Dental Biochemistry 1- (4)

Enzymes, coenzymes,
cofactors

1
 Enzymes
• Almost all enzymes are proteins.
• Enzymes follow the physical and chemical
reactions of proteins.
• They are heat labile, soluble in water,
precipitated by protein precipitating
reagents (ammonium sulfate or
trichloroacetic acid) and contain 16%
weight as nitrogen.
2
 Enzymes are biocatalysts
• Catalysts are substances which accelerate the
rate of chemical reactions, but do not change
the equilibrium.
• Lack of enzymes will lead to block in
metabolic pathways causing inborn errors of
metabolism.
• The substance upon which an enzyme acts, is
called the substrate.
• The enzyme will convert the substrate into the
product or products.
3
 Nomenclature of enzymes

• Early workers gave whimsical names such as

Pepsin, Trypsin, Chymotrypsin, ….etc.

• Later workers gave the trivial names for some

enzymes named by adding the suffix "ase" to
the substrate, as example, enzyme Lactase
acts on the substrate lactose.

• But there may be more than one enzyme

acting on the same substrate.
4
 Classification of enzymes
According to its function
• Class 1. Oxidoreductase:
Transfer of hydrogen, e.g. alcohol dehydrogenase.
• Class 2. Transferase:
Transfer of groups other than hydrogen. e.g.
hexokinase).
• Class 3. Hydrolases:
Cleave bond; adds water, e.g. acetyl choline esterase.

5
• Class 4. Lyases:
Cleave without adding water, e.g. aldolase.
• Class 5. Isomerases:
Intramolecular transfers. Example, triose phosphate
isomerase.
• Class 6. Ligases:
ATP dependent condensation of two molecules, e.g.
acetyl CoA carboxylase.

6
 Holoenzymes
• Some enzymes require molecules other than
proteins for enzymatic activity.
• The term holoenzyme refers to the active enzyme
with its nonprotein component.
• The term apoenzyme is inactive enzyme without
its nonprotein part.
• If the nonprotein part is a metal ion such as Zn
2+ or Fe2+, it is called a cofactor.
• If it is a small organic molecule, it is termed a
coenzyme.
7
8
• Coenzymes that only transiently associate with
the enzyme are called co-substrates. It acts by
donating or accepting hydrogen atoms or
electrons (NAD+, NADP, FAD and FMN).
• Or transferring groups other than hydrogen.

• If the coenzyme is permanently associated with

the enzyme and returned to its original form, it is
called a prosthetic group as FAD.

• Coenzymes frequently are derived from vitamins.

Example, NAD+ contains niacin, FAD contains
riboflavin.
• Also ATP is an example of coenzyme.
9
Salient features of coenzymes:
• Coenzymes are heat stable. They are low-molecular
weight substances.
• The coenzymes combine loosely with the enzyme
molecules and so, the coenzyme can be separated
easily by dialysis.
• When the reaction is completed, the coenzyme is
released from the apo-enzyme, and goes to some
other reaction site.

10
 Function of coenzyme
• The coenzyme is essential for the
biological activity of the enzyme.
• A coenzyme is a low molecular weight
organic substance, without which the
enzyme cannot exhibit any reaction.
• One molecule of the coenzyme is able to
convert a large number of substrate
molecules with the help of enzyme.

11
 Nicotinamide Adenine Dincleotide
(NAD+)
• This is a coenzyme synthesized from
Nicotinamide, a member of vitamin B complex.
• The structure of NAD+ could be written as:
Nicotinamide-Ribose-P-P-Ribose-Adenine
• The reversible reaction of lactate to pyruvate is
catalyzed by the enzyme lactate
dehydrogenase, but the actual transfer of
hydrogen is taking place on the coenzyme,
NAD+.
12
COO- COO-
I Lactate dehydrogenase I
CHOH ←-----------------------------------→ C=O
I NAD+ → NADH I
CH3 CH3

Lactate
Pyruvate

13
Adinosine triphosphate (ATP):
• ATP is considered to be the energy currency in the
body.
• During the oxidation of food stuffs, energy is released,
a part of which is stored as chemical energy in the form
of ATP.
• In the ATP molecule, the second and third phosphate
bonds are 'high energy' bonds.
• For example;
Hexokinase
Glucose --------------------------------→ Glucose-6-
phosphate
ATP → ADP
14
 Mode of action of enzymes
• There are few theories explaining the mechanism of
action of enzymes

1- Lowering of activation energy

• Presence of enzyme in the reaction decrease the
activation energy which is defined as the energy
required to convert all molecules in one mole of a
reacting substance from the ground state to the
transition state.

