The Evolution

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 debated

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 supernova. 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 minerals * 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 molecules!

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 life. * 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. * 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.
Estimations of the Time when Chemical Evolution Occurred * Assume all components of solar system formed at same time, about 4.6 Ga ("giga ago"). * Youngest known moon rocks are 3.8 Ga-correlates to slowing of asteroid bombardment. * 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 molecules. * 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 conditions. * 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 N2. * 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 * 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 prebiotic soup. * 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.
Testing the Predictions of the Chemical Evolution Theory * Miller 1953 Spark-Discharge Experiment * Assumed a reduced 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 forms. * Conclusion- Organic preliminary molecules could have been formed in a reduced atmosphere * Potential problem-Was the early Earth atmosphere really reduced? * Volcanic gas thought to have created the atmosphere on early Earth. * Volcanic gases are rich in oxidized gases-CO2, H2, and N2. * 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 reduced environment, the earth's early atmosphere was oxidized, not reduced, so this is not a likely origin of these chemicals in the early earth envrionment.

* 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 carbon * 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 pressure. * At high temperature and pressure, CH3SH plus carbon monoxide (CO) forms acetic acid (CH3COOH), a building block of organic molecules. * Conclusion-The data suggest that moderately complex organic molecules could have been synthesized at hydrothermal vents.
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.

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 scientists. * 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 hexose monosaccharides. * 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 * 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.
Challenges of Polymerization * 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 polymerization.
Modeling Polymerization Reactions on Ancient Earth * Ferris et al.-Nucleotide reaction/separation/reaction experiments 1. Nucleotides plus minerals mixture allowed to react for 1 day. 2. Remove and collect solids; then add more nucleotides. 3. Repeat steps 1 and 2 for two weeks. 4. Perform gel electrophoresis of collected solids - See nucleic acid macromolecules up to 40 nucleotides in length 5. 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 Catalysts
Catalyst
* A molecule that increases the rate of chemical reaction by lowering the activation energy * We'll come back to this in a future lecture
Proteins and the Prebiotic Soup * 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 for assembly. * Proteins can be catalysts, but cannot act as templates for synthesizing new proteins. * Conclusion: Proteins were most likely not the first living entity

DNA: A Stable, Information-Containing Molecule That Can Act as a Template
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 Catalyst
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 copy. * 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 phosophodiester bonds. * Catalytic RNAs are called "ribozymes."
RNA and the Prebiotic Soup * 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 RNA molecule. * 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 1 (Bartel and Szostak)-Can a ribozyme capable of catalyzing phosphodiester bond formation be created? * Oligo substrate RNAs were prepared: * 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 replicase. * Any replicase activity will cause the pool RNA to be ligated to an oligo substrate RNA. * Protocol: * Mix pool RNAs and oligo substrate RNAs * Pass mixture over an affinity column * RNA attached to column beads binds the 5' tag of ligated RNAs. * 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).
Experiment 2 - In-vitro selection of ribozymes: Can ribozymes with improved activity be created by inexact copying and selection in vitro? * 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. * Results: * Some new pool RNAs had greater ligation efficiency than the original pool RNAs. * Repeating the copy-assay cycle 10 times produced a ribozyme that was very efficient at catalyzing phosphodiester bond formation. * Conclusions: * 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 activity. * Further in-vitro selection experiments produced molecules that could catalyze * 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 evolution.
The self-replicating RNA makes copies of itself using free ribonucleotides in the prebiotic soup. * 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.
Natural selection occurs. * 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.
Chemical evolution gives way to biological evolution 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 organisms.