Cholesterol Synthesis Pathway: Steps, Enzymes & Drugs

The cholesterol synthesis pathway builds cholesterol from acetyl-CoA in the cytosol and endoplasmic reticulum, mostly in the liver: acetyl-CoA → HMG-CoA → mevalonate → isopentenyl pyrophosphate (IPP) → geranyl-PP → farnesyl-PP → squalene → lanosterol → cholesterol. The rate-limiting step is HMG-CoA reductase (HMG-CoA → mevalonate, using 2 NADPH), the enzyme statins inhibit.

Memorize the order as "All Hungry Med Interns Find Some Leftover Cake" and the carbon counts as 2 → 6 → 5 → 10 → 15 → 30 → 27. HMG-CoA reductase is switched on when cell sterols are low (through SREBP-2) and after a meal, and switched off by high sterols, which speed its degradation, and by AMPK when ATP runs low.

The same map explains nitrogen-containing bisphosphonates, which block farnesyl-PP synthase, and two classic enzyme defects: mevalonate kinase deficiency and Smith-Lemli-Opitz syndrome.

The cholesterol synthesis pathway in one line (mnemonic)

All Hungry Med Interns Find Some Leftover Cake = Acetyl-CoA → HMG-CoA → Mevalonate → Isopentenyl pyrophosphate (IPP) → Farnesyl-PP (by way of geranyl-PP) → Squalene → Lanosterol → Cholesterol.

Then count carbons. The number falls only twice: mevalonate loses its carboxyl carbon as CO₂ on the way to IPP (6 → 5), and lanosterol loses three methyl groups on the way to cholesterol (30 → 27).

Cholesterol biosynthesis steps: enzymes, location and cofactors

The textbook outline has three stages: acetyl-CoA to IPP, six IPP to squalene, squalene to cholesterol.

Where cholesterol synthesis takes place. Almost all cells can make some cholesterol, but the liver is the major site. The enzymes work in the cytosol and smooth endoplasmic reticulum: HMG-CoA reductase is an integral ER membrane protein, as are squalene synthase and the enzymes after it. Mitochondria only supply the acetyl-CoA.

Stoichiometry. Each mevalonate takes 3 acetyl-CoA and 2 NADPH (not NADH), and making IPP from it costs 3 ATP. Six IPP form one squalene, and squalene synthase uses 1 more NADPH; later steps use more O₂ and NADPH.

Rate-limiting step: HMG-CoA reductase and its regulation

HMG-CoA reductase (ER membrane, 2 NADPH) catalyzes the irreversible, rate-limiting and committed step for cholesterol and the other isoprenoids.

Sterol sensing: SREBP-2, SCAP and INSIG

1. Low ER cholesterol: SCAP escorts SREBP-2 to the Golgi in COPII vesicles, where site-1 and site-2 proteases release the transcription factor, which enters the nucleus.
2. Nuclear SREBP-2 turns on the reductase and the other synthesis enzymes, the LDL receptor, PCSK9 and INSIG-1.
3. High cholesterol: cholesterol binds SCAP, and oxysterols such as 25-hydroxycholesterol bind INSIG (insulin-induced gene). SCAP then binds INSIG, SCAP-SREBP-2 stays in the ER, and transcription falls.

SREBP-2 is the cholesterol isoform; SREBP-1c, induced by insulin, mainly drives fatty acid synthesis.

Sterol-accelerated degradation

When sterols accumulate in the ER, the reductase binds INSIG, which recruits ubiquitin ligases such as gp78 (AMFR); the tagged enzyme is pulled out of the membrane and destroyed by the proteasome. The key sterol trigger is lanosterol, the first sterol of the pathway, not cholesterol (25-hydroxycholesterol also works), so a backlog of intermediates throttles the enzyme that feeds them. Nonsterol isoprenoids add a brake by slowing translation of reductase mRNA.

Hormones and energy

AMPK switches off acetyl-CoA carboxylase, which catalyzes the committed step of fatty acid synthesis, the same way. Compare every rate-limiting enzyme in this rate-limiting enzymes table.

Acetyl-CoA supply: the citrate shuttle and two HMG-CoA synthases

Acetyl-CoA is made in mitochondria, but cholesterol is built in the cytosol, so acetyl groups travel as citrate:

1. The mitochondrial citrate carrier (SLC25A1) exports citrate in exchange for malate.
2. ATP-citrate lyase spends ATP to split citrate into acetyl-CoA and oxaloacetate. Bempedoic acid blocks this step; SREBP-1c induces the enzyme.
3. The shuttle also turns the reducing power of NADH into NADPH: malic enzyme converts malate to pyruvate, CO₂ and NADPH. The pentose phosphate pathway (rate-limiting enzyme G6PD) also supplies NADPH.

