The Atoms and Molecules of Ancient Earth

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The Atoms and Molecules of Ancient Earth

• Chapter 2

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The Ancient Earth
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How did the earth start?

• The concept of vitalism
• Is the idea that organic compounds arise only
  within living organisms
• Life force outside of jurisdiction of physical
  and chemical laws
• Was disproved when chemists synthesized the
  compounds in the laboratory
• The chemical evolution hypothesis explains how
  complex carbon-containing compounds (and
  eventually life) could have formed from simpler
  molecules.

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Chemical Evolution Hypothesis
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When did chemical evolution take place?

• First a review of atomic structure
• Atoms are composed of electrons orbiting a
  nucleus made of protons and neutrons.
• Each element has a characteristic number of
  protons, the number of neutrons can vary.
• Forms of an element with different numbers of
  neutrons are called isotopes.

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Atomic Structure
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When did chemical evolution take place?

• Radiometric dating can be used to estimate the
  age of the Earth and when life first appeared.
• Radioactive isotopes have unstable nuclei that
  emit particles of radiation (energy) to form new
  daughter isotopes. This is known as radioactive
  decay
• Each radioactive isotope decays at a constant
  rate called its half-life

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Radioactive Decay
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How old is the earth?

• Meteorites formed 4.58 Ga (BYA)
• Moon formed 4.51 Ga.
• Earth must be about the same age,
• No direct radiometric dating is possible because
  Earth was initially molten
• The oldest fossils (from 3.85 Ga) consist of
  carbon grains that have high levels of 12C
  relative to other heavier carbon isotopes. Living
  organisms preferentially take in this lighter 12C
  from their surroundings.

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How old is the earth?
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The Building Blocks of Chemical Evolution
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Elements of Life

• 92 elements critical to organic life
• Most cells are 96 percent hydrogen (H), carbon
  (C), nitrogen (N), and oxygen (O).
• Many are trace elements

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Elements of Life
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Elements of Life

• Elements commonly found in organisms have at
  least one unpaired valence electron.
• It is the presence of unfilled electron orbitals
  that allows formation of chemical bonds that
  attach atoms together.
• Two types of bonds
• Covalent and ionic

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Elements of Life
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Electron Orbitals

• Orbitals are not concentric paths but rather
  where the electron spends 90 of its time

Electron-shell diagrams. Each shell is shown with
its maximum number of electrons, grouped in pairs.
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Covalent Bonds

• Atoms are most stable when each orbital has two
  electrons.
• Atoms can be joined by a covalent bond in which
  each atoms unpaired electrons are shared by both
  nuclei to fill their orbitals

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Non-polar Covalent Bonds

• A nonpolar covalent bond forms when electrons are
  evenly shared between two atoms.

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Polar Covalent Bonds

• If one atom holds the shared electrons more
  tightly than the other, a polar covalent bond
  forms
• An atom in a molecule with a high
  electronegativity will hold the electrons more
  tightly and have a partial negative charge (d),
  whereas the other atom will have a partial
  positive charge (d).

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Polar Covalent Bonds
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Ionic Bonds

• Ionic bonds form when electrons are completely
  transferred from one atom to another
• An atom that loses an electron becomes a
  positively charged cation an atom that gains an
  electron becomes a negatively charged anion.
  These oppositely charged ions attract each other

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Ionic Bonds

• Forms crystalline structures
• Based on the attraction of partial positive to
  partial negative

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Types of Covalent Bonds

• Most organic molecules are formed from several
  types of covalent bonds
• The number of unpaired electrons determines the
  number of bonds an atom can make
• When there are two unpaired electrons in the
  valence shell, two nuclei can share four
  electrons in a double bond. A triple bond can
  form if there are three unpaired electrons

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The Shape of Molecules

• Molecular shape depends on bond angles, which in
  turn depend on the orbitals in the bond

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Molecular and Structural Formulas

• The molecular formula states the numbers and
  types of atoms in a molecule (e.g., H2O, CH4).
• Structural formulas show which atoms are bonded
  together and indicate single, double, or triple
  bonds. Other models show three-dimensional
  geometry

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Quantifying and Concentrationof Molecules

• Molecular weight of a molecule is the sum of the
  mass numbers of all the atoms in the molecule.
• One mole, or 6.022 ? 1023 molecules, has a mass
  equal to the molecular weight expressed in grams
• The concentration of a substance in a solution is
  typically expressed as molarity (M) (moles/liter).

