Enzyme Catalysed Reactions

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Enzyme Catalysed Reactions

Introduction

Enzymes are the natural catalysts present in the bodies of living organisms. They are the globular proteins made to function inside as well as outside the cell. They catalyse thousands of chemical reactions taking place within the living bodies.

Enzymes are needed for the metabolic reactions. If there are no enzymes, metabolism will stop, and life will not exist anymore. In this article, we will talk about various metabolic processes with respect to the human cells and the role of enzymes as catalysts in such reactions. It will provide an overview of the important enzyme catalysed reactions taking place in the cells of living organisms.

Glycolysis

Glucose is used as an energy substance by almost all the living cells. Glycolysis is the first process in obtaining energy from glucose. It is an anaerobic process that can take place in the presence or absence of oxygen. Thus, it occurs in all aerobic as well as non-aerobic organisms.

Glycolysis is the process in which one molecule of glucose is oxidized to two molecules of pyruvic acid by passing it through a series of ten reactions. Each reaction is a sperate enzyme catalysed reaction and used the product of previous reaction as a substrate. During this process, there is net production of two molecules of ATP and two NADH2 molecules.

The process of glycolysis is divided into two phases:

  • Energy investment phase
  • Energy generation phase

Each of these phases includes five reactions. In the energy investment phase, two molecules of ATP are utilised to generate high energy phosphorylated intermediates. In the energy generation phase, four ATP molecules and two NADH2 are generated. So, a total of two ATP and two NADH2 are made in this process.

Below is a brief detail of the enzyme catalysed reactions involved in glycolysis.

Phosphorylation of Glucose

It is first step in the process of glycolysis. During this process, a molecule of ATP is used to make phosphorylated intermediate called glucose-6-phosphate. This phosphorylation reaction is catalysed by enzyme called hexokinase.

Hexokinases are the enzymes that cause phosphorylation of hexose sugars, sugars with six carbon atoms like glucose, fructose, etc. During this process, a molecule of ATP is used as an energy source while an inorganic phosphate ion is combined with a molecule of glucose to make glucose-6-phosphate.

Hexokinases have four isozymes, the enzyme having similar function but different structure. The isozymes I-III cause phosphorylation of hexose sugars in most of the tissues. They are not specific for glucose only and cause phosphorylation of other hexose sugars too, at a very low substrate concentration.

The isozyme IV, also called hexokinase IV or glucokinase has high substrate specificity for glucose. It causes phosphorylation of glucose only, that too at high substrate concentration. Other hexose sugars like fructose cannot be catalysed by hexokinase IV.

Once the glucose is phosphorylated, it is sequestered inside the cytoplasm as it cannot cross the plasma membranes in this form.  

Isomerization of Glucose

The next step in glycolysis is the isomerization of glucose-6-phosphate. The isomerization reaction is catalysed by Phosphoglucose isomerase enzyme that converts glucoe-6-phopshate to fructose-6-phosphate. It is a reversible reaction and can proceed in either directions.

Phosphorylation of Frcutose-6-phosphate

It is another energy investment reaction. During this reaction, another ATP molecule is used as an energy source for the phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate. This second phosphorylation reaction is catalysed by phosphofructokinase-1 enzyme.

The product of this reaction becomes committed to the process of glycolysis. Once fructose-1,6-phosphate is formed, it cannot leave the process to enter some other metabolic process. It must go through the subsequent steps to generate the products.

Breakdown of Fructose-1,6-bisphosphate

During this reaction, a molecule of fructose-1,6-bisphosphate is broken down into two intermediates: glyceraldehyde-3-phosphate and dihydroxyacetone phosphate. This is a reversible reaction that is catalysed by aldolase enzyme.

Isomerization

During the second isomerization reaction of this process, the dihydroxyacetone molecule is converted into glyceraldehyde-3-phosphate. This is because dihydroxyacetone phosphate cannot be processed through the process of glycolysis. Only glyceraldehyde-3-phosphate can pass through the subsequent reactions.

It is also a reversible reaction that is catalysed by triose phosphate enzyme.

With this process, the energy investment phase of glycolysis comes to an end. Two molecules of glyceraldehyde-3-phosphate have been generated till now. Each of them goes through the remaining five reactions of energy generation phase mentioned below.

Oxidation of Glyceraldehyde-3-phosphate

During this reaction, glyceraldehyde-3-phosphate molecule is oxidized along with incorporation of an inorganic phosphate to form 1,3-bisphosphoglycerate. A molecule of NAD+ is used as an oxidizing agent that gets reduced to NADH2. This oxidation reaction is reversible and is catalysed by glyceraldehyde-3-phosphate dehydrogenase enzyme.

