The Origin and Evolution of Life on Earth
Why do we start the discussion of biology with a discussion of geology? Here are some
reasons why one would do this:
- All life on earth is linked to geology; likewise, many surface geologic features and
processes have been influenced by life on earth. The origin and early evolution of the earth
are especially important when looking at the origin and early evolution of life on earth.
- Life chemistry had its origin with the elements available to it during the formation of the
earth. These provided the basic raw materials available for life.
- The evolution of life is in response to changes in environment. Many of these changes
are linked to changes in climate and/or geology.
- All life is (so far) limited to placement upon the earth, so it is crucial that we understand
the processes of the earth.
The Big Bang theory of the formation of the universe
All material in the universe was created in a huge "explosion," creating and defining
matter and space. The sudden cooling of the superheated ejecta facilitated the combination of
atomic components into atoms and molecules. These clouds of gasses eventually cooled and
formed the principle components of galaxies - including stars and planets.
Other theories have been postulated (i.e. the oscillating universe theory which states that
the universe expands and contracts in a cycle every 100 billion years) and these are hotly
Location of the Solar System
Our solar system is located on a spiral arm of the Milky Way galaxy. We are approximately
2/3 of the distance from the core to the outer rim of the galaxy. This distance places us in a
lower-density region of the galaxy - there are some stars near to ours, but this region is
nowhere as congested as the galactic core.
Formation of the solar system
A. The earth formed approximately 4.6 BYA (billion years ago.) Initially, there was a
cloud of gasses and dust particles, possibly originating from the ejected particles of a nearby
B. The cloud gradually contracted and flattened, concentrating about 99% of its mass
in the center with the rest rotating counterclockwise in a flattened disk.
C. As the disk rotated, turbulence was created, causing condensation of the disk into small,
turbular eddies. These gradually accreted together to form protoplanets.
D. These protoplanets further accreted, creating the mature planets of the solar system.
The sun also accreted, pulling in most of the mass. As these accumulated, the pressure
and temperature caused the initiation of thermonuclear fusion. This thermonuclear fusion is
what provides the ultimate source of energy for all life on earth.
In the hot accretions of planetesimals, iron-rich elements condensed first, creating the
cores (the inner and outer cores). Next, the lower-density silicates began to condense and
aggregate, forming the mantle and the crust. Further differentiation of the crust was fueled by
the energy output from radioactive decay deep within the earth
Structure of the earth
There are three clearly defined regions of the earth:
- Cores (inner (1250 km) and outer (2100 km)) - composed primarily of iron (85%) and
nickel. Other heavy elements (such as radioactive elements) are also found here
- Mantle (2900 km) - a "fluid" region primarily composed of oxygen and silica - derived
- Crust (5-70 km) - thin film of "crud" which has floated to the surface. We are simply
passengers, living on this geologic flotsam.
Early Earth Conditions
Theory of Early Earth Conditions-Hot and violent
- Immense heat due to accretion and volcanoes-Earth is molten.
- Earth is bombarded by asteroids, one of which dislodged the moon.
- Cooling causes condensation of H2O to form rain.
- Volcanoes eject gases (CO2, N2, H2), forming the early atmosphere.
- Note that there is no O2 present in the early atmosphere. Any
O2 outgassed would have reacted with the metals of the crust, causing
oxidation. This lack of O2 is crucial for the formation of organic
What is life?
What is life? Life is everywhere, but it resists a simple one-sentence definition. Some of the
properties of life are given below:
- Order Living organisms partition resources and nutrients within their
systems. This is an energy-requiring process which must be maintained for life to continue.
- Reproduction Organisms reproduce their own kind. Life only comes from
- Growth and Development Heritable characters direct the pattern of growth
and development, producing an organism that is characteristic of its species.
- Energy Utilization Organisms take in energy and transform it to do work.
Almost all of life's functions require energy.
- Homeostasis Regulatory mechanisms maintain an organism's internal
environment within tolerable limits, even though the external environment may fluctuate. This
process is known as homeostasis.
- Evolutionary Adaptation Live evolves as a result of the interaction between
organisms and their environment. As the environment is rarely stable, life must adapt to survive
in these new living conditions.
