Glucose aerobic respiration: C6H12O6+6O2→6CO2+6H2O+ATP, showing a high energy yield.

Endosymbiotic Theory & Eukaryotic Complexity

Sequence of events (most accepted):
1. An archaeal host cell engulfs an aerobic $\alpha$ -proteobacterium, which becomes a mitochondrion.
2. A lineage that already has mitochondria later engulfs a cyanobacterium, which becomes a chloroplast (found only in plants and algae).
Evidence summary:
- Double membranes (outer from host, inner from symbiont).
- Similar size and shape to bacteria.
- Circular DNA; they replicate by binary fission (splitting in two).
- Have $70S$ ribosomes; are affected by antibiotics that target bacterial ribosomes.
- Phylogenetics: Organelle genes are genetically similar to bacterial groups.
Outstanding puzzles:
- How the original bacterial cell wall was lost.
- The change in lipid composition (from archaeal to bacterial-type phospholipids).
- The exact timing of nucleus formation compared to mitochondrion capture.
- Multiple secondary and tertiary endosymbioses (e.g., brown algae chloroplasts have four membranes).

Formula & Numerical References Collected

Earth's age: $4.5 \times 10^9\;\text{yr}$ .
First prokaryote fossil: $3.7\text{–}3.5 \times 10^9\;\text{yr}$ .
Cell number after $n$ generations: $N = N_0 2^n$ .
Serial-dilution plate count (general): $\text{CFU}{\,/\,}\text{mL} = \frac{\text{colonies}}{\text{dilution}\times\text{volume plated}}$ .
Methanogenesis reaction: CO2+4H2→CH4+2H2O
Acetogenesis reaction:
2CO2+4H2→CH3COOH+2H2O
Aerobic respiration (glucose): C6H12O6+6O2→6CO2+6H2O+ATP.
Practical / Ethical / Real-World Notes

Comparing results with others is discouraged; focus on your own progress and study efforts.
Correct lab techniques (like keeping things sterile and knowing your tools) are vital for safety and good data.
Protecting the ozone layer is crucial: It formed because of life and shields all surface life.
Understanding early life helps in astrobiology (searching for life on Mars, icy moons) and synthetic biology (designing minimal cells).