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Introduction
1. CARS
2. Psych/soc
3. Bio/biochem
3.1 Structure and function of proteins and their constituent amino acids
3.2 Transmission of genetic information from the gene to the protein
3.3 Heredity and genetic diversity
3.4 Principles of bioenergetics and fuel molecule metabolism
3.4.1 Bioenergetics, free energy, ATP and redox in biology
3.4.2 Carbohydrates
3.4.3 Glycolysis, gluconeogenesis, metabolic regulation
3.4.4 Citric acid cycle, ETP, OP, hormonal regulation
3.5 Assemblies of molecules, cells, groups of cells
3.6 Structure and physiology of prokaryotes and viruses
3.7 Processes of cell division, differentiation, and specialization
3.8 Structure and functions of nervous and endocrine systems
3.9 Structure and functions of main organ systems
4. Chem/phys
Wrapping up
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3.4.4 Citric acid cycle, ETP, OP, hormonal regulation
Achievable MCAT
3. Bio/biochem
3.4. Principles of bioenergetics and fuel molecule metabolism

Citric acid cycle, ETP, OP, hormonal regulation

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The Krebs cycle (TCA, citric acid cycle)

The Krebs cycle, also called the TCA cycle or citric acid cycle, occurs in the mitochondrial matrix. Acetyl CoA (produced from several metabolic pathways) enters the cycle and is processed through a series of reactions that fully oxidize the acetyl group to carbon dioxide.

For each acetyl CoA that enters the cycle, the cell produces:

  • Three NADH
  • One FADH₂
  • One ATP (or GTP)

During the cycle’s early steps, coenzyme A is regenerated, which allows additional acetyl CoA molecules to enter and keep the cycle running.

The Krebs cycle is tightly regulated. When ATP and NADH levels are high (signaling that the cell’s energy needs are being met), key steps in the cycle are inhibited, helping maintain energy homeostasis.

Citric acid cycle with intermediates and energy output
Citric acid cycle with intermediates and energy output

Electron transport chain (ETC) and oxidative phosphorylation

The electron transport chain (ETC) and oxidative phosphorylation occur on the inner mitochondrial membrane, along the cristae. High-energy electrons carried by NADH and FADH2​ (produced largely by the Krebs cycle) move through a series of redox reactions involving FMN, Coenzyme Q, iron-sulfur clusters, and cytochromes (including cytochrome b, c, and aa₃).

As electrons flow from NADH (relatively high energy) to oxygen (the final electron acceptor, relatively low energy), energy is released. The ETC uses that energy to pump protons (H⁺) from the mitochondrial matrix into the intermembrane space, creating an electrochemical proton gradient.

That gradient (the proton motive force) powers ATP synthase. As protons move back into the matrix through ATP synthase, the enzyme uses the released energy to convert ADP into ATP. This ATP-producing step is called oxidative phosphorylation.

The ETC can be disrupted by inhibitors, including some antibiotics, cyanide, azide, and carbon monoxide.

Although NADH is the primary electron donor for the mitochondrial ETC, NADPH is also important. Produced mainly by the pentose phosphate pathway, NADPH supplies reducing power for biosynthetic reactions and antioxidant defenses. These roles help maintain cellular redox balance and can support electron transport efficiency under stress.

Flavoproteins are enzymes that contain flavin cofactors (FAD or FMN). These cofactors allow flavoproteins to participate in redox reactions by accepting and donating electrons. For example, in Complex II of the ETC, FAD accepts electrons during succinate oxidation and transfers them to ubiquinone, linking the citric acid cycle with oxidative phosphorylation for ATP production.

Oxidative phosphorylation

  • Oxidative phosphorylation is the process by which mitochondria convert electron energy into ATP. ATP synthase generates ATP as protons flow down their concentration gradient, a mechanism called chemiosmotic coupling. The ETC pumps protons from the mitochondrial matrix into the intermembrane space, creating a proton motive force (PMF) that drives ATP synthesis as protons return to the matrix.
  • Under optimal conditions, the complete oxidation of one glucose molecule yields about 30-32 ATP, reflecting the tight coupling between the ETC and ATP synthesis. This process is regulated by factors such as ADP availability, substrate levels, oxygen concentration, and ATP feedback.
  • Mitochondria also influence cell fate via apoptosis. Disruptions in oxidative phosphorylation can increase reactive oxygen species (ROS) production, contributing to oxidative stress and cell death.
Electron transport chain and chemiosmotic ATP production
Electron transport chain and chemiosmotic ATP production

