All You Need To Know About the Power of the Krebs Cycle: Understanding Biochemical Reactions for Energy Production

The Krebs cycle, also known as the citric acid cycle or the tricarboxylic acid (TCA) cycle, is a series of biochemical reactions that occur in the mitochondria of eukaryotic cells. It is a central metabolic pathway that plays a crucial role in energy production through the breakdown of carbohydrates, fats, and proteins. In this article, we will explore the various steps involved in the Krebs cycle and their significance.

The Krebs cycle consists of a series of eight reactions that occur in a cyclic manner, with the end product of one reaction acting as the starting substrate for the next reaction. The cycle begins with the acetyl-CoA molecule, which is derived from the breakdown of glucose or fatty acids, entering the cycle and combining with oxaloacetate to form citrate. This reaction is catalyzed by the enzyme citrate synthase and is an irreversible step that commits the acetyl-CoA to the cycle.

The cycle then proceeds through a series of reactions that involve the removal and addition of chemical groups to the citrate molecule, resulting in the formation of ATP, NADH, FADH2, and carbon dioxide. The NADH and FADH2 molecules generated during the cycle then enter the electron transport chain, where they are oxidized to generate ATP through oxidative phosphorylation.

Steps of the Krebs Cycle

1-Citrate Synthase

The first step of the Krebs cycle involves the formation of citrate from acetyl-CoA and oxaloacetate. This reaction is catalyzed by the enzyme citrate synthase and results in the release of CoA-SH. The formation of citrate is an irreversible step that commits the acetyl-CoA to the cycle.

Citrate synthase is a crucial enzyme that plays a central role in the Krebs cycle, also known as the tricarboxylic acid (TCA) cycle or the citric acid cycle. This enzyme is responsible for catalyzing the first step of the cycle, which involves the conversion of acetyl-CoA and oxaloacetate into citrate. In this article, we will explore the structure, function, and regulation of citrate synthase in the Krebs cycle.

Structure of Citrate Synthase:

Citrate synthase is a large enzyme that is found in the mitochondrial matrix of eukaryotic cells. It is composed of two identical subunits, each consisting of approximately 400 amino acid residues. The subunits are arranged in a head-to-head configuration, with a deep cleft between them that serves as the active site for the enzyme.

The active site of citrate synthase contains several amino acid residues that are essential for the catalytic activity of the enzyme. These residues include two cysteine residues, which form a thioester intermediate with acetyl-CoA, and a histidine residue, which acts as a proton acceptor during the catalytic reaction.

Function of Citrate Synthase:

The function of citrate synthase is to catalyze the first step of the Krebs cycle, which involves the conversion of acetyl-CoA and oxaloacetate into citrate. This reaction is an important step in the process of energy production, as it initiates the cyclic series of reactions that result in the generation of ATP.

The catalytic mechanism of citrate synthase involves several steps, including the binding of acetyl-CoA to the enzyme, the formation of a thioester intermediate, and the transfer of the acetyl group to oxaloacetate to form citrate. The reaction is exothermic and results in the release of energy that is utilized by the cell to carry out various metabolic processes.

Regulation of Citrate Synthase:

The activity of citrate synthase is regulated by several factors, including the concentration of reactants and products, the availability of coenzymes, and the presence of allosteric modulators.

One of the most important regulators of citrate synthase is ATP, which acts as an inhibitor of the enzyme. High levels of ATP in the cell signal that energy needs have been met, and therefore, the rate of the Krebs cycle can be reduced. Conversely, low levels of ATP in the cell stimulate the activity of citrate synthase, leading to an increase in the rate of the cycle.

Another important regulator of citrate synthase is the product of the reaction, citrate. High levels of citrate in the cell signal that energy needs have been met, and therefore, the rate of the Krebs cycle can be reduced. Conversely, low levels of citrate in the cell stimulate the activity of citrate synthase, leading to an increase in the rate of the cycle.

In addition to these regulators, citrate synthase is also subject to allosteric regulation by several other molecules, including NADH, succinyl-CoA, and malate. These molecules bind to the enzyme and can either stimulate or inhibit its activity, depending on their concentration and the metabolic needs of the cell.

