S t r u c t u r e   &   O r g a n i z a t i o n :     L e c t u r e  # 3 Vocabulary | Study Questions
The Chemistry of Life: Part 1
Objectives:
  1. Develop a basic understanding of chemistry as it relates to fundamental biological processes:
    1. the relationship between atomic structure and chemical bonding
    2. the three basic kinds of chemical bonds
    3. the nature and significance of chemical reactions
  2. Understand the properties of water that make it essential to life processes.
  1. A fundamental understanding of basic chemical principles is critical to the the comprehension of many biological phenomena.
    Sometimes we lose track of what WE are made up of: atoms/chemicals that are bonded together to form molecules, cells, tissues, organs, organ systems, organisms (e.g. human being). Our make-up conforms to the basic principles of chemistry.
    1. The metabolic processes of life conform to the laws governing atomic structure and chemical reactions.
      -
    2. The structure of life at the cellular and organismal levels are directly influenced by atomic structure and chemical bonding.
      Sarah is held together by chemical bonds. (We all are.)
  2. Chemical elements, atomic structure, and molecules
    Matter is anything that has substance and occupies space. Wave your hands in the air--feel the matter; it's everywhere.
    1. Characteristics of elements
      Simplest forms of matter: elements.
      1. Naturally occurring elements
        Periodic table  There are 92 naturally occuring elements, others can be 'manufactured.'
      2. Biologically important elements
        30 or so biologically important elements, including the following 6: On a percent weight basis, these 6 elements account for well over 95% of living tissue. Of the 6, oxygen is the most common (again, on a % weight basis, not in #): Why? Water. (Complex carbohydrates are also rich with oxygen.)

        3. Atomic Composition of 3 Representative Organisms
        (on a % weight basis)
          Human Alfalfa Bacterium
        Carbon 19.37% 11.34% 12.14%
        Hydrogen 9.31% 8.72% 9.94%
        Nitrogen 5.14% 0.83% 3.04%
        Oxygen 62.81% 77.90% 73.68%
        Phosphorous 0.63% 0.71% 0.60%
        Sulfur 0.64% 0.10% 0.32%
        totals: 97.9% 99.60% 99.72%
        1. Oxygen
          -
        2. Carbon
          -
        3. Hydrogen
          -
        4. Nitrogen
          -
        5. Sulfur
          -
        6. Phosphorous
          -
    2. Molecules
      A molecule is any chemical structure that has two or more atoms.
    3. Compounds
      A compound is a molecule made up of two different kinds of atoms.

      4. All compounds are molecules but not all molecules are compounds. (e.g O2 is a molecule but not a compound. H2O is a molecule and a compound.

  3. Atomic structure and chemical properties
    There are over 100 different kinds of subatomic particles; we will only be discussing 3: protons, neutrons, and electrons.
    1. Nucleus
      The major portion of mass associated with any atom.
      1. Protons (positively charged particles)
        (e.g. Hydrogen has 1 proton in nucleus.) The number of protons will always be constant.
      2. Neutrons (uncharged particles)
        We can have variable number of neutrons. An atom with an unusual number of neutrons (more or less than the # of protons) is called an isotope. (e.g. Carbon has 6 protons yet can have 6, 7, or 8 neutrons. Carbon atoms with the 7 or 8 neutrons are isotopes.)
    2. Energy levels
      Energy levels are concentric spheres arranged in increasing size, surrounding the nucleus. The maximum # of electrons in the first energy level is 2. In the second energy level: 8. In the third: 18.
      1. Electrons (negatively charges particles)
        Move in very precise ways within energy levels at speeds approaching the speed of light. Are about 1/5000th the size of a proton or neutron, which are about the same in mass. The electrical charge has nothing to do with size.
      2. Facilitating energy transformations by manipulating electrons
        In biological systems we perform transform energy constantly (e.g. breakfast: Dr. St. Clair 'recycles' his daughters cereal milk. He is an ATM machine--office: 193 MLBM)) We change food into energy we can use: this processing (energy transformation) is done by moving energized electrons around.
    3. Chemical and physical properties of an atom are determined by:
       
      1. Number of protons and neutrons in nucleus
        (e.g. Look at each of the 6 biologically important elements: what differentiates them?)
      2. Number and position of electrons
        The number of protons always equals the number of electrons in an atom. (Not so in an ion.)
  4. Chemical bonding
    A matter of filling outer energy levels with electrons: if an atom can fill its outer energy level, it becomes physically and chemically stable. (e.g. Helium: 2 protons, 2 electrons: the outer (first) energy level is full, so helium is a couch potato atom: inert: non-reactive. When we look at the biologically important elements, we see that they are reactive: their outer energy levels are not full; they tend to react and form molecules.)

