Chapter 34 — Lipids, Terpenes, and Biosynthesis: How Nature Does Organic Chemistry

"Life starts with acetate. Two carbons at a time, biology builds the membranes that contain it, the energy stores that power it, the hormones that signal in it, the vitamins that protect it. The chemistry is the chemistry of Chapter 28." — paraphrase from a biochemistry text

"Squalene cyclization to lanosterol — a single enzyme converts a 30-carbon linear hydrocarbon into a tetracyclic ring system in one step, with control of all 7 stereocenters. It is one of the most elegant reactions known."

This chapter covers the third great class of biomolecules: lipids. Lipids are biological molecules that are insoluble in water (or soluble only in organic solvents). The class includes: - Fatty acids: long-chain carboxylic acids. - Triglycerides: triesters of glycerol with three fatty acids; energy storage. - Phospholipids: similar to triglycerides but one fatty acid replaced by phosphate + head group; cell-membrane material. - Sterols (cholesterol): 4-ring tetracyclic structures; membrane modulator; hormone precursor. - Terpenes: polymers of isoprene; from monoterpenes (C₁₀) to polyisoprenoids. - Steroid hormones, bile acids, vitamins D, A, E, K: derived from terpenoid biosynthesis.

The unifying chemistry: all lipids are biosynthesized from a single 2-carbon starting material — acetyl-CoA — via iterated Claisen condensations (Ch 28) and a few elaborations. By following one mechanism through one biosynthetic logic, biology builds an entire class of structurally diverse molecules.

By the end of this chapter you should be able to: - Recognize the major lipid classes and their biological roles. - Understand fatty acid biosynthesis (iterative Claisen + reduction + dehydration + reduction). - Apply the isoprene rule to terpene structures. - Outline cholesterol biosynthesis from acetyl-CoA via mevalonate, IPP, squalene, lanosterol. - Recognize how statin drugs work (inhibit HMG-CoA reductase). - Explain β-oxidation as the reverse of fatty acid biosynthesis. - Connect lipid chemistry to cell membrane structure and function.

34.1 Fatty acids: structure and naming

Fatty acids are long-chain carboxylic acids of the general formula $CH_3(CH_2)_n-COOH$. Common chain lengths: 12, 14, 16, 18, 20, 22 carbons (even numbers, because biosynthesis adds 2 carbons at a time from acetate units).

Saturated vs unsaturated

• Saturated fatty acids: no C=C bonds in the chain. Example: palmitic acid (16:0) = $CH_3(CH_2)_{14}COOH$.
• Unsaturated fatty acids: one or more C=C bonds. Example: oleic acid (18:1Δ9) = $CH_3(CH_2)_7CH=CH(CH_2)_7COOH$, with a single cis double bond between C9 and C10.

The shorthand notation: $C_xC_y$ where $x$ is total carbons and $y$ is number of C=C bonds. Δ followed by number gives the position of the C=C (counting from carboxyl end).

Omega numbering

For metabolic and nutritional purposes, fatty acids are also named by counting from the methyl (omega = ω) end: - ω-3: last C=C is 3 carbons from the methyl end. Example: α-linolenic acid (18:3, ω-3). - ω-6: last C=C is 6 carbons from the methyl end. Example: linoleic acid (18:2, ω-6). - ω-9: last C=C is 9 carbons from the methyl end. Example: oleic acid (18:1, ω-9).

The ω-3 and ω-6 designations are biologically significant because mammals cannot synthesize these from scratch — they must be obtained from diet (essential fatty acids).

Common fatty acids

Cis double bonds in unsaturated fatty acids cause kinks in the chain; trans (rare in nature, common in industrial trans fats) keep the chain straight. The kinks affect packing in membranes and physical properties (fluidity, melting point).

Trans fats

In partially hydrogenated vegetable oils, some cis double bonds are isomerized to trans. Trans fats are linked to cardiovascular disease and have been banned or restricted in many countries (FDA banned them in 2018 in the U.S.).

The chemistry: heterogeneous catalysis (typically Ni or Pd at high temperature) of vegetable oil with H₂ partially saturates and partially isomerizes the C=C. Modern food chemistry avoids this (interestification, fractionation, or alternative oils).