Fatty acid synthesis uses the same shuttle (fatty acid synthesis overview).

Tracing labeled carbons. Konrad Bloch's isotope-labeled acetate experiments showed that acetate builds both the rings and the side chain; all 27 carbons of cholesterol come from acetyl-CoA. The only carbon lost before squalene is mevalonate's carboxyl carbon (C1), released as CO₂, so a label there never reaches IPP.

More on the ketone side in the ketogenesis overview.

Mevalonate pathway to isoprenoids: IPP, farnesyl-PP and branch products

Three ATP-using enzymes turn mevalonate into IPP, the 5-carbon isoprene unit, and farnesyl-PP synthase builds geranyl-PP (C10), then farnesyl-PP (C15), from IPP and its isomer DMAPP. Farnesyl-PP and geranyl-PP feed back on mevalonate kinase by competing for its ATP site, and farnesyl-PP is the branch point:

Statins act upstream of every branch, so they lower these isoprenoids too: the basis of their "pleiotropic" effects and one proposed cause of statin muscle symptoms.

Squalene, lanosterol and the last steps to cholesterol

• Squalene synthase joins two farnesyl-PP through presqualene-PP and reduces the product with NADPH: the first step committed to sterols.
• Squalene epoxidase uses O₂ and NADPH to make 2,3-oxidosqualene. Cholesterol triggers its degradation; terbinafine blocks the fungal enzyme, and the human enzyme is only slightly inhibited.
• Lanosterol synthase (oxidosqualene cyclase) folds 2,3-oxidosqualene into lanosterol, the first sterol: the four rings appear here, not at squalene.
• Lanosterol to cholesterol takes about 19 ER reactions. Three methyl groups are removed (CYP51 strips the 14α-methyl as formate, the reaction azoles block in fungi). The last step is either desmosterol → cholesterol (DHCR24, Bloch pathway) or 7-dehydrocholesterol → cholesterol (DHCR7, Kandutsch-Russell); in mice, the Bloch share ranges from 8% to 97% by tissue.

What cholesterol becomes:

• Bile acids: cholesterol 7α-hydroxylase (CYP7A1) is the rate-limiting step. This is one way the body disposes of cholesterol, which it cannot break down.
• Steroid hormones: side-chain cleavage to pregnenolone (CYP11A1) is the rate-limiting step.
• Vitamin D3: UVB converts 7-dehydrocholesterol in the skin to previtamin D; follow it on in vitamin D metabolism.

LDL receptor regulation: synthesis vs uptake

Cells get cholesterol two ways: make it, or take up LDL. The LDL receptor recognizes apoB-100 and apoE, clusters in clathrin-coated pits and carries LDL in; lysosomes free the cholesterol, which leaves through NPC2 and NPC1 (defective in Niemann-Pick type C) toward the ER. Rising cell cholesterol then:

• turns off SREBP-2, so fewer reductase molecules and LDL receptors are made;
• speeds reductase degradation;
• activates ACAT (SOAT1) to store the excess as cholesteryl ester;
• through oxysterols and LXR, induces IDOL, a ubiquitin ligase that degrades the LDL receptor.

About 70% of circulating LDL is cleared by hepatic LDL receptors, and each receptor returns to the surface more than 100 times unless PCSK9 binds it and diverts it to the lysosome. PCSK9 is itself an SREBP-2 target, so drugs that lower liver cholesterol, statins included, raise PCSK9. Particle traffic is mapped in lipoprotein metabolism.

Familial hypercholesterolemia is a clearance defect, not a synthesis defect. Most cases are LDLR variants; APOB and PCSK9 variants also cause autosomal dominant disease, and LDLRAP1 variants a recessive form; about 1 in 200 to 250 people are affected. Homozygotes with almost no working receptors respond poorly to statins, ezetimibe and PCSK9 inhibitors, because all three work through receptors. Compare the other lipid disorders in the familial dyslipidemias mnemonic.

Drugs that act on the cholesterol pathway

• How statins lower LDL: mainly by raising hepatic LDL receptors through SREBP-2, not just by cutting synthesis.
• CoQ10: statins lower CoQ10, but CoQ10 supplements for statin muscle symptoms have not consistently helped in randomized trials.
• Pregnancy: in July 2021 the FDA asked for removal of the class-wide contraindication; most patients should still stop statins once pregnancy is recognized.

Practice the classic question in this HMG-CoA reductase breakdown, and the bone side in bisphosphonates and bone drugs.

Disorders of the pathway: Smith-Lemli-Opitz and mevalonate kinase deficiency

USMLE traps: classic teaching vs current evidence

Browse more pathway reviews on the Biochemistry hub.

