Professional Documents
Culture Documents
Subject: Biochemistry
Date:
June 25, 2014
Title:
(LE 1, Lecture 1.4) Enzymes & Enzyme Kinetics
Lecturer: Dr. Floro B. Madarcos
Batch/section: 2018A
Sem/A.Y.: 1st / A.Y. 2014-2015
Transcribers:
Calupitan, C., Candido, S., Canto, G., Capistrano, D., Base, J.
Trans Subject head:
Evangelista, A. (9369390879/alanaevangelista@gmail.com)
I. Outline
A. Definition of Terms
B. Cofactors of Enzymes
C. Six Major Classes of Enzymes
D. Characteristics of Enzymes
E. Models of Enzyme - Substrate Complex
F. Kinetics of Enzyme - Catalyzed Reactions
G. Illustration of Enzyme Kinetics Using Plots &
Equations
H. Inhibition of Enzymatic Activity
I. Regulation of Enzymatic Activity
J. Factors Affecting Enzymatic Activity
K. Clinical Application of Enzymes
II. Objectives
A. Define the following:
- Enzymes, Apoenzyme, Coenzyme, Holoenzyme,
Metalloenzyme, Regulatory enzyme, Active site of the
enzyme, Allosteric site, Substrate
B. Discuss the cofactors of enzymes
C. Enumerate the six major classes of enzymes
D. Discuss the characteristics of enzymes
E. Explain the models of enzyme-substrate complex
F. Explain enzyme kinetics
- Factors that affect enzyme activity or reaction
velocity
- Ways of expressing enzyme activity
G. Discuss the operation and plots used to illustrate
enzyme kinetics
- Michaelis-Menten kinetics
- Lineweaver-Burke Double Reciprocal Plot
- Michaelis constant and its significance
- Kinetic order of reactions
H. Discuss enzyme inhibition and its effect on reaction
velocity
- Reversible
- Irreversible
I. Discuss the different ways of regulating enzyme
activity
J. Explain the factors affecting enzyme activity
K. Elucidate uses and clinical application of enzymes
A. Definition of terms
1. Enzymes specialized protein catalysts that
accelerate chemical reactions in biologic systems to
about 10^5 to 10^20 times faster than uncatalyzed
reactions but are not consumed during the reactions
they catalyse. At the end these are neither used up but
are regenerated, recycled, reutilized
2. Apoenzyme protein part of an enzyme without any
cofactors or prosthetic groups; catalytically inactive;
cannot increase reaction rate by itself
3. Cofactor small organic or inorganic molecules;
either loosely or tightly bound to apoenzyme that
participates in overall catalytic activity; non-protein part
of enzyme
- Coenzymes small organic molecules often
derived from vitamins
- Prosthetic group an organic molecule
permanently attached to the apoenzyme
- Metal ions inorganic molecules
4. Holoenzyme consists of an apoenzyme and a
cofactor; catalytically active form of enzyme; complete
enzyme complex.
5. Metalloenzyme enzymes that require metal in their
composition; has very high affinity in binding and
retaining metal atoms
6. Regulatory enzyme - catalyzes the rate-limiting or
committed step of a metabolic pathway
7. Active site of the enzyme site where the substrate
binds for a catalytic reaction
8. Allosteric site of the enzyme a site where small
molecules (effectors or regulators) bind and may cause
conformational changes in the enzyme; may cause
active site to be more reactive or less reactive.
9. Substrate molecule acted upon by enzyme to form
product
B. Cofactors of Enzymes
1. Coenzymes (Organic Molecules) - Usually (but not
always) derived or synthesized from B- vitamins and act
as transient carriers of specific functional groups; very
little activity and specificity in the absence of the
enzyme.
III. Lecture
Calupitan, C.| Candido, S.| Canto, G.| Capistrano, D.| Base, J.