34.2 Fatty acid biosynthesis: iterated Claisen

This is one of the most beautiful biosyntheses in nature, and it is exactly the chemistry of Chapter 28.

The starting materials

• Acetyl-CoA (2 carbons): the "primer" — provides the first 2 carbons of the chain.
• Malonyl-CoA (3 carbons; HOOC-CH₂-CO-S-CoA): the chain extender — provides 2 carbons per cycle, with the third carbon released as CO₂.

Malonyl-CoA is made from acetyl-CoA + CO₂ + ATP by acetyl-CoA carboxylase (ACC) — the rate-limiting step of fatty acid biosynthesis.

One cycle: Claisen + reduce + dehydrate + reduce

Each cycle adds 2 carbons via four enzymatic steps. The chain is held throughout by the acyl carrier protein (ACP) as a thioester.

Step 1 (Claisen condensation; β-ketoacyl-ACP synthase): $$\text{acetyl-ACP} + \text{malonyl-ACP} \to \text{β-ketobutyryl-ACP} + CO_2 + \text{ACP-SH}$$

The α-C of malonyl-ACP (which is doubly stabilized: α to two C=O) attacks the carbonyl C of acetyl-ACP. The C=O of acetyl-ACP collapses; ACP-SH leaves; CO₂ is released. Net: β-keto-acyl-ACP, 4 carbons.

This is a decarboxylative Claisen — the CO₂ release provides the thermodynamic driving force.

Step 2 (Reduction; β-ketoacyl-ACP reductase): NADPH reduces the β-keto group to a β-hydroxy group.

Step 3 (Dehydration; β-hydroxyacyl-ACP dehydratase): Loss of water (E2-like elimination of α-H and β-OH) gives an α,β-unsaturated thioester (enoyl-ACP).

Step 4 (Reduction; enoyl-ACP reductase): NADPH reduces the C=C to a saturated chain.

Net for one cycle: chain is now 4 carbons (4:0). Repeat for 6 more cycles to reach 16 carbons (palmitate, 16:0). After cycle 7, a thioesterase releases palmitic acid from ACP-SH.

Total stoichiometry for palmitate

$$8 \text{ acetyl-CoA} + 14 \text{ NADPH} + 14 H^+ + 7 ATP \to \text{palmitic acid} + 8 CoA-SH + 7 ADP + 7 P_i + 14 NADP^+ + 6 H_2O$$

Each cycle uses 1 acetyl-CoA (carbons), 1 ATP (for the malonyl-CoA synthesis), and 2 NADPH (for the two reductions). Palmitate (16C) requires 7 cycles, hence 14 NADPH.

The role of NADPH

NADPH is the reduced cofactor used for biosynthesis. It is generated by: - The pentose phosphate pathway (oxidation of glucose-6-phosphate gives NADPH). - Malic enzyme (oxidation of malate to pyruvate gives NADPH). - Other reactions.

Cells with high biosynthetic activity (liver, adipose, lactating mammary gland) have high NADPH production.

Mechanism Map 34.1: Fatty acid biosynthesis cycle.

Round 1: acetyl-ACP (C2) + malonyl-ACP (C3) → β-ketobutyryl-ACP (C4) + CO₂ + ACP-SH. NADPH reduction: β-ketobutyryl-ACP → β-hydroxybutyryl-ACP. Dehydration: β-hydroxybutyryl-ACP → crotonyl-ACP (α,β-unsaturated). NADPH reduction: crotonyl-ACP → butyryl-ACP (C4).

Round 2: butyryl-ACP (C4) + malonyl-ACP → β-keto C6 acyl-ACP. ... continue.

After 7 rounds: palmitoyl-ACP (C16); thioesterase releases palmitate.

34.3 β-oxidation: fatty acid breakdown

The reverse of biosynthesis (with NADH and FADH₂ instead of NADPH; mitochondrial instead of cytosolic): β-oxidation breaks down fatty acids 2 carbons at a time, releasing acetyl-CoA for the citric acid cycle.

One cycle: dehydrogenate + hydrate + oxidize + thiolyze

For a 16:0 fatty acid (palmitate, on a CoA), one β-oxidation cycle:

Step 1 (Dehydrogenation; acyl-CoA dehydrogenase): FAD oxidizes the α-β bond to an α,β-unsaturated thioester (a fatty enoyl-CoA). FAD → FADH₂. Adds 1.5 ATP per FADH₂ (via the electron transport chain).

