Citric acid cycle Study Guide

📖 Core Concepts Citric Acid (Krebs) Cycle – A series of eight enzyme‑catalyzed reactions that completely oxidize the two‑carbon acetyl‑CoA derived from carbs, fats, or proteins to CO₂, while harvesting energy. Cellular location – Mitochondrial matrix in eukaryotes; cytosol in prokaryotes (ATP synthase uses the plasma‑membrane gradient). Energy carriers produced – 3 NADH, 1 FADH₂, and 1 GTP (or ATP) per acetyl‑CoA; these feed oxidative phosphorylation. Anaplerosis vs. Cataplerosis – Reactions that replenish (e.g., pyruvate → oxaloacetate) or withdraw (e.g., citrate → fatty‑acid synthesis) cycle intermediates. Allosteric regulation – NADH, ATP, acetyl‑CoA, and succinyl‑CoA inhibit key enzymes; Ca²⁺ activates PDH phosphatase, isocitrate dehydrogenase, and α‑ketoglutarate dehydrogenase. 📌 Must Remember Overall per‑acetyl‑CoA reaction \[ \text{Acetyl‑CoA} + 3\text{NAD}^+ + \text{FAD} + \text{GDP (or ADP)} + \text{P}i + 2\text{H}2\text{O} \rightarrow 2\text{CO}2 + 3\text{NADH} + \text{FADH}2 + \text{GTP (or ATP)} + \text{CoA‑SH} \] Products per glucose (2 cycles) 6 NADH, 2 FADH₂, 2 GTP/ATP, 4 CO₂. ATP yield (theoretical) – 38 ATP/glucose (3 ATP per NADH, 2 ATP per FADH₂). Practical yield – 30 ATP/glucose after accounting for shuttle costs, proton leak, and ATP‑synthase efficiency. Key regulatory effectors – NADH & ATP (inhibit), Ca²⁺ (activate), citrate (inhibits PFK‑1). Isoforms – Succinate‑CoA ligase: ADP‑forming (most organisms) vs. GDP‑forming (mammalian tissue‑specific). Enzyme specificity – Isocitrate dehydrogenase: NAD⁺‑dependent in eukaryotes, NADP⁺‑dependent in many prokaryotes; Malate dehydrogenase: NAD⁺ in eukaryotes, quinone‑dependent in most prokaryotes. 🔄 Key Processes Acetyl‑CoA formation – Pyruvate dehydrogenase: \[ \text{Pyruvate} + \text{CoA‑SH} + \text{NAD}^+ \rightarrow \text{Acetyl‑CoA} + \text{NADH} + \text{CO}2 \] Citrate synthase – Acetyl‑CoA + oxaloacetate → citrate. Aconitase – Citrate ⇌ isocitrate (dehydration‑rehydration). Isocitrate dehydrogenase – Isocitrate → α‑ketoglutarate + NADH + CO₂. α‑Ketoglutarate dehydrogenase – α‑KG → succinyl‑CoA + NADH + CO₂. Succinyl‑CoA ligase – Succinyl‑CoA → succinate + GTP/ATP. Succinate dehydrogenase – Succinate → fumarate + FADH₂. Fumarase – Fumarate + H₂O → malate. Malate dehydrogenase – Malate → oxaloacetate + NADH (cycle restarts). 🔍 Key Comparisons NAD⁺‑dependent vs. NADP⁺‑dependent isocitrate dehydrogenase NAD⁺‑dependent: eukaryotes, links to oxidative phosphorylation. NADP⁺‑dependent: many prokaryotes, supplies NADPH for biosynthesis. ADP‑forming vs. GDP‑forming succinate‑CoA ligase ADP‑forming: most organisms → direct ATP generation. GDP‑forming: mammals, provides GTP for gluconeogenesis & protein synthesis. Mitochondrial vs. cytosolic location Eukaryotes: matrix, coupled to inner‑membrane proton gradient. Prokaryotes: cytosol, gradient across plasma membrane. ⚠️ Common Misunderstandings “The cycle makes ATP directly.” – Only one GTP/ATP is synthesized directly; the bulk of ATP comes from NADH/FADH₂ oxidation in the electron‑transport chain. “Each turn yields 3 ATP.” – The 3‑ATP number is the theoretical yield from NADH; actual ATP per turn is lower after shuttles and leak. “All organisms use the same isocitrate dehydrogenase.” – Prokaryotes often use an NADP⁺‑dependent isozyme, changing the redox balance. “Citrate only stays in mitochondria.” – Citrate can be exported for fatty‑acid and cholesterol synthesis. 🧠 Mental Models / Intuition “Fuel‑to‑Fire” model – Acetyl‑CoA is the “fuel” (2‑C); each step is a “spark” that strips away electrons (NADH/FADH₂) and carbon (CO₂), ultimately lighting the “fire” of oxidative phosphorylation. “Bucket‑refill” analogy – Oxaloacetate is the bucket; each turn adds acetyl‑CoA (water) and removes two CO₂ (spill), ending with the bucket ready for the next fill. 🚩 Exceptions & Edge Cases Shuttle variability – Glycerol‑phosphate shuttle consumes 2 ATP, reducing net yield to 36 ATP/glucose; malate‑aspartate shuttle is more efficient. Proton leak & ATP‑synthase slippage – Real cells often produce 30 ATP/glucose. Isoform tissue specificity – Liver and heart may favor GDP‑forming succinate‑CoA ligase for GTP‑dependent pathways. 📍 When to Use Which Choosing NAD⁺ vs. NADP⁺ isocitrate dehydrogenase – Consider organism type (eukaryote vs. prokaryote) and cellular need for NADPH (biosynthesis). Selecting succinate‑CoA ligase isoform – ADP‑forming when direct ATP is required; GDP‑forming when GTP‑dependent biosynthetic steps (e.g., gluconeogenesis) dominate. Evaluating ATP yield calculations – Use 3 ATP/NADH and 2 ATP/FADH₂ for theoretical maximum (38 ATP); adjust downwards for shuttle costs and measured proton‑to‑ATP ratios (30 ATP). 👀 Patterns to Recognize CO₂ release points – Always after decarboxylating dehydrogenase steps (isocitrate DH and α‑KG DH). NAD⁺/FAD reduction steps – Appear immediately after carbon‑carbon bond cleavage (three NADH, one FADH₂ per turn). Regulatory hot spots – Enzymes that bind NADH, ATP, or acetyl‑CoA are common inhibition points (PDH, isocitrate DH, α‑KG DH, citrate synthase). 🗂️ Exam Traps “Every turn makes 1 ATP.” – Only GTP/ATP is made directly; NADH/FADH₂ must be converted via ETC. Confusing NADH vs. NADPH yields – Only NADH from the cycle contributes to ATP; NADPH (if produced by NADP⁺‑dependent enzymes) is used for biosynthesis, not ATP. Assuming mitochondrial and cytosolic cycles are identical – Prokaryotes lack a separate mitochondrial matrix; the same reactions occur in the cytosol, and the proton gradient is across the plasma membrane. Counting six CO₂ per glucose incorrectly – Two cycles (one per pyruvate) release four CO₂, not six; the other two carbons leave as water‑derived hydrogen in NADH/FADH₂. Misidentifying the rate‑limiting step – Often isocitrate dehydrogenase (NAD⁺‑dependent) in eukaryotes; remembering this helps pick the correct answer when asked about control points.