Chapter 2

1. He is wise; all wise men are happy; therefore he is happy. The sky is green; all green
objects are hard; therefore the sky is hard. This sentence is in a book; this book was
published by X; therefore this sentence was published by X.
Note that, although the second syllogism seems rather strange conclusion, the
conclusion does at least follow logically from the premises. Some green objects may
be hard, but grass usually is not! Thus we see that the degree to which we may be
prepared to accept the conclusion of an argument depends very much on the
plausibility of the assumptions, the premises.
2. According to the Shorter Oxford English Dictionary, kinetic is defined as of,
pertaining or relating to, motion: potential means existing in a positional form, not
as motion. Kinetic is of Greek origin. It comes from kinetikos, meaning moving.
Potential derives from the Latin word potentia, potency.
3. This is a tough one. Every living organism is an open system. There are no known
exceptions to this rule. Another might be that all proteins are made of L-amino acids.
D-amino acids exist, but the proteins of which living organisms are not known to
incorporate them (but see Chapter 9).
4. The zero point energy is arbitrary. For example, with gravitational potential energy it
makes no difference to calculations of energy differences whether we consider the
surface of Earth at a particular location, sea level, or the floor of the ocean as the zero
point of energy (neglecting small differences in the acceleration due to gravity). In
each case, the change in potential energy for an object is mgz, where m is the mass of
the object, g is the gravitational acceleration, and z is the height of the object relative
to the zero point energy. As we shall see in Chapter 4, one can do relatively straightforward laboratory experiments to determine the energy difference between the
folded and unfolded conformations of a protein. In contrast, measurement of the
absolute energy of either conformation is effectively impossible.
5. Heres an example:

Uiii = 2
i

ii
Ui2 = 2

U1i = 1
1

Uii2 = 4
2

U12 =3

All values are in the same arbitrary units of energy.

2001-2007 by D.T. Haynie. All rights reserved.

6. The capital Greek letter represents a measurable change in magnitude of some

observable quantity, e.g. temperature of a system. It is used with state functions to
indicate that the value is independent of path. The value of a state function depends
only on the physical state of the system. Path functions are different in kind. A
schematic representation of a path function is given in Fig. 2.5. Although the end
points are the same in panels A and B, the area below the curves is different,
reflecting the differences in path. Path function means a function whose value is
depends on the path. In the context of Fig. 2.2, q and w would not necessarily be the
same for the three paths between state 1 and state 2.
7. The units of Fx are N m. The units of pV are Pa m3 = N m-2 m3 = N m. A
pressure is a force per unit area.
8. U = q + w. q = 0 and w = 96 kJ, so U = 1.96 kJ. This much energy was
expended. We assume that the heat transferred in this process is negligible. If the
womans initial position was at the zero point of potential energy, her final point (4 m
higher) has a potential energy of 1.96 kJ.
9. The energy expended = mgz = 70 kg 9.8 m s2 6 m = 4.1 kJ. This is the
minimum energy required to climb the stairs. The energy conversion process in the
body does not involve complete oxidation.
On the surface of the moon, the energy is 4,116 J 1.6 m s2 / 9.8 m s2 = 670 J.
10. From Chapter 1, Exercise 13, the energy of oxidation of 11 g glucose = 171.6 kJ.
z = w / (mg) = 171.6 kJ / 70 kg / 9.8 m s2 = 250 m.
11. w = pexV = 121 kPa 50 cm2 15 cm 106 m3 / cm3 = 91 J.
12. No change in temperature for the non-adiabatic cases, as heat is transferred from
(endothermic) or to (exothermic) surroundings which are effectively infinite in extent.
In an adiabatic container, an exothermic reaction will increase the temperature and an
endothermic reaction will decrease it.
13. For an adiabatic process q = 0, so U = w. In addition to exchanging no heat with its
surroundings, an isolated system can do no work; hence U = 0. For a process that
occurs at constant volume, w = 0, since only p-V work can be done; thus, U = q.
From Eqn. 2.7, H = qp. If, in addition to occurring at constant pressure, the process
is also adiabatic, q = 0; giving H = 0.
14. Eqn. 2.9 is H = U + (nRT). U = 673 kcal mol1. n = 0, so H = 673 kcal
mol1. The bacteria give off less heat in consuming glucose than is measured in a
bomb calorimeter because they do not completely oxidize the carbohydrate to carbon
dioxide and water.

2001-2007 by D.T. Haynie. All rights reserved.

