1. Written Report on …
Enzymes: Nomenclature
Molecular Model of Protein
Molecular Model of Enzyme Amylase
Submitted by:
Conrad Vincent V. Vivas
BS Chemical Engineering-4
Submitted to:
Engr. Christylene S.Balagtas
ChE-40 Biotechnology
January 12, 2013

2. ChE 40- Biotechnology
Xavier University- Ateneo de Cagayan
Introduction
In this report the main discussion is all about enzymes and its nomenclature. Enzymes
govern all chemical reactions in living organisms. They are specialized proteins that with
fascinating precision and selectivity catalyze biochemical reactions that store and release
energy, pigments in our hair and eyes, digest food that we eat, synthesize cellular building
materials, and protect us by repairing cellular damage and clotting our blood. Enzymes are
sensitive to their environment, responding quickly in the cell. The deficiency or excess of
particular enzymes can cause certain disease or signal problems such as heart attack and other
organ damage.
I. Basic Information about Enzymes
The name “enzyme” was coined by Wilhelm Kunhne, which means “in yeast”, but the
word is now used to mean biological catalyst regardless of their origin.
 (Comes from Greek words “en” = in and “zyme” = yeast)
Yeast Enzymes  production of breads and alcoholic beverages.
(Action of yeast on sugar produces CO2 gas that causes the bread to rise, while
fermentation of sugars in fruit juices with the same yeast enzyme produces
alcoholic beverages)
Enzymes are specialized globular Proteins that acts as biological catalysts, it is used to
increase the rate of biochemical reactions taking place within living systems, without
themselves undergoing any overall change.
 Proteins are polymers of amino acids.
(Proteins are major structural component of all tissue of living organisms and are
necessary for cell repair and muscular growth.)
 Biological catalyst is a substance that mediates or speeds up a specific
biochemical (occurs in living organisms) reactions.
 As catalyst they are not being destroyed or altered upon completion of the
reaction. (Hence it is not consume in the reaction)
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3. ChE 40- Biotechnology
Xavier University- Ateneo de Cagayan
 Enzymes lower the activation energy needed for the reaction to occur or
proceed into product.
Two structural classes of enzymes:
1. Simple enzymes – enzyme composed only of protein (amino acid chains).
2. Conjugated enzymes –enzymes that have a non-protein part in addition to a protein.
Parts of Conjugated Enzyme:
a. Apoenzyme - inactive portion of protein
b. Cofactor- non-protein component of enzyme
c. Coenzyme - enzyme with organic molecule as its cofactor
d. Holoenzyme - active enzyme including cofactor
Apoenzyme + Cofactor = Holoenzyme
Figure 1. parts of conjugated enzyme
Deficiency of enzyme in the human body can lead to various complications.
Ex. Lactose intolerant
 The problem arises because the sugar in milk -- lactose -- does not get broken
into its glucose components. Therefore, it cannot be digested.
 The intestinal cells of lactose-intolerant people do not produce LACTASE, the
enzyme needed to break down lactose.
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4. ChE 40- Biotechnology
Xavier University- Ateneo de Cagayan
II. History of Enzymes
In 1836, the word “catalyst” was coined by Jon Jakob Berzelius
(According to J.J. Berzelius, catalyst refers to materials whose presence would set the
reactions to go to which otherwise would be dormant)
The concept prevailed until 1926, when Willstaetter first could achieve the isolation of
pure enzyme peroxidase
 Horseradish Peroxidase (phenols, which are important pollutant, can be
removed by enzyme-catalyzed polymerization using horseradish peroxidase.)
Almost the same period, +James B. Sumner isolated and crystallize the enzyme Urease
from the jack bean.
(+His work was to earn him the 1947 Nobel Prize.)
 Urease breaks down urea (waste product formed in the liver) into carbon dioxide
and ammonia.
As time pass by, large number of enzymes has been isolated from time to time. By
1985, as many as 2500 enzymes were known.
There needs to be rules for naming!!!
