Chapter 1: Basic Plant Chemistry Concepts

For millions of years, plants have evolved a wealth of shapes and sizes and with them an abundance of highly diverse substances that help them stay alive and reproduce. Sweet fragrances from wild roses, bright pigments in fall leaves, and potent poisons, like those of the deadly nightshade plant, are all part of the huge range of compounds that plants produce to attract, protect, and repel (Figure 1.1). Most importantly, plants contain green chlorophyll, capable of trapping portions of sunlight. With chlorophyll's help, plants generate the basic chemicals that humans could not live without, like oxygen, sugars, fats, amino acids, and vitamins.

This book is an introduction to the chemistry of plants, especially concerning their organic chemistry. As a preparation for the descriptions of the chemistry of plant smells, colors, and defensive plant compounds, this introductory chapter reviews some basic chemistry concepts as they relate to plants.

We begin with a look at elements and their atoms. Plants need to have a set of elements available as nutrients, and in useful form. (It is a set that is not so different from human needs.) Just a couple of these elements—carbon, hydrogen, oxygen, nitrogen, and a few others—assemble to form the abundance of carbon-based organic molecules.

Elements link up by chemical bonds to form compounds. Plants, like all living things on Earth, require the compound water to live and grow. Therefore, a special section addresses the distinct structures of water molecules. They determine the unusual properties of this vital compound and affect how water moves through plants, how minerals are transported in aqueous saps, and where pigments are stored in plant cells.

Every gardener knows that growing plants starts with the right soil. Aside from suitable growing conditions, plants must have a sufficient supply of essential nutrients to be able to synthesize all the compounds that enable them to grow and live. With the proper nutrients and the right growing conditions, plants can produce alluring smells, enticing colors, or defensive substances. A look at the composition of soils leads to a more detailed description of ions, mineral nutrients in soils, and the acid or alkaline nature of growing media. Some soil compositions are also described that make understanding plant life truly challenging.

With a basic knowledge of elements, ions, and compounds in hand, we continue to study how plant compounds interact in chemical reactions that assemble new plant compounds or break them down. Plants must be able to perform these reactions in conditions dictated by their environment, namely at ambient temperatures and mostly in water. However, the environment can also entail highly restrictive conditions. Plants are able to function under harsh conditions thanks to elaborate enzymes and lots of time. Suitable nutrients, with light as the source of energy and with the help of the pigment chlorophyll, allow plants to undergo the numerous reaction steps of photosynthesis. These reactions produce oxygen and simple sugars like glucose. The sugars, in turn, are needed to compose all other organic compounds in plants: cellulose for plant structures, starch in bulbs to store energy, fats and amino acids, as well as plant fragrances, pigments, and toxins. Respiration, the set of reactions in which sugars and fats are broken down, provides the energy for further reactions in plants.

The chapter ends with an introduction to organic compounds and how to understand their structures. A few simple rules are needed to assemble basic organic molecules. Hydrocarbons, consisting of carbon and hydrogen only, will provide an introduction to organic structures. They will be illustrated with some examples of plants that contain specific hydrocarbons.

Just as chemical structures exactly describe the composition of a plant substance and pinpoint which compound is addressed (e.g. caffeine, vanillin, or vitamin C), systematic names of plants, also known as scientific or binomial names, clearly identify a plant. Common names vary regionally, and the same name may describe different plants. For example, the common name “hemlock” can refer to a poisonous, herbaceous plant native to the Mediterranean region or may describe a coniferous tree growing in North America. Add to this native and foreign language names, and the confusion is complete. The scientific name of a plant, on the other hand, describes universally which plant is meant (although it can change sometimes, too, because of new studies of plant relationships). Therefore, scientific names are included with the plant examples. The glossary at the start of this book provides explanations of key expressions (emphasized in the text with italics) and a brief introduction to the structure of scientific plant names.

For successful growth, productivity, and good survival, plants must have a continuous supply of specific nutrients they can then transform into sugars, starch, plant structural materials, colorful pigments, and all the substances that make plant life possible. These nutrients are a collection of elements in various forms and combinations. The periodic table of elements (see the front of this book and Box 1.1) lists all the elements known to this day.^1,2  But only a select few are essential for plant growth, i.e. they must be available to plants for survival. Table 1.1 lists the essential elements and shows some of the forms or combinations in which these elements have to be available so that plants can make use of them as nutrients.^3–5  Some of their major functions in plants are provided as well.

Plant nutrients are required in different amounts, and the quantities needed vary at different stages of plant life. Nutrient elements are considered to be either macronutrients that are required in relatively large amounts or micronutrients that are needed in much smaller amounts, sometimes even as traces only. Nevertheless, all the nutrients must be available. The growth of plants is greatly challenged if too much of a micronutrient or too little of a macronutrient is supplied, or if toxic additional elements are present in the soil. Plants that are able to grow in less-than-ideal environments need to have special adaptations. Some examples are described in Box 1.2.

