Major Metabolic Pathways

Why This Matters

Understanding metabolic pathways is about seeing how cells orchestrate a complex energy economy. These pathways answer fundamental questions you'll encounter throughout General Biology II: How do cells extract energy from food? Why can the brain use ketones but not fatty acids directly? What happens metabolically during fasting versus the fed state?

You're being tested on your ability to connect pathway function to regulation and cellular context. Exams will ask you to predict what happens when a pathway is blocked, why certain tissues prefer specific fuels, and how pathways interconnect under different conditions. Don't just memorize the steps. Know where each pathway occurs, what regulates it, and why it matters.

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Energy-Producing Pathways: Breaking Down Fuel

These pathways extract energy from macronutrients by systematically oxidizing carbon bonds. The key principle: electrons are harvested from fuel molecules and ultimately transferred to oxygen, with the energy released captured as ATP.

Glycolysis

• Glucose → 2 pyruvate in the cytoplasm of all cells, producing a net gain of 2 ATP and 2 NADH per glucose molecule
• Anaerobic capability: doesn't require oxygen, making it essential for red blood cells (which lack mitochondria) and for muscle during intense exercise
• Rate-limiting enzyme: phosphofructokinase-1 (PFK-1), inhibited by ATP and citrate, activated by AMP and fructose-2,6-bisphosphate

Citric Acid Cycle (Krebs Cycle)

• Acetyl-CoA oxidation hub located in the mitochondrial matrix, producing 3 NADH, 1 $FADH_2$, and 1 GTP per turn
• Central metabolic crossroads: accepts carbon skeletons from carbohydrates, fats, and proteins for complete oxidation
• Regulated by energy charge: isocitrate dehydrogenase and $\alpha$-ketoglutarate dehydrogenase are inhibited by NADH and ATP

Electron Transport Chain and Oxidative Phosphorylation

The ETC is where the bulk of ATP gets made. NADH and $FADH_2$ from earlier pathways donate electrons to a series of protein complexes (I through IV) embedded in the inner mitochondrial membrane. As electrons pass along the chain, protons ($H^+$) are pumped into the intermembrane space, creating an electrochemical gradient.

• ATP yield: approximately 30–32 ATP per glucose via this proton gradient
• $O_2$ is the final electron acceptor, which is why you need to breathe. Without oxygen, the chain backs up, NADH can't be reoxidized, and ATP production halts.
• ATP synthase (Complex V) lets protons flow back down their gradient, using that energy to phosphorylate ADP → ATP. This coupling of the proton gradient to ATP synthesis is called chemiosmosis.

Fatty Acid Oxidation (Beta-oxidation)

• Mitochondrial pathway that breaks fatty acids into 2-carbon acetyl-CoA units; each cycle produces 1 NADH, 1 $FADH_2$, and 1 acetyl-CoA
• High ATP yield: a 16-carbon palmitate generates approximately 106 ATP (after accounting for the 2 ATP activation cost), making fat the most energy-dense fuel
• Carnitine shuttle required: long-chain fatty acids need carnitine palmitoyltransferase I (CPT-I) to cross the inner mitochondrial membrane, a key regulatory point inhibited by malonyl-CoA (the product of fatty acid synthesis, which prevents simultaneous synthesis and breakdown)

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Glucose Homeostasis Pathways: Maintaining Blood Sugar

These pathways keep blood glucose within a narrow range regardless of feeding state. The liver acts as the glucose thermostat, storing excess glucose after meals and releasing it during fasting.

Gluconeogenesis

• Makes glucose from non-carbohydrate sources: lactate, glycerol, and glucogenic amino acids are converted to glucose primarily in the liver (and to a lesser extent, the kidneys)
• Bypasses three irreversible glycolytic steps using key enzymes: pyruvate carboxylase, PEPCK, fructose-1,6-bisphosphatase, and glucose-6-phosphatase
• Fasting survival mechanism: maintains blood glucose for glucose-dependent tissues (brain, RBCs) when dietary carbohydrate is unavailable

Glycogenesis and Glycogenolysis

• Glycogenesis stores glucose as glycogen, activated by insulin in the fed state. The liver holds ~100g and muscle holds ~400g of glycogen.
• Glycogenolysis releases glucose from glycogen. Glucagon (liver) and epinephrine (liver and muscle) activate glycogen phosphorylase to mobilize stored glucose.
• Tissue-specific function: liver glycogen maintains blood glucose; muscle glycogen fuels local contraction only, because muscle lacks glucose-6-phosphatase and therefore can't export free glucose into the blood.

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Alternative Fuel Pathways: Adapting to Metabolic Stress

When glucose is scarce or energy demands shift, these pathways provide alternative fuels and metabolic flexibility. Nutritional state dramatically influences which pathways dominate.

