COLLEGE OF MEDICIN AND MEDICAL SCIENCES

Biochemistry
LECTURES
Haitham H. Alnemari

ENZYMES

1 BY : HAITHAM H. ALNEMARI
 Biochemistry ENZYMES

Enzymes
• Bio-catalyst that are produced by living cells and they are protein in

nature.

• Because they are protein in nature they pass the protein characteristics :
a) Colloidal.
b) Heat sensitive ((thermo labial))

• Activation energy: the minimum amount of energy required to bring all

the molecules of the substrate to energy rich state.

• Substrates: are the substances on which the enzymes act to convert

them into products.

• Enzyme decreases the requirement of activation energy.

• Transition state: it is the energy rich state for interacting molecules.

• Important properties of enzymes :

1. Produced by living cells.
2. Catalyze the chemical reactions.
3. Powerful catalyst.
4. They are protein in nature except for riboenzymes.
5. They differ from non-biochemical catalysts that their activity can be regulated.
6. Enzymes have an (Active site)
Active site: is the substrate binding site and it has the catalytic property.
It is a compact structure [secondary and tertiary] made of a chain of amino
acids.
7. Enzymes are highly NOT absolutely specific.

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 Biochemistry ENZYMES

8. Compartmentalization: many enzymes are localized in specific organelles within

the cell. Such compartmentalization:
A. Isolate the reaction substrate or products from other competing
reactions.
B. Provides a favorable environment for the reaction.
C. Organizes thousands of enzymes which present in the cell.
9. Enzymes can be synthesized in an inactive form called
PROENZYMES((zymogens)) . E.g. pepsinogen.

10. Iso-enzymes are those enzymes which have different structure but the same
function.
E.g. creatine phosphokinase
(CPK)1………….. in brain
(CPK)2…………… in heart
(CPK)3…………… in muscle
If these enzymes were found in the serum of the blood in high quantity, this
indicates damage in tissue so enzymes a diagnostic value.

11. Enzymes can be used as drug.

12. Activity of the enzymes can be regulated “regulatory enzymes”

3 BY : HAITHAM H. ALNEMARI
 Biochemistry ENZYMES

v Differentiate between holoenzymes, apoenzymes, co-factor, metal activated

enzyme, prosthetic group, coenzyme, metalloenzyme and isoenzyme.
A. Holoenzyme: it is an enzyme composed from proteinic part and non-
proteinic part.
B. Apoenzyme: it is the proteinic part of the holoenzyme.
C. Co-factor: it is the non-proteinic part of the holoenzyme.
D. Metal activated enzyme: holoenzymes which have a loosely bound
metals on its prosthetic inorganic group.
E. Co-enzyme: specific thermo stable low mol.wt non-protein organic
substance bound tightly in usual.
F. Metalloenzyme: enzyme which has tightly bound metals as its prosthetic
group.
G. Isoenzymes: enzymes which have different structures and same function.

¤ Cardiolipin is the prosthetic group of the enzyme cytochrome

oxidase.
¤ Cu++, Fe++ ions are the metalloenzyme of cytochrome oxidase.
¤ Some vitamins act as co-enzyme:
a. B1 thiamine à form TPP [ thiamine pyrophosphate ] co-enzyme
for pyruvate degyrogenase
b. B2 à FAD [flavin adenine dinucleotide] , FMN [flavin
mononucleotide].
c. B3 à NAD [ nicotinamide adenine dinucleotide ] , NADP
[nicotinamide adenine dinucleotide phosphate ]
d. B5 pantothenic à co-enzyme A [transfer of acyl group]
e. B6 pyridoxine àform co-enzyme [pyridoxal
phosphate]àtransaminase
f. B12 cobalamin à cabamide
g. Biotin à coenzyme in carboxylation reaction.

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 Biochemistry ENZYMES

• Summary:

v Classification of enzymes:
A. Oxido-reductases:
ü Def: enzymes which catalyze the oxidation reduction reaction.
ü Requires two substrates one oxidized and the other is reduced.
ü E.g. Glucose reductase.

NADH2 + glucose à sorbitol + NAD

Coenzyme

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 Biochemistry ENZYMES

B. Transferase:
ü Def: enzymes which catalyze the transfer of C-containing, N-containing and sulfur
containing groups.

Al.T

Glutamic acid pyrovic acid α-ketoglutaric acid Alanine

The responsible enzyme for the previous reaction is a transaminase and

called [Glutamic Pyrovic Transferase GPT ] or [Alanine Transaminase
ALT]
ü This enzyme can be found in the liver normally, but if it is found in the serum of the
blood in high quantity this indicates the presence of a disease in the liver.

