Metabolism & Cellular Respiration – Comprehensive Study Notes

Learning Outcome Topics

• Identify and describe the sequential pathways that convert food energy into ATP:
  • Glycolysis: enzymatic splitting of sugar, ATP & NADH production.
  • Conversion of Pyruvate → Acetyl-CoA in the mitochondrial matrix.
  • Citric Acid (TCA) Cycle: oxidation of acetyl groups → CO_2 & generation of reduced electron carriers.
  • Electron-Transport Chain (ETC) & Oxidative Phosphorylation: majority of ATP synthesis, driven by proton gradient.
  • Fermentation: ATP production & NAD^+ regeneration in the absence of O_2.
• Recognize that many biosynthetic pathways branch from glycolytic or TCA intermediates.

Overview of Cellular Respiration

• Cellular respiration = controlled extraction of energy from food to synthesize ATP.
• Global reaction: \mathrm{C6H{12}O6 + 6\,O2 \rightarrow 6\,CO2 + 6\,H2O + \sim 36\,ATP} (eukaryotic average).
• Key principle: energy transfer occurs as incremental electron transfers, not as one explosive release (contrast with burning sugar).

Redox Reactions & Electron Carriers

• Redox definition: chemical reactions involving electron transfer.
  • "LEO GER": Lose Electrons = Oxidized, Gain Electrons = Reduced.
  • Example schematic: \mathrm{AH + X^+ \rightarrow A^+ + XH} where AH = reducing agent (donor), X^+ = oxidizing agent (acceptor).
• Electron carriers shuttle electrons between metabolic steps:
  • Nicotinamide adenine dinucleotide: \mathrm{NAD^+ \rightleftharpoons NADH + H^+} (carries 2 e^- & 1 H^+)
  • Flavin adenine dinucleotide: \mathrm{FAD \rightleftharpoons FADH_2}
  • Photosynthetic carrier: \mathrm{NADPH} (mentioned as analogous system).

ATP in Living Systems

• ATP formation: endergonic phosphorylation of ADP: \mathrm{ADP + P_i \rightarrow ATP}.
• Two mechanisms supply required energy:
  1. Substrate-level phosphorylation (SLP) – coupling to an exergonic reaction inside glycolysis/TCA.
  2. Chemiosmosis – proton-motive force drives ATP synthase (≈ 90 % of cellular ATP).
• Locations of chemiosmotic ATP synthesis: inner mitochondrial membrane, thylakoid membrane, & aerobic prokaryote plasma membrane.

Three Stages of Respiration

1. Glycolysis – cytosolic, anaerobic compatible.
2. Oxidation of Pyruvate & TCA Cycle – mitochondrial matrix (eukaryotes).
3. Oxidative Phosphorylation – ETC creates H^+ gradient; ATP synthase converts gradient energy → ATP.

Glycolysis (Detailed)

Global Features

• Universally conserved 10-reaction pathway in cytosol.
• Inputs per glucose: 1 Glucose, 2 NAD^+, 2 ATP (investment), 4 ADP + 4 P_i.
• Outputs: 2 Pyruvate, 2 NADH, 4 ATP (gross), 2 ADP.
• Net ATP gain: 2 ATP.
• Oxygen not required.

Phase 1 – Energy Investment (Reactions 1-5)

Phase 2 – Energy Payoff (Reactions 6-10, occurs twice per glucose)

Net Reaction

\mathrm{Glucose + 2\,NAD^+ + 2\,ADP + 2\,Pi \rightarrow 2\,Pyruvate + 2\,NADH + 2\,ATP + 2\,H2O + 2\,H^+}

Oxidation of Pyruvate (Link Reaction)

• Location: mitochondrial matrix (eukaryotes).
• Enzyme complex: Pyruvate dehydrogenase (PDH); multienzyme, highly regulated.
• Reaction (per pyruvate):
  \mathrm{Pyruvate + CoA + NAD^+ \rightarrow Acetyl\hyp CoA + CO_2 + NADH + H^+}
• Two pyruvates per glucose → 2 CO_2 and 2 NADH before TCA entry.

