STEPTRACKERBIOCHEMISTRY | METABOLISM PRINCIPLES | HIGH-YIELD REVIEW

Metabolic Map & Rate-Limiting Enzymes

Where each pathway runs in the cell, what step controls its speed, and which hormones and molecules push the lever.

FOCUS ON
Mitochondria: β-oxidation, TCA, ETC, ketogenesis, PDH. Cytosol: glycolysis, HMP shunt, fatty acid synthesis, steroid synthesis (SER), protein synthesis (RER). Both: heme synthesis, urea cycle, gluconeogenesis. Insulin favors storage (dephosphorylates enzymes); glucagon favors release (cAMP → PKA phosphorylation). Rate-limiting enzymes are the drug and regulation targets.
PATHWAY
RATE-LIMITING ENZYME
ACTIVATORS
INHIBITORS · LOCATION
Glycolysis
Phosphofructokinase-1
AMP, fructose-2,6-bisphosphate
ATP, citrate · cytosol
Gluconeogenesis
Fructose-1,6-bisphosphatase
ATP, acetyl-CoA
AMP, F-2,6-BP · cytosol + mitochondria (pyruvate carboxylase)
TCA cycle
Isocitrate dehydrogenase
ADP
ATP, NADH · mitochondria
Glycogenesis
Glycogen synthase
Glucose-6-P, insulin, cortisol
Epinephrine, glucagon
Glycogenolysis
Glycogen phosphorylase
Epinephrine, glucagon, AMP (muscle), Ca²⁺ (muscle)
G6P, insulin, ATP
HMP shunt
Glucose-6-phosphate dehydrogenase
NADP⁺
NADPH · cytosol
De novo pyrimidine synthesis
Carbamoyl phosphate synthetase II
ATP, PRPP
UTP
De novo purine synthesis
Glutamine-PRPP amidotransferase
—
AMP, IMP, GMP
Urea cycle
Carbamoyl phosphate synthetase I
N-acetylglutamate
— · mitochondria + cytosol
Fatty acid synthesis
Acetyl-CoA carboxylase
Insulin, citrate
Glucagon, palmitoyl-CoA · cytosol
Fatty acid oxidation
Carnitine acyltransferase I
—
Malonyl-CoA · mitochondria
Ketogenesis
HMG-CoA synthase
—
— · mitochondria
Cholesterol synthesis
HMG-CoA reductase
Insulin, thyroxine, estrogen
Glucagon, cholesterol, statins · cytosol/SER
Heme synthesis
ALA synthase
—
Heme, glucose · mitochondria + cytosol

Mechanism — the hormonal switch

InsulinFed state
→
PhosphatasesDephosphorylate
→
Storage onGlycogen synthase, ACC, PFK-2 kinase
Glucagon / epinephrineFasting, stress
→
cAMP → PKAPhosphorylate
→
Release onPhosphorylase, gluconeogenesis, lipolysis

Where pathways run

MITOCHONDRIA
CYTOSOL
BOTH
β-Oxidation
Glycolysis
Heme synthesis
Acetyl-CoA production (PDH)
HMP shunt
Urea cycle
TCA cycle, ETC
Fatty acid synthesis
Gluconeogenesis
Ketogenesis
Cholesterol synthesis
—

How it's tested

COMMON CONFUSIONCPS I (urea, mitochondria, activated by N-acetylglutamate) vs CPS II (pyrimidines, cytosol).
THE TRAPMalonyl-CoA (made during fat synthesis) blocks carnitine acyltransferase I — so the liver doesn't burn the fat it's making.
YOUR APPROACHName the pathway → its rate-limiting enzyme → its location → what the fed vs fasting state does to it.

If you see… think…

Rate-limiting enzyme of glycolysis → PFK-1
Rate-limiting enzyme of gluconeogenesis → fructose-1,6-bisphosphatase
Rate-limiting enzyme of cholesterol synthesis → HMG-CoA reductase (statins)
Rate-limiting enzyme of ketogenesis → HMG-CoA synthase
Rate-limiting enzyme of fatty acid synthesis → acetyl-CoA carboxylase
Molecule blocking fatty acid entry into mitochondria → malonyl-CoA
Activator of CPS I → N-acetylglutamate
Pathways split between mitochondria and cytosol → heme, urea cycle, gluconeogenesis
Strongest activator of PFK-1 → fructose-2,6-bisphosphate
Rate-limiting enzyme of heme synthesis → ALA synthase