The macronutrients—carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)—compose most of a plant structure. They are part of compounds in which the elements’ atoms are linked to each other by chemical bonds to form molecules.⁷  A large portion of hydrogen and oxygen atoms are tied up in water molecules (H₂O), as plants are mostly aqueous systems. Carbon atoms are a required part of all organic compounds. In addition, hydrogen, oxygen, and nitrogen are most common contributors to organic compounds. Phosphorus (P) and sulfur (S) can also be part of organic molecules. Note that the macronutrient elements mentioned are listed in vertical columns or groups on the right-hand side of the periodic table (with the exception of hydrogen). These are the groups that contain nonmetal elements. Their atoms bond to form the organic molecules of plant structures, plant odors, pigments, and defensive substances. In this book, we will mostly discuss organic compounds.

Two gases dominate Earth's atmosphere: nitrogen (N₂), contributing about 78%, and oxygen (O₂), providing about 21%, of our atmosphere. Oxygen molecules are produced by plants during photosynthesis. They participate in the breakdown of plant molecules during respiration, thereby providing energy for plant processes. In other words, oxygen has vital roles not only as part of compounds in plant life but also as oxygen gas.

One might assume that nitrogen gas, as the largest component of air, would be a major direct supplier of the macronutrient nitrogen. Yet, plants cannot directly use this much-needed nutrient from air. Nitrogen molecules are unreactive because of a strong triple bond between the nitrogen atoms (Figure 1.10d). Therefore, plants need the help of beneficial bacteria that convert nitrogen gas into forms that plants can work with, like ammonium (NH₄⁺) and nitrate (NO₃⁻) ions. Many different plants have root nodules with nitrogen-fixing bacteria, as shown in Figure 1.2a. Plants in the legume family, like peas and beans, have such root nodules and are well-known for their nitrogen-fixing abilities. Farmers of former times carefully incorporated plantings of them in their crop rotations to get nitrogen into the soil. Furthermore, some plants have learned to trap and digest insects to obtain another source of useful nitrogen. Insectivorous plants, in their amazing trapping mechanisms, have special enzymes that digest and break down the ensnared insects and their nitrogen-containing proteins and thus obtain additional, useful, nitrogen compounds (Figure 1.2b and c).

On the left-hand side and towards the bottom of the periodic table we find elements that are metals. Among them we find the macronutrients potassium (K), calcium (Ca), and magnesium (Mg). They mostly function as ions (i.e. as atoms with a charge) in the plant system. Metal ions have positive electrical charges; they are cations. Elements that are in the same group of the periodic table tend to have similar properties (a fact that was recognized by Mendeleev when he set out his first periodic table; see Box 1.1). Calcium and magnesium, for instance, both in main group number two, form ions with a 2⁺ charge and react similarly. Elements of the same group, therefore, can sometimes take each other's place in compounds or reactions, as shown in the plant examples in Box 1.2.

Only traces are needed for the micronutrients. Among them we find iron (Fe), copper (Cu), manganese (Mn), zinc (Zn), and molybdenum (Mo). They are metallic elements listed in the short vertical groups in the center of the periodic table, known as transition elements. Two additional essential micronutrients are chlorine (Cl) and boron (B). Chlorine, a nonmetal, must be supplied as chloride (Cl⁻) ions. The name for negatively charged ions is anions. Boron is usually part of more complex anions (See Table 1.1).

The soils that plants grow in supply most of the nutrients. The exception is the element carbon which plants obtain from air as carbon dioxide (CO₂). Less than 1% of air is carbon dioxide, and it is the source of carbon in photosynthesis. Section 1.4 discusses different types of soils and their properties.

Decomposing plant materials are great suppliers of essential elements in useful forms. In tropical rainforests they provide the major source of plant nutrition. If a rainforest is logged and burned down, initially there is a good nutrient supply from the former plant materials. But this rich supply of mineral nutrients is rapidly depleted, as it is washed out by rains and consumed by plants, with no chance for renewal.

Plant nutrients can be made available by wildfires as the heat breaks down complex plant compounds into simpler ones that become part of the soil. If wildfires get too hot, however, nutrients like nitrogen are lost as they escape as gaseous oxides into the air. Some natural environments that regularly experience wildfires have a collection of plants that are fire followers. Plants like fireweed (Epilobium spp.) take advantage of the increase in sunlight and all the newly available nutrients from the ashes after an area has burned (Figure 1.4a).

If soils are lacking adequate amounts of some of the macro- or micronutrients, farmers and gardeners tend to apply fertilizers. Commercial fertilizer packages characteristically display three numbers on their labels, like “10-4-10” or “4-12-4”, which refer to three of the essential macronutrients, N (nitrogen), P (phosphorus), and K (potassium) (Figure 1.4b). Fertilizers must contain them in the form of compounds or ions that plants can make use of, and the numbers relate to the relative weight percentage of the compounds. If soils do not supply the essential nutrients in adequate amounts, plants will turn yellow, shrivel up, have irregular growth, or die. Too much of a nutrient can also kill a plant, as some unlucky gardeners experience after applying too much nitrogen-rich fertilizer.

