Enzymes

3.1 Nature of Enzymes

What are enzyme molecules like?

• An enzyme is a globular protein with a unique tertiary structure, which gives it a unique shape and a
uniquely shaped active site.

• Active site is the part of an enzyme that binds with its substrate.
• Substrate is a substance upon which an enzyme acts in a biochemical reaction. During a reaction, a
substrate binds with the active site of an enzyme to form an enzyme-substrate complex.

• Enzyme-substrate complex is the intermediate formed, temporarily, when an enzyme binds to its
substrate.

E+S⟶ES⟶P+EE+S⟶ES⟶P+E
E = enzyme S = substrate ES = Enzyme-substrate complex P = product

Properties of enzymes
• All enzymes are globular proteins.
• They are biological catalysts: they speed up a reaction.
• They catalyze chemical reactions without being charged or used up.
• They can be used over and over again.
• They lower the energy needed for reactions to take place.
• They are specific: they catalyze one reaction only.
• They are affected by pH, temperature, the concentration of their substrate and the presence of
inhibitors.

What are catalysts?

• A catalyst is a substance that speeds up a reaction; the reaction itself is unaltered. There is no
overall change to:

⇒⇒ the catalyst itself

⇒⇒ the nature of the products
⇒⇒ the energy change that takes place during the reaction

• Not all catalysts are proteins. Some RNA molecules can catalyze some biological reactions.

Why are enzymes specific?

• Enzymes are specific because they have a uniquely shaped active site. The conformation of the
active site (the way in which it is shaped) allows an enzyme to bind to only a certain substrate or
combination of substances.

How do we name and classify enzymes?

• Different enzymes are named in different ways:

⇒⇒ by adding the suffix – ase to the name of the substrate; e.g. sucrase, lipase, urease, etc.
⇒⇒ by the type of reaction that they catalyze; e.g. polymerase, dehydrogenase, etc.
⇒⇒ by the source from which they were first identified; e.g. papayin, intestinal protease, etc.
⇒⇒ by ending the name of the enzyme with 'in', indicating that they are proteins; e.g. pepsin, trypsin,
erypsin, etc

Some enzymes and the reactions that they catalyze

• Proteases: enzymes that act on proteins. Examples include Pepsin, trypsin and erypsin
• Carbohydrases: enzymes that act on carbohydrates. Examples include maltase, sucrase, lactase
and cellulase
• Lipase: an enzyme that hydrolyzes lipids
• ATPase: an enzyme that hydrolyzes ATP
• Dehydrogenase: an enzyme that removes hydrogen ions from a substance
• Polymerase: an enzyme that joins monomers to form a polymer

Enzyme classification and the systematic

nomenclature of enzymes
• Enzymes are grouped into six based on the type of reactions that they catalyze:

1. Oxidoreductases — transfer of hydrogen and oxygen atoms or electrons from one substrate to
another. E.g. Dehydrogenases and oxidases
2. Transferases — transfer of a specific group (a phosphate or methyl, etc.) from one substrate to
another E.g. Transaminases and Kinases
3. Hydrolases — hydrolysis of a substrate E.g. Esterases and digestive enzymes
4. Isomerases — change of the molecular form of a substrate E.g. Fumarases and
Phosphohexoisomerase and
5. Lyases — non -hydrolytic removal of a group or addition of a group to a substrate E.g. Decarboxylases
and aldolases
6. Ligases (Synthetase) — joining of two molecules by the formation of new bonds E.g. Citric acid
synthetase

• In a systematic naming of enzymes decided by the enzyme commission, each enzyme has a name
associated with numbers, such as EC 3.4.11.1. Each part tells us something about the enzyme.
What do Enzymes do for us?
• Some enzymes commonly used in industries include:

⇒⇒ Biochymosin: It is used to produce cheese.

⇒⇒ Lactase: It is used to produce lactose-free milk.
⇒⇒ Proteases, lipases and amylases: They are used in biological washing powders to remove
biological stains. Proteases and amylases are also used in dishwasher detergents. In textiles, proteases
are used to remove hair whereas lipases are used to degrease animal hides.
⇒⇒ Cellulase: It is used in textiles to ‘bio-polish’ cotton fabrics and ‘bio-stone’ denim.
⇒⇒ Pectinase: It is used in food processing to clarify fruit juice.
⇒⇒ Glucose oxidase: It allows easy diagnosis of diabetes by testing urine
⇒⇒ Streptokinase: It is used to dissolve clots of heart-attack patients
3.2 Functions of enzymes
How do enzymes act as catalysts?

• In order for a chemical reaction to take place the reacting molecules must first collide and then have
sufficient energy to trigger the formation of new bonds.

