Notes to Bio115 , Winter 2016, Lecture 1

Hinrich Boeger
Introduction
This lecture will provide you with an introduction into molecular biology and, as the title
indicates, we shall focus on eukaryotes whenever necessary, although many fundamental
insights have been attained by research on bacteria. Indeed, the molecular biology of bacteria
and eukaryotes is essentially the same despite many significant differences suggesting a
common ancestor for all of life on earth.
I shall not follow any particular text book, for I suppose that you are perfectly capable of
reading a text book on your own, without me. Of course, essentially all of the material
presented here is covered by any text book on molecular biology. Several good text books are
available e.g. Molecular biology of the cell by Alberts et al., Molecular biology of the
gene by Watson et al., or Molecular biology, principles and practice by Cox et al.;
Molecular biology by Weaver is a rich source for many historical experiments. And I would
like to encourage you to also read the relevant chapters in any text book of your choice;
different books work for different people. This lecture, however, is mine; it thus presents
molecular biology as I understand it, from my point of view. All slides of this lecture together
with extensive notes will be available via your eCommons account (Resources).
There are four major themes that run through this lecture. Three of which stress that
biology is chemistry. The enzymes of molecular biology catalyze essentially two types of
chemical reaction mechanism. Two additional principles are important for understanding the
biochemistry of these enzymes: thermodynamic coupling and kinetic proofreading; both will
require us to review some principles of thermodynamics.
The fourth theme is philosophical; namely and this is the critical insight Karl R.
Poppers (1902-1994) that knowledge grows by inventing explanatory conjectures and
testing them, logically and experimentally; experimental observations tell us which theoretical
possibilities are false; i.e. we learn from experience by trial and error, by refutation of our
mistaken assumptions ('critical rationalism').
Molecular biology has been extraordinarily successful in its first two decades precisely
because many of its founders sought explanatory conjectures, and refutations; they proceeded
in a manner contrary to inductivism, the mistaken but widespread idea that scientific theories
grow out of and are justifiable by the methodical collection of data (see below). This is the
philosophical thesis of my lecture.
I thus hope that this lecture will also inspire you to reflect on questions such as these:
What is science? What are its aims? How does it work? What are the logical condition for the
growth of knowledge? The consideration of such questions is virtually absent from scientific
curricula and textbooks. I believe this is a great shortcoming of science education. The few
remarks that I will be able to make in this lecture will hardly suffice to rectify this deficit. But
there is nothing that stops you from continuing on this path on your own. I hope you will.
Slide 4