A.Y. 2014-2015
Page 1 of 11
Biochemistry1.4 |Enzyme Classification & Kinetics
Thiamine
Pyrophosphat
e (TPP)
Flavin
Adenine
Dinucleotide
(FAD)
Nicotinamide
Adenine
Dinucleotide
(NAD)
Pyridoxal
Phosphate
(PLP)
Lipoate
Coenzyme A
(CoA)
Biocytin
5
deoxycobala
min
Tetrahydrofol
alate
Enzyme
Pyruvate
dehydrogenase,
isocitrate
dehydrogenase, aketoglutarate
dehydrogenase,
transketolase, aketoacid
dehydrogenase
Succinate
dehydrogenase, Ketoglutarate
dehydrogenase,
Pyruvate
dehydrogenase,
Nitric oxide
synthase
Lactate
dehydrogenase,
other
dehydrogenases
Glycogen
phosphorylase,
-ALA synthase,
Histidine
decardoxylase,
Alanine
aminotransferase
Pyruvate
dehydrogenase
-Ketoglutarate
dehydrogenase
Acetyl CoA
carboxylase
Pyruvate
carboxylase, Acetyl
CoA carboxylase,
Proprionyl CoA
carboxylase
Methylmalonyl
mutase
Thimdylate
synthase
Chemical
Groups
Transferred
Vitamin
Precursor
Aldehydes
Thiamine
(Vitamin B1)
Electrons
Riboflavin
(Vitamin B2)
Hydride ion
(:H-)
Nicotinic acid
(Niacin; B3)
Amino groups
Pyridoxine
(Vitamin B6)
Electrons and
acyl groups
Not required
in diet
Acyl groups
Pantothenic
acid and other
compounds
CO2 in the
form of
bicarbonate
Biotin
H atoms and
alkyl groups
Vitamin B12
One-carbon
groups
Folic acid
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Biochemistry1.4 |Enzyme Classification & Kinetics
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Biochemistry1.4 |Enzyme Classification & Kinetics
Inorganic
(Metal ions or
iron-sulfur
clusters)
Enzyme
Zn+2
Cu+2
Cytochrome oxidase
Mn+2
Arginase, Ribonucleotide
reductase
Mg+2
Ni+2
Urease
Mo
Nitrate reductase
Se
Glutathione peroxidase
Mn+2
Superoxide dismutase
K+
a. Mg+2
i. A cofactor of hexokinase or glucokinase, an
enzyme that catalyzes the phosphorylation of glucose to
glucose 6-PO4 in the presence of ATP; this is the 1st step
of glycolysis.
ii. Kinases usually require Mg++ as a co-factor.
iii. In the phosphorylation of glucose to glucose 6phosphate, Mg+2 is bound to the phosphates of ATP,
making the phosphate ion more positive and susceptible
for nucleophilic attack, hence kinase can easily catalyze
the transfer of the terminal phosphate group of ATP to
glucose, forming glucose 6-phosphate.
b. K+
i. A cofactor of hexokinase/glucokinase, an enzyme
that catalyzes the phosphorylation of glucose to glucose
6-phosphate, the 1st step of glycolysis.
ii. Also a cofactor of pyruvate kinase, an enzyme that
catalyzes the conversion of phosphoenolpyruvate (PEP)
into pyruvate, the last irreversible reaction of glycolysis.
c. Zn+ - is a cofactor of carbonic anhydrase, an
enzyme that catalyzes the synthesis of H2CO3 from CO2
and H2O; it is bound to the active site of the enzyme.
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Biochemistry1.4 |Enzyme Classification & Kinetics
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Biochemistry1.4 |Enzyme Classification & Kinetics
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Biochemistry1.4 |Enzyme Classification & Kinetics
Significance of Km
- concentration of substrate at which half of the
active sites of the enzyme are filled up
- inverse measure of the affinity of the substrate for
the enzyme:
The lower the km, the higher is the affinity; Vmax
is reached at relatively low substrate
concentration.
The higher the km, the lower is the affinity; Vmax
can be reached only at high substrate
concentration
Calupitan, C.| Candido, S.| Canto, G.| Capistrano, D.| Base, J.
A.Y. 2014-2015
Page 7 of 11
Biochemistry1.4 |Enzyme Classification & Kinetics
Uncompetitive inhibitors
decrease both Vmax and
Km, hence the production of
parallel lines in uninhibited
and inhibited reactions.
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Biochemistry1.4 |Enzyme Classification & Kinetics
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Biochemistry1.4 |Enzyme Classification & Kinetics
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Biochemistry1.4 |Enzyme Classification & Kinetics
V. References
Devlin, T. (2011). Textbook of Biochemistry with Clinical
Correlations, Wiley-Liss 7th Edition. New York: A John
Wiley & Sons, Inc., Publication.
Madarcos, F. (2014). Enzymes. Quezon City,Philippines.
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Biochemistry1.4 |Enzyme Classification & Kinetics