It is interesting to compare which of the essential plant elements are also required by the human body. Except for boron, humans need all of the plant elements as well. But in addition, the human diet must provide traces of fluorine (F) and iodine (i), both as anions. Humans also need additional mineral ions, supplied in the form of cations—they are sodium (Na) and traces of cobalt (Co), chromium (Cr), and selenium (Se).

This section serves as a brief review of the structure of atoms as their structures determine how atoms combine by chemical bonds and form molecules. Depending on your previous chemistry knowledge, you may want to carefully read this chapter in preparation for the descriptions of plant substances, or you may choose to browse through it, proceeding directly to those basic concepts that you need to brush up on and returning to more in-depth explanations when needed.

Elements are composed of atoms, the units that compose all matter. Atoms are extremely small; it would take about a million of them to stretch across the period printed at the end of this sentence.¹¹  Nevertheless, their structures determine which element they belong to (hydrogen, carbon, or oxygen), or which elements can form bonds with each other and link up to form compounds. The periodic table (see the front of this book) provides a lot of information about atomic structures.

At the center of each atom is a tiny, highly condensed nucleus that accounts for almost all of an atom's mass. In this nucleus are the positively charged protons and neutral particles called neutrons, as shown in the simple models of a helium (He) atom and a carbon (C) atom in Figure 1.5. They are the subatomic particles that determine the mass of an atom, with the atomic mass unit for a proton or for a neutron being 1 amu (atomic mass unit) or simply 1. The number of protons in the nucleus of an atom determines the identity of an element. Therefore, an element whose atoms have one proton only in its nuclei is always hydrogen. The atoms of the element helium are characterized by two nuclear protons and those of carbon atoms by six protons (Figure 1.5). The number of protons in the atoms of a specific element can be read from the periodic table—it is the same as the atomic number of an element. It also tells us the position of an element in the table and the number of electrons around the nucleus in an uncharged atom.

While all atoms of an element have the same number of protons, the number of neutrons in their nuclei may vary. Isotopes are atoms of the same element, but with different numbers of neutrons. This means their masses are different, too. Some isotopes are stable and very common, like carbon atoms with six neutrons in their nuclei. Together with the masses of their six protons, they have a mass of 12 atomic mass units, written as carbon-12, C-12, or ¹²C (Figure 1.5). Carbon-14 or ¹⁴C is another isotope of carbon. Its atoms have eight neutrons and, therefore, a mass of 14. Atoms of carbon-14 are unstable and decay spontaneously as they are radioactive. ¹⁴C is used in radiocarbon dating, and also in studies that research how plants assemble organic compounds in plant reactions. Oxygen atoms have eight protons and most commonly eight neutrons in their nuclei. A rare, heavier isotope, ¹⁸O, has ten neutrons and is also stable. We will encounter it in studies on photosynthesis in Section 1.6.1.

In a neutral atom, the total number of negatively charged electrons is equal to the number of protons. As the mass of an electron is much smaller than the mass of a proton or neutron, electron masses are usually ignored when calculating the total mass of an atom (as was done for determining the masses of carbon isotopes).

Electrons move at specific distances around the nucleus—with fixed levels of potential energy, called energy levels—or electron shells (Figures 1.5 and 1.6a). The more energy electrons have, the further away they are from the atom's nucleus, and the less they are attracted to the positive charges of the protons. Energy, e.g. in the form of light, can excite electrons and move them to higher energy levels, a process that involves absorption of energy. (When electrons drop again to lower than original energy levels, energy is released, usually in the form of very small amounts of heat.) Colorful plant pigments, such as those in Figure 1.6b, are composed of molecules with many excitable electrons in their bonds. These electrons are easily lifted to higher energy levels and absorb light energy in the process. Chapter 4 on plant pigments will introduce typical bonding patterns in molecules of colorful compounds.

As an introduction to understanding the chemical bonding between atoms, let us look at electrons in more detail. The periodic table shows how many energy levels of electrons are found in the unexcited or ground state of an atom. With each start of a horizontal row of elements in the table, called a period, a new shell or main energy level is added. The first electron shell can accommodate a maximum of two electrons, the second one a total of eight. Electrons in the outermost shells, called the valence shells, accomplish most of the bonding between atoms as they are furthest away from the attractive forces of the nucleus. The group number of an element in the periodic table's main groups is equal to the number of valence electrons. Carbon is in main group number four, and therefore carbon atoms have four valence electrons (Figure 1.5).

