Essential Biochemical Pathways

Why This Matters

Biochemical pathways aren't just isolated reactions to memorize—they're interconnected systems that reveal how cells manage energy, build molecules, and respond to changing conditions. In this course, you're being tested on your ability to trace carbon atoms through metabolism, explain why certain reactions are thermodynamically favorable, and predict how disrupting one pathway affects others. Understanding these pathways means understanding redox chemistry, enzyme regulation, thermodynamics, and coupled reactions in a biological context.

Don't just memorize the steps of glycolysis or the citric acid cycle. Instead, focus on why each pathway exists, what it produces, and how it connects to other metabolic routes. When you can explain why gluconeogenesis isn't simply glycolysis in reverse, or why fatty acid synthesis requires NADPH while beta-oxidation produces NADH, you've mastered the chemistry that drives these biological processes.

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Energy-Harvesting Pathways: Breaking Down Fuel

These pathways extract energy from nutrients by oxidizing carbon compounds, capturing electrons in carrier molecules (NADH, FADH₂), and ultimately generating ATP. The common thread is controlled oxidation—releasing energy in manageable steps rather than all at once.

Glycolysis

• Converts glucose ($C_6H_{12}O_6$) to two pyruvate molecules—net yield of 2 ATP and 2 NADH per glucose, making it the universal entry point for carbohydrate metabolism
• Occurs in the cytoplasm without oxygen—this anaerobic capability allows cells to generate ATP even when oxygen is limited (fermentation follows if oxygen remains unavailable)
• Regulated at three irreversible steps—hexokinase, phosphofructokinase (PFK), and pyruvate kinase control flux; PFK is the committed step and responds to ATP/AMP levels

Citric Acid Cycle (Krebs Cycle)

• Oxidizes acetyl-CoA ($C_2$) to $CO_2$ in the mitochondrial matrix—this is where carbon from all fuel sources (carbs, fats, proteins) is fully oxidized
• Produces 3 NADH, 1 $FADH_2$, and 1 GTP per turn—the real ATP payoff comes later when these electron carriers feed the ETC
• Regulated by substrate availability and product inhibition—high ATP and NADH slow the cycle; this is classic feedback inhibition in action

Electron Transport Chain and Oxidative Phosphorylation

• Creates a proton gradient across the inner mitochondrial membrane—electrons from NADH and $FADH_2$ flow through protein complexes, pumping $H^+$ into the intermembrane space
• ATP synthase couples proton flow to ATP synthesis—approximately 2.5 ATP per NADH and 1.5 ATP per $FADH_2$; this is chemiosmotic coupling in action
• Oxygen is the terminal electron acceptor—forms $H_2O$ and keeps the chain flowing; without $O_2$, electrons back up and ATP production halts

Beta-Oxidation of Fatty Acids

• Breaks fatty acids into acetyl-CoA units in the mitochondria—each 2-carbon unit enters the citric acid cycle, making fats extremely energy-dense
• Each cycle produces 1 FADH₂, 1 NADH, and 1 acetyl-CoA—a 16-carbon palmitate yields ~106 ATP after complete oxidation
• Regulated by fatty acid availability and cellular energy status—carnitine shuttle controls entry into mitochondria; high malonyl-CoA (from fed state) inhibits transport

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Biosynthetic Pathways: Building Molecules

While catabolic pathways break down molecules and release energy, anabolic pathways consume energy to build complex molecules. Notice the pattern: synthesis reactions typically require NADPH (not NADH) and occur in the cytoplasm.

Gluconeogenesis

• Synthesizes glucose from non-carbohydrate precursors—lactate, glycerol, and certain amino acids can all become glucose; primarily occurs in the liver
• Bypasses three irreversible glycolytic steps with different enzymes—pyruvate carboxylase and PEPCK are key; this is why gluconeogenesis costs 6 ATP equivalents while glycolysis yields only 2
• Essential for maintaining blood glucose during fasting—the brain requires ~120g glucose daily; without gluconeogenesis, blood sugar would plummet between meals

Fatty Acid Synthesis

• Builds fatty acids from acetyl-CoA in the cytoplasm—primarily produces palmitate (16:0); occurs when energy and carbon are abundant
• Requires NADPH as the reducing agent—this distinguishes it chemically from beta-oxidation, which produces NADH; the pentose phosphate pathway supplies most of this NADPH
• Fatty acid synthase is a multi-enzyme complex—adds 2-carbon units from malonyl-CoA; acetyl-CoA carboxylase (ACC) is the rate-limiting regulatory enzyme

Pentose Phosphate Pathway

• Generates NADPH and ribose-5-phosphate parallel to glycolysis—branches off at glucose-6-phosphate; the cell's main source of cytoplasmic reducing power
• Oxidative phase produces NADPH; non-oxidative phase interconverts sugars—the balance depends on cellular needs for NADPH versus ribose-5-phosphate
• Critical for antioxidant defense and nucleotide synthesis—NADPH regenerates glutathione; ribose-5-phosphate is essential for DNA/RNA synthesis

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Nitrogen-Handling Pathways: Managing Amino Groups

Nitrogen metabolism presents unique challenges because ammonia ($NH_3$) is toxic. These pathways manage the amino groups from protein breakdown and enable amino acid interconversion.

Amino Acid Metabolism

• Transamination transfers amino groups between molecules—aminotransferases (using PLP cofactor) allow interconversion of amino acids without releasing free ammonia
• Deamination releases ammonia for disposal—glutamate dehydrogenase is key; the resulting $NH_4^+$ must be converted to urea
• Carbon skeletons enter central metabolism at various points—glucogenic amino acids yield pyruvate or citric acid cycle intermediates; ketogenic amino acids yield acetyl-CoA

Urea Cycle

• Converts toxic ammonia to urea for excretion—occurs in liver; urea is water-soluble and much less toxic than ammonia
• Requires 4 ATP equivalents per urea molecule—carbamoyl phosphate synthetase I is the rate-limiting enzyme; this is an energy-expensive but essential detoxification
• Links to the citric acid cycle via fumarate—the "bicycle" connection allows efficient coordination between nitrogen disposal and energy metabolism

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Photosynthesis: Capturing Light Energy

While most of your course focuses on heterotrophic metabolism, understanding photosynthesis reveals the ultimate source of the reduced carbon compounds that fuel all other pathways.

Photosynthesis (Light and Dark Reactions)

• Light reactions in thylakoid membranes convert solar energy to ATP and NADPH—water is split, releasing $O_2$; electron flow through photosystems drives chemiosmosis (similar to mitochondrial ETC, but in reverse direction)
• Calvin cycle in stroma fixes $CO_2$ into glucose—RuBisCO catalyzes the key carbon-fixing step; uses ATP and NADPH from light reactions
• Represents the reverse of cellular respiration in terms of overall chemistry—$6CO_2 + 6H_2O \rightarrow C_6H_{12}O_6 + 6O_2$ is endergonic and requires light energy input

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Quick Reference Table

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Self-Check Questions

1. Which two pathways both produce acetyl-CoA, and where does each occur within the cell?

2. Explain why fatty acid synthesis requires NADPH while beta-oxidation produces NADH—what does this tell you about the chemistry of each process?

3. Compare glycolysis and gluconeogenesis: why can't gluconeogenesis simply run glycolysis in reverse, and which enzymes differ between them?

4. If the electron transport chain is inhibited, how would this affect the citric acid cycle, and why? Trace the connection through electron carriers.

5. A patient has a deficiency in carbamoyl phosphate synthetase I. Which pathway is affected, what toxic compound would accumulate, and what symptoms might result?