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TS Notes

Chemistry, Nucleic Acids, Origin of Life

Fall Biology

Table of contents
  1. Textbook Notes - Chapter 2.1 to 2.2
    1. 2.1: Atoms, Ions, and Molecules: The Building Blocks of Chemical Evolution
      1. Introduction
      2. Atoms, Protons, and Neutrons
      3. Elements and Daltons
      4. Isotopes
      5. Structure of Atoms
      6. Bonds
      7. Ionic Bonding & Ions
      8. Simple Molecules formed with C, H, N, O
      9. Representing Molecules
    2. 2.2: Properties of Water and the Early Oceans
      1. Properties Correlated with Water’s Structure
  2. Video Notes - Chemical Basis for LIfe
    1. Structure of the Atomic Nucleus
    2. Electron Arrangement
    3. Covalent Bonds
    4. Nonpolar and Polar Molecules
    5. Ionic Bonds
    6. Hydrogen Bonds
    7. The Polarity of Water
  3. Textbook Notes - Nucleic Acids and an RNA World
    1. 4.1: What is a Nucleic Acid?
      1. Introduction
      2. Nucleic Acids
      3. Nitrogenous Bases
      4. Drawing Nucleotides
      5. Chemical Evolution in the Production of Nucleotides
      6. How do Nucleotides Polymerize to Form Nucleic Acids?
      7. DNA and RNA Strands Are Directional
      8. Polymerization Requires an Energy Source
    2. 4.2: DNA Structure and Function
      1. The Nature of DNA’s Secondary Structure
      2. Antiparallel Double Helix
      3. Summary of Antiparallel Double Helix
      4. Tertiary Structure of DNA
      5. DNA as an Information-Encoding Molecule
      6. The DNA Double Helix is a Stable Structure
    3. 4.3 RNA Structure and Function
      1. Structural Differences Between RNA & DNA
      2. Tabular Version - DNA vs RNA Structure
      3. RNA’s Versatility
      4. RNA Can Function as a Catalytic Molecule
  4. Video Notes on Nucleic Acids
    1. Nucleic Acid Structure
    2. Tips on Drawing DNA Sequences
    3. Tips on Drawing Nucleotides
    4. Tips on Drawing Nucleic Acids
    5. ATP Hydrolysis
    6. The Double Helix
    7. RNA Folding
  5. Textbook Notes - Chemical Evolution
    1. 2.3: Chemical Reactions, Energy, and Chemical Evolution
      1. How do Chemical Reactions Happen?
        1. Systems & Surroundings, Law of Conservation of Mass
        2. Chemical Equilibrium
        3. Endothermic and Exothermic Changes
      2. What is Energy?
        1. Potential Energy & Chemical Energy
        2. Bond Strength
        3. Kinetic Energy and Thermal Energy
        4. First Law of Thermodynamics
        5. Heat’s Role in Earth’s Beginnings
      3. What Makes a Chemical Reaction Spontaneous?
        1. Entropy
        2. Second Law of Thermodynamics
    2. 2.4: Investigating Chemical Evolution
      1. Miller’s Experiment
        1. Formal Description of Miller’s Experiment
  6. Textbook Notes - Chemical Evolution - 4.4 In Search of the First Life-Form
    1. Introduction
    2. The Process of RNA Synthesis/Copying
    3. How Biologists Study the RNA World
    4. An RNA World May Have Sparked the Evolution of Life
  7. Textbook Notes - Chemical Evolution - 2.4 Origin-of-Life Experiments and the Two Models
    1. Recent Origin-of-Life Experiments
      1. Synthesis of Precursors Using Light Energy
        1. Free Radicals
      2. Concentration and Catalysis in Hydrothermal Vents
        1. As a Catalyst
        2. Evidence of Vent Minerals as Catalysts
      3. The Two Theories
  8. Video Notes on Chemical Evolution
    1. Figure Walkthrough: Potential Energy Change During Chemical Reactions
    2. What Was the Miller-Urey Experiment?
    3. Steven Hawking Asks What Are the Building Blocks of Life and How Did They Come to Be
    4. What is Chemical Evolution?
  9. Video Notes on Chemical Evolution - the Origin of Life
    1. The Mysterious Origins of Life on Earth
    2. Life’s Rocky Start | Deep Sea Vents
    3. What is the Metabolism-First Hypothesis for the Origiin of Life?
    4. What is the RNA World Hypothesis?
    5. The RNA Origin of Life

Textbook Notes - Chapter 2.1 to 2.2

Directions: study chapter 2.1 and 2.2 (up to page 66; stop before the section “Cohesion, Adhesion, and Surface Tension”).

2.1: Atoms, Ions, and Molecules: The Building Blocks of Chemical Evolution

Introduction

  • Four types of atoms - hydrogen, carbon, nitrogen, and oxygen (H, C, N, O) make up about 96% of all matter.
  • Fundamental questions to understanding how simple substances evolved into complex molecules found in living cells:
    1. What is the physical structure of H, C, N, O atoms?
    2. What are the structures of simple molecules (water, CO2, etc.) that serve as building blocks of chemical evolution?
  • Key theme in biology: structure affects function.

Atoms, Protons, and Neutrons

  • An atom is the smallest identifiable unit of matter.
    • Contains a characteristic number of protons, called its atomic number. This is written at bottom left of the symbol.
    • Sum of protons and neutrons in atom is called mass number and is written at top left of symbol.
  • Simple way of depicting an atom: extremely small particles called electrons orbit an atomic nucleus made up of larger particles called protons and neutrons.
    • Every element except hydrogen has one or more neutrons in its nucleus.
    • Protons have a positive electric charge (-1), neutrons are electrically neutral, and electrons have a negative electric charge (-1).
    • Number of protons and electrons in an atom are the same: atom is electrically neutral.

Elements and Daltons

  • Element - a substance that consists entirely of a single type of atom.
  • Dalton (Da) is used to measure the masses of electrons, etc. Masses of protons and neutrons are about 1 Da. An electron’s mass is so small it is usually ignored.
  • The number of protons in an element does not change; if the atomic number in an atom changes, it is no longer the same element.

Isotopes

  • The number of neutrons can vary. Forms of an element with different numbers of neutrons are isotopes.
    • Isotopes of the same element can have different masses because they have different numbers of neutrons.
    • Atomic weight of an element is the average of all masses of naturally occuring isotopes in nature. This is why atomic weight can be slightly different from mass number.
    • Some isotopes are not stable; these are radioactive isotopes. The nucleus will decay and release energy in the form of radiation.

Structure of Atoms

  • The arrangement of electrons around the nucleus helps us understand how different elements behave.
  • Electrons move around the atomic nucleus in regions called orbitals. An orbital can hold up to two electrons (a pair).
  • Orbitals are grouped into levels called electron shells. These are numbered 1, 2, 3, … to indicate how close to how far the levels are from the nucleus.
  • An electron shell contains a specific number of orbitals. Each orbital in a shell is loaded with at least one electron before any orbital can be filled with a second paired electron. Electrons in an atom must also be filled from innermost to outermost.
  • The outermost shell of the element is called the valence shell. Electrons in this shell are valence electrons.
    • The number of unpaired electrons in the atom’s valence shell is its valence.

Bonds

  • A covalent bond is when two atoms share electrons, and the connected atoms form a molecule.
    • Covalent bonds can make atoms more stable (e.g. when the valence shell is not filled with only one electron, but together the valence shell is filled). Shared electrons ‘glue’ atoms together into molecules.
    • The two bonded atoms are written as H-H or H2.
  • Electrons participating in a covalent bond are not always shared equally in the atoms involved. This can heppn in compounds, where atoms of different elements are bonded together.
  • When atoms of different elements bond, they may pull electrons towards their nuclei with different strengths; this is called electronegativity.
    • Electronegativity is caused by the number of protons in the nucleus and the distance between the nucleus and the valence shell.
    • E.g. like a magnet; electronegativity is caused by the strength of the ‘magnet’ and how far away the object is from it.
    • Electronegativities of six most abundant elements in organisms: O > N > S = C = H = P (= being approximate).
  • A bond that involves equally shared electrons is a nonpolar covalent bond.

