Enzymes (General Introduction & Action Mechanism)

This presentation is made for S.Y.Bsc. Students.
The presentation includes the General Introduction & Action mechanism of Enzymes.

1. Enzymes
By: Dr. MohammedAzim Bagban
Assistant Professor
C. U. Shah Institute of Science
Ahmedabad
General Introduction & Enzyme Action

MI 201 Unit:2

3. What is an enzyme?
globular protein
which functions as a
biological catalyst,
speeding up reaction
rate by lowering
activation energy
without being
affected by the
reaction it catalyse
Active
site

4. Enzymes are protein in nature (?)
 Globular protein.
 Ribozymes are RNA molecule with enzymatic
activity.
 Catalytic behaviour of any enzyme depends
upon its primary, secondary, tertiary or
quaternary structure.
 Enzymes of digestive tract and those found in
blood are present in inactive form called
zymogen or proezymes.

5. Etymology and history
•French chemist Anselme Payen was the first to discover an enzyme, diastase,
in 1833.
•A few decades later, when studying the fermentation of sugar to alcohol by
yeast, Louis Pasteur concluded that this fermentation was caused by a vital
force contained within the yeast cells called "ferments", which were thought
to function only within living organisms.
•The conclusion that pure proteins can be enzymes was definitively
demonstrated by John Howard Northrop and Wendell Meredith Stanley,
who worked on the digestive enzymes pepsin (1930), trypsin and
chymotrypsin. These three scientists were awarded the 1946 Nobel Prize in
Chemistry.

6. Enzyme Nomenclature
An enzyme's name is often derived from its substrate or the chemical reaction
it catalyzes, with the word ending in -ase. Examples are lactase, alcohol
dehydrogenase and DNA polymerase.
Different enzymes that catalyze the same chemical reaction are called
isozymes.
The International Union of Biochemistry and Molecular Biology have
developed a nomenclature for enzymes, the EC numbers; each enzyme is
described by a sequence of four numbers preceded by "EC", which stands for
"Enzyme Commission". The first number broadly classifies the enzyme based
on its mechanism.

7. Enzyme Nomenclature
The top-level classification is:
EC 1, Oxidoreductases: catalyze oxidation/reduction reactions
EC 2, Transferases: transfer a functional group (e.g. a methyl or phosphate
group)
EC 3, Hydrolases: catalyze the hydrolysis of various bonds
EC 4, Lyases: cleave various bonds by means other than hydrolysis and
oxidation
EC 5, Isomerases: catalyze isomerization changes within a single molecule
EC 6, Ligases: join two molecules with covalent bonds.

8. Active site
 Enzymes are composed of
long chains of amino acids
that have folded into a very
specific three-dimensional
shape which contains an
active site.

 An active site is a region on
the surface of an enzyme to
which substrates will bind
and catalyses a chemical
reaction.

9. Enzymes are highly specific for the type of
the reaction they catalyze and for their
substrate.

12. Co-factor (Prosthetic group)
A cofactor is a non-protein chemical compound or metallic ion that is
required for an enzyme's activity as a catalyst, a substance that
increases the rate of a chemical reaction.
Cofactors can be considered "helper molecules" that assist in
biochemical transformations. Cofactors can be divided into two types:
inorganic ions and complex organic molecules called coenzymes.
Coenzymes are further divided into two types. The first is called a
"prosthetic group", which consists of a coenzyme that is tightly or even
covalently, and permanently bound to a protein.
he second type of coenzymes are called "cosubstrates", and are
transiently bound to the protein. Cosubstrates may be released from a
protein at some point, and then rebind later.

13. Coenzyme examples

14. Cofactor examples

15. Distribution of Enzyme in cells
Enzyme
Intracellular
Enzyme
Soluble
Enzymes
Particulate
Enzymes
Periplasmic
Enzymes
Extracellular
Enzyme

16. Extracellular Enzymes
An exoenzyme, or extracellular enzyme, is an enzyme that is secreted by a cell
and functions outside that cell. Exoenzymes are produced by both prokaryotic
and eukaryotic cells and have been shown to be a crucial component of many
biological processes.
Most often these enzymes are involved in the breakdown of larger
macromolecules.
The breakdown of these larger macromolecules is critical for allowing their
constituents to pass through the cell membrane and enter into the cell.
For humans and other complex organisms, this process is best characterized by
the digestive system which breaks down solid food.
 Bacteria and fungi also produce exoenzymes to digest nutrients in their
environment, and these organisms can be used to conduct laboratory assays to
identify the presence and function of such exoenzymes.
Some pathogenic species also use exoenzymes as virulence factors to assist in
the spread of these disease-causing microorganisms.

17. Intracellular Enzymes
An endoenzyme, or intracellular enzyme, is an enzyme that
functions within the cell in which it was produced and the majority of
enzymes fall within this category.
Soluble Enzymes: Found within the cytoplasm and associated with
metabolic activity of cytoplasm.
Particulate enzymes: Found within embedded in cell membrane.
Associated with metabolic activity leading to ATP generation.
Periplasmic enzymes: Located in the periplasmic regions and
associated with biosynthesis of cell wall constituents.