15. If the laws of physics were not (approximately) constant in time, the energy required
to climb a flight of stairs on one day would be different from that on another day.
One could also say that because we believe that the laws of physics to be the same
from one day to the next, a physical process carried out one day should give identical
results to a physical process carried on a different day, assuming that all other aspects
of the process are identical. In view of this, it is said that the law of the conservation
of energy is related to the time-symmetry of the electromechanical laws of physics.
16. Because energy is conserved, (60 kg 37 oC 0.8 kcal/kg) + (0.25 kg 62 oC 1
kcal/kg) = 60.25 Tf 0.8 kcal/kg. Solving for Tf gives 37.2 oC. Body temperature
is raised by 0.1 oC. Energy is transferred from the water to the stomach and thence to
the rest of the body. The First Law is taken into account in balancing the energy on
both sides of the equation. Tf is determined by the requirement that energy be
conserved.
17. Eqn. 2.13 is H = CpT. The enthalpy difference between the folded state of a
protein at two temperatures is Hf,2 Hf,1 = Cp,f(T2 T1). The enthalpy difference
between the unfolded state of a protein at two temperatures is Hu,2 Hu,1 = Cp,u(T2
T1). Subtraction of the first equation from the second one gives (Hu,2 Hf,2) (Hu,1
Hf,1) = (Cp,u Cp,f) (T2 T1). This can be rewritten as Hd(T2) = Hd(T1) + Cp,d(T2
T1), where the subscript d stands for denaturation. This is Eqn. 2.14.
18. No, polar moieties have a negative Cp,d, though the magnitude per unit area is
smaller for polar surfaces than for non-polar ones. Polar surfaces do not interact with
water, a highly polar solvent, in the same way as non-polar ones.
19. Eqn. 2.14 tells us that Hd(T2) = Hd(T1) + Cp,d(T2 T1). Using the data given in
the statement of the problem, we have
a) Hd(78 oC) = Hd(25 oC) + Cp,d(78 oC 25 oC)
= 52 kcal mol1 + 1500 cal mol1 K1 53 K
= 130,000 cal mol1
b) Hd(10 oC) = Hd(25 oC) + Cp,d(10 oC 25 oC)
= 52 kcal mol1 + 1500 cal mol1 K1 35 K
= 500 cal mol1
We see from part b) that the enthalpy of unfolding can be negative. This means that,
under suitable conditions heat is absorbed on protein folding. As will become clear in
Chapter 4, however, the entropy of folding is so favorable under such conditions that
the protein does fold.
20. Hd(Tm) v. Tm is nearly a straight line. This corresponds to Cp on protein unfolding.
Linear regression gives a best-fit value of 2.88 0.01 kcal mol1 K1.
Hd(Tm) v. pH, on the other hand, is low at low pH, high at mildly acidic pH, and
low at neutral pH. This would suggest that protein stability - propensity to unfold - is
2001-2007 by D.T. Haynie. All rights reserved.

influenced substantially by changes in pH. This would presumably reflect changes in

protonation/deprotonation of amino acid side chains.
21. The background signal comes from protonation of the phosphate group.
The average heats of injection per mol of peptide are
Asp: 72 cal/(0.64 mM 10 l) = 1.1 kcal mol1
Glu: 54 cal/(0.57 mM 10 l) = 0.95 kcal mol1
His: 55 cal/(0.64 mM 10 l) = 6.9 kcal mol1
Note that His > Asp Glu.
Tripeptides are used to decrease effects of the amino and carboxyl groups.
Pentapeptides would be even better than tripeptides as far as end effects are
concerned, but because they are less soluble than tripeptides they might be harder to
work with under the desired experimental conditions.
One could account for the heat effect of protonation of the peptide termini by doing
control experiments with a small peptide that would exhibit no side chain protonation
effects, for example Gly-Gly-Gly. One would still to assume, though, that
protonation at a terminus was not influence by the central side chain or its charge.
This would not account for the heat effect of solvating the side chains, but because
the peptides were dissolved in aqueous solution to begin with and the heat of dilution
would be small, this contribution could probably be neglected or otherwise shown to
be negligible.
22. No one set of five buffers is objectively best. The choice of a buffer is based on the
requirements of an experiment. General principles are nevertheless involved in the
choice of a buffer for thermodynamic studies. One set of useful buffers is the
following:
Buffer
Acetate

Cacodylate

Imidazole

2001-2007 by D.T. Haynie. All rights reserved.

Rationale
If the experiment is done at constant
temperature and in a pH-regime where
acetate buffers well, acetate is an
excellent choice: the enthalpy of
protonation is very small.
Same as for acetate. One must be
especially careful with this buffer,
however, as it is poisonous.
This buffer is very good for situations in
which protonation or deprotonation of
histidine side chains makes a substantial
contribution to the enthalpy of reaction.

Phosphate

PIPES

Using
imidazole
in
the
buffer
compensates for the heat effect of
ionization of the side chain.
Same as for acetate. This is a popular
buffer for experiments near neutral pH.
Note, however, that the heat capacity
change of protonation is large.
Same as for acetate.

