The Chemistry of Life

Biology is a
multidisciplinary
science.
Living organisms are
subject to basic laws
of physics and
chemistry.
One example is the
bombardier beetle,
which uses chemistry
to defend itself.


Atoms of elements play
important roles in biology
What element is lacking in her diet?
Atoms combine to make
molecules
The bonds between atoms of the same
molecule are intramolecular bonds. The
three types of intramolecular bonds are:

1. Covalent Bonds
2. Ionic Bonds
3. Polar Covalent Bonds
1. Covalent Bonds
The bond is formed by sharing a pair of valence
electrons between two atoms.
The bond can be represented in many ways.


Hydrogen (H
2
)
Name
(molecular
formula)
Electron-
shell
diagram
Structural
formula
Space-
filling
model
2. Polar Covalent Bonds
This bond occurs when a pair of valence
electrons is unequally shared between two
atoms.
The atom with a
larger nucleus
attracts the electron
more and has a
slightly negative
charge.
The other atom is
slightly positive.
3. Ionic Bond
Formed by the transfer of an electron from atom to
atom. This results in the formation of positive
cations, and negative anions. Ions are held
together by electrostatic attraction.

Na
Sodium atom
(an uncharged
atom)
Cl
Chlorine atom
(an uncharged
atom)
Na
+

Sodium ion
(a cation)
Cl

Chlorine ion
(an anion)
Sodium chloride (NaCl)
Properties of Covalent Bonds
Pure Covalent Bonds

Results from largely
equal sharing of
electrons.

Happens when bond
partners have similar
electronegativities or
an electronegativity
difference of <0.5
Polar Covalent Bonds

Results from unequal
sharing of electrons.

Happens when bond
partners have
electronegativity
differences between
0.5 and 1.6
The Role of Electronegativity
Electronegativity is a measure of the strength with
which an atom can attract electrons and can be
found on a periodic table.
The electronegativity difference between two
atoms is calculated by subtracting the smaller
value from the larger value.
Bond Types and
Electronegativity
A difference of < 0. 5 covalent bond
A difference of 0.5 1.6 polar covalent bond
A difference of > 1.6 ionic bond
H
O
H
H
2
O
+ +

Bonds in Water
Oxygen electronegativity =
3.44
Hydrogen electronegativity
= 2.2
Difference
3.44 2.2 = 1.24
Bond Type
Polar covalent
In a water molecule the
oxygen is slightly
negatively charged.
Inter- Molecular Interactions
The properties of
molecules can influence
their interactions with
other molecules. These
are weaker bonds than
intramolecular bonds.

1.hydrogen bonding
2.dipole-dipole
interactions
3.London/dispersion force

Water: A special molecule
a) Hydrogen bonding
Effects: cohesion, adhesion, surface
tension. More energy is needed to break
hydrogen bonds than other intermolecular
bonds, which gives water a high specific
heat capacity.
b) Density
Effects: Ice is less dense so it floats,
insulating water underneath.
Water: A special molecule
c) Polar nature of the bond
Effects: as a solvent, water allows polar
molecules and ionic compounds to
dissolve due to waters polarity
d) Dissociation of intramolecular bonds
Effects: 1 in 10
7
water molecules dissociates
to form H
+
and OH
-
ions.
This is a pH of 7 = NEUTRAL.
Functional Groups
Functional
groups are parts
of larger
molecules.
They greatly
influence
biological
reactivity.
Functional Groups
Hydroxyl alcohols
Carboxyl acids
Amino bases
Carbonyl aldehydes
and ketones

Functional Groups
One biologically important functional group
missing from this list is sulfhydryl, which
contains sulphur. The name of molecules
with this functional group is thiol. The R
represents the rest of the molecule.
Functional Groups
Sulphur forms relatively strong
intermolecular bonds with other sulphurs.
This is important to forming the 3D
structure of proteins.

Extra slides for students without
chemistry background
LE 4-10aa
STRUCTURE
(may be written HO)
NAME OF COMPOUNDS
Alcohols (their specific names
usually end in -ol)
Ethanol, the alcohol present in
alcoholic beverages
FUNCTIONAL PROPERTIES
Is polar as a result of the
electronegative oxygen atom
drawing electrons toward itself.
Attracts water molecules, helping
dissolve organic compounds such
as sugars (see Figure 5.3).
LE 4-10ab
STRUCTURE
NAME OF COMPOUNDS
Ketones if the carbonyl group is
within a carbon skeleton
EXAMPLE
Acetone, the simplest ketone
A ketone and an aldehyde may
be structural isomers with
different properties, as is the case
for acetone and propanal.
Aldehydes if the carbonyl group is
at the end of the carbon skeleton
Acetone, the simplest ketone
Propanal, an aldehyde
FUNCTIONAL PROPERTIES
LE 4-10ac
STRUCTURE
NAME OF COMPOUNDS
Carboxylic acids, or organic acids
EXAMPLE
Has acidic properties because it is
a source of hydrogen ions.
Acetic acid, which gives vinegar
its sour taste
FUNCTIONAL PROPERTIES
The covalent bond between
oxygen and hydrogen is so polar
that hydrogen ions (H
+
) tend to
dissociate reversibly; for example,
Acetic acid Acetate ion
In cells, found in the ionic form,
which is called a carboxylate group.
LE 4-10ba
STRUCTURE
NAME OF COMPOUNDS
Amine
EXAMPLE
Because it also has a carboxyl
group, glycine is both an amine and
a carboxylic acid; compounds with
both groups are called amino acids.
FUNCTIONAL PROPERTIES
Acts as a base; can pick up a
proton from the surrounding
solution:
(nonionized)
Ionized, with a charge of 1+,
under cellular conditions
Glycine
(ionized)
LE 4-10bb
STRUCTURE
(may be written HS)
NAME OF COMPOUNDS
Thiols
EXAMPLE
Ethanethiol
FUNCTIONAL PROPERTIES
Two sulfhydryl groups can
interact to help stabilize protein
structure (see Figure 5.20).
LE 4-10bc
STRUCTURE
NAME OF COMPOUNDS
Organic phosphates
EXAMPLE
Glycerol phosphate
FUNCTIONAL PROPERTIES
Makes the molecule of which it
is a part an anion (negatively
charged ion).
Can transfer energy between
organic molecules.