Synthesis of 3-Phosphoglycerate

It is a reversible reaction during which one phosphate is cleaved from 1,3-bisphosphoglycerate to form 3-phosphoglycerate. A large amount of energy is released during this reaction that is used to phosphorylate a molecule of ADP to form ATP. This energy yielding reaction is also reversible and is catalysed by phosphoglycerate kinase enzyme.

Phosphate group Transfer

The phosphate group in 3-phosphoglycerate is transferred from 3rd carbon to 2nd carbon generating 2-phosphoglycerate. This isomerization reaction is catalysed by phosphoglycerate mutase enzyme.

Dehydration Reaction

The 2-phosphoglycerate molecule undergoes dehydration to form phosphoenolpyruvate. The dehydration reaction is catalysed by enolase enzyme.

Synthesis of Pyruvate

In this final step, phosphoenolpyruvate is converted into pyruvate. It involved breaking of high energy enol pyruvate bond. The energy used in this reaction is used to phosphorylate another molecule of ADP to ATP.

With this reaction, the process of glycolysis is completed with two molecules of ATP, NADH2, and pyruvate as end products.

Decarboxylation of Pyruvate

It is also an example of enzyme catalysed reactions during carbohydrate metabolism. In the presence of oxygen, the pyruvate molecules generated by the process of glycolysis are further oxidized via the oxidative decarboxylation reaction. This reaction takes place within the mitochondria of the cells.

During this reaction, one carbon is removed from pyruvate molecule and is released in the form of carbon dioxide. As a result, the pyruvate gets converted into acetyl CoA with incorporation of CoA. During this reaction, a molecule of NAD+ is also reduced to NADH2.

This oxidation reaction is catalysed by pyruvate dehydrogenase complex. It is not a single enzyme rather a complex of that contains three enzymes and five coenzymes. The oxidative decarboxylation of pyruvate is not a single step reaction. Rather, it includes three enzyme catalysed reaction. Each reaction is catalysed by one enzyme present in the dehydrogenase complex. The detail of these reactions is not necessary at this level.

The net products of this reactions are one molecule of acetyl CoA, NADH2, and carbon dioxide.

Tricarboxylic Acid Cycle

It is the final process for the oxidation of any molecule that enters the cells. Carbohydrates, fatty acids, amino acids, etc. eventually pass through this cyclic process to complete their oxidation. It is the process at which different metabolic processes converge.

This cyclic process takes place within the mitochondria of aerobic organisms in the presence of oxygen. If started with acetyl CoA, it involves 8 enzyme catalysed reactions. The details of these reactions are given below.

Synthesis of Citrate

It is the first reaction of tricarboxylic acid cycle. During this reaction, one molecule of acetyl CoA condenses with the precursor oxaloacetate to form citrate. One molecule of water is utilized during this reaction. It results in removal and release of CoA from acetyl CoA. The reaction is catalysed by citrate synthase enzyme.

Due to synthesis of citrate, this cycle is also called the citric acid cycle.

Isomerization

The next step in the tricarboxylic acid cycle is the isomerization of citrate to isocitrate. It is a reversible reaction catalysed by aconitase enzyme.

Oxidative Decarboxylation of Isocitrate

The isocitrate molecule is converted into alpha-ketoglutarate by removal of one carbon atom. A molecule of NAD+ gets reduced to NADH2 during this oxidation reaction. This reaction is catalysed by isocitrate dehydrogenase enzyme present within the ATP.

Oxidative Decarboxylation of alpha-Ketoglutarate

The alpha-ketoglutarate molecule undergoes oxidative decarboxylation to form succinyl CoA. This reaction is catalyzed by alpha-ketoglutarate dehydrogenase complex, an enzyme complex similar to pyruvate dehydrogenase complex. It also involves incorporation of a CoA molecule to form succinyl CoA along with the reduction of  NAD+to NADH2.

Various amino acids can join this cycle at this step in the form of alpha-ketoglutarate.

Breakdown of Succinyl CoA

Succinyl CoA molecule has a high energy thioester bond. This high energy bond is cleaved by succinate thiokinase enzyme to remove CoA, leaving behind a succinate molecule.

The energy released during this reaction is used to phosphorylate GDP to GTP, which is later used to convert ADP to ATP.

Oxidation of Succinate

In this step, succinate molecule is oxidized to fumarate using FADH as an oxidizing agent. As a result, FADH gets reduced to FADH2. This reaction is catalysed by succinate dehydrogenase enzyme.

Hydration of Fumarate

In the next step, fumarate undergoes hydration to from malate. A molecule of water is used in this reaction. It is a reversible reaction that is catalysed by fumarase enzyme.

Oxidation of Malate

It is the last step in the tricarboxylic acid cycle. A molecule of malate is oxidized to regenerate the oxaloacetate molecule with NAD+ as an oxidizing agent. As a result, third NADH2 molecule of this cycle is generated during this reaction. This oxidation reaction is catalysed by malate dehydrogenase enzyme.

