Table of Contents
Overview
Besides proteins, carbohydrates, lipids, and nucleic acids, cells use many other organic molecules that play crucial, often very specific, roles. In this chapter we focus on two such groups:
- pyrrole compounds
- terpenes (isoprenoids)
Both are examples of “specialized” or “secondary” metabolites: molecules that are not strictly required for basic survival in every organism, but that enable important functions such as light capture, oxygen transport, signaling, or defense.
Pyrrole Compounds
The pyrrole ring
Pyrrole compounds share a common structural feature: the pyrrole ring.
- A pyrrole ring is a five-membered ring with one nitrogen atom and four carbon atoms.
- In simplified form, you can imagine a small pentagon where one corner is nitrogen (N) and the others are carbon (C).
- This ring has a system of delocalized electrons, making it chemically reactive and suitable for binding metals or absorbing light.
The pyrrole ring itself is a relatively simple organic molecule, but in living organisms several pyrrole rings can be linked together to form more complex “macrocycles” (large ring systems). These macrocycles are central to life processes.
Porphyrins: macrocycles built from pyrroles
Four pyrrole rings can be connected in a ring-like structure to form a porphyrin. Porphyrins (and closely related molecules) are often able to bind metal ions at their center.
A general feature:
- 4 pyrrole units → linked into a large, flat, ring-shaped molecule
- central cavity → can “host” a metal ion (e.g., Fe²⁺, Mg²⁺, Co²⁺)
- planar structure → good at absorbing light and/or enabling electron transfer
Small modifications of porphyrins lead to a family of molecules with different biological functions. Three particularly important examples are:
- heme
- chlorophylls (tetrapyrrole-related)
- cobalamin (vitamin B₁₂, corrin ring)
Only the pyrrole-based aspects and the overall roles will be sketched here; photosynthesis, respiration, and metabolism are discussed in later chapters.
Heme: pyrrole and oxygen transport
Heme is a porphyrin-like molecule with an iron ion at its center.
Basic points:
- 4 pyrrole rings → porphyrin framework
- central metal: Fe²⁺ (iron)
- part of larger proteins → for example, hemoglobin and myoglobin in animals, and many enzymes (e.g., cytochromes)
Key functions that depend on the pyrrole-based heme group:
- Binding and transport of oxygen in blood (hemoglobin)
- Storage of oxygen in muscle (myoglobin)
- Electron transfer in cellular respiration (cytochromes in the electron transport chain)
- Catalysis of oxidation reactions in many enzymes (e.g., cytochrome P450 family)
Why the pyrrole system matters:
- The conjugated (electron-rich) ring structure allows heme to absorb and release energy.
- The nitrogen atoms in the pyrrole units help hold the iron ion in an optimal position for reversible binding of oxygen or for electron transfer.
Thus, a relatively simple building block (pyrrole) underlies a complex, metal-containing cofactor that is essential for respiration and energy metabolism.
Tetrapyrroles in photosynthesis: chlorophylls
Chlorophylls are photosynthetic pigments in plants, algae, and cyanobacteria. They are also derived from linked pyrrole units.
Key structural features:
- ring system related to porphyrins (often called a chlorin)
- 4 modified pyrrole units
- central metal: Mg²⁺ (magnesium) instead of iron
- additional side chains (e.g., a long hydrophobic tail in chlorophyll a) that anchor the molecule in membranes
Biological roles that depend on the pyrrole-based ring:
- Absorption of light in specific wavelength ranges (mainly blue and red)
- Conversion of light energy into chemical energy in the light-dependent reactions of photosynthesis
The conjugated electron system of the tetrapyrrole ring makes chlorophyll highly efficient at absorbing light and transferring excitation energy, functions that are elaborated in the chapter on photosynthesis.
Vitamin B₁₂ (Cobalamin) and related corrinoids
Vitamin B₁₂ (cobalamin) is another example of a macrocycle built from pyrrole-like units, though the ring (corrin ring) is slightly different from a classical porphyrin.
