Biological Chemistry II

2.3 Citric acid cycle: reactions and regulation

Citation:

The citric acid cycle, a key part of carbohydrate metabolism, breaks down acetyl-CoA to produce energy-rich molecules. This process, occurring in the mitochondria, involves eight enzymatic reactions that oxidize and decarboxylate substrates, generating NADH, FADH2, and GTP.

Regulation of the cycle is crucial for maintaining energy balance. Allosteric enzymes respond to energy levels, while substrate availability and hormonal signals fine-tune the process. The cycle also serves anabolic functions, providing precursors for various biosynthetic pathways.

Reactions and Enzymes of the Citric Acid Cycle

Cycle Overview and Initial Steps

Citric acid cycle occurs in mitochondrial matrix through eight enzymatic reactions
Cycle begins with condensation of acetyl-CoA and oxaloacetate forming citrate
Citrate synthase catalyzes initial reaction
Aconitase isomerizes citrate to isocitrate via cis-aconitate intermediate

Decarboxylation and Oxidation Steps

Isocitrate dehydrogenase oxidizes isocitrate to α-ketoglutarate
- Releases CO2 and reduces NAD+ to NADH
α-Ketoglutarate dehydrogenase complex catalyzes oxidative decarboxylation of α-ketoglutarate
- Produces succinyl-CoA, NADH, and CO2

Final Steps and Cycle Completion

Succinyl-CoA synthetase converts succinyl-CoA to succinate
- Coupled with GTP formation (ATP in some organisms)
Succinate dehydrogenase oxidizes succinate to fumarate
- Reduces FAD to FADH2
Fumarase catalyzes hydration of fumarate to malate
Malate dehydrogenase oxidizes malate to oxaloacetate
- Reduces NAD+ to NADH
Oxaloacetate regeneration completes the cycle

High-Energy Molecule Formation in the Citric Acid Cycle

NADH and FADH2 Production

Three NADH molecules generated per acetyl-CoA oxidized
- Produced by isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, and malate dehydrogenase
One FADH2 molecule produced by succinate dehydrogenase
- Result of succinate oxidation to fumarate

GTP/ATP Generation and Energy Yield

Succinyl-CoA synthetase reaction produces one GTP (or ATP)
- Occurs through substrate-level phosphorylation
NADH and FADH2 serve as electron donors for electron transport chain
- Drive oxidative phosphorylation and ATP synthesis
Total energy yield from one cycle turn equates to 12 ATP molecules
- Accounts for subsequent oxidative phosphorylation

Regulation of the Citric Acid Cycle

Allosteric Enzyme Regulation

Citrate synthase allosterically inhibited by ATP and NADH
- Signals high cellular energy levels
Isocitrate dehydrogenase activated by ADP and inhibited by ATP and NADH
- Sensitive to cell's energy state
α-Ketoglutarate dehydrogenase inhibited by products and high ATP/ADP ratio
- Products include succinyl-CoA and NADH

Substrate Availability and Cofactor Influence

Acetyl-CoA availability major factor in cycle regulation
- Influenced by pyruvate dehydrogenase complex activity
NAD+/NADH ratio in mitochondrial matrix affects cycle rate
- High NADH concentration slows several steps

Hormonal and Neural Regulation

Calcium ions act as positive regulators
- Activate pyruvate dehydrogenase, isocitrate dehydrogenase, and α-ketoglutarate dehydrogenase
- Link cycle activity to hormonal and neural signals (adrenaline, glucagon)

Amphibolic Nature of the Citric Acid Cycle

Catabolic Functions

Oxidizes acetyl-CoA from various sources (carbohydrates, fats, proteins)
- Generates energy in form of ATP, NADH, and FADH2
Breaks down complex molecules to simpler forms
- Provides energy for cellular processes

Anabolic Functions

Cycle intermediates serve as precursors for biosynthetic pathways
- Oxaloacetate and α-ketoglutarate precursors for aspartate and glutamate synthesis
  - Further converted to other amino acids (arginine, proline)
- Succinyl-CoA precursor for heme biosynthesis and certain amino acids (methionine, isoleucine)
- Citrate exported to cytosol for fatty acid and cholesterol synthesis