15
16
2- Michaelis-Menten theory
• This also called enzyme-substrate complex
theory.

• The enzyme (E) combines with the substrate

(S), to form an enzyme-substrate (ES)
complex, which immediately breaks down to
the enzyme and the product (P).

• E+S → E-S complex → E+P

17
18
3- Fischer's Template theory:
• The explanation is that substrate fits on the
enzyme, similar to lock and key. The key will
fit only to its own lock.
4- Koshland's induced fit theory
• substrate binds to a specific part of the
enzyme, this lead to conformational changes.

19
20
 Active site or active center
• It is the area of the enzyme where catalysis occurs
(i.e. the reaction occur).
• The active site occupies only a small portion of the
whole enzyme.
• Generally active site is situated in a crevice or cleft
of the enzyme molecule.
• The amino acids or groups that directly participate
in making or breaking the bonds (present at the
active site) are called catalytic residues or catalytic
groups. As example Proteolytic enzymes having a
serine residue at the active center called serine
proteases.
21
• The specific substrate bound to the active site.
• During binding, the catalytic group orient itself to
promote exact fitting of substrate to the active site.

22
23
 Thermodynamics:
• From the standpoint of energy, the enzymatic
reactions are divided into three types:
1- Exergonic or Exothermic reaction
• In this reaction energy is released when the
reaction essentially goes to completion. This
reaction is generally irreversible.
• e.g. Urease enzyme
Urea → ammonia + CO2 + energy
• At equilibrium of this reaction, the substrate will be
only 0.5% and product will be 99.5%.
24
2- Isothermic reaction:

• In this reaction, the exchange of energy is

negligible and the reaction is easily reversible.

• e.g. Glycogen +Pi → Glucose-1-phosphate

• At equilibrium of this reaction, 77% glycogen will be

unutilized and 23% glucose-1-phosphate will be
formed.
25
3- Endergonic or Endothermic reaction

• Energy is consumed and external energy is to be

supplied for these reactions. In the body this is
usually accomplished by coupling the endergonic
reaction with an exergonic reaction.

• e.g. Hexokinase reaction

Glucose + ATP → Glucose-6-Phosphate + ADP

26
 Factors influencing enzyme activity
1- Enzyme concentration:
• Velocity of reaction is increased proportionately with
the concentration of enzyme, when substrate
concentration is unlimited.
2- Substrate concentration:
• As substrate concentration is increased, the velocity is
also correspondingly increased in the initial phases; but
the curve flattens afterwards. The maximum velocity
thus obtained is called Vmax.
3- Effect of concentration of products:
• When product concentration is increased, the reaction
is slowed, stopped or even reversed.
27
4- Effect of temperature:
• The velocity of enzyme reaction increases when
temperature of the medium is increased; reaches a
maximum and then falls.
• As temperature is increased, more molecules get
activation energy, or molecules are at increased rate of
motion. So their collision probabilities are increased
and so the reaction velocity is enhanced.
• But when temperature is more than 50°C, heat
denaturation and consequent loss of tertiary structure
of protein occurs. So activity of the enzyme decreased.
• Most human enzymes have the optimum temperature
around 37°C. Certain bacteria living in hot springs will
have enzymes with optimum temperature near 100°C.
28
5- Effect of pH:
• Each enzyme has an optimum pH, on both sides of
which the velocity will be drastically reduced.
• Usually enzymes have the optimum pH between 6
and 8.
• Some important exceptions are Pepsin (with
optimum pH 1-2), alkaline phosphatase (optimum
pH 9-10) and acid phosphatase (4-5).

29
 Enzyme activation
Enzymes activated by different methods as:
• Presence of certain metallic ions, e.g. calcium
activate lipase.
• Conversion of an inactive proenzyme or zymogen
to the active enzyme. E.g. splitting of a single
peptide bond and removal of a small polypeptide
from trypsinogen, the active trypsin is formed.
• Covalent modification, in which activation of
enzyme occur by adding or removing groups
(breaking or making covalent bonds).
30
 Enzyme inhibition

All the reactions in the body are

appropriately controlled. Control of
the whole pathway is achieved by
inhibition of such key enzymes or
regulatory enzymes.