As mentioned earlier, it is the final pathway at which the oxidation of carbohydrates, amino acids, and fatty acids converge. The carbon skeleton of these organic compounds is converted to carbon dioxide and energy released is captured in the form of reduced coenzyme like FADH2 and NADH2.

The cycle not only provides energy but also provides intermediate products for other metabolic reactions. This cycle provides a route by which some amino acids can be used in the synthesis of glucose by the process of gluconeogenesis.

Gluconeogenesis

We have discussed the enzyme catalysed reactions involved in releasing the energy stored in glucose molecules. Gluconeogenesis is the process that involves various enzyme catalysed reaction for the synthesis of glucose from non-carbohydrate sources. It is used as an important pathway for the synthesis of glucose in state of fasting.

Gluconeogenesis is not a simple reversal of glycolysis. Rather, it involves some additional steps to bypass the irreversible steps of glycolysis. The noncarbohydrate sources used for the synthesis of glucose include lactic acid, pyruvic acid, glycerol, and a-keto amino acids.

The details of reactions involved in this process are discussed below.

Carboxylation of Pyruvate

The first step in gluconeogenesis is the carboxylation of pyruvate to from oxaloacetate. The carbon for this reaction is donated by a bicarbonate ion. The carboxylation reaction is catalysed pyruvate carboxylase enzyme. Biotin is used as a coenzyme in this reaction. This reaction takes place within the mitochondria.

Transport of Oxaloacetate

The rest of the reactions of this process occur within the cytosol. For this, oxaloacetate need to be transported across the mitochondrial membranes into the cytoplasm. For this purpose, oxaloacetate is reduced to malate within the mitochondria by mitochondrial malate dehydrogenase enzyme.

Malate is then transported across the mitochondrial membrane into cytosol. Once in cytoplasm, malate is again converted to oxaloacetate by cytoplasmic malate dehydrogenase enzyme.

The rest of reactions then take place in the cytosol, catalysed by cytoplasmic enzymes.

Decarboxylation and Phosphorylation of Oxaloacetate

In this step, one carbon atom is removed from oxaloacetate along with the phosphorylation of the intermediate to form phosphoenolpyruvate. This reaction is catalysed by phosphoenolpyruvate carboxykinase enzyme. This enzyme has activity of carboxylase as well as kinase.

During this reaction, a molecule of GTP is used as an energy source as well as donor of phosphate group. The energy released during the hydrolysis of GTP is used to make high energy thioester bond in phosphoenolpyruvate.

After the synthesis of PEP, the reactions of glycolysis continue in the reverse order until fructose-1,6-bisphosphate is formed. A specific enzyme is needed for the dephosphorylation of fructose-1,6-bisphosphate and for the process to further proceed.

Dephosphorylation of Fructose-1,6-bisphosphate

Fructose-1,6-bisphoate undergoes hydrolysis to generate fructose-6-phosphate. The reaction is catalysed by fructose-1,6-bisphosphatase enzyme. This enzyme is only found in liver and kidneys, the major organs of gluconeogenesis.

The fructose-6-phosphate molecule thus formed undergoes simple reversible isomerization to form glucose-6-phosphate, catalysed by Phosphoglucose isomerase, same enzyme as used in glycolysis.

Dephosphorylation of Glucose

This is the final step in gluconeogenesis. The molecule of glucose-6-phosphate undergoes hydrolysis to generate free glucose molecules. This hydrolysis reaction is catalysed by glucose-6-phosphatase. This enzyme is exclusively present in liver and kidneys, making them the only organs that can release glucose from glucose-6-phosphate.

The release of free glucose molecule completes the process of gluconeogenesis.

Synthesis of Cholesterol

Cholesterol is an important steroid alcohol found in all living cells. It performs several function in the bodies of living organisms. It is an important constituent of all the plasma membranes.

The synthesis of cholesterol is one of the examples of enzyme catalysed reactions. Cholesterol is made by all the cells in the human body. However, large contributions come from liver, adrenal cortex, and reproductive organs.

The reactions involved in this process along with the enzymes are as follows.

Synthesis of HMG-CoA

 It involves two reactions. In the first reaction, two molecules of acetyl CoA condense to form acetoacetyl CoA. It is a reversible reaction catalysed by thiolase enzyme.

In the next reaction, acetoacetyl CoA is converted to 3-hydroxy-3-methyglutaryl CoA by incorporation of another acetate. The acetate residue is donated by acetyl CoA. The extra CoA is released. A molecule of water is also used in this reaction. This is catalysed by HMG CoA synthase enzyme.

Synthesis of Mevalonate

The HMG CoA formed by the previous reactions is reduced to mevalonate by using two molecules of NADPH as reducing agent. It is an irreversible reaction that takes place in the cytosol. The reaction is catalysed by HMG CoA reductase enzyme.