Anaplerotic Reactions and Cycle Maintenance

Anaplerotic reactions replenish cycle intermediates removed for biosynthesis
- Pyruvate carboxylase converts pyruvate to oxaloacetate
- Glutamate dehydrogenase converts glutamate to α-ketoglutarate
Maintain cycle function despite constant removal of intermediates for anabolic processes

Key Terms to Review (32)

Fadh2: FADH2 is a reduced coenzyme derived from riboflavin that plays a crucial role in the metabolism of carbohydrates, fatty acids, and amino acids. It acts as an electron carrier in cellular respiration, specifically in the electron transport chain, contributing to the production of ATP through oxidative phosphorylation.

ATP: ATP, or adenosine triphosphate, is a high-energy molecule that serves as the primary energy currency of the cell. It is essential for driving various biochemical processes, including muscle contraction, active transport, and biosynthesis. ATP is produced in cellular respiration and photosynthesis, linking energy-releasing reactions to energy-consuming activities.

NADH: NADH, or nicotinamide adenine dinucleotide (reduced form), is a crucial coenzyme in cellular metabolism that acts as an electron carrier in redox reactions. It plays a significant role in energy production by facilitating the transfer of electrons during metabolic pathways such as glycolysis and the citric acid cycle, ultimately contributing to ATP synthesis through oxidative phosphorylation.

Malate dehydrogenase: Malate dehydrogenase is an enzyme that catalyzes the reversible conversion of malate to oxaloacetate, utilizing NAD+ as a cofactor to produce NADH in the process. This reaction is crucial for cellular metabolism, as it plays a significant role in the citric acid cycle and also facilitates the transport of reducing equivalents into mitochondria through the malate-aspartate shuttle.

Substrate availability: Substrate availability refers to the presence and concentration of substrates required for enzymatic reactions, impacting the rate and efficiency of metabolic processes. It plays a crucial role in determining how well metabolic pathways function, as enzymes rely on substrates to catalyze biochemical reactions. Variations in substrate availability can lead to changes in metabolic rates and can affect cellular energy production and overall metabolic balance.

Malate: Malate is a four-carbon dicarboxylic acid that plays a crucial role in metabolic processes, particularly in the citric acid cycle and the transport of reducing equivalents across mitochondrial membranes. It serves as both an intermediate in energy production and as a key player in the C4 and CAM pathways of carbon fixation, connecting various metabolic pathways and facilitating cellular respiration and photosynthesis.

Fumarate: Fumarate is a key intermediate in the citric acid cycle, formed from the dehydration of malate by the enzyme fumarase. It plays an important role in both energy production and the metabolism of amino acids, particularly during the conversion of certain amino acids to succinate and ultimately to fumarate, linking amino acid catabolism with the citric acid cycle.

α-ketoglutarate: α-ketoglutarate is a key intermediate in the citric acid cycle and a significant molecule in amino acid metabolism. It plays a crucial role in energy production, being involved in the conversion of carbohydrates, fats, and proteins into usable energy. Additionally, α-ketoglutarate acts as a precursor for several amino acids and is involved in the urea cycle, highlighting its importance in both energy production and nitrogen metabolism.

Feedback Inhibition: Feedback inhibition is a regulatory mechanism in biochemical pathways where the end product of a reaction inhibits an earlier step in the pathway, preventing the overproduction of that product. This process is crucial for maintaining homeostasis within the cell and ensuring efficient use of resources.

GTP: Guanosine triphosphate (GTP) is a nucleotide that serves as a critical energy source and a signaling molecule in cellular processes. It plays a significant role in protein synthesis and cell signaling, particularly in the activation of G-proteins. GTP is involved in various metabolic pathways, making it integral to energy metabolism and cellular regulation.

