ENZYMES

By:
Roselita O. Natividad
Nat. Science – Ateneo de Zamboanga University

➢ are made up of protein molecules

➢ catalyze chemical reactions in the body, thus, they are biologic catalysts
➢ as catalyst, they are highly specific
➢ the name ends in - ase such as amylase, peptidase

Classification according to the type of reaction they catalyze:

1. Oxidoreductases catalyze oxidation and reduction reactions
2. Transferases catalyze the transfer of a group of atoms such as methyl, amino, carboxyl, carbonyl,
phosphoryl, acyl
3. Hydrolases catalyze hydrolysis reactions. These include the esterases, phosphatases, and peptidases
4. Lyases catalyze the addition of atoms or groups of atoms to a double bond to form a single bond or the
removal of two atoms or groups of atoms from adjacent carbons to create a double bond
5. Isomerases catalyze isomerization reactions
6. Ligases, or synthetases, catalyze the joining of two molecules

Common terms associated in Enzyme Chemistry

Apoenzyme is the protein portion of the enzyme

Confactor is the non-protein portion of the enzyme. May be metallic ions such as Zn2+ or Mg2+ or they
may be organic compounds

Coenzymes are organic cofactors (Example are the B Vitamins)

Substrate is the compound on which the enzyme works

Active site is the specific portion of the enzyme to which the substrate binds during the reaction

Factors Affecting Enzyme Activity

➢ Enzyme activity is a measure of how much reaction rates are increased
➢ Activation is any process that initiates or increases the action of an enzyme. Any process that
makes an active enzyme less active or inactive is called inhibition
➢ Competitive inhibitors bind to the active site of the enzyme surface, thus preventing the binding
of substrate
➢ Noncompetitive inhibitors bind to some portion of the enzyme so that its catalytic effectiveness is
slowed

1. Enzyme and substrate concentration

➢ If the concentration of the substrate is kept constant and increases the concentration of the
enzyme, the rate of reaction increases linearly. Because in practically all enzyme reaction the
molar concentration of the enzyme is almost always much lower than that of substrate, thus there
is enough enzymes to react with the substrate

Enzyme concentration
 ➢ If the concentration of the enzyme is kept constant and the concentration of the substrate is
increased, a point is reached after which the rate of the reaction stays the same even if the
concentration of the substrate is increased further. This is because that the point of saturation has
reached. That is, enzymes are all occupied already that increase in the concentration of the
substrate can no longer increase the rate because excess substrate cannot find any active sites to
attach to.

Substrate concentration

2. Temperature
➢ temperature affects enzyme activity because it changes the three-dimensional structure of the
enzyme. Once the optimum temperature is reached, any further increase in temperature causes
changes in enzyme conformation. The substrate may then not fit properly onto the changed
enzyme surface resulting to a decrease in the reaction

Temperature

3. pH
➢ enzymes operates best at a certain pH. Any extreme change in pH will denature the enzyme

Mechanism of Action
1) Lock-and-key model. This model assumes that the enzyme is a rigid three-dimensional body. The body
that contains the active site has a restricted opening into which only one kind of substrate can fit. The
substrate’s overall shape and charge distribution allow it to enter and interact with the enzyme’s
active site.
 2) Induced-fit model. In this model the enzymes modifies the shape of the active site to accommodate
the substrate. The non-covalent interactions between the enzyme and the substrate change the 3-
dimensional structure of the active site, conforming the shape of the active site to the shape of the
substrate.

Enzyme regulation
1) Feedback control. Formation of a product inhibits an earlier reaction in the sequence. That is, the
reaction product of one enzyme may control the activity of another. In short, the concentration of
products influences the rate of reaction.

E1 E2 E3
A B C D

2) Allosterism. In this reaction, an interaction takes place at a position other than the active site but
affects the active site, either positively or negatively

3) Protein modification. This modification is usually a change in the primary structure mostly by the
addition of a functional group covalently bound to the Apoenzyme to either activate or inhibit the
reaction
Role of Metal Ions as Cofactors in the Enzyme
➢ the functional groups of proteins can easily participate in acid-base reactions, forming certain
types of transient covalent bonds and also take part in charge-charge interactions
➢ although, enzymes can catalyze such reaction but they can only do so with the help of cofactors
which essentially act as the enzymes “chemical teeth”
➢ they are of two types:
o metalloenzymes – with built-in metals
o metallo-activates enzyme – in which enzymes are added for activity
➢ hasten enzyme reactions
➢ explains why we need trace amounts of certain elements in our diet
➢ it also explains, the toxic effect of some heavy metals such as Cd, Hg, because they can replace Zn
➢ the important metals falls in to parts :
o alkali and alkaline earth metals – rarely found in tight complexes with proteins
o transition – because of their electronic configuration, they are most often involved in
catalysis
➢ provide a high concentration of (+) charge that is useful in binding small molecules
o also act as Lewis acid, thus effective electrophile
➢ because of their directed valences, it allows them to interact with 2 or more ligands and so metal
ions help orient the substrate within the active site
➢ as a consequence, the substrate-metal ion complex polarizes the substrate and promote catalysis
➢ finally, because transition metals have 2 or more valence states, they can mediate redox reactions

Organic molecules as coenzymes

➢ such as NAD are transiently associated with a given enzyme molecule so that they function as co-
substrate
➢ some coenzymes are known as prosthetic groups because they are permanently associated with
their proteins often by covalent bond
➢ many of the vitamins (especially water-soluble) are coenzymes

source coenzymes type of reaction

biotin biocytin carboxylation

panthotenate CoA acyl transfer
B12 cabalmin coenzymes alkylation
B2 flavin coenzymes oxidation – reduction
Niacin nicotinamide coenzymes oxidation – reduction

Questions
1. Differentiate between cofactor and coenzyme?
2. What is the role of cofactors in enzyme catalysis?
3. Inhibition of enzyme activity may be reversible or irreversible. Describe each.
4. What are the two types of enzyme inhibitors? Describe each.
5. How do enzymes differ to that of ordinary catalysts in terms of their functions? Describe each.
6. Trypsin cleaves polypeptide chains at the carboxyl side of a lysine or arginine residue. Chymotrypsin
cleaves polypeptide chains on the carboxyl side of an aromatic amino acid residue or nonpolar, bulky
side chain. Which is more specific? Explain.