Library Core Topics
Foundational Science Series

Core Topics: Biochemistry Pathways

High-yield reference for carbohydrate metabolism, energy production, and metabolic regulation — mapped to USMLE Step 1/2 CK foundational science objectives.

How to Use This Resource

Each pathway section includes: Core Concepts (location, net reaction), Key Enzymes (regulatory steps), and High-Yield Facts (clinical correlations, deficiencies). Use for active recall, spaced repetition, and integration with clinical cases.

Glycolysis

Cytoplasmic glucose breakdown to pyruvate with ATP production

Location & Net Reaction
  • Location: Cytoplasm (all cells)
  • Net Reaction: Glucose + 2 NAD⁺ + 2 ADP + 2 Pi → 2 Pyruvate + 2 NADH + 2 ATP + 2 H₂O + 2 H⁺
  • Energy Yield: 2 ATP (net), 2 NADH per glucose
  • Aerobic: Pyruvate → acetyl-CoA → TCA cycle
  • Anaerobic: Pyruvate → lactate (regenerates NAD⁺)
Key Regulatory Enzymes
Hexokinase/Glucokinase
Step 1: Glucose → G6P; irreversible
PFK-1
Step 3: F6P → F1,6BP; rate-limiting
Pyruvate Kinase
Step 10: PEP → pyruvate; irreversible
Pyruvate Fate & Cori Cycle
  • Aerobic: Pyruvate → acetyl-CoA (pyruvate dehydrogenase) → TCA cycle
  • Anaerobic: Pyruvate → lactate (LDH); regenerates NAD⁺ for continued glycolysis
  • Lactate Dehydrogenase (LDH): Pyruvate + NADH ↔ Lactate + NAD⁺
  • Cori Cycle: Lactate (muscle/RBC) → blood → liver → gluconeogenesis → glucose → blood → muscle
  • Substrate-level phosphorylation: Steps 7 (PGK) and 10 (pyruvate kinase)
High-Yield: Glycolysis
Rate-Limiting Step
PFK-1 is the key regulatory enzyme; activated by AMP, F2,6BP; inhibited by ATP, citrate
Hexokinase vs Glucokinase
Hexokinase: all tissues, low Km, inhibited by G6P; Glucokinase: liver/pancreas, high Km, not inhibited
Anaerobic Glycolysis
RBCs rely exclusively on anaerobic glycolysis (no mitochondria); lactate production prevents NAD⁺ depletion
Clinical Correlation
Pyruvate kinase deficiency → hemolytic anemia; PFK-1 deficiency (Tarui disease) → exercise intolerance

Gluconeogenesis

De novo glucose synthesis from non-carbohydrate precursors

Location & Substrates
  • Location: Liver (primarily), kidney cortex, intestinal epithelium
  • Substrates: Lactate (Cori cycle), amino acids (all except Leu, Lys), glycerol (from triglycerides), propionyl-CoA (odd-chain FA)
  • Energy Cost: 6 ATP equivalents per glucose (vs 2 ATP produced in glycolysis)
  • Physiologic Role: Maintains blood glucose during fasting (4+ hours)
4 Unique Bypass Enzymes
1
Pyruvate Carboxylase
Pyruvate → oxaloacetate (mitochondria; requires biotin, ATP)
2
PEPCK
Oxaloacetate → PEP (requires GTP)
3
Fructose-1,6-Bisphosphatase
F1,6BP → F6P (rate-limiting step)
4
Glucose-6-Phosphatase
G6P → glucose (ER lumen; liver/kidney only)
Regulation
  • Reciprocal to glycolysis: When one pathway is active, the other is inhibited
  • Fructose-2,6-bisphosphate: Activates PFK-1 (glycolysis); inhibits F1,6BPase (gluconeogenesis)
  • Hormonal control: Glucagon ↑ cAMP → ↓ F2,6BP → favors gluconeogenesis; Insulin has opposite effect
  • Allosteric: Acetyl-CoA activates pyruvate carboxylase; AMP inhibits F1,6BPase
  • Substrate availability: Alanine (from muscle) is major gluconeogenic amino acid
High-Yield: Gluconeogenesis
Key Mnemonic
"Pathway Produces Fresh Glucose" = Pyruvate carboxylase, PEPCK, Fructose-1,6-BPase, Glucose-6-Pase
Tissue Specificity
Glucose-6-phosphatase only in liver/kidney → muscle cannot release free glucose (trapped as G6P)
Fasting States
0-4h: glycogenolysis; 4-16h: gluconeogenesis + glycogenolysis; 16h+: gluconeogenesis + ketogenesis
Clinical Correlation
Von Gierke disease (G6Pase deficiency) → severe fasting hypoglycemia, lactic acidosis, hepatomegaly

