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                                   THE CHEMISTRY OF LIFE

    Take Note: While the AP Biology exam does not test directly on this material, it is important
    to have a solid understanding of the concepts in this chapter in order to properly understand
    the biochemistry that is to follow. It is important that you have a working knowledge of the
    elements that are important for life, the role of isotopes in biology, and the different types of
    bonds that form between elements. The properties of water are extremely important, as well as
    the behavior of acids and bases.

2.1       Chemical Elements
Matter is defined as anything that has mass and takes up space. Both living and nonliving matter
is composed of elements, the simplest forms of matter that cannot be broken down to simpler
substances with different chemical or physical properties. Six of the elements that occur in
nature--carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur (CHNOPS)--are important
for life and make up 98% of the body weight of organisms.

Elements consist of tiny particles called atoms, the smallest unit of an element that displays the
properties of the element. Atoms contain specific numbers of protons, neutrons, and electrons.
Protons and neutrons are in the nucleus of an atom; electrons move around the nucleus. Protons
are positively charged particles; neutrons have no charge. Both have 1 atomic mass unit (amu) of
weight. Electrons are negatively charged particles located in orbitals outside the nucleus. Protons
and neutrons in the nucleus determine the mass number of an atom. The atomic number indicates
the number of protons and the number of electrons in electrically neutral atoms.

Isotopes are atoms of a single element that differ in their numbers of neutrons. A carbon atom
with 8 rather than 6 neutrons is unstable; it releases energy and subatomic particles and is thus a
radioactive isotope. Radioactive isotopes have many uses, including serving as tracers in
biological experiments and medical procedures. An example is radioactive iodine that is used to
detect tumors in the thyroid gland. High levels of radiation can destroy cells and cause cancer;
careful use of radiation can sterilize products and kill cancer cells.

2.2       Compounds and Molecules
Ions form when atoms lose or gain one or more electrons. An ionic bond is an attraction between
oppositely charged ions. It is formed when electrons are transferred from one atom to another
atom. For example, sodium loses an electron, forming a positive charge, and chlorine gains an
electron to give it a negative charge. The ionic bond that forms between them results in the
formation of sodium chloride, NaCl.

Covalent bonds form when atoms share one or more pairs of electrons. There are single, double,
and triple covalent bonds. In polar covalent bonds, the sharing of electrons is not equal. If the
molecule is polar, the more electronegative atom carries a slightly negative charge and the other
atom carries a slightly positive charge. In nonpolar covalent bonds, sharing of electrons is equal
(i.e., the electrons are not attracted to either atom to a greater degree).

8                                                                                       Chapter 2
 Take Note: The properties of water are important in all of Biology. Be sure you fully
 understand the properties of water so that you can apply the knowledge gained in this section
 to other topics as you proceed through your study of Biology.

2.3      Chemistry of Water
All living things are 7090% water. The polarity of water molecules allows hydrogen bonding to
occur between them. In a water molecule, the sharing of electrons by oxygen and hydrogen is not
equal; the oxygen atom is more electronegative, attracting the electrons closer to it, and thus
assuming a partial negative charge. As a result, the hydrogens develop a partial positive charge.

A hydrogen bond is a weak attraction between a slightly positive hydrogen atom and a slightly
negative oxygen or nitrogen atom within the same or a different molecule. Many hydrogen bonds
taken together are relatively strong and help maintain the structure and function of cellular
molecules such as proteins and DNA. Water's polarity and hydrogen bonding account for its
unique properties. These properties, described below, allow living things to exist and carry on
cellular activities. Because of hydrogen bonding, water is liquid between 0 C and 100 C, which
is essential for the existence of life.

    1. High heat capacity. The temperature of liquid water rises and falls more slowly than that
       of most other liquids because the hydrogen bonds between water molecules hold more
       heat. This protects organisms from rapid temperature changes and helps them maintain
       homeostatic temperature.

    2. High heat of vaporization. Hydrogen bonds between water molecules require a relatively
       large amount of heat to break. This property moderates Earth's surface temperature;
       permitting living systems to exist. When animals sweat, evaporation of the sweat
       removes body heat, thus cooling the animal.

