Biolo1100 Chapter 2 Chemistry
  1. An atom is the smallest particle of an element  .
    • An element has unique chemical properties and is made of one kind of atom.

      An atom is made of 3 kinds of smaller particles:

      • protons are positively charged
      • neutrons have no charge and are electrically neutral
      • electrons are negatively charged

      The nucleus of an atom contains protons and neutrons.

      Electrons orbit the nucleus in different energy levels.

      Carbon plays a central role in life.


    • The number of protons of an atom is its atomic number, and gives the element unique chemical properties.

      Atoms are electrically neutral: they always have an equal number of protons and electrons.

      • How many electrons does Oxygen have?
        • 8

    • Electrons circulate around the nucleus in paths with different energy levels called electron shells.

      Lower electron shells possess lower energy, and electrons tend to occupy lower shells first, since they are most stable there.

      The first shell can hold up to 2 electrons.

      The 2nd and 3rd shells can hold up to 8 electrons.

      An atom is most stable when its outermost shell is filled.

    • Carbon has an incomplete outermost shell with 4 vacancies for electrons.

      Thus Carbon can form chemical reactions with many kinds of atoms.

      This versatility allows Carbon to play a central role in many biological reactions.


  2. Atoms can gain or lose one or more electrons and become charged ions  .
    • Ions are atoms that have gained or lost one or more electrons.

      A sodium atom has 11 protons and 11 electrons.

      • It becomes a positively charged ion when it loses one electron.

      Conversely, a chlorine atom has 17 protons and 17 electrons.

      • It becomes a negatively charged ion when it gains one electron.

      Both ions are stable because they now have a complete complement of electrons (8) in their outermost shells.


  3. Atoms and ions can be linked to each other by forming bonds  .
    • Ionic   bonds form when ions   of opposite charge are attracted to each other.
      • Ionic bond

        1. A sodium atom (Na) can donate an electron to a chlorine atom (Cl).

        2. The positively charged sodium ion and the negatively charged chloride ion are attracted to each other.

        3. Sodium chloride (NaCl, or table salt) is composed of alternating sodium and chloride ions held together by strong ionic bonds.


    • Covalent   bonds form when atoms share electrons to make a molecule  .
      • Covalent bond

        Two hydrogen atoms can share each of their single electrons and create a strong attraction called a covalent bond.

        Two or more atoms linked by covalent bonds form stable molecules with unique properties.

        Thus a hydrogen gas molecule (H2) has a covalent bond (a pair of shared electrons) between two hydrogen atoms.



    • Hydrogen   bonds form between the partially charged ends of polar   molecules.

    • In a water molecule (H2O), one oxygen atom forms a covalent bond with each of 2 hydrogen atoms by sharing one electron pair with each hydrogen.

      The oxygen atom attracts the shared electrons more strongly than the hydrogen atoms, forming polar covalent bonds.

      Due to this unequal sharing of electrons, water is a polar molecule with a partially positive "pole" at the hydrogen end and a partially negative "pole" at the oxygen end.


    • Hydrogen bond

      The partial positive charges of the hydrogen atoms of one water molecule (H2O) are attracted to the partial negative charge of the oxygen atom of another molecule.

      These weak attractions (dotted lines in the diagram) between polar molecules are called hydrogen bonds.

      Note that the strong bonds between hydrogen and oxygen atoms within water molecules are covalent bonds.

      Summary: hydrogen bonds are weak.



  4. The hydrogen   bonds between polar water molecules give water unique properties.
    • Due to numerous hydrogen bonds, water has many unique properties to support life.

      • High cohesion and surface tension.

      • Good solvent for polar and ionic substances.

    • The tendency for water molecules to stick together is called cohesion.

      Cohesion due to hydrogen bonds allows water to be pulled from beneath the soil to great heights in trees.

      Note: Trees take up water via roots, while photosynthesis (the process of producing their food with light) occurs in leaves.

    • Many hydrogen bonds let water molecules stick together, giving water great cohesion, and lets water form a strong surface at the boundary with air.

      This surface tension allows spiders and water striders to walk on water.

      Water also adheres to other surfaces, forming a meniscus in a graduated cylinder.



    • The partial charges on water molecules are attracted to the charged sodium and chloride ions of salt (NaCl).

      The water molecules separate the ions from the crystal and dissolve the salt to make a solution.

      Substances such as NaCl dissolved in liquid are called solutes.

      Water is a good solvent for ionic or polar substances, which are said to be "hydrophilic" (water-loving) and form a solution in water.

  5. The covalent   bonds in water sometimes dissociate to form hydroxide   ions and hydrogen   ions.
    • A small percent of the molecules in water can dissociate into a negatively charged OH- (hydroxide ion) and a positively charged H+ hydrogen ion ( proton ) in a reversible reaction.
  6. The concentration of hydrogen   ions in a solution determines a chemical property called pH   .
    • pH scale

      Pure water has the same concentration of hydrogen ions and hydroxide ions; this is represented as 7 (neutral) on a pH scale from 0 to 14.

