Directions and Rates of
Biochemical Processes
Chapter 5
Ludwig Boltzmann, an Austrian
physiscist, working around 1906 favored
the idea that the behavior of atoms
accounts for all chemical transformations.
At this time few thought that atoms were
real. The idea was first theorized by
Democritus in the 5th century B.C. then
was abandoned for 2000 years.
About the time Boltzmann was working
Albert Einstein proposed that Brownian
movement was probably due to atoms.
They did not communicate. Boltzmann
despaired that his life’s work had been a
waste and hung himself. Today his ideas
are called the First and Second Laws of
Thermodynamics.
Thermodynamics is the study of the
relationships between different forms of
energy. His work also involved kinetics,
the study of rates of reactions. In
general 2 questions must be asked:
1.Which way will the reaction go?
2.How fast will it go?
Ex. of rate Why does gasoline or oil burn
quickly but take millions of years to form?
Ex. of direction, Why does water fall down?
Biological processes also have a definite
direction. Predicting it lies in understanding
that energy gets converted from one form to
another. Thermodynamics governs all energy
changes.
Work requires energy because it is
movement against a force. Energy for
work can be stored in a battery
(potential) and used when the movement
(kinetic) is needed.
Rearranging atoms in a chemical
reaction is a form of work.
Making a molecule of ATP requires
putting together 3 negatively charged
phosphate groups (goes against electrical
force) but stores energy as potential
energy. ATP can later be used to do
work. ATP ADP; muscles move.
Going back to predicting the direction
of a reaction, much was learned by
watching steam engines. As coal
burned the engine caused movement.
However, energy is not destroyed or
created, it just changes form. The First
Law of Thermodynamics states the total
amount of energy in any process stays
the same.
The Second Law of Thermodynamics
states that in any process the amount of
energy available to do work decreases.
According to the second Law of
thermodynamics muscle contraction can
only convert part of the potential energy
in ATP into muscular contraction
(kinetic). The rest becomes heat
because of the random movement of
molecules.
Energy is measured in calories, the
amount of energy needed to raise the
temperature of one gram of water one
degree Celsius. Food is measured in
Calories (1000x larger units than
calories). Whenever energy changes
form, more energy turns to work. Heat
loss is a result of energy transformation.
Reactions usually go in the direction of
heat loss.
To predict the direction of a chemical
reaction you need to know how much
free energy there is minus the energy for
doing work. (G) Every chemical
reaction involves a change in free
energy. When 2 reactants form new
products the change in energy is equal to
the free energy of the products minus the
free energy of the reactants.(Δ G)
Δ G + G products minus G reactants.
All processes that release energy are
exergonic which give off heat.
ATP  ADP + P.
Reactions that require input of energy are
endergonic.
ADP + P  ATP is endergonic, required
heat in calories.
In all exergonic processes, free energy
decreases so Δ G is negative. If free
energy increases, Δ G is positive.
Endergonic reactions are not
spontaneous.
ATP + H2O  ADP + P
(reactants)
(products)
H replaces the O in the ATP’s 3rd
phosphate group. 2 bonds break, O-H
and P-O. The new P-O bond is more
stable. Free energy decreases when
unstable bonds break and stable bonds
form.
The free energy of the products
( ADP + P) hass less than free energy of
the reactants.
Biochemists call the unstable bonds of
ATP high – energy bonds (~).
ATP can be written out as:
adenine + ribose + P ~ P ~ P.
The free energy for the breakdown of
ATP  ADP is -7.3 kcal/mole. A mole
is 6.02 x 1023. The breakdown of ATP is
the most common source of energy for
biochemical processes.
When an exergonic reaction drives an
endergonic reaction the 2 processes are
coupled. A coupled process must be
exergonic overall.
Energy from splitting ATP drives
reactions in small steps. Reactions are
coupled by enzymes (proteins) that speed
up biochemical processes.
Enzymes do not change the free energy of
the reaction like sliding down a hill of ice
rather than dirt., the reaction happens
faster. In muscle contraction, an enzyme
couples the breakdown of ATP to the
contraction of muscle filaments.
The Second Law of Thermodynamics,
that energy for work always decreases
implies the amount of disorder in the
universe always increases. A measure of
disorder is entropy. Entropy is high
when things are disordered and low when
ordered. Entropy tends to increase as is
can be used to do work.
A process that converts an orderly
arrangement to a less orderly arrangement
can perform work. Burning wood
converts the well – ordered molecules of
cellulose to disordered molecules of CO2
and H2O. Energy from this reaction can
cook or heat. A process to convert a
disorderly arrangement to an orderly one
consumes energy. For a tree to grow, light
energy and O2 are used to build cellulose.
Cells use energy and maintain
concentration of molecules inside the
cell that are different than those outside
of the cell. Cells must perform work to
keep their internal environment constant.
When no energy is available to perform
work the difference between the inside
and outside disappear - lethal for the
cell.
Therefore free energy depends on the
concentration of molecules. The greater
the difference in a concentration
gradient the more work can be done.
Reaction A B
Reactant
Product
As B accumulates there is less free
energy available for the reaction.
When the free energy of B = the free
energy of A, Δ G = 0. The reaction is not
downhill, equilibrium is reached.
Thermosynamics can predict where
equilibrium lies.
When a substance absorbs heat and
temperature increases the molecules bounce
more rapidly – kinetic energy. The
minimum energy needed to start a reaction
is called activation energy.
Catalysts lower activation energy.