    3. Water is a solvent. Water dissolves a great number of substances (e.g., salts, large polar
       molecules). Ionized or polar molecules that are attracted to water are hydrophilic ("water
       loving"); whereas non-ionized and nonpolar molecules that cannot attract water are
       hydrophobic ("water fearing"). A solution contains dissolved substances called solutes.

    4. Cohesion and adhesion. Cohesion allows water to flow freely without molecules
       separating. Adhesion is ability to adhere to polar surfaces. These characteristics allow
       water to rise up a tree from the roots to the leaves through small tubes. Adhesion of water
       to walls of vessels prevents water columns from breaking apart. Cohesion allows
       evaporation from leaves to pull water columns from roots.

    5. Water has a high surface tension. Water is relatively difficult to break through at its
       surface. This property permits a rock to be skipped across a pond surface and supports
       insects walking on the surface of water.

    6. Ice is less dense than water. Below 4 C, hydrogen bonding becomes more rigid but more
       open, causing expansion. Because ice is less dense, it floats; therefore, bodies of water
       freeze from the top down. If ice was heavier than water, ice would sink and bodies of
       water would freeze solid. This property allows ice to act as an insulator on bodies of
       water, thereby protecting aquatic organisms during the winter.

    Chapter 2                                                                                      9
     Take Note: A solid understanding of acids and bases is important for your understanding of
     the biochemistry presented in the next few chapters. Take time now to be sure you understand
     these concepts, so that you can properly understand the information that is to come.

2.4      Acids and Bases
A small fraction of water molecules dissociate to produce an equal number of hydrogen ions and
hydroxide ions. The pH scale indicates acidity and basicity (alkalinity) of a solution. pH is the
measurement of free hydrogen ions, expressed as a negative logarithm of the H+ concentration
(-log [H+]). Solutions with equal numbers of H+ and OH- are neutral. In acidic solutions, there are
more hydrogen ions than hydroxide ions; these solutions have a pH less than 7. In basic solutions,
there are more hydroxide ions than hydrogen ions; these solutions have a pH greater than 7. Cells
are sensitive to pH changes.

Biological systems often contain buffers that help keep the pH within a normal range. Buffers
keep pH steady and within normal limits in living organisms. Buffers stabilize pH of a solution
by taking up excess hydrogen (H+) or hydroxide (OH-) ions, keeping the pH of the blood in a
narrow range so that the body can maintain homeostasis. For example, carbonic acid helps keep
blood pH within normal limits: H2CO3  H+ + HCO3-.

Multiple Choice Questions

1.     Which of the following statements is NOT true regarding the properties of water?
         A. Hydrogen bonds require a good deal of energy to break.
         B. Water cools more slowly than other liquids.
         C. The hydrogen bonds between water hold more heat energy.
         D. Water reaches its boiling point more slowly than substances with a lower specific heat.
         E. Water's surface tension arises due to hydrogen bonds between water molecules.

2.     In a molecule of DNA, the bonds holding the side chains must be very strong, whereas the bonds
       holding the rungs of the ladder between the nucleic acids must break during DNA replication. What
       types of bonds are present between adenine and thymine and cytosine and guanine in a DNA
           A. nonpolar covalent
           B. ionic
           C. polar covalent
           D. hydrogen
           E. hydrophobic interactions

3.     Van der Waals interactions and hydrogen bonds and ionic bonds are weak interactions. Therefore,
         A. their cumulative effects reinforce molecular structure, making them biologically significant.
         B. they are not found in organic molecules.
         C. they occur between molecules that are a long distance apart.
         D. they occur when two atoms that are equally electronegative are attracted to one another.
         E. they occur when cations and anions attract each other and transfer electrons.

10                                                                                           Chapter 2
4.   Ionic bonds involve the
        A. equal sharing of electrons.
        B. transfer of electrons.
        C. uneven sharing of electrons.
        D. asymmetric distribution in molecules.
        E. hydrogen atom bonding of a hydrogen atom to one electronegative atom.