  • A bond that involves assymetrically shared electrons is a polar covalent bond. In a polar covalent bond, electrons spend most of their time closer to the nucleus of the most electronegative atom.

  • Example: the water molecule. Written as H2O (two hydrogen and one oxygen atom).
  • Electrons involved in covalent bonds in water are not shared equally but are held much more tightly by the oxygen nucleus than by the hydrogen nuclei.
  • Because electrons are shared unequally in each O-H bond, they spend more time near the oxygen atom, giving it a partial negative charge (recall electrons have a negative charge); they spend less time near the hydrogen atoms, giving them a partial positive charge.
  • Lowercase delta is used for this. O has δ- and H has δ+

Ionic Bonding & Ions

  • Ionic bonds are similar to covalent bonds, but electrons in ionic bonds are completely transferred from one atom to another.
    • This electron transfer gives each of the two resulting atoms a full valence shell.
  • Atoms or molecules that carry full charges instead of partial charges that come from polar covalent bonds are called ions. The sodium ion is written as Na⁺.
    • Positively charged ions are called cations (KAT-eye-un).
    • Negatively charged ions are called anions (AN-eye-un).
  • Examples:
    • E.g. sodium atom (Na) has three electron shells with one lone electron in its valence shell. They can lose that electron to leave them with a second full shell, which is more energetically stable. Because it has one more proton than it has electrons, the atom has a net electric charge of +1.
    • E.g. chlorine atoms (Cl) tend to gain an electron, filling their outermost shell. The resulting ion has a net charge of -1, because it has one more electron than proton.
    • E.g. sodium cations and chloride anions form sodium chloride (NaCL, table salt); held together by strong opposite charges in their ions.
  • Covalent bonds share electrons to make both more stable. Ionic bonds are between atoms that have full charges (-1 or +1) and attract strongly.
  • The electron-sharing continuum. Equal sharing of electrons to complete transfer of electrons.
    • Nonpolar covalent bonds. Atoms have no charge, atoms are shared equally.
    • Polar covalent bonds Atoms have a partial charge because of electronegativity; electrons spend more time around certain atoms in the bond.
    • Ionic bonds. Atoms have full charges that are directly opposite each other to form strong bonds.
  • Note - most compounds present in living organisms are formed with either nonpolar or polar covalent bonds.

Simple Molecules formed with C, H, N, O

  • CH4 (Methane) is formed when four hydrogen atoms are convalently bonded with each of the four unpaired electrons of a carbon atom.
  • NH3 (Ammonia) is formed when three hydrogen atoms are covalently bonded with three unpaired electrons in nitrogen.

  • H2O (Water) is formed when two hydrogen atoms bond with two unpaired electrons in oxygen.

  • Atoms with more than one unpaired electron in the valence shell can also form double bonds or triple bonds.
  • CO2 (Carbon Dioxide) is formed when a pair of unmatched electrons in two oxygen atoms are bonded with two pairs of unmatched electrons in a carbon atom.

  • N2 (Molecular Nitrogen) is formed when the three unmatched electrons in each of two nitrogen atoms bond.

  • There are different 3-dimensional geometries to these simple molecules.
    • N2 and CO2 have simple linear structures. There are only two atoms in N2, so the model can only be linear. In CO2, the two C=O bonds repel each other 180 degrees apart.
    • CH4 has a tetrahedral structure, which allows the four C-H bonds to get as far away from each other as possible.
    • Water’s bond geometry is bent rather than linear. Has four orbitals in valence shell that repel each other, but two orbitals are filled with unshared electron pairs, which pushes the O-H bonds closer together.

Representing Molecules

  • Molecular formulas are compact, but don’t have much information. Just indicate numbers and types of atoms in molecules. e.g. CO2, H2O, etc.
  • Structural formulas indicate which atoms are bonded together. Single, double, and triple bonds are represented by single, double, and triple dashes. e.g. O=C=O.
  • Ball-and-stick models take up more space than structural formulas both provide information on three-dimensional shapes and indicate sizes of atoms.
  • Space-filling models are difficult to read but accurately depict the relative sizes of atoms and their spatial relationships.

2.2: Properties of Water and the Early Oceans

  • Life is based on water; it arose in an aqueous environment.
    • 75 percent of volume in a typical cell is water.
  • Water is an excellent solvent - an agent for dissolving, or getting substances into solution.
    • e.g. dumping sugar into coffee; the sugar dissappears as the sugar molecules disperse in the aqueous solution. Sugar molecules are separated and interact with water’s partial charges.
  • Substances are likely to come into contact with one another when they are solutes (dissolved into a solvent like water).

Properties Correlated with Water’s Structure

  • Water has small size, highly polar covalent bonds, and a bent shape resulting in unique polarity among molecules.
  • ==Water is an efficient solvent.==
  • Recall that…
    • …the covalent O-H bond is polar (difference in electronegativites of hydrogen and oxygen). Oxygen atom has partial negative charge and hydrogen atom has partial positive charge.
    • …water molecules are bent. This shape makes the partial negative charge on the oxygen atom stick out away from partial positive charges on the hydrogen atoms, gives the water molecule a polar nature.
    • When molecules are polar, they carry a partial positive charge on one side and a partial negative charge on the other.
  • When two water molecules approach each other, the partial positive charge on hydrogen attracts the partial negative charge on oxygen. This is an example of a hydrogen bond.
    • Hydrogen bonds also form between water molecules and polar solutes, like sugar glucose, or between water and ions, like Na⁺ and Cl⁻from table salt.
    • Substances that interact with water this way are hydrophilic (water-loving). Almost any ionic compound and polar molecule can dissolve in water.
  • Nonpolar molecules do not readily dissolve into aqueous solutions. Substances that do not interact with water are hydrophobic (water-fearing).
    • Interactions of hydrophobic molecules with water are minimal or nonexistent; surrounding water molecules form hydrogen bonds with each other.
    • These are hydrophobic interactions.
  • When hydrophobic molecules are close to each other, they are further stabilized by weak electrical attractions, known as van der Waals interactions.
  • Example: octane (C8H18), a component of gasoline, is a nonpolar molecule; when put in water it is forced to interact with itself, because water is more stable when it interacts with itself rather than with nonpolar molecules.
    • Analogy: Unstable conditions are -1 and 1, stable condition is 0. Combining an unstable -1 with a stable 0 yields -1, still an unstable condition; combining an unstable -1 with an unstable +1 yields a stable 0.

Video Notes - Chemical Basis for LIfe

Structure of the Atomic Nucleus

  • Five important atoms: Hydrogen, Carbon, Nitrogen, Oxygen, and Chlorine.
  • Protons are positively charged.
  • Electrons are negatively charged.
  • Each atom has the unique number of protons. Protons + Neutrons = Mass Number
  • Most elements have two or more isotopes whose atoms differ in both mass number and neutral number.

Electron Arrangement

  • A cloud of negatively charged electrons surrounds the nucleus.
  • In an uncharged atoms, the number of electrons = the number of protons.
  • Electrons occupy energy levels called energy shells.
    • Innermost shell can hold at most two electrons, the next few shells can hold up to 8 electrons apiece.
    • The chemical properties of an atom depends on the # of electrons in its outermost electron shell.
    • An atom is most stable when its outermost shell is full.
    • Two electrons for hydrogen, eight election for larger items
  • By transfering or sharing electrons, atoms can complete their outer shells and bond.