TCA Cycle (Krebs Cycle)

Mitochondrial oxidation of acetyl-CoA to CO₂ with NADH/FADH₂ production

Location & Net Reaction
  • Location: Mitochondrial matrix (all cells with mitochondria)
  • Net Reaction (per acetyl-CoA): Acetyl-CoA + 3 NAD⁺ + FAD + GDP + Pi + 2 H₂O → 2 CO₂ + 3 NADH + FADH₂ + GTP + 2 H⁺ + CoA
  • Per Glucose: 6 NADH, 2 FADH₂, 2 GTP (→ ATP), 4 CO₂
  • Amphibolic: Both catabolic (energy production) and anabolic (biosynthetic precursors)
Key Enzymes
Citrate Synthase
Acetyl-CoA + OAA → citrate; irreversible
Isocitrate Dehydrogenase
Isocitrate → α-KG; rate-limiting; produces NADH + CO₂
α-KG Dehydrogenase
α-KG → succinyl-CoA; produces NADH + CO₂
Succinate Dehydrogenase
Succinate → fumarate; produces FADH₂; Complex II of ETC
Regulation & Anaplerosis
  • Energy status: ATP/ADP ratio, NADH/NAD⁺ ratio (high energy → inhibition)
  • Calcium: Activates isocitrate DH, α-KG DH, pyruvate DH (muscle contraction signal)
  • Substrate availability: Acetyl-CoA, OAA levels
  • Anaplerotic reactions: Replenish cycle intermediates (e.g., pyruvate → OAA via pyruvate carboxylase)
  • Cataplerotic reactions: Remove intermediates for biosynthesis (e.g., OAA → glucose, citrate → fatty acids)
High-Yield: TCA Cycle
Rate-Limiting Enzyme
Isocitrate dehydrogenase is the primary regulatory step; activated by ADP, inhibited by ATP, NADH
Unique Enzyme
Succinate dehydrogenase is the only TCA enzyme embedded in inner mitochondrial membrane (Complex II)
Vitamin Cofactors
B1 (TPP), B2 (FAD), B3 (NAD), B5 (CoA), B7 (biotin for pyruvate carboxylase)
Clinical Correlation
Fumarase deficiency → encephalopathy; α-KG DH autoantibodies → primary biliary cholangitis

Oxidative Phosphorylation

Electron transport chain and ATP synthesis via chemiosmotic coupling

Location & ETC Complexes
  • Location: Inner mitochondrial membrane
  • Complex I (NADH dehydrogenase): NADH → CoQ; pumps 4 H⁺
  • Complex II (Succinate DH): FADH₂ → CoQ; pumps 0 H⁺ (from TCA cycle)
  • Complex III (Cytochrome bc1): CoQ → cytochrome c; pumps 4 H⁺
  • Complex IV (Cytochrome c oxidase): Cytochrome c → O₂; pumps 2 H⁺; O₂ is final electron acceptor
  • Complex V (ATP synthase): H⁺ gradient drives ATP synthesis from ADP + Pi
ATP Yield & P/O Ratio
  • Chemiosmotic coupling: Proton gradient (ΔpH + ΔΨ) drives ATP synthase rotation
  • P/O Ratio: ~2.5 ATP per NADH (10 H⁺ pumped / 4 H⁺ per ATP); ~1.5 ATP per FADH₂ (6 H⁺ pumped)
  • Total per Glucose: ~30-32 ATP (glycolysis + TCA + ETC; varies by shuttle system)
  • Proton leak: Some H⁺ bypass ATP synthase → heat production (thermogenesis)
Inhibitors & Uncouplers
AgentTargetEffect
RotenoneComplex IBlocks NADH → CoQ
Antimycin AComplex IIIBlocks CoQ → cyt c
Cyanide, CO, AzideComplex IVBlocks O₂ reduction → death
OligomycinATP SynthaseBlocks H⁺ channel → no ATP
DNP, ThermogeninInner membraneUncouples → heat, no ATP
High-Yield: Oxidative Phosphorylation
Final Electron Acceptor
Oxygen at Complex IV → H₂O; without O₂, ETC stops → no ATP → cell death
Uncouplers
DNP (2,4-dinitrophenol), thermogenin (UCP-1) in brown fat → proton leak → heat instead of ATP
Cyanide Poisoning
Binds Complex IV (cytochrome a3) → blocks O₂ use → histotoxic hypoxia; treat with nitrites + thiosulfate
Mitochondrial Diseases
Maternal inheritance; affect high-energy tissues (muscle, brain); lactic acidosis common