Anaplerotic reactions: Anaplerotic reactions are metabolic pathways that replenish the intermediates of the citric acid cycle (Krebs cycle), ensuring its continuous operation. These reactions are essential for maintaining the balance of metabolites within the cycle, allowing it to function efficiently in energy production and biosynthesis, especially during times when intermediates are drawn off for other metabolic processes.

Catabolic Functions: Catabolic functions refer to the metabolic processes that break down complex molecules into simpler ones, releasing energy stored in chemical bonds. These functions are crucial for providing the energy necessary for various cellular activities and are a key component of cellular respiration, including processes like the citric acid cycle. By dismantling larger biomolecules, catabolic pathways contribute to maintaining the overall energy balance in living organisms.

Anabolic functions: Anabolic functions are metabolic processes that build complex molecules from simpler ones, requiring energy input in the form of ATP. These functions are crucial for growth, repair, and maintenance of tissues, as they contribute to the synthesis of proteins, nucleic acids, and other essential biomolecules. Understanding anabolic functions is vital for comprehending how cells utilize energy and resources to create macromolecules necessary for life.

Enzyme kinetics: Enzyme kinetics is the study of the rates at which enzyme-catalyzed reactions occur, focusing on how various factors influence these rates. It helps to understand the relationship between substrate concentration and reaction velocity, ultimately revealing how enzymes function in metabolic pathways and how they are regulated. This understanding is crucial for grasping mechanisms like feedback inhibition and allosteric regulation that affect enzyme activity.

Metabolic flux: Metabolic flux refers to the rate at which substrates and products flow through a metabolic pathway, essentially quantifying how much of a certain metabolite is produced or consumed over time. This concept is crucial in understanding how cells regulate their biochemical pathways in response to varying conditions, ensuring that metabolic processes efficiently meet the energy and biosynthetic demands of the cell.

Decarboxylation: Decarboxylation is the biochemical process of removing a carboxyl group (-COOH) from a molecule, releasing carbon dioxide (CO2) in the process. This reaction is crucial in various metabolic pathways, particularly in the conversion of organic acids into more energetically favorable molecules during cellular respiration, including the citric acid cycle.

FAD: FAD, or flavin adenine dinucleotide, is a redox cofactor involved in various metabolic reactions, particularly in the citric acid cycle. It serves as an electron carrier, accepting electrons during reactions and subsequently donating them in the electron transport chain, playing a crucial role in cellular respiration and energy production.

Succinyl-CoA: Succinyl-CoA is a crucial intermediate in the citric acid cycle, formed from the conversion of α-ketoglutarate. This molecule plays a significant role in energy production and biosynthesis, connecting various metabolic pathways by facilitating the generation of ATP and serving as a substrate for the synthesis of heme and other biomolecules.

Succinate: Succinate is a four-carbon dicarboxylic acid that plays a key role in the citric acid cycle as an intermediate formed during the conversion of succinyl-CoA to succinate. This transformation is catalyzed by the enzyme succinyl-CoA synthetase, which also generates GTP or ATP, depending on the specific organism. Succinate serves as a crucial substrate for further reactions within the cycle, linking various metabolic pathways and influencing the regulation of cellular respiration.

Isocitrate: Isocitrate is a six-carbon intermediate compound in the citric acid cycle, formed from citrate by the enzyme aconitase. It plays a crucial role in energy production as it is further processed to produce NADH and ATP, contributing to cellular respiration and energy metabolism.

Citrate: Citrate is a key intermediate in the citric acid cycle, also known as the Krebs cycle or tricarboxylic acid (TCA) cycle. It is formed by the condensation of acetyl-CoA with oxaloacetate, catalyzed by the enzyme citrate synthase. Citrate plays a vital role in cellular metabolism, serving as a precursor for various biosynthetic pathways and contributing to the regulation of energy production.

Succinyl-coa synthetase: Succinyl-CoA synthetase is an enzyme that plays a critical role in the citric acid cycle by catalyzing the reversible conversion of succinyl-CoA to succinate, coupled with the phosphorylation of GDP to GTP or ADP to ATP. This reaction not only helps in energy production but also links various metabolic pathways, showcasing the importance of this enzyme in cellular respiration and metabolism.