Step 2 (Hydration; enoyl-CoA hydratase): Water adds across the C=C, giving a β-hydroxy acyl-CoA. The OH ends up on the β-C (anti-Markovnikov-like; hydration of an enoyl-CoA gives the β-hydroxy product because the β-C is the one stabilized by the C=O).

Step 3 (Oxidation; β-hydroxyacyl-CoA dehydrogenase): NAD⁺ oxidizes the β-OH to a β-keto group. NAD⁺ → NADH. 2.5 ATP per NADH.

Step 4 (Thiolysis; β-ketoacyl-CoA thiolase): A second CoA-SH attacks the β-keto, cleaving the C-C bond between α and β. This is essentially a retro-Claisen condensation. Products: acetyl-CoA (the cleaved 2-C piece) and a fatty acyl-CoA shortened by 2 carbons.

The acyl-CoA continues to the next cycle. Acetyl-CoA enters the citric acid cycle.

Energy yield

For palmitate (16:0), 7 cycles of β-oxidation → 8 acetyl-CoA + 7 FADH₂ + 7 NADH. Each acetyl-CoA in citric acid cycle → 1 ATP + 3 NADH + 1 FADH₂ (over 8 steps). Each NADH ≈ 2.5 ATP; each FADH₂ ≈ 1.5 ATP via electron transport chain.

Total ATP yield from palmitate: - β-oxidation: 7 × (1.5 + 2.5) = 28 ATP from FADH₂ and NADH. - Acetyl-CoA from citric acid cycle: 8 × (1 + 3×2.5 + 1×1.5) = 8 × 10 = 80 ATP. - Subtract 2 ATP for activation (palmitate → palmitoyl-CoA, forming 2 high-energy phosphate bonds).

Net: ~106 ATP per palmitate, vs. ~32 ATP per glucose. Per carbon, fatty acids yield ~50% more ATP than glucose — which is why fat is the body's preferred energy storage.

34.4 Triglycerides and phospholipids

Triglycerides: energy storage

A triglyceride (or triacylglycerol) is a triester of glycerol with three fatty acids: $$\text{Glycerol} + 3 \text{ fatty acids} \to \text{triglyceride} + 3 H_2O$$

Triglycerides are the energy storage form of lipids in animals (in adipose tissue) and plants (seeds and oils).

Mechanism of triglyceride synthesis: glycerol + three acyl-CoAs → glyceride + three CoA-SH (acyl substitution, Family II from Ch 26).

Mechanism of breakdown: lipase enzymes hydrolyze each ester bond → free fatty acids + glycerol.

Phospholipids: membrane material

Phospholipids have: - Glycerol backbone. - Two fatty acid esters (positions C1 and C2). - Phosphate at C3, connected to a polar head group (choline, ethanolamine, serine, inositol, etc.).

The two non-polar fatty acid tails + the polar phosphate-head group make phospholipids amphiphilic. They self-assemble in water into lipid bilayers — the basis of every cell membrane.

Common phospholipids: - Phosphatidylcholine (PC): head group = choline (positively charged); the most common membrane lipid. - Phosphatidylethanolamine (PE): head group = ethanolamine. - Phosphatidylserine (PS): head group = serine; on the inner leaflet. - Sphingomyelin: a different class (uses sphingosine instead of glycerol).

Membrane structure

A lipid bilayer consists of two layers of phospholipid molecules, with the polar head groups facing the aqueous environment (outside and inside the cell) and the nonpolar tails facing each other (the membrane interior).

The bilayer is: - ~5 nm thick. - Fluid (lateral diffusion of lipids). - Selectively permeable (small nonpolar molecules pass; ions need transporters).

Cholesterol is incorporated into the membrane to modulate fluidity.

34.5 Terpenes: the isoprene rule

Terpenes are a vast class of natural products built from isoprene units (2-methyl-1,3-butadiene, $CH_2=C(CH_3)CH=CH_2$, C₅).

The isoprene rule (Ruzicka, 1922): most terpenes consist of isoprene units linked head-to-tail or head-to-head.