*International Union of Biochemistry and
Molecular Biology (IUBMB)
Named and classified enzymes
Figure 2. Discovered Enzymes through time
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5. ChE 40- Biotechnology
Xavier University- Ateneo de Cagayan
III. Enzyme Nomenclature
Enzymes are classified and named (by IUBMB) according to the nature of the chemical
reactions they catalyze and not on their structure.
(Unlike in organic chemistry, where nomenclature of compounds are mainly based on its
structures)
 suffix -ase indicates an enzyme
Some examples:
 Urease - hydrolysis of Urea
 DNA polymerase - polymerization of nucleotides
 Protease - hydrolysis of peptides
 suffix –in is also used to name enzyme
(Enzymes that were named before the specific reaction they catalyzed were
known!)
Ex. Pepsin, thrombin and Trypsin
Two Naming Systems:
1. Trivial name or Recommended name: everyday use
 Gives no idea of source, function or reaction catalyzed by the enzyme.
 Ex. Pepsin, thrombin and Trypsin
2. Systematic name: has two parts, a.) substrates b.) name of Rxn
Name of substrate(s) +name of reaction catalyzed (group classification) with –ase suffix
Ex. Lactate dehydrogenase
Suffix -ase
Substrate name of rxn catalyzed
Substrates are reagent molecules upon which enzymes act.
The enzyme has spatial binding sites for the attachment of its substrate forming enzyme-
substrate. These sites are called activation centers of the enzyme. Substrates bind to these
centers forming the enzyme-substrate complex.
According to IUBMB, Enzymes are grouped into six major classes on the basis of the
reaction they catalyzed:
1. Oxidoreductase is an enzyme that catalyzes oxidation-reduction rxn.
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6. ChE 40- Biotechnology
Xavier University- Ateneo de Cagayan
2. Transferase is an enzyme that catalyzes the transfer of functional group from one
molecule to another.
3. Hydrolase is an enzyme that catalyzes hydrolysis reactions in which the addition of
water molecule to a bond causes the bond to break.
4. Lyase is an enzyme that catalyzes the addition of a group to a double bond or the
removal of a group to form a double bond in a manner that does not involve hydrolysis
or oxidation.
5. Isomerase is an enzyme that catalyzes the rearrangement of the functional group within
a molecule, converting the molecule into another molecule isomeric with it.
6. A ligase is an enzyme that catalyzes the bonding together of two molecules into one
with the participation of ATP.
Within each of six main classes of enzymes are subclasses. Table 1 gives further
information about enzyme subclass terminology.
Main Classes Selected Types of Reaction Catalyzed
Subclasses
Oxidoreductases Oxidases Oxidation of a substrate
Reductases Reduction of a substrate
Dehydrogenase Introduction of double bond (oxidation) by formal
removal of two H atoms from substrate, the H being
accepted by coenzyme.
Transferases Transminases Transfer of an amino group between substrate
Kinases Transfer of phosphate group between substrate
Hydrolases Lipases Hydrolysis of ester linkages in lipids
Proteases Hydrolysis of amide linkages in proteins
Nucleases Hydrolysis of sugar-phosphate ester bonds in nucleic acid
Carbohydrases Hydrolysis of glycosidic bonds in carbohydrates
Phosphatases Hydrolysis of phosphate-ester bonds
Lyases Dehydratases Removal of H2O from substrate
Decarboxylases Removal of CO2 from substrate
Deaminases Removal of NH3 from substrate
Hydratases Addition of H2O of a substrate
Isomerases Racemases Conversion of D to L isomer, or vice versa
Mutases Conversion of one constitutional isomer another
Ligases Synthases Formation of new bond between two substrate, with the
participation of ATP
Carboxylases Formation of a new bond between a substrate and CO2,
with the participation of ATP
Table 1. Six Major Classification of Enzymes According to Reactions they catalyzed.
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7. ChE 40- Biotechnology
Xavier University- Ateneo de Cagayan
IV. Reference(s):
Rao, D.G. (2010). Introduction to biochemical engineering. 2nd Edition. Singapore:
McGraw-Hill Education Private limited. pg 62-67.
Stephen, H.S. 2007. General, organic and biological Chemistry. 4th Edition. New York:
wylie&Sons Inc. pg 640-644
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