Inductivism. Common sense holds that the human mind, at least initially, is a blank slate, an
empty bucket. Knowledge enters it by observation. Truth is manifest to everyone who is
willing and able to see it. Scientific laws or theories are discovered by repeated observation;
and therefore reducible to observation. Observed regularities are extended to instances of
which we have no experience; i.e. it is claimed that the future is like the past. And the more
often we have made a specific observation in the past, the more confident we may be that the
same observation will be made in the future. In short, empirical evidence provides
(probabilistic) support for conclusions that go beyond the available evidence. This notion is
sometimes called inductive probability or inductive logic. It aims at the verification of
theories (thus, positivism).
The notion of inductive probability was first introduced by Pierre-Simon Laplace (17491827). He calculated the probability that the sun will rise tomorrow, given that it has risen n
number of days in the past. According to Laplace, this probability is given by (n +1) / (n + 2)
(Laplace rule of succession).
Despite its popularity, inductivism is a mistaken. The reasons are many:
(i) Truth is not manifest whatsoever. Rather, truth is difficult to attain; and even if we
were in its possession, we have no means of knowing so. All observations, including all
measurements, are impregnated by theory, they are theory-laden; empirical observations can
be, and often are, false. Thus, inductivism fails before taking its first step (Popper, 1972). The
mistaken belief that truth is manifest (the common sense theory of knowledge) begs for
authoritarian answers, for it has to explain falsity (Popper, 1963).
(ii) Even if our observations were unproblematic, scientific theories cannot be justified by
empirical evidence. The reason is simple: Proof would require an infinite number of
observations; but our observations are always finite; and they pertain to the past and present,
but never the future.
(iii) Positivists address this latter problem by claiming that repeated past observation
justifies our expectation of future observations (of the same kind). However, this principle of
induction is untenable. It leads to absurd result. I mention only one here: that I will be alive
tomorrow is, according to Laplace, more probable today than it was 10 years ago, for I have
observed repeatedly over those 10 years indeed without exception that I was alive the
following day. As desirable as this conclusion might be, nobody seriously believes this
conclusion to be true. The same argument would have applied to many people who are now
dead, revealing that the argument is false. The notion that the future is like the past has been
refuted many times. The rule of succession, applied to the probability of the suns ascension
tomorrow, yields a prediction that contradicts modern physics.
(iv) The most important objection against inductivism, perhaps, is that inductivism does
not seek explanation, but data. However, data, no matter how many, dont explain anything;
theories do, namely the data.
Thus, theories can neither be proved or justified, in any way or by any number of
observation. As explanations theories always transcend the data and therefore cannot be
obtained from observation. Theories are inspired guesses. As such, neither observation nor
reason may be regarded as sources of our knowledge or theories (Popper, 1963). Even
regularities, the object of discovery of induction, are generally observed only after they have
been anticipated what we see, or not, is a function of our conscious and unconscious

expectations. The latter are often innate. Induction, the formation of a believe by repetition, is
a myth (Popper, 1972).
If empirical evidence cannot be used to verify hypotheses, or attain theories, then, what is
its role in science? After all, we think of science as a discipline in which empirical
observation play an important role. The solution of this problem is 'critical rationalism'.
Critical rationalism. Briefly, critical rationalism holds that we acquire knowledge by
inventing theories and criticizing them, logically and empirically (by experimental testing), in
order to force decisions between them. Empirical observations do not tell us which theories
are true, but which ones are false. The growth of knowledge or the learning process is
not a repetitive or a cumulative process but one of error-elimination. It is Darwinian selection,
rather than Lamarckian instruction (Popper, 1972).
Thus, in as much as our aim, qua scientists, is to attain knowledge, we must propose
explanatory theories and device experimental tests that may falsify them. Because
explanations transcend the data, they are generally independently testable; i.e. they allow for
predictions other than the observations that they were originally invented to explain.
Only those hypotheses or theories contribute to the growth of knowledge that allow for
the deduction of consequences that potentially can stand in conflict with experimental
observations; hypotheses must be falsifiable or testable. The larger the set of its predictions
that may clash with observation (the empirical content of a theory), the better the theory.
Empirical evidence contributes to the growth of knowledge only by refutation of theoretical
possibilities; we learn from experience by refutation.
Falsification, contrary to verification (proof), requires no more but a finite number of
observations that contradict theoretical expectation. (Logically, a single observation is
sufficient for refutation.) From false conclusions follows the falsehood of one or more their
premises (modus tollens of logic). We must seek falsification, which is possible, and not
verification, which is not.
A theory that has withstood critical testing is said to have been corroborated. We may
accept a corroborated theory, but only tentatively, for it too may be shown to be false and may
be overthrown by a better theory in the future, namely a theory that explains more (because it
has a larger empirical content) and corrects the errors of the earlier theory. (Correction may
even include earlier empirical observations.) All of human knowledge, including textbook
knowledge, is conjectural; it consists, at best, of hypotheses that have proved their mettle,
that have been corroborated experimentally (Popper, 1963).
Against this theory it has been objected that theories cannot be falsified either, because of
the conjectural nature of our observations. (Observations are theory-laden.) If a conflict arises
between theoretical prediction and experimental observation it is not known whether our
theory is false, or our observation, or any other background knowledge that we used in the
process (e.g. the assumption that the scientist who conducted the experiment is competent as
well as honest). Thus, experiments always test the whole system of human knowledge, rather
than any specific theory. (This is sometimes called the Duhem-Quine problem.) This
criticism is countered by approaching a scientific problem with two or more competing
theories, i.e. with a plurality of theoretical solutions. Then our experimental tests decide
between competing systems that differ only over the theories at stake (Popper, 1963). If the

