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Chemistry & Living Systems

Chemistry Notes BI 171
  1. If it takes up space and has mass then it matters - actually it is matter. There are numerous terms that relate to the basic or fundamental unit of matter - the atom. ELEMENTS are pure substances which means that they consist of only one type of atom. A COMPOUND consists of two or more different kind of atoms or ions in definite proportions.
    1. ATOMS are the smallest particles into which an element can be divided and still show the properties of that element. Atoms cannot be further divided by ordinary chemical and physical means.
      1. Atoms are composed of PROTONS, NEUTRONS, and ELECTRONS.
      2. An atom's NUCLEUS includes a set number of protons and a variable number of neutrons.
        1. The ATOMIC NUMBER is the number of protons.
        2. The ATOMIC MASS is the number of protons and neutrons.
        3. ISOTOPES are atoms of the same element with different numbers of neutrons.
      3. A set number of electrons, equal to the number of protons, orbits around the nucleus.
        1. IONS are atoms or molecules with a positive or negative charge due to a deficit or excess of electrons.
        2. Electrons are attracted by the nucleus but repelled by each other; they move in ORBITALS.
        3. Electrons occur in discrete ENERGY LEVELS. The energy levels nearest the nucleus (the levels with the lowest energy) are filled first.
      4. An atom's chemical properties are largely a result of THE NUMBER OF ELECTRONS IN THE OUTERMOST ENERGY LEVEL.
        1. An atom with a full outer level is INERT.
        2. Atoms with unfilled outer levels will react with other atoms to fill or empty those levels.

  2. Molecules are groups of atoms held together by MOLECULAR BONDS, which are links of pure energy based on shared or transferred electrons.
    1. COVALENT BONDS form when atoms share electrons, which creates a molecular orbital around the nuclei.
      1. A SINGLE BOND results from the sharing of one pair of electrons.
      2. DOUBLE BONDS and TRIPLE BONDS result from the sharing of two or three pairs of electrons.
      3. NONPOLAR COVALENT BONDS occur between two atoms that share electrons equally.
      4. POLAR COVALENT BONDS occur where the shared electrons spend more time around one of the nuclei which results in a slight negative charge around that atom and a slight positive charge around the other atom.
      5. HYDROGEN BONDS are weak bonds that involve the attraction between a polar molecule with a negative pole and a polar molecule with a hydrogen atom bearing a slight positive charge.
    2. IONIC BONDS occur between positively- and negatively-charged ions.

  3. Water is essential to life. Cells are largely composed of water and exist in a watery medium.
    1. The polarity of water molecules and the hydrogen bonds between them affects the physical properties of water related to temperature.
      1. Water has a HIGH SPECIFIC HEAT. Heat energy must first break the hydrogen bonds between molecules before their speed of movement can be increased. This feature moderates the temperature of organisms and their environment.
      2. Water has a HIGH HEAT OF FUSION and resists the change to ice.
      3. Water has a HIGH HEAT OF VAPORIZATION. Hydrogen bonds hold liquid water molecules together, and a molecule must have a high velocity to escape as a gas. By evaporating, water removes heat from its surroundings such as when a person sweats and thus lowers their temperature.
    2. Water's hydrogen bonds affect its mechanical properties.
      1. COHESION is the tendency of like molecules to cling to each other. SURFACE TENSION is the tendency of water molecules at the surface of liquid water to stick to each other but not to the molecules of air above them.
      2. ADHESION is the tendency of unlike molecules to cling together. CAPILLARITY is the tendency of a liquid such as water to move upward through a narrow space such as the tubes carrying water and nutrients high into a plant stem.
      3. Ice is less dense than water and floats on it.
      4. Water has been called the universal SOLVENT, a substance that can dissolve SOLUTES including polar molecules and ions.
        1. HYDROPHILIC substances dissolve readily in water.
        2. HYDROPHOBIC substances do not dissolve readily in water.
      5. Water molecules tend to IONIZE, or dissociate, into a hydrogen ion, H+, and a hydroxide (hydroxyl) ion, OH_.
        1. An ACID is any substance that gives off hydrogen ions when dissolved in water.
        2. A BASE is any substance that accepts hydrogen ions when dissolved in water. Such substances are called ALKALINE or BASIC.
        3. The pH scale measures the concentration of H+. More information on pH here.
        4. BUFFERS moderate changes in pH.