31
1- Competitive inhibition:
• In this type, the inhibitor will be a structural analog
of the substrate. There will be similarity in three-
dimensional structure between substrate (S) and
inhibitor (I).

• The inhibitor molecules are competing with the

normal substrate molecules for attaching with the
active site of the enzyme.

• E + S → E-S → E + P
• E + I → E-I
32
• Since E-I (enzyme-inhibitor complex) can react only
to reform the enzyme and inhibitor, the number of
enzyme molecules available for E-S formation is
reduced.

• Competitive inhibition is usually reversible. Excess

substrate abolishes the inhibition. If substrate
concentration is enormously high when compared
to inhibitor, then the inhibition is reversed.

• For example, the succinate dehydrogenase reaction

is inhibited by malonate, which are structural
analogs of succinate.

33
Clinical significance:
• Pharmacological action of many drugs may be
explained by the principle of competitive inhibition.
As example:
• Sulphonamides are commonly employed
antibacterial agents. Bacteria synthesize folic acid
by combining PABA with pteroylglutamic acid. .
Bacteria wall is impermeable to folic acid. Sulpha
drugs, being structural analogs of PABA, will inhibit
the folic acid synthesis in bacteria, and then die.
The drug nontoxic to human cells, because human
beings cannot synthesizes folic acid.
34
Methotrexate is structural analog to folic
acid, and so can competitively inhibit
folate reductase enzyme. This is essential
for DNA synthesis and cell division.
Therefore, methotrexate is used as an
anticancer drug.

35
2- Noncompetitive inhibition
• A variety of poisons, such as iodoacetate, heavy
metal ions (silver, mercury) and oxidizing agents act
as irreversible noncompetitive inhibitors.

• The inhibitor usually binds to different domain on

the enzyme, other than the substrate binding site.

• Since these inhibitors have no structural

resemblance to the substrate, an increase in the
substrate concentration generally does not relieve
this inhibition.
36
• Cyanide inhibits cytochrome oxidase. Fluoride
will remove magnesium ions and will inhibit
the enzyme, enolase, and consequently the
glycolysis.
• The inhibitor combines with the enzymes and
reaction becomes irreversible.
• The velocity of the reaction is reduced.
• Increasing substrate concentration will abolish
the competitive inhibition, but will not abolish
non-competitive inhibition.
37
3- Allosteric regulation:
• Allosteric enzyme has one catalytic site where
the substrate binds and another separate
allosteric site where the modifier binds
(allo=other).
• Allosteric enzymes are utilized by the body for
regulating metabolic pathways. Such a
regulatory enzyme in a particular pathway is
called the key enzyme or rate limiting
enzyme.
38
39
 Isoenzymes
• They are physically distinct forms of the same
enzyme activity. Multiple molecular form of
an enzyme is described as isoenzymes or
isozymes. They synthesized from various
tissues
• Ex. Lactate dehydrogenase has 5 forms.
• The study of isoenzymes is useful to
understand diseases of different organs.

40
 Clinical enzymology
• Plasma contains many functional enzymes which
are actively secreted into plasma. For example,
enzymes of blood coagulation.
• On the other hand, there are a few non-functional
enzymes in plasma, which are coming out from cells
of various tissues due to normal wear and tear.
• Their normal levels in blood are very low, but are
drastically increased during cell death (necrosis) or
disease.
• Therefore, assays of these enzymes are very useful
in diagnosis of diseases.
41
 Lactate Dehydrogenase (LDH):
Isoenzymes of LDH
• LDH enzyme is a tetramer with 4 subunits. But the
subunit may be either H (heart) or M (muscle)
polypeptide chains. These two are the products of 2
different genes.
• S0 5 combinations of H and M chains are possible;
H4, H3M, H2M2, M3H and M4 varieties, forming 5
isoenzymes. All these 5 forms are seen in all
persons.

