UNIT- II
General Characteristics of Enzymes
• ENZYME
– Usually a protein, acting as catalyst in specific biochemical reaction
• Each cell in the human body contains 1,000s of different enzymes
– Every reaction in the cell requires its own specific enzyme
• Most enzymes are globular proteins
– A few enzymes are made of RNA
• Catalyze biochemical reactions involving nucleic acids
• Enzymes undergo all the reactions of
• proteins
– Enzymes denaturation due to pH or temperature change
• A person suffering high fever runs the risk of denaturing certain
Enzyme
Structure
• SIMPLE ENZYMES
Composed only of protein
• CONJUGATED ENZYMES
Composed of:
– Apoenzyme • The apoenzyme can’t catalyze its
• Conjugate enzyme reaction without its cofactor.
without – The combination of the apoenzyme
its cofactor with the cofactor makes the
conjugated enzyme functional.
• Protein part of a • Holoenzyme = apoenzyme + cofactor
conjugated enzyme – The biochemically active conjugated
enzyme.
– Coenzyme (Cofactor)
• Non-protein part of
Coenzymes and cofactors
• Coenzymes provide additional chemically reactive functional groups
• besides those present in the amino acids of the apoenzymes
– Are either small organic molecules or inorganic ions
• Metal ions often act as additional cofactors (Zn2+, Mg2+, Mn2+ & Fe2+)
– A metal ion cofactor can be bound directly to the enzyme or to a
coenzyme
• COENZYME
– A small organic molecule, acting as a cofactor in a conjugated
enzyme
• Coenzymes are derived from vitamins or vitamin derivatives
•– Many vitamins act as coenzymes, esp. B-vitamins
Enzyme definitions
Term Definition
Enzyme Protein only enzyme that facilitates a chemical reaction
(simple)
Coenzyme Compound derived from a vitamin (e.g. NAD+) that assists an
enzyme in facilitating a chemical reaction
Cofactor Metal ion (e.g. Mg2+) that that assists an enzyme in facilitating a
chemical reaction
Apoenzyme Protein only part of an enzyme (e.g. isocitrate dehydrogenase) that
requires an additional coenzyme to facilitate a chemical reaction (not
functional alone)
Holoenzyme Combination of the apoenzyme and coenzyme which together
facilitating a chemical reaction (functional)
Enzyme • Suffix of an enzyme –ase
– Lactase, amylase, lipase or protease
Nomenclature • Denotes an enzyme
• Enzymes are named • Some digestive enzymes have the suffix –
according to the in
• These enzymes were the first ones to be
type of reaction they – Pepsin, trypsin & chymotrypsin
studied
catalyze and/or their • Prefix denotes the type of reaction the
substrate enzyme catalyzes
– Oxidase: redox reaction
• Substrate = the reactant – Hydrolase: Addition of water to break one
upon component into two parts
which the specific enzyme • Substrate identity is often used together
acts with the reaction type
– Enzyme physically binds – Pyruvate carboxylase, lactate
to the substrate dehydrogenase
Substrate
Enzyme Enzyme/substrate complex
6 Major Classes of
Based on the type of reaction they catalyze
Enzymes
The table explains the functions of enzymes and how they are classified and name
Enzyme Class Reaction Catalyzed Examples in Metabolism
Oxidoreductase Redox reaction (reduction Examples are dehydrogenases catalyse
& oxidation) reactions in which a substrate is oxidised or
reduced
Transferase Transfer of a functional group Transaminases which catalyze the transfer
from 1 molecule to another of amino group or kinases which catalyze
the transfer of phosphate groups.
Hydrolase Hydrolysis reaction Lipases catalyze the hydrolysis of lipids, and
proteases catalyze the hydrolysis of
proteins
Lyase Addition / removal of atoms Decarboxylases catalyze the removal of
to / from double bond carboxyl groups
Isomerase Isomerization reaction Isomerases may catalyze the conversion of
an aldose to a ketose, and mutases transfer
functional group from one atom to another
within a substrate.
Ligase Synthesis reaction Synthetases link two smaller molecules
(Joining of 2 molecules into are form a larger one.
