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BCH 321
Lecture Notes
Enzymes
Properties of Enzymes
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Enzyme are protein catalysts
Enzyme show a high catalytic efficiency
Enzymes are highly specific
Some enzymes contain a nonprotein cofactor that needed enzymatic activity
Enzyme activity can be regulated
The basic mechanism by which enzymes catalyze chemical reactions begins with the
binding of the substrate (or substrates) to the active site on the enzyme. The active
site is the specific region of the enzyme which combines with the substrate. The
binding of the substrate to the enzyme causes changes in the distribution of electrons
in the chemical bonds of the substrate and ultimately causes the reactions that lead to
the formation of products. The products are released from the enzyme surface to
regenerate the enzyme for another reaction cycle.
The active site has a unique geometric shape that is complementary to the geometric
shape of a substrate molecule, similar to the fit of puzzle pieces. This means that
enzymes specifically react with only one or a very few similar compounds.
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Enzymes are typically large proteins, contain an active site.
Lock and Key Theory: The specific action of an enzyme with a single substrate
can be explained using a Lock and Key analogy first postulated in 1894 by Emil
Fischer. In this analogy, the lock is the enzyme and the key is the substrate. Only
the correctly sized key (substrate) fits into the key hole (active site) of the lock
(enzyme). Smaller keys, larger keys, or incorrectly positioned teeth on keys
(incorrectly shaped or sized substrate molecules) do not fit into the lock (enzyme).
Only the correctly shaped key opens a particular lock. This is illustrated in graphic
on the left.
Induced Fit Theory: Not all experimental evidence can be adequately explained
by using the so-called rigid enzyme model assumed by the lock and key theory.
For this reason, a modification called the induced-fit theory has been proposed.
The induced-fit theory assumes that the substrate plays a role in determining the
final shape of the enzyme and that the enzyme is partially flexible. This explains
why certain compounds can bind to the enzyme but do not react because the
enzyme has been distorted too much. Other molecules may be too small to induce
the proper alignment and therefore cannot react. Only the proper substrate is
capable of inducing the proper alignment of the active site.
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Substrate binds to active site in highly 3D specific orientation.
View binding of substrate (protein to be digested) to active site of digestive
enzyme chymotrypsin.
Enzyme + Substrate form temporary chemical bonds, both weak and strong.
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Enzyme facilitates bringing substrates into exact alignment needed for
transition state to be achieved. This often involves temporary changes in shape
of enzyme, called Induced Fit.
Net effect of enzyme is to lower activation energy.
Enzyme dissociates from product after reaction is complete (thousandths of a
second typically)
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Enzyme is unchanged, able to recycle again
Typical equation: E + S E-S complex E + P
Explore Lysozyme as a sample enzyme
o Lysozyme is an enzyme that hydrolyzes (breaks down) the cell walls
of bacteria. Lysozyme is very common; it is found in saliva, in
digestive fluids, even in body secretions. It is one of the first lines of
defense against bacterial infection.
o Lysozyme is a small enzyme, a single polypeptide chain with both
alpha helix and beta sheet regions.
o view the lysozyme-substrate complex. Explore various settings, and
observe the fit between enzyme and substrate.
Enzymes accelerate chemical reactions by factors of
1010 to 1015
1. Difference between presence or absence of enyzme is enormous.
2. Example: breakdown of urea (nitrogenous waste in urine) would take about a
year without enzyme, only millionth of a second with enzyme.
3. Enzymes characterized by a turnover number: typically 1000s to millions of
reactions per second
4. Cell chemistry is absolutely dependent on enzyme; if one type of enzyme if
lost, that reaction will no longer occur at useful rates, for practial purposes will
not occur at all.
Enzymes are named by adding the suffix -ase
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Example 1: the enzyme deoxyribonuclease, or DNAse, breaks down DNA
Example 2: the enzyme lactase attacks the disaccharide sugar lactose
Exceptions: a few very familiar enzymes retain older names: trypsin,
chymotrypsin, etc.
Specificity of enzymes is variable
1. Some enzymes work on one unique substrate only
2. Others will accept a variety of substrates that have certain types of chemical
similarity; will work better on some, poorer on others
Many enzymes require cofactors
1. some enzymes have tightly bound helpers called coenzymes or cofactors
2. Cofactors can be single metal ions (Mg, Zn, Co, Mn, etc)
3. Cofactors can be small organic molecule called coenzyme
Many enzymes can be inhibited
1. A molecule with very similar 3-D shape to the substrate may bind to active
site, block substrate. This is called a competitive inhibitor.
2. Competitive inhibition always depends on relative concentrations of substrate
and inhibitor. More inhibitor, more inhibition. Less inhibitor, less inhibition.
3. Something that changes protein structure (e.g. by binding to the enzyme at
some site outside the active site) can block enzyme activity. This is called
noncompetitive inhibition.
Enzyme activity can be regulated in different ways
1. Consider Regulatory problem of cell: thousands of enzymes, each with a
"mind of its own". Yet cell needs overall stability.
2. Example: synthesis of a certain amino acid. Reaction scheme looks like this:
3. Suppose supply of E in cell increases (e.g. eat a meal rich in E). How to shut
down synthesis of E?
4. Cell's answer: Enzyme 1 is reversibly inhibited by E. Note that E is not the
substrate, and chemically so different that it cannot bind to active site. How
does E shut down Enzyme 1?
5. Enz 1 is a special type of enzyme called an allosteric enzyme. It causes
feedback inhibition. Allosteric enzymes contains two distinct subunits, one
with active site (binds substrate A and catalyzes reaction), one with allosteric
site (binds E).
6. When E binds, causes shape change in the enzyme, this is transmitted to block
activity of active site.
7. Net result: whole pathway is turned on or off as a unit by end-product. Called
Feedback inhibition. Crucial to cell regulation.
Factors Affecting
Reactions:
1. Substrate concentration
2. Temperature
3. pH
the
Velocity
of
Enzyme-catalyzed