2-Aconitase

Aconitase is an enzyme that plays a critical role in the Krebs cycle, also known as the tricarboxylic acid (TCA) cycle or the citric acid cycle. This enzyme catalyzes the reversible isomerization of citrate to isocitrate, which is an essential step in the cycle. In this article, we will explore the structure, function, and regulation of aconitase in the Krebs cycle.

Structure of Aconitase:

Aconitase is a large enzyme that is found in the mitochondrial matrix of eukaryotic cells. It is a homodimeric protein, meaning that it is composed of two identical subunits, each consisting of approximately 800 amino acid residues. The subunits are arranged in a head-to-tail configuration, with a deep cleft between them that serves as the active site for the enzyme.

The active site of aconitase contains a cluster of iron-sulfur (Fe-S) atoms that are essential for the catalytic activity of the enzyme. These atoms are coordinated by several cysteine residues and are involved in the transfer of electrons during the catalytic reaction.

Function of Aconitase:

The function of aconitase is to catalyze the reversible isomerization of citrate to isocitrate, which is an important step in the Krebs cycle. This reaction involves the removal of a water molecule from citrate, followed by the addition of a water molecule to isocitrate, resulting in a change in the position of the double bond in the molecule.

The catalytic mechanism of aconitase involves the binding of citrate to the enzyme, followed by the formation of a citrate-aconitase complex. This complex undergoes a series of conformational changes that result in the isomerization of the molecule to isocitrate. The reaction is exothermic and results in the release of energy that is utilized by the cell to carry out various metabolic processes.

Regulation of Aconitase:

The activity of aconitase is regulated by several factors, including the concentration of reactants and products, the availability of coenzymes, and the presence of allosteric modulators.

One of the most important regulators of aconitase is the concentration of reactive oxygen species (ROS) in the cell. ROS can react with the Fe-S cluster in the enzyme, leading to the inactivation of aconitase. This mechanism serves as a protective mechanism for the cell, as it prevents the accumulation of ROS, which can damage cellular components and lead to cell death.

Another important regulator of aconitase is the product of the reaction, isocitrate. High levels of isocitrate in the cell signal that energy needs have been met, and therefore, the rate of the Krebs cycle can be reduced. Conversely, low levels of isocitrate in the cell stimulate the activity of aconitase, leading to an increase in the rate of the cycle.

In addition to these regulators, aconitase is also subject to allosteric regulation by several other molecules, including ATP, ADP, and NADH. These molecules bind to the enzyme and can either stimulate or inhibit its activity, depending on their concentration and the metabolic needs of the cell.

3-Isocitrate Dehydrogenase

Isocitrate dehydrogenase (IDH) is an enzyme that plays a vital role in the Krebs cycle, also known as the citric acid cycle or the tricarboxylic acid (TCA) cycle. This enzyme catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate, producing NADH in the process. In this article, we will explore the structure, function, and regulation of IDH in the Krebs cycle.

Structure of Isocitrate Dehydrogenase:

IDH is a large enzyme that is found in the mitochondrial matrix of eukaryotic cells. It is a homodimeric protein, meaning that it is composed of two identical subunits, each consisting of approximately 400-500 amino acid residues. The subunits are arranged in a head-to-tail configuration, with a deep cleft between them that serves as the active site for the enzyme.

The active site of IDH contains several amino acid residues that are essential for the catalytic activity of the enzyme. These residues are involved in the binding of isocitrate and NAD+ to the enzyme, as well as the transfer of electrons during the catalytic reaction.

Function of Isocitrate Dehydrogenase:

The function of IDH is to catalyze the oxidative decarboxylation of isocitrate to α-ketoglutarate, an important step in the Krebs cycle. This reaction involves the removal of a carboxyl group from isocitrate, followed by the transfer of two electrons and a proton to NAD+, producing NADH in the process.

The catalytic mechanism of IDH involves the binding of isocitrate and NAD+ to the enzyme, followed by the formation of a complex between the two molecules and the enzyme. This complex undergoes a series of conformational changes that result in the decarboxylation of isocitrate and the transfer of electrons to NAD+, producing NADH and α-ketoglutarate.

Regulation of Isocitrate Dehydrogenase:

The activity of IDH is regulated by several factors, including the concentration of reactants and products, the availability of coenzymes, and the presence of allosteric modulators.

