Glycolysis / Pyruvate Dehydrogenase

Vocabulary flashcards covering key concepts from glycolysis, glucose transport, and pyruvate metabolism discussed in the lecture notes.

TCA Cycle (Citric Acid Cycle / Krebs Cycle)

A central metabolic pathway located in the mitochondrial matrix that oxidizes acetyl-CoA, derived from carbohydrates, fats, and proteins, to carbon dioxide (CO2). Its primary role is to generate high-energy electron carriers (NADH and FADH2) for the electron transport chain and produce guanosine triphosphate (GTP), which can be converted to ATP. This cycle is amphibolic, meaning it participates in both catabolic and anabolic processes.

Primary Function of TCA Cycle

The main function of the TCA cycle is to generate the reduced electron carriers, NADH and FADH_2. These carriers then donate their electrons to the electron transport chain, driving the synthesis of the vast majority of cellular ATP. Additionally, the cycle supplies critical intermediates for various biosynthetic pathways, acting as a metabolic hub.

Factors Regulating TCA Cycle Activity

The activity of the TCA cycle is tightly regulated to match the cell's energy demands. Key regulatory factors include:1. Substrate Availability: Levels of acetyl-CoA and oxaloacetate (OAA).2. Product Inhibition: High concentrations of NADH and ATP (indicators of high energy) inhibit key enzymes. Succinyl-CoA and citrate can also act as feedback inhibitors.3. Allosteric Activation: ADP and Ca^{2+} (indicators of low energy or muscle contraction) activate certain enzymes.

Accomplishments of TCA Cycle for the Cell

The TCA cycle achieves several vital functions for the cell:1. Energy Generation: Produces the majority of the reduced electron carriers (NADH, FADH_2) that fuel ATP synthesis via oxidative phosphorylation. It also directly produces one molecule of GTP (or ATP) per cycle via substrate-level phosphorylation.2. Precursor Supply: Provides intermediates for the synthesis of glucose (via gluconeogenesis), amino acids, heme (for porphyrins), and fatty acids.3. Metabolic Hub: Integrates the metabolism of carbohydrates, fats, and proteins, serving as a central point where catabolic pathways converge and anabolic pathways diverge.

Key Regulated Enzymes of TCA Cycle

The primary regulated enzymes that control the flux through the TCA cycle are:1. Citrate Synthase: Catalyzes the first step.2. Isocitrate Dehydrogenase: A major rate-limiting enzyme.3. \alpha-Ketoglutarate Dehydrogenase Complex: Another key regulatory point, similar in mechanism to pyruvate dehydrogenase complex.

Citrate Synthase

The enzyme that catalyzes the irreversible condensation of acetyl-CoA and oxaloacetate to form citrate, initiating the TCA cycle. It is a key regulatory enzyme, inhibited by high concentrations of ATP, NADH, succinyl-CoA, and citrate (product inhibition).

Isocitrate Dehydrogenase

A crucial enzyme in the TCA cycle that catalyzes the oxidative decarboxylation of isocitrate to \alpha-ketoglutarate, producing the first NADH and a molecule of CO_2. It is a major regulatory enzyme, allosterically activated by ADP and Ca^{2+} (signaling low energy or muscle activity) and inhibited by ATP and NADH (signaling high energy).

\alpha-Ketoglutarate Dehydrogenase Complex

A multi-enzyme complex that catalyzes the oxidative decarboxylation of \alpha-ketoglutarate to succinyl-CoA, producing the second NADH and another molecule of CO_2. This complex is analogous to the pyruvate dehydrogenase complex, requiring the cofactors thiamine pyrophosphate (TPP), lipoate, FAD, NAD+, and Coenzyme A. It is inhibited by its products, succinyl-CoA and NADH.

Anaplerotic Reactions in TCA Cycle

Reactions that replenish the intermediates of the TCA cycle. When TCA cycle intermediates are drawn off for various biosynthetic pathways (cataplerotic reactions), anaplerotic reactions are essential to maintain the cycle's integrity. A prime example is the pyruvate carboxylase reaction, which converts pyruvate to oxaloacetate, supporting both the TCA cycle and gluconeogenesis.

Succinate Dehydrogenase (Complex II of ETS)

The only enzyme of the TCA cycle that is directly embedded in the inner mitochondrial membrane, rather than residing in the matrix. It catalyzes the oxidation of succinate to fumarate and, in this process, reduces FAD to FADH2. Critically, the FADH2 produced remains bound to the enzyme and directly transfers its electrons into the electron transport chain via Complex II, bypassing Complex I.

Electron Transport System (ETS)

A series of protein complexes (Complexes I-IV) and mobile electron carriers (Coenzyme Q and Cytochrome c) located in the inner mitochondrial membrane. The primary function of the ETS is to accept electrons from NADH and FADH2 (generated during glycolysis, TCA cycle, and fatty acid oxidation) and successively pass them to molecular oxygen (O2), the final electron acceptor. This electron flow releases energy used to pump protons, creating an electrochemical gradient.