Metabolism of fatty acids and proteins

Metabolism of fats

  • Fats are digested in the small intestine. Their components are packaged into chylomicrons for transport through the lymphatic system and bloodstream, delivering lipids to tissues. In cells, ester hydrolysis by lipases in the cytosol converts triglycerides into free fatty acids and glycerol. Each fatty acid is then “activated” by forming a thioester bond with CoA, a reaction that requires ATP.
  • In β-oxidation, these acyl-CoA molecules are sequentially cleaved into two-carbon units of acetyl-CoA, generating FADH2​ and NADH in the process. Acetyl-CoA enters the Krebs cycle, while FADH2​ and NADH deliver electrons to the ETC, ultimately driving ATP synthesis. Per gram, fats yield more energy than any other macronutrient.
β-oxidation of fatty acids
β-oxidation of fatty acids
  • In the liver, when carbohydrate availability is low, excess acetyl-CoA can be converted into ketone bodies (acetoacetate, β-hydroxybutyrate), which serve as alternative energy sources for tissues such as the brain.

Saturated and unsaturated fats

  • Saturated fatty acids have no carbon-carbon double bonds
  • Unsaturated fatty acids contain one or more double bonds, affecting their fluidity and metabolic processing.

Anabolism/synthesis of fats

  • Cells don’t only break down fats; they can also perform anabolism of fats, synthesizing fatty acids and triglycerides from acetyl-CoA. This is a form of non-template synthesis, where complex biomolecules like lipids (and polysaccharides) are built without following a nucleic-acid-encoded template. These pathways support energy storage, membrane structure, and signaling.

Metabolism of proteins

  • Proteins are hydrolyzed into amino acids by peptidases. The amino groups are removed and converted into nitrogenous waste such as urea (or uric acid in certain species).
  • The remaining carbon skeleton can be converted into pyruvate, acetyl-CoA, or other metabolic intermediates, depending on the amino acid. These carbon skeletons can enter the Krebs cycle or serve as substrates for gluconeogenesis, linking protein catabolism to the cell’s energy and biosynthetic needs.

Hormonal regulation and integration of metabolism

Hormones help coordinate metabolism by signaling when to store fuel and when to mobilize it, so tissues receive energy when they need it. Both hormone structure (peptide, steroid, or amino-acid derived) and tissue-specific metabolism influence how cells respond.

For example, the pancreas secretes insulin (a peptide hormone) when blood glucose rises. Insulin promotes glucose uptake - especially in muscle and adipose - and encourages storage as glycogen or fat. In contrast, glucagon (also secreted by the pancreas) rises when blood glucose is low and stimulates glycogenolysis and gluconeogenesis in the liver, increasing circulating glucose.

Epinephrine and cortisol

  • Further integration comes from hormones like
    • Epinephrine (adrenaline), which accelerates glycogen breakdown in muscle during acute stress
    • Cortisol, a steroid hormone that increases protein and fat catabolism and upregulates gluconeogenesis over longer periods.

Individual tissues thus maintain specialized roles:

  • Muscle primarily uses glucose for rapid ATP production
  • Adipose stores excess energy as triglycerides
  • The liver coordinates overall fuel distribution, converting substrates (e.g., amino acids, lactate, glycerol) into glucose or ketone bodies as needed.

Hormonal regulation of fuel metabolism

  • Hormonal regulation also shapes fuel metabolism across feeding, fasting, and exercise states. In the fed state, insulin predominates, promoting glucose uptake and storage. During fasting or exercise, glucagon and epinephrine rise, mobilizing glycogen and fatty acids to maintain blood glucose and energy output.

Obesity and regulation of body mass

  • Chronic energy imbalance can lead to obesity, characterized by increased adipose tissue mass. This can contribute to hormonal dysregulation, including reduced insulin sensitivity and metabolic syndrome.
  • Both genetic factors and hormonal feedback loops (e.g., involving leptin and ghrelin, which regulate hunger and satiety) contribute to regulating body mass, highlighting how integrated hormonal signals can maintain - or disrupt - energy homeostasis.