One of the most important regulators of IDH is the product of the reaction, α-ketoglutarate. High levels of α-ketoglutarate in the cell signal that energy needs have been met, and therefore, the rate of the Krebs cycle can be reduced. Conversely, low levels of α-ketoglutarate in the cell stimulate the activity of IDH, leading to an increase in the rate of the cycle.

Another important regulator of IDH is the availability of NAD+, which is necessary for the enzyme to function. When NAD+ levels are low, the activity of IDH is inhibited, leading to a decrease in the rate of the Krebs cycle.

In addition to these regulators, IDH is also subject to allosteric regulation by several other molecules, including ATP, ADP, and Ca2+. These molecules bind to the enzyme and can either stimulate or inhibit its activity, depending on their concentration and the metabolic needs of the cell.

4-Alpha-Ketoglutarate Dehydrogenase

Alpha-ketoglutarate dehydrogenase (α-KGDH) is a multi-enzyme complex that plays a crucial role in the Krebs cycle, also known as the citric acid cycle or the tricarboxylic acid (TCA) cycle. This enzyme complex catalyzes the oxidative decarboxylation of alpha-ketoglutarate (α-KG) to succinyl-CoA, producing NADH in the process. In this article, we will explore the structure, function, and regulation of α-KGDH in the Krebs cycle.

Structure of Alpha-ketoglutarate Dehydrogenase:

α-KGDH is a large enzyme complex that is found in the mitochondrial matrix of eukaryotic cells. It is composed of three subunits, named E1, E2, and E3. The E1 subunit contains the active site for the enzyme, where the oxidative decarboxylation of α-KG takes place. The E2 subunit contains a covalently bound lipoamide prosthetic group that serves as a carrier of the reaction intermediates. The E3 subunit contains a flavin adenine dinucleotide (FAD) prosthetic group that is involved in the regeneration of NAD+.

The three subunits are arranged in a head-to-tail configuration, forming a large complex that is approximately 10 times larger than a typical enzyme. The E2 subunit is connected to the E1 and E3 subunits by flexible linkers that allow for the movement of reaction intermediates between the active sites.

Function of Alpha-ketoglutarate Dehydrogenase:

The function of α-KGDH is to catalyze the oxidative decarboxylation of α-KG to succinyl-CoA, an important step in the Krebs cycle. This reaction involves the removal of a carboxyl group from α-KG, followed by the transfer of two electrons and a proton to NAD+, producing NADH in the process.

The catalytic mechanism of α-KGDH involves several steps, beginning with the binding of α-KG to the E1 subunit of the enzyme complex. The α-KG is then oxidatively decarboxylated, with the release of CO2 and the formation of a high-energy intermediate called an acyl-enzyme. This intermediate is then transferred to the lipoamide prosthetic group on the E2 subunit, where it is further processed to produce succinyl-CoA and reduce the lipoamide group. Finally, the reduced lipoamide group is oxidized by the E3 subunit, transferring electrons to FAD and ultimately regenerating NAD+.

Regulation of Alpha-ketoglutarate Dehydrogenase:

The activity of α-KGDH is regulated by several factors, including the concentration of reactants and products, the availability of coenzymes, and the presence of allosteric modulators.

One of the most important regulators of α-KGDH is the product of the reaction, succinyl-CoA. High levels of succinyl-CoA in the cell signal that energy needs have been met, and therefore, the rate of the Krebs cycle can be reduced. Conversely, low levels of succinyl-CoA in the cell stimulate the activity of α-KGDH, leading to an increase in the rate of the cycle.

Another important regulator of α-KGDH is the availability of NAD+, which is necessary for the enzyme to function. When NAD+ levels are low, the activity of α-KGDH is inhibited, leading to a decrease in the rate of the Krebs cycle.

5-Succinyl-CoA Synthetase

Succinyl-CoA synthetase (SCS) is an enzyme that plays a critical role in the Krebs cycle, also known as the citric acid cycle or the tricarboxylic acid (TCA) cycle. This enzyme catalyzes the conversion of succinyl-CoA to succinate, producing ATP in the process. In this article, we will explore the structure, function, and regulation of SCS in the Krebs cycle.