C. Hydrolayses.
ü Def: enzymes that catalyze the breakdown of a certain compound by addition of water
molecule.
ü E.g. lactase. Lactose -----à glucose + galactose

D. Lyses.
ü Def: enzymes which catalyze the breakdown of organic compound.
ü Lyases differ from other enzymes in that they only require one substrate for the
reaction in one direction, but two substrates for the reverse reaction
ü Fructose by lyase enzyme called [fructose 1,6 biphosphatase] is cleaved to
glyceralaldehyde 3-phphsphate + dihydroxyaceton 3-phosphate

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 Biochemistry ENZYMES

E. Isomerases.
ü Def: enzymes that catalyze the conversion between isomers.
ü The enzymes which catalyze the transforming between hexoses` isomers are called
hexoisomerase.
ü E.g. glucoseà fructoes

F. Ligases.
ü Def: enzymes which catalyze the connection between two molecules.

f
CO2 + Pyruvate carboxylase

Pyruvic_acid Oxaloacetic_acid

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 Biochemistry ENZYMES

v Summary: (important)

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 Biochemistry ENZYMES

v How does the enzyme increase the rate of the reaction?

1. Enzyme is lowering the amount of activation energy.

Activation energy: is the minimum amount of energy required to
initiate a chemical reaction.

2. Enzyme stabilizes the transition state.

Transition state: is energy rich state of interacting molecules.

Enzyme Substrate
Enzyme + Substrate Enzyme + Product
complex
E+S E+P
g [ES]

Michaelis-Menten model of enzyme mechanism

Enzyme substrate complex [ES] is the transition state

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 Biochemistry ENZYMES

v Models of the enzyme-substrate complex:

1. Lock and key models:
Ø The active site in the enzyme has a fixed shape so a specific type of
substrate can bind to the active site.
Ø There should be complementation between the enzyme and the
substrate.
Ø This theory is true for absolute specificity enzymes and cannot
explain change in the enzymatic activity in the presence of allosteric
modulators.

2. Induced-fit model: (Koshland)

Ø The active site is flexible.
Ø When the active site identifies the substrate it brings a change in the
active site shape so it can accommodate the substrate.
Ø This model similar to the rubber gloves.

v Factors that affect the enzyme activity:

1. Substrate concentration. [S]
2. Enzyme concentration. [E]
3. Product concentration.[P]
4. Temperature.
5. Acidity or alkalinity pH
6. Inhibitors.
7. Agonists.
8. Antagonists.

1. Substrate concentration:
§ When we draw the relation between [S] and the rate of the reaction
we get a hyperpola diagram.
§ If you increase [S] the enzyme activity increase the rate of the
reaction.
§ Explaining: the enzyme has a limited capacity for binding with S if
the amount of S goes beyond this capacity the activity of the enzyme
remains constant it won`t further increased.
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 Biochemistry ENZYMES

§ Km : is the substrate concentration when the maximum velocity

(Vmax) in its half.

v Important conclusions about Michaelis-Menten kinetics:

1. Characteristics of Km: Km ((the Michaels constant))is characteristic
of an enzyme and its particular substrate . Km reflects the affinity of
the enzyme for that substrate. Km is numerically equal to the [S] at
which the reaction velocity is equal to ½ Vmax. Km does not vary
with the [E].

a. Small Km reflects High affinity.

Because low [S] is needed to half-saturate the enzyme that is, reach a
velocity that is ½ Vmax.

b. Large Km reflects low affinity.

Because a high [s] is needed to half-saturate the enzyme.

Q) After having a meal the concentration of the glucose is arises . In the human
body there are two enzymes in order to phosphlyrate the glucose.

1. Glucokinase………. High Km
2. Hexokinase…………low Km
Which enzyme will act after having a meal?
Glucokinase will act because it has a high Km it has a low affinity so it requires
more concentration of substrate to act.

11 BY : HAITHAM H. ALNEMARI
 Biochemistry ENZYMES

2. Enzyme concentration:
• Increase [E] à increase the speed of the reaction.
• If we plot the relation between [E] and the rate of the reaction
we get a hyperbola curve.

• In the beginning of the reaction the rate of the reaction is directly

proportional to [E].
• With continuing to add more E the rate of the reaction reaches its
maximum velocity and it won`t further increased.
3. Temperature:
• As you increase the temperature the rate of the reaction increased
into a certain temperature called OPTIMUM TEMPERATURE.
• Optimum temperature: it is the temperature in which the rate of the
reaction begins to drop.

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 Biochemistry ENZYMES

Rate of the
reaction

• This curve called parabola.

• Why does rate of the reaction begin to drop after optimum
temperature?
Because enzymes are protein in nature the high temperature
may cause denaturation of these enzymes and the enzyme
loses its catalytic power.
• The optimum temperature for the body is 37⁰C à 38.4⁰C.

4. Acidity or alkalinity [pH]

• Every enzyme requires a pH where its function is maximum.

Optimum pH

13 BY : HAITHAM H. ALNEMARI
 Biochemistry ENZYMES

• Optimum pH: is the pH value where the rate of the reaction is

maximum.
• Optimum pH varies from enzyme to enzyme.