predictions of both theories, say A and B, disagree with the data, then we will have to
critically reanalyze the background knowledge (e.g. the data). But if our test results conform
to the prediction of theory A, but not B, then we consider B refuted, rather than our
background knowledge. Thus there may be no falsification before the emergence of a better
theory (Lakatos, 1970). This is always so in the case of probabilistic theories; refutation and
corroboration are closely linked (Boeger, 2014).
References
Boeger, H. (2014). Nucleosomes, transcription, and probability. Molecular biology of the cell
25, 3451-3455.
Lakatos, I. (1970). Methodology of Scientific Research Programmes; in Criticism and the
Growth of Knowledge; edit. Lakatos, I. Musgrave, A. (Cambridge University Press).
Popper, K.R. (1963). Conjectures and refutations (New York: Routledge Classics).
Popper, K.R. (1972). Objective knowledge (Oxford: Clarendon Press).
Slide 5
Nothing in molecular biology makes sense without an appreciation of the function of
enzymes almost all of which are proteins and their structural properties. I shall therefore
begin this lecture with considerations about catalysis, and protein structure. Since we start
with proteins rather than DNA, we shall follow, to some extent, the central dogma (shown in
this slide) in reverse order, i.e, from proteins to genes. This order also roughly traces the
historical development of molecular biology.
Slide 6
As you will have learned in your cell biology class, all of live is composed of cells, either
of solitary cells, or of many specialized cells derived from a single cell by cell division. (This
fundamental biological theory was first suggested by the physiologists Theodor Schwann in
1839.)
This lecture is dedicated mostly to one particular type of cell, the eukaryotic cell (gr.
proper, nucleus). As you already know, eukaryotic cells are distinguished from their
prokaryotic relatives by a set of characteristic features; for instance, the cell nucleus from
which they derive their name, chromosomes, the Golgi apparatus, mitochondria, the
centrosome, mitosis, and meiosis (sexual reproduction), exo- and endocytosis. The oldest
fossils considered eukaryotic cells are about 1.2 billion years old (the earth is about 4.6 billion
years old, and life on earth is older than 3.5 billion years).
Slide 7
What do we mean by molecular biology? There are two rather different notions of
molecular biology. Both of them have existed side by side from the very beginning. The first
notion is very general in character: Molecular Biology is the attempt to understand any
biological problem at the level of atoms and molecules. This broad definition offers little help
to provide us with a central theme for our lecture. Furthermore it may be asked whether it is