Worked USMLE-style vignettes

Vignette 1: the muscle aches. A 58-year-old man with an LDL cholesterol of 190 mg/dL starts a new drug. Six weeks later his LDL has fallen by about half, but his thighs ache and his creatine kinase is mildly raised. The drug most likely inhibits which reaction?

Answer: HMG-CoA → mevalonate (HMG-CoA reductase; a statin).

Why the distractors are wrong:

• Acetoacetyl-CoA + acetyl-CoA → HMG-CoA (HMG-CoA synthase): the step before the statin target.
• Citrate → acetyl-CoA (ATP-citrate lyase): bempedoic acid is activated in liver, not muscle, and lowers LDL only about 15–25%.
• Cholesterol uptake by NPC1L1: ezetimibe lowers LDL only about 15–20%.

If weakness and a high creatine kinase persist for months after stopping the statin, think immune-mediated necrotizing myopathy (anti-HMG-CoA reductase antibodies).

Vignette 2: the newborn with fused toes. A newborn boy has microcephaly, ptosis, a cleft palate, hypospadias, Y-shaped fusion of the second and third toes and an extra digit on each foot. Serum cholesterol is low and 7-dehydrocholesterol is markedly raised. Which enzyme is deficient?

Answer: 7-dehydrocholesterol reductase (DHCR7), the last step: Smith-Lemli-Opitz syndrome, autosomal recessive.

Why the distractors are wrong:

• HMG-CoA reductase: a block there would deplete every downstream intermediate, so 7-dehydrocholesterol could not pile up.
• Mevalonate kinase: causes periodic fevers and mevalonic aciduria, not 7-dehydrocholesterol excess.
• Lanosterol 14α-demethylase (CYP51): acts well upstream of 7-dehydrocholesterol; the azole target in fungi.

Vignette 3: fevers after vaccines. A 2-year-old girl has had fevers every few weeks since her 2-month vaccines, each lasting about 4 days, with tender cervical lymph nodes, abdominal pain, diarrhea and a rash. She is well between episodes, and urinary mevalonic acid is raised during a fever. Which enzyme is deficient, and what is the long-term treatment?

Answer: Mevalonate kinase (mevalonate → mevalonate-5-phosphate), the mild form of mevalonate kinase deficiency (HIDS); long-term treatment is IL-1 blockade such as canakinumab.

Why the distractors are wrong:

• HMG-CoA reductase: it makes mevalonate, so its loss would lower mevalonate, not raise it; statins are not recommended here.
• Mitochondrial HMG-CoA synthase: its deficiency causes hypoketotic hypoglycemia with encephalopathy and hepatomegaly, not periodic fevers.
• 7-dehydrocholesterol reductase: Smith-Lemli-Opitz presents with malformations at birth.

Confirm with MVK genetic testing, not a serum IgD level.

Vignette 4: the bone drug. A 67-year-old woman with osteoporosis starts weekly alendronate. Which enzyme does the drug inhibit inside osteoclasts?

Answer: Farnesyl-PP synthase; without farnesyl and geranylgeranyl groups, osteoclasts cannot prenylate small GTPases and stop resorbing bone.

Why the distractors are wrong:

• HMG-CoA reductase: the statin target, upstream of farnesyl-PP synthase.
• Squalene epoxidase: terbinafine blocks the fungal enzyme.
• Making nonfunctional ATP analogs: how non-nitrogen bisphosphonates such as etidronate act; alendronate contains nitrogen.

Key takeaways

• Order: acetyl-CoA → HMG-CoA → mevalonate → IPP → geranyl-PP → farnesyl-PP → squalene → lanosterol → cholesterol ("All Hungry Med Interns Find Some Leftover Cake"; carbons 2 → 6 → 5 → 10 → 15 → 30 → 27).
• Where: cytosol and smooth ER, mainly in the liver; acetyl-CoA arrives from mitochondria as citrate.
• Rate-limiting: HMG-CoA reductase (2 NADPH); on with low sterols (SREBP-2) and feeding, off with INSIG-driven degradation, AMPK and statins.
• Drug map: bempedoic acid (ATP-citrate lyase), statins (reductase), nitrogen-containing bisphosphonates (farnesyl-PP synthase); ezetimibe and PCSK9 inhibitors raise LDL receptors without blocking synthesis.
• Diseases: Smith-Lemli-Opitz (DHCR7, high 7-dehydrocholesterol); mevalonate kinase deficiency (periodic fevers, IL-1 blockade); familial hypercholesterolemia is a receptor defect.