Ketogenesis

• Produces ketone bodies from excess acetyl-CoA in liver mitochondria when acetyl-CoA accumulates faster than the citric acid cycle can use it (typically because oxaloacetate is being diverted to gluconeogenesis)
• Three ketone bodies: acetoacetate, $\beta$-hydroxybutyrate, and acetone. The first two serve as fuel for other tissues; acetone is exhaled (the fruity breath in diabetic ketoacidosis).
• Brain's alternative fuel: unlike fatty acids, ketones cross the blood-brain barrier, providing up to 70% of brain energy during prolonged fasting

Pentose Phosphate Pathway

• Runs parallel to glycolysis in the cytoplasm, generating NADPH for biosynthesis and antioxidant defense, plus ribose-5-phosphate for nucleotide synthesis
• Two phases: the oxidative phase produces NADPH; the non-oxidative phase interconverts sugars based on cellular needs
• Critical for RBC protection: NADPH keeps glutathione in its reduced form, which neutralizes reactive oxygen species. G6PD deficiency (the rate-limiting enzyme of the oxidative phase) leaves RBCs vulnerable to oxidative damage, causing hemolytic anemia.

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Biosynthetic Pathways: Building Cellular Components

These anabolic pathways use energy and precursors to synthesize molecules the body needs. They're typically active in the fed state when energy and substrates are abundant.

Fatty Acid Synthesis

• Cytoplasmic pathway that converts acetyl-CoA into fatty acids using NADPH (supplied largely by the pentose phosphate pathway)
• Key enzyme: acetyl-CoA carboxylase (ACC) produces malonyl-CoA, the committed step. ACC is activated by insulin and inhibited by glucagon and AMPK.
• Fatty acid synthase complex adds 2-carbon units to the growing chain, primarily producing palmitate (16:0) as the end product

Cholesterol Biosynthesis

• Multi-step pathway in liver cytoplasm and ER: acetyl-CoA → mevalonate → squalene → cholesterol
• Rate-limiting enzyme: HMG-CoA reductase, the target of statin drugs. It's inhibited by cholesterol itself (feedback inhibition) and by glucagon.
• Essential functions: maintains cell membrane fluidity, and serves as the precursor for bile acids, vitamin D, and steroid hormones

Purine and Pyrimidine Metabolism

• De novo synthesis vs. salvage pathways: cells can build nucleotides from scratch or recycle bases from nucleic acid breakdown
• Purines (adenine, guanine) are degraded to uric acid in humans; elevated levels cause gout
• Pyrimidines (cytosine, thymine, uracil) are degraded to $CO_2$, $NH_3$, and water, which is less clinically problematic than purine accumulation

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Nitrogen Handling Pathways: Processing Protein

Amino acid metabolism generates toxic ammonia that must be safely eliminated. The urea cycle is the liver's solution to this nitrogen disposal problem.

Urea Cycle

• Converts toxic ammonia to urea across two compartments: it begins in the mitochondrial matrix and continues in the cytoplasm of liver cells. Urea is water-soluble and excreted by the kidneys.
• Rate-limiting enzyme: carbamoyl phosphate synthetase I (CPS I), activated by N-acetylglutamate. Arginase catalyzes the final step, releasing urea from arginine.
• Links to the citric acid cycle: fumarate produced in the urea cycle feeds into the TCA cycle, connecting the two pathways (sometimes called the "bicycle" concept).

Amino Acid Metabolism

• Transamination transfers amino groups between molecules. Aminotransferases (ALT, AST) shuffle nitrogen between amino acids and $\alpha$-keto acids. Clinically, elevated ALT and AST in blood indicate liver damage.
• Oxidative deamination removes amino groups as free ammonia for urea synthesis. Glutamate dehydrogenase is the key enzyme here.
• Metabolic fates vary: amino acids are classified as glucogenic (carbon skeletons → glucose), ketogenic (carbon skeletons → ketones/acetyl-CoA), or both. Only leucine and lysine are purely ketogenic.

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Plant-Based Energy Capture: Photosynthesis

While not a human metabolic pathway, photosynthesis is the ultimate source of the chemical energy in our food. Understanding it completes the picture of biological energy flow.

Photosynthesis (Light Reactions and Calvin Cycle)

• Light reactions occur in the thylakoid membranes. They capture solar energy to produce ATP and NADPH, while splitting water to release $O_2$ as a byproduct. The two photosystems work in series: light hits Photosystem II first, then Photosystem I.
• Calvin Cycle (light-independent reactions) occurs in the chloroplast stroma. It uses the ATP and NADPH from the light reactions to fix $CO_2$ into G3P, which is then used to build glucose.
• Foundation of food chains: virtually all dietary carbohydrates, fats, and proteins trace back to photosynthetic carbon fixation

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Quick Reference Table

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Self-Check Questions

1. Which two pathways both produce acetyl-CoA, and how do their contributions differ during fasting versus the fed state?

2. A patient has a deficiency in carnitine palmitoyltransferase I (CPT-I). Which pathway is directly impaired, and what compensatory pathway would you expect to be upregulated?

3. Compare and contrast gluconeogenesis and glycogenolysis: When does each predominate, and why can muscle glycogenolysis not directly contribute to blood glucose?

4. If a question asks you to explain how the body maintains brain function during a 48-hour fast, which three pathways would you discuss and in what sequence?

5. Both fatty acid synthesis and cholesterol biosynthesis require NADPH. Which pathway supplies this NADPH, and what other critical function does this pathway serve?