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									Life and Chemistry:
 Small Molecules
2                     Life and Chemistry: Small Molecules


    • Water and the Origin of Life’s Chemistry
    • Atoms: The Constituents of Matter
    • Chemical Bonds: Linking Atoms Together
    • Chemical Reactions: Atoms Change Partners
    • Water: Structure and Properties
    • Acids, Bases, and the pH Scale
    • Properties of Molecules
2                  Water and the Origin of Life’s Chemistry


    • The earliest chemical signatures of life on Earth
      are about 4 billion years old.
    • The presence of water, possibly brought by
      comets striking the Earth, was critical in making
      conditions suitable for life.
    • Environmental conditions conducive to life
      evolved during the Hadean period.
Figure 2.1 A Geological Time Scale
2                        Atoms: The Constituents of Matter


    • All matter is composed of atoms.
    • Each atom consists of at least one proton and
      one electron.
    • Atoms have mass. The mass comes mostly from
      the proton and a neutrally charged body called a
      neutron.
2                                           Charges and Mass




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Figure 2.2 The Helium Atom
2                         Atoms: The Constituents of Matter


    • Each element contains only one type of atom.
    • Information on elements is arranged in logical
      order in a table called the periodic table.
    • The periodic table arranges elements left to right
      based on their atomic number, and in columns
      based on similarities in their properties.
Figure 2.3 The Periodic Table (Part 1)
Figure 2.3 The Periodic Table (Part 2)
2                        Atoms: The Constituents of Matter


    • Each element has a unique atomic number
      which is the number of protons found in an atom
      of the element.
    • The mass number is the number of protons plus
      the number of neutrons.
    • The mass number is used as the weight of the
      atom, in units called daltons.
    • Each element has a unique symbol: H is
      hydrogen, C is carbon, Na is sodium, and Fe is
      iron.
2                        Atoms: The Constituents of Matter


    • All atoms of an element have the same number of
      protons, but not necessarily the same number of
      neutrons.
    • Atoms of the same element that have different
      atomic weights are called isotopes.
Figure 2.4 Isotopes Have Different Numbers of Neutrons
2                        Atoms: The Constituents of Matter


    • Some isotopes are radioisotopes, which emit
      energy as alpha, beta, and gamma radiation from
      their nuclei.
    • Radioactive decay transforms the original atom
      into another atom, usually of another element.
2                         Atoms: The Constituents of Matter


    • The region in which an electron travels is called
      the electron’s orbital.
    • The orbitals constitute a series of electron shells,
      or energy levels, around the nucleus.
    • Two electrons at most can occupy each orbital.
2                          Atoms: The Constituents of Matter


    • The first shell is the innermost shell and has just
      one orbital, called the s orbital.
    • The s orbital fills first and its electrons have the
      lowest energy.
    • The second shell is next closest to the nucleus
      and has one s and three p orbitals.
    • The second shell can accommodate eight
      electrons, two per orbital.
Figure 2.6 Electron Orbitals
2                                           Electron Orbitals

    • Orbital 1: 2 electrons
    • Orbital 2: 8 electrons
    • Orbital 3: 8 electrons


    • The lower the shell the more stable the element.
    • When the outer shells are full the more stable.
    • Electrons want to be stable and in the lowest
      shell.
2                                         Carbon Atom




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2                          Atoms: The Constituents of Matter


    • The outermost shell of an atom determines how it
      reacts with other atoms.
    • Generally, if eight electrons are in the outer shell,
      the atom is stable and does not tend to react.
    • Atoms which do not have eight electrons in the
      outermost shell will share, gain, or lose electrons
      to arrive at a stable state.
2                Chemical Bonds: Linking Atoms Together


    • A molecule is two or more atoms bonded
      together.
    • A chemical bond is an attractive force that links
      two atoms together.
2                Chemical Bonds: Linking Atoms Together


    • A covalent bond is formed by sharing of a pair of
      electrons between two atoms.
    • In hydrogen molecules (H2), a pair of electrons
      share a common orbital and spend equal amounts
      of time around each of the two nuclei.
    • The nuclei stay some distance from each other
      due to mutually repelling positive charges.
Figure 2.8 Electrons Are Shared in Covalent Bonds




                               Properties of Molecules
2                  Chemical Bonds: Linking Atoms Together


    • Molecules made up of more than one type of atoms are
      called compounds.
    • Every compound has a molecular weight that is the sum
      of all atoms in the molecule.