Fumarase: Fumarase is an enzyme that catalyzes the reversible hydration of fumarate to malate in the citric acid cycle. This reaction is crucial for the continuation of the cycle, which plays a significant role in cellular respiration and energy production. Fumarase functions as a key player in the metabolic pathway that converts carbohydrates, fats, and proteins into usable energy, emphasizing its importance in cellular metabolism.

Aconitase: Aconitase is an enzyme that plays a critical role in the citric acid cycle, catalyzing the isomerization of citrate to isocitrate through a two-step process. This enzyme is important for facilitating energy production in aerobic respiration and helps regulate the flow of metabolites within the cycle, impacting overall cellular metabolism.

Isocitrate dehydrogenase: Isocitrate dehydrogenase is an important enzyme in the citric acid cycle that catalyzes the conversion of isocitrate to alpha-ketoglutarate while reducing NAD+ to NADH. This enzyme plays a critical role in energy production and cellular respiration, linking the cycles of glucose metabolism to the production of electron carriers for ATP synthesis.

α-ketoglutarate dehydrogenase complex: The α-ketoglutarate dehydrogenase complex is a multi-enzyme complex that catalyzes the conversion of α-ketoglutarate to succinyl-CoA in the citric acid cycle, also known as the Krebs cycle. This reaction is significant because it represents the third oxidative decarboxylation step in the cycle, where carbon dioxide is released and energy-rich NADH is produced. The regulation of this enzyme complex plays a crucial role in controlling the overall rate of the citric acid cycle and cellular metabolism.

Citrate synthase: Citrate synthase is an essential enzyme in the citric acid cycle that catalyzes the condensation of acetyl-CoA and oxaloacetate to form citrate. This reaction is a crucial step in energy production, linking carbohydrate, fat, and protein metabolism to ATP synthesis through oxidative phosphorylation.

Oxaloacetate: Oxaloacetate is a four-carbon dicarboxylic acid that plays a critical role in the citric acid cycle, also known as the Krebs cycle. It acts as both a substrate and an intermediate, facilitating the conversion of acetyl-CoA into energy-rich compounds. Furthermore, oxaloacetate is important in carbohydrate metabolism and serves as a precursor for gluconeogenesis and amino acid synthesis, linking various metabolic pathways.

Oxidative phosphorylation: Oxidative phosphorylation is the process by which ATP is produced in cells through the transfer of electrons from electron donors to electron acceptors in the electron transport chain, coupled with the generation of a proton gradient across the mitochondrial membrane. This process connects energy production from nutrients with the synthesis of ATP, highlighting its role in cellular respiration and energy metabolism.

NAD+: NAD+ (nicotinamide adenine dinucleotide) is a vital coenzyme that functions as an electron carrier in various metabolic reactions. It plays a critical role in redox reactions, helping to transfer electrons from one molecule to another, thus facilitating energy production in cellular processes such as glycolysis, the citric acid cycle, and fatty acid oxidation and synthesis. Its ability to exist in an oxidized form (NAD+) and a reduced form (NADH) is essential for maintaining the balance of metabolic pathways.

Succinate dehydrogenase: Succinate dehydrogenase is an enzyme that plays a crucial role in both the citric acid cycle and the electron transport chain. It catalyzes the conversion of succinate to fumarate while reducing flavin adenine dinucleotide (FAD) to FADH2. This enzyme links the citric acid cycle with oxidative phosphorylation, as the FADH2 produced is subsequently utilized in the electron transport chain to generate ATP through chemiosmosis.

Substrate-level phosphorylation: Substrate-level phosphorylation is a process in cellular metabolism where ATP is produced directly from the transfer of a phosphate group from a high-energy substrate to ADP, without the involvement of an electron transport chain. This mechanism is crucial for generating energy in both glycolysis and the citric acid cycle, providing a rapid way to produce ATP in the absence of oxygen or during anaerobic conditions.

Table of Contents

⚗️biological chemistry ii review