Krebs cycle (TCA, citric acid cycle)

  • Occurs in mitochondrial matrix; acetyl CoA fully oxidized to CO₂
  • Yields per acetyl CoA: 3 NADH, 1 FADH₂, 1 ATP (or GTP)
  • Regulated by ATP/NADH levels; inhibited when energy is sufficient

Electron transport chain (ETC) and oxidative phosphorylation

  • Located on inner mitochondrial membrane (cristae); uses NADH and FADH₂ electrons
  • Electron flow pumps protons, creating proton motive force for ATP synthase
  • Oxygen is final electron acceptor; inhibitors (cyanide, CO, some antibiotics) can block ETC

Oxidative phosphorylation

  • ATP synthase produces ATP via chemiosmotic coupling (proton gradient)
  • Complete glucose oxidation yields ~30-32 ATP
  • Regulated by ADP, substrate, oxygen, and ATP feedback; disruptions can increase ROS and trigger apoptosis

Flavoproteins and NADPH

  • Flavoproteins (with FAD or FMN) participate in redox reactions in ETC
  • NADPH (from pentose phosphate pathway) supports biosynthesis and antioxidant defense

Metabolism of fatty acids and proteins

Metabolism of fats

  • Fats digested, packaged as chylomicrons, transported to tissues
  • Lipases hydrolyze triglycerides to free fatty acids + glycerol; fatty acids activated to acyl-CoA
  • β-oxidation: acyl-CoA cleaved to acetyl-CoA, producing FADH₂ and NADH; acetyl-CoA enters Krebs cycle
    • Fats yield more energy per gram than other macronutrients
  • In liver, excess acetyl-CoA forms ketone bodies (acetoacetate, β-hydroxybutyrate) during low carbohydrate states

Saturated and unsaturated fats

  • Saturated: no carbon-carbon double bonds
  • Unsaturated: one or more double bonds

Anabolism/synthesis of fats

  • Fatty acids and triglycerides synthesized from acetyl-CoA (non-template synthesis)
  • Supports energy storage, membrane structure, signaling

Metabolism of proteins

  • Proteins hydrolyzed to amino acids; amino groups removed (urea or uric acid)
  • Carbon skeletons converted to pyruvate, acetyl-CoA, or Krebs cycle intermediates

Hormonal regulation and integration of metabolism

  • Hormones (insulin, glucagon, epinephrine, cortisol) coordinate fuel storage and mobilization
    • Insulin: promotes glucose uptake/storage (muscle, adipose)
    • Glucagon: stimulates glycogenolysis, gluconeogenesis (liver)
    • Epinephrine: accelerates glycogen breakdown (muscle, acute stress)
    • Cortisol: increases protein/fat catabolism, upregulates gluconeogenesis (chronic stress)
  • Tissue specialization:
    • Muscle: rapid ATP from glucose
    • Adipose: stores triglycerides
    • Liver: coordinates fuel distribution, gluconeogenesis, ketone body production
  • Hormonal regulation shifts with feeding, fasting, exercise (insulin vs. glucagon/epinephrine dominance)
  • Obesity: chronic energy imbalance, hormonal dysregulation (insulin resistance, metabolic syndrome)
    • Body mass regulated by genetic factors and hormones (leptin, ghrelin) affecting hunger/satiety

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Citric acid cycle, ETP, OP, hormonal regulation

The Krebs cycle (TCA, citric acid cycle)

The Krebs cycle, also called the TCA cycle or citric acid cycle, occurs in the mitochondrial matrix. Acetyl CoA (produced from several metabolic pathways) enters the cycle and is processed through a series of reactions that fully oxidize the acetyl group to carbon dioxide.

For each acetyl CoA that enters the cycle, the cell produces:

  • Three NADH
  • One FADH₂
  • One ATP (or GTP)

During the cycle’s early steps, coenzyme A is regenerated, which allows additional acetyl CoA molecules to enter and keep the cycle running.

The Krebs cycle is tightly regulated. When ATP and NADH levels are high (signaling that the cell’s energy needs are being met), key steps in the cycle are inhibited, helping maintain energy homeostasis.

Electron transport chain (ETC) and oxidative phosphorylation

The electron transport chain (ETC) and oxidative phosphorylation occur on the inner mitochondrial membrane, along the cristae. High-energy electrons carried by NADH and FADH2​ (produced largely by the Krebs cycle) move through a series of redox reactions involving FMN, Coenzyme Q, iron-sulfur clusters, and cytochromes (including cytochrome b, c, and aa₃).

As electrons flow from NADH (relatively high energy) to oxygen (the final electron acceptor, relatively low energy), energy is released. The ETC uses that energy to pump protons (H⁺) from the mitochondrial matrix into the intermembrane space, creating an electrochemical proton gradient.

