CHEM 440

CHEM 440
Biochemistry I J. D. Cronk Syllabus Previous lecture | Next lecture
Lecture 2. Life, thermodynamics, and water

Friday 2 September 2016
Life and thermodynamics. The geometric, electronic, and bulk properties of

water relevant to biological systems. Noncovalent (weak electrostatic) forces.
The hydrophobic effect: Nonpolar and amphipathic species in water.
Thermodynamic analysis of the hydrophobic effect. Colligative properties;
osmosis, diffusion, and dialysis.
Reading: Voet, Voet and Pratt, 4th ed. (VVP4e); Chapters 1 and 2.
Summary
Biological systems are subject to the same physicochemical laws that govern non-living
systems. It is important therefore to understand explicitly how basic thermodynamic
principles are applied in biochemistry and biology. Therefore we undertake a review of
the thermodynamics appropriate for application to biological systems. For example, we
can usually treat processes in living organisms and tissues as occurring at constant
pressure and temperature, with little or no change in volume. Thermodynamic methods
valid in general for such processes will be useful in this specific biological context. To
illustrate, the free energy function is used to interpret both the formation of a DNA
double helix from separate single strands and the hydrophobic effect. The physical
and chemical properties of water are of great relevance to biochemistry. The
hydrophobic effect, an especially important case, is a consequence of the properties of
water and aqueous environments.
A brief review of chemical thermodynamics
The first law of thermodynamics is equivalent to the law of conservation of energy.

For example, in a process occurring at constant pressure and volume involving exchange
of heat between a system and its surroundings, the enthalpy change (ΔH) for the
system will be exactly balanced by ΔH for the surroundings so that the net ΔH is zero.
Conservation of energy applies to all processes, but says nothing about the direction
that a process obeying it will operate in. A further aim of thermodynamics is to be able
to predict whether or not a process will occur within a system without the input of
energy from the surroundings. If so, the process is said to be spontaneous. In order to
make such predictions, it is first necessary to define entropy, S. Roughly speaking,
entropy is a measure of the number of ways that energy can be distributed within a
system. The second law of thermodynamics states that the total entropy of the
system and surroundings always increases for a spontaneous process.
For biochemical systems, it would be convenient to have a means to evaluate whether or
not a process is spontaneous without having to consider the surroundings. The state
function known as Gibbs free energy, G (sometimes referred to simply as free
energy), which is defined by the equation G = H − TS that combines the state functions
enthalpy and entropy (T is the temperature in K), is the key quantity that allows us to
make this determination. The change in free energy of a system for a process occurring
at constant temperature is given as ΔG = ΔH − TΔS. A spontaneous process corresponds
to a decrease in the free energy of the system.
Key thermodynamic equations for biochemistry
The relationship between free energy and

chemical equilibrium is one of the most
important results of chemical
thermodynamics, and it retains this status in
biochemistry. The equations at right, (1) -
(4), are the key thermodynamic relations that
are essential for you to know. The equations
are general in form, so it is also necessary to
understand how they are used in specific
examples. The quantity ΔG°′ is the
biochemical standard free energy
change, which is based on the definition of a biochemical standard state. In all these
relations, the prime [′] denotes biochemical standard conventions in order to clearly
distinguish from chemical convention (physical chemistry standard conventions) for
which all the relations above are the same, sans prime symbol. The key distinction to
bear in mind for these conventions is for the standard hydrogen or hydronium ion
concentration. While the physical chemistry standard [H+] is 1 M (just like for any solute
species), in the biochemical convention the standard [H+] is specifically defined as 1 ×
10−7 M, or pH 7.
Properties of water
Since so many of the processes of living organisms occur in aqueous media, it is of

fundamental importance to understand physicochemical properties of water. Given the
complexity of the liquid state, especially that of water, accomplishing this is much more
of a challenge than one might first imagine. Let us nonetheless at least consider some of
the outstanding features of water, and try to get at what are the most relevant and
important from a biochemical viewpoint. With water making up most of the weight of
typical organisms, it is appropriate to think of water as the solvent of life, and we'll
examine the properties of water as a solvent and the principles of aqueous solution
chemistry.
One very notable feature of water is its great capacity and tendency to form hydrogen
bonds with itself and solutes with hydrogen-bonding ("H-bonding") groups. This
underlies water's great cohesiveness, manifest in some unusual properties such as high
melting point, boiling point, and surface tension. Molecules with a number of functional
groups capable of hydrogen bonding with water tend to be quite soluble in water. Since
water is a polar molecule, it also interacts well with ions and polar molecules.
Water is unquestionably an excellent solvent for many polar and charged species, yet it
is a rather poor solvent for nonpolar molecules. Amphipathic molecules such as
detergents or phospholipids can form micelles or bilayer structures in which the
nonpolar portions of the amphipathic molecules are are sequestered together, while the
polar or charged portions are exposed to the aqueous surroundings.
What is the basis of the solvent properties of water? The interactions of water with ions,
dipoles, and H-bond acceptors and donors are strong. The dipole of water interacts
strongly with charges, and we should note here that the rather large dielectric constant
of water weakens electrostatic forces between charged solute groups. Water molecules
ought to be able to interact somewhat favorably with nonpolar species by van der Waals
attractions.
If we are to understand water as a solvent, we will have to venture beyond "like