Covalent Bonds

  • A covalent bond is the sharing of outer-shell electrons by two atoms.
  • E.g. Hydrogen has one electron but needs 2 complete its outer shell.
    • H-H covalent bond can be formed; each atom shares the other electron. The outer shell is completed.
  • Other examples: CH4 (Methane), O2 (Oxygen), H2O (Water)

Nonpolar and Polar Molecules

  • Electronegativity - tendency for atoms to pull electrons towards themselves.
  • In a covalent bond H-H, both nuclei have the same electronegativity. This is nonpolar.
  • In a covalent bond H2O, the nucleus of oxygen attracts the electrons more; it ‘hogs’ it.
    • Therefore, electrons spend more time around the oxygen molecule than the hydrogen molecules.
    • The oxygen molecule has a partial negative charge (electrons are negative).
    • The hydrogen molecules have a partial positive charge.
  • Think: polar = skewed, drastically contrasting (poles).
    • If two atoms have same electronegativity, not polar
    • If two atoms have different electronegativity, is polar
  • Think: electronegativity = magnet, the strength depends on the strength of the magnet itself as well as how far the object is from the magnet.

Ionic Bonds

  • Sometimes, atoms complete their outer shells by stealing or giving away atoms instead of sharing them.
  • ions are formed when atoms lose or gain an electron to complete their shells.
  • Electrical implications of ions
    • If an atom loses an electron, it has a positive charge (it lost a negatively-charged electrion).
    • If an atom gains an electron, it has a negative charge (it gained a negatively-charged electron.)

Hydrogen Bonds

  • Water molecules tend to stick together.
  • Covalent bonds between hydrogen and oxygen atoms are polar
    • Share electrons unequally
  • Remember that in H2O water molecule:
    • Hydrogen molecule has slight positive charge
    • Oxygen molecule has slight negative charge
  • If we have two hydrogen molecules A and B:
    • The oxygen molecule of B will attract to the hydrogen molecule of A
    • This is called a hydrogen bond.
    • We can continue stacking up several weak covalent bonds through it being polar (uneven).
  • Many biological processes require on hydrogen bonds.
    • Keeps proteins folded in a three-dimensional shape.
    • Two strands of DNA held together by hydrogen bonds.

The Polarity of Water

  • Water has many properties
    • Takes lots of heat energy to change water
    • Individual water molecules are polar and stick together by hydrogen bonds
  • Atoms in H2O are in a constant ‘tug-of-war’ for electrons.
  • The polarity of water keeps it attracted to each other (hydrogen bonds)
  • Each molecule can hydrogen bond to four other molecules
    • 2 unpaired electrons in oxygen atom
    • 1 unpaired electron in each hydrogen atom
  • This gives water special properties like:
    • High boiling point
    • Surface tension

Textbook Notes - Nucleic Acids and an RNA World

4.1: What is a Nucleic Acid?

Introduction

  • Life began when chemicals evolved to the point where molecules could promote their own replication.
  • Deoxyribonucleic Acid (DNA) stores genetic information and is replicated using proteins.
  • RNA world hypothesis says that there was a stage in life’s evolution where ribonucleic acid (RNA) stored genetic information and catalyzed its own replication.
    • Did life on Earth begin with DNA first?
    • Did it do some replicating, evolving into a molecule just before RNA?
    • Did RNA precede DNA and proteins?

Nucleic Acids

  • Nucleic acids are polymers, like proteins.
  • Instead of being assembled from amino acids, nucleic acids are made up of nucleotides.
  • There are three components of a nucleotide.
    • A phosphate group.
    • A five-carbon sugar.
      • A central component in the nucleotide.
      • Five carbons in the sugar are usually labelled with numbers and prime (') symbols. For example, base is attached to 1’ carbon and phosphate group attached to 5’ carbon.
    • A nitrogenous (contains nitrogen) base.
  • Phosphate group bonds to a sugar molecule, which bonds to the base.
TermDefinition
ribonucleotidesmonomers of RNA (ribonucleic acid). sugar is ribose.
deoxyribonucleotidemonomers of DNA (deoxyribonucleic acid). sugar is deoxyribus.
deoxy-prefix for ‘lacking oxygen’.

Nitrogenous Bases

  • purines - consist of double rings formed from nine atoms.
    • adenine (A) (note - has ‘nine’ in name)
    • guanine (G) (note - has ‘nine’ in name)
  • pyrimidines - consist of single rings formed from six atoms.
    • cytosine (C)
    • uracil (U) (used by ribonucleotides)
    • thymine (T) (used by deoxyribonucleotides)

Drawing Nucleotides

phosphate
usually represented as a circle.
sugar
usually represented as a pentagon with an upright tail.
nitrogenous base
usually represented as a hexagon.
covalent bond
usually represented with a line.

Chemical Evolution in the Production of Nucleotides

  • If nucleic acids played a role in chemical evolution of life, then there must have been at least some nucleotides present in prebiotic oceans.
  • Most biologists accept the idea that amino acids could have been synthesized early in Earth’s history.
    • Nitrogenous bases and types of sugars[^1] can be synthesized under conditions like those in early Earth oceans, particularly deep-sea hydrothermal vent systems.
      • Reactive minerals on the surface of walls in deep-sea vents bind to ribose, effectively enriching and concentrating ribose[^2] from a pool of diverse sugars.

How do Nucleotides Polymerize to Form Nucleic Acids?

  • **Once nucleotides formed, how would they polymerize to form nucleic acids?
  • Nucleotides polymerize through condensation reactions between hydroxyl on sugar component of one nucleotide and phosphate group of another nucleotide.
    • Forms a new covalent bond between the two nucleotides, and a molecule of water is released.
  • Bridge formed by phosphate group called phosphodiester linkage (phosophodiester bond).
  • When phosphodiester linkages join ribonucleotides together, the polymer produced is RNA.
  • Phosphodiester linkages between deoxyribonucleotides produces DNA.

DNA and RNA Strands Are Directional

  • A chain of linked sugars and phosphates in a nucleic acid acts as a backbone.
  • The phosphate backbone of a nucleic acid is directional.
    • In a strand of RNA/DNA,
      • One end has an unlinked 5’ phosphate
      • Another end has an unlinked 3’ hydroxyl
  • Order of different nucleotides forms the primary structure of the nucleic acid.
  • Sequence of bases in RNA/DNA is always written in a 5’ to 3’ direction.
    • This is logical; RNA and DNA are synthesized in this direction.
    • Nucleotides are only added at 3’ end.

Polymerization Requires an Energy Source

  • The joining of nucleotides into nucleic acids decreases entropy and therefore is not spontaenous.
  • Energy is needed to tip the balance _in favor of polymerization).
  • Nucleic acid polymerization can take place in cells b/c potential energy of nucleotides are raised by reactions that add +2 phosphate groups to the 5’ phosphates of ribonucleoside or deoxyribonucleoside monophosphates, which create nucleoside triphosphates’.
  • Nucleoside triphosphates are activated nucleotides; adenosine triphosphate, ATP.
    • Equivalent used in DNA synthesis: deoxyadenosine triphosphate (dATP).
  • Phosphates are negatively charged, and charges repel.
    • Linking 2 or more phosphates together creates covalent bonds that carry lots of potential energy.
    • Energy is released when phosphates form new, more stable bonds with other atoms.

4.2: DNA Structure and Function

  • Primary structure of DNA is similar to primary strucutre of proteins.
  • DNA molecules have a sugar-phosphate backbone created by phosphodiester linkages and a sequence of any of 4 bases that extend from it.
  • DNA also has a secondary structure.

The Nature of DNA’s Secondary Structure

  • Discovery of DNA’s secondary structure was one of the biggest scientific breakthroughs of the 20th century.
  • Many clues as to the structure of DNA:
    • Chemists knew the molecule had a sugar-phosphate backbone.
    • Number of purines in a DNA molecule equal to number of pyridines, #T = #A, #C = #G.
    • Rosalind Franklin and Maurice Wilkins used X-ray crystallography to find distances between groups of atoms in the molecule.
      • Three distances were repeated: 0.34, 2.0, 3.4 nm[^3]
      • Could infer a regular and repeating structure.

