Enzymes

Structure, Classification &

Mechanism of Action.

By: Anam Tariq

Lecturer SCN
November, 17th 2020.
 ENZYMES

• Enzymes are proteins that increase the rate of

reaction by lowering the energy of activation.
• They catalyze nearly all the chemical reactions
taking place in the cells of the body.
• Not altered or consumed during reaction.
• Reusable.
• Enzyme molecules contain a special pocket or
cleft called the active sites.
 Apoenzyme and Holoenzyme

• The enzyme without its non protein moiety is

termed as apoenzyme and it is inactive.
• Holoenzyme is an active enzyme with its non
protein component.
• Co factor:
A cofactor is a non-protein chemical compound
that is bound (either tightly or loosely) to an
enzyme and is required for catalysis.

• Types of Cofactors:
• Coenzymes.
• Prosthetic groups.
 Types of Cofactors
• Coenzyme:
The non-protein component loosely bound to
apo-enzyme by non-covalent bond.
• Examples : vitamins or compound derived
from vitamins.
• Prosthetic group:
The non-protein component tightly bound
to the apo-enzyme by covalent bonds is
called a Prosthetic group.
 Enzyme Specificity

• Enzymes have varying degrees of

specificity for substrates.
• Enzymes may recognize and catalyze:
- a single substrate
- a group of similar substrates
- a particular type of bond
Energy of Activation:

• All chemical reactions require some amount of energy

to get them started. This energy is called activation
energy.
• It is First push to start reaction.
Mechanism of Action of Enzymes
• Enzymes increase reaction rates by
decreasing the Activation energy:
• Enzyme-Substrate Interactions:
‒ Formation of Enzyme substrate complex
by:
‒ Lock-and-Key Model
‒ Induced Fit Model
Enzymes
Lower a
Reaction’s

Activation
Energy
 Lock-and-Key Model
• In the lock-and-key model of enzyme action:
- the active site has a rigid shape
- only substrates with the matching shape can fit
- the substrate is a key that fits the lock of the
active site
• This is an older model and does not work for all
enzymes.
 Induced Fit Model
• In the induced-fit model of enzyme action:
- the active site is flexible, not rigid.
- the shapes of the enzyme, active site, and substrate
adjust to maximize the fit which improves catalysis.
- there is a greater range of substrate specificity
• This model is more consistent with a wider range of
enzymes.
 Enzyme substrate complex
• Step 1:
• Enzyme and substrate combine to form
complex
• E + S ES
• Enzyme Substrate Complex

+
• Step 2:
• An enzyme-product complex is formed.

• ES EP

ES transition EP
state
• Step 3: The enzyme and product separates.

• EP E + P

The
product
is made
Enzyme
is ready
EP for
another
substra
te.
 What Affects Enzyme Activity?
• Three factors:
1.Environmental Conditions.
2.Cofactors and Coenzymes.
3.Enzyme Inhibitors.

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 1. Environmental Conditions

1. Extreme Temperature are the most

dangerous. High temps may denature (unfold)
the enzyme.
2. pH (most like 6 - 8 pH near neutral)
3. substrate concentration .

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 Cofactors and Coenzymes
• Inorganic substances (zinc, iron) and vitamins
are sometimes need for proper enzymatic
activity.
• Example:
Iron must be present in the quaternary
structure - hemoglobin in order for it
to pick up oxygen.