Within their main energy levels, electrons occupy orbitals which can be described as the three-dimensional spaces where an electron can be found with about 90% probability (Figure 1.7). Each orbital can hold a maximum of two electrons. The first two electrons of each energy level are in an orbital that is spherical in shape and called the s-orbital (Figure 1.7a). Hydrogen and helium atoms have their electrons in s-orbitals. Starting with the second electron shell, the first two electrons of this energy level are in an s-orbital, while the next six electrons occupy three barbell-shaped orbitals called p-orbitals, oriented along the x, y, and z axes in space (Figure 1.7b and c).

As this book is mostly concerned with organic compounds, we now focus on the orbitals of a carbon atom when it forms bonds with four other atoms (Figure 1.7d). The four valence electrons of carbon are located singly in four equivalent orbitals. These orbitals are combinations or hybrids between s- and p-orbitals. As they all contain negatively charged electrons, they repel each other, and, as a consequence, are as far apart from each other as possible, which is toward the corners of an imaginary tetrahedron (shown in red in Figure 1.7d). This orbital arrangement determines the shape of molecules in which carbon atoms form single bonds to four other atoms. The molecular shapes, in turn, affect how molecules interact with each other. Figure 1.7e shows a “wedge-and-dash” picture that is commonly used to point out the tetrahedral arrangement of bonds around a carbon atom in a molecule. An even simpler picture of carbon with its four valence electrons is the electron-dot structure shown in Figure 1.7f. It can be used to explain bonding of carbon, as discussed next.

Valence electrons do the bonding between atoms. When two atoms form a chemical bond, they either lose or gain electrons from their valence shells and become ions, or they share electrons and form covalent bonds. By forming a chemical bond, atoms strive to obtain a stable set of electrons with a full valence shell, i.e. a noble gas configuration. By losing or gaining electrons, or by sharing electrons, atoms each obtain eight electrons in their valence shells, with the exception of hydrogen which can have a maximum of two electrons.

Many nutrients in soils are supplied as ions. (See Table 1.1.) When atoms of metal elements form cations, they lose electrons from their valence shells. This results in an imbalance of protons and electrons and creates atoms with an overall positive charge. Examples are ions of sodium (Na⁺), potassium (K⁺), calcium (Ca²⁺), or aluminum (Al³⁺). Atoms of some nonmetal elements, like chlorine, acquire additional electrons to reach a full valence shell. This results in a surplus of negative charges and the formation of negatively charged anions, like Cl⁻. In soils, nutrients to plants can also be in the form of complex ions, like ammonium (NH₄⁺) ions or anions like phosphates (PO₄³⁻) or carbonates (CO₃²⁻). Cations and anions attract each other due to electrostatic forces and form ionic bonds. They combine in fixed proportions to form ionic compounds, also known as salts. Ions in solid salts form three-dimensional, regular arrangements, called lattices. Figure 1.8 illustrates the formation of an ionic bond between a sodium and a chlorine atom and shows part of the lattice pattern between sodium and chloride ions. In formulas of ionic compounds, like NaCl, CaCO₃, or K₃PO₄, the overall negative and positive charges of the ions are balanced, and number subscripts show the correct proportions.

Atoms of nonmetal elements like carbon, hydrogen, or oxygen form bonds with other nonmetal atoms by sharing electrons from their valence shells. Their orbitals overlap and combine to form bonding orbitals. This type of bond is called a covalent bond. Electron-dot structures can be used to illustrate the shared valence electrons. Figure 1.9 shows the structures of hydrogen (H₂) and methane (CH₄) molecules. Each molecule is shown as an electron-dot structure, with its shared valence electrons doing the bonding, and as a “ball-and-stick” model that shows the shape or geometry of the molecule. For methane, a “wedge-and-dash” picture is shown as well. We will find covalent bonds almost exclusively in the molecules discussed in this book, i.e. in water molecules and in the molecules of sugars, fats, plant fragrances, pigments, and toxins.

Single covalent bonds composed of two bonding electrons are most easily drawn as a single line between atoms. Figure 1.10 shows single bonds in the molecules of hydrogen (H₂) and methane (CH₄). Double bonds, with four-electron bonding, are drawn as double lines, as in the molecule of oxygen (O₂). Triple bonds are drawn as triple lines, as shown in the structure of a nitrogen molecule (N₂).

Every living plant and animal on Earth needs water. It is the most abundant liquid on Earth, and its properties affect all living beings. Because water is so common, we often overlook how unusual a compound it is. Here are a couple of its unusual properties:

• Water is a liquid over a very large temperature range, from 100 °C (212 °F) all the way down to 0 °C (32 °F). Water in its liquid form is most useful to plants.

• Water heats up—and cools down—very slowly compared to other liquids. This is an important advantage for plants that live in or near water and that cannot be moved away when rapid temperature changes occur.

• Water has a tendency to cling to surfaces. It has a high-surface tension, higher than most other liquids. Water molecules cling to each other, too. This allows plants to transport water from their root hairs to the tips of their leaves.