5.   In the following reaction

     C6H12O6 + 6O2  6CO2 + 6H2O

     glucose is
        A. reduced.
        B. an anion.
        C. oxidized.
        D. a cation.
        E. electronegative.

6.   One of the most common biological fluids which may be outside of the neutral pH range of 68 is
       A. saliva.
       B. gastric juice.
       C. mucus.
       D. semen.
       E. urine.

7.   A buffer works by
        A. accepting hydrogen ions from the solution when they are in excess.
        B. irreversibly combining with hydrogen ions to neutralize a base.
        C. dissociating to yield OH- ions to neutralize an acid.
        D. donating hydrogen ions when they are in excess.
        E. balancing the reaction between CO2 and H2O.

8.   Evaporative cooling occurs because
        A. molecules with the greatest kinetic energy are the most likely to leave as a gas.
        B. water's low heat of vaporization converts water to a gas.
        C. when water is heated, the kinetic energy of molecules decreases and the liquid
            evaporates more rapidly.
        D. molecules do not move fast enough to overcome attractions to other molecules.
        E. hydrogen bonds form as water evaporates absorbing heat energy.

9.   As water travels through xylem tissue
        A. hydrogen bonding attracts water to the walls of the cells to counteract gravity.
        B. it forces water out of the root hairs as it travels from source to sink.
        C. it is actively transported by the use of ATP.
        D. it moves through aquaporins from one xylem cell to the next.
        E. hydrogen bonds are not able to form because of the speed of the water molecules
            moving up the xylem.

     Chapter 2                                                                                         11
10. It is improbable that the hydrogen atoms in two water molecules would be attracted to one another and
    the oxygen atoms would repel one another because
         A. hydrogen atoms have a partial negative charge and will be attracted to one another.
         B. the slightly positive hydrogen of one molecule is attracted to the slightly negative oxygen of
             another molecule.
         C. the opposite ends of water molecules have similar charges.
         D. hydrogen is more electronegative than oxygen, and the electrons spend more time closer to the
             oxygen atom.
         E. its two hydrogen atoms are joined to the oxygen atom by single covalent bonds.

Free Response Question

Water is a very unique molecule and is very important to biological systems. As an example, water striders,
spiders, and other arthropods are able to walk across water.

        A. Discuss three properties of water that make this possible.

        B. Explain why humans are not able to walk across water.

        C. Propose a hypothesis for the structure of arthropod legs to facilitate this phenomenon.

Annotated Answer Key (MC)

 1.   C; Hydrogen bonds do not hold heat energy, rather they require heat energy to be broken. They are
      strong enough to maintain the integrity of the DNA molecule.

 2.   D; Hydrogen bonds are readily broken and reformed, an ideal combination for the location between
      nucleic acids of the DNA strand.

 3.   A; Van der Waals forces are found in many organic molecules. These interactions usually occur
      between molecules that are a great distance apart and are not the same as covalent or ionic bonds, as
      represented by choices D and E. When viewed as a whole these interactions are very important
      biologically, especially in protein structure.

 4.   B; Ionic bonds involve attractions between ions of opposite charge. The charges of these atoms or
      compounds are acquired due to the loss or gain of one or more electrons. This transfer of electrons is
      a relatively weak bond as compared to the sharing of electrons in a covalent bond.

 5.   B; During aerobic respiration, a molecule of glucose is oxidized to produce ~38 molecules of ATP.
      When a molecule is oxidized, it loses electrons. Molecules that are reduced actually gain electrons.

 6.   B; Saliva, semen, urine, and mucus are all found within a relatively neutral pH range of 68. The pH
      scale ranges from 014, with 7 being neutral. Gastric juice has a very acidic pH, usually around 2, due
      to the presence of HCl in the stomach for chemical digestion.

 7.   A; Buffers function in pairs. When the weak acid dissolves in water it forms a weak base. The two
      work together to counter any small shift in pH to maintain a suitable environment for many biological
      processes to occur.

 8.   A; Water has a very high heat of vaporization. When water is heated, the kinetic energy of molecules
      actually increases and those water molecules are the most likely to leave. Hydrogen bonds actually
      break as water evaporates.

12                                                                                            Chapter 2
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