The document outlines a group assignment focused on enzyme structure, classification, and mechanisms of action, including preparation guidelines for a PowerPoint presentation. Key learning objectives include defining enzymes, explaining their functions, and understanding their specificity and classification. Additionally, it covers various factors affecting enzyme activity, including cofactors, environmental conditions, and inhibitors.

1. Enzyme Structure, classification
&
mechanism of action
T. Mutibvu
tmutibvu@gmail.com
1

2. Group assignment/ presentation
• Prepare a PowerPoint presentation on ‘Enzyme
assays’
• Presentation time: 10 minutes
• Use standard PowerPoint techniques
– Include at most 6 points per slide
– Include about 6 words per bullet
– Make sure the slides are readable from a distance
– NB: NO ANIMATIONS/stylish transitions (penalty)
• Dress accordingly. NB: marks will be deducted for
inappropriate dressing
2

3. Aspect Component Score
Group ID and leader
A B
C
D E
Subject
matter
Introduction 5
Measuring [enzyme] 5
Assay methods 15
Important additional
details
5
Conclusion &
references
5
Presentation
quality
Slide quality &
content
5
Slide numbering &
editorials
5
Presenter
composure, voice
projection & clarity
5
Presenter
appearance
5
Time keeping 5
Total 60
3

4. OR
We write a quiz after we are done with the
section
4

5. Learning Objectives
• By the end of the lecture, the student
should be able to :
–Define enzymes and related terms (active
site, apoenzyme, holoenzyme, prosthetic
group)
– Explain the Ea
–Describe the structure of enzymes
–Understand the mechanism of action
–Describe & explain the classification of
enzymes 5

6. Importance
• Enzymes play an important role in Metabolism,
Diagnosis & Therapeutics
• All biochemical reactions are catalyzed by enzymes
• [Enzyme] in blood is of diagnostic significance e.g
good indicator of disease e.g myocardial infarction
• Enzymes can be used therapeutically
6

7. Define enzymes
(Biological Catalysts)
• Enzymes are proteins that increase the rate of
reaction by lowering the activation energy (Ea)
• They catalyze nearly all the chemical reactions
taking place in the cells of the body
• Not altered or consumed during reaction
• Reusable 7

8. Active site
• Enzyme molecules contain a special pocket or
cleft called the active sites
9

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 11

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
12

11. Terms used in enzymology
• 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
13

12. 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
14

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

14. Specificity
• Specificity
– Unlike inorganic catalysts, enzymes are more
specific toward their substrates and for the type
of reactions they catalyze
– Enzymes exhibit different types of specificity;
• Absolute specificity: act on one substrate type
– Succinate dehydrogenase (TCA cycle) catalyzes
only the oxidation of succinate to fumarate
16

15. • Absolute group specificity: Act on a very small
group of substrates having the same functional
group but at different rates
– Alcohol dehydrogenase oxidizes both ethanol and
methanol which have a common hydroxyl group
– Hexokinase phosphorylates glucose but also fructose
and mannose
• Relative group specificity: enzymes exhibiting
relative group specificity act upon more than
one group of substrates
– Trypsin catalyzes the hydrolysis of both ester and
amide bonds
Specificity
17

16. Specificity
Specificity
• Stereospecificity: a given enzyme can act upon only
particular stereoisomers
– L-amino acid oxidase acts only on L-amino acid
not on its D-form
– Similarly D-amino oxidase acts only on D-amino
acid
• The enzymes are so specific since the active site of
each enzyme has a particular shape, size and charge
to bind certain substructure only and to catalyze the
conversion of these substrates
18

17. Activation energy
All chemical reactions require some amount of
energy to get them started
OR
• It is the first push needed to start reaction
• This energy is called Ea
Terms used in enzymology
19

18. Mechanism of Action of Enzymes
• Enzymes increase reaction rates by
decreasing the Ea :
• Enzyme-Substrate Interactions:
‒ Formation of Enzyme substrate complex by:
‒ Lock-and-Key Model
‒ Induced Fit Model
21

19. Enzymes
Lower a
Reaction’s
Ea
22

20. 23

21. Lock-and-Key Model
• In the lock-and-key model of enzyme action:
- Active site has a rigid shape
- only substrates with 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
24

22. 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
25

23. Enzyme-substrate complex
• Step 1:
• Enzyme and substrate combine to form a
complex
• E + S ES
– Enzyme - Substrate Complex
+
27

24. Enzyme-product complex
• Step 2:
• An enzyme-product complex is formed
• E
ES
S EP
EP
E
ES
S EP
EP
transition
transition
state
state
28

25. Product
• The enzyme and product separate
• EP
EP E
E +
+ P
P
The product
is made
Enzyme is
ready
for
another
substrate.
EP
EP
29

26. 30
What affects enzyme activity
What affects enzyme activity?
?
• Three (main) factors:
Three (main) factors:
1.
1. Environmental Conditions
Environmental Conditions
2.
2. Cofactors and Coenzymes
Cofactors and Coenzymes
3.
3. Enzyme Inhibitors
Enzyme Inhibitors
30