• Liquid water has a higher density than its solid form, a very unusual property among compounds. Because of this, ice will float on water, and ponds and lakes freeze from the top on down, not the other way round.

A closer examination of water molecules provides explanations for these unique properties. H₂O molecules have an angular shape (Figure 1.11). Hydrogen and oxygen atoms form a covalent bond by sharing electrons with the bonding orbitals each obtaining a pair of electrons. But the shared electrons are not equally distributed between the atoms. It is the nature of the compact, electronegative oxygen atom to pull the bonding electrons somewhat closer, away from the hydrogen atoms. This gives oxygen atoms in water molecules a partial negative charge (δ−), leaving a slightly positive charge on the hydrogen atoms (δ+). As a result, water molecules are polar, and the bonds in them are polar covalent.

When water molecules approach each other, the slightly positive ends become attracted to the oxygen atoms, and the water molecules become connected to each other in a huge network. The bonds between water molecules are called hydrogen bonds (Figure 1.12). Their strength is much weaker than covalent bonds or bonds between ions. Yet, hydrogen bonds determine many properties of water. They are also the most important bonds within very large molecules, like proteins or nucleic acids, where they determine the shapes of the molecules and their functioning.

Hydrogen bonding explains many of the extraordinary phenomena relating to water. The huge network of interconnected molecules in liquid water requires large amounts of energy to absorb heat, much more so than separate molecules would. Therefore, a body of water, like a lake, heats up and cools down slowly. At 4 °C, water has its highest density. When it cools further down and forms ice, there is still hydrogen bonding between the H₂O molecules, but the molecules are arranged more loosely. This results in a lower density of ice than of water and explains why ice floats on water.

In plants water is picked up through the root hairs (Figures 1.13 and 1.14a) and the plants seem to “pull up” the water. Actually, as water molecules cling strongly to each other through hydrogen bonding, they move in an uninterrupted network, due to capillary action, from the root hairs all the way to the leaves where large amounts of water evaporate through tiny openings called stomata (singular: stoma) (see Figures 1.13 and 1.14b).¹² 

Water is often called the universal solvent because it can dissolve more substances than any other liquid. The polar nature of water explains why it can dissolve salts and sugars and other polar compounds. The transport of compounds in the aqueous plant system is determined by their water-solubility (or insolubility). Water can dissolve many salts from soil. When an ionic compound, like sodium chloride, is placed in water, the polar water molecules are attracted to the individual ions (Figure 1.15). The partially negative charges on oxygen atoms in water molecules are attracted to cations, like sodium ions (Na⁺), whereas the partially positive charges on the hydrogen atoms of water are attracted to anions, like chloride (Cl⁻), as shown in Figure 1.15. Water molecules thus surrounding ions in a solid ionic compound break up the lattice and dissolve the salt. Plants can easily absorb nutrients in the form of aqueous solutions. Ionic nutrients dissolved in water can be pulled up by the root hairs and follow the route of water molecules through a system of vascular tissues called the xylem (Figure 1.13).

The old chemistry saying “like dissolves like” helps us remember that polar water can dissolve other polar compounds. Sugars, like glucose, are polar organic compounds. Glucose and other sugars have numerous OH groups that water molecules can form hydrogen bonds with, as shown in Figure 1.16. Surrounded by water molecules, the sugar molecules become separated from the solid crystals and dissolve. Sugars and other water-soluble organic molecules can be transported in plants as aqueous solutions in vascular tissues called the phloem.

Water is a poor solvent for nonpolar substances like oxygen (O₂). If molecules have an even distribution of bonding electrons as in O₂, polar water cannot surround them by forming hydrogen bonds. Yet, plants (and animals) that live in water need adequate amounts of oxygen for vital metabolic processes like respiration. To obtain the needed oxygen, plants that live partially in water have special adaptations. Water lilies (Figure 1.17a) have large, waxy leaves that shade the water, keeping it cool and allowing some air oxygen to dissolve. Reeds, like tules (Scirpus acutus, Figure 1.17b), have stems filled with spongy air chambers that can transport air oxygen to water-locked plant parts. (These structures made tules useful materials for building boats as the reeds float on water.) Plants that are completely immersed in water, like Elodea (Figure 1.17c), depend on an initial supply of oxygen in water. Once growing, these plants produce an even larger amount of oxygen through photosynthesis, making water plants like Elodea important suppliers of oxygen for aquaria and ponds.

In pure water, about one out of every 550 million water molecules separate or dissociate into hydrogen ions (H⁺) and hydroxide ions (OH⁻) (eqn (1.1)). The ions are surrounded by water molecules, shown by appending (aq). Between the ions and H₂O molecules, there is a dynamic equilibrium, meaning there is a continuous back-and-forth movement between the separated ions and the water molecules, with most of the reaction on the side of the undissociated H₂O (indicated by the direction of the lower arrow).