23. A biochemist might also require that the standard state be defined at a specific pH.
This is because most biochemical reactions occur at or near pH 7.0, making it a
convenient standard.
24. The unfolding of a protein is like the melting of an organic crystal in several ways. In
a crystal, individual units, e.g. individual urea molecules, are packed very close to
each other, forming a lattice. As urea molecules are uncharged, a urea crystal must be
held together by van der Waals interactions. The situation is similar in the core of a
protein, where the atoms of amino acid side chains are in close contact. Moreover,
just as the relative position of individual units is effectively constant in a crystal, so
too the core of a protein molecule is relatively rigid under native conditions. When
heat is added, vibrations increase, and when these are large enough the orderly array
breaks down. If the crystal is pure, melting occurs over a very narrow range of
temperatures. Similarly, the vibrations of amino acid side chains increase in
magnitude when a protein solution is heated. There may be larger-scale motions as
well, as the atoms of a protein form a complete, covalently-linked unit. When so
much heat has been added that the van der Waals forces are no longer great enough to
prevent large-scale fluctuations, the protein unfolds, often cooperatively. This results
to a greater or lesser degree in the complete solvation of the polypeptide chain.
Exceptions to this rule do occur and these will be discussed in Chapter 5.
25. Analysis of the crystallographic structure of baboon -lactalbumin has revealed that
several water molecules remain bound to the calcium ion in the binding site. That is,
the binding process removes only some of the water molecules in the solvation shell.
The enthalpy of solvation of a particular water molecule depends on how many
molecules are already bound to the ion. The enthalpy change is greatest for the first
water molecule and progressively smaller for subsequent ones. The enthalpy
difference between the bound and unbound states of calcium in -lactalbumin is
therefore only a few kilocalories per mole.
26. It seems practically impossible to design an experiment to test whether the First Law
applies to all living organisms. Why? We do not know if living organisms are
peculiar to Earth. New species are still being discovered, so we do not even know of
the existence of every species on Earth. And even if we did know of all species and
where each individual was located, how could one test whether the First Law applies
to all individuals? The best one could possibly do, it seems, would be to select
individuals for careful examination and then assume that what is true of them is also
true of all individuals. One could choose individuals representing major classes of
2001-2007 by D.T. Haynie. All rights reserved.

organism. The experiments would have to involve a means of quantifying and

comparing energy input (solid food, liquid food, gaseous food, heat) and energy
output (solid waste, liquid waste, gaseous waste, heat).
27. The enthalpy change on protein unfolding is usually large and positive under
normal conditions (T > 0). Heat must be absorbed for the protein to unfold. Heat
energy is required to disrupt the bonds by which the folded protein structure is held
together. These include hydrogen bonds, hydrophobic bonds, or van der Waals
interactions, and salt bridges, or ionic interactions. Something similar occurs when
ice cubes are used to cool a drink. The solid water absorbs heat from its surroundings
(a warmer liquid), resulting in an increase in the temperature of the ice. Eventually,
the melting point of ice is reached, and the hydrogen bonds that hold the ice together
are broken. This process occurs first on the exterior of the cube and moves inward
until all the ice is gone. As the liquid surroundings are cooled, they are also diluted.
28. The conservation of matter is a statement of the First Law of thermodynamics, but
only under certain conditions. The conditions are that all nuclei of a system are
absolutely stable. Modern physics, however, has revealed that unstable atomic nuclei
can decay. Nuclear events are not usually of direct interest to the biological scientist,
and so nuclear energy need not be taken into account in most calculations. For
instance, in attempting to rationalize the result of a bomb calorimetry experiment, one
supposes the conservation of matter holds. In light of this, it is particularly interesting
that the energy living things depend on comes from the Sun, which radiates nuclear
energy in the form of electromagnetic radiation.
29. The change in the number of moles of gas is 0.5:
1 (carbon dioxide) + 1 (diatomic nitrogen) 1.5 (diatomic oxygen) = 0.5
Thus, H = U + 0.5RT. Plugging in what is known and solving for H gives
H = 152300 cal mol1 + 0.5 1.9872 cal mol1 K1 298 K
= 152 kcal mol1
The difference between H and U for this reaction is less than 1%.
30. The atomic weights of oxygen and hydrogen are, respectively, 16 g mol1 and 1 g
mol1. So, the work done on lifting a single water molecule a distance of 300 m on
the surface of Earth is
w = Fx = max = 0.018 kg mol1 / (6.02 1023 mol1) 9.8 m s2 300 m
= 8.8 1023 J.
Where does the energy come from for the tree to accomplish this?
31. There are several ways in which one can show that heat is not a fluid in the sense that
water is a fluid. Here are three of them. One, heat can be transferred through
2001-2007 by D.T. Haynie. All rights reserved.

vacuum. This is essentially what happens when the Sun transfers its heat energy to
Earth. Two, the mass of a block of material is independent of its temperature. Three,
an indefinite amount heat can be extracted from a solid by friction.
32. Humans expend energy in a variety of ways. There are four major classes of energy
loss: solid matter, liquid matter, gaseous matter, and heat. Solid matter is lost by
defecating, urinating, vomiting, exhaling and so on. Further metabolism of these
solid materials is possible, but it is generally more advantageous for humans to
expend energy to locate less degraded sources of food energy than to continue to
metabolise such waste products. We also lose heat energy to the environment. The
rate of loss of heat energy depends of course on the temperature. We use clothes to
help regulate the rate of loss of heat energy. We also expend energy by perspiring.
The salty water covering ones body after a vigorous workout is not condensation
from the atmosphere but a bodily secretion. This water helps to cool the body by
absorbing heat. This works particularly effectively because sweat is salty, and the salt
increases the amount of heat energy water will absorb before evaporating (see
Chapter 5).

2001-2007 by D.T. Haynie. All rights reserved.