Chemical Evolution Occurred Early in Earth's History
Radiometric dating technique determines age of rocks.
Estimations of the Time when Chemical Evolution Occurred
- Unstable-decay by emitting either radiation or particles.
- Particle-emitting isotopes decay to daughter isotopes.
- Rate of decay for a specific isotope is constant and has a specific half-life.
- Using radioactive isotopes to determine age of rocks.
- Measure ratio of daughter isotopes to parent isotope in a rock sample.
- Estimate the ratio that existed at the time the rock formed.
- Calculate number of elapsed half-lives since the rock formed.
- Assume all components of solar system formed at same time, about 4.6 Ga ("giga
- Youngest known moon rocks are 3.8 Ga-correlates to slowing of asteroid
- Oldest known cell fossils are found in rocks dated 3.5 Ga.
- Conclusion-Chemical evolution occurred in the 300 million years between cessation
of asteroid bombardment (3.8 Ga) and age of oldest known cell fossils (3.5 Ga).
Building Blocks of Chemical Evolution
- 96% of every organism is composed of the elements C, H, O, N.
- These elements were present in the forms of CO2, H2O,
N2 and some CH4, H2, and NH3
Chemical Modeling of Chemical Evolution Reactions
- Formaldehyde (H2CO) and hydrogen cyanide (HCN) are simple,
carbon-containing inorganic molecules that are key intermediates in forming larger organic
- Can H2CO and/or HCN be produced by an input of energy to the types
of molecules available 3.8 Ga?
- Pinto et al.-Hypothesis: CO2 + 2H2 + energy ---->
H2CO + H2O
- Prepared computer model of all possible reactions.
- Model used energy from photons of sunlight, which knock electrons from
valence orbitals and create free radicals. (Fig. 2.11)
- Specified concentrations and temperature based on estimates of early Earth
- Higher temperature increases number of collisions.
- Higher concentration of reactants increases collisions.
- Specified reaction rates in the model based on measurements from
laboratory experiments under controlled conditions.
- Model indicates appreciable quantities of formaldehyde are produced.
- Zahnle develops a similar model showing HCN could also form.
Reduction of carbon was a key step in chemical evolution.
- Carbon is the most versatile molecule found in biological tissues.
- Each carbon atom can form four bonds with other molecules.
- Carbon atoms form the skeleton of organic molecules.
- Carbon atoms can be linked in many arrangements.
- A wide variety of molecular shapes is possible.
- Functional groups added to carbon skeleton impart a variety of chemical
reactivities to carbon molecules.
- Reduction of CO2 by H2 forms H2CO, which
is used as a building block to form
organic compounds (compounds containing at least one C-C bond).
For carbon to be reduced, early atmosphere must have contained CH4,
H2, and NH3
(molecules that can give up electrons).
- Volcanic ash is known to be rich in CO2, H2O, and
- Recent evidence indicates it also has small amounts of CH4,
H2, and NH3.
Once organic molecules formed, only heat was needed to drive formation of more complex
organic molecules to complete chemical evolution.
- Heat was widely available on early Earth as thermal energy.
- Heat + potential chemical energy in bonds of organic compounds was sufficient to
drive formation of more complex organic compounds.
Conditions in the Oceans at the Time of Chemical Evolution
- Earth cools; water condenses from atmosphere, forms rains.
- Rainwater dissolves salts from rocks, forms oceans.
- Salts are most abundant substances leached from rocks.
- Salts are held by ionic bonds
- Chemical evolution may have begun in a salty ocean of pH 7.
Chemical Evolution-Theory and Hypothesis Testing
Oparin and Haldane
Testing the Predictions of the Chemical Evolution Theory
- First to propose the idea of chemical evolution (1923).
- Pattern component-Increasingly complex carbon-containing molecules formed in the
atmosphere and ocean of ancient Earth.
- Process component: radiant and kinetic energy are converted into chemical energy in
the bonds of large molecules.
- Four steps of chemical evolution theory-predictions of the theory:
- First molecules formed were small, carbon-containing compounds like formaldehyde
(H2CO) and hydrogen cyanide (HCN).
