Biochemistry Pathway Explainer
Metabolic pathways walked through enzyme-by-enzyme — cofactors, regulation, thermodynamics.
What it does
Pick a pathway — or part of one — and Clara walks through it enzyme-by-enzyme. For each step you get the catalytic chemistry, the cofactors, the regulation, and the thermodynamics. Useful for both organic-thinking chemists and pre-med biochemistry students.
Highlights
- ✓Per-step enzyme mechanism (not just 'A goes to B')
- ✓Cofactor and metal-ion involvement
- ✓Allosteric and hormonal regulation
- ✓Standard free energy (ΔG'°) for each step
What you get back
- →Pathway overview and physiological purpose
- →Per-enzyme: EC number, reaction, cofactors, mechanism, regulation, ΔG'°
- →A flow diagram of metabolites
- →Textbook references (Lehninger, Berg/Stryer)
What it looks like
An illustration of the kind of answer Clara gives, laid out the way the live tool shows it.
Pathway
Glycolysis — investment phase (steps 1–3)
Investment phase — 2 ATP consumed
Step 1
Hexokinase (or glucokinase in liver/β-cells)
EC 2.7.1.1 / 2.7.1.2
Reaction
Glucose + ATP → Glucose-6-phosphate + ADP
Mechanism
The C6-OH of glucose acts as the nucleophile, attacking the γ-phosphate of ATP via a pentacoordinate (trigonal-bipyramidal) transition state. Phosphate transfer proceeds with inversion at phosphorus. Hexokinase undergoes induced-fit closure on glucose binding — this excludes water from the active site and prevents wasteful ATP hydrolysis.
Example ask
“Walk me through the investment phase of glycolysis — steps 1 through 3 — including the regulation of PFK-1.”
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