reasonable to examine all biological problems at the level of atoms and molecules.
Historically molecular biology has first and foremost been concerned with a specific
molecular problem: what is the chemical nature of biological information and how is it
expressed? The most fundamental aspects of this problem had been solved no later than the
early 1960ies, and many molecular biologists started to apply their tools and paradigms to
other biological problems. By now, Francis Crick s tongue in cheek definition of molecular
biology as everything that a molecular biologist is interested in, has become reality.
In parallel, however, the project of understanding at ever greater depth the molecular
mechanisms that govern the flow of biological information has also continued unabated.
For the purpose of this lecture, we will adopt the following, narrower, description of
molecular biology: (next slide).
Slide 8
Molecular biology is concerned with the molecular structures and mechanisms that carry
biological information and govern its flow from the gene into the cytoplasm, and from
generation to generation.
Central to this description is the notion of biological information. But, what does this
admittedly vague notion mean? As we shall see, the pursuit into the chemical foundations of
biological inheritance eventually revealed that biological information is sequence
information.
Slide 9
The most fundamental property of living beings is their ability to reproduce with only
minor variations, on the basis of information that is bequeathed from cell to cell, and
generation to generation, in the form of distinct units called genes. Living beings are thus not
only subject to the laws of physics and chemistry, but also to the vagaries of history, as the
information is subject to random changes and selection (Darwin's theory of evolution). This is
a unique feature of life, which distinguishes it from unanimated matter.
The picture of this slide shows an adult fruit fly, Drosophila melanogaster. Research on
this little fly, about 2.5 mm in length, has fundamentally shaped our understanding of the
molecular biology of pattern formation of multicellular organisms, including the human
being, and we will again return to Drosophila later in this lecture.
As any living being, Drospophila is endowed with elaborate purposive structures; i.e.
structures that serve a specific purpose, but ultimately one goal: reproduction. Jacques
Monod (1910-1976) called reproduction the essential teleonomic project (gr. end,
purpose), Francois Jacob (*1920), the dream of all living beings to become two.
For instance, Drosophila bears two large complex eyes, each composed of 800
ommatidia, with each ommatidium containing eight photoreceptor cells for visual perception.
About two thirds of the Drosophila nervous system is dedicated to its visual system. On the
second of its three thorax segments it carries two wings that beat about 220 times per second
during flight. The following thorax segment is endowed with halteres, little rotating knobs
that serve as stabilizers of flight, and are a unique feature of all flies. Each one of the three
thorax segments furthermore carries one pair of legs for walking. All these structures
essentially serve the task of seeking a mating partner.
After fertilization the female lays about 400 eggs into rotten fruit or decaying mushrooms

using a tube like structure, the ovipositor, at the end of its abdomen. Embryogenesis takes no
longer than 24 hours after which a larva hatches from the egg. The larva feeds on
microorganism within the fruit, and on the sugars of the fruit sap. Eating for growth is the
main purpose of the larva. Within 4 days the larva molts twice before encapuslation in the
puparium, where it undergoes metamorphosis, a uniquely shared character of all
holometabolic insects. During metamorphosis the adult fly develops, which has little
resemblance with the larva, but looks just like the parent fly. The adult fly initiates a new life
cycle, inheriting its information to the next generation; its members will thus be endowed with
the largely the same properties as their parents.
The reduplication and inheritance of biological information is subject to random
mutation, providing the basis for evolution by selection, which gives rise to new species
whose shared inherited information reflects their phylogenetic relationships. There are about
1450 Drosophila species alone, about 120,000 fly species, and at least 1 million insect
species.
Slide 10
Flies can be very different in appearance, but they are always recognizable by their
halteres, inherited from their common ancestor.
Insects belonging to the taxon pterygota (all insect with wings) moths, butterflies, bees,
beetles, bugs, and the dragon flies, for instance all inherited from their common ancestor
two pairs of wings, the posterior pair of which has been transformed into halteres in flies,
whereas the anterior pair hardened into elytra in beetles, protecting their delicate hind wings
and abdomen.
Insects belong to a larger group called euarthropods. Other euarthropods, like the
Indonesian millipede or the tropical jumping spider (see slide), dont have wings, but share
with insects the segmental organization of their body plan, and an exoskeleton made out of
chitin due to information inherited from a common ancestor. Biological systems contain
inheritable information.
Slide 11
At the chemical level biological information is expressed in form of precisely defined
networks of chemical reactions, such as the one shown here, where nodes represent chemical
species and connecting edges realized chemical transformations between them. (Transitions
highlighted in bold represent the glycolytic pathway and the citric acid cycle.)
The topology or graph (nodes and edges) of the chemical network determines the
properties of the organism, be it a single cell, or a multicellular organism. Although the
number of different chemical reactions that occur in any cell appears staggering, it only
represents a minor fraction of all possible chemical reactions. How then does the cell generate
defined chemical networks that represent only a small subset of all possible chemical
reactions? The answer to this question is catalysis.
Slide 12
As a chemical reaction progresses from its reactants to its products, the free energy (see
below) of the system increases until it reaches a maximum. The corresponding molecular
configuration is called the transition state of the reaction. The difference in free energy