dissolves like" with some more careful analysis. If we imagine a process in which initially
separated water and solute mix, the thermodynamics are tricky because although water
interacts so well with solutes, its interacts with quite well with itself, as may some
solutes such as salts. Thus, for the case of an ionic solid that dissolves endothermically,
ΔH of the process is not favorable, but ΔS of forming the more dispersed solution is
positive (and thus favorable). For solutes with nonpolar character, on the other hand, the
interactions between solute molecules in the undissolved initial state and between solute
molecules and water molecules in the dissolved state are both considerably weaker. Yet
it is still possible for the solute-solvent interactions to be a little better than the
interactions in the separated materials. The enthalpy change (ΔH) of the process is then
slightly negative; even so, the solubility may still be quite low, indicating that ΔG is
positive. We would be led in this case to the counterintuitive conclusion that ΔS is
negative. This large negative ΔS for the formation of aqueous solutions of nonpolar
solutes is the basis of the what is usually called the hydrophobic effect.
Chemical properties of water: Acid-base chemistry
Please review these topics: Autoionization of water and pH. Acids, bases, and buffers in
aqueous systems.
In biochemistry, especially in discussion of amino acid and protein chemistry, we will

make frequent use of the concept of pKa of an ionizable group. Starting with the
chemical equation for the ionization of a weak acid (see figure below, left), the acid
dissociation equation (top equation), we derive the usual equilibrium expression,
giving the equilibrium constant the special designation Ka (2nd equation). Taking the
negative logarithm (base 10) of both sides of this equation leads to a definition of pKa in
terms of pH and the log(10) of the ratio of concentrations of the anionic conjugate base
and unionized acid (not shown).
This equation can be rearranged to express pH in terms of pKa and the log ratio of
conjugate base to acid, yielding what is known as the Henderson-Hasselbalch equation
(3rd equation, at left).
These equations are very useful for buffer
calculations and in determining the
proportions of conjugate pairs that exist at a
given pH. It is easy to see, for instance, that
at a pH equal to the pKa of a weak acid HA,
the population of unionized acid molecules is
exactly balanced by the number of molecules of the conjugate base. At a pH above that
of the pKa, the anionic form will predominate, and at low pH, the unionized acid species
is favored.
Exercise: Derive the Henderson-Hasselbalch equation for the ionization equilibrium BH+
= H+ + B:. Which form predominates at low pH? Compare this equilibrium with that for
the dissociation of the neutral acid HA above, and consider the effect of transferring the
ionizable group from an aqueous environment to a non-polar environment. Are the
respective pKa's affected equally, or is one affected more than the other? Explain.
Learning objectives
Recount the properties of water and how they relate to biochemical and biological
phenomena.
Perform all relevant applications from study of acid-base equilibria (pH calculations for
strong acids and bases, weak acids or weak bases, buffers; treatment of polyprotic
systems, Henderson-Hasselbalch equation, definition and interpretation of titration
curves).
State and briefly discuss the significance of the first and second laws of
thermodynamics.
Recognize the applicability of the free energy function to biological systems.
Clearly distinguish between thermodynamic and kinetic views of processes.
Recall that systems at constant temperature and pressure spontaneously approach an
equilibrium characterized as the minimum of the free energy function, G. Equivalently,
ΔG = 0 at equilibrium.
Define the biochemical standard state and the biochemical standard free energy
change, ΔG°′.
Recall the key thermodynamic relations, and apply them to biochemical processes,
primarily (but not limited to!) chemical reactions occurring at constant temperature
and pressure.
Page updated 9-3-2016
References
1. Donald Voet, Judith G. Voet, Charlotte W. Pratt. Fundamentals of Biochemistry, 4th

ed.; Ch.1 & Ch.2.
2. Nelson DL & Cox MM. Ch.2 - Water. Lehninger Principles of Biochemistry (4ed, 2005.
Freeman)
3. Creighton, TE. Proteins: Structure and Molecular Properties (2nd ed, 1993. Freeman).
4. Asimov, I. Life and Energy (1962, Doubleday). This is a classic by my lights, worth
reading if you can find it. Reading this book in high school convinced me to become a
biochemist!

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Biochemistry I J. D. Cronk Syllabus Previous lecture | Next lecture

Lecture 2. Life, thermodynamics, and water

Life and thermodynamics. The geometric, electronic, and bulk properties of

A brief review of chemical thermodynamics

The first law of thermodynamics is equivalent to the law of conservation of energy.

Key thermodynamic equations for biochemistry

The relationship between free energy and

Since so many of the processes of living organisms occur in aqueous media, it is of

If we are to understand water as a solvent, we will have to venture beyond "like

Chemical properties of water: Acid-base chemistry

In biochemistry, especially in discussion of amino acid and protein chemistry, we will

1. Donald Voet, Judith G. Voet, Charlotte W. Pratt. Fundamentals of Biochemistry, 4th

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