That gradient (the proton motive force) powers ATP synthase. As protons move back into the matrix through ATP synthase, the enzyme uses the released energy to convert ADP into ATP. This ATP-producing step is called oxidative phosphorylation.

The ETC can be disrupted by inhibitors, including some antibiotics, cyanide, azide, and carbon monoxide.

Although NADH is the primary electron donor for the mitochondrial ETC, NADPH is also important. Produced mainly by the pentose phosphate pathway, NADPH supplies reducing power for biosynthetic reactions and antioxidant defenses. These roles help maintain cellular redox balance and can support electron transport efficiency under stress.

Flavoproteins are enzymes that contain flavin cofactors (FAD or FMN). These cofactors allow flavoproteins to participate in redox reactions by accepting and donating electrons. For example, in Complex II of the ETC, FAD accepts electrons during succinate oxidation and transfers them to ubiquinone, linking the citric acid cycle with oxidative phosphorylation for ATP production.

Oxidative phosphorylation

  • Oxidative phosphorylation is the process by which mitochondria convert electron energy into ATP. ATP synthase generates ATP as protons flow down their concentration gradient, a mechanism called chemiosmotic coupling. The ETC pumps protons from the mitochondrial matrix into the intermembrane space, creating a proton motive force (PMF) that drives ATP synthesis as protons return to the matrix.
  • Under optimal conditions, the complete oxidation of one glucose molecule yields about 30-32 ATP, reflecting the tight coupling between the ETC and ATP synthesis. This process is regulated by factors such as ADP availability, substrate levels, oxygen concentration, and ATP feedback.
  • Mitochondria also influence cell fate via apoptosis. Disruptions in oxidative phosphorylation can increase reactive oxygen species (ROS) production, contributing to oxidative stress and cell death.

Metabolism of fatty acids and proteins

Metabolism of fats

  • Fats are digested in the small intestine. Their components are packaged into chylomicrons for transport through the lymphatic system and bloodstream, delivering lipids to tissues. In cells, ester hydrolysis by lipases in the cytosol converts triglycerides into free fatty acids and glycerol. Each fatty acid is then “activated” by forming a thioester bond with CoA, a reaction that requires ATP.
  • In β-oxidation, these acyl-CoA molecules are sequentially cleaved into two-carbon units of acetyl-CoA, generating FADH2​ and NADH in the process. Acetyl-CoA enters the Krebs cycle, while FADH2​ and NADH deliver electrons to the ETC, ultimately driving ATP synthesis. Per gram, fats yield more energy than any other macronutrient.
  • In the liver, when carbohydrate availability is low, excess acetyl-CoA can be converted into ketone bodies (acetoacetate, β-hydroxybutyrate), which serve as alternative energy sources for tissues such as the brain.

Saturated and unsaturated fats

  • Saturated fatty acids have no carbon-carbon double bonds
  • Unsaturated fatty acids contain one or more double bonds, affecting their fluidity and metabolic processing.

Anabolism/synthesis of fats

  • Cells don’t only break down fats; they can also perform anabolism of fats, synthesizing fatty acids and triglycerides from acetyl-CoA. This is a form of non-template synthesis, where complex biomolecules like lipids (and polysaccharides) are built without following a nucleic-acid-encoded template. These pathways support energy storage, membrane structure, and signaling.

Metabolism of proteins

  • Proteins are hydrolyzed into amino acids by peptidases. The amino groups are removed and converted into nitrogenous waste such as urea (or uric acid in certain species).
  • The remaining carbon skeleton can be converted into pyruvate, acetyl-CoA, or other metabolic intermediates, depending on the amino acid. These carbon skeletons can enter the Krebs cycle or serve as substrates for gluconeogenesis, linking protein catabolism to the cell’s energy and biosynthetic needs.

Hormonal regulation and integration of metabolism

Hormones help coordinate metabolism by signaling when to store fuel and when to mobilize it, so tissues receive energy when they need it. Both hormone structure (peptide, steroid, or amino-acid derived) and tissue-specific metabolism influence how cells respond.

For example, the pancreas secretes insulin (a peptide hormone) when blood glucose rises. Insulin promotes glucose uptake - especially in muscle and adipose - and encourages storage as glycogen or fat. In contrast, glucagon (also secreted by the pancreas) rises when blood glucose is low and stimulates glycogenolysis and gluconeogenesis in the liver, increasing circulating glucose.

Epinephrine and cortisol

  • Further integration comes from hormones like
    • Epinephrine (adrenaline), which accelerates glycogen breakdown in muscle during acute stress
    • Cortisol, a steroid hormone that increases protein and fat catabolism and upregulates gluconeogenesis over longer periods.

