CHAPTER 2

Water, Weak Bonds, and the

Generation of Order Out of Chaos

Our senses—vision, taste, smell, hearing, and touch—allow us to

experience the world. We delight in the softness of a kitten’s fur and the
loudness of its purr through touch and hearing. Remarkably, these
sensuous pleasures depend on weak, reversible chemical bonds. 1
 Chapter 2: Outline

2.1 Thermal Motions Power Biological Interactions

2.2 Biochemical Interactions Take Place in an Aqueous
Solution
2.3 Weak Interactions Are Important Biochemical
Properties
2.4 Hydrophobic Molecules Cluster Together
2.5 pH Is an Important Parameter of Biochemical
Systems

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 Section 2.1 Thermal Motions Power
Biological Interactions
• Weak bonds permit dynamic interactions that form the
basis of biochemistry and life itself.

• Brownian motion is the movement of molecules powered

by random fluctuations of environmental energy.

• Brownian motion of water initiates many biochemical

interactions.

DID YOU KNOW?

One angstrom (Å) = 0.1 nanometer (nm) = 1 × 10–10 meter (m). It is
named after Swedish physicist Anders Jonas Ångström (1814–1874),
who expressed wavelengths as multiples of 1 × 10–10 meter. That
length was subsequently named an angstrom.

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Section 2.2 Biochemical Interactions Take
Place in an Aqueous Solution
Learning objective 4: Describe the chemical properties
of water and explain how water affects biochemical
interactions.

• Water is a polar molecule, with the oxygen atom carrying

a slightly negative charge and the hydrogen atoms
carrying slightly positive charges.

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 2.2 Biochemical Interactions Take Place in
an Aqueous Solution
• The polarity of water allows the Figure 2.1 Hydrogen bonding
formation of hydrogen bonds between in water molecule
water molecules and accounts for the
cohesiveness of water.

• The polarity of water also accounts

for its ability to dissolve many
important biochemicals.

• The inability of water to dissolve

nonpolar molecules results in an
important organizing principle called Hydrogen bonds (shown as dashed green
the hydrophobic effect. lines) are formed between water molecules to
produce a highly ordered and open structure.

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Redwood Forest

Hydrogen bonding allows

water to travel from the
roots to the top leaves of
the giant redwoods.

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 Section 2.3 Weak Interactions Are
Important Biochemical Properties
Learning objective 5: Describe the types of noncovalent,
reversible interactions and explain why reversible
interactions are important in biochemistry.

• Electrostatic interactions
• Hydrogen bonds
• Van der Waals interactions
• Hydrophobic effect

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 Section 2.3 Electrostatic interactions are
between electrical charges
• Electrostatic interactions, also called ionic bonds or salt bridges,
are the interactions between distinct electrical charges on atoms
• The energy of an electrostatic interaction between two charges
is given by Coulomb’s law:

• E is the energy, q1 and q2 are the charges on the ions, D is the dielectric
constant, r is the distance between the two ions, and k is the proportionality
constant.
• The dielectric constant (D) is 1 in a vacuum and 80 in water. Thus,
water weakens electrostatic interactions.

Sodium chloride dissolves in water. As the sodium ions disperse,

their positive charges are neutralized by the partially negative charges
of the oxygen atoms of water. The chloride ions are surrounded by the
partially positive charges on the hydrogen atoms.

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 Hydrogen Bonds Form Between an
Electronegative Atom and Hydrogen
• Hydrogen bonds are not unique to water molecules and can occur
whenever hydrogen is covalently bonded to an electronegative atom.

• Water disrupts hydrogen bonds between two molecules by competing for

the hydrogen-bonding capability.

Figure 2.5 Disruption of hydrogen bonds.

Competition from water molecules disrupts
hydrogen bonds in other molecules.

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 van der Waals Interactions Depend on
Transient Asymmetry in Electrical Charge
• Nonpolar and uncharged
molecules can interact
electrostatically with van
der Waals interactions.
• The basis of the van der
Waals interaction is that
transient asymmetry in
the electron distribution
of one molecule will
induce complementary
asymmetry in a nearby Figure 2.6 The energy of a van der Waals interaction as two
atoms approach each other. The energy is most favorable at
molecule. the van der Waals contact distance. The energy rises rapidly
owing to electron–electron repulsion as the atoms move closer
together than this distance.
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Gecko uses van der Waals interactions

Figure 2.7 The power of van der Waals interactions. Geckos

can cross a ceiling, held only by weak bonds called van der Waals
forces. 11
 Weak Bonds Permit Repeated Interactions
• Hydrogen bonds contribute to the stability of the DNA
double helix. However, these bonds are weak enough to
be broken by the enzymes of DNA metabolism, thereby
allowing access to the genetic information.

Figure 2.8 Stabilization of the double helix. Hydrogen bonds between

adenine and thymine and between guanine and cytosine base pairs
stabilize the double helix. 12
 Pause and digest time!

Let’s think about the biochemical advantage of using weak

bonds (vs strong bonds) in biological molecules?