Enzymes are biological catalysts. Most
enzymes are proteins. Enzymes allow
organisms to lower activation energy
and shorten the time to attain
equilibrium which is essential to life.
Kinetic theory helps us understand why
some thermodynamically favored
reactions take place and others do not.
The presence of an active enzyme
allows a cell to use ATP in specific
ways; contraction of a muscle, pumping
of ions in or out of a cell, or making
other molecules. Enzymes bind to the
reacting molecule (substrate) making a
chemical reaction go 1 million x faster
than it normally would.
Ex. At 0 degrees C. one molecule of
catalase can break down 5 million
molecules of H2O2/minute. Enzymes
are specific. Each one catalyzes only
one reaction. This is because of their
shape (remember proteins have a
secondary, tertiary, and sometimes
quaternary shape) and interactions with
the substrate.
Most enzymes are large, globular
proteins with irregular shapes. Each
enzyme has an “active site” where it
will bind with the substrate molecularly
(like jigsaw puzzle pieces). Binding
lowers activation energy for a particular
reaction. Enzymes bond temporarily to
substrates by weak covalent bonds,
even H bonds and ionic bonds.
Binding of enzyme and substrate is
reversible. Some enzymes can alter and
release more than 600,000x per second.
Interactions between enzymes and
substrates occur one molecule at a time.
The rate of reactions depends on
temperature as well as concentration of
reactants, and how much enzyme is
present.
Forming noncovalent bonds between
enzymes and substrates leaves the
enzyme unchanged. The enzyme
briefly changes the shape of the
substrate. Enzymes bring substrates
together in position to unite. The
enzyme can alter covalent bonds on
substrates and they break more easily.
The changed substrate is a transition
state intermediate between starting
molecules and the final product. This
lasts a billionth of a second. Once the
activation energy is changed the enzyme
leaves.
In some cases the enzyme may lend an
atom or ion. Enzymes work best at
certain temperatures, pH values, and salt
concentrations. In mammals most work
best at body temperature.
Some chemical reactions work better at
higher temperatures because mlecules
possess more kinetic energy. Increasing
the temperature of an enzyme only
works to a point because enzymes are
proteins, bonds loosen and break. When
a protein loses its shape and activity it is
said to be denatured.
In organisms temperatures higher than
40 degrees C. are usually unfavorable.
A few can survive like archaebacteria
that live in hot springs. Enzymes also
have only a small range of pH where
they work. pH can alter an enzyme by
adding or removing atoms changing its
shape and the way it binds to a
substrate.
Most cell enzymes require an
environment between 6 and 8 but
pepsin in the stomach works best at 2.
The more food you put in your stomach
the higher the pH gets and at 5 the
enzyme stops working. Some enzymes
act as acids and bases. They can donate
or accept H ions to a reaction. By
regulating pH cells control what
enzymes can do.
Highly acid environments are usually
unfavorable. This makes vinegar a good
preservative for pickled foods. Northern
bogs (cranberry and blueberry) are also
strange places where vegetation like peat
moss floating on water will not decay
after it dies. Layers build up and finally
you can jump and bounce on mats of
peat.
Enzymatic reactions must occur in small
steps with each step of a process being
controlled by a different enzyme. There
are 10 different reactions and 10
different enzymes necessary for the
initial part of the breakdown of glucose.
Most organisms including bacteria use
these same 10 steps. The complexity is
due to 4 reasons.
1.Chemical transformations are complex
and require many steps.
2.Many reactions are endergonic to
preceding exergonic reactions. ATP
ADP. (espeially synthesis of large
molecules from small ones, anabolism).
3.Many ergonic reactions would produce
too much heat. (such as breaking down
food, catabolism).
4.In some reactions intermediate
products are starting molecules for
synthesis of building blocks. Ex.
Intermediate steps in breakdown of
sugars to CO2 and H2O are precursors
for amino acids (building blocks of
protein).
The variety of molecules in cells gives
rise to many reactions. Enzymes regulate
the rate of these reactions in response to
environmental change. Organisms have
ways to detect when they have built
enough of a substance to avoid wasting
energy. Ex. Cells make the amino acid
isoleucine from threonine. This requires 5
enzymatic reactions which is energetically
expensive.
When enough isoleucine has
accumulated it shuts down this pathway
by a negative feedback loop. Other
molecules besides end products can
inhibit the action of an enzyme. Enzymes
that normally recognize the shape of an
enzyme can be fooled into binding to
molecules that are similar in size and
shape.
Molecules similar to the substratecan
block an enzymes active site and prevent
the enzyme from working. This is
inhibition by physical shape. In CO
poisoning , CO competes for a site on the
hemoglobin molecule..
Unlike CO most steric inhibitors are
reversible. Steric inhibitors can also be
overcome if the concentration of
substrate is high. The enzyme will bind
to the substrate enough to block the
inhibitor
Substrates and inhibitors compete for the
same enzyme so the more concentrated
substrate is the more effective the
binding. The action of steric inhibitors
is called competitive inhibition.
Some inhibitors are noncompetitive.
Ex. Lead blocks specific groups out of
the active site, which changes the shape
and chemistry of the enzyme.
Inhibitors that bind to enzymes at other
than the active sites are allosteric
inhibitors. Noncompetitive inhibitors
may bind to an an enzyme temporarily,
others irreversibly. Penecillin
irreversibly binds to enzymes necessary
for bacteria to make cell walls. Most
enzymes have evolved so that their
active shape is their most stable shape.