between the transition state and the reactants is referred to as the activation energy. While the
equilibrium distribution of the reaction exclusively depends upon the free energy difference
between reactants and products, the rate constant of the reaction, k, depends on the activation
energy of the reaction according to the formula shown, where kB is the Boltzmann constant, h
is Plancks constant, T is the absolute temperature in Kelvin.
The chemistry of living beings is organic chemistry, i.e. biochemical molecules are
carbon based compounds. From a biological point of view, the most important property of
organic chemistry is that the activation energies of organic reactions are high at ordinary
temperature and pH. In the absence catalysis, organic reactions are, therefore, exceedingly
slow.
Slide 13
Catalysts accelerate reactions by lowering the activation energy of the reaction; unlike
the reactants, the catalyst is not consumed in the reaction. Catalysts cannot change the
equilibrium of a chemical reaction; since both forward and backward reaction proceed
through the same transition state, the catalyst necessarily accelerates both reactions equally.
As we shall see, this remarkable symmetry is a consequence of the second law of
thermodynamics. And it is for this reason that organisms evolved enzymes for thermodynamic
(energetic) coupling to allow for anabolic processes (see below).
Slide 14
Biological catalysts are called enzymes (from gr. inside; yeast; the term was
coined by Wilhelm Friedrich Khne, 1837-1900). They recognize chemical compounds with
great specificity; we say that enzymatic catalysis is stereospecific enzymes recognize
specific substrates and release specific products. As we shall see that this selectivity is
entailed in the three-dimensional structure of biological catalysts; almost all of which are
proteins. Enzymatic catalysis is accomplished essentially by stabilization of the transition
state.
Slide 15
The biological purpose of stereospecific catalysis is selection of chemical reactions. This
important notion, without which most of molecular biology cannot be understood, is
demonstrated in this figure by an analogy. Here, a chemical compound is represented by a ball
in a box. We shake the box, imitating the random thermal motion of molecules. The ball can
escape the box by jumping over either one of the four confining walls, the walls are analogous
to the activation energy of alternative chemical reactions. Since the walls are high and of
equal height, the ball will jump over a wall only seldom and equal probabilities for all four
walls. Now imagine, we selectively remove wall 1. Upon shaking the box the ball will almost
always escape by taking path 1. Molecules can thus be guided along a precisely defined path
of chemical transitions. Cells generate reaction networks by catalyzing some reactions and
not others.
Text books generally stress the fact that enzymes accelerate chemical reactions. This is
correct, but the emphasis on acceleration misses the crucial point: enzymatic (stereospecific)
catalysis serves to select specific reactions from the large number of all possible reactions.

Slide 16
We can use stereospecific catalysis for accelerating and thus selecting specific
reactions, but it is not possible to accelerate only one of the two directions of a chemical
reaction. To understand this principle and its biological implications, we have to briefly
review some thermodynamics.
We shall see that chemically molecular biology is concerned with the formation of only
two types of bonds: the phosphoester bond and the peptide or amide bond. We shall consider
this biochemistry in some detail. For guidance, we shall focus on three theoretical aspects
(i)
kinetic proofreading
(ii)
energetic coupling
(iii)
reaction mechanism.
Points (i) and (ii) will require some thermodynamic background knowledge.
A brief review of the first and second law of thermodynamics
In thermodynamics, we call the object of interest 'the system' (circle), and the rest of the
universe its 'surroundings'. The system may be a heat engine, a reaction tube in the laboratory,
or a cell. The surroundings are decomposed into idealized reservoirs (colored rectangles) with
which the system may exchange energy.
In the 19th century physicists started to realize that heat was another form of energy with
unique properties (see below); they distinguished, therefore, between heat and all other forms
of energy, which are collectively called 'work'. Thus, there are two basic types of reservoirs,
the heat reservoir or heat bath with which the system may exchange heat, and the work
reservoir, which may be further decomposed into sub-reservoirs depending on the type of
energy that is exchanged for instance a volume reservoir against which the system may
expand (or contract) and thus exchange mechanical work, W, with the surroundings according
to W = pV W, where p is the pressure of the reservoir, and V is the change in system
volume. The heat reservoir or heat bath is considered infinitely large compared to the system
and therefore maintains the same temperature, even when exchanging heat with the system.
A state function is a function whose value only depends on the state of the system, i.e., its
chemical composition, temperature, pressure and volume, but not its history. Thus, for any
cyclical process, the change in a state function is zero. We may now state the first (i) and
second law (ii) of thermodynamics:
(i) The first law
There is a state function U, called the internal energy of the system, with

U = Q + W ,
where, by definition, Q > 0 if heat flows into the system, and W > 0 if work is done on the
system. (Both heat flowing out of the system and work done by the system is < 0). The first
law implies that the (internal) energy of an isolated system, i.e. a system that does not
exchange energy (including matter) with its surroundings, is constant. Thus, the energy of the
universe is constant. For this reason the first law is also called the 'law of energy
conversation'. A critical insight that made its discovery possible and is implied by the first
law is that heat is energy.

(ii) The second law

There is a state function S, called the entropy. The total change (system + surroundings =
universe) in S for any process is larger or equal to zero:

S total 0 ;
furthermore, the entropy change in the surroundings is limited to the heat bath and is given by
S res =

Q
;
T

the entropy of the work reservoir does not change.

Note that S res > 0 if heat flows into the reservoir (and thus out of the system), for Q < 0
according to the sign convention in (i); and S res < 0 if heat flows out of the reservoir (and
thus into the system), for Q > 0.) The equality sign in S total 0 applies only for quasi-static
processes, i.e., processes for which the system is infinitesimally close to thermodynamic
equilibrium at all times. We call processes that are not quasi-static spontaneous. All natural
processes are spontaneous and hence, according to the second law, increase the entropy of the
universe. The surroundings plus the systems together form an isolated system, i.e. no energy
or matter can flow into or out of the system. The entropy of an isolated system ever increases
until reaching a maximum.
The word entropy was introduced by Rudolf Clausius (1822-1888) in 1865 (Gr.
transformation content).
Slide 17
As mentioned earlier, catalysts cannot accelerate the forward reaction of a chemical
reaction without accelerating the backward reaction, too; and therefore cannot change the
equilibrium of a chemical reaction. This symmetry is a consequence of the second law of
thermodynamics. We shall prove this statement by assuming the opposite and showing that
our assumption leads to a contradiction with the second law. (That is, we apply the modus
tollens, see above.)
Our model system encompasses molecules A and B, which can be chemically converted
into each other and is coupled to the heat reservoir HT at temperature T. Let B have lower
energy than A, the reaction, therefore, releases energy as it proceeds from A to B; i.e., the
reaction from A to be B is 'exothermic'. We furthermore assume the reaction is in equilibrium,
i.e. forward and backward reaction proceed at equal speeds:

k1[A] = k2 [B] ,
where k1, k2 are the rate constants of the reaction. Thus, in equilibrium the concentration ratio
[A] / [B] = k2 / k1 assumes a characteristic value at temperature T.
Now suppose that one direction of the reaction is catalyzed by a catalyst, C, but not the
other, say the reaction from A to B. Let k1C be the rate constant for A B in the presence of
C, where k1C >> k1 . Upon removal of C, A B , but not A B becomes slower and there
will be a net flow from B to A. This requires absorption of energy from the heat reservoir
because the reaction from A to B is exothermic; the opposite reaction, therefore, is