Synthesis of 5-Pyrophosphomevalonate

It is a two-step phosphorylation of mevalonate catalysed by kinases. In each step, one phosphate is donated by a molecule of ATP that gets hydrolyzed to ADP.

Decarboxylation of 5-Pyrophosphomevalonate

The 5-pyrophosphomevalonate undergoes decarboxylation to form isopentyl pyrophosphate (IPP). This reaction is catalysed by decarboxylase enzyme. One molecule of ATP is also utilized during this reaction.

Isomerization of IPP

This is a reversible reaction during which IPP is converted to dimethyl pyrophosphate (DPP) catalysed by isomerase enzyme.

Condensation of IPP and DPP

In the next step, one molecule of IPP and one molecule of DPP condense to form a ten-carbon compound called geranyl pyrophosphate (GPP). Two phosphate residues are released during this reaction.

Condensation of IPP and GPP

One molecule of IPP and GPP condense to form a 15-carbon compound called farnesyl pyrophosphate (FPP). It is also catalysed by transferase enzyme with the release of two phosphate residues.

Formation of Squalene

Two molecules of FPP condense together and undergo second reduction to form squalene. NADPH is used as a reducing agent. The reaction is catalysed by squalene synthase. This reaction also involves the release of two phosphate residues.

Synthesis of Cyclic Lanosterol

In the next step, squalene undergoes reduction to form cyclic lanosterol. It is a complex process consisting of several steps all catalysed by enzyme associated to endoplasmic reticulum. The enzyme involved is called squalene monooxygenase.

Conversion of Lanosterol to Cholesterol

It is a multistep process that takes place within the ER. The final product is cholesterol consisting of 27 carbons.

All these reactions in the synthesis of cholesterol are examples of enzyme catalysed reactions.

Urea Cycle

Urea cycle is a process by which harmful nitrogenous waste ammonia is converted into less harmful urea that can later be excreted in the form of urine.

Urea cycle involves five reactions, the first two of which occur in mitochondria. The enzyme catalysed reactions involved in urea cycle are as follows.

Formation of Carbamoyl Phosphate

One molecule of ammonia and a bicarbonate ion combine together to form carbamoyl phosphate within the mitochondria using two molecules of ATP. The reaction takes place within the mitochondria and is catalysed by carbamoyl phosphate synthetase I enzyme.

Formation of Citrulline

Here, the carbamoyl part of carbamoyl phosphate is transferred to a molecule of ornithine resulting in the formation of citrulline. This reaction is catalysed by ornithine transcarboxylase enzyme.

An inorganic phosphate ion is released during this reaction. The citrulline thus formed is transferred to cytoplasm where the rest of reactions of urea cycle take place.

Formation of Argininosuccinate

Once citrulline is in the cytoplasm, it combines with aspartate to form argininosuccinate. One nitrogen comes from ammonia while the other comes from aspartate. The reaction is catalysed by argininosuccinate synthase.

Degradation of Argininosuccinate

In the next step, argininosuccinate undergoes lysis to form fumarate and arginine. Fumarate leaves the urea cycle while arginine acts as a precursor for urea. This reaction is catalysed by argininosuccinate lyase enzyme.

Synthesis of Ornithine and Urea

In the final step, arginine undergoes hydrolysis to form urea and ornithine. Urea leaves the cycle to be excreted as a waste product while ornithine is transported into the mitochondria to be used again.

This final reaction is catalysed by arginase enzyme that is present exclusively in the liver.

Summary

  • Enzymes are the natural catalysts that are required for all the metabolic reactions taking place within the living cells.
  • Several examples of catalysed reactions can be found occurring all the time within the cells of living organisms. Some of the famous metabolic reactions have been discussed in this article.
  • Glycolysis is a process by which energy is extracted from glucose under aerobic or anaerobic conditions. It involves a series of ten enzyme catalysed reactions.
  • Pyruvate generated from glycolysis undergoes enzyme catalysed oxidative decarboxylation to be used in tricarboxylic acid cycle.
  • Tricarboxylic acid cycle consists of a series of enzyme catalysed reactions by which the final oxidation takes place and carbon skeleton is converted into carbon dioxide.
  • Gluconeogenesis consists of enzyme catalysed reactions for the synthesis of glucose from non-carbohydrate sources.
  • Cholesterol synthesis has also been discussed as an example of enzyme catalysed reactions.
  • Urea cycle is a part of nitrogen metabolism in mammals that involves converting ammonia into urea by a series of five enzyme catalysed reactions.

References

  1. Denise R. Ferrier, Lippincott Illustrated Reviews, Biochemistry, Ed. 6th
  2. Rodwell, Kennelly, Harper’s Illustrated Biochemistry, Ed. 30th