100Q BIOPHYSICS: MOLECULAR BIOLOGY BASICS

D. ALLAN DRUMMOND

Abstract. I will answer the following 4% of the 100 questions:

(1) Explain how a system of chemical reactions can be represented as ODEs
and PDEs. What approximations are involved?
(2) What is the Central Dogma of Molecular Biology?
(3) What are the differences between entropy, free energy, and enthalpy?
(4) Explain the difference between equilibrium and steady-state.

1. The Central Dogma of Molecular Biology

Question: What is the Central Dogma of Molecular Biology?
The central dogma: Information is carried by the genes (DNA which is tran-
scribed to RNA), and expressed in proteins. Information flows from DNA to RNA
to proteins, but not the reverse.

transcription translation
DNA −−−−−−−−→ RNA −−−−−−−→ Protein

Figure 1. The Central Dogma of Molecular Biology.

According to Francis Crick, “Once information has passed into protein, it cannot
get out again.”
I will summarize the basic physiological process by which this happens below.
An outstanding site that will show-and-tell you everything you need to know about
transcription and translation is UCLA’s Tutorials in Molecular Biology at http:
//www.lsic.ucla.edu/ls3/tutorials/gene_expression.html.
Transcription and translation proceed similarly for all forms of life, with differ-
ences primarily between prokaryotes (organisms without cell nuclei, like bacteria)
and eukaryotes (like yeast and most higher life forms). Prokaryotes have a fairly
simple process that turns DNA into RNA and then into one or more proteins with-
out any editing or splicing; translation can begin while transcription is still taking
place. Eukaryotes, with their DNA walled off in the nucleus, can and do perform
elaborate editing of RNA before it is transported outside the nucleus to the trans-
lating ribosomes.
During transcription, a complex protein called RNA polymerase binds to a por-
tion of the DNA called a promoter, unzips the DNA locally, and begins transcribing
the DNA into messenger RNA (mRNA) until it reaches a stop signal. At this point
we eukaryotes start slicing and dicing the mRNA to produce a “mature” mRNA
strand, while prokaryotes have already begun pounding out protein. Let’s assume
a mature mRNA strand makes it to a ribosome, as it eventually will in all species.
1
2 D. ALLAN DRUMMOND

Ribosomes are massive two-subunit molecules composed of several proteins and

RNA strands. With the help of many transfer RNA molecules (tRNAs), which
carry amino acids to the translation site, the ribosome steps down the mRNA three
bases (one codon) at a time, adding one of twenty amino acids to an output chain
depending on the bases in the current locked-in codon. When the ribosome reaches
the end of the mRNA, translation stops, and the chain of amino acids achieves its
final folded shape as a protein.
In this way, information contained in DNA is transcribed into RNA which is
translated into protein. The Central Dogma states that this is the way of the world.
A few notable exceptions remind us that we’re right to bristle at the word “dogma.”

1.1. Exceptions to the Central Dogma. First, retroviruses, which turn RNA
into DNA. (A nice introduction to retroviruses can be found at http://www-micro.
msb.le.ac.uk/335/Retroviruses.html.) The retrovirus you’re most likely to know
is HIV-1, a human retrovirus, though they afflict a wide variety of species, from
fungi to flies to mice to us. Most RNA viruses inject mRNA into a cell, causing viral
proteins to be produced by the ribosomes. Retroviruses, by contrast, inject capsids
inside which viral RNA and an enzyme called reverse transcriptase hide. Reverse
transcriptase turns RNA into DNA much the way DNA polymerase turns DNA into
RNA; the DNA then migrates to the cell nucleus and is incorporated into the host
DNA. Viral replication then uses only the cell’s normal machinery. (See Figure 2.)
This RNA-to-DNA cycle reverses the first part of the Central Dogma, which is why
we call them retroviruses. Cocktail party note: David Baltimore shared the 1975
Nobel Prize in Medicine or Physiology for his discovery of reverse transcriptase.

The Life Cycle of a Retrovirus

©1998 by Alberts, Bray, Johnson, Lewis, Raff, Roberts, Walter
. http://www.essentialcellbiology.com
Published by Garland Publishing, a member of the Taylor & Francis Group.

