CHEM 5006: ENZYMES

Semester 1 | A.Y 2024-2025 Nica Leilannie Bellosillo

• How enzymes speed up the chemical
MODULE OUTLINE reaction: enzymes accelerate
I. Enzymes reactions by lowering the free energy
of activation
MAIN TOPIC

ENZYMES

• Proteins that act as catalysts within

living cells
• The human body has thousands of
enzymes
• Not consumed during the reaction
• Most effective catalysts known
• Most enzymes are globular proteins
• Reactions
• All enzymes are proteins and
• Chemical reactions- are happening
undergo all the reactions of proteins
in our bodies all the time
including denaturation
• These reactions help us break down
• Enzyme Property – approximately
food and make energy
3000 enzymes in a single cell.

• Types of Enzymes: Simple and

• How do enzymes work: enzymes are
conjugated
required to break down the carbs,
• Simple enzyme: enzyme composed
protein and fats we eat into
only of protein (amino acid chains)
molecules our body can use
• Conjugated enzyme: Enzyme that
has nonprotein part in addition to a
protein.

• Terms Used with Enzyme

• Apoenzyme: the protein part of a
conjugated enzyme
• Holoenzyme: Biochemically active
conjugated enzyme
o Apoenzyme + cofactor =
holoenzyme
➢ Active site: pocket or cleft in the
enzyme where the reaction occurs or
the specific portion of the enzyme to
which a substrate binds during
reaction.
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➢ Proenzyme: inactive form of enzymes ➢ Transferases: Group transfer
➢ Cofactor: a nonprotein portion of an reactions.
enzyme that is necessary for catalytic ➢ Hydrolases: Hydrolysis reactions.
function; examples are metallic ions ➢ Lyases: Addition of two groups to a C-
such as Zn2+ and Mg2+. C double bond, or removal of two
➢ Coenzyme: a nonprotein organic groups to create a C-C double bond.
molecule, frequently a B vitamin, that ➢ Isomerases: Isomerization reactions.
acts as a cofactor (organic cofactor) ➢ Ligases: The joining to two molecules.
➢ Substrate: the reactant bound at
active site
➢ Cofactors are important for the
chemically reactive enzymes
➢ Cofactors are small organic
molecules or Inorganic ions
➢ Enzyme active site - Relatively small
part of an enzyme’s structure that is
involved in catalysis.
ENZYMES
• Oxidoreductase - enzyme catalyzes
an oxidation–reduction reaction
➢ Oxidation and reduction reactions are
always linked to one another
➢ An oxidoreductase requires a
coenzyme that is either oxidized or
reduced as the substrate in the
reaction.
➢ E.g., Lactate dehydrogenase is an
oxidoreductase, and the reaction
catalyzed is shown below

• Transferase - enzyme that catalyzes

CLASSIFICATION OF ENZYMES
the transfer of a functional group
• Enzymes are commonly named after
from one molecule to another
the reaction or reactions they
➢ Two major subtypes: Transaminases
catalyze.
and Kinases
• Ex.: lactate dehydrogenase, acid
➢ Transaminases - catalyze transfer of
phosphatase.
an amino group to a substrate
➢ Six major groups according to the
➢ Kinases - catalyze transfer of a
type of reaction catalyzed
phosphate group from adenosine
➢ Oxidoreductases: Oxidation-
triphosphate (ATP) to a substrate
reduction reactions.
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➢ Hydrolase - enzyme that catalyzes a
hydrolysis reaction
➢ The reaction involves addition of a
water molecule to a bond to cause
bond breakage

• Lyase - is an enzyme that catalyzes

the addition of a group to a double
bond or the removal of a group to
form a double bond in a manner that
does not involve hydrolysis or
oxidation

