Notes on enzymes

1. ENZYMES
Biological sciences

2. ENZYMES
 Usually a protein, acting as a catalyst in a
specific biochemical reaction.
 Each reaction in the cell requires its own
specific enzyme.
 Most enzymes are globular proteins and few
are made of RNA.
 RNA enzymes catalyze biochemical
reactions involving nucleic acids.

3. ENZYME DEFINITIONS
 Enzyme
Protein only enzyme that facilitates chemical reaction.
 Coenzyme
Compound derived from a vitamin (e.g NAD+) that assist
enzyme in facilitating a chemical reaction.
 Cofactor
Metal ion(Mg) that assist an enzyme in facilitating a
chemical reaction.
 Apoenzyme
Protein part of enzyme that requires an additional
coenzyme to facilitate a chemical reaction.
 Holoenzyme
Combination of the apoenzyme and coenzyme which
together facilitate chemical reaction.

4. ENZYME STRUCTURE
 Simple Enzymes –
 Composed of only proteins.
 Conjugated Enzymes
 Apoenzyme -
 Conjugate enzyme without its cofactor
 Protein part of conjugated enzymes.
 Coenzyme(Cofactor)
 Non protein part of conjugated enzyme.
Apoenzyme + Coenzyme = Conjugate Enzyme
Apoenzyme + Cofactor = Holoenzyme

5. COENZYMES AND COFACTORS
COENZYME
 Provides 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 (Zn, Mg, Mn
and Fe)
 A metal ion cofactor can be bound directly to the enzyme
or to a coenzyme.
 Coenzymes are derived from vitamins or vitamin
derivatives especially vitamin B.

6. ENZYME NOMENCLATURE
 Enzyme are named according to the type of reaction they catalyze and/or their substrate.
ENZYME CLASS REACTION
CATALYZED
EXAMPLES IN METABOLISIS
OXIDOREDUCTASE Redox reaction,
Reduction and
oxidation.
e.g
Dehydrogenases
TRANSFERASE Transfer of functional
group from one
molecule to another
Transaminases
HYDROLASE Hydrolysis reaction Lipases
LYASE Addition/ removal of
atoms to /from double
bond.
Decarboxylases
ISOMORASE Isomerization reaction Isomerases
LIGASE Synthesis reaction Synthetase

7. ENZYME ACTIVE SITE
 The specific portion of an enzyme (location) where
the substrate binds while it undergoes chemical
reaction.
 An enzyme can have more than one active site.
 The common acids R-groups (side-chain) in the
active site are important for determining the
specificity of the substrate.

8. ENZYME - SUBSTRATE COMPLEX
 This is formed when the substrate binds to an enzyme
active site and it is formed temporarily.
 It allows the substrate to undergo its chemical reaction
much faster.
Lock and Key Enzyme Action
 The substrate(key) fit exactly into the rigid enzyme(lock)
 Complementary shape and geometry between enzyme
and substrate.
 Upon completion of a chemical reaction. The products
are released from the active site, so the next substrate
molecule can bind.
 Many enzymes are flexible and constantly change their
shape of the active site, so the next substrate molecule
can bind.
 This conformation allows substrate to bind .

9. ENZYME SPECIFICITY
 Absolute specificity
 An enzyme will catalyze a particular reaction for only one
substrate.
 Catalase has absolute specifications for Hydrogen peroxide
 Unease catalyzes only the hydrolysis of urea.
 Group specificity
 Enzyme will act only on similar substrate that have a
specific functional group.
 Hexokinase adds a phosphate group to hexoses.
 Carboxypeptidase cleaves amino acids one at a time from the carboxyl
and of the peptide chain.

10.  Linkage Specificity
 The enzyme will act on a particular type of chemical
bond, irrespective of the rest of the molecular structure.
 Phosphatases hydrolyze phosphate-ester bonds in all types of
phosphate esters.
 Chymotrypsin catalyzes the hydrolysis of peptide bonds.
 Stereochemical Specificity
 Chirality is inherent in an active site (as amino
acids are chiral compounds)
 L-amino acid oxidase catalyzes L- amino acids but not D-amino
acids

11. FACTORS AFFECTING ENZYME ACTIVITY
 Enzyme activity
Measure of rate at which enzyme converts substrates to
products in biochemical reaction.
 Factors
i. Temperature
ii. Substrate concentration
iii. Enzyme concentration
iv. PH
1.Temperature (t)
 With increased t the enzyme kinetic energy increases
thus
 more colissions
 increased reaction rate

12. OPTIMUM TEMPERATURE
 The temperature at which the enzyme exhibits maximum
activity.
 The optimum t of enzymes = 37c
 When t is increased beyond the optimum, changes in the
enzymes tertiary structure occur, inactivating &
denaturing it.
 Little activity is seen at low temperatures.
2.PH
 Optimum pH is the pH at which enzyme exhibits
maximum activity.
 Most enzymes are active over a very narrow pH range.
 Small changes in pH can result in enzyme denautaration
& loss of function.

