Enzymes are protein catalysts that speed up biochemical reactions without being consumed. They have specific three-dimensional structures with active sites that bind substrates and catalyze their conversion to products. There are six main enzyme classes defined by their catalyzed reaction types. Enzyme activity is affected by factors like substrate and enzyme concentration, pH, temperature, and inhibitors. Enzymes lower activation energy and use lock-and-key or induced-fit binding to catalyze reactions efficiently through transition states. Many require cofactors like vitamins and metal ions to function. Enzyme kinetics describe how rates change with conditions and inhibition mechanisms. Enzymes are essential to all living functions but some inhibitors like nerve gases are toxic.

2. ENZYMES
Outline
Definition
Characteristics of enzymes
Types of enzymes
Factors effecting enzyme activity

3. The Definition and Characteristics of Enzymes
• Enzymes are catalysts that increase the rate of a
reaction without being changed themselves.
• Characters:
 a protein
 Catalyst
 effects rate of reaction and not the equilibrium
 unchanged at the end of reaction
 effective in smaller quantities
 efficient and specific
 reaction can be reversed
 activities affected by surroundings
 may need helpers – cofactors/coenzymes
 involve in multiple steps of biochemical pathways

4. Classification of enzymes
 6 main classes according to International
Union of Biochemistry and Molecular
Biology (IUBMB):
1. Oxidoreductase
2. Transferase
3. hydrolase
4. lyase
5. isomerase
6. ligase

5.  Function: catalyzes oxidation-reduction reactions
(transfer of electrons)
 e.g. alcohol dehydrogenase
 Other e.g. Biliverdin reductase; Glucose oxidase
1.OXIDOREDACTASES1.OXIDOREDACTASES

6.  Function: catalyzes reactions involving
transfer of functional groups
 e.g. Hexokinase
 Other e.g. Glycoaldehyde transferase; DNA
nucleotidylexotransferase
2.TRANSFERASES2.TRANSFERASES

7.  Function: catalyzes hydrolytic reactions
involving use of water mol.
 e.g. Triacylglycerol lipase
 Other e.g. -amino acid esterase;
Oxaloacetase; trypsin
H2O
3. HYDROLASES3. HYDROLASES

8.  Function: catalyzes cleavage of C-C, C-O, C-
N and other bonds by other means than by
hydrolysis or oxidation.
 e.g. Lysine decarboxylase
 other e.g.: threonine aldolase [EC 4.1.2.5];
Other e.g. cystine lyase, pyruvate
decarboxylase
4. LYASES4. LYASES

9.  Function: catalyzes intramolecular transfer of
groups
 e.g. Maleate isomerase
 Other e.g. Inositol-3-phosphate synthase;
Maltose epimerase]
5. ISOMERASES5. ISOMERASES

10.  Function: catalyzes the joining of two molecules with
concomitant hydrolysis of the diphosphate bond in
ATP or a similar triphosphate
 e.g. Pyruvate carboxylase
 Other e.g. GMP synthase; DNA ligase
6. LIGASES6. LIGASES

11. Enzymes are protein and all proteins are not
enzyme
 exhibits characteristics like other proteins
 primary structure
 amino acid sequence
e.g.: human pancreatic lipase (467 amino acids)
N-Met1-…-Ser171-...-Asp194-...-His281-…-Cys467-C
human trypsin (247 amino acids)
N-Met1-…-His63-…-Asp107-…-Ser200-…-Ser247-C

12. Lysozyme’s tertiary structure
Anti-parallel
-sheet
(3)
-helix
(5)

13. Aspartate carbamoyltransferase’s quartenary structure
 2 catalytic
trimers
 3 regulatory
dimers

14. Active site of Enzyme:
• The active site is the region of the enzyme that binds the
substrate, to form an enzyme–substrate complex, and
transforms it into product (Binding site).
• The active site is a three-dimensional entity, often a cleft
or crevice on the surface of the protein, in which the
substrate is bound by multiple weak interactions (non-
covalent bond).
• Two models have been proposed to explain how an
enzyme binds its substrate: the lock-and-key model
and the induced-fit model.

15. Lock and Key hypothesis
E + S ES E + P
Proposed by Emil Fischer (1894): the shape of the substrate
and the active site of the enzyme are thought to fit together
like a key into its lock.