RNA
envelope
new progeny virus particles
single-stranded RNA each containing reverse
retrovirus transcriptase

capsid
VIRAL BUDDING

reverse
transcriptase
plasma membrane
of host cell CYTOSOL
ENTRY INTO ASSEMBLY
CELL AND LOSS
OF ENVELOPE

LOSS OF
VIRAL CAPSID envelope protein capsid protein reverse transcriptase

RNA
TRANSLATION TRANSLATION

TRANSCRIPTION BY HOST
RNA CELL RNA POLYMERASE
MAKES MANY RNA COPIES
DNA
INTEGRATION OF DNA integrated DNA
SYNTHESIS OF A COPY INTO HOST of virus
DNA/RNA AND THEN A DNA CHROMOSOME
DNA/DNA DOUBLE HELIX BY
REVERSE TRANSCRIPTASE DNA
portion of
host cell
chromosome

Figure 2. How a retrovirus defies the Central Dogma.

 100Q BIOPHYSICS: MOLECULAR BIOLOGY BASICS 3

Second, prions. A standard way to talk about information flow in the context
of the Central Dogma is this: DNA determines mRNA, which determines protein
sequence, which determines protein structure (fold), which determines protein func-
tion. Thus DNA, the genotype, is responsible for the proteins, the phenotype. Prions
are proteins that induce proteins with a common sequence to fold into a different
structure, and thus a new phenotype. In mice, a normal protein apparently respon-
sible for keeping Purkinje cells alive can be induced to misfold by a prion protein
with the same sequence but a different folded structure. The misfolding is infec-
tious: newly misfolded prion proteins induce others to misfold, and so on. In this
way, structural (and thus functional) information is passed from protein to protein
without any DNA involvement, again contradicting the Central Dogma.

1.2. Interesting Questions. Why is the Central Dogma true? Are there evolu-
tionary reasons to presume the stability of the Central Dogma (i.e., is there selective
pressure maintaining the firewall between nucleic acids and proteins)?

2. Reaction Kinetics
Question: Explain how a system of chemical reactions can be represented as ODEs
and PDEs. What approximations are involved?
See the handout provided.

3. Entropy, Free Energy, and Enthalpy

Question: What are the differences between entropy, free energy, and enthalpy?
First, why care about entropy, free energy and enthalpy? Because these quantities
tell us important things about the direction of chemical reactions, let us make
predictions about the relative concentrations of reactants at equilibrium, tell us
how stable chemical species are and where their stability comes from, and tell us
how much energy is required to get a reaction to take place. All these things help
us understand the biophysics of the phenomena we study.
Next, what are some simple differences? Units, for starters. Entropy carries units
of J/K, energy per degree kelvin. Enthalpy carries units of energy (typically called
heat when talking about enthalpy), as does free energy.
Entropy for a closed system is governed by the second law of thermodynamics,
∆S ≥ 0. Enthalpy and free energy are governed by the first law, the law of con-
servation of energy. Thus for a closed system entropy must always increase, while
enthalpy and free energy must always stay the same.
A basic diagram to keep in mind which relates all three of these concepts is
Figure 3.

3.1. Precise Thermodynamic Definitions. Consider a thermodynamic system

at equilibrium which has N states and is at temperature T . Each state n has energy
En . The probability Pn for the system to be in state n is
1 − En
Pn = e kT ,
Q
4 D. ALLAN DRUMMOND

where
N
X En
Q≡ e− kT
n=1
is called the partition function and k is Boltzmann’s constant, 1.3807 × 10−23 J/K.
While Q isn’t a quantity of ultimate interest to us, we can use it to compute almost
all such quantities. For example, as Figure 3 implies, as we look at entropy, enthalpy
and free energy we will need to start from a basic system energy, the internal energy
U defined as the average
N N
X X 1 − En
U= En Pn = En e kT .
n=1 n=1
Q
The entropy S of the system is defined as
N
X
S = −k Pn ln Pn ,
n
with Pn defined as above. The entropy quantifies how “spread out” the system
is over its N microstates, probabilistically speaking. If all the states are equally
likely (implying all have the same energy, or that states with equal energy are
indistinguishable), then Pn = N1 and we get S = k ln N , the equation Boltzmann
had inscribed on his tombstone (though he used W instead of N —those crazy
Austrians). The second law of thermodynamics states that the entropy of a closed

­ TS

U F
Internal Energy Helmholtz Free Energy = U ­ TS

Energy needed to create a system; energy Energy needed to create a system minus
attributable to the microscopic, random the energy you get "for free" by the

+ PV
fluctuations present in the system. spontaneous transfer of heat from the
environment.

