A2.1 Origins of cells

Outline the conditions that are thought to have existed on prebiotic Earth, including atmosphere, temperature, UV radiation, volcanic activity and asteroid bombardment.

A2.1.1— Conditions on early Earth and the prebiotic formation of carbon compounds.

Atmosphere: "reducing atmosphere"; Lots of Ammonia and Hydrogen; very little oxygen.

Temperature: Significantly warmer than today due to asteroid collision and planet formation.

UV radiation: no ozone to block radiation ∴ intense UV rays reached planet

Volcanic Activity: volcanic eruptions released gases into the atmosphere.

Asteroid bombardment: constant from forming solar system.

State that the conditions of prebiotic Earth may have caused a variety of carbon compounds to form spontaneously.

A2.1.1— Conditions on early Earth and the prebiotic formation of carbon compounds.

Conditions of prebiotic Earth may have caused a variety of carbon compounds to form spontaneously.

Discuss the challenges of defining matter as living or nonliving.

A2.1.2— Cells as the smallest units of self-sustaining life.

Traditional definition says the living things:

• have cells/DNA

• processes of life like growth and reproduction

But, there are many counter examples to this definition.

i.e.

• mature red blood cells do not contain DNA. Does this mean they are not alive?

• Mules are sterile hybrids and can not reproduce.Does this mean they are not alive?

Discuss the reasons why cells are considered to be living.

A2.1.2— Cells as the smallest units of self-sustaining life.

• Cells are the smallest unit of self sustaining life

• Cells contain all components to carry out all eight process of life: (MRS GREN) Metabolism, Reproduction, (response to) Stimuli, Growth, Reproduction, Excretion, Nutrition, Homeostasis

Discuss the reasons why viruses are considered to be non-living.

A2.1.2— Cells as the smallest units of self-sustaining life.

• unable to reproduce outside a host cell.

• rely on host cells for many processes such as nutrition and growth.

• Do not possess a metabolism

Outline the intermediate stages needed for the evolution of the first cells on prebiotic Earth.

A2.1.3— Challenge of explaining the spontaneous origin of cells.

SCLSC

1. Simple organic molecules (amino-acids and hydrocarbons, fatty acids) were formed by inorganic compounds

2. Catalysis (heat + radiation) accelerated chemical reactions

3. Larger organic molecules were assembled from smaller molecules

4. Self replication was able to take place for some (like RNA)

5. Compartmentalization (package into vesicles) allow internal cell chemistry to differ from external cell chemistry.

Discuss limitations in testing hypotheses about the evolution of the first cells.

A2.1.3— Challenge of explaining the spontaneous origin of cells.

• cells spontaneously originated a very LONG time ago, making their evolution difficult to study as evidence may be destroyed or distorted.

• very first protocell did not fossilize

• cells may have originated deep in the ocean making reaching and collecting samples challenging.

• uncertainty of exact conditions of prebiotic earth meaning it cannot be exactly replicated and tested.

Outline the methodology, results and conclusion that can be drawn from Miller and Urey's experiments into the origin of biologically relevant carbon compounds.

A2.1.4— Evidence for the origin of carbon compounds.

Methodology:

to simulate earths prebiotic conditions to show spontaneous formation of organic molecules could occur.

Set up closed system with:

• water to simulate ocean (boiled H2O so that it would evaporate)

• a gas inlet to add reducing gases (methane, ammonia, H)

• chemical sparks to simulate electric storms

• cooling condenser turns steam into liquid H2O

• collected resulting molecules from trap

Results:

• Primordial soup contained basic organic monomers including amino-acids.

Conclusion:

Non-living synthesis of organic molecules was possible in early Earth conditions.

Discuss the benefits and limitations of the Miller-Urey apparatus as a model for a natural phenomena.

A2.1.4— Evidence for the origin of carbon compounds.

