DO NOT PRINT THIS PAGE. Click HERE for your print-friendly copy.

The Molecules that Make Plant Cells...Different

By now, you should be very familiar with the four basic types of biological macromolecules, their subunits, and their functions. Recall...

Recall that a polymer is a long chain of repeating subunits that are (more or less) identical.


Everyone here has had first year biology, and so should have a basic understanding of how DNA and RNA work. But in case you've forgotten, here is a very brief and extremely simple baby overview of genetics.

The basic structure and function of DNA is conservative across taxa, and is one of the most unifying characters of life on earth. There is nothing significantly different about plant DNA, compared to that of other taxa, other than the instructions encoded in plant DNA.

As in animals, ATP (and GTP)--components of nucleic acids, when in polymer form--are the "energy currency" of the cell. Their high-energy phosphate bonds yield 7.3kcal/mole, upon hydrolysis.


In most organisms, protein comprises more than 50% of the biomass of the individual. In plants, however, cellulose makes up the bulk of the organism, with protein coming in a distant second.

Like other organisms, plants use about 20 different kinds of amino acids to construct their unique proteins, but there is nothing significantly different about plant proteins compared with those of other organisms. They are constructed the same way, with different proteins having characteristic structure

As in other organisms, proteins in plants may be structural (often helical or pleated sheets), or functional (enzymes, usually with complex tertiary or quaternary structure).

(What is an essential amino acid? What are the essential amino acids for Homo sapiens? (lys, trp, thr, met, his, phe, leu, val, ileu) And where do we get them? Do plants require any essential amino acids?)


In animals, carbohydrates are used primarily for short-term energy storage.
In plants, however, carbohydrates are not only used for energy storage, but also make up the main structure of the organism itself.
Simple Carbohydrates (Sugars)
The three most abundant simple sugars synthesized by plants are
  • glucose - the primary sugar used for energy in cellular respiration. (In animals and many other organisms, it's also the primary transport sugar moved around via the blood stream or other transport systems in the body--but not in plants!)
  • sucrose - the a major transport sugar in plants, is intimately involved with water movement through phloem (as we'll see later).
  • fructose - another storage sugar, primarily sequestered in aqueous solution as polysaccharides called fructans

    The simplest carbohydrates are monosaccharides, which consist of a single carbon ring. Next up are the disaccharides, consisting of two carbon rings. Recall also that some molecules may have the same chemical formula but different physical arrangement of the atomic components, and are isomers of one another. (For example, glucose and fructose are isomers of one another. Sucrose, the most common form of sugar transported by plants, is a disaccharide composed of glucose and fructose.)

    Monosaccharides are quite stable, highly water-soluble, and are thus excellent candidates for physical structure, transport and energy storage.

    Complex Carbohydrates
    Chains of sugar molecules may be manufactred by the plant, and these are known as polysaccharides. Short chain polysaccharides are known as oligosaccharides (oligos is Greek for "short".). Manufacture of sugar polymers requires the removal of one -OH from one sugar and an H from the other, which join to form a molecule of water. The reaction is thus a dehydration reaction. To break the bond of a polysaccharide, water must be added back and joined to the resulting monomers in their original form (an -OH on one molecule and an -H on the other), a process you all recall as hydrolysis (literally, "splitting with water").

    Starch is one of the defining biological macromolecules of Plantae and its closest relatives. Starch, a polymer of glucose, comes in two forms:

    ...and is used for long-term energy storage, sequestered as starch granules inside plant cells. Starch granules may play other roles as well, as we'll see.

    The enzyme responsible for starch synthesis is known as starch synthetase. It joins the C-1 of one glucose to the C-4 of the next to form an alpha-1,2 glycosidic bond. Fructans are another storage polysaccharide, but these are composed of primarily of fructose. After starch and sucrose, fructans are probably the most abundant storage carbohydrates in plants. Synthesized from fructose and sucrose in the plant vacuoles, fructans may be linear or branched, with a basic trisaccharide structure known as a kestose(fructose and sucrose polymer):

    Because fructans are water soluble, they can be stored in much higher concentrations than starches, which are stored as relatively voluminous granules.

    Our friend CELLULOSE is the most abundant organic molecule on the planet.

    Cellulose is found in the form of microfibrils that make up the main structural molecules of the plant cell wall.

    Like starch, cellulose is a polymer of glucose. But a subtle shift in chemical structure changes it from highly digestible nutrient into The Perfect Structural Material for plants.

    You may recall from other courses that glucose can exist in two structural forms, alpha (on the left) and beta (on the right):

    In aqueous solution in the plant cell, these two forms flip back and forth, and stay in equilibrium, about 50:50. But when the glucose molecules join to form polymers, there can be more of one form or the other.