one, forming a new chemical
bond,
Enzyme Active Site
• Active site
– The specific portion of an enzyme
(location) where the substrate binds
while it undergoes a chemical reaction
• The active site is a 3-D ‘crevice-like’ cavity
formed by secondary & tertiary structures
of the protein part of the enzyme
– Crevice formed from the folding of the
protein
• Aka binding cleft
Stoker 2014, Figure 21-2 p750
– An enzyme can have more than only
one
active site
– The amino acids R-groups (side chain)
in the active site are important for
Enzyme – Substrate
Complex
• When the substrate binds to the enzyme active site an
Enzyme-Substrate Complex is formed temporarily
– Allows the substrate to undergo its chemical reaction much faster
Timberlake 2014, Figure 4, p.738 Timberlake 2014, Figure 3, p.737
Lock & Key Model of Enzyme
•
Action
The active site is fixed, with a rigid shape (LOCK)
• The substrate (KEY) must fit exactly into the rigid enzyme (LOCK)
• Complementary shape & geometry between enzyme and substrate
– Key (substrate) fits into the lock (enzyme)
• Upon completion of the chemical reaction, the products are released from
the active site, so the next substrate molecule can bind
Stoker 2014, Figure 21-3 p750
Induced Fit Model of
Enzyme Action
• Many enzymes are flexible & constantly change their shape
– The shape of the active site changes to accept & accommodate the
substrate
• Conformation change in the enzyme’s active site to allow the
substrate to bind
• Analogy: a glove (enzyme) changes shape when a hand
(substrate) is inserted into it
Stoker 2014, Figure 21-4 p751
Enzyme Specificity
• Absolute Specificity
– An enzyme will catalyze a particular reaction for only one substrate
– Most restrictive of all specificities
• Not common
– Catalase has absolute specificity for hydrogen peroxide (H2O2)
– Urease catalyzes only the hydrolysis of urea
• Group Specificity
– The enzyme will act only on similar substrates that have a specific
functional group
• Carboxypeptidase cleaves amino acids one at a time from the
carboxyl end of the
peptide chain
• Hexokinase adds a phosphate group to hexoses
Enzyme Specificity
• Linkage Specificity
– The enzyme will act on a particular type of chemical bond, irrespective
of the
rest of the molecular structure
– The most general of the enzyme specificities
• Phosphatases hydrolyze phosphate–ester bonds in all types of
phosphate esters
• Chymotrypsin catalyzes the hydrolysis of peptide bonds
• Stereochemical Specificity
– The enzyme can distinguish between stereoisomers
– Chirality is inherent in an active site (as amino acids are chiral
compounds)
Factors Affecting Enzyme
Activity
Enzyme activity
• Measure of the rate at which an enzyme converts substrate to products
in a biochemical reaction
4 factors affect enzyme activity:
• Temperature
• pH
• Substrate concentration: [substrate]
• Enzyme concentration: [enzyme]
Stoker 2014,
p756
Enzyme Inhibition
• ENZYME INHIBITOR
– A substance that slows down or stops the normal catalytic
function of
an enzyme by binding to the enzyme
• Three types of inhibition:
– Reversible competitive inhibition
– Reversible non-competitive inhibition
– Irreversible inhibition
Reversible Competitive
•Inhibition
A competitive inhibitor resembles the
substrate
– Inhibitor competes with the substrate for
binding to the active site of the enzyme
– If an inhibitor is bound to the active site:
Prevents the substrate molecules to
access the active site
– Decreasing / stopping enzyme
activity
Stoker 2014, Figure 21-11
• The binding of the competitive inhibitor to p758
the active site is a reversible process
– Add much more substrate to outcompete
the competitive inhibitor
•
Reversible Noncompetitive Stoker 2004, Figure 21.11, p.634
Inhibition
• A non-competitive inhibitor decreases
enzyme activity by binding to a site on
the enzyme other than the active site
– The non-competitive inhibitor alters
the tertiary structure of the enzyme
& the active site
• Decreasing enzyme activity
• Substrate cannot fit into active
site
– Process can be reversed only by
lowering the [non-competitive
inhibitor]
• Example:
– Heavy metals Pb2+ & Hg2+ bind to –
SH of Cysteine, away from active
site Stoker 2004, Figure 21.12, p.634
Irreversible
Inhibition
• An irreversible inhibitor inactivates an enzyme
by binding to its active site by a strong covalent bond
– Permanently deactivates the enzyme
– Irreversible inhibitors do not resemble substrates
• Addition of excess substrate
doesn’t reverse this process
– Cannot be reversed
• Chemical warfare (nerve gases)
• Organophosphate insecticides
Stoker 2014, p759
Drugs Inhibiting Enzyme Activity
• Many prescription drugs inhibit enzymes
• ACE Inhibitors
– Inhibit Angiotensin-Converting Enzyme
• Lowers blood pressure
• Sulfa drugs
– Antibiotics acting as competitive inhibitors of bacterial enzymes
• Involved in conversion of PABA to Folic acid
– Deficiency of folic acid retards bacterial growth, eventually killing
them
• Penicillin's
– β-lactam antibiotics inhibit transpeptidase
• Transpeptidase enzyme strengthens the cell wall
– Forms peptide cross links between polysaccharides strands in
bacterial cell walls
– Without transpeptidase enzyme (inhibited by Penicillin) >>>
Medical Uses of
Enzymes
• Enzymes can be used in diagnosis & treatment of certain diseases
• Lactate dehydrogenase (LDH) is normally not found in high levels in
blood, as it is produced in cells
– Increased levels of LDH in the blood indicate
myocardial iinfarction (MI) (Heart attack)
– Tissue plasminogen activator (TPA) activates the enzyme plasminogen
that dissolves blood clots
• Used in the treatment of MI
• There is no direct test to measure urea in the blood
– Urease converts urea into ammonia, which is easily
measured & is used as urea indicator
• Blood Urea Nitrogen (BUN) is used to measure kidney function
– High urea levels in the blood indicate kidney malfunction