27. 31
Environmental Conditions
Environmental Conditions
1. Extreme temperatures;
– the most dangerous
– high temps may denature (unfold) the enzyme
2. pH (most like 6 - 8 pH near neutral)
3. Substrate concentration [S]
31

28. 32
Cofactors and Coenzymes
Cofactors and Coenzymes
• Inorganic substances (zinc, iron) and
vitamins (respectively) are sometimes
need ed for proper enzymatic activity
• Example:
Iron must be present in the quaternary
structure - haemoglobin in order for it to
pick up oxygen 32

29. Environmental factors
Environmental factors
• Optimum temperature :The temp at which
enzymatic reaction occurs fastest.
33

30. Environmental factors
Environmental factors
• pH also affects the rate of formation of
enzyme-substrate complexes
–Most enzymes have an optimum pH of around 7
(neutral)
• However, some prefer acidic or basic conditions
34

31. 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)
35

32. Enzyme Inhibitors
• Competive - mimic substrate, may block active site, but may dislodge it.
37

33. Enzyme Inhibitors
• Noncompetitive
38

34. Irreversible inhibition:
- Suicide inactivators;
•These molecules bind permanently with the
enzyme;
•Reduce the [enzyme]
•Example, cyanide irreversibly inhibits the
enzyme cytochrome oxidase (respiration)
•If this cannot be used, death will occur
39

35. Enzyme
nomenclature
40

36. Protein
ase
Substrate Name + -ase
Love that ‘ase’!
Love that ‘ase’!
41

37. Carbohydrate
ase
Name that Enzyme !!!
42

38. 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 43

39. 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
44

40. Enzyme classification
• Enzymes can be classified into 6 major classes based on nature &
type of reaction catalyzed:
– 1. Oxidoreductases: oxidation or reduction reactions by
transfer of hydrogen or electrons e.g. succinate dehydrogenase
– 2. Transferases: transferring functional groups between donors
and acceptors
• the amino, acyl, phosphate, one-carbon and glycosyl groups
are major moieties that are transferred e.g., glutamic
pyruvic transminase
– 3. Hydrolases: special class of transferases in which the donor
group is transferred to water
– 4. Lyases: remove the groups of water, ammonia or CO2 from
the substrate to cleave double bonds or conversely, add these
groups to double bonds e.g. fumarase.
45

41. Enzyme classification
5. Isomerases: heterogeneous group of enzymes that catalyze
isomerizations (i.e. structural rearrangements within a molecule). These
include cis-trans, keto-enol, and adose-ketose interconversions. Mutases
involve the intramulecular transfer of a group such as phosphoryl group
6. Ligases (synthetases): involved in synthetic reactions where
two molecules are joined together at the expense of
breakdown of nucleosidetriphosphates
• The formation of aminoacyl tRNAs, acetyl coenzyme A & glutamine are
reactions catalyzed by ligases, e.g. pyruvic carboxylase
46

42. Enzyme class Reactions classified
1 Oxidoreductases Oxidation and reduction of substances (usually
involves hydrogen transfer)
Dehydrogenases Transfer of hydrogen atoms from substrate to NAD*
Oxidases Transfer of hydrogen atoms from substrate to
oxygen
Oxygenases Partial incorporation of oxygen to substrate
Peroxidases Transfer of electrons from substrate to hydrogen
peroxide
2 Transferases Transfer of a chemical group (such as a methyl
group, amino group, phosphate from one molecule
to another
Phosphorylases Addition of orthophosphate to substrate
Transaminases Transfer of amino group from one substrate to
another
Kinases Transfer of phosphate from ATP to substrate
47

43. 3 Hydrolases Cleavage of bonds by the addition of water
Phosphatases Removal of phosphate from substrate
Peptidases Cleavage of peptide bonds
4 Lyases Addition of groups to double bonds (-C=C-, -
C=O-, -C=N-)
Decarboxylase
s
Removal of carbon dioxide from substrate
5 Isomerases Rearrangement of atoms of a molecule
6 Ligases Formation of new bonds using energy from
(simultaneous) beakdown of ATP
7 Synthetases Joining two molecules together
Types of enzymes and reactions catalysed
48

44. Principle of the international
classification
Each enzyme has a classification number
consisting of four digits:
•Example, EC: (2.7.1.1) HEXOKINASE
49

45. • 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 A PHOSPHATE
ACCEPTOR)
• 1. SPECIFIC NAME
ATP-D-HEXOSE-6-PHOSPHOTRANSFERASE (Hexokinase)
50

46. H O
O H
H
O H
H
O H
CH 2O H
H
O H
H H O
O H
H
O H
H
O H
CH 2O PO 3
2
H
O H
H
2
3
4
5
6
1 1
6
5
4
3 2
ATP ADP
M g2+
glucose glucose-6-phosphate
Hexokinase
1. Hexokinase catalyzes:
Glucose + ATP  glucose-6-P + ADP
51

47. Oxidoreductases, Transferases and Hydrolases
52

48. Lyases, Isomerases and Ligases
53