Key features:
- ring derived from pyrrole units (corrin)
- central metal: Co³⁺ (cobalt)
- large and complex structure, with additional side chains and a nucleotide-like portion
Biological significance:
- acts as a coenzyme in various metabolic reactions (e.g., rearrangement of carbon skeletons, methyl group transfers)
- essential in humans for:
- normal function of the nervous system
- synthesis of certain amino acids and nucleotides
- formation of red blood cells
Only certain prokaryotes can synthesize vitamin B₁₂ completely; animals (including humans) must obtain it directly or indirectly from microorganisms via their diet.
Other biologically relevant pyrrole derivatives
Beyond these well-known examples, many other molecules contain pyrrole or pyrrole-like units:
- Bile pigments (e.g., bilirubin, biliverdin)
- derived from heme breakdown
- important in waste processing and can act as antioxidants
- Some alkaloids and natural pigments
- for instance, certain red and purple pigments in marine organisms
- Signal and sensory molecules
- e.g., retinal (visual pigment) is not a pyrrole itself but works closely with a lysine residue in opsin to form the light-sensitive rhodopsin complex; different structural classes can cooperate in light sensing.
The unifying theme: pyrrole rings contribute to molecules that can bind metals, transfer electrons, or interact with light—functions that are central to respiration, photosynthesis, and signaling.
Terpenes – Isoprenoids
Basic building block: isoprene unit
Terpenes (or isoprenoids) form one of the largest and most diverse families of natural products. They are built from repeated units of a simple 5‑carbon molecule, the isoprene unit.
An isoprene unit has 5 carbon atoms and 8 hydrogen atoms:
- molecular formula: $$\text{C}_5\text{H}_8$$
Terpenes can be envisioned as “chains” or “rings” constructed by joining these C₅ units in different ways.
General formula (for many terpenes):
- $$\text{C}_5\text{H}_8)_n$$, where $$n$$ is the number of isoprene units.
Because of this, terpenes are often classified according to how many C₅ units (isoprene units) they contain.
Classification by isoprene units
Some common classes of terpenes and their approximate carbon counts:
- Hemiterpenes: 1 isoprene unit → C₅
- Monoterpenes: 2 isoprene units → C₁₀
- Sesquiterpenes: 3 isoprene units → C₁₅
- Diterpenes: 4 isoprene units → C₂₀
- Sesterterpenes: 5 isoprene units → C₂₅ (less common)
- Triterpenes: 6 isoprene units → C₃₀
- Tetraterpenes: 8 isoprene units → C₄₀
Many biologically important terpenoids are modified terpenes—they may contain additional groups such as oxygen, or have been rearranged. These are often called terpenoids or isoprenoids in a broader sense.
Biological functions of terpenes
Despite their common chemical origin, terpenes perform extremely diverse roles in living organisms. A few major roles include:
- components of essential oils and plant scents
- pigments involved in light absorption and protection
- precursors of hormones and vitamins
- structural components of membranes
- defense substances against herbivores, microbes, or competitors
Monoterpenes and sesquiterpenes: scents and defense
Monoterpenes (C₁₀) and sesquiterpenes (C₁₅) are often volatile—easily evaporating at normal temperatures.
They are major components of:
- Essential oils from plants (e.g., mint, lavender, citrus, conifers)
- Characteristic odors of herbs and spices (e.g., thymol, menthol, limonene, pinene)
Biological roles:
- Attraction of pollinators and seed dispersers through fragrant floral and fruit scents
- Defense:
- against herbivores (bitter tastes, toxic effects)
- against microbes and fungi (antimicrobial activity)
- Communication:
- some insects use terpene derivatives as pheromones (chemical signals).
From a human perspective, these compounds are important in:
- perfumery and flavoring
- traditional and modern medicine (some have anti-inflammatory, antimicrobial, or other pharmacological properties)
- pest control (e.g., natural insect repellents).
Diterpenes: pigments and resins
Diterpenes (C₂₀) are structurally more complex and less volatile. Many plant resins and some defensive compounds are diterpenes.
Important biological roles include:
- components of plant resins (e.g., conifer resins that protect wounds)
- precursors of certain plant hormones (e.g., gibberellins are diterpenoid growth regulators)
- participation in signaling and responses to stress.