17. Induced fit hypothesis
proposed in 1958 by Daniel E. Koshland, Jr.: the
binding of substrate induces a conformational change
in the active site of the enzyme.
In addition, the enzyme may distort the substrate,
forcing it into a conformation similar to that of the
transition state

18. For example, the binding of glucose to hexokinase induces
a conformational change in the structure of the enzyme such
that the active site assumes a shape that is complementary to
the substrate (glucose) only after it has bound to the enzyme.

19. Coenzyme and Cofactor
Many enzymes require the presence of small, nonprotein units to carry
out their particular reaction.
 Coenzyme: complex organic molecule
Cofactor: inorganic ions, such as Zn2+ or Fe2+

20. Holoenzyme: A complete catalytically-active enzyme together
with its coenzyme or metal ion (cofactor) is called as
holoenzyme.
Apoenzyme: The protein part of the enzyme on its own
without its cofactor/ coenzyme is termed as apoenzyme.

22. Enzyme Kinetics
Activation energy: For a biochemical reaction to proceed, the energy barrier
needed to transform the substrate molecules into the transition state has to be
overcome. The energy required to overcome this energy barrier is known as
activation energy.
It is the magnitude of the activation energy which determines just how fast the
reaction will proceed. It is believed that enzymes increase the rate of reaction by
lowering the activation energy for the reaction they are catalyzing.

23. Enzyme Kinetics
Factors affecting enzyme activity
1. Substrate concentration
2. Enzyme concentration
3. pH
4. Temperature
5. Inhibitors

24. 1. Substrate concentration
A
B
At low substrate concentrations a doubling of substrate concentration
leads to a doubling of reaction rate, whereas at higher substrate
concentration the enzyme becomes saturated and there is no further
increase in reaction rate (hyperbolic curve)

25. 2. Enzyme concentration
When substrate concentrations is saturating, a doubling of the enzyme
concentration leads to a doubling of rate of reaction

26. 3. pH
Each enzyme has an optimum pH at which the rate of the reaction
that it catalyzes is at its maximum. Slight deviations in the pH from
the optimum lead to a decrease in the reaction rate.

28. A
C
B
4. Temperature
Elevated temperature increases the rate of an enzyme-catalyzed reaction by
increasing the thermal energy of the substrate molecules which helps to
overcome energy barrier or achieve activation energy.
However, a second effect comes into play at higher temperatures.which causes
denaturation of the enzyme and decrease the rate of reaction.

29.  Substances which bind to enzyme & disrupt the enzyme
activity by blocking the production of ES-complex or E + P
Many inhibitors exist, including normal body metabolites,
foreign drugs and toxins.
Enzyme inhibition can be of two main types: irreversible
or reversible.
Reversible inhibition can be subdivided into competitive
and noncompetitive.
5. Enzyme Inhibition

30. Irreversible Inhibition
An irreversible inhibitor binds tightly, often covalently, to the
active site of the enzyme, permanently inactivating the
enzyme.
They often form covalent bond with amino acid at active site.
Examples: diisopropylphosphofluoridate (DIPF),
iodoacetamide and penicillin.
Reversible Inhibition
 Involves the noncovalent links between
inhibitor and enzyme

31. Reversible Competitive Inhibition
A competitive inhibitor competes with the substrate
molecules for binding to the active site of the enzyme due to
close structural similarities with the substrate molecule.
At high substrate concentration, the effect of a competitive
inhibitor can be overcome.
e.g.: succinate dehydrogenase (E);
succinate (S); malonate (I)

32. Reversible Non-competitive Inhibition
A noncompetitive inhibitor binds at a site other than the active site of the
enzyme and decreases its catalytic rate by causing a conformational
change in the three-dimensional shape of the enzyme.
Inhibitor dont have any structural similarities with the substrate molecule
e.g.: prostaglandin synthase (E); arachidonate (S); aspirin (I)

33. Enzyme inhibitor: harmful or beneficial?
 Sarin – the nerve gas
Action – inhibits acetylcholinesterase from hydrolyzing
acetylcholine to acetate & choline
Effect – acetylcholine gather at end of nerve, causing
symptoms such as fuzzy eyesight, extreme sweating,
loss of motor functions control & paralysis
acetylcholinesterase – enzyme in the body which has an
important function in nerve regulation and control
 Penicillin – antibacterial agent
Action – covalently attaches to bacterial glycoprotein
peptidase active site, preventing peptidoglycan
peptide bond cross-linking
Effect – prevents cell wall synthesis; exposing bacterial
cell to osmotic lysis; bacteria cannot reproduce
glycoprotein peptidase – bacterial enzyme catalyzing cross-linking
of peptidoglycan peptide bonds, the main cell wall polymer

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