161Zero to Genetic Engineering Hero - Chapter 6 - Processing Enzymes
X-gal is considered a “normal” small molecule
with a “normal” rate of movement for a small
molecule. A “normal” amount can be estimated
at up to 10
collisions per second. In the world
of biochemistry, each molecule can have up to
100,000,000,000,000,000,000 or 100 quintillion
collisions with other molecules each second! If you
were an atom or small molecule, this is the equiv-
alent of you brushing elbows with every person on
earth 17 billion times each second. In other words,
every protein enzyme in the cell, such as beta-ga-
lactosidase, has MANY opportunities to interact
with its substrate, X-gal, hundreds or thousands
of times each second. This is why an enzyme can
cause a chemical reaction to happen. You might
recall RNA polymerase can typically add 50 ribo-
nucleotides to an RNA transcript each second.
A single catalase enzyme can turn thousands of
hydrogen peroxide molecules into oxygen and
water every second.
This can be simplified into knowing that mole-
cules typically interact (“bump”) a billion times a
second with other molecules within the cell. This
means that often two molecules will bump into
one another countless times per second and it
might take millions of bumps before a substrate
“key” bumps into the enzyme “lock”, resulting in
a chemical reaction.
• The strength of interaction between molecules:
The most important factor in determining the
operation or decision making in a cell is bonding.
The specic interaction between molecules is the
“logic” that drives specic events in cells. In the
X-gal example, the protein enzyme beta-galacto-
sidase has the right structure and composition
to be able to bind quite specically to X-gal, and
X-gal alone. It does not bind to other molecules in
the cell with any notable strength or specicity. It
is ‘beta-galactosidase’s job’ to bind specically to
X-gal and catalyze the chemical reaction that cuts
off a sugar ring allowing X-gal to dimerize and
become colorful (Figure 6-6).
If the interaction is strong, the substrate is more
likely to get “locked” in place in the protein enzyme
active site, the site at which the chemical reac-
tion happens. If the bonding interaction between
the enzyme and the substrate is weak, then the
substrate will not “lock” into place in the enzyme
active site. The strength of an interaction between
molecules is dened by its dissociation constant,
discussed in the breakout below.
The same principles apply to the thousands of other
protein enzymes in a cell. But what is an interaction?
What does it mean when a substrate gets “locked into
place”? In the next sections, we’ll dig a little deeper
into atoms, molecules, and the bonding that makes
it all happen so that we may answer these questions.
Before learning what causes the interactions between
substrates, protein enzymes and having a more
in-depth discussion about chemical reactions, we
need to see what an atom is.
An atom is very small and generally considered the
smallest unit of matter. A single atom is usually about
300 picometers in width, which is 0.0000000003
meters, or about a million times thinner than a
human hair. An atom has two essential attributes:
Nucleus: a very dense core called a nucleus,
contains sub-atomic particles called protons
(which are positively charged), and neutrons
(which have no charge). The nucleus makes up
more than 99% of the mass of each atom and has
a positive charge.
Electron clouds: electrons are very small nega-
tively charged atomic particles that orbit the
nucleus very fast in “cloud-like” patterns. The
electron clouds are called orbitals, and they are
Dissociation constant Web Search Breakout
Theequilibrium dissociation constant (K
) is used to evaluate and rank strengths of molecular interac-
tions. You can search for this, as well as “Enzyme Kinetics”, “Michaelis-Menten Kinetics” and “Specicity
Constant” online to learn more in-depth. Each of these topics discusses how the strength of bonding
between a substrate and an enzyme relate to the specicity of the chemical reaction (how well a substrate
“locks in place”), as well as the speed of the chemical reaction.
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