Benefits:

• artificial representations of natural phenomena are useful when direct observation or experimentation is difficult

• simplifications of complex systems

Limitations:

• they may be oversimplified and/or cannot represent all aspects of a system

• models are only as accurate as the scientific knowledge on which they are based

Outline the cause and consequence of the spontaneous formation of membranes and vesicles by amphipathic molecules such as fatty acids and phospholipids on prebiotic Earth.

A2.1.5— Spontaneous formation of vesicles by coalescence of fatty acids into spherical bilayers.

Cause:

• bilayers spontaneously form stable spherical structures in water, due to their hydrophobic tails

Consequence:

• the formation of membranes was a crucial step in the origin of living cells as they could developed their own internal chemistry, different from that of the surroundings

State that modern cells use DNA as the genetic material and enzyme proteins as catalysts of metabolism.

A2.1.6— RNA as a presumed first genetic material.

Modern cells use DNA as the genetic material and enzyme proteins as catalysts of metabolism.

List properties of RNA that suggest it was the first genetic material.

A2.1.6— RNA as a presumed first genetic material.

• RNA can self replicate

• RNA has some catalytic activity in other biochemical reactions

• ribozymes in ribosomes are still used to catalyze peptide bond formation

• short

• simple

Compare the genetic stability of RNA and DNA.

A2.1.6— RNA as a presumed first genetic material.

• DNA is more genetically stable than RNA

• DNA has a deoxyribose sugar that contains one less oxygen-containing hydroxyl group than Ribose sugar present in RNA

• The hydrogen bonds holding together the double-helical structure of DNA add additional stability

• The use of thymine rather than uracil further enhances DNA stability. Thymine is much less susceptible to mutation than uracil and those that do occur are easier to repair.

Outline the ribosomal ribozyme as a type of RNA that is still used as a catalyst.

A2.1.6— RNA as a presumed first genetic material.

• The ribosome contains a ribozyme that forms the peptide bond between amino acids during translation.

• The ribozyme catalyzes the peptide bond formation between amino acids

Define LUCA

A2.1.7— Evidence for a last universal common ancestor.

Last Universal Common Ancestor

• Small, single-celled prokaryote (bacteria and archaea)

  • Eukaryotes emerged later

• It probably lived in the high-temperature water of deep sea vents near ocean-floor magma flows around 4 billion years ago. HYDROTHERMAL vents. 

• LUCA emerged after the formation of the first cells but still relatively early in Earth's history

• If LUCA were the first cell, we would expect a simpler, more uniform biochemistry. Instead, LUCA likely possessed a complex and diverse set of cellular processes.
  

Discuss why the LUCA is not thought to be the first cell, but rather is thought to be the last common ancestor to all living cells

A2.1.7— Evidence for a last universal common ancestor.

• The first cells were likely some sort of membrane surrounding a self replicating molecule like RNA

• LUCA is an inferred evolutionary intermediate that links the abiotic phase of Earth's history with the first traces of microbial life in rocks

• Before LUCA there was a common ancestor of all life that was likely one of these simple cells, those before LUCA have gone extinct, but LUCA was the last before species branched off

Explain the use of deductive reasoning to predict what genes were present in the LUCA cells.

A2.1.7— Evidence for a last universal common ancestor.

• If an evolutionary tree is constructed for a shared gene and it matches the accepted evolutionary tree for bacteria and archaea

• deductive reason tells us that a gene has been inherited from a common ancestor of bacteria and archaea.

• This suggests that LUCA had the gene.

• Genes needed for chemautrophic and anaerobic metabolism were present in LUCA, environment with these conditions were found in/around hydrothermal vents → LUCA lived around these vents

List characteristics of the LUCA

A2.1.7— Evidence for a last universal common ancestor.

• small, single-celled prokaryotic cell,

• was an obligate anaerobe (did not use oxygen)

• was a chemoautotroph, obtaining energy from hydrogen and converting carbon dioxide and nitrogen into essential organic compounds

Compare the estimated dates for the evolution of the first cells and of the LUCA cells to the age of Earth.