13.  Each enzyme has its characteristic optimum pH which is
usually falls within physiological pH range 7.0 – 7.5.
 Digestive enzymes are exceptions
 Pepsin (stomach) = 2.0
 Trypsin (Ileum) = 8.0
3. Substrate Concentration
If enzyme is kept at constant and substrate is increased
 Reaction rate increases until a saturation point is met.
 At saturation the reaction rate stays the same even if the
substrate is increased .
 At saturation point substrate molecules are bound to all
available active sites of enzyme molecules.
Reaction takes place at the active site
 If all active sites are occupied the reaction is at its maximum
rate.
 Each enzyme molecule is working at its maximum capacity

14. 4.ENZYME CONCENTRATION
If the substrate is kept constant and the enzyme is
increased.
 The reaction rate increases
 The greater the enzyme , the greater the reaction rate.
RULE: The rate of an enzyme catalyzed reaction is
always directly proportional to the amount of the enzyme
present.
In a living cell;
 The substrate is much higher than the enzyme.
 Enzymes are not consumed in the reaction.
 Enzymes can be reused many times.

15. ENZYME INHIBITION
 Enzyme inhibitor
 A substance that slows down or stops the normal catalytic
function of an enzyme by binding to the enzyme.
Types
i. Reversible competitive inhibition
ii. Reversible non-competitive inhibition
iii. Irreversible inhibition
i. Reversible competitive inhibition
 A competitive inhibitor resembles the substrates.
Inhibitor competes with the substrate for binding to the active site
; prevents the substrate molecules to access the active site.
decreasing / stopping the enzyme activity.
 The of the competitive inhibitor to active site is a reversible
process;
add more substrate to outcompete the competitive inhibitor

16. II. REVERSIBLE NON-COMPETITIVE INHIBITION
A non competitive inhibitor decreases enzyme activity by
binding to a site on the enzyme other than the active site.
 It alters the tertiary structure of the enzyme and active
site:
Decreasing enzyme activity.
Substrate can not fit into the active.
 Process can be reversed only by lowering the non-
competitive inhibitor.
Example
Heavy metals: Pb and Hg bind to –SH of Cysteine away
from the active site:
disrupt the secondary and the tertiary structure.

17. IV. IRREVERSIBLE INHIBITION
Inactivates an enzyme by binding to a active site by strong
covalent bond.
 Permanently deactivates the enzyme
 Do not resemble substrates
Addition of excess substrate doesn’t reverse this process –
cannot be reversed.
Examples
 Chemical warfare (Nerve gas)
 Organophosphate (insecticides)
Allosteric Enzymes
 Have quartenary structure.
 Compound of two or more protein chains.
 Posses two or more binding sites.
Active site
Regulatory site

18.  Active and regulatory sites are distinct from each other in
shape and location.
 Binding of a regulatory molecule to its regulatory site
causes changes in the 3-d structure of the enzyme and
active site.
 Binding of a positive regulator up-regulate enzyme
activity.
 Enhances active site, more able to accept substrate.
 Binding of negative regulator (non-competitive inhibitor)
down-regulates enzyme activity.
 Compromises active site, less able to accept
substrate.

19. FEEDBACK CONTROL
 A process in which activation or inhibition of one of the
earlier reaction steps in a reaction is controlled by a
product of this reaction sequence.
 One of the mechanism in which allosteric enzymes are
regulated.
 Most biochemical process proceed in several steps and
each step is catalyzed by a different enzyme.
 The product of each step is the substrate for the next
step/enzyme.
 Inhibition of enzyme 1 by product D
 A enzyme 1 B enzyme 2 C enzyme 3 D
Reaction 1 Reaction 2 Reaction 3
Converts reagent A
into product B
Converts reagent B
into product C
Converts reagent C into
product D

20. PROTEOLYTIC ENZYMES AND ZYMOGENS
 Second mechanism of allosteric enzyme regulation production
of an enzyme in an inactive form.
 Activated when required (right at time and place)
 Proteolytic enzymes – catalyze the breaking of peptide bond in
proteins.
 To prevent the enzymes from destroying the tissues, that
produced them, they are released in an inactive form
(Zymogens)
 Most digestive and blood clotting enzymes ate proteolytic.
Blood clotting enzymes breakdown proteins within the blood so
that they can form the clot.
 Activation of a zymogen requires removal of a peptide
fragment from the zymogen structure.
Changing the 3-D shape affecting the active site.
 E.g Pepsinogen (zymogen)
 pepsin (active proteolytic enzyme)