1. Enzymes are protein catalysts that lower the activation energy of biochemical reactions and increase their rates without being consumed. 2. They are classified into six main categories based on the type of reaction they catalyze. 3. Enzyme activity is affected by environmental factors like temperature and pH, as well as cofactors that bind enzymes. Inhibitors can also decrease enzyme activity.

1. Enzyme Structure, classification
and
mechanism of action

2. Importance
• Enzymes play an important role in
Metabolism, Diagnosis, and Therapeutics.
• All biochemical reactions are enzyme
catalyzed in the living organism.
• Level of enzyme in blood are of diagnostic
importance e.g. it is a good indicator in
disease such as myocardial infarction.
• Enzyme can be used therapeutically such as
digestive enzymes.

3. • Virtually all reactions in the body are
mediated by enzymes, which are protein
catalysts, usually within cells, that increase the
rate of reactions without being changed in the
overall process

4. Define enzymes
(Enzymes as Biological Catalysts)
• Enzymes are proteins that increase the rate of
reaction by lowering the energy of activation
• They catalyze nearly all the chemical reactions
taking place in the cells of the body.
• Not altered or consumed during reaction.
• Reusable

5. NOMENCLATURE
• Each enzyme is assigned two names. The first
is its short, recommended name, convenient
for everyday use.
• The second is the more complete systematic
name, which is used when an enzyme must be
identified without ambiguity

6. Recommended name
Most commonly used enzyme names have the
suffix “-ase” attached to the substrate of the
reaction, such as glucosidase and urease. Names
of other enzymes include a description of the
action performed, for example, lactate
dehydrogenase (LDH) and adenylyl cyclase. Some
enzymes retain their original trivial names, which
give no hint of the associated enzymatic reaction,
for example, trypsin and pepsin.

7. Systematic name
• In the systematic naming system, enzymes are
divided into six major classes each with
numerous subgroups. For a given enzyme, the
suffix -ase is attached to a fairly complete
description of the chemical reaction catalyzed,
including the names of all the substrates, for
example, lactate:nicotinamide adenine
dinucleotide (NAD+) oxidoreductase.

8. ACTIVE SITES
• Enzyme molecules contain a special pocket or
cleft called the active sites.

9. Lock-and-Key Model
• In the lock-and-key model of enzyme action:
- the active site has a rigid shape
- only substrates with the matching shape can fit
- the substrate is a key that fits the lock of the
active site
This explains enzyme
specificity
This explains the loss
of activity when
enzymes denature

10. 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.

11. Important Terms to Understand
Biochemical Nature
And Activity of Enzymes
• 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.

12. Types of Cofactors
• Coenzyme:
The non-protein component, loosely bound to apoenzyme
by non-covalent bond. Coenzymes or cosubstrates only
transiently associate with the enzyme and dissociate from the
enzyme in an altered state (for example, NAD+).
• 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.
• permanently associated with the enzyme

13. 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

15. Important Terms to Understand
Biochemical Nature
And Activity of Enzymes
Activation energy or Energy of Activation:
• All chemical reactions require some amount of
energy to get them started.
OR
• It is First push to start reaction.
This energy is called activation energy.

16. 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

17. Enzymes
Lower a
Reaction’s
Activation
Energy

19. Lock-and-Key Model
• In the lock-and-key model of enzyme action:
- the active site has a rigid shape
- only substrates with the matching shape can fit
- the substrate is a key that fits the lock of the active site
• This is an older model, however, and does not work for all
enzymes

20. Induced Fit Model
• In the induced-fit model of enzyme action:
- the active site is flexible, not rigid
- the shapes of the enzyme, active site, and substrate adjust
to maximumize the fit, which improves catalysis
- there is a greater range of substrate specificity
• This model is more consistent with a wider range of enzymes

21. Enzyme-substrate complex
• Step 1:
• Enzyme and substrate combine to form
complex
• E + S ES
• Enzyme Substrate Complex
+

22. Enzyme-product complex
• Step 2:
• An enzyme-product complex is formed.
• ES EP
ES EP
transition
state

23. Product
• The enzyme and product separate
• EP E + P The product
is made
Enzyme is
ready
for
another
substrate.
EP

24. 28
What Affects Enzyme Activity?
• Three factors:
1. Environmental Conditions
2. Cofactors and Coenzymes
3. Enzyme Inhibitors

25. 29
1. Environmental Conditions
1. Extreme Temperature are the most
dangerous
- high temps may denature (unfold) the
enzyme.
2. pH (most like 6 - 8 pH near neutral)
3. substrate concentration .

26. 30
2. 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.

27. Environmental factors
• Optimum temperature The temp at which
enzymatic reaction occur fastest.

28. Environmental factors
• pH also affects the rate of enzyme-
substrate complexes
–Most enzymes have an optimum pH of
around 7 (neutral)
• However, some prefer acidic or basic conditions

29. Substrate Concentration and Reaction Rate
• The rate of reaction increases as substrate
concentration increases (at constant enzyme
concentration)
• Maximum activity occurs when the enzyme is
saturated (when all enzymes are binding substrate)

30. Michaelis-Menten equation

31. Michaelis-Menten Kinetics
V
[S]
V = Reaction velocity
Rate of P formation
Vmax
V = Vm* [S]
Km + [S]

32. Michaelis-Menten Kinetics
• Adding S  More P formation  Faster V
• Eventually, reach Vmax

33. Vmax
Vmax
More Enzyme
Enzyme Kinetics

34. • 1. Km characteristics: Km, the Michaelis constant, is characteristic of an enzyme
and its particular substrate and reflects the affinity of the enzyme for that
substrate. Km is numerically equal to the substrate concentration at which the
reaction velocity is equal to one half Vmax. Km does not vary
with enzyme concentration.
• a. Small Km: A numerically small (low) Km reflects a high affinity of the enzyme for
substrate, because a low concentration of substrate is needed to half-saturate the
enzyme—that is, to reach a velocity that is one half Vmax .
• b. Large Km: A numerically large (high) Km reflects a low affinity of enzyme for
substrate because a high concentration of substrate is needed to half saturate the
enzyme.