                      Chemical Bonds
    Covalent - Sharing
    Ionic - Giving
    Hydrogen - Between Molecules
2                Chemical Bonds: Linking Atoms Together


    • Covalent bonds are very strong.
    • Each covalent bond has a predictable length, angle,
      and direction, which makes it possible to predict the
      three-dimensional structures of molecules.
    • A double covalent bond occurs when atoms share
      two pairs of electrons; in triple covalent bonds
      atoms share three electron pairs.
Figure 2.10 Covalent Bonding With Carbon




                              Properties of Molecules
2                                                REACTION MODELS




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2                Chemical Bonds: Linking Atoms Together


    • Electrons are not always shared equally between
      covalently bonded atoms.
    • The attractive force that an atom exerts on
      electrons is called electronegativity.
    • When a molecule has nuclei with different
      electronegativities, an electron spends most of its
      time around the nucleus with the greater
      electronegativity.
2                Chemical Bonds: Linking Atoms Together


    • Unequal sharing of electrons causes a partial
      negative charge around the more electronegative
      atom, and a partial positive charge around the
      less electronegative atom, resulting in a polar
      covalent bond.
    • Molecules that have polar covalent bonds are
      called polar molecules.
Figure 2.11 The Polar Covalent Bond in the Water Molecule




                               Properties of Molecules
2                Chemical Bonds: Linking Atoms Together


    • Hydrogen bonds may form within or between
      atoms with polar covalent bonds.
    • The d– portion of one molecule has a weak
      attraction to the d+ portion of another molecule.
      Each of these attractions is called a hydrogen bond.
    • Hydrogen bonds do not share electrons.
    • Although hydrogen bonds are weak, they tend to be
      additive, and they are of profound biological
      importance.
Figure 2.12 Hydrogen Bonds Can Form between or within Molecules




                              Properties of Molecules
2                                     HYDROGEN BONDS




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2                                     HYDROGEN BONDS




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2                Chemical Bonds: Linking Atoms Together


    • Ionic bonds involve a complete transfer of one or
      more electrons.
    • Ions are formed when an atom loses or gains
      electrons.
    • Positively charged ions are called cations.
    • Negatively charged ions are called anions.
Figure 2.13 Formation of Sodium and Chloride Ions




                               Properties of Molecules
2                 Chemical Bonds: Linking Atoms Together


    • Ionic bonds are formed by the electrical
      attraction between ions with opposite charges.
    • Table salt has chloride and sodium ions, held
      together by ionic bonds.
    • When salt is introduced into water, the partial
      charges of the water molecules can easily
      interfere with the ionic bonds.
Figure 2.14 Water Molecules Surround Ions




                              Properties of Molecules
2                 Chemical Bonds: Linking Atoms Together


    • Polar molecules tend to be hydrophilic.
      Substances that are ionic or polar often dissolve
      in water due to hydrogen bonds.
    • Nonpolar molecules are called hydrophobic
      because they tend to aggregate with other
      nonpolar molecules.
    • Nonpolar molecules are also attracted to each
      other via relatively weak attractions called van
      der Waals forces.
2             Chemical Reactions: Atoms Change Partners


    • Chemical reactions occur when atoms combine or
      change partners.
    • In a chemical reaction, reactants are converted to
      products.
    • A chemical reaction can be written as an
      equation. The equation must balance because
      matter is neither created nor destroyed.
Figure 2.15 Bonding Partners and Energy May Change in a Chemical Reaction




                              Properties of Molecules
2             Chemical Reactions: Atoms Change Partners


    • Changes in energy usually accompany chemical
      reactions.
    • Stored energy, such as that in chemical bonds, is
      called potential energy and is available for future
      use.
    • We can measure the potential energy of
      molecules and express it in units of heat called
      calories.
    • A calorie is the amount of heat required to raise
      the temperature of one gram of pure water from
      14.5°C to 15.5°C.
2                            Water: Structure and Properties


    • Due to its shape, polarity, and ability to form
      hydrogen bonds, water has some unusual
      properties.
                    Properties of water
    1. Cohesive and Adhesive
    2. High Specific Heat
    3. High Boiling Point
    4. Good Evaporative Coolant
    5. Less Dense as a solid
    6. Good Solvent
2                            Water: Structure and Properties


    • Ice is held in a crystalline structure by the
      orientation of water molecules’ hydrogen bonds.
    • Each molecule forms hydrogen bonds with four
      other molecules.
    • These four hydrogen bonds increase the space
      the water molecules take up, so water expands as
      it freezes, and ice is less dense than liquid water.
    • For these reasons, ice floats in liquid water.
Figure 2.16 Hydrogen Bonds Hold Water Molecules Together (Part 1)




                              Properties of Molecules
Figure 2.16 Hydrogen Bonds Hold Water Molecules Together (Part 2)




                              Properties of Molecules
2                                         Winter Pond life




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2                           Water: Structure and Properties