      A substance that increases concentrations of hydrogen ions has a pH lower than 7 and is an acid.

      A substance that lowers concentrations of hydrogen ions has a pH greater than 7 and is a base.

      An acidic solution has a high concentration of hydrogen ions with a low pH.

      A basic (alkaline) solution has a low concentration of hydrogen ions with a high pH.


  7. Four classes of macromolecules are important to life.
    • Carbohydrates
      • Carbohydrates (carbon and water) are made of C, H, and O, and can also be called sugars.

        Like water, these molescules are polar.

        The simplest carbohydrates (simple sugars) are monosaccharides.

        Larger carbohydrates (complex sugars) are called polysaccharides.

          In addition to starch, polysaccharides include cellulose and glycogen.


      • The simplest sugars (monosaccharides) are composed of one ring of carbohydrates, and can provide quick energy.

        Examples include glucose, fructose, and galactose.


      • Complex sugars (polysaccharides) are made of multiple monosaccharides.

        The strong covalent bonds between the simple sugars can be broken down by digestion for energy.

        The shortest polysaccharides are disaccharides such as sucrose (table sugar).

        Starch is an example of a longer, larger polysaccharides that is easily digestible.


      • glycogen fat Glucose is the most important sugar for life.

        Polysaccharides are digested into glucose, which is used as a source of energy.

        Some excess glucose is stored in muscles and liver of animals as the polysaccharide glycogen, which can be broken down to glucose for energy needs.

        Additional excess glucose is converted into fat for long-term energy storage.


    • Lipids
      • Lipids comprise 3 major types.
        • fats

        • sterols

        • phospholipids

      • Fat molecules are triglycerides, each containing a glycerol head attached to 3 fatty acid tails.

        A fatty acid is a long chain of carbon and hydrogen atoms (hydrocarbon).

        The nonpolar hydrocarbons are hydrophobic ("afraid" of water) and are insoluble in water.

        The dense covalent bonds make fats ideal for long-term energy storage.

      • Sterols are lipids with 4 carbon rings.

        • Cholesterol is an important component of animal cell membranes, and is also required to synthesize steroid hormones.

        • Steroid hormones such as estrogen and testosterone are built through chemical modifications to cholesterol precursor molecules.

      • A phospholipid is similar to a fat molecule except it has:

        • a hydrophilic (polar) phosphate group

        • 2 hydrophobic (nonpolar) fatty acid tails

        Phospholipids are major components of cell membranes.

    • Proteins
      • Proteins are made from 20 different kinds of subunits called amino acids.

        Amino acids are composed of a central carbon joined to

        • an amino group which often loses an electron.

        • a carboxyl group which often gains an electron.

        • a side chain unique to each of 20 different kinds of amino acids.

        The polar amino acids are linked by covalent bonds to form polypeptide chains called proteins.

        Many proteins are enzymes that play a critical role in many biological reactions.

      • Weak hydrogen bonds fold each protein into a unique 3-dimensional shape that determine its function.

      • Enzymes such as lactase help speed up chemical reactions.

        1. An active site on the protein's surface binds a particular substrate such as lactose.

        2. The tight fit allows the enzyme to break the covalent bond between the simple sugars.

        3. The products of the reaction are the 2 sugars, which are released.

        All of the chemical reactions in a living organism make up its metabolism, keeping it alive.



      • Changes in a protein's environment, such as temperature or pH, can cause it to lose the weak hydrogen bonds in a process is called denaturation.

        This denatured protein with a deformed 3-dimensional shape often loses some of its function.


    • Nucleic acids

    • Nucleic acids (DNA and RNA) are made of nucleotide subunits.

      Nucleotides are composed of a five-carbon sugar, a phosphate group, and a nitrogen-containing base.

      The sugar is

      • deoxyribose (missing an oxygen) in DNA (Deoxyribonucleic Acid)
      • ribose (with an extra oxygen) in RNA (Ribonucleic Acid)

      Two chains of nucleotides form a double helix with sugar-phosphate backbones held together by hydrogen bonds.


    • Four different nitrogen-containing bases are found in the nucleotides of DNA:

      Adenine (A), Guanine (G), Cytosine (C), and Thymine (T).

      In RNA, Uracil (U) takes the place of Thymine (T).


    • The two chains of a DNA double helix are complementary to each other:

      • they are held together by specific hydrogen bonds between nitrogen-containing bases.

      Adenine (A) always forms 2 hydrogen bonds with Thymine (T).

      Guanine (G) always forms 3 hydrogen bonds with cytosine (C).