Key Concepts of ETS

The fundamental principles underlying the Electron Transport System include:1. Electron Flow: Electrons move spontaneously from compounds with higher electron potential (e.g., NADH) to those with lower potential (e.g., O_2), releasing energy.2. Redox Reactions: Sequential oxidation and reduction reactions occur as electrons are passed between components.3. Proton Pumping: The energy released from electron transfer is coupled to the active pumping of protons (H^+) from the mitochondrial matrix to the intermembrane space, building a proton gradient.4. Chemiosmosis: The utilization of this proton gradient's potential energy by ATP synthase to drive the synthesis of ATP.

Oxidative Phosphorylation

The metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing energy which is used to reform ATP from ADP and Pi. This process occurs by way of the electron transport system and ATP synthase, where the oxidation of NADH and FADH2 generates a proton motive force, which then drives the phosphorylation of ADP.

Accomplishments of ETS & Oxidative Phosphorylation for the Cell

Together, the ETS and oxidative phosphorylation are the major energy-generating pathways in aerobic organisms, accomplishing:1. Massive ATP Generation: They produce the vast majority of ATP molecules from the complete oxidation of glucose and other fuels, far exceeding the ATP yield of glycolysis alone.2. Regeneration of Electron Acceptors: They reoxidize NADH and FADH_2 back to NAD^+ and FAD, which are essential coenzymes required to sustain glycolysis and the TCA cycle.3. Efficient Energy Conversion: They efficiently convert the chemical energy stored in reduced coenzymes into a usable form (ATP) for cellular processes, while also producing water as a byproduct.

Mitochondrial Respiratory Complex I (NADH Dehydrogenase)

The largest of the mitochondrial respiratory complexes, located in the inner mitochondrial membrane. It accepts electrons from NADH, oxidizes it to NAD^+ (which can then return to glycolysis and the TCA cycle), and passes these electrons through flavin mononucleotide (FMN) and iron-sulfur clusters to Coenzyme Q (ubiquinone). Critically, the energy released from this electron transfer is used to pump 4 protons (H^+) from the mitochondrial matrix into the intermembrane space.

Mitochondrial Respiratory Complex II (Succinate Dehydrogenase)

Identical to the succinate dehydrogenase enzyme of the TCA cycle, this complex is also embedded in the inner mitochondrial membrane. It accepts electrons from FADH_2 (generated during the oxidation of succinate to fumarate) and passes them to Coenzyme Q. Unlike Complexes I, III, and IV, Complex II does NOT pump protons across the membrane.

Mitochondrial Respiratory Complex III (Cytochrome bc1 Complex)

Located in the inner mitochondrial membrane, this complex accepts electrons from reduced Coenzyme Q (QH2) and passes them, via iron-sulfur clusters and cytochromes bL, bH, and c1, to the mobile electron carrier Cytochrome c. During this process, which involves a 'Q cycle,' 4 protons (H^+) are pumped from the mitochondrial matrix to the intermembrane space.

Mitochondrial Respiratory Complex IV (Cytochrome c Oxidase)

The final complex in the electron transport chain, located in the inner mitochondrial membrane. It accepts electrons from Cytochrome c and transfers them to the ultimate electron acceptor, molecular oxygen (O2), reducing O2 to water (H_2O). This crucial step also involves the pumping of 2 protons (H^+) from the mitochondrial matrix into the intermembrane space.

Proton Pump in ETS

Specific protein complexes (Complexes I, III, and IV) within the electron transport system that actively transport protons (H^+) from the mitochondrial matrix to the intermembrane space. This movement is energetically driven by the exergonic flow of electrons through the complexes, creating an electrochemical gradient (proton motive force) across the inner mitochondrial membrane.

Proton Gradient (Proton Motive Force)

The electrochemical potential energy generated across the inner mitochondrial membrane by the active pumping of protons (H^+) during electron transport. This gradient consists of two components: a difference in proton concentration (pH gradient, with lower pH in the intermembrane space) and an electrical potential difference (matrix is more negatively charged). This stored energy is then harnessed by ATP synthase to produce ATP.

ATP Synthase (Complex V)

A multi-subunit enzyme, also known as Complex V or F0F1-ATPase, universally found in the inner mitochondrial membrane. It functions as a molecular motor that utilizes the energy stored in the proton gradient (proton motive force) to catalyze the synthesis of ATP from ADP and inorganic phosphate (Pi). It consists of two main parts: the F0 subunit embedded in the membrane (proton channel) and the F_1 subunit protruding into the matrix (catalytic site).