• Isomerase – catalyzes the

isomerization (rearrangement of
atoms) reactions.
➢ Substrate Concentration - At a
• Ligase - catalyzes the formation of a constant enzyme concentration, the
bond between two molecules enzyme activity increases with
involving ATP hydrolysis increased substrate concentration.
➢ the concentration at which it reaches
its maximum rate, and all the active
ENZYME ACTIVITY
• A measure of how much a reaction sites are full

rate is increased. ➢ Turnover Number: Number of

• We examine how the rate of an substrate molecules converted to

enzyme-catalyzed reaction is product per second per enzyme

affected by: molecule under conditions of

o Enzyme concentration optimum temperature and pH

o Substrate concentration.
o Temperature.
o pH
➢ Enzyme concentration - Enzymes
are not consumed in the reactions
they catalyze
➢ At a constant substrate
concentration, enzyme activity
increases linearly with increase in
enzyme concentration
➢ The greater the enzyme
concentration, the greater the
reaction rate.
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➢ Temperature - Higher temperature ➢ Trypsin: Optimum pH = 8.0
results in higher kinetic energy which
HOW AN ENZYME BINDS ITS
causes an increase in number of
SUBSTRATE
reactant collisions, therefore there is
• MODELS OF ENZYME ACTION
higher activity.
➢ Optimum temperature:
➢ Lock and Key Model – proposed by
Temperature at which the rate of
Emil Fischer
enzyme catalyzed reaction is
➢ Explains specificity by comparing the
maximum
active site to a lock and the substrate
➢ Optimum temperature for human
to a key
enzymes is 37ºC (body temperature)
➢ The enzyme is a rigid three-
➢ Increased temperature (high fever)
dimensional body.
leads to decreased enzyme activity
➢ The enzyme surface contains the
active site

➢ Above a certain temperature, activity

begins to decline because the
enzyme begins to denature

➢ pH - pH changes affect enzyme

activity
➢ Drastic changes in pH can result in ➢ Induced Fit Model – proposed by
denaturation of proteins Daniel Koshland
➢ Optimum pH: pH at which enzyme ➢ According to this model the enzyme
has maximum activity modifies the shape of the active site
➢ Most enzymes have optimal activity to accommodate the substrate
in the pH range of 7.0 - 7.5 ➢ The active site becomes modified to
➢ Exception: Digestive enzymes accommodate the substrate.
➢ Pepsin: Optimum pH = 2.0 •
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➢ Noncompetitive inhibitor - any
substance that binds to a portion of
the enzyme other than the active site
and thereby inhibits the activity of the
enzyme.
➢ Enzyme Inhibitor - a substance that
slows down or stops the normal
catalytic function of an enzyme by
binding to it
o Inhibitors bind to the enzyme
and alter the conformation of
the enzyme.
o Inhibitors could be reversible
or irreversible.
o Application: Drugs with cause
complete inactivation of
MECHANISM OF ACTION enzymes from essential
pathways will cause death and
therefore such drugs can e
used as antibiotics
➢ Reversible Inhibition
➢ binds noncovalently to the enzyme
(such as by forming H bonds or salt
bridges with the enzyme).
➢ Reversible inhibition can be reversed
by removal of the inhibitor.
➢ Reversible inhibitors can be
competitive, noncompetitive and
➢ Lock and Key model – explains the
uncompetitive
phenomenon of competitive
o Competitive Inhibitors -
inhibition
compete with the substrate for
➢ Induced Fit model – explains
the same active site
noncompetitive inhibition
o will have similar charge &
➢ Activation - any process that initiates
shape
or increases the activity of an enzyme
o Noncompetitive Inhibitors-
➢ Inhibition - any process that makes
do not compete with the
an active enzyme less active or
substrate for the same active
inactive.
site
➢ Competitive Inhibitor - any
o binds to the enzyme at a
substance that binds to the active site
location other than active site
of an enzyme thereby preventing
binding of substrate.
LECTURE #1 | ENZYMES
o Uncompetitive inhibition - ➢ Competitive inhibition can be
inhibitor binds to the enzyme reduced by simply increasing the
substrate complex concentration of the substrate.