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 Section 2.4 Hydrophobic Molecules
Cluster Together
• Hydrophobic molecules such as benzene tend to
cluster together in aqueous solutions.

• This clustering of hydrophobic molecules in water is called the hydrophobic

effect.

• The hydrophobic effect is powered by the increase in the entropy of water

that results when hydrophobic molecules come together.

• The hydrophobic effect is a powerful organizing force in biological systems.

Figure 2.9 The hydrophobic effect.

The aggregation of nonpolar groups in
water leads to an increase in entropy
owing to the release of water molecules
into bulk water.

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 Membrane formation and protein folding are
powered by the hydrophobic effect
• Phospholipids have hydrophilic and hydrophobic
properties. Such a molecule, with two distinct
chemical personalities, is called an amphipathic or
amphiphilic molecule. When exposed to water,
phospholipids form membranes.

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 Functional Groups Have Specific Chemical Properties

• Although there are

many different
biomolecules, only
a limited number of
functional groups
are found in these
molecules.

• Functional groups
are arrays of atoms
that have
distinctive chemical
properties.

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 Pause and digest…

How does the following statement apply to biochemistry:

Order can be generated by an increase in randomness.

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Section 2.5 pH Is an Important Parameter
of Biochemical Systems
Learning objective 6: Define pH and explain why
changes in pH may affect biochemical systems.

• pH is the measure of H+ concentration of a solution.

• Controlling pH is a crucial function in biological systems.
• Gastric esophageal reflux disease (GERD) is a
pathological condition that results when the esophagus is
exposed to the acid of the stomach.

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 Applications of Biochemistry
A common example of a pathological
modification of environmental pH is
gastroesophageal reflux disease, or Also known as Acid Reflux
GERD. A chronic digestive disease, GERD
develops when stomach acid refluxes into
the esophagus. The backwash of acid,
frequently experienced as heartburn,
irritates the lining of the esophagus by
exposing the tissue to very acidic
conditions (pH 1 to 2). GERD can cause
chronic inflammation in the esophagus
that can lead to complications, including
esophageal ulcers and esophageal
cancer. Risk factors for GERD include
smoking and obesity.

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 Water Ionizes to a Small Extent

• The equilibrium constant Keq for the dissociation of water

is given by

• Kw, the ion product of water, is

DID YOU KNOW?
given by
In chemistry, equilibrium is the
KW = Keq × [H2O] condition in which the
concentrations of reactants and
• This can be simplified to products have no net change
KW = [H+][OH−] over time.

• The pH of any solution is defined as

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 An Acid Is a Proton Donor, Whereas a
Base Is a Proton Acceptor
• Acids ionize to form a proton and a base.

• The chemical formed upon ionization of an acid is

called its conjugate base.
• Conversely, the acid formed when a base binds a
proton is called its conjugate acid.

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 Acids Have Differing Tendencies to Ionize
• The ionization equilibrium of a weak acid is given by

• The equilibrium constant for this reaction is

• The larger Ka, the stronger the acid.

• We can derive a relationship between pH and the ratio of acid to
base by first manipulating the formula for the ionization of the acid.

• Taking the logarithm of both sides gives

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 Acids Have Differing Tendencies to Ionize

• The log(1/Ka) is the pKa of the acid.

• Substituting pH for log(1/H+) and pKa for log of (1/Ka) yields the
Henderson–Hasselbalch equation:

• When [A–] = [HA], log ([A–]/[HA]) equals 0 and pH = pKa.

• For any acid, at pH > pKa, [A–] predominates.

• At pH < pKa, [HA] predominates.

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Diagram Depicting a Variety of Conjugate
Acid–Base Pairs

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 Buffers Resist Changes in pH

• An acid–base
conjugate pair resists
changes in the pH of
a solution.

• In other words, it acts

as a buffer. A buffer is
most effective at a
pH near its pKa.
Figure 2.12 The titration curve for
acetic acid. Notice that near the pKa
of acetic acid, the pH does not
change much with the addition of
more base 25
 Buffer Action between weak base and
strong acid

Figure 2.13 Buffer action. The addition of a strong acid—say, 1 M HCl—to pure water
results in an immediate drop in pH to near 2, as the blue line shows. In contrast, the addition
of acid to 0.1 mM sodium acetate (Na+CH3COO−) results in a much more gradual change in
pH until the pH drops below 3.5, as shown by the red line.
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The Titration Curves of Three Important
Weak Acids

Figure 2.14 Notice that the regions of buffering capacity differ.

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 Buffers Are Crucial in Biological Systems
• The pH of blood is buffered by the conjugate acid-base
pair of carbonic acid and bicarbonate (H2CO3/HCO3–).
• The CO2 produced in aerobic respiration (Chapter 19)
reacts with water to produce the weak acid carbonic
acid. Carbonic acid then ionizes to produce a proton and
bicarbonate.

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 Making Buffers Is a Common Laboratory
Practice

• Buffers that resist pH changes over a range of pH values

can be made by using the Henderson–Hasselbalch
equation and simple chemistry.

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