18. Mechanism of enzyme action
The enzymatic reactions takes place by binding of the
substrate with the active site of the enzyme molecule
by several weak bonds.
E + S ‹--------› ES --------› E + P

Formation of ES complex is the first step in the
enzyme catalyzed reaction then ES complex is
subsequently converted to product and free enzyme.

19. "Lock and key" or Template model

20. Induced-fit model

21. Mechanism of enzyme action
The enzymatic reactions takes place by binding of the
substrate with the active site of the enzyme molecule
by several weak bonds.
E + S ‹--------› ES --------› E + P

Formation of ES complex is the first step in the
enzyme catalyzed reaction then ES complex is
subsequently converted to product and free enzyme.

23. Features of enzyme active site :

The active site of an enzyme is the region that binds the
substrates (and the cofactor, if any).
 It also contains the residues that directly participate in the
making and breaking the bonds. These residues are called the
catalytic groups. In essence, the interaction of the enzyme and
substrate at the active site promotes the formation of the
transition state.
The active site is a three-dimensional cleft formed by groups that
come from different parts of the amino acid sequence
Substrates are bound to enzymes by multiple weak attractions as
products needs to be released after the completion of the
reactions. Strong bonding inhibits the process.

25. "Lock and key" or Template model

26. 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 maximize the fit,
which improves catalysis.

- there is a greater range of
substrate specificity

27. Enzyme Specificity

28. Enzyme Specificity

37. Factors affecting reaction velocity

Temperature
Hydrogen ion concentration (pH)
Substrate concentration
Enzyme concentration
Products of the reaction
Presence of activator/inhibitor
Time

38. Effect of Temperature

Temperature(
o
C)
Reaction
Velocity
(v0)

39. Effect of pH
Reaction
Velocity
(v0)
pH
Pepsin
Trypsin
q
r

40. Rate of the reaction or velocity is directly proportional to
the Enzyme Concentration when sufficient substrate is
present.








Accumulation of Product in a reaction causes inhibition of
enzyme activity.

41. Effect of Substrate Concentration


Substrate Concentration/arbitrary
Units
Reaction
Velocity
(v0)

42. Enzyme Kinetics
oStudy of reaction rate and how they changes in
response to change in experimental parameter is
known as kinetics.

oAmount of substrate present is one of the key factor
affecting the rate of reaction catalyzed by an enzyme in
vitro.

43. Effect of Substrate Concentration on Reaction
Velocity

44. References
oStryer L, Berg JM, Tymoczko JL (2002). Biochemistry (5th ed.). San Francisco: W.H. Freeman. ISBN 0-7167-4955-6.open access
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doi:10.1042/bst20160400. PMID 28408493.
o Murphy JM, et al. (2014). "A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties". Biochemical
Journal. 457 (2): 323–334. doi:10.1042/BJ20131174. PMC 5679212. PMID 24107129.
oadzicka A, Wolfenden R (January 1995). "A proficient enzyme". Science. 267 (5194): 90–931. Bibcode:1995Sci...267...90R.
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o Holmes FL (2003). "Enzymes". In Heilbron JL (ed.). The Oxford Companion to the History of Modern Science. Oxford: Oxford University
Press. p. 270. ISBN 9780199743766.
oNomenclature Committee. "Classification and Nomenclature of Enzymes by the Reactions they Catalyse". International Union of
Biochemistry and Molecular Biology (NC-IUBMB). School of Biological and Chemical Sciences, Queen Mary, University of London. Archived
from the original on 17 March 2015. Retrieved 6 March 2015.
o Nomenclature Committee. "EC 2.7.1.1". International Union of Biochemistry and Molecular Biology (NC-IUBMB). School of Biological and
Chemical Sciences, Queen Mary, University of London. Archived from the original on 1 December 2014. Retrieved 6 March 2015.
o Anfinsen CB (July 1973). "Principles that govern the folding of protein chains". Science. 181 (4096): 223–30. Bibcode:1973Sci...181..223A.
doi:10.1126/science.181.4096.223. PMID 4124164.
o Dunaway-Mariano D (November 2008). "Enzyme function discovery". Structure. 16 (11): 1599–600. doi:10.1016/j.str.2008.10.001. PMID
19000810.
oHasim, Onn (2010). Coenzyme, Cofactor and Prosthetic Group – Ambiguous Biochemical Jargon. Kuala Lumpur: Biochemical Education. pp.
93–94.
o "coenzymes and cofactors". Retrieved 2007-11-17.
o "Enzyme Cofactors". Archived from the original on 2003-05-05. Retrieved 2007-11-17.
oCrane FL (December 2001). "Biochemical functions of coenzyme Q10". Journal of the American College of Nutrition. 20 (6): 591–8.
doi:10.1080/07315724.2001.10719063. PMID 11771674. Archived from the original on 16 December 2008.

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