➢ Noncompetitive inhibition (allosteric

site)
➢ the inhibitor binds to a site other than
the active site, thereby changing the
conformation of the active site. The
substrate no longer fits

➢ Competitive Inhibition – the

inhibitors fit into the active site,
thereby preventing the substrate
from entering the

➢ A noncompetitive enzyme inhibitor

decreases enzyme activity by binding
to a site on an enzyme other than the
active site.
➢ Causes a change in the structure of
the enzyme and prevents enzyme
activity.
➢ Increasing the concentration of
substrate does not completely
➢ Reversible Competitive Inhibition overcome inhibition.
➢ A competitive enzyme inhibitor: ➢ Examples: Heavy metal ions Pb2+,
resembles an enzyme substrate in Ag+, and Hg2+.
shape and charge ➢ Heavy metal poisoning is an example
➢ Binds reversibly to an enzyme active of noncompetitive inhibitor
site and the inhibitor remains
unchanged (no reaction occurs) ➢ Uncompetitive Inhibition
➢ The enzyme - inhibitor complex ➢ Inhibitors binds to with enzyme-
formation is via weak interactions substrate complex
(hydrogen bonds, etc.).
LECTURE #1 | ENZYMES
➢ Drugs to treat cases of poisoning by • They are in use for cancer therapy,
methanol or ethylene glycol act as gout, etc.
uncompetitive inhibitors • IMPORTANCE OF ENZYME INHIBITORS
➢ Tetramethylene sulfoxide and 3- • Use to elucidate the mechanism of
butylthiolene 1-oxide are enzyme action
uncompetitive inhibitors of liver • Many drugs and poisons are enzyme
alcohaldhydrogenase inhibitors

➢ Irreversible Inhibition - Some

substances combine covalently with • Enzyme Specificity
enzymes to inactivate them • Absolute specificity - Enzyme will
irreversibly. catalyze only one reaction
➢ Almost irreversible enzyme inhibitors • Most restrictive of all specificities and
are toxic substances, either natural or is not common
synthetic • Example: Catalase is an enzyme with
➢ An irreversible enzyme inhibitor absolute specificity for hydrogen
inactivates enzymes by forming a peroxide (H2O2 )
strong covalent bond with the
enzyme’s active site. • Group specificity - Enzyme will act
➢ The enzyme is permanently only on molecules that have a
deactivated specific functional group
➢ The actions of chemical warfare • Example: Carboxypeptidase cleaves
agents (nerve gases) and organo- amino acids, one at a time, from the
phosphate insecticides are based on carboxyl end of the peptide chain
irreversible inhibition.
• Linkage specificity
• Enzyme will act on a particular type
CLINICAL SIGNIFICANCE OF ENZYME
of chemical bond, rest of the
INHIBITION
molecular structure is not considered
• The usefulness of the most important • Most general of the common
pharmaceutical agents, specificities – Example: Phosphatases
antimetabolites, is based on the hydrolyze phosphate–ester bonds in
concept of competitive enzyme all types of phosphate esters
inhibition
• The antimetabolites are structural • Stereochemical specificity
analogues of normal biochemical • Enzyme will act on a particular
compounds stereoisomer
• As competitive inhibitors, they • Chirality is inherent in an active site
compete with the naturally substrate • ʟ-amino-acid oxidase will only
for the active site of enzyme and block catalyze the oxidation of the ʟ-form of
the formation of undesirable an amino acid but not its ᴅ-form
metabolic products in the body
LECTURE #1 | ENZYMES
EMZYME REGULATION

➢ Feedback control
➢ A process in which the formation of a
product inhibits an earlier reaction in
the sequence
➢ The reaction product of one enzyme
may control the activity of the other

➢ Proenzymes or zymogems (inactive

precursor)
➢ A protein that becomes an active
enzyme after undergoing a chemical
change
o Trypsin’s inactive form is called
trypsinogen

➢ Allosterism - An enzyme regulation in

which the binding of a regulator on
one site on the enzyme modifies the
enzyme’s ability to bind the substrate
in the active site
➢ Protein modification – The
modification is usually a change in
the primary structure typically by the
addition of a functional group bound
to apoenzyme
➢ Isoenzymes – Enzymes that perform
the same function but have different
combination of subunits and thus
different quaternary structures