- Small molecules react, forming sugars, amino acids, and nitrogenous bases; and the
- Small molecules of prebiotic soup link together to form nucleic acids and proteins.
- A single molecule acquires the ability to self-replicate, becoming the first living
entity and marking the end of chemical evolution, beginning of biological evolution.
Experimental evidence indicates step 1 of the Oparin-Haldane chemical evolution
hypothesis is plausible-Small organic molecules could have formed in the atmosphere and
hydrothermal vents of early Earth.
- Miller 1953 Spark-Discharge Experiment
- Assumed a reducing atmosphere-NH3, H2, and
CH4 (gases), and H2O (water vapor).
- Electrical discharge created sparks (= kinetic energy).
- Results-In one week, a deep red solution containing HCN and H2CO
- Conclusion- Organic preliminary molecules could have been formed in a
- Potential problem-Was the early Earth atmosphere really reducing?
- Volcanic gas thought to have created the atmosphere on early Earth.
- Volcanic gases are rich in oxidized gases-CO2, H2,
- Water plus oxidized gases plus a spark does not yield HCN,
H2CO, or other small carbon-containing molecules.
- Secondary Conclusion-While the Miller experiment shows that
formaldehyde and HCN can form under a reducing environment, the earth's early atmosphere
was oxidizing, not reducing, so this is not a likely origin of these chemicals in the early earth
- Bar-Nun and Chang studied an oxidized atmosphere plus sunlight-like radiation.
- Used water vapor and an oxidized gas-carbon monoxide (CO).
- High-energy radiation from a lamp mimicked sunlight radiant energy.
- Results-A wide variety of reduced-carbon compounds (H2CO,
acetaldehyde, CH4) formed. Varying temperature and ratios/types of oxidized gases
gave similar results.
- Conclusion-The data support the hypothesis that sunlight can trigger
reduction of carbon from a mixture of volcanic gases (Step 1 of chemical evolution).
- Wachtershauser and Huber-Chemical evolution at hydrothermal vents
- Oceanic hydrothermal vent environment:
- Intense pressure
- Superheated water (up to 450oC)
- Contains dissolved compounds of iron, sulfur, nickel, and reduced
- Deposits the dissolved compounds in the 4oC water,
forming "black smokers."
- Could the kinetic energy in superheated water, plus reduced carbon compounds, have
triggered chemical evolution at hydrothermal vents?
- Vents emit methyl mercaptan (CH3SH) at high temperature and
- At high temperature and pressure, CH3SH plus carbon
monoxide (CO) forms acetic acid (CH3COOH), a building block of organic
- Conclusion-The data suggest that moderately complex organic
molecules could have been synthesized at hydrothermal vents.
The Origin of Small Organic Molecules in the Prebiotic Soup
The Second Step in the Oparin and Haldane Theory
Evidence/observations that support the occurrence of amino acids in prebiotic soup:
- Amino acids form readily in Miller's spark-discharge experiment, so they could have formed
in conditions of early Earth..
- Amino acids may have been seeded from outer space.
- Interstellar dust that constantly falls on Earth contains hydrogen cyanide and
aldehydes, key reactants in forming amino acids.
- Murchison meteorite landed on Earth 1969, contained 18 different amino acids.
- Conclusions: Amino acids could have formed in the ancient oceans or plashed in
after meteorite impacts. The origin of amino acids is no longer considered a problem by most
- Unresolved problem: In amino acid chemical evolution, why did only left-handed
enantiomers emerge during chemical evolution?
- Although two forms of every amino acid except Glycine (which has no enatomers)
exist in nature, only the left-handed form are found in living beings
Sugars and the prebiotic soup
- Evidence that supports the occurrence of sugars in the prebiotic soup:
- Monosaccharides form readily in Miller's spark-discharge experiment.
- Heating H2CO molecules in solution forms almost all the pentose and
- Conclusion: The formation of sugars is not a real issue anymore
- Unresolved Problems
- Laboratory simulations of early Earth -- Different pentoses and hexoses form in
approximately equal amounts; but for RNA to form, ribose should have been dominant.