Classification by carbon count

Biosynthesis: from acetyl-CoA via mevalonate

The biosynthesis of all terpenes starts from acetyl-CoA via the mevalonate pathway:

1. 3 Acetyl-CoA → 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA): two Claisen-like condensations.
2. HMG-CoA + 2 NADPH → mevalonate (mevalonic acid): reduction by HMG-CoA reductase (the rate-limiting step, drug target for statins).
3. Mevalonate + 3 ATP → isopentenyl pyrophosphate (IPP): phosphorylation and decarboxylation.
4. IPP ↔ DMAPP (dimethylallyl pyrophosphate): isomerization, gives the two essential monomers.

IPP and DMAPP are the universal C₅ building blocks of all terpenes. They differ by one double bond position.

Chain extension: head-to-tail coupling

DMAPP + IPP → geranyl pyrophosphate (GPP, C₁₀). Mechanism: the DMAPP's pyrophosphate leaves; the resulting allylic carbocation is attacked by IPP's terminal C=C; deprotonation gives GPP.

GPP + IPP → farnesyl pyrophosphate (FPP, C₁₅). Same mechanism.

FPP + IPP → geranylgeranyl pyrophosphate (GGPP, C₂₀). Same.

These linear polyisoprenoids are the precursors to mono-, sesqui-, di-, tri-, and tetraterpenes via various cyclization and modification reactions.

Cyclization to monoterpenes (C₁₀)

GPP can cyclize via cationic cyclization to give monoterpenes: - Limonene (citrus): 6-membered ring + one isopropenyl group. - α-pinene (pine): bridged bicyclic. - Menthol (peppermint): cyclohexane with hydroxyl.

Each cyclization is enzyme-catalyzed; a specific cation is generated and trapped at a specific position.

34.6 Cholesterol and steroid hormone biosynthesis

Cholesterol (C₂₇) is the most-studied sterol. Its biosynthesis from acetyl-CoA is one of biology's most elegant pathways.

From acetyl-CoA to squalene

Following the mevalonate pathway: - 18 Acetyl-CoA → 6 IPP/DMAPP (C₃₀). - 2 GPP (C₂₀) condense head-to-head to give squalene (C₃₀, the linear triterpene precursor of cholesterol).

Wait — let me restate: the C₃₀ squalene is built from 6 IPP+DMAPP units, which in total is 18 acetyl-CoA equivalents.

Squalene cyclization to lanosterol

The most spectacular reaction in biosynthesis. Squalene synthase (or oxidosqualene cyclase) folds the 30-carbon linear hydrocarbon squalene into the tetracyclic lanosterol in a single step. The mechanism:

1. Epoxidation of one C=C of squalene (by squalene monooxygenase) gives 2,3-oxidosqualene.
2. Protonation of the epoxide and opening generates a tertiary carbocation.
3. Cationic cyclization cascade: the carbocation initiates a series of intramolecular C=C attacks. Each attack generates a new ring and a new cation.
4. Migrations: methyl and hydride shifts occur to relieve strain.
5. Deprotonation completes the polycyclization, giving lanosterol with 4 fused rings and 7 stereocenters set in one step.

The reaction is enzyme-catalyzed cationic polyene cyclization. It is one of the most elegant reactions in biology, controlling 7 stereocenters from one substrate in one step.

From lanosterol to cholesterol

Lanosterol has 30 carbons. Cholesterol has 27 carbons. The difference: 3 methyl groups are removed by oxidation steps: 1. The C14 methyl is oxidized to a carboxylic acid and decarboxylated. 2. The two C4 methyls are similarly removed. 3. Some C=C bonds are hydrogenated; others are introduced.

Total: ~25 enzymatic steps from acetyl-CoA to cholesterol. Each step is a known organic mechanism.

Cholesterol's downstream products

Cholesterol is the precursor of: - Steroid hormones: testosterone, estradiol, progesterone, cortisol, aldosterone (made by enzymes in adrenal glands and gonads). - Vitamin D: from 7-dehydrocholesterol via UV light + thermal isomerization. - Bile acids: cholic acid, chenodeoxycholic acid (made in liver, secreted into bile, used to emulsify fats for digestion). - Membrane sterol: cholesterol modulates membrane fluidity in animal cells.

Biological Connection 34.1: Steroid hormone biosynthesis.