Pentose Phosphate Pathway

NADPH production and ribose synthesis for biosynthesis and antioxidant defense

Location & Phases
  • Location: Cytoplasm (all cells; high in liver, adipose, adrenal cortex, RBCs)
  • Oxidative Phase (irreversible): G6P → ribulose-5-P + 2 NADPH + CO₂
  • Non-Oxidative Phase (reversible): Sugar interconversions (ribose-5-P ↔ glycolytic intermediates)
  • No ATP produced or consumed — pathway serves biosynthetic needs
Key Enzyme & Products
  • Rate-Limiting Enzyme: Glucose-6-phosphate dehydrogenase (G6PD)
  • NADPH Functions:
    • Reductive biosynthesis (fatty acids, cholesterol)
    • Glutathione reduction (antioxidant defense via glutathione reductase)
    • Respiratory burst in phagocytes (NADPH oxidase → superoxide)
    • Cytochrome P450 system (drug detoxification)
  • Ribose-5-Phosphate: Nucleotide synthesis (DNA, RNA, ATP, NAD⁺, FAD, CoA)
G6PD Deficiency
  • Epidemiology: Most common enzyme deficiency worldwide; X-linked recessive
  • Pathophysiology: ↓ NADPH → ↓ reduced glutathione → oxidative damage to RBCs → hemolysis
  • Triggers: Oxidative stress (infections, fava beans, sulfonamides, antimalarials like primaquine, dapsone)
  • Findings: Heinz bodies (denatured Hb), bite cells (splenic macrophage removal), acute hemolytic anemia
  • Protection: Confers resistance to Plasmodium falciparum malaria
High-Yield: Pentose Phosphate Pathway
Primary Purpose
NADPH production (not ATP!) for reductive biosynthesis and antioxidant defense
G6PD Triggers
Mnemonic: "Favabeans" = Fava beans, Antimalarials, Sulfonamides, Anti-TB drugs, Beans (fava)
RBC Vulnerability
RBCs lack mitochondria → rely on PPP for NADPH → G6PD deficiency causes hemolysis under oxidative stress
Respiratory Burst
NADPH oxidase uses NADPH to make superoxide (O₂⁻) → kills phagocytosed bacteria; defective in CGD

Glycogen Metabolism

Glucose storage (glycogenesis) and mobilization (glycogenolysis)

Glycogenesis (Synthesis)
  • Location: Cytoplasm (liver, muscle primarily)
  • Activated glucose: UDP-glucose (from G1P + UTP)
  • Glycogen Synthase: Adds glucose via α-1,4 glycosidic bonds; rate-limiting enzyme
  • Branching Enzyme: Creates α-1,6 bonds every ~10 residues → increases solubility and access points
  • Primer: Glycogenin (autoglucosylating protein) initiates chain
Glycogenolysis (Breakdown)
  • Glycogen Phosphorylase: Cleaves α-1,4 bonds → glucose-1-P; rate-limiting enzyme; requires pyridoxal phosphate (B6)
  • Debranching Enzyme: Removes α-1,6 branches (transferase + α-1,6-glucosidase activities)
  • Phosphoglucomutase: G1P ↔ G6P
  • Glucose-6-Phosphatase: G6P → glucose (liver/kidney only); releases free glucose into blood
  • Muscle: Lacks G6Pase → G6P used locally for glycolysis (cannot release glucose)
Hormonal Regulation
Insulin (Fed State)
Activates glycogen synthase (dephosphorylation); inhibits phosphorylase → glycogen storage
Glucagon/Epinephrine (Fasting/Stress)
↑ cAMP → PKA → activates phosphorylase kinase → activates phosphorylase; inhibits synthase → glycogen breakdown
High-Yield: Glycogen Metabolism
Tissue Differences
Liver: Maintains blood glucose (has G6Pase); Muscle: Local energy only (no G6Pase)
Glycogen Storage Diseases
Von Gierke (Type I, G6Pase), Pompe (Type II, lysosomal α-1,4), Cori (Type III, debranching), McArdle (Type V, muscle phosphorylase)
Key Cofactor
Pyridoxal phosphate (B6) required for glycogen phosphorylase activity
Clinical Pearls
McArdle disease → exercise intolerance, no lactate rise with exercise; Pompe → cardiomegaly, hypotonia (infantile)
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Evidence & Further Reading