Lecture 2 (BES 108, OITE)

Lecture 2: Organisms in Their Environment

• Lecture was given on January 10, 2025, in BES 108D.
• The lecturer was Dr. Benazir Alam.
• The topic was the history of life on Earth, focusing on prokaryotes (bacteria and archaea).

Topic 1: Prokaryotes: Bacteria and Archaea (Chapter 25)

• Early Earth conditions made the origin of life possible.
• Abiotic synthesis of small organic molecules (e.g., amino acids, nitrogenous bases).
• Joining of these molecules into macromolecules (e.g., proteins, nucleic acids).
• Encapsulation of molecules into protocells with membranes maintaining internal chemistry.
• Origin of self-replicating molecules allowing inheritance.

Synthesis of Organic Compounds on Early Earth

• The solar system formed 4.6 billion years ago, and early Earth was bombarded by asteroids and comets.
• This bombardment vaporized water, preventing oceans from forming until 4.2-3.9 billion years ago.
• Early Earth's atmosphere had little oxygen and contained water vapor and volcanic gases (e.g., nitrogen, nitrogen oxides, carbon dioxide, methane, ammonia, hydrogen, hydrogen sulfide).
• As Earth cooled, water vapor condensed into oceans, and hydrogen escaped into space.

Further Synthesis of Organic Compounds on Early Earth

• In the 1920s, Oparin and Haldane hypothesized the early atmosphere was a reducing environment, ideal for organic molecule formation.
• They theorized that organic compounds formed from simpler molecules using energy from lightning and UV radiation.
• Haldane suggested the presence of a "primitive soup" in early oceans from which life arose.
• Miller and Urey's 1953 lab experiments demonstrated abiotic synthesis of organic molecules in a reducing atmosphere is possible.
• Early organic compounds may have been synthesized near volcanoes or deep-sea vents.
• Miller-Urey-type experiments showed organic molecule formation with various possible atmospheres.

Early Earth's Organic Compounds & Volcanic Eruptions

• 1953 Miller-Urey experiment compared to 2008 reanalysis shows variations in the mass of amino acids synthesized in simulated volcanic eruptions.

Organic Compounds and Deep-Sea Vents

• Some deep-sea alkaline vents release water with high pH (9-11) and warm temperatures (40-90°C).
• This environment could be suitable for abiotic organic molecule synthesis and the origin of the first cells.
• A pH gradient would have existed between the vent interior and the surrounding ocean water, providing potential energy for organic compound synthesis.

Abiotic Synthesis of Macromolecules

• Amino acids and other organic molecules may be present in meteorites.
• RNA monomers might have been produced spontaneously from simple molecules.
• Scientists have produced polymers of organic molecules using heat, clay or rock as catalysts and without enzymes or ribosomes.
• Minerals in clay and rock can provide catalytic surfaces for the polymerization of small molecules into larger chains (like proteins and RNA).

Protocells

• A protocell is a theoretical model of an early life form, resembling a cell but lacking complex structures.
• Protocells can be thought of as a transitional step from non-living chemistry to living organisms.
• Protocells might have been fluid-filled vesicles with a membrane-like structure that spontaneously formed from lipids in water.
• Adding clay may increase the rate of vesicle formation.
• Vesicles exhibit simple reproduction and metabolism while maintaining an internal environment separate from their surroundings.

Role of Montmorillonite Clay

• Montmorillonite clay, common in early Earth, is composed of silicate layers.
• Clay provides surfaces for concentrating organic molecules, increasing the chance of reactions to form vesicles.
• The presence of clay enhances the rate of vesicle self-assembly.

Self-Replicating RNA

• RNA, not DNA, was likely the first genetic material.
• RNA plays a role in protein synthesis and can act as an enzyme-like catalyst (ribozyme).
• Ribozymes catalyze various reactions, such as making complementary RNA copies using nucleotide building blocks, potentially signifying a self-replication process.
• Natural selection in early organic molecules might have produced stable, self-replicating ribozymes, defining a possible "RNA world".
• Small RNA molecules, capable of replicating and storing genetic information about protocells, played a vital role.
• Early protocells carrying RNA might have limited function.
• RNA could provide a template for the emergence of DNA.
• DNA's greater stability and better replication could have led to its dominance.

Transition from RNA to DNA

• Accurate replication was favored as genomes grew in size.
• The development of DNA marked a pivotal point that paved the way for the proliferation and evolution of new life forms.

The Fossil Record

• The fossil record shows changes in the history of life.
• Sedimentary rocks, which form layers called strata, are a primary source of fossils.
• Fossils offer an incomplete record due to limitations in preservation and discoveries.
• The record is biased toward organisms that lived for long periods, were widespread, and had hard parts.

How Rocks and Fossils are Dated

• Sedimentary strata provide relative ages of fossils.
• Dating relies on radiometric dating techniques analyzing the decay of radioactive isotopes to determine the absolute ages of fossils.
• Each radioisotope has a characteristic decay rate or half-life, unaffected by environmental factors.
• Radiocarbon dating can accurately date organic material up to 75,000 years.

Radiometric Dating

• Living organisms contain various isotopes (e.g., carbon-12, carbon-14), with carbon-14 being radioactive.
• After death, the uptake of carbon-14 stops, allowing its decay.
• Measuring the ratio of carbon-14 to carbon-12 can estimate the fossil's age.
• Dating older fossils uses surrounding rock strata's age markers.

The Geologic Record

• The geologic record shows the evolution of life's diversity across geologic time.
• Early geological time periods are documented in the fossil record.
• The timeline includes the appearance of prokaryotes, eukaryotes, multicellular organisms, and specific geologic events, such as the Cambrian explosion.

Oxygen Revolution

• Early rise in atmospheric oxygen levels was largely due to oxygenic photosynthetic prokaryotes.
• Later increases in atmospheric oxygen might be attributed to the evolution of eukaryotic cells containing chloroplasts.
• The "oxygen revolution" around 2.7-2.4 billion years ago led to the extinction of many anaerobic groups, causing some surviving organisms to adapt through cellular respiration.