liminfoMetabolic Pathway Reference
Free reference guide: Metabolic Pathway Reference
About Metabolic Pathway Reference
The Metabolic Pathway Reference is a comprehensive biochemistry cheat sheet covering 26 core metabolic pathways organized into six categories: carbohydrate metabolism (glycolysis, TCA cycle, electron transport chain, pentose phosphate pathway, gluconeogenesis, glycogen metabolism, Cori cycle), lipid metabolism (beta-oxidation, fatty acid synthesis, cholesterol/mevalonate pathway, ketogenesis, citrate shuttle), and amino acid metabolism (urea cycle, transamination, BCAA catabolism, one-carbon/folate metabolism).
The nucleotide metabolism section includes de novo purine synthesis with HGPRT salvage pathway, pyrimidine synthesis with thymidylate synthase as a chemotherapy target, and purine degradation to uric acid via xanthine oxidase. Special pathways cover oxidative stress defense (SOD, catalase, glutathione peroxidase), heme biosynthesis from succinyl-CoA and glycine, and the malate-aspartate shuttle for NADH transport.
Each pathway entry lists key enzymes, regulatory steps, cofactors, subcellular locations, ATP/NADH yields, and clinical correlations (G6PD deficiency, Lesch-Nyhan syndrome, maple syrup urine disease, gout, porphyrias). Links to KEGG, MetaCyc/BioCyc, and Reactome databases are included for further exploration.
Key Features
- Complete glycolysis, TCA cycle, and oxidative phosphorylation with enzyme names, ATP/NADH yields, and regulatory enzymes
- Lipid metabolism pathways: beta-oxidation (carnitine shuttle, per-cycle yields), de novo fatty acid synthesis (FAS complex), and mevalonate/cholesterol pathway with statin targets
- Amino acid catabolism: urea cycle intermediates, transamination with ALT/AST enzymes, and branched-chain amino acid (BCAA) degradation with MSUD clinical link
- Nucleotide metabolism: purine de novo and salvage pathways, pyrimidine synthesis with 5-FU and methotrexate drug targets, and uric acid/gout connection
- Special pathways including ROS defense (SOD, catalase, GPx, glutathione reductase), heme biosynthesis, Cori cycle, malate-aspartate shuttle, and one-carbon metabolism
- Database links to KEGG pathway maps (hsa00010, hsa00020, hsa00071), MetaCyc/BioCyc/HumanCyc/EcoCyc, and Reactome pathway browser
- Key enzyme regulation, rate-limiting steps, cofactor requirements (NAD+, FAD, PLP, THF, B12), and subcellular compartmentalization noted for each pathway
- Clinical correlations for metabolic disorders: G6PD deficiency, Lesch-Nyhan syndrome, maple syrup urine disease (MSUD), diabetic ketoacidosis, gout, and porphyrias
Frequently Asked Questions
How much ATP does complete glucose oxidation produce?
Complete oxidation of one glucose molecule through glycolysis (2 ATP, 2 NADH), pyruvate dehydrogenase (2 NADH), TCA cycle (6 NADH, 2 FADH2, 2 GTP), and oxidative phosphorylation yields approximately 30-32 ATP total. Each NADH produces about 2.5 ATP and each FADH2 about 1.5 ATP via the electron transport chain complexes I-V.
What are the key regulatory enzymes of glycolysis and gluconeogenesis?
Glycolysis is regulated by three irreversible enzymes: hexokinase (step 1), phosphofructokinase-1/PFK-1 (rate-limiting step 3), and pyruvate kinase (step 10). Gluconeogenesis bypasses these with pyruvate carboxylase + PEPCK, fructose-1,6-bisphosphatase (FBPase), and glucose-6-phosphatase (G6Pase, found only in liver and kidney).
How does fatty acid beta-oxidation work and what is its ATP yield?
Beta-oxidation occurs in the mitochondrial matrix after activation and carnitine shuttle transport (CPT-I/II). Each cycle removes 2 carbons, producing 1 FADH2, 1 NADH, and 1 acetyl-CoA. Palmitate (C16) undergoes 7 cycles yielding 8 acetyl-CoA, 7 FADH2, and 7 NADH, totaling approximately 106 ATP after TCA cycle and oxidative phosphorylation.
What connects the urea cycle to the TCA cycle?
The urea cycle and TCA cycle are linked through fumarate. Argininosuccinate lyase (ASL) in the urea cycle produces fumarate as a byproduct when converting argininosuccinate to arginine. This fumarate enters the TCA cycle where it is converted to malate and then oxaloacetate, creating the "Krebs bicycle" connection between nitrogen disposal and energy metabolism.
What drugs target nucleotide synthesis pathways?
Key chemotherapy targets include thymidylate synthase (inhibited by 5-fluorouracil/5-FU, blocking dTMP synthesis), dihydrofolate reductase/DHFR (inhibited by methotrexate, blocking THF regeneration needed for both purine and pyrimidine synthesis). For gout treatment, allopurinol and febuxostat inhibit xanthine oxidase to reduce uric acid production from purine degradation.
What is the role of the pentose phosphate pathway (PPP)?
The PPP serves two main functions: the oxidative phase produces 2 NADPH per glucose-6-phosphate (regulated by G6PD), which is essential for reductive biosynthesis and ROS defense via glutathione. The non-oxidative phase generates ribose-5-phosphate for nucleotide synthesis. G6PD deficiency impairs NADPH production, leading to hemolytic anemia due to inadequate ROS protection in red blood cells.
How does cholesterol synthesis work and where do statins act?
Cholesterol is synthesized via the mevalonate pathway: 3 acetyl-CoA condense to HMG-CoA, which is reduced to mevalonate by HMG-CoA reductase (the rate-limiting enzyme). Mevalonate is then converted through IPP, GPP, FPP, squalene, and lanosterol to cholesterol. Statin drugs (atorvastatin, simvastatin) competitively inhibit HMG-CoA reductase, lowering cholesterol production.
Is this metabolic pathway reference free to use?
Yes, this reference is completely free with no sign-up, no download, and no usage limits. All content is processed locally in your browser without sending data to any server. It is designed as a quick-reference cheat sheet for biochemistry students, medical students, researchers, and healthcare professionals and is part of liminfo.com's free science tools.