Bayan Abusheikha

Minna Mushtaha

19

Mamoun Ahram

Marah Bitar

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Classificationofenzymes

-Some enzymes, called simple enzymes, are completely protein. Others, called conjugated enzymes, are composed of a protein portion called the apoenzyme and one or more nonprotein portions.

-Apoenzyme is an inactive form of enzyme lacking the association of coenzymes and/or cofactors. Activation of the enzyme occurs upon binding of an organic or inorganic cofactor.

-Holoenzyme is a complete and catalytically active form of enzyme. An apoenzyme together with its cofactor is a holoenzyme.

-Cofactors are small non-protein inorganic molecules that carry out chemical reactions that cannot be performed by the standard 20 amino acids. Examples of cofactors include metal ions, like iron and zinc. Coenzymes are the organic equivalent of cofactors.

Simple enzymes don’t need cofactors/coenzymes, but conjugated ones do.

-Enzymes are classified and named according to the reaction they catalyze. The chemical reaction catalyzed is the specific property that distinguishes one enzyme from another. Enzymes are also named according to the chemical nature of the substrate. Enzymes’ names end with the suffix “-ase”.

ATPase breaks down ATP, and ATP synthase synthesizes ATP.

-Some enzymes have common names, like the proteolytic enzyme trypsin.

-Scientists divided the basic reaction types and the enzymes catalyzing them into six broad, numbered classes: (1) oxidoreductases, (2) transferases, (3) hydrolases, (4) lyases, (5) isomerases, and (6) ligases.

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1- Oxidoreductases:

Theseenzymesareresponsibleforoxidation/reductionreactions,whichinvolvetransferringelectronsorhydrogenatoms.Theyaredividedinto4classes:

a- Dehydrogenases

They accept and donate electrons in the form of hydride ions or hydrogen atoms. Usually an electron-transferring coenzyme, such as NAD+/NADH or FAD/FADH2, acts as an electron donor or acceptor. One example is lactate dehydrogenase: It works by transferring 2 electrons to NAD+ (reducing it). LDH in muscles produces lactate molecules in anaerobic respiration, which are released into the blood. LDH in heart cells turns lactate molecules into pyruvate again and uses it as fuel. The level of LDH in the blood is a marker for myocardial infarction (heart failure).

Anotherexampleisalcoholdehydrogenase:

b- Oxidases

These enzymes catalyze hydrogen transfer to molecular oxygen to produce hydrogen peroxide as a byproduct. One example is glucose oxidase in the following reaction:

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c- Peroxidases

Peroxidases catalyze the oxidation of a substrate by reducing hydrogen peroxide H₂O₂.

Example: Glutathione peroxidase.

Glutathione is an important anti-oxidant. It prevents the damage of DNA and membranes when the peroxidase gives electrons to free radicals and reactive oxygen species.

Glutathione disulfide is the product of oxidation. It can be reduced back to glutathione by glutathione reductase.

AreactionofanoxidaseisusuallycoupledwithareactionofaperoxidasetogetridoftheH₂O₂.

d- Oxygenases

They oxidize the substrate by introducing molecular oxygen to it. The reduced product is water, not hydrogen peroxide. The enzyme can be a monooxygenase if one oxygen atom is introduced to the substrate and a dioxygenase if two oxygen atoms are introduced.

Example: Lactate-2-monooxygenase, which oxidizes lactate to acetate.

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Another example: Heme dioxygenase

2- Transferases

Transferases are enzymes that transfer a functional group, e.g. a methyl group or a phosphate group, from one compound (generally regarded as a donor) to another compound (generally regarded as an acceptor).

-Example: Kinases. These are very important transferases, especially in metabolism. They move a phosphate group from a highly energetic molecule, like ATP, to a substrate.

-Phosphofructokinase catalyzes the transfer of a phosphate group from ATP to fructose-6-phosphate to produce ADP and fructose-1,6-bisphosphate (which has a higher energy now because a phosphate group was introduced to it).

-Another example: Transaminases. the amino group from an amino acid is donated to a

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keto acid, forming a new amino acid and the keto acid corresponding to the donor amino acid (interconversion of amino acids). The body uses this reaction to produce the amino acids that it needs. -These enzymes are clinically important to indicate some diseases, like liver diseases, when their concentration in blood is measured.

-This reaction is very important in Krebs cycle. Notice that in reactions catalyzed by transferases, there are at least two substrates and two products. Dr Nafeth said we should know at least three keto acids with their corresponding amino acids:

1. Glutamate and a-ketoglutarate 2. Pyruvate and alanine 3. Aspartate and oxaloacetate

3- Hydrolases

In hydrolysis reactions, C-O, C-N, or C-S bonds are cleaved by the addition of H₂O in the form of OH- and H+ to the atoms forming the bond. Peptidases, esterases, lipases, glycosidases, and phosphatases are all hydrolytic enzymes named according to the type of bond that is cleaved. -Example: Proteases. They catalyze proteolysis (the hydrolysis of a peptide bond in a protein).