Antiparallel Double Helix

  • Watson and Crick analyzed the size and geometry of 3 nucleotide components:
    • Deoxyribose
    • Phosphate
    • Base
  • Determined that:
    • the distance of 2.0 nm represented the width of the helix
    • the distance of 0.34 nm was the distance between bases stacked in a spiral
  • Observations:
    • only purine-pyrimidine fits in the 2-nm wide sugar-phosphate backbone.
      • purine-purine too big, pyrimidine-pyrimidine too small
    • complimentary base pairing based on hydrogen bonding
    • patterns of hydrogen bonding could form only if bases are opposite strands flipped 180 degrees relative. These are antiparallel.
    • antiparallel strands predicted to form a double helix.
  • Carbon-nitrogen rings are mostly nonpolar, although each base has polar groups for hydrogen bonds.
    • In aqueous solutions[^4], hydrophobic interactions caused DNA to twist into a helix to minimize contact between hydrophobic base and water molecules.
  • Strands are stabilized by base stacking.
    • Results from van der Waals interactions between adjacent bases.
    • Rotated orientation of interior base pairs lets rings of adjacent bases stack on top of each other like coins.
    • Double helix is hydrophilic overall and soluble in aqueous solutions.
  • Major and minor grooves allow access to proteins.

Summary of Antiparallel Double Helix

The double helix is shaped and stabilized by hydrogen bonding between complementary base pairs, hydrophobic interactions, and van der Waals interactions.

Tertiary Structure of DNA

  • DNA in cells is found in compact three-dimensional structures.
  • Total length of DNA in each cell is about 6 feet long. Needs to be compact.
  • When DNA becomes wound too tightly or losely, it twists on itself to form supercoils, which are compact and 3-dimensional structures.

DNA as an Information-Encoding Molecule

  • Watson and Crick’s model revealed DNA as a biological resevoir of information.
  • Information consists of a sequence of nucleotides in nucleic acid.
  • Four nitrogenous bases are like letters in an alphabet.
  • DNA stores important information.
  • DNA can perform its own synthesis.
    1. Separate strand; break complementary base pairs.
      • This can be done by breaking hydrogen bonds with heat or enzyme-catalyzed reaction.
    2. Each strand of DNA serves as a template for formation of a new strand.
      • Template strand is combined with complementary strand.
    3. Strands polymerize to form sugar-pohsphate backbone.
      • Produces two identical daughter molecules.
  • Does the structure of DNA allow it to be replicated?

    It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism. -Watson and Crick

The DNA Double Helix is a Stable Structure

  • DNA is highly structured; regular, symmetric, held together.
  • DNA from fossils that are 10k-s of years old; they are the same sequence of bases as when they were alive.
  • Stability of DNA reveals why it is so effective as information storage.
  • Structure of DNA is simple and nonreactive; never ben observed to cataylze any reaction in any organism.
  • No support for the idea that life began with DNA alone; instead, life began with RNA.

4.3 RNA Structure and Function

Structural Differences Between RNA & DNA

  • Primary structure
    • RNA has a primary structure of four types of nitrogenous bases from a sugar-phosphate backbone.
    • Two differences:
      1. Sugar in sugar-phosphate backbone is ribose, not deoxyribose.
      2. Pyrimidine base thymine does not exist in RNA; uses a related base, uracil.
    • Hydroxyl (OH) group in 2’ carbon of ribose is much more reactive than hydrogen atom on 2’ carbon of deoxyribose.
    • Hydroxyl group can attack phosphate linkage between nucleotides when RNA molecules fold in different ways.
      • Generates a break in the sugar-phosphate backbone.
    • The extra hydroxyl group makes RNA less stable than DNA.
  • Secondary structure
    • RNA molecules have secondary structure that results from complementary base pairing between purine and pyrimidine bases.
    • purine and pyrmidine bases in RNA usually hydrogen bond with complementary bases in the same strand, rather than in a different strand.
    • Within-strand base pairing: one part of the RNA strand folds over and aligns with bases on another part of the same strand.
      • Hydrogen bonding with complimentary bases results in a helical structure like the double helix of DNA.
      • Stem-and-loop configuration.
  • Tertiary structure
    • RNA molecules have tertiary structure that arises when secondary structures fold into more complex shapes.
    • Pseudoknot structure is an example of 3-d shapes formed by base pairing in distant regions of folded RNA molecules.
    • RNA molecules with different base sequences can have different shapes and chemical properties.
      • More diverse in size, shape, and reactivity than DNA molecules.

Tabular Version - DNA vs RNA Structure

Level of StructureDNARNA
PrimarySequence of deoxyribonucleotides: bases are A, T, G, CSequence of ribonucleotides: bases are A, U, G, C
SecondaryTwo antiparallel strands twist into a double helix, stabilized by hydrogen bonding, hydrophobic bonding, hydrophobic interactions, and van der Waals interactionsSingle strand folds back on itself to form a double-helical ‘stem’ and an unpaired ‘loop’.
TertiaryDouble helical DNA forms compact structures by wrapping around histone proteins or twisting into supercoils.Secondary structures fold to form a wide variety of distinctive three-dimensional shape.

RNA’s Versatility

  • RNA molecules are highly versatile.
    • A nucleic acid like DNA, but RNA folds into complex three-dimensional shapes like proteins.
  • Structural flexibility of RNA molecules lets them perform many tasks.
    • Central dogma introduced RNA as an intermediate between DNA and protein.
    • Messenger RNA transmits information needed to synthesize polypeptides.
    • RNA molecules help regulate the production of messenger RNA from DNA, process and edit information stored in messages, and catalyze synthesis of proteins.

RNA Can Function as a Catalytic Molecule

  • Four types of nucleotides in RNA molecules are no match for 20 amino acid residues in proteins.
  • RNA has a degree of structural and chemical complexity.
  • Capable of forming structures that catalyze a number of chemical reactions.
  • RNAs are called ribozymes (RNA enzymes), catalyze reactions similar to protein enzymes.
    • Ribozyme catalyzes hydrolysis and condensation of phosphodiester linkages in RNA.
    • Ribozymes catalyze important reactions in cells.
    • For example, responsible for catalytic activity of ribosomes that polymerize amino acids to form polypeptides.
  • 3-dimensional nature of ribozymes are vital to catalytic activity.
  • Ribozymes were a watershed event in origin-of-life research.
  • The fact that ribozymes could catalyze formations of phosphodiester bonds raised the possibility that RNA could polymerize a copy of itself; such a molecule would be the first living identity.

Video Notes on Nucleic Acids

Nucleic Acid Structure

  • DNA polymer - one of two twisted stands that make up a DNA molecule.
  • Cells make nucleic acid polymers by linking together four types of monomers, called nucleotides.
  • Each nucleotide consists of a
    • Sugar (deoxyribose in DNA)
    • Phosphate group
    • Nitrogen-containing[^1] base (G, A, C, T)
  • Letters in a sentence, sequence of nucleotides carries information.
  • The DNA of every organism has a unique nucleotide sequence.
    • DNA can be millions of nucleotides in length.
  • DNA consists of two strands of nucleotides that twist around each other.
    • This forms a double helix.
    • Strands are held together by hydrogen bonds between pairs of nitrogenous bases.
    • A pairs with T, G pairs with C.
  • RNA Polymer - typically single-stranded.
  • Instead of deoxyribose, has a sugar called ribose.
  • Uses a different base (uracil, U) instead of thyamine (T).
  • Copied from part from part of DNA, so shorter than DNA.
    • Dozens to thousands of nucleotides.

Tips on Drawing DNA Sequences

  • DNA molecules are large, complex, & important.
  • There are many different models for DNA.
  • Use models that ignore most of DNA structure, but be familiar with the basics so you know what it represents.
  • Double-stranded DNA is shaped like a ladder.
    • Uprights made of sugars and phosphate groups.
    • Rungs made of nitrogenous bases that come in four varieties (G with C, A with T)
  • How is genetic information stored in DNA?
    • Particular sequence of letters (-T-C-T-A-G-C-)
    • Thousands of letters in a sequence of gene.
    • The sequence of gene determines the physical trait.
    • If a mutation occurs, causing change in DNA sequence, the protein may change.
  • Only focus on a small segment of a gene.
    • In general, plants with similar DNAs are likely to be more related.