Tricarboxylic Acid (Citric Acid, Krebs) Cycle

General Properties

• Cyclic pathway in mitochondrial matrix; requires acetyl-CoA.
• Runs continuously if substrates & oxidized carriers (NAD^+/FAD) are available.
• Each "turn" (per acetyl-CoA) yields:
  • 3 NADH
  • 1 FADH$_2$
  • 1 GTP (≅ ATP by nucleoside diphosphate kinase)
  • 2 CO$_2$
• Oxaloacetate regenerated → cycle ready for another acetyl-CoA.

Stepwise Highlights

1. Citrate synthase: Acetyl-CoA + oxaloacetate → citrate; CoA released.
2. Aconitase: Citrate ⇄ cis-aconitate ⇄ isocitrate (isomerization).
3. Isocitrate dehydrogenase: Oxidation → \alpha-ketoglutarate + CO_2 + NADH.
4. \alpha-Ketoglutarate dehydrogenase: Similar to PDH; yields succinyl-CoA, CO_2, NADH.
5. Succinyl-CoA synthetase: Substrate-level phosphorylation → succinate + GTP.
6. Succinate dehydrogenase (Complex II of ETC): Succinate → fumarate + FADH$_2$.
7. Fumarase: Fumarate + H_2O → malate.
8. Malate dehydrogenase: Malate → oxaloacetate + NADH.

Additional Notes

• Fatty acid β-oxidation & some amino acids generate acetyl-CoA → feed into cycle.
• Intermediates serve as precursors for anabolic pathways (glutamate, heme, fatty acids, etc.).

Electron Transport Chain (ETC) & Oxidative Phosphorylation

Architecture

• Located in the inner mitochondrial membrane; organized into 3 large enzyme complexes + 2 mobile carriers.
  1. Complex I (NADH dehydrogenase)
  2. Complex II (succinate dehydrogenase – FADH$_2$ input, no proton pump)
  3. Ubiquinone (Q) – lipid-mobile.
  4. Complex III (cytochrome bc$_1$)
  5. Cytochrome c – soluble peripheral protein.
  6. Complex IV (cytochrome c oxidase) – reduces O2 → H2O.

Proton Motive Force (PMF)

• Electron flow is coupled to pumping H^+ from matrix → inter-membrane space.
• PMF components:
  • Electrical: membrane potential \Delta V (matrix negative).
  • Chemical: \Delta pH (matrix alkaline).
• ETC converts redox energy of NADH/FADH$_2$ → electrochemical gradient.

ATP Synthase (Complex V)

• Multisubunit rotary engine; Fo (membrane) & F$_1$ (matrix) sectors.
• Uses H^+ flow down gradient to synthesize ATP: \mathrm{ADP + Pi + n\,H^+{intermembrane} \rightarrow ATP + n\,H^+_{matrix}}.
• ~90 % of cell’s ATP produced via this chemiosmotic mechanism.

Metabolism Without Oxygen – Fermentation

• Problem: NAD^+ consumed in glycolytic step 6 must be regenerated; ETC requires O_2.
• Solution: Fermentation pathways oxidize NADH → NAD^+ while reducing pyruvate or its derivative.

Lactic Acid Fermentation (e.g., muscle cells under hypoxia)

\mathrm{Pyruvate + NADH \rightarrow Lactate + NAD^+}

• Allows glycolysis to persist; yields only 2 ATP per glucose (glycolytic net).

Alcohol (Ethanolic) Fermentation (yeast, some bacteria)

Two-step sequence:

1. \mathrm{Pyruvate \rightarrow Acetaldehyde + CO_2} (pyruvate decarboxylase).
2. \mathrm{Acetaldehyde + NADH \rightarrow Ethanol + NAD^+} (alcohol dehydrogenase).

Integration of Metabolism

• Catabolism of carbohydrates, lipids, proteins converges on glycolysis or TCA intermediates.
  • Example: β-oxidation of fatty acids → acetyl-CoA.
  • Amino acid deamination → pyruvate, \alpha-ketoglutarate, succinyl-CoA, etc.
• Anabolism draws from the same pools ⇒ TCA & glycolysis are hubs for biosynthesis.

Ethical, Philosophical & Practical Connections

• Understanding cellular energy flow underpins medical interventions for metabolic disorders (e.g., diabetes, mitochondrial diseases).
• Controlled fermentation exploited in food/beverage industries; also raises considerations about biofuel production.
• Knowledge of ETC pivotal for antibiotic & pesticide development targeting unique respiratory components.
• Illustrates evolutionary conservation of core metabolic pathways across life domains, reinforcing the unity of biology.