Cholesterol → pregnenolone (lose 6 carbons) → various pathways: - Pregnenolone → progesterone → various corticosteroids (cortisol, aldosterone) in adrenal cortex. - Pregnenolone → androstenedione → testosterone in testes. - Testosterone → estradiol (aromatization of A ring) in ovaries and testes.

Each step is enzyme-catalyzed but uses standard organic mechanisms (hydroxylation, oxidation, reduction, dehydration).

34.7 Statins: blocking cholesterol biosynthesis

The statins are the most-prescribed drug class for cardiovascular disease prevention. They work by inhibiting HMG-CoA reductase, the rate-limiting step of cholesterol biosynthesis.

Mechanism of statin action

Statins are competitive inhibitors that mimic the HMG-CoA substrate. They bind to HMG-CoA reductase's active site, preventing the natural substrate from binding.

Examples: - Lovastatin (Mevacor): the first statin, derived from a fungus (1976 discovery by Akira Endo). - Simvastatin (Zocor): semi-synthetic. - Atorvastatin (Lipitor): synthetic; was the top-selling drug in history (~$130 billion lifetime sales). - Rosuvastatin (Crestor): a more-potent statin. - Pravastatin, Fluvastatin, Pitavastatin: other variants.

By blocking cholesterol biosynthesis, statins: - Lower LDL cholesterol by 30–60%. - Reduce cardiovascular events (heart attack, stroke) by 25–35%. - Used preventively in millions of patients worldwide.

The statin discovery is one of the great achievements of pharmacology. Akira Endo (the discoverer) was nominated for the Nobel Prize multiple times.

Biological Connection 34.2: How statins help heart disease.

1. Statin enters bloodstream after oral administration.
2. Reaches the liver (the major site of cholesterol synthesis).
3. Inhibits HMG-CoA reductase → less cholesterol synthesis.
4. Liver responds by upregulating LDL receptors (to take up LDL cholesterol from blood).
5. LDL cholesterol drops in plasma.
6. Less LDL means less plaque formation in arteries → fewer heart attacks and strokes.

The chemistry: statins compete with HMG-CoA for HMG-CoA reductase's active site. They mimic the substrate's transition state — a textbook example of medicinal chemistry done right.

34.8 The unifying principle

All of lipid biosynthesis can be summarized as:

1. Start from acetyl-CoA (the universal 2-carbon currency).
2. Iterated Claisen condensations (Ch 28) build chains: fatty acids straight; terpenes via mevalonate then C₅-C₅ couplings.
3. Reductions, dehydrations, oxidations introduce double bonds, hydroxyls, etc.
4. Cyclizations (often cationic) form rings: polyene cyclization for cholesterol, terpenes.
5. Late-stage modifications (oxidation, methylation, conjugation) generate diversity.

A few mechanisms (Claisen, reduction, cyclization) generate enormous structural diversity. This is why mechanism-first chemistry is so powerful: master the few mechanisms, and you understand the many products.

34.9 Summary

1. Lipids: fatty acids, triglycerides, phospholipids, sterols, terpenes.
2. Fatty acids: long-chain carboxylic acids; saturated or unsaturated; ω-3, ω-6, ω-9.
3. Fatty acid biosynthesis: iterated Claisen + reduce + dehydrate + reduce. 2 carbons per cycle from acetyl-CoA + malonyl-CoA. NADPH-driven.
4. β-oxidation: the reverse process. 2 carbons per cycle, releasing acetyl-CoA.
5. Triglycerides: triesters of glycerol; energy storage.
6. Phospholipids: membrane material; amphiphilic; form bilayers.
7. Terpenes: built from isoprene units (C₅). Mono (C₁₀) → tetra (C₄₀) → polyterpenes.
8. Mevalonate pathway: from 3 acetyl-CoA via HMG-CoA, mevalonate, IPP, DMAPP.
9. Cholesterol: from acetyl-CoA via mevalonate, then squalene, then lanosterol cyclization.
10. Squalene cyclization: cationic polyene cyclization → tetracyclic lanosterol with 7 stereocenters set in one step.
11. Cholesterol → steroid hormones, vitamin D, bile acids.
12. Statins: HMG-CoA reductase inhibitors; lower cholesterol; reduce heart attacks/strokes.

Chapter 35 turns to drug design — how chemistry is applied to make medicines, with capstone treatment of the thalidomide story.