Tips on Drawing Nucleotides

  • Molecules like nucleotides are hard to see because they are so small.
  • Space-filling models are difficult to see; structural formula is better.
  • Ribose
    • OH group at 2’ and 3’ carbon
  • Deoxyribose
    • OH group at 3’, H group at 2’ carbon
  • Simplification!
    • Leave out hydrogens and carbons, which are implied by corners of the model.
    • Sugar left to a pentagon, if different types of sugar not necessary.
    • Phosphate group as sugar connected by 5’ carbon item.
    • Nitrogenous base as a hexagon with letter indicating type.
    • Simplified model useful to draw several nucleotides.

Tips on Drawing Nucleic Acids

  • DNA is a type of nucleic acid, which is a polymer of nucleotides.
  • When nucleotides polymerize, a covalent bond forms between the three-prime carbon of one sugar molecule and the phosphate group of another.
  • The phosphate groups and sugars form the backbone.
    • Arrowhead represents the side of the chain where the 3’ carbon has a free OH group.
  • In the other strand, they are reversed.
  • Nitrogenous bases pair in the center and pair in a specific way.
    • One-ring cytosine form three hydrogen bonds with double-ring guanine.
    • One-ring thyamine forms three hydrogen bonds with double-ring adenine.

ATP Hydrolysis

  • What is the source of acid used for nucleic acid polymerization?
  • Monomers of nucleic acids are nucleotides. Imagine them moving around in a disordered manner.
    • Nucleotides are organized by condensation reactions, become ordered.
  • In spontaneous reactions:
FromTo
ReactantsProducts
High potential energyLow potential energy
Low entropyHigh entropy
  • The process is not spontaneous, because entropy does not decrease.
  • Nucleotide activiation is activated with more phosphates.
    • Each phosphate has a negative charge.
    • Repulsion between negative charges makes bonds between phosphates weak.
    • Increase potential energy.
    • Potential to form new, stronger bonds has increased.
  • Condensation reactions.
    • Two phosphates are removed in one nucleotide and the remaining phosphate makes a strong bond with the 3’ carbon in another nucleotide.
    • Different in bond strength releases heat.
    • Condensation reactions with activated nucleotides are spontaneous.
      • Increase in molecular motion as heat is released increases entropy.
  • ATP: Adenosine Triphosphate.
    • Activated nucleotide.
    • When ATP + H2O, splits into AMP[^2] + inorganic pyrophosphate (2 phosphate molecules), which have formed stronger bonds with water.
    • Decrease in potential energy.
    • Hydrolysis. Released as heat.

The Double Helix

  • 3-dimensional arrangement of molecules must explain stability of life (traits passed) and the mutability of life (change fo evolution to happen).
  • Genes - located inside the nucleus of cells, associated with chromosomes.
  • Genes needed to be made of DNA or proteins
    • DNA doesn’t seem very interesting - repeated units of phosphate, sugar, and bases.
    • This view persisted for a long time.
  • Powerful technique for solving molecular structure: x-ray crystallography.
    • Determine position of every single atom in the molecule with respect to every other molecule.
    • DNA is not an easy molecule to work with.
  • Maurice Wilkins - trained as a physicist, drawn to problem of the gene.
    • Rosalind Franklin; talented crytallographer.
    • Recipe for disaster; worked against each other often.
  • Biological molecules come in many shapes.
    • Suspected DNA might be a helix of some kind.
    • How would the bases arrange?
  • Initially, Watson and Crick’s the model was wrong (bases on the outside). Franklin dismissed their effort.
  • Pauling preparing a copy of DNA; a triple helix similar to the one that they had been shamed in abandoning.
  • Photo 51, diffraction pattern was a helix.
    • A double helix, not a triple helix.
    • The two backbones led in opposite directions.
    • The bases need to be on the inside.
  • The number of As and Ts was the same, the number of Gs and Cs was the same.
  • Discovered the arrangement of the bases, which revealed how DNA works.
  • Complimentary nature of DNA. Could easily make a new complimentary copy just be obeying pairing rules. Solved gene replication.
  • Answers how information is stored and how mutations emerge.

RNA Folding

  • When nucleic acid is relieved of being locked with another strand, it can take on any shape it wants to (does not need to be a double helix).
  • RNA structues are more varied than what DNA can be.
  • Can interact with itself.
  • Can achieve what, for instance, a protein molecule can achieve.
  • Not just an informational molecule, but a biocatalyst.

Textbook Notes - Chemical Evolution

2.3: Chemical Reactions, Energy, and Chemical Evolution

  • Chemical evolution theory supporters say simple molecules in the atmosphere and oceans participated in reactions that produced larger and more complex molecules.

  • Two environments.
    • The atmosphere in early Earth had many gases (from volcanoes). Water vapor, carbon dioxide, & nitrogen primarily, molecular hydrogen and carbon monoxide in lesser numbers.
    • Deep-sea hydrothermal vents were where very hot rocks contacted cracks in the seafloor. Deep-sea vents have lots of gases like carbon dioxide and molecular hydrogen, as well as reactive metals like nickel & iron.
  • Very little happens when CO2, N2, H2, CO, and water vapor interact on their own.
    • How did these molecules evolve to produce large and complex substances in living cells?

How do Chemical Reactions Happen?

  • Take, for example, gases that come out of volcanoes to produce carbonic acid:
    • CO2(*g*) + H2O(*g*) ⇌ CH2O3(*aq*)
    • The expression is balanced.
      • 1 carbon atom
      • 3 oxygen atoms
      • 2 hydrogen atoms
    • chemical (*state*) indicates the state of the chemical.
      • l for liquid.
      • g for gas.
      • aq for aqueous.
Systems & Surroundings, Law of Conservation of Mass
  • Interacting molecules are systems, and everything else is the surroundings.
  • Ignore surroundings and focus on the system.
  • System as being closed relative to its surroundings.

  • Mass of reactants always equal to mass of products.

  • Law of Conservation of Mass
    • Mass cannot be created or destroyed.
    • It must be rearranged through chemical reactions.
Chemical Equilibrium
  • Chemical equilibrium (indicated by ⇌).
    • Driving reactions
      • CO2(*g*) + H2O(*g*) ⇌ CH2O3(*aq*)
      • Adding more CO2 will drive the reaction to the right, creating more CH2O3.
      • Removing CO2 or adding more CH2O3 will drive the reaction to the left.
    • Temperature
      • H2O(l) ⇌ H2O(g) (liquid water and water vapor).
      • Equilibrium cna be altered by changes in temperature.
      • System absorbs thermal energy from surrounding environment; liquid water molecules change from liquid to gas.
Endothermic and Exothermic Changes
  • When thermal energy is absorbed by the system, it is endothermic (‘within heating’).
    • H2O(l) → H2O(g) is endothermic. Energy is absorbed to vaporize liquid water.
  • When thermal energy is released to the surroundings, it is exothermic (‘outside heating’).
    • H2O(g) → H2O(l) is exothermic. Energy is released when the environment is cooled and vaporized water turns into liquid water

What is Energy?

