ENZYMES

ENZYME - a biological catalyst.

- WIth the exception of some RNAs that catalyze their own self-cleavage, all enzymes are proteins.
- Enzymes can increase the rate of a reaction by a factor of 10​9 ​to 10​20​ over an uncatalyzed reaction.
● Some catalyze the reaction of only one compound.
- Others are ​stereoselective​; e.g. enzymes that catalyze the reactions of only L-amino acids.
- Others catalyze reaction of​ specific​ types of compounds or bonds; e.g. trypsin catalyzes hydrolysis of peptide bonds
by the carboxyl groups of Lys and Arg.
● Examples of enzymes
- Urease

- Trypsin​: catalyzes the hydrolysis of peptide bonds formed by carboxyl group of lysine and arginine.

CLASSIFICATION OF ENZYMES
- Enzymes are commonly named after the reaction/s they catalyze.
- E.g. lactate dehydrogenase (speeds up the removal of hydrogen from lactate - an oxidation reaction), acid phosphatase
(catalyzes the hydrolysis of phosphate ester bonds under acidic conditions).
- Most enzymes end in “-ase” except pepsin, trypsin, and chymotrypsin - all enzymes of the digestive tract.
● Enzymes are classified into six major groups according to the type of reaction catalyzed.

Reactions Definitions Examples

1. Oxidoreductase Oxidation-reduction reactions.

2. Transferases Group transfer reactions.

3. Hydrolases Hydrolysis reactions

4. Lyases Addition of two groups to a C-C double

bond, or removal of two groups to
create a C-C double bond.

5. Isomerases Isomerization reactions.

6. Ligases Joining of two molecules

ENZYME TERMINOLOGY
● Apoenzyme ​- the protein part of an enzyme.
● Cofactor ​- a nonprotein portion of an enzyme that is necessary for catalytic function; e.g.
metallic ions such as Zn​2+​ and Mg​2+​.
● Coenzyme ​- a nonprotein organic molecule, frequently a B vitamin, that acts as a cofactor.
- B vitamins: important group of coenzymes, which are essential for enzyme activity.
- Heme: another important coenzyme, which is part of several oxidoreductases as well
as of hemoglobin.
● Substrate ​- the compound/s whose reaction an enzyme catalyzes.
● Active site ​- the specific portion of the enzyme to which a substrate binds to during a reaction.
- Schematic diagram of the active site of an enzyme participating components shown
on the right:
● Activation ​- any process that initiates or increases the activity of an enzyme.
● Inhibition ​- any process that makes an active enzyme less active or inactive.
● Competitive inhibitor ​- a substrate that binds to the active site of an enzyme, thereby
preventing binding of substrate.
● Noncompetitive inhibitor ​- any substance that binds to a portion of the enzyme other than the
active site, thereby inhibits the activity of the enzyme.

ENZYME ACTIVITY​ ​- a measure of how much a reaction rate is increased.

● Factors that affect enzyme activity:
- Enzyme concentration
- Substrate concentration
- Temperature
- pH

Factors Effect Diagrams

Enzyme concentration Directly proportional

Substrate concentration Saturation curve - the rate does not

increase continuously once it reaches the
saturation point. In this case, the rate
stays the same even if we increase the
substrate concentration further, since
substrate molecules are bound to all
available active sites of the enzymes.
 Temperature When we start at a low temperature, an
increase in temperature first causes an
increase in rate. However, protein
conformations are very sensitive to
temperature changes. Once the optimal
temperature is reached, any further
increase in temperature alters the enzyme
conformation (hence, substrate may not fit
properly, and rate of reaction decreases).

Optimal temperature: mostly around 37°C

(physiological temperature)

Reversible at small change from optimal

temperature.

pH As the pH of its environment changes the

conformation of a protein, pH-related
effects resemble those observed when the
temperature changes. Each enzyme
operates best at a certain pH.

Reversible at a narrow pH range.

Irreversible at extreme pH values (either
acidic or basic).

MECHANISM OF ACTION
● Enzyme-substrate complex ​- an intermediate compound formed by the combination of catalysts and substrates.

Model Mechanism

Lock-and Key Model - The enzyme is a rigid three-dimensional

body.
- The enzyme surface contains the active
site.