endothermic; it absorbs heat. We now reintroduce the catalyst, the old equilibrium will be
attained, which requires the conversion of some A molecules into B molecules until
[A] / [B] = k2 / k1 is again obtained, releasing energy, which we harness for work by coupling
the system to a work reservoir. Thus we have obtained a cyclical (chemical) process whose
only effect is the conversion of some heat, Q, into work, W.
According to the second law, this is impossible: Since entropy is a state function and the
system (A, B) is in the same state at the beginning and end of the process, S sys = 0 . In
contrast, because heat Q was absorbed by the system (Q > 0), the change in entropy of HT,
S res = Q / T , is negative. Hence, the total change in entropy S res + S sys is negative, in
contradiction of the second law of thermodynamics; the notion that a catalyst may catalyze
only one direction of a chemical reaction and thus affect the equilibrium of the reaction,
stands in contradiction to the second law. Note that fundamentally the same argument may be
used to prove the following general result:
Slide 18
No process is possible whose sole result is the absorption of heat from a reservoir and
the conversion of this heat into work.
This is the Kelvin-Planck statement of the second law of thermodynamics. It establishes
the unique status of heat energy among all forms of energy. While every other form of energy
(i.e., work) can be completely converted into heat, heat can never be completely converted
into work.
(The Kelvin-Planck statement is equivalent to our formulation of the second law. It is
easily derived from our formulation of the second law; as we have seen. The reverse however
is hard.)
Slide 19
The second law does not imply that heat cannot be converted into work whatever; after
all, this is what a steam engine does. However, conversion of heat into work by some
(cyclically operating) engine requires two heat baths, one colder than the other, for we can
compensate for the loss of entropy in the warmer heat bath, QH / TH , by transfer of a
smaller amount of heat, QC < QH , to the colder heat bath, fulfilling the second law's
requirement that
Q
Q
H C 0.
TH TC
The difference between these two, QC QH , can be used for work. (Note that work done by
the system is negative by sign convention.) From this inequality, it is easily seen that the
thermal efficiency of the engine W / QH i.e., the amount of work that can be done per
unit of heat absorbed from the heat reservoir obeys the following law:

10

TC
TH

Thus, 1 TC / TH is the upper limit for the efficiency of the engine and only depends on the
temperatures of the two heat baths. It thus applies to any engine; and is therefore a universal
upper bound for the efficiency of a heat engine. This upper bound is approached only for ideal
quasi-static processes. (The actual efficiency of realistic engine is much smaller.) The greater
the temperature difference between the two reservoirs, the greater the maximal efficiency of
the engine.
Slide 20
By considering the reversal of the process shown in this slide, transfer of heat from a cold
reservoir to a hot reservoir, we may infer that
No process is possible whose sole result is the transfer of heat from a cooler to a hotter
reservoir.
This is the Clausius statement of the second law of thermodynamics. (It can be proved
that it is equivalent to the Kelvin-Planck statement.) The process shown is that of a heat pump
(refrigerators are heat pumps). Thus, work energy needs to be converted into heat in order to
cool a body. A refrigerator requires energy (i.e., work).
Now, consider the problem of heating your house. The second law allows you to heat
your house by using energy to pump heat from the surroundings, the cold heat bath, into your
house, the hot reservoir; i.e. by running a heat pump. The energy eventually added to your
house per unit of work 'consumed' by the heat pump is

QH QC + (QH QC ) QC + W QC
=
=
=
+1 .
W
W
W
W
The ratio = QC / W is called the coefficient of performance for the heat pump. Its
theoretical upper limit is given by

TC
.
TH TC

(Derive this inequality.) Thus, for an outside temperature of 5C (273K; a cold winter at the
coast of California) and 25C (298K) for your house, the maximal coefficient of performance
is 273 / 20 = 13.65 . This value is obtainable only, if the engine runs quasi-statically or
'reversibly', which practically is impossible. Nonetheless, the coefficient of performance of
modern heat pumps ranges between 2 and 7. Hence, QH / W , the amount of heat generated
per unit of work, can range between 3 and 8, as opposed to 1 for the direct conversion of work
(e.g. oil or coal) into heat. According to the U.S. Energy Information Administration 42% of
energy spent in American households is used for space heating, another 18% for water
heating. We could cut the total amount of energy 'consumption' by at least 40%, if we used
heat pumps for heating. (The question of why we don't do this must be discussed elsewhere.)
As mentioned earlier, almost all biological catalysts are proteins. The importance of
biological catalysis, and therefore of proteins, is not understood without the concept of
energetic coupling. We first briefly review the concept of 'Gibbs free energy'.