As all life on Earth is based on water, the balance or imbalance of hydrogen and hydroxide ions influences life in general and plants in particular. If an aqueous system has a surplus of hydrogen ions, it is called acidic, and acids are compounds that release hydrogen ions when dissolved in water. In contrast, bases release hydroxide ions into water, and a high concentration of hydroxide ions leads to an alkaline or basic medium. The measure of the pH is based on water. In everyday life, we hear of acid rain, the pH of foods, or of plant soils needing the proper pH. The pH-scale (Figure 1.18) is a measure of acidity or alkalinity. The scale ranges from 0 to 14, with pH 7 being neutral and representing the pH of pure water—a balance of hydrogen and hydroxide ions. A pH value below 7 refers to an acidic medium. Above pH 7 means the medium is alkaline or basic. The pH scale is a logarithmic scale, with a factor of ten between each pH unit. Therefore, a medium that has a pH of 6 is ten times more acidic than one with a pH of 7, and water in a swamp or bog with a pH of 4 is a thousand times more acidic than pure water.

Rain without any pollutants has a pH around 5.6 because CO₂ from the air mixes with water to form carbonic acid, H₂CO₃ (eqn (1.2)). As a weak acid, carbonic acid is only partially dissociated into ions (note the back reaction to the undissociated H₂CO₃).

In a desert, lakebeds without any outlets tend to be strongly alkaline. As water evaporates, high concentrations of salts like calcium carbonate accumulate in the lake water. The dissolving salts react further with water and produce hydroxide ions, as shown in eqn (1.3).

Plants themselves contain various organic acids and bases. We notice the sour taste of acids like citric acid in lemons, or oxalic acid and malic acid in rhubarb (Figure 1.19a). These acids release hydrogen ions into the aqueous plant saps. As they are weak acids, they do not affect the pH of the plant dramatically. Strong acids that are fully dissociated into ions, like hydrochloric acid, are not found in plants. As for bases in plants, the most well-known ones are the alkaloids, like caffeine in coffee plants (Figure 1.19b). Alkaloids are organic plant compounds that often act as defensive substances in plants. They have nitrogen atoms in their structures and tend to be weakly basic when dissolved in the aqueous plant saps. We will encounter them in Chapter 5 on plant poisons.

Water and its properties affect all aspects of plant life. Last, but not least, water is required for photosynthesis (see Section 1.6). The splitting of water molecules, accomplished by green plants, algae, and some bacteria during photosynthesis, provides living things with oxygen and the basic sugars needed for composing further vital compounds. Water is truly a life-giving compound.

The soils that plants grow in supply water and mineral nutrients. Soils are highly diverse, complex mixtures. They contain tiny rock fragments composed of ionic compounds, dead and decaying plant and animal materials, and diverse societies of organisms (Figure 1.20).¹³  When moisture in the soil dissolves some of the salts and rocky materials, plants can pick up nutrients in solution through their root hairs. The structure of the soils that plants grow in, their mineral content, water-holding ability, aeration, and their acidity or alkalinity all determine how well a plant will grow in them.

Sandy soils (Figure 1.20a) with relatively large particles of quartz (i.e. silicon dioxide; SiO₂) have equally large air spaces between the particles. This allows water to pass freely between the sand grains and to run off rapidly. The result is that little water is retained, and dissolved nutrients also drain off rapidly. Nevertheless, as a benefit to plants, sandy soils are well aerated and promote the processes of respiration and of healthy growth of plant roots. In contrast, the soil type that we know as clay (Figure 1.20c) consists of very fine particles called micelles. Negatively charged ions, like silicate (SiO₃²⁻), aggregate at the surface of the micelles and attract cations like potassium ions (K⁺), magnesium ions (Mg²⁺), and calcium ions (Ca²⁺). Plants in clays get adequate supplies of these nutrients. However, the charged surfaces of clay micelles hold tenaciously to polar water molecules so that clays turn soggy in heavy rains, leaving root systems with little oxygen. When clays dry out, they form cracked surfaces. The experienced gardener adds good compost (Figure 1.20b) to clay soils, with lots of decomposing plant material, to loosen up the soil and make water and minerals better available to plants. Compost is rich in humic acids—the deep-brown to black biomaterials in fertile soils.^14,15  (Their name is derived from “humus” which is Latin for “earth”.) Humic acids are products of degradation of plant and animal materials and are composed of complex organic macromolecules. Humic acids help regulate soil pH, retain water in the soil, bind metal ions, and can transform and absorb toxic pollutants. They are thus highly desirable materials in soils.

