The

Chemical
Basis of Life
 Key Concepts
1. Strong chemical bonds
• Nonpolar covalent bonds
• Polar covalent bonds
• Ionic bonds
2. Weak chemical bonds
• Hydrogen bonds
• Nonpolar interactions
3. Acids and bases
• Water dissociation
• The pH scale
• Buffers
Outline: Insightful Questions to Ask
1. What are chemical bonds?
2. What determines the number of bonds in which
an atom can participate?
3. What determines the type of chemical bond?
4. What is hydrogen bonding and why does it
matter?
5. What are the connections between water
dissociation, pH, and acid-base reactions?
6. What functional chemical groups commonly
affect biological systems?
 The Basics about Bonds
• Chemical bonds always involve electrons.
• Electrons “orbit”
in shells around
the nucleus of
an atom.
• General rule:
Electrons in the
outermost shell
affect the
chemical
reactivity of the
atom.
 The Basics about Bonds
• For all biologically-relevant atoms, each electron
shell can hold a certain number of electrons
– 1st shell: 1 or 2 electrons
– Subsequent shells: 1 to 8 electrons each

• Foundational concept: Atoms tend to be most

stable when their outermost (“valence”) shell has
the maximum number.
– Atoms that have incomplete valence shells interact
with electrons of other atoms to complete their shell.
1. An atom of carbon is most stable
when it forms _____ bond(s) with
other atoms.
A. one
B. two
C. four
D. six
 Understanding Bonds
• Bonds form when atoms share or transfer electrons.
 Understanding Bonds
Covalent Bonds
• Single bond involves the
sharing of 2 electrons.
• Double bonds share 4
electrons.
• Triple bonds share 6
electrons.

Test Your Understanding

1. Why do oxygen atoms
readily form double
bonds with other oxygen
atoms?
 Understanding Bonds
Ionic Bonds
• Transfer of electron(s) from
one atom to another results in
electrostatic attraction.

Test Your Understanding

1. In what sense is this a bond?
2. What happens to this bond
when NaCl is placed in water?
Would the same be true of a
covalent bond?
Fate of Ionic Bonds in Water
Fate of Covalent Bonds in Water

But its covalent

bonds remain
intact.
 Understanding Bonds
• What determines whether two atoms form a
covalent bond or an ionic bond?
• ELECTRONEGATIVITY
– Definition: The ability of an atom to attract
electrons towards itself in a chemical bond.
– Electronegativity depends on:
1. The number of protons in the atom’s nucleus.
2. The distance (atomic radius) between the nucleus
and the outer shell in which the electron is orbiting.
Understanding Electronegativity

Decreasing atomic radius

Increasing number of protons in atomic nucleus
 Understanding Electronegativity
• Key generalization: The greater the difference in
electronegativity between two atoms, the more
likely they will form an ionic bond.

– Ionic bond
Na = 0.93, Cl = 3.16 3.16 – 0.93 = 2.23
– Covalent bond
C = 2.55, H = 2.20 2.55 – 2.20 = 0.35

• What about values that are in-between?

– This is what determines the polarity of a bond.
 Understanding Bonds
• Water has two polar covalent bonds
• H and O do not
share electrons
equally.
– Electronegativity
O = 3.44
H = 2.20
1.24
Thus, water has a
partial ionic nature –
i.e., it is polar.
 Understanding Bonds
• If we could get really
small, what would we see
when a polar covalent
bond forms?

Test Your Understanding

1. Which atom is the most
electronegative, the
yellow or the red one?
2. Why is the final state
colored orange?
Top 10 Covalent Bonds in Biomolecules
Covalent Electronegativity
Bond Atom 1 Atom 2 Difference Polarity
C-C 2.55 2.55 0.00 nonpolar
C-S 2.55 2.58 0.03 nonpolar
C-H 2.55 2.20 0.35 nonpolar
S-H 2.58 2.20 0.38 nonpolar
N-O 3.04 3.44 0.40 nonpolar
C-N 2.55 3.04 0.49 nonpolar
N-H 3.04 2.20 0.84 polar
C-O 2.55 3.44 0.89 polar
O-H 3.44 2.20 1.24 polar
P-O 2.19 3.44 1.25 polar
 Polarity Affects Properties
Polar Compounds Nonpolar Compounds
• Tend to associate with other • Tend to associate with other
polar molecules (why?) nonpolar molecules (why?)
• Are hydrophilic (“water- • Are hydrophobic (“water-
loving”) fearing”)
• Examples: sugars, ions • Examples: fats, oils, waxes

Amphipathic Compounds
• Have some chemical groups that are
polar and other groups that are
nonpolar, all on the same molecule
• Examples: proteins, phospholipids
Summary: Bonding and Charge
Remember this Example?

What do the dotted

lines represent?
 Hydrogen Bonds
• They’re not really bonds at all, but rather
weak electromagnetic attractions due to the
partial (dipole) charges on polar molecules.
3. Which of the red lines depicts a
hydrogen bond?
A. R-CH3 H2N-R
B. R-C=O H2N-R
C. R-C N-R
O H
D. All of these.
E. A and B only.
 Hydrogen Bonding Occurs When…
• A hydrogen atom attached to another atom by
a polar covalent bond is attracted to an
electronegative atom in another molecule.
H atom attached to an
O atom by a polar
covalent bond…
H atom attached to an …is attracted to an
N atom by a polar electronegative N
covalent bond… atom.
…is attracted to an NOTE: Hydrogen bonds
electronegative O are always denoted with
atom, producing a dotted or dashed lines.
hydrogen bond.
 Importance of Hydrogen Bonds
• Hydrogen
bonding affects
the shape (and
therefore
function) of
proteins,
including the
enzymes that
catalyze
essential
processes in
your cells!
Importance of Hydrogen Bonds

• Hydrogen bonding is
responsible for base-
pairing in DNA, which
enables organisms to pass
on heritable traits.
 Understanding Acids & Bases
• Certain compounds dissolved in water will
promote the release of H+ or OH-.
– Acids stimulate release of H+ (or uptake of OH-)
– Bases stimulate release of OH- (or uptake of H+)
• Where do the H+ and OH- come from?
– Dissociation of water:
 Understanding Acids & Bases
Test Your Understanding
1. Which of these molecules is acting like an
acid and which is acting like a base?
Acid Base

NH2  NH3+
Full equation: NH2 + H2O  NH3+ + OH-

COOH  COO -
Full equation: COOH + OH-  COO- + H2O
 Understanding the pH Scale

• pH = - log[H+]
• Change of
1 pH unit =
10-fold change
in [H+]
• Acidic range:
[H+] > 10-7M
pH < 7
• Basic range:
[H+] < 10-7M
pH > 7
 Understanding Buffers
• Buffers resist pH changes by either releasing
or taking up H+, thereby stabilizing cells.
• Important buffer in blood plasma:

CO2 + H2O HCO3- + H+

Test Your Understanding

1. In which direction would the reaction tend to
resist acidification? …promote acidification?
Understanding
Functional
Groups

• Learn the names,

structures, and
properties of
these functional
groups.
• Pay attention to
polar/nonpolar
features and
acid/base
functions.