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Quantifying and Concentrationof Molecules

• Example
• Water, H2O
• Hydrogen MW 1 X 2 molecules 2
• Oxygen MW 16 X1 molecule 16
• Molecular weight of water is 18
• 18 grams of water would contain exactly 6.022 x
  1023 water molecules

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Energy
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Energy

• Capacity to do work
• Two types of energy
• Potential energy
• Stored
• Example?
• Kinetic energy
• Energy of motion
• Example?
• Can change from one form to another

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Laws of Thermodynamics

• The first law of thermodynamics
• Law of energy conservation
• Energy is conservedit cannot be created or
  destroyed, but it can be transferred or
  transformed
• Second Law of Thermodynamics
• Energy changes are not 100 efficient
• Energy conversions increase disorder, or entropy
  (the amt of disorder in a system)
• Some energy is always lost as heat

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Laws of Thermodynamics
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Potential energy and Atoms

• Electrons have potential energy because of how
  they are arranged in relation to the nucleus
• It takes work to move the negative electron
  farther away from the nucleus

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Potential energy and Atoms
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Chemical Reactions
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Chemical Reactions

• Chemical reactions are the breaking and reforming
  of bonds
• Have products and reactants
• Two types of reactions
• Endothermic reactions must absorb heat and
  energy to proceed
• Exothermic reactions release heat and energy

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Spontaneous Reactions

• Spontaneous reactions continue on their own
  without external influence
• Doesnt mean fast
• Reactions tend to occur spontaneously if the
  products have lower potential energy
• And, if the products have higher entropy

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Spontaneous Reactions
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Gibbs Free-Energy Change

• The Gibbs free-energy change (DG) determines
  whether a reaction is spontaneous or requires
  energy.
• DG lt 0 indicates a spontaneous reaction
• An exergonic reaction
• DG gt 0 indicates a reaction that requires energy
  input to occur
• An endergonic reaction
• DG 0 indicates a reaction that is at equilibrium

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Temperature, Concentration and Reactions

• High temperatures and high concentrations cause
  more reactant collisions and faster reaction
  rates.

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Redox Reactions

• In a reduction-oxidation (redox) reaction, one
  molecule loses electrons (is oxidized), another
  gains electrons (is reduced)
• An electron donor is always paired with an
  electron acceptor (energy coupling)

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Redox Reactions

• The shift in electron position in a redox
  reaction results in a reduction in potential
  energy

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Carbon and Chemical Reactions
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Carbon

• Contains four available bonds
• Very reactive
• Almost all molecules found in organisms contain a
  CC bond and are called organic molecules

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Organic Molecules
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Complex Carbon Compounds

• Reduced carbon compounds contain a lot of
  potential energy in their bonds
• Allows for complex compounds present in
  organisms
• Carbon provides the structural framework of
  organic compounds, and functional groups
  containing H, N, or O atoms bonded to C determine
  their behavior

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Water
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Characteristics of Water

• Life on earth depends on water
• Great solvent
• Due to its polar nature
• The O has a partial negative charge (d), and the
  H atoms carry partial positive charges (d)
• Hydrogen bonds between H2O and other polar
  molecules or ions help the substances stay in
  solution

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Properties of Water

• The structure of water is unusual
• small size, bent shape, highly polar covalent
  bonds, and overall polarity are unique.
• Unusual physical properties
• it expands as it changes from a liquid to a solid
• extraordinarily large capacity for absorbing heat.

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Properties of Water

• Ice crystalizes is a set pattern, a crystal
  lattice
• Fewer hydrogen bonds in water than in ice
• Water molecules pack tighter
• Ice is less dense and floats

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Properties of Water

• Water has an extremely high specific heat and
  heat of vaporization.
• Cools the earth
• Cools our bodies

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Properties of Water

• Strongly cohesive
• Causes water to bead
• Allows insects to walk on water
• Allows plants to get water from roots

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pH

• pH is a scale of the ratio of H molecules to OH
  molecules.
• Water pH is 7 (Ratio is 11)
• Acids have higher H ratio
• Bases have higher OH ratio

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Isomers

• Isomers are molecules with the same molecular
  formula but different structures
• Isomers include structural isomers, geometric
  isomers, and optical isomers.

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Structural Isomer
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Geometric Isomers
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Optical Isomers

• Optical isomers are mirror images of each other
• Also called enantiomers
• Just like hands
• All amino acids except glycine have optical
  isomers, but only left-handed forms are found
  in cells.

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Structural Isomer

• All amino acids except glycine have optical
  isomers, but only left-handed forms are found
  in cells.