    • Compared to other nonmetallic substances, ice
      requires a lot of heat to melt because hydrogen
      bonds must be broken.
    • The opposite process, freezing, requires water to
      lose a great deal of heat.
2                           Water: Structure and Properties


    • A great deal of heat energy is required to change
      the temperature of liquid water because the
      hydrogen bonds must be broken.
    • Specific heat is the number of calories needed to
      raise one gram of a substance 1oC. The specific
      heat of liquid water is 1.
    • Liquid water has a higher specific heat than most
      other small molecules in liquid form.
2                           Water: Structure and Properties


    • The heat of vaporization is the amount of heat
      needed to change a substance from its liquid
      state to its gaseous state.
    • A lot of heat is required to change water to a
      gaseous state because the hydrogen bonds of the
      liquid water must be broken.
    • Evaporation has a cooling effect by absorbing
      calories.
    • Condensing has the opposite effect, releasing
      heat.
2                             Water: Structure and Properties


    • Water has a cohesive strength because of
      hydrogen bonds.
    • The cohesive strength of water molecules allows
      the transport of water from the roots to the tops of
      trees.
    • Water has high surface tension, which means that
      the surface of liquid water is relatively difficult to
      puncture.
2                             Water: Structure and Properties


    • Water is the solvent of life.
    • Living organisms are over 70 percent water by
      weight and many reactions take place in this
      watery environment.
    • A solution is a substance (the solute) dissolved
      in a liquid (the solvent).
2                            Acids, Bases, and the pH Scale


    • Some substances dissolve in water and release
      hydrogen ions (H+); these are called acids. Their
      release is called ionization.
    • Other substances dissolve in water and release
      hydroxide ions (OH–); these are called bases.
    • Acids donate H+; bases accept H+.
2                              Acids, Bases, and the pH Scale


    • Acids release H+ ions in solution.
    • If the reaction is complete, it is a strong acid, such
      as HCl.
    • The carboxyl group (—COOH) is common in
      biological compounds. It functions as an acid
      because
         —COOH  —COO– + H+
2                            Acids, Bases, and the pH Scale


    • Bases accept H+ in solution.
    • NaOH ionizes completely to Na+ and OH–. The
      OH– absorbs H+ to form water. It is a strong
      base.
    • The amino group (—NH2) is an important part of
      many biological compounds; it functions as a
      weak base by accepting H+:
        —NH2 + H+  —(NH3)+
2                            Acids, Bases, and the pH Scale


    • Water is really a weak acid and has a slight
      tendency to ionize into H+ and OH–.
    • This ionization is very important for living
      creatures and the chemical reactions they must
      perform because the H+ ion is so reactive.
2                            Acids, Bases, and the pH Scale


    • pH is the measure of hydrogen ion concentration.
    • It is defined as the negative logarithm of the
      hydrogen ion concentration in moles per liter.
    • The pH scale indicates the strength of a solution
      of an acid or base. The scale values range from 1
      through 14.
    • A pH 7 means the concentration of hydrogen ions
      is 1 x 10–7 moles per liter of water.
Figure 2.18 pH Values of Some Familiar Substances




                              Properties of Molecules
2                                         pH scale




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2                            Acids, Bases, and the pH Scale


    • A buffer is a mixture of a weak acid and its
      corresponding base.
    • Because buffers can react with both added bases
      and acids, they make the overall solution resistant
      to pH change.
    • Buffers illustrate the law of mass action:
        Addition of reactants to one side of a reaction
         drives the reaction in the direction that uses
         that component.
Figure 2.19 Buffers Minimize Changes in pH




                               Properties of Molecules
2                                       Properties of Molecules


    • Chemists use the characteristics of composition,
      structure, reactivity, and solubility to help classify
      molecules.
    • Two other properties that influence the behavior
      of molecules are the presence of recognizable
      functional groups, and the existence of isomers of
      molecules.
2                                   Properties of Molecules


    • Functional groups give specific properties to
      molecules.
    • Functional groups are covalently bonded to
      organic molecules.
    • Amino acids are biological molecules that contain
      both a carboxyl group and an amino group.
Figure 2.20 Some Functional Groups Important to Living Systems (Part 1)




                               Properties of Molecules
Figure 2.20 Some Functional Groups Important to Living Systems (Part 2)




                               Properties of Molecules
Figure 2.20 Some Functional Groups Important to Living Systems (Part 3)




                               Properties of Molecules
2                                    Properties of Molecules


    • Isomers are molecules that have the same
      chemical formula but different arrangements of
      the atoms.
    • Structural isomers differ in terms of how atoms
      are joined together.
    • Optical isomers are mirror images of each other.
    • Optical isomers can occur whenever a carbon has
      four different atoms or groups attached to it.
Figure 2.21 Optical Isomers




                              Properties of Molecules

								
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