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- Proteolytic enzymes differ in their degree of substrate specificity. Trypsin is greatly specific. It is a digestive enzyme that breaks peptide bonds on the carboxyl side of Lys and Arg residues. Thrombin is also very specific. It participates in blood clotting by breaking the bond between Arg and Gly. 4- Lyases These enzymes remove groups from substrates with the associated formation or remove double bonds between C-C, C-O, or C-N without hydrolysis (using water). - Example: Aldolase breaks down frucrose-1,6-bisphosphate into dihydroxyacetone phosphate (precursor of plasmalogens) and glyceraldehyde-3-phosphate.

-Example: Enolase. It interconverts phosphoenolpyruvate and 2-phosphoglycerate by forming or removing double bonds. Notice here that water is used only as a source of electrons. It does not break the molecule.

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5- Isomerase

Many biochemical reactions simply rearrange the existing atoms of a molecule—that is, create isomers of the starting material. Enzymes that rearrange the bond structure of a compound are called isomerases; they hardly use any energy, whereas enzymes that catalyze movement of a phosphate from one atom to another are called mutases. -Example: Phosphoglucoisomerase isomerizes glucose-6-phosphate to fructose-6-phosphate. -Example: Phosphoglycerate mutase transfers a phosphate group from carbon #3 to carbon #2 of phosphorylated glycerate.

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6- Ligases

Ligases synthesize C-C, C-S, C-O, and C-N bonds in reactions coupled with the cleavage of a high-energy phosphate bond in ATP or another nucleotide. -Example: Pyruvate carboxylase. It uses energy to add a fourth carbon to pyruvate. -Be aware of the difference between kinases and ligases. Kinases add a phosphate group from ATP to a substrate. Ligases use the energy of ATP to connect molecules together. -The enzyme forms a complex (in the transition state) with pyruvate and carbon dioxide. A phosphate group is added to pyruvate so that it becomes a high energy molecule. This energy is used to connect the two molecules together.

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Type Main function

Examples

1-Oxidoreductases Catalyze oxidation and reduction reactions.

They are divided into 4 subgroups.

a- Dehydrogenases They accept and donate electrons in the form of hydride ions or hydrogen atoms. They are closely associated with NADH and FADH2.

-lactate dehydrogenase

-alcohol dehydrogenase

b- Oxidases Catalyze hydrogen transfer to molecular oxygen to produce hydrogen peroxide as a byproduct.

-glucose oxidase

c- Peroxidases Catalyze the oxidation of a substrate by reducing hydrogen peroxide H₂O₂.

-glutathione à glutathione disulfide

d- Oxygenases They oxidize the substrate by introducing molecular oxygen to it. The reduced product is water, not hydrogen peroxide.

- lactate-2-monooxygenase

-heme dioxygenase

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2-Transferases Transferases are enzymes that transfer a functional group from one compound to another.

-Kinases transfer phosphate groups

-transaminases transfer amino groups from an amino acid to a keto acid

3-Hydrolases C-O, C-N, or C-S bonds are cleaved by the addition of H₂O in the form of OH- and H+ to the atoms forming the bond.

-proteases

-trypsin and thrombin are very specific hydrolases.

4-Lyases Remove groups from substrates with the associated formation or remove double bonds.

-aldolase Enolase

5-Isomerase Catalyze intramolecular rearrangements. There are isomerases and mutases.

-glucose-6-phosphate à fructose-6-phosphate (phosphoglucoisomerase) -3-P glycerate à 2-P glycerate (phosphoglycerate mutase)

6-Ligases Join C-C, C-O, C-N, and C-X bonds by consuming ATP or other nucleotide triphosphates.

Pyruvate+HCO3- +ATP à oxaloacetate +ADP+ Pi

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Kinetics The study of Kinetics deals with the rates of chemical reactions. For the reaction A à P, the rate of reaction v is the amount of P formed or amount of A consumed per unit time t. -The mathematical relationship between the rate of the reaction and the concentration of the reactants is the rate law. v:velocity(rate)[A]:concentrationofAK:rateconstant(1/sec) -This equation describes how the concentration of the reactants affects the rate of the reaction during a certain period. -The rate depends on the concentration [A] and a rate constant k. It is directly proportional to the concentration. If the concentration is doubled, the rate will also be doubled. -The equation above is a first order reaction since only one substrate affects the rate. -If the rate depends on the concentrations of two substrates, it is a second order reaction.

v= k [A][B] -If the reaction does not depend on any substrate concentration, it is a zero order reaction.

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Enzyme kinetics The study of enzyme kinetics addresses the biological roles of enzymatic catalysis. -Enzyme-catalyzed reactions have hyperbolic plots. -At lower concentrations, initial rate is highly affected by the concentration of the substrate. The rate rises linearly as the concentration increases. Then, it begins to level off (plateau) and approach a maximum at higher substrate concentration. -The hyperbolic plot is also known as the saturation plot because at high concentrations of substrate, all the enzymes are occupied. Further explanation: -At a fixed concentration of enzyme, Vₒ (initial velocity) is almost linearly proportional to [S] (substrate concentration). -However, Vₒ is nearly independent of [S] when [S] becomes larger. -Vmax is achieved when the catalytic sites of the enzymes are saturated with substrate. At higher concentrations, the rate is ultimately dependent on the catalytic ability of the enzyme. -Vmax is also the turn over number, which is the number of substrate molecules converted into product per unit time when the enzyme is fully saturated. It is a measure of the catalytic ability of the enzyme.

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