  • Starch (and glycogen, "animal starch") are composed entirely of alpha-glucose.
  • Cellulose is composed entirely of beta-glucose. It is constructed by a different set of enzymes (cellulose synthases), which forms beta-1,4 glycosidic bonds between the component glucose monomers.

    The digestive enzymes capable of breaking down chains of alpha glucose--found in the vast majority of heterotrophs--do not recognize nor bind to beta-glucose chains. Only a few types of organisms can produce enzymes capable of digesting the beta-glucose chain that is cellulose. (Can you name some of them?)

    Think of the evolutionary implications of the tiny shift that occurred when an enzyme appeared that linked beta-glucoses together, instead of alpha-glucoses. And then think of how rare the mutation that allowed any organisms to break that mighty chain!


    These are molecules composed primarily of single or branched fatty acid chains.

    Fats are nonpolar and hydrophobic, and thus are neither soluble nor miscible in water.

    Lipids serve structural roles in cell membranes (e.g., phospholipids), and are also important players in plant metabolism. Lipids may be... Structural Lipids
    1. Phospholipids
    As in all eukaryotes, phospholipids are a major structural component of plant cell membranes.

    2. Waxes and Cutins
    Plant epidermal cells secrete fatty acids, which polymerize upon exposure to O2 to form cutins and waxes. These may branch and cross-link, forming complex, hydrophobic, 3-D blobs that help retain water inside the plant, prevent undesired entry of water and protect the plant against invading fungal pathogens. The protective layer is known as the cuticle, composed of cutin impregnated with wax (cuticular wax).

    The cuticle prevents water loss through the epidermal cells, but also necessitates the existence of stomates, gas-exchange pores, in terrestrial plants with a thick cuticle.

    Cutins and waxes are also major structural components of cell walls in higher, terrestrial plants. Cutin and waxes form matrices around plant cells, and the complex fatty barrier effectively prevents water from traveling through any such barrier.

    Suberin A special type of wax, known as suberin is especially important in the cells of the outermost layer of woody plant bark, known as cork. All plants that produce true, botanical wood produce a layer of cork, which is largely impervious to water and gases. (The cork of the Cork Oak, Quercus suber, is used to make wine corks for this very reason; it's from this plant that suberin gets its name.)

    As we'll see later, suberin also plays a vital role in the root's ability to selectively allow only certain substances into the plant.

    The cork (outermost layer of the bark of woody plants is the main location you'll find suberin. It's arranged in layers alternating with waxes to prevent water loss from woody stems that no longer have an epidermal layer.

    We'll also find that suberin plays a very important role in the transport of water through the root cortex, preventing interstitial entry of water into the root, and hence, creating a selectively-permeable membrane into the root in a layer called the endodermis.

    Plant Compounds and Homo sapiens
    Various species of plants manufacture waxes unique to their taxa, and many are of commercial importance. Carnauba wax, used as a polish for everything from cars to floorsis extracted from the leaves of the Carnauba Wax Palm (Copernicia cerifera) of the Amazon. (So long, car polish...)

    Steroids are lipids whose basic structure is that of four connected hydrocarbon rings. Functional groups attached to this basic steroid backbone determine the function of the many different steroids found in living organisms.

    A hydroxyl group in the carbon-3 position makes the steroid a sterol (an alcohol; remember?). These function to stabilize plasma membranes. Sitosterol is the main form found in plants and their closest relatives, green algae:

    Cholesterol, the main plasma-membrane stabilizing sterol in animal cells is quite rare in plants:

    Steroids also may function as hormones, or be hormone precursors. The discovery of estrogen- and progesterone-like compounds in plants has spawned a new area of biomedical research, not only in cancer treatment, but also in the treatment of symptoms associated with menopause.

    More Organic Compounds

    Plants produce a huge, diverse assemblage of organic compounds such as those above as well as many others. Organic compounds may be produced by plants to serve as All these are derived from that single product of photosynthesis: 3-phosphoglyceraldehyde (p-gal). Hence, a plant needs only CO2, H2O, sunlight and some soil minerals (macro- and micronutrients) in order to survive and thrive. A plant is the complete autotroph.

    Plants respire, of course, just as animals and other heterotrophs do. But heterotrophs rely on autotrophs for life, and could not survive without them. Plants produce the essential nutrients needed by heterotrophs to serve as coenzymes, cofactors, etc.

    Plants produce all the vitamins they need to serve as enzymatic cofactors. Animals, however, either never had the metabolic ability to produce these things, or have lost them via mutations. Such mutations would be lethal in a plant, but an animal can survive (or even benefit) from such a genetic change as long as it can eat plants to provide the lost nutrient. Humans and other primates cannot produce Vitamin C (though many animals can). Hence, we suffer from scurvy (bleeding gums, joint swelling and pain, weight loss, etc.) if deprived of our necessary ascorbic acid.