42
• M4 form is seen in skeletal muscles; while H4 form
is seen in heart.
• Normally LDH-2 (H3M1) concentration in blood is
greater than LDH-1 (H4); but this pattern is reversed
in myocardial infarction; this is called flipped
pattern. The isoenzymes are usually separated by
cellulose acetate electrophoresis.
• In myocardial infarction, LDH activity is increased.
Within a few hours after the heart attack, the
enzyme level starts to increase, reaches a peak on
the 5th day, and reaches normal levels by 10-12
days.
43
 Creatine Kinase (CK):
• Ck value in serum is increased in myocardial
infarction. The CK level starts to rise within 3 hours
of infarction.

• Therefore CK estimation is very useful to detect

early cases.

• The CK level is not increased in hemolysis or in

congestive cardiac failure; and therefore Ck has an
advantage over LDH.

44
CK and Muscle Diseases
• The level of CK in serum is very much elevated in
muscular dystrophies. The level is very high in the
early phases of the disease.

• CK level is highly elevated in crush injury, fracture

and acute cerebrovascular accidents.

• Estimation of total CK is employed in muscular

dystrophies and MB isoenzyme is estimated in
myocardial infarction.
45
Isoenzymes of CK
• CK is a dimer. The subunits are called B for brain and
M for muscle. Therefore, three isoenzymes are seen
in circulation.
• MM (CK3) is originating from skeletal muscles. MB
(CK2) is from heart and BB (CK1) is from brain.
• Hence, the detection of MB- isoenzyme is important
in myocardial infarction.
• The most sensitive and earlier marker of acute
myocardial infarction (AM) is either Troponin I or
Troponin T.
46
 ALanine amino transferase (ALT)
• In old literature, it was called as serum glutamate
pyruvate transaminase (SGPT). The enzyme needs
pyridoxal phosphate as coenzyme.
• Normal serum level of ALT for male is 13-35 U/L and for
female is 10-30 U/L.
• Very high values (100 to 1000 U/L) are seen in acute
hepatitis, either toxic or viral in origin.
• Both ALT and AST levels are increased in liver disease,
but ALT˃˃ AST. Rise in ALT levels may be noticed several
days before clinical such as jaundice is manifested.
• Moderate increase (25 to 100 U/L) may be seen in
chronic liver diseases such as cirrhosis, and
malignancy in liver.
47
 Alkaline Phosphatase (ALP)
• ALP is a nonspecific enzyme which hydrolyses
aliphatic, aromatic or heterocyclic
compounds. The pH optimum for the enzyme
reaction is between 9 and 10.
• It is produced by osteoblasts of bone, and is
associated with the calcification process.
Normal serum value of ALP is 40-125 U/L.
• In children the upper level of normal value
may be more, because of the increased
osteoblastic activity in children.
48
• Moderate increase (2-3 times) in ALP level is
seen in hepatic diseases such as infective
hepatitis, alcoholic hepatitis or hepatocellular
carcinoma.

• Very high levels of ALP (10-12 times of upper

limit) may be noticed in extrahepatic
obstruction (obstructive jaundice) caused by gall
stones or by pressure on bile duct by carcinoma
of head of pancreas or enlarged lymph nodes.

49
 Enzyme patterns (profile) in diseases

I. Hepatic diseases
• Alanine amino transferase (ALT):
Marked increase in parenchymal diseases.

• Alkaline phosphatase (ALP):

Marked increase in obstructive liver disease.

50
II. Myocardial infarction
• Creatine kinase (CK-MB):
First enzyme to rise following infarction, CK-MB
isoenzyme is specific.

• Aspartate amino transferase (AST):

Rises after the rise in CK and return to normal in 4-5
days.

• Lactate dehydrogenase (LDH):

Last enzyme to rise. LDH-1 becomes more than 2
(Flipped pattern).
51
III. Muscle diseases
• Creatine kinase (CK-MM):
Marked increase in muscle diseases. CK-MM
fraction is elevated.

IV. Bone diseases

• Alkaline phosphatase (ALP):
Marked elevation in osteoblastic bone
activity as in rickets. Heat labile bone.
52
V. Prostate cancer
• Prostate specific antigen (PSA):
Marker of prostate cancer. Mild increase in
benign prostate enlargement.

• Acid phosphatase (ACP):

Marker of prostate cancer. Metastatic bone
disease especially from a primary from
prostate. Inhibited by L tartrate.
53
 THANKS

54