Chapter 24a

Early Life and Conditions
- Exploration of early Earth conditions that allowed life to emerge.
- Description of structural and metabolic adaptations in prokaryotes.
- Comparison of mechanisms that promoted genetic diversity in early prokaryotes.
- Upcoming classes will explore different prokaryote lineages and their functional roles in the biosphere.

Abundance:
- Prokaryotes are the most abundant organisms on Earth.
- They inhabit extreme and normal environments.
- In a handful of soil, there are more prokaryotes than there have been humans throughout history.
Historical Context:
- Earliest cells were prokaryotes, appearing in the fossil record approximately 3.8 billion years ago.
- Prokaryotes are defined as single-celled organisms.
- They are classified under Domain Archaea and Domain Bacteria.
- Early prokaryotes existed in clusters resembling stepping stones or floated freely.

Hypothesis: The first organic molecules may have arrived on Earth via meteorites (e.g. Murchison meteorite, containing >80 amino acids).
Earth's early atmosphere included volcanic gases (nitrogen, nitrogen oxides, carbon dioxide, methane, ammonia, hydrogen).
As Earth cooled, water vapor condensed to form oceans; much hydrogen escaped into space.
1920s - Oparin & Haldane hypothesized that organic compounds formed from simpler molecules.
Haldane later suggested that early oceans were a solution of organic molecules, or what we also call ‘primordial soup’.
In 1953, Miller and Urey tested the hypothesis of Oparin & Haldane to determine what the true ‘recipe’ of primordial soup consisted of, and they found it consisted of many different kinds of amino acids.

RNA monomers are produced spontaneously from simple molecules; small organic molecules polymerize when they are concentrated on hot sand, clay, or rocks.
Polymerization is the process of substances bonding together.
Amino acids may have acted as weak catalysts for early Earth chemical reactions.

Definition: Protocells are fluid-filled vesicles with membrane-like structures.
Vesicles can spontaneously form when lipids or organic molecules are exposed to water, creating a lipid bilayer.
Protocells can demonstrate reproductive capabilities, metabolism, and maintain internal chemical environments distinct from their surroundings.

RNA is believed to have been the first genetic material, rather than DNA.
Vesicles with self-replicating, catalytic RNA could reproduce and pass on properties to daughter protocells.
RNA may have preceded DNA as a template for genetic material; ribozymes in RNA can catalyze various reactions and create RNA copies.

Stromatolites:
- One of the oldest fossil types, layered rocks formed from prokaryotic activities dating back to 3.5 billion years ago.
- Stromatolites were primarily formed by cyanobacteria, which significantly contributed to atmospheric oxygen.
- Ancient prokaryotic cell fossils found in 3.4 billion-year-old rocks in Australia.
- Surviving prokaryote lineages either adapted or avoided the early aerobic conditions that arose.

Most prokaryotes are unicellular, some form colonies.
Typical dimensions range from 0.5 to 5 µm, considerably smaller than the 10 to 100 µm dimensions of many eukaryotic cells.
Varied shapes include:
1. Spheres (cocci)
2. Rods (bacilli)
3. Spirals

Functions of cell walls: Maintain shape, protect the cell, prevent bursting in hypotonic environments.
Composition differences:
- Bacterial Cell Walls: Contain peptidoglycan, a network of sugars linked by polypeptides.
- Archaeal Cell Walls: Composed of polysaccharides and proteins, but lack peptidoglycan.

The Gram stain method reveals bacterial cell wall composition:
- Gram-positive Bacteria: Feature simpler walls with extensive peptidoglycan, appearing purple/blue in stain.
- Gram-negative Bacteria: Show less peptidoglycan and have an outer membrane, may appear pink due to a counter stain; also more likely to be antibiotic resistant.

Salmonella typhi:
- A gram-negative bacilli infecting the intestinal tract causing typhoid fever.
Chlamydia trachomatis:
- A gram-negative cocci causing sexually transmitted infections and complications such as infertility.

Capsule: A protective layer allowing adherence to substrates.
Endospore: Dormant cells resistant to unfavorable conditions (found in some bacteria).
Fimbrae: Hair-like appendages aiding adhesion.
Pili: Longer than fimbrae, facilitating DNA exchange.

Many prokaryotes possess flagella for mobility; structure varies across bacteria, archaea, and eukaryotes, indicating independent evolution.
Exhibit taxis, the ability to move in response to stimuli; includes chemotaxis (movement toward/away from chemicals).

Prokaryotes are structurally simpler than eukaryotes
Prokaryotic cells lack complex compartmentalization
Some prokaryotes do have specialized membranes that perform metabolic functions
Prokaryotes have considerably less DNA than eukaryotes.
Most of the genome consists of a single circular chromosome
The genetic material is not enclosed inside a membrane; it is located in the nucleoid region
Some species of bacteria also have smaller rings of DNA called plasmids
There are some differences between prokaryotes and eukaryotes in DNA replication, transcription, and translation.

Autotrophs: Can synthesize their own food.
- Photoautotrophs: Utilize light and CO2 (e.g. cyanobacteria).
- Chemoautotrophs: Use inorganic chemicals and CO2 (e.g. Sulfolobus).
Heterotrophs: Cannot produce their own food.
- Photoheterotrophs: Use light and organic compounds (e.g. Chloroflexus spp.).
- Chemoheterotrophs: Utilize organic compounds (e.g. Clostridium botulinum).

Obligate Aerobes: Require oxygen for cellular respiration.
Obligate Anaerobes: Poisoned by oxygen, utilizing anaerobic respiration with electron acceptors other than O2.
Facultative Anaerobes: Can grow in both the presence and absence of oxygen.

Nitrogen is essential for the production of amino acids and nucleic acids in all organisms.
Certain prokaryotes facilitate nitrogen fixation, converting atmospheric N2 to ammonia (NH3).

Prokaryotic cells can cooperate to exploit resources; for instance, Cyanobacteria like Anabaena have specialized cells called heterocysts that perform photosynthesis and nitrogen fixation, helping to exchange metabolic products.