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Enzyme classification and properties

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ENZYMES

Definitions--

♦ A biomolecule either Protein or RNA, that catalyse a specific chemical reaction, enhance the rate of a reaction by providing a reaction path with a lower activation energy

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Fundamental Properties

1) Catalytic power-speeding up reactions 10⁸ to 10²⁰ fold.

They speed up reactions without being

used up.

2) Specificity

a) for substrate - ranges from absolute to relative

b) for reaction catalyzed

3) Regulated-- some enzymes can sense metabolic signals.

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Catalytic Power

Catalytic Power is defined as the Ratio of the Enzyme-Catalyzed Rate of a Reaction to the Uncatalyzed Rate

e.g. Urease-

• At 20°C, the rate constant for the enzyme-catalyzed reaction is 3 X 10⁴/sec
• the rate constant for the uncatalyzed hydrolysis of urea is 3 X 10¹⁰/sec
• 10¹⁴ is the ratio of the catalyzed rate to the uncatalyzed rate of reaction

Specificity

Defined as the Selectivity of Enzymes for the Reactants Upon which They Act

• In an enzyme-catalyzed reaction, none of the substrate is diverted into nonproductive side reactions, so no wasteful by-products are produced.

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The substances upon which an enzyme acts are traditionally called- substrates

The selective qualities of an enzyme are collectively recognized- specificity

The specific site on the enzyme where substrate binds and catalysis occurs is called- active site

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Regulation

Regulation of Enzyme Activity Ensures That the Rate of Metabolic Reactions Is Appropriate to Cellular Requirements

• essential to the integration and regulation of metabolism

Achieved by various ways

• Inhibitor
• Activator
• Hormonal
• Rate of synthesis

History

• As early as the late 1700s and early 1800s, the digestion of meat by stomach secretions and the conversion of starch to sugars by plant extracts and saliva were known. However, the mechanism by which this occurred had not been identified

• In the 19th century, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur came to the conclusion that this fermentation was catalyzed by a vital force contained within the yeast cells called "ferments", which were thought to function only within living organisms. He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells.

• In 1878 German physiologist Wilhelm Kühne (1837–1900) first used the term enzyme. The word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment used to refer to chemical activity produced by living organisms
• In 1897 Eduard Buchner began to study the ability of yeast extracts that lacked any living yeast cells to ferment sugar. In a series of experiments at the University of Berlin, he found that the sugar was fermented even when there were no living yeast cells in the mixture
• He named the enzyme that brought about the fermentation of sucrose "zymase". In 1907 he received the Nobel Prize in Chemistry“ for his biochemical research and his discovery of cell-free fermentation"

Classification and Nomenclature

1. Often named by adding the suffix -ase to the name of the substrate upon which they acted

e.g. Urease, DNA Polymerase

2. Names bearing little resemblance to their activity

e.g. catalase - the peroxide-decomposing enzyme

Proteolytic enzymes (proteases) of the digestive tract

Trypsin- Gr. Word Tryein means to wear down

Pepsin- Pepsis means digestion

IUB nomemclature

1956 - to create a systematic basis for enzyme nomenclature

• 4 digit numbered code
• first digit - major class
• Second digit - sub class
• third digit - sub sub class
• final digit - specific enzyme

2.7.1.1�ATP: glucose phosphotransferase

2- class name (transferase)

7- subclass name (phosphotransferase)

1- sub sub class (hydroxyl group as acceptor)

1- specific enzyme (D- glucose as phosphoryl group acceptor)

Enzyme classification

• Six classes

1. Oxidoreductase- transfer of reducing equivalents from one redox system to another

e.g. Alcohol Dehydrogenase

Lactate dehydrogenase

cytochrome oxidase

2. Transferase

functional group is transferred from one compound to another

e.g. kinases

transaminase

phosphorylase

3. Hydrolase

cleave C-O, C-N, C-S or P-O etc bonds by adding water across the bond

e.g. lipase

acid phosphatase

(important in digestive process)

4. Lyases

cleave C-O, C-N, or C-S bonds but do so without addition of water and without oxidizing or reducing the substrates

e.g. aldolase

fumarase

Carbonic anhydrase

5. Isomerase

catalyze intramolecular rearrangements of functional groups that reversibly interconvert to optical or geometric isomers

e.g. Triose isomerase

phosphohexose isomerase

mutase

6. Ligase

catalyze biosynthetic reactions that form a covalent bond between two substrates utilizing ATP-ADP interconversion

e.g. glutamine synthetase

DNA- ligase

Specificity

• highly specific compared to other catalyst
• catalyzes only specific reaction

3 types

1. Stereospecificity/ optical specificity
2. Reaction specificity
3. Substrate specificity

Optical specificity

• able to recognise optical isomers of the substrate
• Act only on one isomer

e.g. enzymes of amino acid metabolism (D & L Amino acid oxidase)

Isomerase do not exhibit stereospecificity

Reaction Specificity

• catalyze only one specific reaction over substrate

e.g. amino acid can undergo deamination, transamination, decarboxylation and each is catalysed by separate enzyme

Substrate specificity

specific towards their substrates

e.g. glucokinase and galactokinase- both transfer phophoryl group from ATP to different molecule

3 types

1. Absolute
2. Relative substrate
3. broad

Absolute substrate specificity

• Act only on one substrate

e.g. urease

Relative substrate specificity

• act on structurally related substrates
• Further divide into
• Group dependent- act on specific group e.g. trypsin- break peptide bond between lysine and arginine, Chymotripsin act on aromatic AA
• Bond specificity- act on specific bond e.g. proteolytic enzyme, glycosidase

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Broad specificity

• Act on closely related substrates

e.g. hexokinase- act on many hexoses

Chemical Nature & Properties of Enzyme

• Protein or RNA
• Tertiary structure and specific conformation- essential for catalytic power
• Holoenzyme- functional unit
• Apoenzyme & coenzyme

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• Monomeric Enzyme- made of a single polypeptide e.g. ribonuclease, trypsin

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• Oligomeric Enzyme- more than one polypeptide e.g. LDH, aspartate carbamoylase

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• Multienzyme complex- specific sites to catalyse different reactions in sequence. Only native conformation is active not individual e.g. pyruvate dehydrogenase

Multienzyme Complexes and �Multifunctional Enzymes

• In a number of metabolic pathways, several enzymes which catalyze different stages of the process have been found to be associated noncovalently, giving a multienzyme complex.

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• Examples: Pyruvate Dehydrogenase Complex; Electron Respiratory Chain

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• In other cases, different activities may be found on a single multifunctional polypeptide chain. The presence of multiple activities is on a single polypeptide chain is usually the result of a gene fusion event