Plants are very sensitive to the pH of the soils they grow in. Many plant processes involve hydrogen ions, and soil pH affects them. The environment around roots is slightly acidic as the fine root hairs give off CO₂ as a product of respiration. According to eqn (1.2), soil moisture combines with CO₂ to form carbonic acid. The released hydrogen ions can be exchanged for metal ions. Most plants do best in soils with a pH not too far from neutrality, with some plants, like azaleas and rhododendrons, needing acidic soils with a pH between 4.5 and 5.5, and some vegetables preferring a somewhat alkaline soil. If the soil pH is high, essential metal ions, like iron ions, get tied up as water-insoluble hydroxides and are thus not available to plants. On the other hand, acidic soils make metal ions highly available. A very low pH frees too high a concentration of metal ions for healthy plant growth.

Environments with ample rainfall, like a rainforest (Figure 1.21a), tend to have acidic soils because mineral salts that can neutralize the slightly acidic rainwater are continuously washed out. Water-logged moorlands and bogs are acidic and are characterized by low-growing vegetation. Limestone and dolomite areas (Figure 1.21b), on the other hand, have alkaline soils. Their carbonates slowly dissolve in water (it is in limestone areas that we find caves) and in the process form hydroxide ions in water (eqn (1.3)).

Strongly acidic soils that have high metal concentrations can be found close to some springs (Figure 1.22a) or in mine tailings. These environments are either devoid of plants, or only specialist plants that can survive in them. High soil alkalinity, with pH values of 9 or more, is found in arid areas like alkaline lake beds (Figure 1.22b) of deserts where rain is scarce and salts build up.

While some salts, like carbonates, affect the pH when they dissolve, others, like sodium chloride, dissociate into ions without further reactions with water and do not influence the pH. Nevertheless, the high concentrations of ions in soils destroy the osmotic balance that must exist between plant cells and their aqueous surroundings. The membranes and cell walls that bind living plant cells (Figure 1.23) are not solid barriers. Water molecules diffuse freely back and forth through them. As if to even out differences in salt content on the inside of the cell and the outside, water molecules tend to diffuse to the side where there is a higher salt concentration in a process called osmosis. In saltwater marshes and in salty desert soils, we find a higher salt concentration on the outside of plant cells that bound the salty water, and water molecules have a great tendency to move out of the plant cells. This makes the cells more and more desiccated and shriveled up. Only plants with highly specialized cell mechanisms can survive in such environments, and plant names like pickleweed or Salicornia (sal being Latin for salt) reflect these adaptations (Figure 1.22c).

Sodium chloride and similar salts in soils are a serious problem in agriculture. Irrigation leaches salts out of the soils and into the groundwater. Repeated reuse of water leads to increasing soil salinity and makes the soils useless for growing crops.

Many subtle and complex chemical reactions in plants change the rate of growth of stems and leaves, the color of their fruits, the intensity of odors in blossoms, or the decomposition of their leaves. During photosynthesis plants trap carbon dioxide and, with water, light, and chlorophyll, transform it into glucose. These plant processes involve chemical reaction steps in which existing compounds interact with each other to form new compounds.

Whenever a chemical reaction occurs, whether it is in a laboratory or in a living organism like a plant, bonds between atoms get broken and new bonds are formed, thus leading to new combinations of atoms and new molecules. The chemical compositions of the materials at the beginning of the reaction, the reactants, and of the resulting products are different. This is expressed in their different chemical formulas. Energy is required to get the reactions going, and is mostly in the form of heat. Other forms of energy, like light, can induce reactions, too. Some chemical reactions release energy overall; they are exergonic reactions (exothermic if the release is in the form of heat energy). Other chemical processes need a steady input of energy to keep going and are called endergonic (or endothermic) reactions.

To apply these statements to chemical processes occurring in plants, let us consider the general equation for photosynthesis (eqn (1.4)).

The composition of the reactants on the left side of the equation and of the products on the right side is obviously very different. Sunlight supplies the energy to get the process started and is required to keep photosynthesis going.

Chemical reactions in plants encounter restricted conditions. The reactions have to occur at ambient temperatures given by the environment, and many plant reactions have to take place in aqueous plant saps, with the reactants dissolved in water. (In contrast, a chemical reaction that is carried out in a laboratory can be performed in any suitable solvent and can be accelerated by heating the mixture.) In spite of restrictions, plants produce elaborate products. How do plants accomplish this? With time and highly specialized catalysts! Plant reactions are complex, multistep reactions that progress in controlled reaction steps.

Catalysts are chemical compounds that speed up chemical reactions by lowering the activation energy, i.e. the energy that is required to get the reaction going. Catalysts interact with a reactant and form an activated complex with it that, in turn, will react much faster with other reactants. The catalysts then separate or regenerate to interact with more reactants. Therefore, catalysts are not used up during a chemical reaction. Catalysts in living organisms are called enzymes and are among the most sophisticated substances. They are often large protein molecules with defined three-dimensional shapes that enable them to interact with only certain reactants, and only in specific ways or orientations.

The chemical reactions in living organisms that are catalyzed by enzymes are known as metabolism. Metabolic reactions can involve the synthesis of larger molecules (anabolism) or the breakdown of larger molecules into smaller ones (catabolism).

