Enzymes

Introduction
All enzymes are protein. Catalytic activity of the enzyme depends on the integrity of their native protein
conformation. Catalytic activity will be lost/destroyed by enzymes that will be broken or denatured.
Primary, secondary, tertiary, and quaternary structures of proteins are essential for catalytic activity.
Some enzymes require cofactors or coenzymes or both for their activity.

Cofactor Enzyme
Cu2+ Cytochrome oxidase
Table 1.0: Some inorganic elements serve as cofactors for
Fe2+/Fe3+ Cytochrome oxidase
Catalase enzymes.
Peroxidase
K+ Pyruvate kinase
Mg2+ Pyruvate kinase
Hexokinase
Glucose-6-phosohatase
Mn2+ Arginase
Ribonucleotide reductase
Mo Dinitrogenase
Ni2+ Urease
Se Glutathione peroxidase
Zn2+ Carboxy peptidase A & B
Carbonic anhydrase
Alcohol dehydrogenase

Coenzyme Chemical group transferred Dietary precursor in mammals

Biocytin CO2 Biotin
Coenzyme A Acyl groups Pantothenic acid and other
compounds
5’-Deoxyadenosylcobalamin H atoms and alkyl groups Vitamin B12
(Coenzyme B12)
Flavin adenine dinucleotide Electrons Riboflavin (Vitamin B2)
Lipoate Electrons and acyl groups Not required in diet
Nicotinamide adenine Hydride ion (:H-) Nicotinic acid (Niacin)
dinucleotide
Pyridoxal phosphate Amino group Pyridoxine (Vitamin B6)
Tetrahydrofolate One-carbon group Folate
Thiamine pyrophosphate Aldehydes Thiamine (Vitamin B1)
Table 2.0: Some coenzymes that serve as transient carriers of specific atoms or functionals groups
 Figure 1.0: Prosthetic group (ie. Heam group)

A coenzyme/metal ion is very tightly/covalently bound to the

enzyme protein is called “prosthetic group”.

Figure 2.0: Simple diagram for holoenzyme.

A complete, catalytically active enzyme together with its

bound coenzyme/metal ion is called “holoenzyme”.

The protein part of such an enzyme is called “Apoprotein”.

Apoprotein Coenzyme

No. Class Type of reaction catalyzed

1 Oxidoreductase Transfer of electrons (Hydride
ions/H atoms)
2 Transferases Group transfer reaction
3 Hydrolases Hydrolysis reactions (Transfer of
functionals groups to water)
4 Lyases Addition of groups of double
bonds/formation of double
bonds by removal of groups
5 Isomerases Transfer of groups within
molecules to yield isomeric
forms
6 Ligases Formation of C-C, C-S, C-O, and
C-N bonds by condensation
reactions coupled to ATP
cleavage
Table 3.0: International Classification of Enzymes
Chemical transformation
Chemical transformation is the surface of the active group is lined with amino acid residues with
substituent groups that bind the substrate and catalyze.

Active site
The distinguish feature of enzyme-catalyzed reaction takes place within the confines of a pocket on the
enzyme is called active site.

Substrate
The molecules is bound with active site and acted upon by the enzyme.

Commonly the reaction rate of enzymes (highly effective catalysts) 105 - 1017.

Enzyme-Catalyzed Reaction = Enzyme + Substrate (ES Complex)

Function of enzymes and other catalysts depend on the lower activation energy for a reaction and
enhance the reaction rate.

Enzyme does not affect the equilibrium of a reaction.

Enzymatic rate enhancements are derived from weak interactions (H bonds and hydrophobic and ionic
interactions) between substrate and enzyme.

Enzyme active site and substrate specificity

Enzymes have active sites. Active sites are specific and have unique amino acid residue to bind the
specific substrate. There may be one/more substrates for each type of enzyme depending on the
chemical reaction. Sometimes, a single reactant substrate is broken down into multiple products and 2
substrates may come together to create one large molecule. However, 2 reactants might enter the
reaction, both become modified, and leave the reaction as 2 products. The active site binds with
substrate. Therefore, this site is composed by unique combination of amino acid residues (side chains/R
groups). Each amino acid residues can be large/small; weakly acidic/base; hydrophilic/hydrophobic;
positively charged/negatively charged/neutral. Specific chemical environment is created by the position,
sequences, structures, and properties of these residues in the active site. A specific chemical substrate
makes the enzyme specific to its substrate.

Active site and environmental condition

Enzyme’s active site is affected by environmental conditions. Increasing the environmental
temperature increases reaction rates. Because when the temperature is rising, the molecules are
moving more quickly and come to contact with each other. Increasing/decreasing the temperature
outside of an optimal range can affect chemical bonds and change the shape of enzyme. If the enzyme
changes shape, the active site may no longer bind with the appropriate substrate and the rate of
reaction will decrease. Temperature and pH cause enzymes to denature.
Induces fit and enzyme function.
For long years, scientists believe that enzyme-substrate binding took place in “Lock and Key” fashion.
According to the modern asserted that the enzyme and substrate fit together perfectly in one
instantaneous step. Current research supports a more refined view which is called induced fit. When
enzyme and substrate come together, their interaction causes a mild shift in the enzyme’s structure that
confirms an ideal binding arrangement between the enzyme and the substrate. This dynamic binding
maximizes the enzyme’s ability to catalyze its reaction.

Enzyme-Substrate Complex
Enzyme-substrate complex is formed when an enzyme binds its substrate. This complex is lower the
activation energy and promotes rapid progression by providing certain ions/chemical groups that form
covalent bonds with molecules. Enzymes promote chemical reactions by bringing substrates together in
an optimal orientation, lining up the atoms and bonds of one molecule with the atoms and bonds of the
molecule. It can contort the substrate molecules and facilitate bond breaking. The active site of an
enzyme creates an ideal environment (slightly acidic/non-polar environment). After the completion of
the reaction, the enzyme will return to its original state. One of the important properties of enzymes is
that they remain ultimately unchanged by the reactions they catalyze. After an enzyme is done
catalyzing a reaction, it releases its products (substrates).

Competitive and non-competitive inhibition

The cell uses specific molecules to regulate enzymes to promote/inhibit certain chemical reactions. It is
necessary to inhibit an enzyme to reduce a reaction rate, and there is more than one way for this
inhibition to occur. In competitive inhibition, an inhibitor molecule is similar enough to a substrate that
it can bind to the enzyme’s active site to stop it from binding to the substrate. It competes with the
substrate to bind the enzyme. In non-competitive inhibition, an inhibitor molecule binds to the enzyme
at a location other than the active site (an allosteric site). The substrate can still bind to the enzyme, but
the inhibitor changes the shape of the enzyme, so it is no longer in optimal position to catalyze the
reaction.

Allosteric inhibition and activation

In non-competitive allosteric inhibition, inhibitor molecules bind to an enzyme at the allosteric site.
Their binding induces a conformational change that reduces the affinity of the enzyme’s active site for
its substrate. The binding of this allosteric inhibitor changes the conformation of the enzyme and its
active site, so the substrate is not able to bind. It prevents the enzyme from lowering the activation
energy of the reaction and the reaction rate is reduced. Allosteric inhibitors are not the only molecules
that bind to allosteric sites. Allosteric activators can increase reaction rates. They bind to an allosteric
site which induces a conformational change that increases the affinity of the enyme’s active site for its
substrate. It increases the reaction rate.