Induced-fit Model - The active site becomes modified to

accommodate the substrate.
 Competitive Inhibition - When a competitive inhibitor enters the
active site, the substrate cannot enter.

Non-competitive Inhibition - The inhibitor binds itself to a site other

than the active site (allosterism), thereby
changing the conformation of the active
site.
- The substrate still binds itself but there is
no catalysis.

Take note:
● Enzyme kinetics in the presence and absence of inhibitors shown on the right:
● Both the the lock-and-key model and the induced fit model emphasize the
shape of the active site.
● However, the chemistry of the active site is the most important.
● Just five amino acids participate in the active site in more than 65% of the
enzyme studied to date:
His > Cys > Asp > Arg > Glu ​(from most to least common)
● Four of these amino acids have either acidic or basic side chains; the fifth has a
sulfhydryl group (-SH).

CATALYTIC POWER
● Enzymes provide an alternative pathway for reaction:
(a) The activation energy profile for a typical reaction.
(b) A comparison of the activation energy profiles for a catalyzed and uncatalyzed reactions.
ENZYME REGULATION
● Feedback Control ​- an enzyme-regulation process where the product of a series of enzyme-catalyzed reactions inhibits an
earlier reaction in the sequence.
- The inhibition may be competitive or noncompetitive.
- The accumulation of the final product serves as a message that tells enzyme 1 to shut down because the cell has
enough final product for its present needs. Shutting down enzyme 1 stops the entire process.

● Proenzyme (zymogen) ​- an inactive form of an enzyme that must have part of its polypeptide chain hydrolyzed and removed
before it becomes active.
○ E.g. ​trypsin​, a digestive enzyme:
- It is synthesized and stored in the pancreas as trypsinogen, which has no enzyme activity.
- It becomes active only after a six-amino acid fragment is hydrolyzed and removed from the N-terminal end
of its chain.
- Removal of this small fragment changes not only the primary structure but also the tertiary structure,
allowing the molecule to achieve its active form.
● Allosterism ​- enzyme regulation based on an event occurring at a place other than the active site.
○ Allosteric enzyme ​- an enzyme regulated by this mechanism.
○ Negative modulation ​- inhibition of an allosteric enzyme.
○ Positive modulation ​- stimulation of an allosteric enzyme.
○ Regulator ​- a substance that binds to an allosteric enzyme.
○ Regulatory site ​- the site to which a regulator attaches itself.
○ Allosteric effect ​- binding of the regulator to a site other than the active site changes the shape
of the active site: as shown on the right
○ Effects of binding activators and inhibitors to allosteric enzymes: the enzyme has an equilibrium
between ​T form ​(less active form) and the ​R form ​(more active form):

● Protein modification ​- the process of affecting enzyme activity by covalently modifying it.
- The best known example of protein modification involves phosphorylation/dephosphorylation.
- E.g. pyruvate kinase (PK): the active form of the enzyme; it is activated by phosphorylation to pyruvate kinase
phosphate (PKP):
 ● Isoenzyme (isozymes) ​- an enzyme that occurs in multiple forms; each catalyzes the same reaction.
- E.g. lactate dehydrogenase (LDH): catalyzes the oxidation of lactate to pyruvate.
- The enzyme is a tetramer of H and M chains.
- H​4​ is present predominantly in heart muscle, and is allosterically inhibited by high levels of pyruvate (its product) and
has a higher affinity for lactate (its substrate).
- M​4​ is present in predominantly in the liver and in skeletal muscle, and favors the production of lactate.
- The isoenzymes of lactate dehydrogenase (LDH): the electrophoresis gel depicts the relative isozyme types found in
different tissues:

ENZYMES USED IN MEDICINE

TRANSITION STATE ANALOG - a molecule whose shape mimics the transition of a substrate.
● Proline racemase reaction ​- pyrrole 2-carboxylate mimics the planar transition state reaction:
● Abzymes ​- an antibody that has catalytic activity because it was created using a transition state analog as an immunogen.
(a) The molecule below is a transition analog for the reaction of an amino acid with pyridoxal-5’-phosphate.
(b) The abzyme is then used to catalyze the reaction that follows after: