ENZYMES

2 ENERGY OF ACTIVATION

• Most reactions do not start spontaneously

• They require energy, such as a spark, to get started.
• This is called activation energy
CHEMICAL REACTIONS

• Chemical reactions need an initial input of energy = THE

ACTIVATION ENERGY
• During this part of the reaction the molecules are said to be in a
transition state.
REACTION PATHWAY (EXOTHERMIC)
AN ENDOTHERMIC REACTION
Transition state

Activation
energy

Free
Products
energy

Reactants

Reaction coordinate
MAKING REACTIONS GO FASTER

• Increasing the temperature makes molecules move faster

• Biological systems are very sensitive to temperature
changes
• Enzymes can increase the rate of reactions without the
need to increase the temperature
• They do this by lowering the activation energy
• They create a new reaction pathway “a short cut” .
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
AN ENZYME CONTROLLED PATHWAY

Enzyme controlled reactions proceed 108 to 1011 times faster than

corresponding non-enzymic reactions.
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-FACTORS

• Cofactor:

• 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 apoenzyme by non-
covalent bond.
• Examples : vitamins or compound derived from vitamins.
• Prosthetic group
The non-protein component, tightly bound to the apoenzyme by
covalent bonds is called a Prosthetic group.
THE SUBSTRATE

• The substrates of enzymes are the reactants that are

activated by the enzymes
• Enzymes are specific to their substrates
• The specificity is determined by the active site.

© 2017 Paul Billiet ODWS

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
FACTORS AFFECTING ENZYMES

• substrate concentration
• pH
• temperature
• inhibitors.
• Co-factors
SUBSTRATE CONCENTRATION: NON-ENZYMIC REACTIONS

Reaction
velocity

Substrate concentration

The increase in velocity is proportional to the substrate

concentration.
© 2017 Paul Billiet ODWS
SUBSTRATE CONCENTRATION: ENZYMIC
REACTIONS

Vmax

Reaction
velocity

Substrate concentration
• Faster reaction but it reaches a saturation point when all the enzyme
molecules are occupied
• Alter the concentration of the enzyme then Vmax will change too.

© 2017 Paul Billiet ODWS

THE EFFECT OF PH
Optimum pH values

Enzyme
activity
Trypsin

Pepsin

1 3 5 7 9 11

© 2017 Paul Billiet ODWS pH

THE EFFECT OF PH

• Extreme pH levels will produce denaturation

• The structure of the enzyme is changed
• The active site is distorted and the substrate molecules will no longer fit in it
• At pH values slightly different from the enzyme’s optimum value, small
changes in the charges on the enzyme and it’s substrate molecules will occur
• This change will affect the binding of the substrate with the active site.

© 2017 Paul Billiet ODWS

THE EFFECT OF TEMPERATURE

• Q10 (the temperature coefficient) = the increase in reaction

rate with a 10°C rise in temperature
• For chemical reactions the Q10 = 2 to 3
• Enzyme-controlled reactions follow this rule as they are
chemical reactions
• BUT at high temperatures proteins denature
• The optimum temperature for an enzyme controlled reaction
will be a balance between the Q10 and denaturation.

© 2017 Paul Billiet ODWS

 The effect of temperature
Optimum

Increasing
number of Denaturation
Enzyme collisions (Q10)
activity

0 10 20 30 40 50
Temperature / °C

© 2017 Paul Billiet ODWS

THE EFFECT OF TEMPERATURE
• For most enzymes the optimum temperature is about
30°C
• Many are a lot lower,
cold water fish will die at 30°C because their
enzymes denature
• A few bacteria have enzymes that can withstand
very high temperatures up to 100°C
• Most enzymes however are fully denatured at 70°C.

© 2017 Paul Billiet ODWS

COFACTORS AND COENZYMES

• Inorganic substances (zinc, iron) and

vitamins (respectively) 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.

23
 NAMING ENZYMES

• The name of an enzyme in many cases end in –ase

• For example, sucrase catalyzes the hydrolysis of sucrose

• The name describes the function of the enzyme

For example, oxidases catalyze oxidation reactions

• Sometimes common names are used, particularly for the

digestion enzymes such as pepsin and trypsin

• Some names describe both the substrate and the function

• For example, alcohol dehydrogenase oxides ethanol
ENZYMES ARE CLASSIFIED INTO SIX FUNCTIONAL CLASSES (EC
NUMBER CLASSIFICATION) BY THE INTERNATIONAL UNION OF
BIOCHEMISTRY AND MOLECULAR BIOLOGY (I.U.B.M.B.)
ON THE BASIS OF THE TYPES OF REACTIONS THAT THEY
CATALYSE
• EC 1. Oxidoreductases

• EC 2. Transferases
• EC 3. Hydrolases
• EC 4. Lyases
• EC 5. Isomerases
• EC 6. Ligases
 Principle of the international
classification

Each enzyme has classification number

consisting of four digits:
Example, EC:   (2.7.1.1) HEXOKINASE
• EC: (2.7.1.1) these components indicate the following groups
of enzymes:

• 2. IS CLASS (TRANSFERASE)

• 7. IS SUBCLASS (TRANSFER OF PHOSPHATE)

• 1. IS SUB-SUB CLASS (ALCOHOL IS PHOSPHATE

ACCEPTOR)
• 1. SPECIFIC NAME
ATP,D-HEXOSE-6-PHOSPHOTRANSFERASE (Hexokinase)
 6 CH2OH 6 CH OPO 2
2 3
ATP ADP
5 O 5 O
H H H H
H H
4 1 4 H 1
OH H OH
Mg2+
OH OH OH OH
3 2 3 2
H OH Hexokinase H OH
glucose glucose-6-phosphate