  • Energy - the capacity to do work or supply heat.
    • Capacity: stored potential or active motion.
Potential Energy & Chemical Energy
  • Stored energy is potential energy.
  • An object gains or loses its ability to store energy b/c of its position.
  • Potential energy is related to sharing electrons in covalent bonds.
    • Electrons far from atomic nuclei, bond is long and weak.
      • Greater capacity to be broken apart into new, stronger bonds during reaction.
    • Electrons closer to one or both atoms, bond becomes short and strong.
      • Lesser capacity to be broken apart into new, stronger bonds during reaction.
  • Molecule’s chemical energy is its ability to form stronger bonds is a type of potential energy.
Bond Strength
  • Electronegativities of atoms affect positionof shared electrons.
  • Example:
    • Unequal sharing (polar), low potential energy, short & strong bonds.
      • O-H. (All electrons are with O, which has much higher electronegativity).
    • Mostly equal sharing, increasing potential energy, medium-length & power bonds.
      • N-H. (Electrons are relatively in the middle, but nitrogen has a slightly larger electronegativity than hydrogen.)
    • Equal electron sharing, high potential energy, long & weak bonds.
      • C-H. (Electrons are equally shared b/c both have same weak electronegativities.)
Kinetic Energy and Thermal Energy
  • Energy of motion is kinetic energy.
    • All molecules have at least a little kinetic energy because they are always moving.
    • Kinetic energy in molecular motion is thermal energy.
  • Thermal energy.
    • Temperature of an object measures how much thermal neergy a molecule possesses.
      • Cold object has low temperature. Molecules are moving slower.
      • Hot object has high temperature. Molecules are moving faster.
    • Two objects with diffferent temperatures that come into contact undergo heat transfer.
First Law of Thermodynamics
  • Energy is conserved.
    • It cannot be created or destroyed, only transferred.
  • Energy can only change from one form to another.
Heat’s Role in Earth’s Beginnings
  • Energy transformation is at the ❤️️ of chemical evolution.
    • Molecules in early Earth were exposed to lots of energy.
  • Kinetic energy (in the form of heat) was present in cooling molten mass that formed the planet.
  • Atmosphere and surface of Earth heavily exposed to electricity.
    • Lightning & radiation from the Sun.
  • Energy was stored in the chemical bonds of molecules.

What Makes a Chemical Reaction Spontaneous?

  • Chemical reactions are spontaneous if they can happen on their own.
    • Do not need any additional influence, like added energy.
  • Two factors determining if a reaction is spontaneous.
    • Products have lower potential energy than reactants.
      • Shared electrons in products are more tightly held than those in reactants.
      • 2H2(g) + O2(g) → 2H2O(g)
        • Electrons in O-H bonds of water are held more tightly than in H-H and O=O bonds.
        • Products have lower potential energy than reactants.
    • *Product molecules are less ordered than reactant molecules.
      • Glucose is a single, highly ordered molecule.
      • When glucose burns in air, breaks into gaseous CO2 and H2O(g).
        • Are less ordered than reactant glucose molecules.
Entropy
  • Entropy is the amount of disorder in a system or surrounding environment.
    • Entropy increases when the products of a chemical reaction are less ordered than reactant molecules.
  • Spotaneous reactions can occur without appearing to increase the entropy.
    • 2H2(g) + O2(g) → 2H2O(g)
      • Potential energy drops.
      • Difference in potential energy released as heat and light.
        • Vaporizes the water produced.
  • Potential energy & entropy can be used to determine if a reaction is spontaneous or not.
Second Law of Thermodynamics
  • In all spontaneous reactions, entropy always increases.
    • Must consider both the system and the environment.
  • Consider The Hindenburg.
    • 2H2(g) + O2(g) → 2H2O(g).
      • Molecular hydrogen and diatomic oxygen.
      • Combine to release lots of energy.

2.4: Investigating Chemical Evolution

  • Chemical evolution proposed by Alexander I. Oparin in 1924.
    • Today, considered a formal scientific theory.
  • Answe tehq eustion:
    • Can complex organic[^1] compounds be synthesized from simple molecules in Earth’s early sphere?
      • Recreate stpes of chemical evolution in laboratory?

Miller’s Experiment

  • Experimental setup designed to produce a microcosm of early Earth.
  • Large glass flask: represents the atmosphere.
    • Contained gases CH4, NH3, H2 (high potential energy).
  • Connected to a smaller flask by glass tubing.
    • Tiny ocean (200mL of H2O(l)).
  • Miller constantly boiled the water.
    • This added H2O(g) to the large-flask gases.
    • Vapor cooled and condensed; flowed back into smaller flask (boiled again)
      • Water vapor circulated continuously throughout the system.
      • ‘Rain’ may carry atmosphere interactions into the ‘ocean’.
  • Cannot just boil molecules.
    • Even at boiling point, starting molecules are stable.
    • Do not undergo spontaneous chemical reactions.
      • Different form of energy needed for substances to react.
  • Miller sent electrial discharges to electrodes in the atmosphere.
    • ‘Lightning bolts’ added pulses of intense electrical energy.
  • Results.
    • Days of continuous boiling and sparking, solution was pink.
    • After a week, was deep red and cloudy.
    • Mini-ocean had lots of hydrogen cyanide and formaldehyde.
      • Chemicals are poisonous, but highly reactive.
        • Can promote synthesis of larger and more complex compounds.
      • Samples contained amino acids.
        • Building blocks of proteins.
Formal Description of Miller’s Experiment
AspectContent
QuestionCan simple molecules and kinetic energy lead to chemical evolution?
HypothesisChemical evolution of organic molecules will occur in environments simulating early Earth conditions.
Null HypothesisChemical evolution will not occur in early Earth simulations.
Prediction of HypothesisIf kinetic energy is added to a mix of simple molecules, complex organic compounds will be produced.
Prediction of Null HypothesisNo complex organic compounds will be produced.
ResultsSamples from solution contained formaldehyde, hydrogen cyanide, and several complex compounds with C=C bonds, like amino acids (e.g. glycine).
ConclusionChemical evolution occurs readily if simple moelcules with high free energy are exposed to a source of kinetic energy.

Textbook Notes - Chemical Evolution - 4.4 In Search of the First Life-Form

Introduction

  • Theory of chemical evolution: life began as a self-replicator
    • Self-replicator: a moelcule that existed by itself in solution *without being enclosed in a membrane.
  • To make copies:
    1. Provide a template that could be copied.
    2. Catalyze polymerization reactions that link monomers into a copy of the template.
  • Origin of life researchers propose the first life form was RNA.
  • RNA is a sequence of bases analoous to letters.
    • It can function as an information-containing molecule.
    • Information in RNA can be used to make copies via complementary base pairing.

The Process of RNA Synthesis/Copying

  1. To replicate a single-stranded DNA, create a complementary copy of RNA.
    • The original strand is used as a template.
    • Free ribonucleotides form hydrogen bonds w/ complementary bases on template.
  2. The strand is polymerized when 3’ hydroxyls and 5’ phosphates on adjacent nucleotides link together via condensation reactions.
    • Result: double-stranded RNA molecule.
  3. Hydrogen bonds broken by heating or catalyzed reaction.
    • Newly made complementary RNA molecule exists independent of original template.

How Biologists Study the RNA World

  • Researchers test RNA world hypothesis by establishing an environment in the lab that selects ribozymes that catalyze key steps required in RNA world.
  • Two experiments in David Bartel’s laboratory:
    • Generate a RNA molecule that could catalyze template polymerization.
      • Mimic process of natural selection, target characteristics of molecules instead of organisms.
      • Isolated a ribozyme that could add 14 nucleotides to an RNA strand.
    • Select a ribozyme that could make RNA nucleotides.
      • Began with a large pool of randomly generated RNA sequences.
      • Selected RNAs that could catalyze the addition of a uracil base to ibose sugar.
      • Purified a ribozyme that could perform this task 1 million times more efficiently than uncatalyzed reaction.
        • Molecular evolution occured in reaction tubes.
  • Biologists are producing impressive catalytic activites from RNA molecules.