11

Slide 21
Most systems of interest to chemists and biologists are systems that may be viewed as
systems coupled to a volume reservoir and a thermal reservoir, an open reaction tube in the
laboratory for instance. For such a system the second law of thermodynamics may be
expressed in terms of state functions of the system only, because in this instance heat
exchanged with the heat reservoir is also a state function, called enthalpy. This can be easily
seen as follows:
Since the only work reservoir is the volume reservoir, the only work done on the system
is volume-pressure work, -pV, where p is the pressure of the reservoir and the system (since
they are coupled). Thus, the first law of thermodynamics becomes

U = Q pV

for constant p.

With H U + pV , it follows

H = Q

for constant p.

Since U, p, and V are state functions, H is a state function, too. From the second law it thus
follows
S total = S sys + S res

= S sys H / T
0
and hence, with G H TS

(for constant p)

G 0

for all processes at constant p and T (i.e., coupled to heat and volume reservoir). G is called
Gibbs free energy (after Josiah Williard Gibbs, 1839-1903). For every naturally occurring (i.e
spontaneous) process at constant p and T
G < 0 .

Note that this statement is nothing else but the second law of thermodynamics again, for the
special case of a system that is coupled to a heat and a volume reservoir (and no other
reservoir).
Slide 22
Processes for which G < 0 are called exergonic. Thus, all naturally occurring processes
(in systems coupled to a heat and temperature reservoir) are exergonic. Exergonic must not
be confused with exothermic, which means H > 0 . Processes for which G > 0 are called
endergonic (not to be confused with endothermic, i.e. , H < 0 ).
Many important biochemical reactions, for example polymerization reactions, which will
be at the center stage of this lecture, are endergonic, and hence do not occur spontaneously.
And yet nucleic acids (DNA and RNA) and protein molecules (all are polymers) are
continually synthesized inside cells. How is this possible?
Slide 23
As we have seen, the second law of thermodynamics implies the impossibility of a
catalyst that catalyzes the forward direction but not the backward direction of a chemical

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reaction, or vice versa. And yet biological catalysts, enzymes, can promote endergonic
reactions.
This remarkable feat is accomplished by the mechanistic coupling of two chemical
reactions. This coupling allows for endergonic reactions to proceed when coupled to a
sufficiently exergonic reaction (energetic or thermodynamic coupling) the total change in
free energy is the sum of the partial free energy changes to assures that the total change in
Gibbs free energy is negative.
One of the most often used reactions by cells to drive energetically unfavorable,
endergonic, reaction is the hydrolysis of ATP to ADP, which under cellular conditions is
highly exergonic. Thus, in every reaction that involves ATP hydrolysis we observe biology
paying its dues to the second law of thermodynamics. In 3.5 billion years of evolution, life did
not manage to invent a 'unidirectional catalyst' that could subvert, i.e. invalidate, the second
law of thermodynamics. The second law is a well-tested and corroborated theory, by biology.
Slide 24
The preceding discussion is summarized in this slide. It shows that energetic coupling
allows to decrease entropy within the cell (in the course of polymerization reactions, for
instance) at the expense of generating entropy in the surroundings, which means the export of
energy from the cells into its surroundings in the form of heat (i.e. random molecular motion).
Slide 25
Enzymes are, with very few (but important) exceptions, proteins. As Francis Crick (19162004) pointed out in his famous 1957 essay 'On protein synthesis', which laid down the
foundations for molecular biology: the main function of proteins is to act as enzymes. If we
want to understand biological information, we have to start with an exploration of the
chemical nature of proteins.

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