5. Product concentration:
• As you increase the product concentration you decrease the rate of
the reaction.
• The excess amount of product accumulates and occupies the active site
of the enzyme.

3.5
3
rate of 2.5
reaction
2
1.5
1
0.5
0
0 0.5 1 1.5 2 2.5 3

product concentration

14 BY : HAITHAM H. ALNEMARI
 Biochemistry ENZYMES

6. Inhibitors:
• Def: substances which inhibit (stop) the enzyme activity.
• Classification:

1) Competitive inhibitors:
v The molecule resembling the substrate.
v (I) can bind to the active site of the enzyme and so it can form
enzyme inhibitor complex EI.
v Decreases the affinity of enzymes for substrate.
v Excessive concentrations of substrate will break the EI complex
and then S can bind to the enzyme.
v Reversible.
v It depends on S and I.
v Km is affected by competitive inhibitors ,Km is increased so the
affinity decreased.
2) Non-competitive inhibitors:
v The shapes of the (I) and (S) are not alike.
v (I) will NOT bind to the active site.
v No influence on the affinity, affinity of E for S remains the same
but the catalytic power decreases.
v Excessive concentrations of S have NO effect.
v It may be reversible when it makes temporary bonds, or
irreversible when it makes permanent bonds.
v Vmax affected by non-competitive inhibitors.

15 BY : HAITHAM H. ALNEMARI
 Biochemistry ENZYMES

• Regulation of enzyme activity.

§ Enzymes are the drivers for the process of metabolism.

§ If you regulate enzymes you regulate metabolism.
§ Steroid hormones and thyroid hormones regulate the
synthesis of enzymes in the human body.

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 Biochemistry ENZYMES

A. Allosteric enzymes:
o Allosteric Greek word means other site or other space.
o Allosteric enzymes: they are a type of enzyme where you can
regulate their activity.
o These enzymes contain two sites:
I. Active site for substrate.
II. Regulatory site or allosteric site for modulator or regulator.

o Modulator or regulator is called ligand.

o Ligand influences the active site it may increase or decrease the
catalytic power.
o If the ligand decreases the catalytic power it is called inhibitor.
o If the ligand increases the catalytic power it is called activator.

B. Irreversible covalent modification:

o It contains hydrolysis of the covalent bond.
o E.g. pepsinogen à pepsin.

C. Reversible covalent modification

o E.g. methyl group addition, acetic acid and phosphoralytion.
The attachment of these groups to the enzymes especially
phosphoric acid cans regulate the activity of the enzyme.

D. Control of the enzyme synthesis:

o This control is achieved by the help of hormones.

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 Biochemistry ENZYMES

• Clinical importance of enzymes:

- Ethoilogical imp. Absence of enzymes lead to a case called ((inborn
errors of metabolism.))
- Diagnostic and prognostic imp.
§ Amylase à pancrease and salivary gland.
§ Acid phosphatase à prostate.
§ Alkaline phosphatase à bone and biliary
§ Aldolaseà mauled
§ A SGPT (ALT) à liver
§ A. SGOT à heart
§ CPK 1 à brain
§ CPK 2 à heart
§ CPK 3 à muscles

The measurements of those enzymes’ levels in the serum of the blood indicate the
presence of a disease ((because the enzyme comes out to blood because of a damage of
the cells)) also indicates the prognosis of the disease is it getting better or worse?

- Therapeutic imp.
§ Streptokinase is administrated in case of acute myocardial
infarction.
§ Digestive enzymes.
§ L-Asparaginase is used to treat cancer.
§ For genetic diseases the enzyme might be given to the
patient directly.

• Enzymes in the daily life:

1. Enzymes have been used since the dawn of mankind in cheese
manufacturing and indirectly via yeasts and bacteria in food
manufacturing.
2. Enzymes oxidise ethanol to acetic acid. This reaction has been
used in vinegar production for thousands of years.
3. Leather industry uses proteolytic and lipolytic enzymes in leather
processing.

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 Biochemistry ENZYMES

4. Isolated enzymes were irst used in detergents in the year 1914.

5. Enzymes are now widely used to prepare the fabrics that your
clothing, furniture and other household items.

6. Enzymes are used by the pulp and paper industry for the removal
of “stickies”, the glues, adhesives and coatings that are introduced
to pulp during recycling of paper.
7. It was possible to make wine, beer, vinegar and cheeses, for
example, because of the enzymes in the yeasts and bacteria that
were utilized.
8. Enzymes have also been used to turn starch into sugar.
9. Corn and wheat syrups are used throughout the food industry as
sweeteners.

• Important notes:
1. Do NOT ignore the references.
2. Look for the full name of the abbreviated enzymes.
3. If you notice a wrong statements or missing information please inform
the student and the writer about that.

Wish you all the luck

19 BY : HAITHAM H. ALNEMARI