Structure of Succinyl-CoA Synthetase:

SCS is a dimeric enzyme that is composed of two identical subunits, each consisting of three domains. The first domain binds succinyl-CoA, the second domain binds a nucleotide (either ADP or GDP), and the third domain is responsible for catalysis.

The active site of SCS is located at the interface between the two subunits, where succinyl-CoA and the nucleotide bind. The binding of these substrates induces a conformational change in the enzyme, bringing the catalytic site into the correct position for ATP synthesis.

Function of Succinyl-CoA Synthetase:

The function of SCS is to catalyze the conversion of succinyl-CoA to succinate, producing ATP in the process. This reaction involves the transfer of a phosphate group from the nucleotide substrate to a molecule of GDP or ADP, producing ATP or GTP, respectively.

The catalytic mechanism of SCS involves several steps, beginning with the binding of succinyl-CoA to the enzyme’s active site. The succinyl group is then transferred to a histidine residue on the enzyme, forming a thioester intermediate. This intermediate is then attacked by a phosphate group from the nucleotide substrate, producing ATP or GTP and releasing succinate.

Regulation of Succinyl-CoA Synthetase:

The activity of SCS is regulated by several factors, including the concentrations of reactants and products, the availability of coenzymes, and the presence of allosteric modulators.

One of the most important regulators of SCS is the concentration of ATP in the cell. When ATP levels are high, the activity of SCS is inhibited, leading to a decrease in the rate of the Krebs cycle. Conversely, when ATP levels are low, the activity of SCS is stimulated, leading to an increase in the rate of the cycle.

Another important regulator of SCS is the availability of coenzymes, specifically CoA and ADP or GDP. The availability of CoA limits the rate of succinyl-CoA formation, and the availability of ADP or GDP limits the rate of ATP or GTP synthesis.

In addition to these regulators, SCS is also subject to allosteric regulation by several metabolites. For example, succinyl-CoA itself can act as an inhibitor of SCS, while ADP or GDP can act as activators. This allosteric regulation helps to ensure that the rate of the Krebs cycle is tightly controlled and responsive to the needs of the cell.

6-Succinate Dehydrogenase

Succinate dehydrogenase (SDH) is an enzyme that plays a critical role in the Krebs cycle, also known as the citric acid cycle or the tricarboxylic acid (TCA) cycle. This enzyme catalyzes the conversion of succinate to fumarate, while also participating in the electron transport chain. In this article, we will explore the structure, function, and regulation of SDH in the Krebs cycle.

Structure of Succinate Dehydrogenase:

SDH is a complex membrane-bound enzyme that is composed of four subunits: SDHA, SDHB, SDHC, and SDHD. SDHA and SDHB are the catalytic subunits, while SDHC and SDHD are involved in the electron transfer pathway.

The active site of SDH is located in SDHA, where the conversion of succinate to fumarate occurs. The catalytic site contains a prosthetic group called flavin adenine dinucleotide (FAD), which is required for the enzyme’s function.

Function of Succinate Dehydrogenase:

The function of SDH is to catalyze the conversion of succinate to fumarate, while also participating in the electron transport chain. The reaction catalyzed by SDH involves the transfer of two electrons from succinate to FAD, producing FADH2 and fumarate.

The electrons transferred to FADH2 are then passed down the electron transport chain to complex III, where they are used to generate a proton gradient across the mitochondrial membrane. This gradient is then used to generate ATP through the action of ATP synthase.

Regulation of Succinate Dehydrogenase:

The activity of SDH is regulated by several factors, including the concentrations of reactants and products, the availability of cofactors, and the presence of allosteric modulators.

One of the most important regulators of SDH is the concentration of succinate in the cell. When succinate levels are high, the activity of SDH is stimulated, leading to an increase in the rate of the Krebs cycle. Conversely, when succinate levels are low, the activity of SDH is inhibited, leading to a decrease in the rate of the cycle.

Another important regulator of SDH is the availability of cofactors, specifically FAD and CoQ10. The availability of these cofactors limits the rate of electron transfer through the electron transport chain, which in turn limits the rate of ATP synthesis.

