F A C U L T Y O F M E D I C I N E

F a l l 2 0 2 2
Faculty of Medicine
Basic Medical Sciences
Medical Biochemistry & Molecular Biology
BMS131, LEC05
Introduction to Medical Enzymology

P r o f . R e e m M . S a l l a m
M e d . B i o c h e m i s t r y &
M o l e c u l Faculty
a ofr MedicineB i o l o g y
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Intended Learning Outcomes
By the end of this lecture, you should be able to:

• Define most commonly used enzyme-related

terms
• Explain different systems of enzyme
nomenclature.
• Identify the nature and general properties of
enzymes

Faculty of Medicine 3
ENZYMES
• Enzymes are biological catalysts.
• Most enzymes are proteins (globular proteins with
specialized 3-D shapes).
• All reactions in the body are mediated by enzymes.
• Some enzymes have names that give no idea of
function or reaction catalyzed by the enzyme. e.g.:
pepsin, trypsin, thrombin

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 What is a catalyst?
A catalyst increases
the rate of the
reaction without
being changed in the
overall process.

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Enzymes Nomenclature
Convenient (Trivial Name)
Most commonly used
Short name, for everyday use
• Substrate name + “-ase”
e.g.: glucosidase, Urease
Or:
• First name is of substrate
• Second, ending in “ASE”
indicating type of reaction
catalyzed.
e.g.: lactate dehydrogenase,
Adenylyl cyclase
Systematic (According to International
Union of Biochemistry & Molecular
Biology, IUBMB) Not easy for general use
More complete, Unambiguous, informative
Six major classes:
1. Oxidoreductases
2. Transferases
3. Hydrolases
4. Lyases
5. Isomerases
6. Ligases
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Enzymes Nomenclature; according to IUBMB
Class Action (Catalyze which reaction?)
Oxidoreductases Oxidation-reduction (one substrate is oxidized & other is
reduced ) e.g. Lactate dehydrogenase.
Transferases Group transfer (e.g. Transaminase)
Hydrolases Cleavage of bonds by addition of water (breakdown) e.g.
Urease (has absolute specificity to urea)
Lyases Removal of groups by mechanism other than hydrolysis
(e.g. Pyruvate decarboxylase)
Isomerases Interconversion of isomers (e.g. phosphoglucose isomerase)
Ligases Formation of bonds and new compounds (coupled to hydrolysis
of high energy phosphates; e.g. Pyruvate carboxylase) 7
Enzyme Commission Number
(EC number)

According to the IUBMB, all enzymes are

assigned an “EC” number, which is composed
of four digits.
Example
Recommended (convenient): Lactate Dehydrogenase
Systematic name: Lactate:NAD+ Oxidoreductase
EC number: 1.1.1.27 (Just for you to know)

Lactate
dehydrogenase
Lactic acid Pyruvic acid
+ NAD+ + NADH + H+

NAD+ is considered a coenzyme, co-substrate

Active Site of an Enzyme
• A special pocket or cleft
• Formed by folding of the
protein
• Contains AA side chains
that participate in
substrate binding &
catalysis

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 Induced-Fit Model of Substrate
Binding to Enzyme
• Substrate (S) binds to Enzyme (E) à Enyme –substrate complex (ES)
à conformational change in the enzyme à catalysis à Enzyme–
product (EP) complex à E + P

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Efficiency of Enzyme = Catalytic power of enzymes

• Enzyme-catalyzed reactions are highly efficient

• Enzymes increase the rate of reaction by a factor of 102 - 108 or higher.
• The turnover number (Kcat): The number of substrate molecules converted to
product /enzyme molecule/ second
• For example:
• The kcat for chymotrypsin, is 100 per second i.e. 100 molecules of substrate
(proteins) are converted to product /enzyme molecule/ second
• In 10 seconds, 1000 molecules of substrate (proteins) are converted to product /enzyme
molecule.
• In 1 second, 20 molecules of chymotrypsin will convert 2000 molecules of substrate
(proteins) to product (cleaved proteins)

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Enzyme’s Specificity
• Enzymes are highly specific.
• They interact with one or a few substrates
• They catalyze only one type of chemical reaction

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 Holoenzyme & Apoenzymes
• Some Enzymes require non-
protein molecules to be
active.
• Holoenzyme: the active
enzyme with its non-protein
component.
• Apoenzyme (inactive) : the
enzyme without its non-
protein molecule.

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 The non-protein part
(Cofactor & Coenzyme)
• Cofactors are metal ions,
e.g.: Zinc and Iron. • Co-substrates: are
• Coenzymes:
• Small organic molecules
• Commonly derived from
vitamins.
• e.g. NAD+ (from vitamin
B3), and FAD (from
Vitamin B2).
coenzymes that only
transiently associate with
the enzyme. They • Prosthetic group:
dissociates from the a coenzyme that
enzyme in an altered state is permanently
(e.g. NAD+) associated with
the enzyme. e.g.
FAD, biotin
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Regulation of Enzymes’ Activity
• Regulation means Increased or Decreased rate of enzyme-catalyzed
reaction in response to the surrounding needs.

• i.e. The rate of product formation responds to cellular needs

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Location of Enzymes within the cell
• Localization of enzymes in specific organelles
within the cell = Compartmentalization.
• What are the benefits of compartmentalization?
1. Isolate the reaction substrate or product
from other competing reactions.
2. Provide favorable environment for the
reaction (e.g. the optimum pH)
3. Organize the thousands of enzymes present
in cell into their required pathways. 17
 SUMMARY
• Enzymes are protein catalysts that increase the velocity of a chemical reaction.

• Enzymes are not consumed during the reaction.

• They contain a special cleft called the active site, which contains AA side chains
that participate in substrate binding and catalysis.

• The active site binds to the substrate, forming and ES complex. Binding will
cause a conformational changes in the enzymes induced-fit that allows
catalysis.
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References:
• Harvey, Richard A., Ph. D. (2022). Lippincott's illustrated reviews:
Biochemistry. Philadelphia: Wolters Kluwer Health, 8th ed, Chapter 5,
pp 53

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