Atoms, molecules and bonds

Goals

1. To understand the different ways that atoms bond together to form molecules.

2. To understand how the biological properties of molecules depend on the way their atoms bond together.

3. To get the background in basic chemistry needed to understand the large biological molecules that will be discussed in later classes.

4. To understand how the chemical structure of water has important consequences

5. To understand the nature of acids and bases and the pH scale

Outline:

Atomic structure

nucleus

protons -- determine which element

neutrons -- determine what isotope of that element

electrons -- confer chemical properties

electrons are organized in electron shells

atoms like to have their outermost shells full

Chemical bonds

covalent bonds: atoms sharing pairs of electrons

atom	number of possible bonds
H	1
O	2
N	3
C	4

can make single, double, or triple bonds by sharing 1, 2 or 3 pairs of electrons

electronegativity -- the affinity of the nucleus for electrons

O	high electronegativity
N	fairly high electronegativity
C, H	low electronegativity

polar bonds: covalent bonds between atoms of differing electronegativity (C-O, O-H, N-H, C-N) -- one atom will have a slight negative charge, the other a slight negative

nonpolar bonds: covalent bonds between atoms of the same electronegativity (O-O, N-N, C-C, H-H, C-H)

polar molecules -- polar bonds that don't balance each other out (e.g., water)

nonpolar molecules -- either all nonpolar bonds (e.g., methane), or polar bonds that balance each other (e.g., carbon dioxide)

ionic bonds: stealing electrons

electronegativity difference so great that electron is not shared, it is transferred

creates two ions that are attracted to each other

The chemical nature of water

• it has polar bonds
• it's bent
• it's a polar molecule

  because of this it can form hydrogen bonds

Hydrogen bonds

• weaker than covalent or ionic bonds
• form between molecules
• temporary
• must have N or O involved to happen

  causes water molecules to be very attracted to each other, and to other molecules that can form H-bonds

Consequences -- note: you should understand why these things are true, and what their biological significance is

Water is highly cohesive

Water has high surface tension

Water can act as a solvent for ions and polar molecules (hydrophilic)

Water is highly adhesive to large molecules with polar regions (hydrophilic)

Water will not dissolve nonpolar molecules (hydrophobic)

Water floats when frozen

Acids, bases and buffers

The polar covalent bonds in water allow it to occasionally dissociate into H⁺ and OH^-

[H⁺] [OH^-] = 10^-14 M

pH = -log[H⁺]

acids raise [H⁺] of a solution, lowering pH

bases raise [OH^-] of a solution, raising pH

buffers absorb H⁺ and/or OH^- out of solution, stabilizing pH

Vocabulary

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