chapter 02

Bio1100 Chapter 2

The chemistry of biology

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.
  Thus Carbon has an atomic number of 6.
  Atoms are electrically neutral: they always have an equal number of protons and electrons.
  - How many electrons does Oxygen have?
    - 8 - the same as its atomic number
- Electrons circulate around the nucleus 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 1st 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 electron shell is filled.
  Stable atoms tend not to react or combine with other atoms.
- 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.
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 (Na) atom has 11 protons and 11 electrons.
  - It becomes a positively charged ion when it loses one electron.
  Conversely, a chlorine (Cl) 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.
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 to form a strong attraction called a covalent bond.
    Two or more atoms linked by covalent bonds make stable molecules.
    Thus a hydrogen gas molecule (H₂) has a covalent bond (a pair of shared electrons) between two hydrogen atoms.
    A double bond is the sharing of four electrons as seen in an oxygen gas molecule (O₂): it has one double bond with two pairs of electrons.
- Hydrogen bonds form between the partially charged ends of polar molecules.
- A water molecule (H₂O) has two polar covalent bonds: 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; this unequal sharing of electrons makes these covalent bonds polar.
  Water is a polar molecule with a partially (δ) positive "pole" at the hydrogen end and a partially (δ) negative "pole" at the oxygen end.
- Hydrogen bond
  The partial (δ) positive charges of the hydrogen atoms of one water molecule (H₂O) are attracted to the partial (δ) negative charge of the oxygen atom of another molecule.
  These weak attractions (dotted lines in the diagram) between polar molecules are hydrogen bonds.
  Note that the strong bonds between hydrogen and oxygen atoms within water molecules are covalent bonds.
  Tutorial
Comparison of the different types of bonds
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.
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.
The concentration of hydrogen ions in a solution determines a chemical property called pH .
- pH scale
  Pure water has the same concentration of hydrogen and hydroxide ions; this is 7 (neutral) on a pH scale from 0 to 14.
  If hydrogen ion concentrations increase, the pH is lower than 7 and is an acid.
  If hydrogen ion concentrations decrease, the pH is greater than 7; it 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.