Tymoczko • Berg • Stryer

Biochemistry:
A Short Course
Third Edition

CHAPTER 2
Water, Weak Bonds,
and the Generation
of Order Out of
Chaos

© 2015 W. H. Freeman and Company

Chapter 2 Outline
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.

Water is a polar molecule, with the oxygen atom carrying a slightly negative charge and
the hydrogen atoms carrying slightly positive charges.
The polarity of water allows the formation of hydrogen bonds between 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 the hydrophobic effect.
 Electrostatic interactions are also called ionic bonds or salt bridges.

The energy of an electrostatic interaction between two charges is give 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 a proportionality constant.

The dielectric constant is 1 in a vacuum, and 40 in water. Thus, water weakens

electrostatic interactions.
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.
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
one molecule will induce complementary asymmetry in a nearby molecule.
 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.
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.

Membrane Formation is Powered by the Hydrophobic Effect

Phospholipids have hydrophilic and hydrophobic properties. When exposed to

water, phospholipids form membranes.
Protein Folding is Powered by the Hydrophobic Effect
 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.
 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.
 Water Ionizes to a Small Extent

The equilibrium constant Keq for the dissociation of water is given by:

Kw, the ion constant of water, is given by:

This can be simplified to:

 Water Ionizes to a Small Extent

The pH of any solution is defined as:

 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.
 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.

 Acids Have Differing Tendencies to Ionize

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:

 Acids Have Differing Tendencies to Ionize

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

Substituting pH for log(1/H+) and pKa for log of (1/Ka) yields the
Henderson-Hasselbalch equation:
 Acids Have Differing Tendencies to Ionize

When [A-] = [HA], log ([A-]/[HA]) equals 0, and

pH =pKa.

For any acid, at pH > pKa, A- predominates.

At pH < pKa, HA predominates.
 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.
 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.
 Making Buffers Is a Common Laboratory Practice

Buffers that resist pH changes over range of pH can be made by using the
Henderson-Hasselbalch equation and simple chemistry.