1. Hexokinase catalyzes:
Glucose + ATP  glucose-6-P + ADP
Oxidoreductases are classified as EC 1 in the EC number classification of enzymes. Oxidoreductases can be further classified
into 22 subclasses:
•EC 1.1 includes oxidoreductases that act on the CH-OH group of donors (alcohol oxidoreductases)
•EC 1.2 includes oxidoreductases that act on the aldehyde or oxo group of donors
•EC 1.3 includes oxidoreductases that act on the CH-CH group of donors (CH-CH oxidoreductases)
•EC 1.4 includes oxidoreductases that act on the CH-NH 2 group of donors (Amino acid oxidoreductases, Monoamine oxidase)
•EC 1.5 includes oxidoreductases that act on CH-NH group of donors
•EC 1.6 includes oxidoreductases that act on NADH or NADPH
•EC 1.7 includes oxidoreductases that act on other nitrogenous compounds as donors
•EC 1.8 includes oxidoreductases that act on a sulfur group of donors
•EC 1.9 includes oxidoreductases that act on a heme group of donors
•EC 1.10 includes oxidoreductases that act on diphenols and related substances as donors
•EC 1.11 includes oxidoreductases that act on peroxide as an acceptor (peroxidases)
•EC 1.12 includes oxidoreductases that act on hydrogen as donors
•EC 1.13 includes oxidoreductases that act on single donors with incorporation of molecular oxygen (oxygenases)
•EC 1.14 includes oxidoreductases that act on paired donors with incorporation of molecular oxygen
•EC 1.15 includes oxidoreductases that act on superoxide radicals as acceptors
•EC 1.16 includes oxidoreductases that oxidize metal ions
•EC 1.17 includes oxidoreductases that act on CH or CH 2 groups
•EC 1.18 includes oxidoreductases that act on iron-sulfur proteins as donors
•EC 1.19 includes oxidoreductases that act on reduced flavodoxin as a donor
•EC 1.20 includes oxidoreductases that act on phosphorus or arsenic in donors
•EC 1.21 includes oxidoreductases that act on X-H and Y-H to form an X-Y bond
•EC 1.97 includes other oxidoreductases
Classification of transferases into subclasses
EC number Examples Group(s) transferred
methyltransferase and 
EC 2.1 single-carbon groups
formyltransferase
EC 2.2 transketolase and transaldolase aldehyde or ketone groups
acyl groups or groups that become 
EC 2.3 acyltransferase
alkyl groups during transfer
glycosyltransferase, hexosyltransferase, glycosyl groups, as well as hexoses
EC 2.4
and pentosyltransferase  and pentoses
riboflavin synthase and  alkyl or aryl groups, other than methyl
EC 2.5
chlorophyll synthase groups

EC 2.6 transaminase, and oximinotransferase nitrogenous groups

phosphorus-containing groups;
phosphotransferase, polymerase, and 
EC 2.7 subclasses are based on the acceptor
kinase
(e.g. alcohol, carboxyl, etc.)
EC 2.8 sulfurtransferase and sulfotransferase sulfur-containing groups
EC 2.9 selenotransferase selenium-containing groups
molybdenumtransferase and 
EC 2.10 molybdenum or tungsten
tungstentransferase
Hydrolases are classified as EC 3 in the EC number classification of enzymes. Hydrolases can be further classified
into several subclasses, based upon the bonds they act upon:

•EC 3.1: ester bonds (esterases: nucleases, phosphodiesterases, lipase, phosphatase)

•EC 3.2: sugars (DNA glycosylases, glycoside hydrolase)
•EC 3.3: ether bonds
•EC 3.4: peptide bonds (Proteases/peptidases)
•EC 3.5: carbon-nitrogen bonds, other than peptide bonds
•EC 3.6 acid anhydrides (acid anhydride hydrolases, including helicases and GTPase)
•EC 3.7 carbon-carbon bonds
•EC 3.8 halide bonds
•EC 3.9: phosphorus-nitrogen bonds
•EC 3.10: sulphur-nitrogen bonds
•EC 3.11: carbon-phosphorus bonds
•EC 3.12: sulfur-sulfur bonds
•EC 3.13: carbon-sulfur bonds
Lyases are classified as EC 4 in the EC number classification of enzymes. Lyases can be further classified into seven
subclasses:

•EC 4.1 includes lyases that cleave carbon–carbon bonds, such as decarboxylases (EC 4.1.1), aldehyde lyases (EC
4.1.2), oxo acid lyases (EC 4.1.3), and others (EC 4.1.99)
•EC 4.2 includes lyases that cleave carbon–oxygen bonds, such as dehydratases
•EC 4.3 includes lyases that cleave carbon–nitrogen bonds
•EC 4.4 includes lyases that cleave carbon–sulfur bonds
•EC 4.5 includes lyases that cleave carbon–halide bonds
•EC 4.6 includes lyases that cleave phosphorus–oxygen bonds, such as adenylyl cyclase and guanylyl cyclase
•EC 4.99 includes other lyases, such as ferrochelatase
Subclasses of Isomerase

EC5.1 Racemases, epimerases

EC 5.2 Cis-trans isomerases

EC 5.3 Intramolecular oxidoreductases

EC 5.4 Intramolecular transferases

EC 5.5 Intramolecular lyases

Ligases are classified as EC 6 in the EC number classification of enzymes. Ligases can be further classified into six
subclasses:

•EC 6.1 includes ligases used to form carbon-oxygen bonds

•EC 6.2 includes ligases used to form carbon-sulfur bonds
•EC 6.3 includes ligases used to form carbon-nitrogen bonds (including argininosuccinate synthetase)
•EC 6.4 includes ligases used to form carbon-carbon bonds
•EC 6.5 includes ligases used to form phosphoric ester bonds
•EC 6.6 includes ligases used to form nitrogen-metal bonds, as in the chelatases