• Activation energy is the energy which is required to produce a collision that is powerful enough to
start off a chemical reaction.

• An enzyme is able to catalyze a reaction by lowering the activation energy required for the reaction.
More reactants molecules can meet this lower energy requirement and so the reaction proceeds
more quickly.

How do enzymes lower activation energy?

• There are two models of enzyme action; the Lock-and-key model and the induced-fit-model.

1. Lock-and-key model — this model proposes that the shapes of the substrate molecules are
complementary (completely fit) to that of the active site. The complementary substrate molecule binds
with the active site of the molecule to form the enzyme-substrate complex. The complex causes the
reactants to enter a transition (intermediate) state in which the activation energy is lowered. However, the
model does not explain how the intermediate reduces activation energy. This model was first proposed by
a German biochemist named Fischer.
2. Induced-fit-model — this model suggests that the active site and the substrate are not naturally
complementary in shape, but the binding of substrate molecules produces a conformational change
(change in shape) in the active site that allows the substrate and active site to bind fully. In the induced-
fit-mode, the conformational charge of the active site puts the substrate molecules under tension, so they
enter a transitional state and are able to react due to the lowed activation energy. This model was
proposed by Koshland.

Why do some enzymes need cofactos?

• Holoenzyme is an active enzyme which is made from two molecules called apoenzyme and cofactor.
• Apoenzyme is the protein part of a Holoenzyme.
• Cofactor is a small non-protein particle of the Holoenzyme.
• Cofactors include mineral ions or coenzymes (organic molecules, usually derived from vitamins
which act as cofactors). NAD and FAD are coenzymes derived from the vitamins niacin and riboflavin
respectivel

3.3 Factors affecting the functions of enzymes

• The turnover rate is the number of molecules of reactants that form enzyme-substrate complexes
with each molecule of an enzyme per second.
• The turnover rate and, therefore, the activity of the enzyme are influenced by a number of external
factors including temperature, pH, substrate concentration and inhibitors.
• Enzymes work best within specific ranges of temperature and pH.
• Optimum temperature is the temperature at which an enzyme works most efficiently.
• Effect of temperature: Increasing the temperature generally increases reaction rates because the
molecules are moving more quickly and are more likely to come into contact with each other.
• The Effect of pH: Enzymes function in a narrow pH value. Significant changes in temperature and
pH denature enzymes.
• Denaturation is the alternation of the tertiary structure of a protein.
• The Effect of substrate concentration: Increasing the concentration of the substrates usually
increases the rate of enzymatic activities by increasing collusions among substrate molecules.
However, increasing the concentration beyond Vmax (the maximum rate of enzyme action) will have no
effect on the activity of an enzyme.

• The effect of enzyme concentration: increasing the concentration of an enzyme will increase the
reaction time. However, this will not increase the activity of the enzyme.

How do other substances affect enzyme activity?

• Inhibitors are substances that bind to enzymes and prevent them from forming enzyme-substrate
complexes. There are two types of inhibitors:

1. Irreversible inhibitors bind strongly to enzymes, usually by covalent bond, permanently altering the
structure of the enzyme molecule and inactivating it. .
2. Reversible inhibitors bind to enzymes only weakly and the bond that holds breaks easily releasing
the inhibitor. This allows the enzyme to become active again.
There are two main kinds of reversible inhibitors; competitive inhibitors and non-competitive inhibitors.
Competitive inhibitors are molecules that inhibit enzyme activity by competing with the substrate for the
active site. They have shapes that are complementary to all, or part, of the active site of an enzyme. In
competitive inhibition, increasing substrate concentration decreases the effect of the inhibitor.
Non-competitive inhibitors are molecules that alter the conformation of the active site by binding with
the allosteric sites of the enzymes; they prevent the substrates from binding and inhibit enzyme activities.
They do not compete with the substrates for the active site. In non-competitive inhibition, increasing
substrate concentration has no effect on the effectiveness of the inhibitor.
Allosteric site is a binding site on an enzyme other than the active site.

How do inhibitors control enzyme activity in living cells?

• Many substances are produced in cells as a result of a metabolic pathway (a series of reactions),
controlled by different enzymes.

• Inhibition of any enzyme in a metabolic pathway will interrupt the whole process.

• In some metabolic pathways in living cells, the end product of a pathway acts as a non-competitive
inhibitor of the enzyme that catalyzes the first stage of the series.

• End-product inhibition is a type of enzyme inhibition that occurs when an end product inhibits the
enzyme controlling the first stage of a reaction sequence.

• When the end product is required by the cells, it will be removed by a chemical substance; so it stops
acting like an inhibitor.

• Activator is a substance that removes an inhibitor.