Coupling of ATP Synthesis by ATP Synthase

ATP synthesis by ATP synthase is a process called chemiosmotic coupling. Protons (H^+) flow down their electrochemical gradient from the intermembrane space back into the mitochondrial matrix through the F0 subunit of ATP synthase. This proton flow causes the F0 subunit to rotate, which in turn drives conformational changes in the catalytic sites of the F1 subunit, leading to the phosphorylation of ADP by Pi to form ATP (ADP + P_i \rightarrow ATP).

Inhibitors of ETS

Compounds that block electron flow in the electron transport system at specific points, preventing the formation of the proton gradient and subsequently inhibiting ATP synthesis. Examples include:1. Complex I Inhibitors: Rotenone (a pesticide) and Amytal (a barbiturate).2. Complex III Inhibitors: Antimycin A (an antibiotic).3. Complex IV Inhibitors: Cyanide (CN^-), Carbon Monoxide (CO), and azide (N_3^-).

Inhibitors of ATP Synthase

Compounds that directly target and inhibit the function of ATP synthase, preventing the synthesis of ATP despite continued electron transport and proton pumping (though the proton gradient would eventually build to an extreme level). The classic example is Oligomycin, an antibiotic that binds to the F_0 subunit of ATP synthase, blocking the proton channel and thus preventing $H^+ flow through the enzyme.

Uncouplers (e.g., DNP, Thermogenin)

Molecules or proteins that dissipate the proton gradient across the inner mitochondrial membrane without allowing the protons to pass through ATP synthase. They achieve this by making the membrane permeable to protons, allowing $H^+ to re-enter the mitochondrial matrix without driving ATP synthesis. This 'uncouples' electron transport from oxidative phosphorylation, meaning energy from electron flow is released as heat instead of being captured in ATP. Examples include 2,4-dinitrophenol (DNP) and thermogenin (uncoupling protein 1, UCP1) found in brown adipose tissue.

Glycolysis

A universal cytoplasmic pathway that metabolizes one molecule of glucose into two molecules of pyruvate (or lactate under anaerobic conditions). This process generates a net yield of 2 ATP molecules (via substrate-level phosphorylation) and 2 NADH molecules. Glycolysis is the initial step in glucose catabolism and can proceed under both anaerobic and aerobic conditions, making it an essential pathway in nearly all cells.

Glucose transporter (GLUT)

A family of 14 facilitative glucose transporters (GLUT-1 to GLUT-14) found in the plasma membrane of various cells. These proteins mediate the entry of glucose into cells by facilitated diffusion, moving glucose down its concentration gradient without directly consuming ATP.

GLUT4

An insulin-dependent glucose transporter primarily found in adipose tissue cells and muscle cells. In the basal state, GLUT4 is sequestered in intracellular vesicles. In response to insulin binding to its receptor (or muscle contraction), these vesicles translocate to the cell membrane, increasing the number of GLUT4 transporters on the surface and thereby enhancing glucose uptake into these tissues, lowering blood glucose levels.

Glucokinase (Hexokinase IV)

An isoform of hexokinase predominantly found in liver cells and the pancreatic \beta-cells. Unlike hexokinase I-III, glucokinase has a high Km (low affinity) for glucose and a high V{max} (high capacity). It is not inhibited by its product, glucose-6-phosphate. These properties allow it to act as a glucose sensor, effectively trapping glucose in the liver for storage (as glycogen or fat) when blood glucose levels are high, and regulating insulin release from pancreatic \beta-cells.

Hexokinase (I-III)

Enzymes that catalyze the phosphorylation of glucose to glucose-6-phosphate in most tissues throughout the body, serving as the first committed step in glycolysis. Hexokinase isoforms I-III have a low K_m (high affinity) for glucose, allowing them to efficiently phosphorylate glucose even at low concentrations. They are inhibited by their product, glucose-6-phosphate, providing feedback regulation.

Phosphofructokinase-1 (PFK-1)

The most important rate-limiting and key regulatory enzyme in glycolysis, catalyzing the irreversible phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate using ATP. PFK-1 activity is allosterically regulated: it is activated by AMP and fructose-2,6-bisphosphate (F2,6BP, its most potent activator) and inhibited by ATP and citrate (indicators of abundant energy or biosynthetic precursors).

Fructose-2,6-bisphosphate (F2,6BP)

A potent allosteric activator of Phosphofructokinase-1 (PFK-1), significantly increasing the rate of glycolysis. F2,6BP is synthesized by Phosphofructokinase-2 (PFK-2). Its levels rise in the liver in the fed state, particularly in response to insulin, thereby promoting glucose utilization.

Phosphofructokinase-2 (PFK-2)

A bifunctional enzyme (part of a complex) that synthesizes fructose-2,6-bisphosphate from fructose-6-phosphate and also degrades it. PFK-2 activity is hormonally regulated (e.g., by insulin and glucagon) to modulate the cellular levels of F2,6BP, which in turn controls the activity of PFK-1 and thus the overall flux through glycolysis.