An RNA World May Have Sparked the Evolution of Life

  • Most discovered ribozymes exist in modern cells and play important roles in protein synthesis.
  • If ribozymes removed from cells, proteins would no longer be made.
    • suggests: RNA preceded proteins.
  • Evolution of protein enzymes marked the end of the RNA world.
    • It provided the means to catalyze reactions for life to emerge in cellular form.
  • Established 3/5 characteristics of life:
    1. Information. Proteins and ribozymes process information in nucleic acids to synthesize proteins.
    2. Replication. Enzymes (and maybe riboyzmes) replicate nucleic acids that store hereditary information.
    3. Evolution. Random changes in nucleic acids can lead to the synthesis of different proteins & ribozyes. This can allow for evolution of new functions.
  • If this happened in a hydrothermal vent:
    • Molecular assemblages of nucleic acids & proteins constantly fed thermal & chemical energy.
    • Enzymes moust have evolved to store energy in something more portable.

Textbook Notes - Chemical Evolution - 2.4 Origin-of-Life Experiments and the Two Models

Recent Origin-of-Life Experiments

*Comes from 2.4 of Edition 6 of textbook.

  • Production of complex molecules from simple molecules supports claim that the formation of a ‘prebiotic soup’ was possible.
  • Researchers pointed out that early atmosphere had CO, CO2, and H2, not CH4 and NH3 (used in Miller’s experiment).
  • Follow-up experiments occuring under more realistic conditions.

Synthesis of Precursors Using Light Energy

  • Synthesis of formaldehyde from carbon dioxide & hydrogen.
    • CO2(g) + 2 H2(g) → CH2O(g) + H2O(g)
    • Researchers show formaldehyde molecules can react with each other to produce large organic compounds, like sugars.
    • Does not occur spontaneously.
  • Research group constructed computer model of Earth’s early atmosphere.
    • Model listed all possible chemical reactions that could occur.
    • Included reactions that occur when molecules are struck by sunlight.
      • Light is a source of energy.
    • Computer moldel included reactions that produce highly reactive free radicals.
      • CO2(g) + 2 H2(g) + sunlight → CH2O(g) + H2O(g)
      • Balances energy involved.
  • Energy in sunlight could be converted into chemical energy by generating radicals that spontaneously form bonds in formaldehyde.
  • Similar model: researchers show that hydrogen cyanide was an important precursor of molecules required for life.
    • Organic compounds with relatively high potential energy could have accumulated, and groundowrk would have been in place for the prebiotic soup model of chemical revolution.
Free Radicals
  • Inferred chemical evolution occured when large quantities of high-energy photons bomboarded the planet.
  • Atoms in hydrogen moelcules and CO2 molecules have full valence shells through covalent bonding.
    • Makes molecules unreactive.
  • Energy in the form of photons or intense electrical energy in lightning (like in Miller’s experiment) can break up molecules by knocking apart shared electrons.
    • Fragments that result are free radicals.
    • Have unpaired electrons in their outermost shells and are very reactive.

Concentration and Catalysis in Hydrothermal Vents

  • Stumbling block in prebiotic soup model: preucrsor molecules would have become diluted when they entered the early oceans.
    • Without concentration, how could formaldehyde and hydrogen cyanide meet and form large, complex molecules?
  • Surface metabolism model: reactants recruited in a defined space.
    • Layer of reactive minerals in walls of deep sea-vent chimneys.
    • Dissolved gases attracted by minerals and concentated on vent-wall surfaces.
  • Not only would vent wall minerals bring reactants together, but be critical to the rate of reactant product formation.
    • Potential reactions can be spontaneous but would not occur[^1] without a catalyst.
As a Catalyst
  • Catalysts provide appropriate chemical environment for reactants to interact with each other.
    • Example: synthesis of acetic acid from carbon dioxide and hydrogen:
      • 2 CO2(aq) + 4 H2(aq) → CH3COOH(aq) + 2 H2O(l)
      • Spontaneous reaction driven by chemical energy stored in H2.
  • Importance:
    • Acetic acid can be formed under conditions that simulate a hydrothermal vent environment.
    • Key intermediate in ancient metabolic pathway that produces acetyl CoA, a molecule used by cells throughout tree of life.
Evidence of Vent Minerals as Catalysts
  • Vent minerals could have served as catalysts in synthesis of acetic acid.
  • Catalysts perform the same reactions in modern cells contain minerals similar to those found in hydrothermalv ents.
    • Preliminary results: a variety of carbon-based molecules are formed under early Earth conditions.
    • Precursors of synthesis of nucleotides.

The Two Theories

TheoryProcess
Prebiotic Soup ModelSimple molecules like N2, NH3, and CO were present in the atmosphere of ancient earth. Energy in sunlight drove reactions among simple molecules to produce molecules like formaldehyde and hydrogen cyanide. Stimulated by heat, the products formed more complex molecules like ribose, glycine, and acetaldehyde.
Surface Metabolism ModelSimple molecules like N2, NH3, and CO were present in early oceans and hydrothermal events. Vent minerals catalyzed spontaneous reactions among high-energy molecules to produce, for instance, acetic acid. Concentration and heat formed more complex molecules like ribose.

Video Notes on Chemical Evolution

Figure Walkthrough: Potential Energy Change During Chemical Reactions

  • What makes a chemical reaction spontaneous?
    • Large drop in potential energy as reactants converted to products.
  • What causes the change in energy?
  • Reactants: 2 H2 + O2.
    • Covalent bonds. Electrons are shared equally
    • Form nonpolar covalent bonds.
    • Same electronegativities.
    • Are held ‘losely’.
  • Product: 2 H2O.
    • Two water molecules.
    • Bonds are polar covalent; oxygen atom has higher electronegativity than hydrogen.
    • Shared electrons are held ‘tightly’.
    • Polar bonds have lower potential energy.
  • High potential energy to low potential energy.
    • Difference in potential energy means there is a drop in energy; what happened to the rest of the energy?
    • Changed to kinetic energy and released in heat and light.
    • Many reactions form a very powerful energy outburst.

What Was the Miller-Urey Experiment?

  • Once believed that leaving food out to rot would cause animals to suddenly appear.
    • Spontaneous generation.
  • “Omne vivum ex vivo”, life only comes from life.
    • Rats, maggots, microbes are too complex to simply ‘poof’ into existent.
  • Drawin: theory of evolution.
    • Under the right situations, simple creatures turn into more complex ones.
  • Is it possible that simple life cells could come from nonliving matter?
    • Alexander Oparin published “The Origin of Life’
      • Thoughts on the progression of life:
        1. Simple molecules
        2. Molecules of life (biomonomers)
        3. Macromolecules
        4. Polymer Complexes
        5. Metabolic Networks
        6. Living Cells
      • Early ocean as a soup of complex molecules produced by natural reactions.
  • How to test or observe?
  • Stanley Miller came up with an idea: simulate early Earth conditions in a lab.
  • Simulated early water conditions.
    • Added hydrogen, ammonia, and methane.
    • Added a condensor to cool the atmosphere, allowing water molecules to fall into ocean like rain.
    • Added sparks in the atmosphere to simulate lightning.

  • Not to create life, but test simple molecules to biomonomers.

  • Oceans had amino acids and other complex molecules.
  • Gave rise to a field of reearch: prebiotic chemistry.
  • Scientist’s don’t know if gases used by Miller were the most accurate.
    • Experiments show many different sources of environments work.
  • Molecules of life formed everywhere.
  • Significant:
    • Not perfect simulation, but demonstrated that biomolecules can form from simple molecules.
    • Transformed speculation into science.

Steven Hawking Asks What Are the Building Blocks of Life and How Did They Come to Be

  • How did biological machinery come about?
  • Amino acids
    • Early building blocks of life.
    • How did they first form?
  • 4 billion years back in time
    • Where do basic building blocks come from?
      • Randomly appear?
    • Stanley Miller & Harold Urey
  • Magnets as atoms.
  • When energy is applied, interesting things happen.
    • Amino acids and molecules can form by themselves.
    • Just need the right energy and the right surroundings.
  • Proteins from amino acids.
    • Miller produced 5 amino acids.

What is Chemical Evolution?