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 Environmental factors
• Optimum temperature: The temperature at
which enzymatic reaction occur fastest.
 Environmental factors
• pH also affects the rate of enzyme-substrate
complexes
–Most enzymes have an optimum pH of around 7
but some prefer acidic or basic conditions.
 Substrate Concentration and Reaction
Rate
• The rate of reaction increases as substrate concentration
increases (at constant enzyme concentration)
• Maximum activity occurs when the enzyme is saturated
(when all enzymes are binding substrate)
 Enzyme Inhibitors
• Competive - mimic substrate, may block active site, but may dislodge it.
 Enzyme Inhibitors
• Noncompetitive
 Classification of Enzymes
• Enzymes were classified by first appending the suffix –
ase to a descriptor for the type of reaction catalyzed.
• For example, enzymes that remove hydrogen atoms are
generally referred to as dehydrogenases,
– enzymes that hydrolyze proteins as proteases
– enzymes that catalyze rearrangements in con-figuration as
isomerases.
• As more enzymes were discovered these early
naming conventions increasingly resulted in the
appearance of multiple names for the same enzyme
and duplication in the naming of enzymes exhibiting
similar catalytic capabilities.
• To address these problems the International Union
of Biochemistry (IUB) developed a system of
enzyme nomenclature in which each enzyme has a
unique name and code number that identify the
type of reaction catalyzed and the substrates
involved.
• Enzymes are grouped into the following six
classes.
1. Oxidoreductases: enzymes that catalyze oxidations
and reductions.
2. Transferases: enzymes that catalyze transfer of
moieties such as glycosyl, methyl, or phosphoryl
groups.
3. Hydrolase: enzymes that catalyze hydrolytic
cleavage of C - C, C - O, C - N, and other covalent
bond.
4. Lyases: enzymes that catalyze cleavage of C -C, C -
O, C -N, and other covalent bonds by atom
elimination, generating double bonds.
5. Isomerases: enzymes that catalyze geometric or
structural changes within a molecule.
6. Ligases: enzymes that catalyze the joining together
(ligation) of two molecules in reactions coupled to
the hydrolysis of ATP.
• Enzymes are classified into six functional classes by
I.U.B. On the basis of the types of
reactions that they catalyzes.
• EC 1. Oxidoreductases
• EC 2. Transferases
• EC 3. Hydrolases
• EC 4. Lyases
• EC 5. Isomerases
• EC 6. Ligases
Oxidoreductases, Transferases and Hydrolases
Lyases, Isomerases and Ligases
 Regulatory Enzymes
• “In a multi step enzymatic process there will be one
enzyme which will be responsible for the overall rate
of that process”.
• This critical rate limiting enzyme is called the
regulatory enzyme.
• Regulatory enzyme shows enhanced or decreased
catalytic activities in response to other molecules
(signals) in the cells.
 Regulation by Non-Covalent
Modification
• This type of enzymes presents two binding
sites.
– the substrate of the enzyme and the effectors.
• Effectors binds on allosteric sites by non
covalent bond.
• This non covalent bonding of effectors will
either result in inhibition or activation of
enzyme activity.
 Allosteric Inhibition
• Enzymes can be inhibited when an effector
(negative effector) combines with allosteric
site of enzymes.
• Feedback inhibition: Allosteric enzymes can
be inhibited by the product of its own catalytic
product.
• Excess product inhibition of enzyme
activity decrease product.
 Allosteric Activation
• Enzymes can be activated when an effector
called positive effector combines with
allosteric site of enzyme.
• Feedback activation:
• Decrease product activation of enzyme
activity increase synthesis of product.
 Regulation of enzymes by Covalent
modification
• Enzymes can be regulated by covalent
modification.
• Mostly done by addition or deletion of
phosphate group from specific serine,
threonine or tyrosine.
• Addition or removal of phosphate group
results either in activation or inhibition of
enzymes.
 Enzymes in clinical diagnosis
• Enzymatic diagnosis is a method to diagnose
diseases by measuring the content and
changes of certain substances in the body or
through the changes of the original enzyme
activity in the body.
• Serum acid phosphatase activity will be
elevated in the body of patients with prostate
cancer or hyperparathyroidism.
• glucose oxidase can be used to detect glucose
content in diabetes diagnosis.
• urease can be used to measure the urea
content to diagnose liver and kidney lesions.
• cholesterol oxidase can be used to measure the
content of cholesterol in the blood to diagnose
hyperlipidemia.
• glutaminase can be used to measure glutamine
content in cerebrospinal fluid to diagnose
cirrhosis and hepatic coma.
• DNA polymerase can be used to test whether
the gene is normal or whether there is any
oncogenes exists in the body.
 Cardiac Enzymes
• Cardiac enzymes also known as cardiac biomarkers,
include myoglobin, troponin, creatine kinase and
LDH.
• Cardiac enzymes are released into the circulation
when myocardial necrosis occurs as seen in
myocardial infarction.
• CPK-MB is used to assist diagnoses of an acute
myocardial infarction.
• CK is found in the heart, muscles, small intestine,
brain, and uterus.
• Incase of heart attack injured heart muscle cells
release CK-MB into blood.
• Higher CK-MB may point more directly to heart
damage.
• Releases within 24hrs and fall back to normal within
48 hours.
• Aspartate transaminase ( AST): peaks at 24-
48 hrs and fall back to normal by 72hrs.
• LDH-1: peaks at 3-4 days and remain elevated
for 10-14 days.
 Enzymes as Medicines
• Used as therapeutic purposes.
• For digestive disorder: lipases, proteinases and
amylases.
• For Blood coagulation: Urokinase and streptokinase.
• In Ointments:vHyaluronidase.
• Cancer Treatments:vL-Asparaginase.