    5. From the third energy level out, if an atom can get 8 electrons in the outer energy level, it becomes chemically and physically stable: the octet rule.

    (e.g. Water: By sharing electrons, the atoms become stable: the hydrogen atoms gain an electron by sharing with oxygen atom, which gains two electrons through the sharing. Therefore the atoms have filled their outer energy levels, becoming chemically and physically stable.) Then we blew up (added energy to) a hydrogen gas/oxygen gas baloon and made water vapor.

    1. Ionic bonding
       
      1. Based on the transfer of electron(s) between atoms.
        Transfer is the operative word. The atom becomes an ion (charged) because the # of electrons no longer equals the # of protons.
      2. Attraction between atoms based on electrostatic charge differences
        A negatively charged ion (1 more electron than proton) and a positively charged ion (1 more proton than electron) will bond together: an ionic bond. (e.g. Sodium chloride figure 3.3a (e.g. #2: Christi-um + Tomium)
    2. Covalent bonding
      figure 3.3b
      1. Based on the sharing of electron(s) between atoms.
        The electron is not transferred, as in ionic bonding, but SHARED.
      2. Sharing may be equal (non-polar) or unequal (polar).
        When the sharing is equal (non-polar) there is no molecular charge (e.g. H2). When the sharing is not equal (polar) the result is a positively charged end (pole) and a negatively charged end (e.g. water: H2O).
        For our purposes we're going to say that non-polar covalent bonds occur between atoms of the same element, and polar covalent bonds occur between atoms of different elements. Covalent bonds are slightly stronger than ionic bonds.
    3. Hydrogen bonding
      1. Based on electrostatic attractions between molecules whose constituent atoms are polar covalently bonded.
        figure 3.3c(e.g. the alpha helix of polypeptide (protein) chain. Water (a polar-covalently bonded molecule): the positively charged ends and negatively charged ends are attracted to one another, forming hydrogen bonds.)
      2. Individually, hydrogen bonds are weak but collectively they are quite strong.
        Individual hydrogen bonds are easily broken and reformed.
  5. Chemical reactions
    The movement of electrons.
    1. Oxidation-reduction reactions:
      When an atom or molecule gives up or gains an electron. In a reduction reaction, an electron is gained. In an oxidation reaction, an electron is given up. When we are transforming energy in biological systems, we manipulate electrons using oxidation-reduction reactions.figure 3.4
    2. Condensation
      Small molecules bonding together to form a larger molecule.figure 3.5 Examples: combining amino acids into proteins; combining two monosaccharides into a disaccharide. (Note: carbon can form four covalent bonds: the ultimate tinker-toy element. Look at the previous figure and count the carbons and their bonds.)
    3. Hydrolysis
      A larger molecule is broken down into smaller molecules (the opposite of condensation).figure 3.6 Examples: breaking down a disaccharide into a monosaccharide; Grape Nuts: we don't have the enzymes to break down fiber, but we do to break down the starch. Another: when we consume chicken protein, we break them down into amino acids to be incorporated into human proteins.

      4. Remember: in biological systems, we consistently make use of enzymes in the above reactions. Also: condensation, like on a mirror after you shower, is not a condensation reaction (they're different).

  6. Biologically important properties of water
    Life without water?
    1. Polar nature of water
      The basis of all of the following properties:
    2. Water as a solvent
      Water dissolves well. It's the 'universal solvent.' (e.g. NaCl: water will separate the ions).
    3. Thermal properties of water
      If you boil a quart of water, it takes a lot of energy to break all those hydrogen bonds. (e.g. sweat: when water evaporates it takes heat from the body surface; a dog panting.)
    4. Cohesive and adhesive properties of water
      Cohesive: like substances stick together (e.g. band-aid to itself). Adhesive: unlike substances stick together (e.g. band-aid to skin). This is important in the plant world, for example, because it allows water to be moved through a plant (i.e. a 360 ft. Redwood).