  • The first living cells came about through chemical evolution.
  • Evolution: Change over time.
  • Biological evolution: Changes in things that are able to reproduce.
    • Not random change - adaptive change. Better able to survive in their environments.
    • Requires:
      • Reproduction
      • Variation
      • Selection
  • Chemical evolution: How do things become reproducible?
    • Chemical system: groups of molecules that interact with each other.
    • Often evolve towards simplicity.
      • Iron corrodes to rust.
      • Proteins break down when exposed to heat.
    • Simple chemistry arises into something complex.
  • Chemical evolution needs:
    • Repetitive production
      • Does not depend on reproduction. In fact, answers ‘reproduction’ component in biological evolution.
    • Variation
    • Selection
  • Powerful natural events take place naturally.
    • Heating, cooling (day night)
    • Eruptions of volcanic geysers
    • Rise and fall of oceans
    • Repetitively produce new molecules and systems.
  • ‘Living’ components automatically form.
    • Fatty Acid concentrations that are high enough bunch into a ball.
    • Fatty Acids form skins; edges can fuse together.
    • ‘Hollow container’ similar to skin of a living cell.
    • Can trap other molecules inside and act as an entirely new environment.
    • Fatty acid membrane.
      • Cannot live by themselves, but the development of these and other components demonstrate important principles of chemical energy.
  • Chemistry can give rise to life.

Video Notes on Chemical Evolution - the Origin of Life

The Mysterious Origins of Life on Earth

  • Source
  • Billions of years ago, simple organic compounds assmebled into complex reproducible compouds.
    • Gave rise to every one of billions of species in our planet since.
  • Earth was almost entirely devoid of a suitable environment for living things in its early days.
    • Widespread volcanic activity
    • Atmosphere with hostile conditions.
  • Elements and compounds for life: hydrogen, nitrogen, methane, carbon dioxide, phosphate, ammonia.
    • How to co-mingle and react?
    • Need a solvent: water.
  • All life needs a source of energy.
  • Life forms:
    • Autotrophs. Plants, generate their onw energy.
    • Heterotrophs. Animals, consume other organisms for their energy.
    • First organism: autotrophy.
  • Locations that meet criteria.
    • Places on land or close to surface of ocean have access to sunlight.
    • UV radiation on Earth’s surface was too harsh for life to survive.
    • Hydrothermal vents on the ocean floor are covered in seawater.
  • Hydrothermal vent
    • Fissure in Earth’s crust.
    • Seawater seeps into the magma chambers and is ejected back out at high temperatures with rich minerals and simple compounds.
    • Energy is concentrated in chemical gradients of thermal vents.
  • Last Universal Common Ancestor (LUCA)
    • What does LUCA look like?
    • Scientists identify genes across three domains of life.
      • Archaea, bacteria, eukarya
    • Must have been inherited in a common ancestor.
    • LUCA lived in a hot, oxygen-free place and harvested energy from a chemical gradient.
  • Two tkinds of hydrothermal vent
    • Black smoker. Release acidic, carbon dioxide rich water, heated to 100s of degrees Clesius. Packed with metals essential to life. Too hot for LUCA.
    • White smoker. Probably it.
  • Lost City favored for the cradle of life.

Life’s Rocky Start | Deep Sea Vents

  • Source
  • Dark ocean floor - more than a mile below the surface - explorers found mineral-rich hydrothermal vents.
    • Like underwater volcanoes.
  • Reached almost 600 degrees; yet life *thrived.**
  • Not off the sun’s energy, but chemical energy.
    • life can thrive without sunlight.
    • Extreme temperature and pressure; yet extreme to us is not extreme to microbes.
    • Could this dark and unlikely environment be where life began?
  • Life’s building blocks in the conditions of a deep sea vnet.
    • Miller-Urey experiment in high pressure.
    • Pressure bombs - things can explode.
    • Model the environment of the deep sea vents in a small gold tube.
      • nothing happened.
    • Basic gasses (nitrogen, CO2), etc.
      • Hold in a gold tube, but nothing happens.
    • Squeezing and heating had no effect.
  • The spark kickstarts the chemistry.
    • It’s missing the spark.
  • Try putting rocks and minerals in.
    • Put in “early earth cocktail”
    • Run the experiment again.
    • Atoms reform into new organic molecules: amino acids.
  • When powdered rocks and minerals are put in the capsules, organic molecules form.

What is the Metabolism-First Hypothesis for the Origiin of Life?

  • Mystery of the origin of life has not been solved.
    • Macromolecules: genes and proteins.
  • Cellular metabolism - a sum total of all controlled chemical reactions that occur inside a cell.
    • Eat and digest an apple - bits are given to the bloodstream.
    • Cells’ metabolism transforms food into new parts of the cell.
  • Biological evolution (Darwinian evolution) can create highly complex structures and systems.
  • How can something make copies of itself and mutate?
  • Macromolecule-first Models: metabolism generated automatically.
    • Comes with formation of amino acids, chains, etc.
  • First, needed to generate building blocks.
    • Produce junk along with amino acids.
      • Tar paradox
      • Looking at wrong conditions?
  • Some aspect of modern metabolism must have existed before the macromolecules could have come.
    • If an ancient environment existed that was producing macromolecules, natural selection would favor any macromolecule that could enhance the environmental chemical reactions that produced its building blocks.
    • Widely shared traits are probably the oldest.
  • Reverse Citric Acid Cycle
    • Found in microbes
    • Feeds on things like CO2 and H2`.
    • Very common in the early Earth.
    • Bind to produce larger pathways to build sugars, fats, and amino acids.
    • Avoiding tar paradox.
  • Find a system that generates macromoelcuels from simple elements.
  • metabolism-first hypothesis: some aspect of modern metabolism existed naturally in the environment before genes and proteins.

What is the RNA World Hypothesis?

  • Did chains of RNA exist first and kickstart life?
  • Chains of RNA are found abundantly in all living cells.
    • Chemical cousin to DNA.
  • RNA chains can replicate & evolve with their environments.
  • RNA World Hypothesis: **Earth’s chemistry was producing random chains of RNA. These began competing with each other for survival. Eventually formed living cells. Survival machines for RNA to live inside.
  • Researchers find that base pairing lets RNA evolve.
  • Template for its own replication.
    • Complementary strand is born with exact inverse sequence.
    • Water is heated; both chains are broken and act as templates.
    • Sometimes, mutations slip in; chains that compete for survival.
    • True evolution can operate on chains of RNA.
    • Base pairing gives RNA a special ability:
      • Water cool enough for base pairing but no enough nucleotides for pairing;
      • Chains will fold up and base pair with themselves sometimes.
      • Certain sticky bases point out can cause unique chemical reactions.
      • Many different shapes of RNA are ribozymes.
        • Some can join molecules together or split them apart.
        • Shape determined by sequence, shape determines function.
  • How difficult would it be to develop survival functions?
    • Build nucleotides out of chemicals it ifnds in its environment?
    • Some randomly generated chains could randomly generate nucleotides.
    • PCR to generate random mutations.
    • Highly efficient ribozymes actively participate in their own survival.
    • Blur the line between living things and simple chemistry.
  • Unsolved question: how did the backbone get put together?
    • Other molecules: self-assembling proto-RNA

The RNA Origin of Life

  • Map out evolution to single-celled life.
  • DNA is a good way to store information but doesn’t do much else.
  • Cells rely on other molecules to survive.
  • Proteins are good molecular machines, but cannot store information (need DNA).
  • DNA needs protein to function, proteins need DNA to function.
  • Answer: RNA.
    • RNA came first.
    • RNA can store information, or perform various functions.
  • RNA World Hypothesis.
    • Billions of years ago, self-replicating RNA formed.
    • Self-replicating RNAs formed and developed.
  • Competed - survival of the fittest.
  • RNAs developed the ability to develop proteins.
  • Critical RNAs mutated into DNA. Stable archive of genetic information.
  • Life becam emore complex with good accidents and several tiny steps.
  • Slice, dice, transform, encode molecules.