At the atomic level, atoms, ions, and molecules are
particles flying through space at high velocities, bouncing off each other
and the organized surfaces of solid barriers at high rates of speed. When particles collide that
can interact chemically, you may get a
reaction that changes them. This reaction goes on at a rate,
designated k, Q, or V (for
velocity) that is affected by the circumstances. Usually,
a test tube full of particles needs a little "boost" to get
a significant number of them reacting with each other. The
energy needed to get a sizable reaction going is called activation
Page about the "bump" of activation energy, and how a catalyst
can lower it.
Activation energy can be supplied by something that
increases the chances of the reaction happening - heat, which speeds up
the velocity of the particles, is a common activation energy source.
A common measurement applied to reactions is the Q10,
which is the change a rate undergoes when the temperature is raised 10o
C. Many reaction rates come close to doubling with this seemingly
minor change in temperature.
A lot more on Q10.
reactions, energy is released, as the energy state of the products,
the energy still in the system, is lower than that of the reactants. If enough energy is released that
it can provide
activation energy for more reactions, the reaction will continue, fueling
itself. This is an exergonic reaction - an example
would be a burning piece of paper, a fast oxidation reaction that, once
started with enough heat, releases enough heat itself to burn the rest of
the available paper. Many reactions require constant energy input to
run - these are endergonic
reactions. In biological systems, reactions are often coupled - an exergonic
reaction will be used to provide energy to an endergonic one.
Commonly, the exergonic transfer of phosphate
groups, usually from Adenosine Triphosphate (ATP),
can energize molecules in a way that makes them less stable and more likely to
A discussion of the reaction types.
Discussion of endergonic reactions.
One should remember that, even
though the Second
Law of Thermodynamics (the Entropy Law) states that ordered
systems tend to gradually fall apart, this rule does not apply where
available energy can be used to build, sustain, and repair parts of
the system. And even though complex molecules will occasionally break
apart by themselves, they are generally repaired or replaced.
Breakdown is an important process in living systems, but it is breakdown
of specific molecules at specific times, rigidly controlled.
Introduction to the 2nd Law.
How the 2nd Law works in physics.
Another approach to getting reactions
going is to reduce
the activation energy they require to start - this is done by catalysts, which
in biological systems are almost always enzymes.
"grab" reactants (called substrates when
enzymes are involved) in surface dents called active sites
various ways, greatly increase the chances of their reacting, lowering
the energy needed to get them to react. Once reacted, the new product
or products no longer fit in the active site and are
released by the enzyme, which can then grab new substrates.
How catalysts affect activation energy.
Enzymes as catalysts.
A lot about enzymes.
Enzyme activity can be measured with a
reaction rate or with a turnover
number, the number of substrates an enzyme molecule can process in
second. Some reactions are sped up many thousands of times by
enzymes over what might happen without them. The chemistry of our
cells, Life as we know it,
could not proceed without enzymes. The turnover number is a kind of
ideal maximum - it assumes that there are substrates available to be
grabbed when products are released, which is not always true. Some
enzyme-catalyzed reactions are kept closer to maximum possible rate by
confining them to small spaces within a cell - if the substrates and
enzymes are jammed in a small chamber together, it will be easier for them
to interact. This is part of the reason why eukaryote cells have so
many specialized chambers inside them.
Use of turnover numbers in research. (Article)
As substrates are added to a
system with a constant amount of enzymes,
the overall reaction rate follows a pattern called
Kinetics. Take a look at the
graph - you'll see that as
substrate is added, it quickly gets grabbed by available enzymes and the
reaction rate shoots up. However, as more and more substrate gets
added, the enzymes get busier and busier - it's less and less likely that
an added substrate will find an unoccupied enzyme it can attach to - and
the upswing of the reaction rate lessens. The steep rise curves over to a
more-and-more horizontal line. When the line is completely
horizontal, all of the enzyme molecules are busy all the time, no matter how much more
substrate is added, and the rate is as fast as it's going to get - this is
the maximum rate under these circumstances, called Vmax.
Another term, the
Constant, represented as Km,
is set at the substrate concentration for which the rate is half of Vmax.
This becomes a useful way to compare enzymes, and it can measure their binding
strength or affinity. An enzyme with a high affinity
is very "sticky" for substrates, holding onto them longer.
The enzyme molecules will become occupied more
quickly and hit Vmax quickly
with small amounts of substrate. This can be useful when an
enzyme-catalyzed reaction needs to be done constantly in the presence of
substrate, but it's better done at a relatively slow rate. In a
pathway that depends upon multiple enzymes, as substrates become plentiful
the enzyme with the lowest Km (or the enzyme in a lower supply) may become the limiting factor,
a sort of bottleneck in the system - it is this effect, with the buildup
of a toxic
intermediate molecule, that can make an overdose of acetaminophen deadly,
killing the liver cells that are processing it.
Introduction to Michaelis-Menten.
The graph mentioned in the text.
More on Michaelis-Menten.
More on the Michaelis Constant.
Effects of enzyme concentration.