Sources

• Craig M, et al. Biochemistry, Cholesterol — StatPearls, NCBI Bookshelf (2023)
• Berg JM, et al. Biochemistry, 8th ed., Section 26.2 (cholesterol synthesis) — Macmillan Learning
• Berg JM, et al. Biochemistry, 8th ed., Section 26.3 (regulation) — Macmillan Learning
• Berg JM, et al. Biochemistry, 8th ed., Figure 22.29 — Macmillan Learning
• Bloch K. The Biological Synthesis of Cholesterol, Nobel Lecture — NobelPrize.org (1964)
• Feingold KR. Cholesterol Lowering Drugs — Endotext, NCBI Bookshelf (2026)
• Feingold KR. Introduction to Lipids and Lipoproteins — Endotext, NCBI Bookshelf (2024)
• Sizar O, et al. Statin Medications — StatPearls, NCBI Bookshelf (2024)
• Bansal AB, Cassagnol M. HMG-CoA Reductase Inhibitors — StatPearls, NCBI Bookshelf (2023)
• Ganesan K, et al. Bisphosphonate — StatPearls, NCBI Bookshelf (2023)
• Rahimi N, Gupta S. Biochemistry, Ketogenesis — StatPearls, NCBI Bookshelf (2025)
• Chauhan K, et al. Vitamin D — StatPearls, NCBI Bookshelf (2023)
• Nowaczyk MJM, Wassif CA. Smith-Lemli-Opitz Syndrome — GeneReviews, NCBI Bookshelf (2020)
• Lengvári L, et al. Mevalonate Kinase Deficiency: An Updated Clinical Overview and Revision of the SHARE Recommendations — Front Immunol (2024)
• Mevalonate Kinase Deficiency — MedlinePlus Genetics, NLM
• Smith-Lemli-Opitz Syndrome — MedlinePlus Genetics, NLM
• Familial Hypercholesterolemia — MedlinePlus Genetics, NLM
• Horton JD, et al. SREBPs: Activators of the Complete Program of Cholesterol and Fatty Acid Synthesis in the Liver — J Clin Invest (2002)
• Radhakrishnan A, et al. Sterol-Regulated Transport of SREBPs from Endoplasmic Reticulum to Golgi: Oxysterols Block Transport by Binding to Insig — PNAS (2007)
• Song BL, et al. Insig-Mediated Degradation of HMG CoA Reductase Stimulated by Lanosterol, an Intermediate in the Synthesis of Cholesterol — Cell Metab (2005)
• Ness GC, et al. Insulin and Glucagon Modulate Hepatic 3-Hydroxy-3-Methylglutaryl-Coenzyme A Reductase Activity by Affecting Immunoreactive Protein Levels — J Biol Chem (1994)
• Easom RA, Zammit VA. Acute Effects of Starvation and Treatment of Rats with Anti-Insulin Serum, Glucagon and Catecholamines on the State of Phosphorylation of Hepatic 3-Hydroxy-3-Methylglutaryl-CoA Reductase In Vivo — Biochem J (1987)
• Lu XY, et al. Feeding Induces Cholesterol Biosynthesis via the mTORC1–USP20–HMGCR Axis — Nature (2020)
• Gill S, et al. Cholesterol-Dependent Degradation of Squalene Monooxygenase, a Control Point in Cholesterol Synthesis beyond HMG-CoA Reductase — Cell Metab (2011)
• Mitsche MA, et al. Flux Analysis of Cholesterol Biosynthesis In Vivo Reveals Multiple Tissue and Cell-Type Specific Pathways — eLife (2015)
• Kavanagh KL, et al. The Molecular Mechanism of Nitrogen-Containing Bisphosphonates as Antiosteoporosis Drugs — PNAS (2006)
• FDA Requests Removal of Strongest Warning Against Using Cholesterol-Lowering Statins During Pregnancy — U.S. Food and Drug Administration (2021)
• Atorvastatin Calcium Tablets Label — DailyMed, NLM (2025)
• NEXLETOL (Bempedoic Acid) Label — DailyMed, NLM (2026)
• ZETIA (Ezetimibe) Label — DailyMed, NLM (2025)
• ILARIS (Canakinumab) Label — DailyMed, NLM (2026)
• Terbinafine Tablets Label — DailyMed, NLM (2026)
• Fluconazole Tablets Label — DailyMed, NLM (2025)
• HMG-CoA Reductase, P04035 — UniProtKB
• Mevalonate Kinase, Q03426 — UniProtKB
• Farnesyl Pyrophosphate Synthase, P14324 — UniProtKB
• Squalene Synthase, P37268 — UniProtKB
• Squalene Monooxygenase, Q14534 — UniProtKB
• Lanosterol 14-Alpha Demethylase, Q16850 — UniProtKB
• Dehydrodolichyl Diphosphate Synthase, Q86SQ9 — UniProtKB