- Chirality-Why did only right-handed sugars emerge during chemical evolution?
Nucleotides and the prebiotic soup
- Purines (A and G) are readily synthesized in the laboratory from reactions of HCN.
- Pyrimidines (C, T, U) are never synthesized under the same conditions, so the origin of
pyrimidines needs explaining in the chemical evolution theory.
- As you can see, we've got big problems here...
The Origin of Macromolecules in the Prebiotic Soup
The Third Step in the Oparin and Haldane Theory
Macromolecules Polymerize from Monomers
Challenges of Polymerization
- Amino acids polymerize to form proteins.
- Nucleotides polymerize to form RNA or DNA.
- Polymerization occurs by condensation reactions-Remove a molecule of H2O
from two monomers to form a bond between them.
- De-polymerize by hydrolysis-Add a molecule of H2O to the bond between
monomers to break the bond.
Modeling Polymerization Reactions on Ancient Earth
- Hydrolysis dominates in the chemical equilibrium over condensation.
- Polymerization decreases entropy; hydrolysis increases it.
- Polymers are less stable energetically than monomers.
- Addition of heat or electrical sparks to solutions of monomers does not drive
- Ferris et al.-Nucleotide reaction/separation/reaction experiments
- Nucleotides plus minerals mixture allowed to react for 1 day.
- Remove and collect solids; then add more nucleotides.
- Repeat steps 1 and 2 for two weeks.
- Perform gel electrophoresis of collected solids - See nucleic acid macromolecules up
to 40 nucleotides in length
- Repeat procedure using amino acids - See proteins up to 55 amino acids long.
- Conclusion: Muddy tide pools and beaches of ancient Earth could have become
covered with macromolecules.
Proteins-Highly Variable Macromolecules, Some of Which Act as
Proteins and the Prebiotic Soup
- A molecule that increases the rate of chemical reaction by lowering the activation
- We'll come back to this in a future lecture
- Chemical evolution theory predicts the first living entity was a self-replicating molecule.
- Could proteins have been the first living entities?
- Arguments in favor of proteins as the first living entities:
- Prebiotic soup likely contained many different proteins due to polymerization
from amino acids on mineral surfaces.
- Proteins are the most efficient catalysts known-A self-replicating molecule
must act as a catalyst to assemble and polymerize its copy.
- Arguments against proteins as the first living entities:
- Assembly of a copy requires a template that provides the pattern/instructions
- Proteins can be catalysts, but cannot act as templates for synthesizing new
- Conclusion: Proteins were most likely not the first living entity
DNA: A Stable, Information-Containing Molecule That Can Act as a
DNA and the Prebiotic Soup
- Lack of chemical reactivity means that DNA is not an effective catalyst.
- In a living organism, no DNA molecule has ever been shown to have catalytic properties,
but some RNA molecules are catalytic in living organisms.
- Conclusion: DNA was most likely not the first living entity
RNA - An Information-Containing Molecule That Can Act as a Template or a
Differences between the Structures of RNA and DNA
- RNA is typically single-stranded; DNA is double-stranded.
- RNA has the pyrimidine uracil; DNA has the pyrimidine thymine instead.
- The sugar in RNA is ribose; the sugar in DNA is deoxyribose.
- DNA forms complementary base pairs between two DNA molecules, which together make a
double helical structure; RNA forms complementary base pairs between different parts of one
molecule, resulting in stem-loop structures.
RNA can function as a template
- An RNA molecule can serve as an information source for making copies of itself.
- The primary structure of an existing RNA molecule is the template for making a
- Complementary base-pairing rules determine nucleotide sequence in the new strand.
- Six basic steps in copying an RNA molecule:
- Step 1 - Free ribonucleotides pair with complementary bases on existing template
RNA molecule by hydrogen bond formation.
- Step 2 - Phosphodiester bonds form between the newly added ribonucleotides,
linking them together into a new strand of RNA.
- The polarity of the new strand is opposite that of the template.
- The bases of the new strand are complementary to those of the template.
