Introduction to Biochemistry
Living organisms operate within the same
physical laws that apply to physics and
chemistry:
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Conservation of Mass, Energy
Laws of Thermodynamics
Laws of Chemical Kinetics
Principles of Chemical Reactions
Living organisms are composed of lifeless
molecules that conform to the physical laws
of nature.
Electronegativity
• nonpolar bond: electrons are shared equally
H 2,
Cl2:
• polar bond: electrons are shared unequally
because of the difference in electronegativity.
HCl:
Bond Polarity
A polar bond can be pictured using partial
charges:
+

H
Cl
2.1
 = 0.9
3.0
Electronegativity
Difference
Bond Type
0 - 0.5
Nonpolar
0.5 - 2.0
Polar
2.0 
Ionic
MOLECULAR SHAPE
• When atoms form a covalent bond, the
valence electron pairs arrange themselves to
be as far away from each other as possible.
• This change to the orientation of the valence
electrons is Hybridization.
• Symmetry of shape will also determine
polarity of molecule or functional group.
•Methane: CH4 – tetrahedral shape – equal 109.5
angle between valence electrons; symmetrical;
nonpolar
Ammonia: NH3 – pyramidal shape – equal 107 angle
between valence electrons; asymetrical shape –
polar molecule
To determine if a molecule is polar or
nonpolar, must consider both
electronegativity and shape
Which of the following is the essential characteristic of
a polar molecule?
a. Contains double or triple bonds
b. Is formed at extremely low temperatures
c. Contains ions as part of the structure
d. Has an asymmetrical distribution of electrical charge
e. Contains the element oxygen
Van der Waals forces:
•intermolecular forces of attraction
Examples: London forces, dipole-dipole forces, hydrogen bonds
LONDON FORCES
• London forces are weak
because (1) partial charges are
involved and (2) because they
are temporary. They arise from
the random movement of
electrons in atoms and
molecules.
a) small collection of nonpolar molecules
b) a nonpolar molecule may temporarily have a slight excess of
electrons in one portion of the molecule
c) During the brief interval that these temporarily polar molecules exist,
they are attracted to each other
Hydrogen bonds: strongest intermolecular bonds
The Essential Role of Water
•H2O is the key to understanding the behavior
of macromolecules. It is the solvent of life and
all living transformations occur in an aqueous
environment.
Water is a Polar Molecule
• The structure of water consists of two
hydrogen atoms bonded to one oxygen.
• The hydrogen side of the water molecule has a
slight positive charge. On the other side of the
molecule a negative charge exists.
• Because of the polar structure, water
molecules tend to form weak bonds with one
another and with other substances which are
charged.
• HYDROGEN BONDS are individually weak, but
collectively strong.
Properties of water
• Water has a high specific heat.
• Specific heat is the amount of energy required
to change the temperature of a substance.
• Because water has a high specific heat, it can
absorb large amounts of heat energy before it
begins to get hot. It also means that water
releases heat energy slowly when situations
cause it to cool.
• Water does not undergo changes in
temperature easily.
• The temperature of the water within living
organisms tends to change more slowly than
does that of the surrounding air or soil, so that
the living cells are protected against
temperature fluctuations.
• This kind of protection is important because
many biochemical reactions will take place
only within a narrow range of temperatures.
• Water is a universal solvent. This feature also
enables water to carry solvent nutrients in living
organisms.
• Water is an unusually versatile solvent because its
polar molecules are attracted to charged and
polar substances. When ions or polar substances
are surrounded by water molecules, they dissolve
and are called solutes.
• Hydrophilic substances have an affinity for water.
• Hydrophobic substances do not; they seem to
repel water.
• Water has a high surface tension.
• This phenomenon also causes water to stick to
the sides of vertical structures despite
gravity's downward pull.
• Water's high surface tension allows for the
formation of water droplets and waves, allows
plants to move water (and dissolved nutrients)
from their roots to their leaves, and the
movement of blood through tiny vessels in the
bodies of some animals.
Cohesion and Adhesion
Acids, bases and pH
•
•
•
•
Water can dissociate into H+ and OH- ions
Acids:(pH 0 to 6.9): high concentrations H+
Bases:(pH 7.1 to 14) high concentrations OHHuman blood must be within range of 7.357.45. Control of pH is very important.
Buffers
• A buffer is an aqueous solution that has a highly stable
pH. If you add acid or base to a buffered solution, its
pH will not change significantly.
• An acid-base buffer typically consists of a weak acid,
and its conjugate base
• An acid donates a proton. The chemical that remains
after the proton is donated is a base.
• HNO3
NO3Acid
conjugate base
• When a base accepts a proton, it becomes an acid
because it now has a proton that it can donate.
• The bicarbonate buffering system is an
important buffer system in the acid-base
homeostasis of living things, including
humans.
• In this system, carbon dioxide (CO2) combines
with water to form carbonic acid (H2CO3),
which in turn rapidly dissociates to form
hydrogen ion and bicarbonate (HCO3- )
• When H+ are added to the solution, some of
the base (HCO3-) component of the buffer is
converted to the weak-acid(H2CO3)
component . This uses up most of the H+
added.
• When OH- are added to the solution, protons
are dissociated from some of the weak-acid
molecules of the buffer, converting them to
the base of the buffer. This releases H+ ions.
Types of Reactions
• Dehydration
synthesis
• Hydrolysis
• Neutralization
• Oxidation-Reduction
Dehydration synthesis
• aka Condensation reactions
• Form a covalent bond between two molecules
by removing a water molecule
• Anabolic reaction: creates bigger molecules
Hydrolysis
• Adds a water
molecule to
break a
covalent bond
• Catabolic
reaction:
creates smaller
molecules
Neutralization
• Acid + Base
Salt + Water
• Antacids are supposed to decrease the
amount of hydrochloric acid in the stomach by
reacting with excess acid.
• Some of the ingredients in antacids are: milk
of magnesia (Mg(OH)2, calcium carbonate
(CaCO3), sodium bicarbonate (NaHCO3)
Oxidation -Reaction
• OIL RIG: Oxidation is loss (of electrons)
Reduction is gain
• In biological systems, usually means gain or
loss of H+ (protons)
• Coupled reactions are an important way to
transfer energy (cellular respiration and
photosynthesis)
Functional Groups
• Functional groups are clusters of atoms with
characteristic structure and functions.
• Generally, they are polar covalent groups
• They increase the solubility of a substance in
water.
• The hydroxyl (OH) groups in glucose are what
make this sugar soluble