    The one nutrient needed by animals that plants do not manufacture is cholesterol. Herbivores must be able to metabolically manufacture cholesterol, whereas carnivores can obtain it by eating herbivores. The farther up the food chain an animal is, the less deleterious is might be to lose a nutrient's synthetic pathway, since the organism's prey (or host) will likely provide the necessary nutrients.

    It's a delicate balance between saving energy via loss of synthetic pathways versus the risk of nutrient deficiency in a nutrient-poor environment.

    Secondary Metabolites: Plant Defense

    Plants are literally rooted to the spot. They can't flee predators/herbivores. But that certainly doesn't mean they are defenseless. Plants are masters of chemical warfare.

    Metabolites are just what the name implies: compounds made via metabolic reactions. Primary metabolites are those found in all cells, and are necessary for normal cellular function and energy transduction. They include the biolgical macromolecules and simple sugars.

    Secondary metabolites are complex chemical compounds that are NOT found in every cell, and not found in every species of plant. Once thought to be waste products of metabolism, they are now know to be vital for many plant functions, including

    Like animal hormones, plant secondary metabolites are usually produced in a specific location of the plant, and then transported for storage (usually in vacuoles) to another part of the plant.

    The compounds often follow a Circadian rhythm, with concentration varying in a diurnal cycle, or seasonally, or even with environmental influence, depending on the plant producing it and the specific compound being produced.

    Three major types of secondary metabolites:

    These are produced by plants primarily as a means to deter herbivores, and, as one might expect from such a compound, they mimic some of the naturally occurring compounds in animals and compete for the same receptors in animal cells.

    The first alkaloid formally described from a plant was morphine from the opium poppy. Though it was described in 1806, it had been used by people as a painkiller and as a recreational drug for centuries before Western scientists figured out what it was. Many synthetic opioids are now in production by pharmaceutical companies that have taken the basic formula of morphine and changed it to mitigate some of its more harmful effects.

    Cocaine is another well-known alkaloid with pharmaceutical use. It, too, has been modified and now synthetic derivatives serve as local anesthetics (lidocaine, marcaine, etc.).

    Caffeine is produced by several different types of plants, primarily in the family Rubiaceae (coffee, tea, Cacao). In nature, it inhibits the growth of nearby seedlings, preventing competition for soil resources. This effect is known as allelopathy.

    Theophyllines are similar stimulants produced by tea plants, and are even more powerful stimulants that caffeine. But because they are generally found in lower concentration in leaves than caffeine, most people are not aware of their effects. (But when you drink a cup of tea...)

    Nicotine is another stimulant meant to deter herbivores. What's with us humans, anyway?

    Atropine is found in a number of different plants. One local source is the Angel's Trumpet, which also produces some other very deadly alkaloids.

    If you've ever been to the ophthalmologist and had your pupils dilated, you've had the joy of atropine. Though it's now used medicinally, it was once used as aid! (See what you missed if you didn't come to class?) (Our friend Atropa belladona...)

    The most common secondary metabolites in plants, there are more than 22,000 described!

    Terpenes may serve as photosynthetic accessory pigments (carotenoids), hormones (giberellins, abscisic acid), plasma membrane components (sterols), or electron transport molecules (ubiquinone, plastoquinone), which we'll discuss as they come up.

    The basic subunit of terpenes is isoprene (C5H8), and other terpenoids are classified by the number of isoprene subunits they contain. Isoprene itself is produced in vast quantities by plants, especially on hot days. The Smoky Mountains were "smoggy" long before the cars arrived: isoprene is a major component of smog in forested areas, where plants produce it to stabilize plasma membranes in photosynthetic cells and thylakoids when it's very hot.

    Common terpenes include:

    Essential oils are usually mono- or sesquiterpenoids that create the aroma that plants use to attract pollinators, deter herbivores, kill fungi or bacteria, or inhibit the growth of competing plants.

    What are some examples?
    Are all essential oils NICE?

    Taxol has gotten considerable press as a potential anti-cancer agent. It was first discovered in the rare Pacific Yew Tree (Taxus brevifolia), but similar compounds have now been isolated from other, less endangered yew species. Synthetic versions have since been made in the lab, giving hope for cancer patients as well as for the conservation of the yew trees.

    Rubber is a HUGE terpene, consisting of hundreds or thousands of isoprene units. It starts out as milky latex and is processed into the flexible, bouncy substance with so many commercial uses and applications.