Individual tissues thus maintain specialized roles:

  • Muscle primarily uses glucose for rapid ATP production
  • Adipose stores excess energy as triglycerides
  • The liver coordinates overall fuel distribution, converting substrates (e.g., amino acids, lactate, glycerol) into glucose or ketone bodies as needed.

Hormonal regulation of fuel metabolism

  • Hormonal regulation also shapes fuel metabolism across feeding, fasting, and exercise states. In the fed state, insulin predominates, promoting glucose uptake and storage. During fasting or exercise, glucagon and epinephrine rise, mobilizing glycogen and fatty acids to maintain blood glucose and energy output.

Obesity and regulation of body mass

  • Chronic energy imbalance can lead to obesity, characterized by increased adipose tissue mass. This can contribute to hormonal dysregulation, including reduced insulin sensitivity and metabolic syndrome.
  • Both genetic factors and hormonal feedback loops (e.g., involving leptin and ghrelin, which regulate hunger and satiety) contribute to regulating body mass, highlighting how integrated hormonal signals can maintain - or disrupt - energy homeostasis.
Key points

Krebs cycle (TCA, citric acid cycle)

  • Occurs in mitochondrial matrix; acetyl CoA fully oxidized to CO₂
  • Yields per acetyl CoA: 3 NADH, 1 FADH₂, 1 ATP (or GTP)
  • Regulated by ATP/NADH levels; inhibited when energy is sufficient

Electron transport chain (ETC) and oxidative phosphorylation

  • Located on inner mitochondrial membrane (cristae); uses NADH and FADH₂ electrons
  • Electron flow pumps protons, creating proton motive force for ATP synthase
  • Oxygen is final electron acceptor; inhibitors (cyanide, CO, some antibiotics) can block ETC

Oxidative phosphorylation

  • ATP synthase produces ATP via chemiosmotic coupling (proton gradient)
  • Complete glucose oxidation yields ~30-32 ATP
  • Regulated by ADP, substrate, oxygen, and ATP feedback; disruptions can increase ROS and trigger apoptosis

Flavoproteins and NADPH

  • Flavoproteins (with FAD or FMN) participate in redox reactions in ETC
  • NADPH (from pentose phosphate pathway) supports biosynthesis and antioxidant defense

Metabolism of fatty acids and proteins

Metabolism of fats

  • Fats digested, packaged as chylomicrons, transported to tissues
  • Lipases hydrolyze triglycerides to free fatty acids + glycerol; fatty acids activated to acyl-CoA
  • β-oxidation: acyl-CoA cleaved to acetyl-CoA, producing FADH₂ and NADH; acetyl-CoA enters Krebs cycle
    • Fats yield more energy per gram than other macronutrients
  • In liver, excess acetyl-CoA forms ketone bodies (acetoacetate, β-hydroxybutyrate) during low carbohydrate states

Saturated and unsaturated fats

  • Saturated: no carbon-carbon double bonds
  • Unsaturated: one or more double bonds

Anabolism/synthesis of fats

  • Fatty acids and triglycerides synthesized from acetyl-CoA (non-template synthesis)
  • Supports energy storage, membrane structure, signaling

Metabolism of proteins

  • Proteins hydrolyzed to amino acids; amino groups removed (urea or uric acid)
  • Carbon skeletons converted to pyruvate, acetyl-CoA, or Krebs cycle intermediates

Hormonal regulation and integration of metabolism

  • Hormones (insulin, glucagon, epinephrine, cortisol) coordinate fuel storage and mobilization
    • Insulin: promotes glucose uptake/storage (muscle, adipose)
    • Glucagon: stimulates glycogenolysis, gluconeogenesis (liver)
    • Epinephrine: accelerates glycogen breakdown (muscle, acute stress)
    • Cortisol: increases protein/fat catabolism, upregulates gluconeogenesis (chronic stress)
  • Tissue specialization:
    • Muscle: rapid ATP from glucose
    • Adipose: stores triglycerides
    • Liver: coordinates fuel distribution, gluconeogenesis, ketone body production
  • Hormonal regulation shifts with feeding, fasting, exercise (insulin vs. glucagon/epinephrine dominance)
  • Obesity: chronic energy imbalance, hormonal dysregulation (insulin resistance, metabolic syndrome)
    • Body mass regulated by genetic factors and hormones (leptin, ghrelin) affecting hunger/satiety