In addition to these regulators, SDH is also subject to allosteric regulation by several metabolites. For example, malonate can act as an inhibitor of SDH by binding to the enzyme’s active site and preventing the binding of succinate. This allosteric regulation helps to ensure that the rate of the Krebs cycle is tightly controlled and responsive to the needs of the cell.

7-Fumarase

Fumarase, also known as fumarate hydratase, is an enzyme that plays a critical role in the Krebs cycle, also known as the citric acid cycle or the tricarboxylic acid (TCA) cycle. This enzyme catalyzes the reversible hydration of fumarate to form L-malate. In this article, we will explore the structure, function, and regulation of fumarase in the Krebs cycle.

Structure of Fumarase:

Fumarase is a homodimeric enzyme composed of two identical subunits, each with a molecular weight of approximately 55 kDa. The active site of fumarase is located in a deep cleft between the two subunits, where the conversion of fumarate to L-malate occurs. The active site contains a divalent metal ion, typically iron or zinc, which is required for the enzyme’s function.

Function of Fumarase:

The function of fumarase is to catalyze the reversible hydration of fumarate to form L-malate. This reaction is an important step in the Krebs cycle, as it provides an additional source of energy by producing a molecule of ATP through substrate-level phosphorylation.

The reaction catalyzed by fumarase involves the addition of a water molecule to the double bond in fumarate, resulting in the formation of L-malate. This reaction is reversible, and L-malate can be converted back to fumarate through the action of malate dehydrogenase, providing another opportunity for energy production.

Regulation of Fumarase:

The activity of fumarase is regulated by several factors, including the concentrations of reactants and products, the availability of cofactors, and the presence of allosteric modulators.

One of the most important regulators of fumarase is the concentration of fumarate in the cell. When fumarate levels are high, the activity of fumarase is inhibited, leading to a decrease in the rate of the Krebs cycle. Conversely, when fumarate levels are low, the activity of fumarase is stimulated, leading to an increase in the rate of the cycle.

In addition to this regulation, fumarase is subject to allosteric regulation by several metabolites. For example, ATP and citrate can act as inhibitors of fumarase by binding to the enzyme’s active site and preventing the binding of fumarate. This allosteric regulation helps to ensure that the rate of the Krebs cycle is tightly controlled and responsive to the needs of the cell.

8-Malate Dehydrogenase

Malate dehydrogenase (MDH) is a key enzyme in the Krebs cycle, also known as the citric acid cycle or the tricarboxylic acid (TCA) cycle. MDH catalyzes the conversion of L-malate to oxaloacetate, an important step in the Krebs cycle. In this article, we will explore the structure, function, and regulation of MDH in the Krebs cycle.

Structure of Malate Dehydrogenase:

MDH is a homodimeric enzyme composed of two identical subunits, each with a molecular weight of approximately 35 kDa. The active site of MDH is located in a cleft between the two subunits, where the conversion of L-malate to oxaloacetate occurs. The active site contains a divalent metal ion, typically either NAD+ or NADP+, which serves as a cofactor required for the enzyme’s function.

Function of Malate Dehydrogenase:

The function of MDH is to catalyze the reversible conversion of L-malate to oxaloacetate. This reaction is an important step in the Krebs cycle, as it provides the starting material for the next cycle. The reaction catalyzed by MDH involves the removal of two hydrogen atoms from the carbon atom adjacent to the carboxyl group in L-malate, producing a molecule of NADH and a molecule of oxaloacetate.

Regulation of Malate Dehydrogenase:

The activity of MDH is regulated by several factors, including the concentrations of reactants and products, the availability of cofactors, and the presence of allosteric modulators.

One of the most important regulators of MDH is the concentration of oxaloacetate in the cell. When oxaloacetate levels are high, the activity of MDH is inhibited, leading to a decrease in the rate of the Krebs cycle. Conversely, when oxaloacetate levels are low, the activity of MDH is stimulated, leading to an increase in the rate of the cycle.

In addition to this regulation, MDH is subject to allosteric regulation by several metabolites. For example, ADP and AMP can act as activators of MDH by binding to the enzyme and increasing its activity. This allosteric regulation helps to ensure that the rate of the Krebs cycle is tightly controlled and responsive to the needs of the cell.