    Cardiac glycosides induce heart attack in large concentrations (as in when eaten by an unsuspecting herbivore noshing on Foxglove or other cardiac glycoside-producing plants). But modified and taken in small quantities, these compounds can actually slow and strengthen the heartbeat. Many of the most toxic plant families (e.g., Asclepiaceae (milkweeds), Apocynaceae (dogbane)) produce cardiac glycosides. Cardiac glcosides taste NASTY, and are important in the aposematic protection of butterflies that feed on milkweeds as larvae.

    A Tale of an Unfortunate Bluejay

    Phenolic Compounds
    If you've taken organic chemistry, then you know that a phenol is simply an aromatic carbon ring with a hydroxyl group attached. But plants do know how to use a phenol! If only we could figure out what they're doing with them.

    Phenolics are found in almost all plant cells, and the function of many is not well understood. Many are pigments, such as flavonoids, the most recently famous of which is resveratrol, found in red grapes (and red wine). This compound not only is reported to lower serum cholesterol levels (mechanims not known), but also is an estrogen mimic that may be helpful in treating breast cancer.

    Anthocyanins are phenolic pigments ranging in color from dark red to purple. Flavones and flavonols are pale ivory-colored pigments that may convert to sugar when temperatures are very cold.

    Different flavonoids are used by plants to attract micorhizzal fungi, or bacterial symbionts to set up a mutualistic relationship.

    Tannins are bitter-tasting phenolic compounds employed by flowering woody plants as defense against herbivores. These are found in high concentrations in wood, as well as the outer layers of unripe fruit (why?).
    And as their name implies, these compounds can be used to denature protein and "tan" animal hides.

    Salycilate is our friend. First discovered in willow bark (Salix sp.for which the compound is named), this is the active ingredient in aspirin. But did the willow tree kindly make aspirin for US?

    Salycilate is vital to the plant for SAR: Systemic Acquired Resistance, a sort of plant immune response seen in many flowering plants (Anthophyta). When the plant is injured by bacteria or fungi in one area of the plant, salycilates are involved in a complex chemical cascade that allows the neighboring tissues of the plant and the rest of its body to later resist attack by the same and similar pathogens!

    The activation of the SAR response requires accumulation of endogenous salicylic acid, which is triggered by the presence of a pathogen. In the best-studied model system of the SAR response is known from Wall Cress (Arabidopsis thaliana). In this plant, the high concentration of salicylic acid activates a molecular signal transduction pathway that is identified by a gene called nim1 (also known as npr1 or sai1). The pathway results in heightened immunity to all pathogens in uninfected parts of the plant.

    Plant toxins have affinity for existing receptors in animals.

    Chemical pathways that lead to production of toxic compounds are adaptive, and mutations that result in such pathways may lead to those mutant individuals leaving more offspring then their tastier conspecifics. But does it always work? Not if you have a clever herbivore who has evolved behaviors that make your poisons ineffective!

    Lignin is the second most abundant of all organic molecules, and it is localized in plant cell walls. Lignin forms a polymer comprised of three large alcohol subunits (coumaryl (primarily in flowering plants), coniferyl (primarily in gymnosperms), and sinapyl (primarily in grasses)), and the structure of lignins varies widely with species.

    Lignin provides compressional strength to the cell wall, unlike the flexible strength conferred by cellulose. Without lignin, terrestrial plants probably could not have reached the sizes they do today, as cellulose does not provide enough resistance to gravity itself.

    Waterproof, lignin is also useful in directing water flow through the xylem, as the cellular subunits of xylem are rich in lignin.

    Lignin, Cellulose, Fungi, and Wood Rot
    Lignin is nearly indestructible. There are almost no organisms on earth (with the exception of a few types of fungi) that can break down lignins. Its natural color is reddish-brown. By looking at the color of a rotting log, you can tell which type of fungal (i.e., Wood Rot Decay Fungi) decomposer has been at work.

    Fungi categorized as Brown Rot Fungi feed mainly upon celluloses, and cannot fully break down lignin. Wood broken down by these fungi tends to look reddish-brown in color because of the liginin residues, and falls apart in relatively large chunks as the network of cellulose is destroyed.

    These fungi are more common in cool, wet climates, such as the rainforests of the Pacific northwest.

    By contrast, fungi categorized as White Rot Fungi can fully break down and utilize lignin (as well as cellulose and hemicellulose polymers), so wood being broken down by these fungi appears greyish white (due to the cellulose residues lating longer). Wood affected with "white rot" will more gradually lose its strength, and become spongy, rather than fall apart in blocks/cubes.

    Lignin's first role in plants may have been as a natural microbe inhibitor, and only later was it sequestered for other uses.

    Unfortunately, it's not a nice compound when extracted during the manfacture of wood pulp, as it breaks down into toxic aromatic compounds that are dumped into nearby water. A paper mill is not a good neighbor.