35. Michaelis Constant (Km)
V = Vm * [S]
Km + [S]
Key Points:
1.Km has same units as [S]
2.At some point on graph, Km must equal [S]

36. V = Vm * [S] = Vm * [S] = Vm
[S] + [S] 2 [S] 2
When V = Vm/2
[S] = Km

37. Vmax
V = Vm* [S]
Km + [S]
Km
[S]

38. V = Vm* [S]
Km + [S]
• Small Km  Vm reached at low concentration [S]
• Large Km  Vm reached at high concentration [S]
Vmax
Vmax/2
Km
[S]

39. V = Vm* [S]
Km + [S]
Michaelis Constant (Km)
• Small Km  Substrate binds easily at low [S]
• High affinity substrate for enzyme
• Large Km  Low affinity substrate for enzyme
Vmax
Vmax/2

40. Key Points
• Km is characteristic of each substrate/enzyme
• Vm depends on amount of enzyme present
• Can determine Vm/Km from
• Michaelis Menten plot V vs. [S]
• Lineweaver Burk plot 1/V vs. 1/[S]

41. Lineweaver Burk Plot
V = Vm* [S]
Km + [S]
1 = Km + [S] =
V Vm [S]
Km + [S]
Vm [S] Vm[S]
1 = C * 1 + 1
V [S] Vm

42. LineweaverBurk Plot
1
V

43. Enzyme Inhibitors
S
I
E
Competitive
Competes for same site as S
Lots of S will overcome this
S
E
P
Non-competitive
Binds different site S
Changes S binding site S
cannot overcome this
Effect similar to no
enzyme
I

44. Competitive Inhibitor
[S]
Vmax
Vmax/2
Km
Normal
Km
Same Vm
Higher Km
Inhibitor

45. Vmax
With inhibitor
Vmax
Vmax/2
Vmax/2
Lower Vm
Same Km
Km
[S]
Non-competitive Inhibitor

46. Enzyme Inhibitors
• Competive - mimic substrate, may block active site, but
may dislodge it.

47. Enzyme Inhibitors
• Noncompetitive

48. Competitive inhibition
• This type of inhibition occurs when the inhibitor binds reversibly to the
same site that the substrate would normally occupy and, therefore,
competes with the substrate for binding to the enzyme active site.
• 1. Effect on Vmax: The effect of a competitive inhibitor is reversed by
increasing the concentration of substrate. At a sufficiently high [S], the
reaction velocity reaches the Vmax observed in the absence of inhibitor,
that is, Vmax is unchanged in the presence of a competitive inhibitor
• 2. Effect on Km: A competitive inhibitor increases the apparent Km for a
given substrate. This means that, in the presence of a competitive
inhibitor, more substrate is needed to achieve half Vmax.

49. Noncompetitive inhibition
• This type of inhibition is recognized by its characteristic effect causing a
decrease in Vmax. Noncompetitive inhibition occurs when the inhibitor
and substrate bind at different sites on the enzyme. The noncompetitive
inhibitor can bind either free enzyme or the ES complex, thereby
preventing the reaction from occurring
• 1. Effect on Vmax: Effects of a noncompetitive inhibitor cannot b
overcome by increasing the concentration of substrate. Therefore,
noncompetitive inhibitors decrease the apparent Vmax of the reaction.
• 2. Effect on Km: Noncompetitive inhibitors do not interfere with the
binding of substrate to enzyme. Therefore, the enzyme shows the same
Km in the presence or absence of the noncompetitive inhibitor, that is, Km
is unchanged in the presence of a noncompetitive inhibitor

50. 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

51. Enzymes Are Classified into six functional
Classes (EC number Classification) by the
International Union of Biochemists (I.U.B.).
on the Basis of the Types of
Reactions That They Catalyze
• EC 1. Oxidoreductases
• EC 2. Transferases
• EC 3. Hydrolases
• EC 4. Lyases
• EC 5. Isomerases
• EC 6. Ligases

52. Principle of the international
classification
Each enzyme has classification number
consisting of four digits:
Example, EC: (2.7.1.1) HEXOKINASE

53. • 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)

54. H O
OH
H
OH
H
OH
CH2OH
H
OH
H H O
OH
H
OH
H
OH
CH2OPO3
2
H
OH
H
2
3
4
5
6
1 1
6
5
4
3 2
ATP ADP
Mg2+
glucose glucose-6-phosphate
Hexokinase
1. Hexokinase catalyzes:
Glucose + ATP  glucose-6-P + ADP

55. Oxidoreductases, Transferases and Hydrolases

56. Lyases, Isomerases and Ligases