A2.1.8— Approaches used to estimate dates of the first living cells and the last universal common ancestor.

Luca existed:

• 2.3 and 3.5 billion years ago

First cells existed:

• 3.5 to 4.1 billion years ago.

Earth is:

• 4.5 billion years old.

Describe stromatolites as the earliest direct evidence of fossilized life.

A2.1.8— Approaches used to estimate dates of the first living cells and the last universal common ancestor.

• Stromatolites are formed when mats of cyanobacteria in shallow sea water trap sediments and secrete calcium carbonate, slowly building rocky mounds over the years.

• Structures made by bacteria that live in water and do photosynthesis

• When they get covered up, bateria moves up towards the light (needed for photosynthesis)

• Movement makes layers which minerals precipitate in, makes fossilized stromatolites

Outline the use of isotopes and the molecular clock for estimating dates of the first cells and of the LUCA cells.

A2.1.8— Approaches used to estimate dates of the first living cells and the last universal common ancestor.

isotopes:

• Evidence of microscopic life can be trapped in the rocks and analyzed using ratios of chemical isotope

• earliest evidence of life is found in rocks containing fossil-like structures with isotopes suggesting may be the remains of living organisms

Molecular clock:

• The molecular clock approach uses differences in the genomes of species to tell how much time has passed since they shared a common ancestor

• the number of differences in the genomes of two species is proportional to the time since they diverged from a common ancestor.

Describe the conditions present at a white-smoker hydrothermal vent.

A2.1.9— Evidence for the evolution of the last universal common ancestor in the vicinity of hydrothermal vents.

• high concentrations of H, CO2, FE

• metal-laden

• intensely hot plumes caused by seawater interacting with magma erupting through the ocean floor

• high pH

• contain bacteria

Explain how knowledge of the genes present in the LUCA cells can provide evidence that the cells lived in the vicinity of hydrothermal vents.

A2.1.9— Evidence for the evolution of the last universal common ancestor in the vicinity of hydrothermal vents.

• The genes needed for chemoautotrophic, anaerobic metabolism were present in LUCA .

• The environment with conditions for chemoautotrophic, anaerobic metabolism are found in and around hydrothermal vents.

• Therefore, LUCA must have lived in the vicinity of hydrothermal vents.

• Deduction

Origins of Cells/Earth

1. 4.5 bya: swirling gas + dust to form earth bc gravity

2. 4.4 bya: water vapor and extraplanetary objects

3. Prebiotic Earth (before life): earth was hot solid ball, no ozone, lots of radiation, nuclear and chem rxns 

4. Prebiotic Atm: (atmosphere 1 = Hydrogen and helium) --> (atmosphere 2 = Methane, Ammonia, CO2, water vapor)

5. inorganic --> organic monomers

6. polymerization (mono --> polymeres)

7. self replication

8. ball of life/proto-cell

9. Oparin-Haldane

10. Miller-Urey Experiment

Oparin-Haldane Hypothesis

1. inorganic → organic

2. monomere → polymere

3. self-replicating polymers

4. formation of cell (coacervative proto-cell)

Organic Molecules

any molecule that contains the element "carbon"
with exception of CO, CO2, CO3^2-, CH4 and must be found in living organisms
ex: carbohydrates, lipids, proteins, nucleic acid

Spontaneous Origin of Cells (Abiogenesis)

living organisms can be formed from non-living matter

• Oparin-Haldane proposed spontaneous carbon compound formation is possible in pre-biotic earth conditions

• Miller-Urey confirmed it

Miller-Urey Experiment

test 1st step of Oparin-Haldane Hypothesis

1. boiled water & evaporates

2. combine with methane, ammonia, hydrogen gas

3. electrodes to stimulate lightning

4. cooling condenser

5. collect molecules

Conclusion:

1. inorganic can make organic

2. spontaneous carbon compounds is possible