H G
Enthalpy = U + PV Gibbs Free Energy = U + PV ­ TS

Energy needed to create a system plus the Energy needed to create a system and
energy needed to make room for it. make room for it minus the energy you get
"for free" from the environment.

Figure 3. The relationship between entropy S, free energy G (or

F ), and enthalpy H (after http://hyperphysics.phy-astr.gsu.
edu/hbase/thermo/thepot.html).
 100Q BIOPHYSICS: MOLECULAR BIOLOGY BASICS 5

system always increases, and we can now interpret that to mean the probabilities
tend toward N1 , which means the distribution of the number of particles at each
energy level E, n(E), has an exponential distribution (the Boltzmann distribution).
The enthalpy H of the system is defined as
H ≡ U + P V.
The free energy of the system comes in two varieties. Most of the time, we want
the Gibbs free energy G, but sometimes we’ll want the Helmholtz free energy F . We
have
G = U − TS + PV = H − TS
F ≡ −kT ln Q = U − T S
The relations for F can be obtained by plug-and-chug methods from the defini-
tion of S above; just note that ln Pn = − E
kT − ln Q and simplify.
n

3.2. Useful Chemistry Definitions. Let’s say I have two compounds A and
B that can interconvert under certain conditions (for example, cis- and trans-2-
butene, which interconvert at high temperature or in the presence of a strong acid).
I tell you that the difference in free energies at 298K (= 25◦ C), ∆G◦ = GA − GB =
−0.69kcal/mol. What can you tell me about A and B?
You should be able to tell me a couple very important things. First, A must be
more stable than B at that temperature, because it has a lower free energy. Second,
their equilibrium concentrations can be obtained using the relation
∆G◦ = −RT ln Keq
where R is the ideal gas constant (= 8.3144 J/mol-K), T is the absolute tempera-
ture, and
[A]
Keq = ,
[B]
the ratio of the concentrations of A and B at equilibrium. (Note that top-bottom
in Keq is equivalent to left-right in ∆G◦ .)
Enthalpy is often called the heat of formation, and quantifies the strength of
the bonds present. Enthalpy is typically measured using a calorimeter, burning
the compound in question to see how much energy is released when its bonds are
broken.
If I tell you ∆H for a reaction, what can you tell me? Well, if ∆H < 0 in a
reaction, then the products have stronger bonds than reactants, and vice versa for
∆H < 0 (reactants have stronger bonds). In the latter case, the reaction may still
proceed from reactants to products if there is an entropy decrease that more than
compensates for the increase in enthalpy, because this leads to a favorable free
energy decrease.

4. Equilibrium vs. Steady State

Question: Explain the difference between equilibrium and steady-state.
Trick Question Alert!
There are two kinds of equilibrium: dynamic equilibrium, and static equilibrium.
The former requires energy for its maintenance, while the latter does not. “Equilib-
rium,” unqualified, tends to refer to thermodynamic equilibrium, which is a static
equilibrium. The term is inherently imprecise.
6 D. ALLAN DRUMMOND

Steady state refers to any unchanging state, regardless of how it is maintained,

and corresponds to both kinds of equilibrium. If the system state is represented as
some vector S, then
dS
S is at steady state ⇐⇒ = 0.
dt
Can we have steady state without static equilibrium? Yes. For example, in a
chemical reaction in which reactive species A and B react to form compound AB, we
can imagine an equilibrium in which the forward rate of reaction precisely matches
the reverse rate, leading to no net change in concentrations, but in which reactions
still proceed apace.
Can we have static equilibrium without steady state? No. Static or thermody-
namic equilibrium is a superset of steady state. If a system is in thermodynamic
equilibrium, it is not changing. Keep Figure 4 in mind.

Steady State
Static
Equilibrium

Figure 4. The relationship between static equilibrium and steady state.

You may have come across the notion of thermodynamically reversible processes,
in which each step is assumed to diverge only infinitesimally from equilibrium,
allowing us to use equilibrium assumptions at each step. This is an approximation,
not a violation of the fact that systems at equilibrium do not change.