Biochemistrypedia · the Deppmann Lab
You understand a molecule once you can turn it over in your hands.
Most students meet biochemistry as a wall of terms to get past before the exam, and never reach the part where it's astonishing. This is the version where you change something and watch the reaction answer back — until you walk away understanding why a thing happens, not just remembering that it does. Hemoglobin stops being four letters on a slide and becomes a real protein, found by a real person, that you can rotate yourself.
For students who'd rather understand it than survive it.
Start with Chapter 1 → ▶ Play the Metabolism Arcade Browse the units ↓
Chapters · 30 live now
Unit 1 · Foundations
- Interlude · Alchemy & Vitalism Vitalism: How Chemistry Captured Life Before biochemistry could begin, one idea had to die — this is its seventy-year retreat.
- Introduction to Biochemistry & the Cell Introduction to Biochemistry and Cell Biology: Compartments Create Control Why can one missing enzyme kill a child before age three? The answer is compartments.
- Water and Weak Interactions Water, Weak Bonds, and the Generation of Order The second law says everything should fall apart. Water's own disorder pays for life's order.
Unit 2 · Proteins
- Amino Acids Amino Acids: How One Side Chain Decides Everything The R group sets the chemistry — charge, pKa, and the Glu→Val swap behind sickle cell all fall out of it.
- Protein Three-Dimensional Structure Protein Three-Dimensional Structure: How a Sequence Folds Itself More shapes than the age of the universe allows, folded in milliseconds — the answer is constraints.
- Techniques in Protein Biochemistry Techniques in Protein Biochemistry: Purify It, Then Prove It Pull one protein out of a soup of ten thousand others — then prove you got it.
Unit 3 · Enzymes & Binding
- Enzymes and Bioenergetics Basic Concepts of Enzyme Action Can an enzyme make an impossible reaction happen? No — it can only make a possible one fast.
- Mechanisms and Inhibitors Enzyme Kinetics: The Michaelis–Menten Model Why doesn't doubling the substrate keep doubling the rate? Enzymes saturate.
- Molecular Recognition & Allostery Protein Binding, Molecular Recognition, and Allostery One O₂ pulls the iron 0.4 Å; that twitch rotates the whole tetramer. Cooperativity is mechanics.
Unit 4 · Sugars, Lipids & Membranes
- Carbohydrates & the Sugar Code Carbohydrates: One Hydroxyl Decides Storage or Structure Flip a single hydroxyl on glucose and you decide whether the polymer feeds you or holds a plant up.
- Lipids & Membrane Architecture Lipids: The Building Blocks That Refuse to Polymerize Shape is destiny: a single cis double bond is the difference between lard and olive oil.
- Membranes & Transport Membranes: The Impermeable Sheet That Builds Itself Cystic fibrosis is, at bottom, a story about one protein that never reaches the right membrane.
Unit 5 · Signaling & Digestion
- Cell Signaling Signal-Transduction Pathways: How Cells Compute With Molecular Switches One epinephrine molecule mobilizes millions of glucose molecules; amplification is the whole story.
- Digestion & Absorption Digestion: Turning a Meal into Cellular Biomolecules Digestion is one chemical reaction run three ways — and trypsin is the master switch.
Unit 6 · Central Metabolism
Play these pathways. Wire the cell, run the regulators through a fast, and diagnose a broken enzyme in the Metabolism Arcade.- Metabolism: Foundations Metabolism: Basic Concepts and Design Metabolism is an energy economy; learn its grammar before any pathway teaches its vocabulary.
- Glycolysis Glycolysis: The Investment-and-Payoff Pathway Why does a cell spend ATP to make ATP? The first three steps are a deliberate investment.
- Glucose Homeostasis Gluconeogenesis: Pushing Glucose Back Uphill Four new enzymes, three compartments, real ATP spent uphill: how the body builds glucose from scratch.
- The Citric Acid Cycle The Pyruvate Dehydrogenase Complex: The One-Way Gate to the Cycle One machine, three enzymes, five coenzymes, a 14 Å swinging arm — and no way back once carbon walks through.
- The Citric Acid Cycle The Citric Acid Cycle: Harvesting Electrons The citric acid cycle does not make ATP. Its real product is high-energy electrons.
- Cellular Respiration Oxidative Phosphorylation: The Electron-Transport Chain Electron flow and ATP synthesis are two separate machines linked by one thing: the proton gradient.
- Cellular Respiration The Proton-Motive Force and ATP Synthase Peter Mitchell saw the proton gradient in 1961, was ridiculed for seventeen years, and was vindicated.
Finished the unit? Take the unit review →
Unit 7 · Photosynthesis
- Photosynthesis Photosynthesis: The Light Reactions Two photon-driven uphill boosts, wired so water splits, oxygen leaves, and NADPH gets made.
- Photosynthesis The Calvin Cycle: Fixing Carbon from Thin Air Every carbon in every sugar, protein, and strand of DNA on Earth was pulled out of thin air by this loop.
Unit 8 · Fuels, Fat & Nitrogen
Play these pathways. Wire the cell, run the regulators through a fast, and diagnose a broken enzyme in the Metabolism Arcade.- Glucose Homeostasis The Pentose Phosphate Pathway: NADPH and Five-Carbon Sugars It makes no ATP, and that is the point: NADPH and ribose-5-phosphate are the products that matter.
- Lipid Metabolism Fatty Acid Degradation: The β-Oxidation Spiral Fat comes apart two carbons at a time — and palmitate's ~106 ATP only balance if you keep the books.
- Lipid Metabolism Fatty Acid Synthesis: Building the Chain Two Carbons at a Time Cytoplasm, ACP, NADPH: three choices that keep building fat from colliding with burning it.
- Lipid Metabolism Lipid Synthesis: Building Cholesterol from Acetyl-CoA From two-carbon acetate to a 27-carbon ring: master HMG-CoA reductase and the statins follow.
- Nitrogen Metabolism Protein Turnover and Amino Acid Catabolism: Tag, Recognize, Destroy, Recycle A protein's lifespan runs from minutes to a lifetime, set by tags the cell reads and acts on.
Finished the unit? Take the unit review →
Unit 9 · Supplements
- Supplement · Nucleotide Metabolism Nucleotide Metabolism: Build It, Recycle It, or Pay in Uric Acid Nucleotides are too expensive to throw away — gout, Lesch-Nyhan, and allopurinol live where recycling breaks.
- Supplement · Integration of Metabolism Integration of Metabolism: How the Body Switches Fuels Fed, fasting, starving: two hormones switch every pathway in this course on and off in a timed sequence.
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