Module 11: Enzymes

Enzymes are biological catalysts that speed up chemical reactions inside cells.
• Most enzymes are proteins
◦ enzymes can also be composed of RNA; ribozymes.
• Enzymes interact with specific molecules, allowing them to proceed down a specific
biochemical pathway.
• Enzymes are necessary to produce a consistent and abundant supply of ATP, which provides
the energy required by cells to sustain life.
• Detoxifying toxic substances; alcohol dehydrogenase breaks down alcohol to facilitate its
removal from the body.

Enzymes facilitate the transformation of initial substances called substrates into different
molecules called products.
• Enzymes that build molecules are often called syntheses. An isomerase, like ribose isomerase,
is an enzyme that rearranges a molecule into its isomer.

As substrates are transformed into products during a chemical reaction, they go through an
intermediate transition state.
‣ The chemical reaction is at its highest energy at the transition state.

• The difference between the energy level of the substrate and the energy level of the transition
state is called the activation energy.
◦ Activation energy is the energy needed to overcome the energy barrier of breaking and
reforming bonds for a reaction to proceed.

Every enzyme has an active site, a pocket where it binds its substrates.
◦ formed at the tertiary or quaternary level of protein structure and is where the chemical
transformation of substrate to product occurs.
◦ Most enzymes act on a specific, preferred substrate, although some will act on multiple
substrates that are similar to each other.
◦ When the substrate enters the active site of the enzyme, the substrate and the enzyme
bind together to form an enzyme-substrate complex.
◦ The enzyme and substrate(s) interact through transient hydrogen bonding and ionic and
hydrophobic interactions between the substrate and the R-groups of the enzyme's amino
acids.
‣ These non-covalent bonds position the substrate(s) in ways that favor a specific
chemical reaction to occur.

There are two important things to remember about how enzymes work.

• First, the reaction does not permanently change the enzyme's chemistry or conformation.
‣ Although the enzyme facilitates the reaction that converts substrates into products,
and while the enzyme will often change its shape, or conformation, during the
reaction, it reverts to its original conformation once the reaction is completed

• Second, enzymes exhibit remarkable substrate specificity. The induced-fit model of enzyme
reactions has replaced the lock-and-key model. The induced-fit model builds on the same
basic idea — that the enzyme is specific to one "correct" substrate — but it also takes into
account that the enzyme changes its shape in response to the presence of the substrate. The
 specificity of the enzyme to the substrate allows cells to regulate metabolic reactions very
closely. Often an enzyme that works on glucose will not bind any other sugar isomers, which
allows the cell to regulate exactly which reactions are happening at any given time. However,
enzymes can be "tricked" if a chemical has a region that can bind to the active site.

Some enzymes require substances known as cofactors in order to be biologically functional

catalysts.
• Cofactors are typically involved in the transfer of chemical groups between molecules, helping
transform substrates into final products.
• Some cofactors are metal ions such as iron (Fe2+ and Fe3+), magnesium (Mg2+), and zinc
(Zn2+), which are involved in electron transfer.

• Coenzymes are small organic cofactors that bind to enzymes

◦ For example, coenzyme A interacts with acetyl groups in fatty acid synthesis and pyruvate
oxidation pathways of cellular respiration. Coenzyme A plays such an important role in
these reactions, among many others, that it is present in all living cells. Other common
coenzymes include molecules such as ATP, NAD+, and NADP+; the latter two are
essential in cellular respiration and photosynthesis, respectively. Both coenzymes and
inorganic cofactors can bind tightly or transiently to the active site and help the enzyme-
substrate complex form.

Enzymes lower activation energy of biochemical reactions, but the substrates still need to have
enough kinetic energy to reach their transition state, allowing the reaction to occur.

The temperature at which the enzyme works best is called the enzyme's optimum temperature.
• Lowering the temperature decreases kinetic energy, so fewer chemical reactions reach the
necessary activation energy, even with an enzyme present.
◦ Increasing the temperature increases the Brownian motion (random movement) of the
substrate molecules, increasing the number of collisions between substrates and
enzymes.
‣ Also, increased vibrations in the bonds of the substrates reduce their stability, making
them more likely to break. Thus, raising temperature generally increases the reaction
rate.
◦ if the temperature is too high, the increased kinetic energy can irreversibly denature the
enzyme by breaking down some of the bonds that hold together the three-dimensional
structure of the enzyme.
‣ Denatured enzymes are no longer able to catalyze biochemical reactions.
‣ Fevers are dangerous!!
• the increased temperature over an extended period of time can denature human
proteins.

Not all enzymes have the same optimum temperature; most human enzymes have an
optimum temperature around 37°C (human body temperature).
• Many of our enzymes denature above 50°C.

Enzymes are also sensitive to changes in pH.

• Each enzyme has an optimal pH at which it functions most effectively.
◦ If the pH is below an enzyme's optimum, the enzyme becomes inappropriately
protonated, which can change the shape of its active site as well as its interactions with
the substrates.
◦ As a result, when the pH is suboptimal it is more difficult for the enzyme-substrate
complex to form.
◦ Likewise, if the pH is too high, the enzyme becomes inappropriately deprotonated, which
will have similar effects on the enzyme's conformation.
◦ In addition, extreme pH can disrupt the bonds holding the three-dimensional structure of
the enzyme together, causing the enzyme to denature.

Enzymes catalyze almost all of the chemical reactions required for life, but only some of them are
active at any given time.
• A cell regulates enzymes by turning them off or on. Some enzymes begin in the "on" position
and are active until something specifically inhibits them.
• Others begin in the "off" position until something activates them.
• The regulation mechanisms used by the cell are reversible, which means that a cell can turn
enzymes on or off as needed.

• In feedback inhibition, the products of an enzymatic pathway bind to and inhibit enzymes in
the pathway.
◦ Feedback inhibition often involves the product inhibiting an enzyme near the very
beginning of the pathway, so that there are fewer intermediates produced that are already
committed to the pathway.
‣ Feedback inhibition tells us what is inhibiting the enzyme, but it does not tell us how
the enzyme is being inhibited.

In competitive inhibition, inhibitor molecules that are similar to the substrate bind to the
enzyme's active site but do not react.
• Because the active site is occupied by the inhibitor, the enzyme cannot bind any substrates to
catalyze the reaction.
• As a result, inhibitor molecules compete with substrate molecules for the active site and overall
reduce the rate of the reaction catalyzed by the enzyme.

Allosteric inhibition, also known as non-competitive inhibition, involves inhibitors that do not
bind to the active site. Instead, allosteric inhibitors bind to an allosteric site separate from the
active site.
• The binding of an allosteric inhibitor to an enzyme changes the conformation of the enzyme so
that the active site is no longer able to bind to the substrate.
• Allosteric inhibition turns enzymes off; conversely, allosteric activation turns enzymes on.
Enzymes regulated by an allosteric activator are inactive until the allosteric activator binds to
the allosteric site.
• Before the allosteric activator binds, the active site is inaccessible to the substrate. Upon
binding the allosteric activator, the enzyme undergoes conformational changes, exposing the
active site and allowing the substrate to bind to it.