written report on enzymes-nomenclature

7/29/2019 Written Report on Enzymes-nomenclature

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Written Report on

Enzymes: Nomenclature

Submitted by:

Conrad Vincent V. Vivas

BS Chemical Engineering-4

Submitted to:

Engr. Christylene S.Balagtas

ChE-40 Biotechnology

January 10, 2013

Molecular Model of Protein

Molecular Model of Enzyme Amylase


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ChE 40- Biotechnology

Xavi er Un iv ers it y- At en eo de Cag ay an

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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 Proteins that acts as biological catalysts, itis 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 specificbiochemical (occurs in living organisms) reactions.

As catalyst they are not being destroyed or altered upon completion of thereaction. (Hence it is not consume in the reaction)

Enzymes lower the activation energy needed for the reaction to occur orproceed into product.

Two structural classes of enzymes:

1. Simple enzymes enzyme composed only of protein (amino acid chains).2. Conjugated enzymesenzymes that have a non-protein part in addition to a protein.


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Parts of Conjugated Enzyme:

a. Apoenzyme - inactive portion of proteinb. Cofactor- non-protein component of enzymec. Coenzyme - enzyme with organic molecule as its cofactord. Holoenzyme - active enzyme including cofacor

Apoenzyme + Cofactor = Holoenzyme

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 brokeninto its glucose components. Therefore, it cannot be digested.

The intestinal cells of lactose-intolerant people do not produce LACTASE, theenzyme needed to break down lactose.

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, whioch are important pollutant, can beremoved by enzyme-catalyzed polymerization using horseradish peroxidase.)

Figure 1. parts of conjugated enzyme


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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 dioxideand 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

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 - indicates an enzymeSome examples:

Urease - hydrolysis of Urea DNA polymerase - polymerization of nucleotides Protease - hydrolysis of peptides

Figure 2. Discovered Enzymes through time


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suffix is also used to name enzyme(Enzymes that were named before the specific reaction they catalyzed was

known!)

Example. 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 RxnName of substrate(s) +name of reaction catalyzed (group classification) with 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. 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.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 ofwater 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 theremoval 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 withina 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 onewith the participation of ATP.


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Within each of six main classes of enzymes are subclasses. Table 1 gives further

information about enzyme subclass terminology.

Main Classes SelectedSubclasses

Types of Reaction Catalyzed

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.

IV. Reference(s):

Rao, D.G. (2010). Singapore:

McGraw-Hill Education Private limited. pg 62-67.

Stephen, H.S. 2007. . New York:

wylie&Sons Inc. pg 640-644

written report on enzymes-nomenclature

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