In addition, some photosynthetic pigments are derived from diterpenoid precursors (though the best-known pigment examples align more classically with tetraterpenes, described below).
Triterpenes: precursors of steroids
Triterpenes (C₃₀) are assembled from six isoprene units. A key triterpene skeleton, squalene, serves as a precursor to steroid molecules.
Biological importance:
- Squalene is an intermediate in the biosynthesis of sterols, such as:
- cholesterol (in animals)
- phytosterols (in plants)
- Steroids derived from triterpenes include:
- many hormones (e.g., sex hormones, some stress hormones)
- bile acids
- other signaling molecules
Thus, through the isoprenoid pathway, simple C₅ units ultimately give rise to major regulatory substances that control growth, metabolism, and reproduction.
Tetraterpenes: carotenoids and related pigments
Tetraterpenes (C₄₀) are composed of eight isoprene units and often appear as carotenoids, an important group of pigments.
Carotenoids:
- typical colors: yellow, orange, red (e.g., in carrots, tomatoes, autumn leaves)
- occur in plants, algae, some bacteria, and in animals that obtain them via diet
Main biological roles:
- Light harvesting and energy transfer in photosynthesis:
- accessory pigments that extend the range of usable light beyond what chlorophyll absorbs
- Photoprotection:
- help protect photosynthetic organisms from damage by excess light and reactive oxygen species
- Coloration for signaling:
- in animals, carotenoids contribute to bright colors in feathers, scales, and skin, used in mate choice, camouflage, or warning signals
- Precursors of vitamins:
- e.g., β-carotene is a precursor of vitamin A (retinol), important for vision and epithelial health.
Carotenoids illustrate how terpenoid-based molecules can bridge the functions of light absorption, protection, and signaling across very different organisms.
Isoprenoids in membranes: dolichols, ubiquinone, and others
Some terpenoids are key components or cofactors in cell membranes and electron transport systems.
A few examples:
- Ubiquinone (coenzyme Q):
- contains an isoprenoid “tail” that anchors it in the inner mitochondrial membrane
- functions as a mobile electron carrier in the electron transport chain of cellular respiration
- Dolichols:
- long-chain polyisoprenoids
- involved in glycoprotein synthesis by helping attach sugar chains to proteins in the endoplasmic reticulum
- Prenylated proteins:
- some proteins have isoprenoid groups covalently attached (“prenylation”)
- this helps position them correctly in membranes and can affect cell signaling.
These examples highlight that terpenoids are not only pigments and scents but also structural and functional elements deeply embedded in core cellular processes.
Ecological and evolutionary significance of terpenes
Because terpenes are so chemically diverse and easily modified, they have been repeatedly “recruited” by evolution for different tasks:
- protection (toxins, repellents, antiseptics)
- attraction (scents, colors)
- internal regulation (hormones, signaling compounds)
- energy conversion (photosynthetic pigments, electron carriers)
For many groups of organisms, especially plants, the specific mix of terpenoids they produce is important for their ecological interactions and can even serve as a taxonomic characteristic in systematics.
Summary
- Pyrrole compounds are based on a five-membered ring containing nitrogen. Combined into larger ring systems (porphyrins, corrins), they form key cofactors such as:
- Heme (iron–porphyrin), essential for oxygen transport and electron transfer
- Chlorophylls (magnesium–tetrapyrroles), essential for light capture in photosynthesis
- Vitamin B₁₂ (cobalamin), vital for several metabolic reactions.
- Terpenes (isoprenoids) are built from repeated 5‑carbon isoprene units. Variations in the number and arrangement of these units yield:
- Monoterpenes and sesquiterpenes: volatile scents, defense compounds, pheromones
- Diterpenes: components of resins, plant hormones
- Triterpenes: precursors of sterols and steroid hormones (e.g., cholesterol derivatives)
- Tetraterpenes (carotenoids): pigments for light harvesting, photoprotection, and coloration
- various membrane-associated and signaling molecules, such as ubiquinone and dolichols.
Although they are not counted among the “big four” macromolecules, pyrrole derivatives and terpenoids are indispensable for key life processes, including respiration, photosynthesis, metabolism, communication, and defense.