- Step 3 - H-bonds joining the new strand to template are broken by heating or
catalysis, releasing the new RNA strand.
- Steps 4-6 - Steps 1-3 are repeated with the new RNA strand acting as the template.
The product RNA strand is an exact copy of the original template RNA molecule.
RNA can function as a catalyst.
- Primary structure varies from one RNA molecule to another; different RNA molecules exist
- Secondary structure varies from one RNA to another; different RNAs have different shapes.
- Some RNA molecules have catalytic activity (Altman and Cech, Nobel Prize 1989).
- Certain RNA molecules of Tetrahymena catalyze condensation and hydrolysis of
- Catalytic RNAs are called "ribozymes."
RNA and the Prebiotic Soup
Experiment 1 (Bartel and Szostak)-Can a ribozyme capable of catalyzing phosphodiester
bond formation be created?
- RNA can act as a template, but is not as good a template as DNA.
- RNA can act as a catalyst, but is not as good a catalyst as proteins.
- Only RNA can act as both template and catalyst.
- The "RNA world" hypothesis-The first living entity was probably a self-replicating
- No self-replicating RNAs exist today in nature.
- Can a self-replicating RNA (i.e., an "RNA replicase") be created in the laboratory?
- Essential features of an RNA replicase:
- Able to catalyze the formation of phosphodiester bonds between nucleotides
- Able to read a template strand and select the complementary nucleotide for
inclusion in the new strand
Experiment 2 - In-vitro selection of ribozymes: Can ribozymes with improved activity be
created by inexact copying and selection in vitro?
- Oligo substrate RNAs were
- Tagged at 5' end with a specific sequence.
- At 3' end have the sequence G-U-G-A-C.
- Pool RNAs were prepared:
- Each has hairpin loop with C-A-C-U-G at base of loop
- Each has a 220-nucleotide random sequence:
- In some, the sequence may be capable of acting as an RNA
- Any replicase activity will cause the pool RNA to be ligated to
an oligo substrate RNA.
- Mix pool RNAs and oligo substrate RNAs
- Pass mixture over an affinity column
- RNA attached to column beads binds the 5' tag of ligated
- Nonligated pool RNAs wash out of the column.
- Conclusion: The random sequences on some pool RNAs did show
catalytic activity (i.e., were ribozymes that catalyzed phosphodiester bond formation between the
pool RNA and an oligo substrate RNA).
- Copy the pool RNAs that showed catalytic activity.
- Use a method that gives inexact copies.
- Some copies may have better catalytic activity than the original.
- Repeat the protocol of Experiment 1 = selection of catalytic ribozymes.
- Assay the reaction rate-the number of ligation reactions per hour.
- Some new pool RNAs had greater ligation efficiency than the original
- Repeating the copy-assay cycle 10 times produced a ribozyme that
was very efficient at catalyzing phosphodiester bond formation.
- A key step in chemical evolution was re-created in the lab-A
ribozyme that had one characteristic of a replicase was created.
- In-vitro selection experiments can produce ribozymes with improved
- Further in-vitro selection experiments produced molecules that could
- Amide bond formation in amino acids
- Peptide bond formation in proteins
- Phosphodiester bonds leading to polymerization of nucleotides
Natural Selection of the First Living Entity in the Prebiotic Soup-A Model for
the Transition from Chemical Evolution to Biological Evolution
A self-replicating RNA molecule appears in the prebiotic soup as the result of chemical
The self-replicating RNA makes copies of itself using free ribonucleotides in the prebiotic
Natural selection occurs.
- The RNA cannot match up complementary ribonucleotides to its template perfectly.
- Many inexact copies (mutations) are made randomly, which produces diversity in the
population of self-replicating RNAs.
Chemical evolution gives way to biological evolution over time.
- Mutants that are more efficient self-replicators produce more copies of themselves,
dominating the population.
- Less efficient self-replicators may be destroyed by UV radiation or a chemical reaction
before they can copy themselves.
- Evolution results - changes in the composition of
the population over time.
- Biological evolution begins when natural selection of the self-replicating molecule occurs.
- Natural selection then becomes the primary mechanism for creating the diversity of living