There are many types of chemical reactions. The processes of photosynthesis and respiration involve numerous oxidation–reduction reactions. The oxidation of a compound (or an element or ion) always involves the loss of electrons of the reacting atom. But oxidation is often easier to recognize in the form of an addition of oxygen, as in the formation of CO₂ as the product of respiration, or in the loss of hydrogen, as in the conversion of water into oxygen gas during photosynthesis. Reduction reactions (which always go together with oxidation processes) are the opposite: They involve the gain of electrons or the gain of hydrogen or loss of oxygen. During photosynthesis, CO₂ gets reduced as it loses oxygen.

We will encounter further types of plant reactions as we go along, and they will be explained in the respective chapters. The next section focuses on the reaction steps that plants evolve in the process of photosynthesis.

Until about 2.5 billion years ago, the Earth's atmosphere contained scarcely any oxygen gas.^16,17  This started to change when some cyanobacteria (formerly called blue-green algae) evolved photosynthetic pigments that were capable of trapping light energy from the sun and converting it into chemical energy. This led to the synthesis of simple sugars and, as a waste product, to the formation of oxygen. Initially, the atmospheric oxygen concentration was only around 1%. Much later in Earth's history, marine algae (i.e. phytoplankton) also evolved photosynthesis, and the oxygen content in air increased rapidly. At present our atmosphere has an oxygen content of about 21%. Green plants, algae, and cyanobacteria are the champions that are capable of performing oxygenic (i.e. oxygen-generating) photosynthesis (Figure 1.24).

The overall, balanced reaction equation of photosynthesis (eqn (1.5)) can be written as:

This equation is a general and greatly simplified reaction equation as photosynthesis involves many complex reaction steps. Aside from light, water, carbon dioxide, and the pigment chlorophyll (specifically: chlorophyll a), the reactions during photosynthesis require specific enzymes, proteins, and some metal ions as catalysts. In addition, other pigments, like the carotenoids, are also involved. They are called accessory pigments, and we will encounter them in Chapter 4 on plant pigments.

O₂ is merely a by-product of photosynthesis, albeit the most important one for life on Earth. O₂ is continuously produced biologically via the oxidation of water. Humans and animals need oxygen for respiration and to gain energy for further reactions. So do plants, but more oxygen is produced by plants than is used up in respiration. Some of the oxygen is transformed into ozone in the upper atmosphere and forms a protective ozone layer that keeps away harmful UV radiation. The simple organic sugars that are products of photosynthesis are, in turn, required for the biosynthesis of all other organic plant products, like fats and oils, the plant structural materials, and their pigments, perfumes, and poisons. Humans and animals depend on basic plant products, like many sugars, fats, and amino acids, that their systems cannot produce. Therefore, photosynthesis is indeed the key to life on Earth.

The reaction steps during photosynthesis can be divided into two major sets: light reactions and the light-independent Calvin cycle (also known as the carbon-fixation reactions). The reactions involve several oxidation and reduction steps. A brief summary of their requirements and their products, with their interconnections, is shown in Table 1.2.

The light reactions (the “photo” part) occur along stacked membranes inside the chloroplast (see Figure 1.23 of a plant cell) and take place when sunlight is available. During the light reactions, photosynthetic plants, algae, and bacteria split water molecules into O₂ and H⁺. Chlorophyll molecules, surrounded by proteins, capture light energy and transform it into a flow of electrons (e⁻) in an oxidation reaction of water (eqn (1.6)):

Chlorophyll is helped in this process by carotenoid accessory pigments. Electrons in the chlorophyll molecules get excited and are passed along in a series of reactions that lead to high energy compounds, namely adenosine triphosphate (ATP). ATP is needed to power the reaction steps in the Calvin cycle. Nicotinamide adenine dinucleotide phosphate (NADP⁺), an electron acceptor, is transformed into NADPH in a reduction reaction. NADPH is required for the reactions of the Calvin cycle as well.

For a long time it was debated whether H₂O or CO₂ is the source of the oxygen that is produced during photosynthesis. It was observed that some ancient hot-springs bacteria undergo nonoxygenic photosynthesis, in a reaction of CO₂ with H₂S (instead of H₂O), and form yellow sulfur (S) and simple sugars, here shown as a carbohydrate unit (CH₂O) (eqn (1.7)).¹⁸ 

This observation led to the hypothesis that the source of oxygen during oxygenic photosynthesis must be from water and not from CO₂. The hypothesis was later confirmed by incorporating the heavier ¹⁸O isotopes into CO₂, and into H₂O, respectively, and following their pathways by instrumental analysis. Only if the supplied water molecules were marked with ¹⁸O, did the O₂ formed during photosynthesis processes also carry the heavier isotopes.

The light-independent reactions of the Calvin cycle (the “synthesis” part) are named after Melvin Calvin who elucidated the reaction steps in the 1940s. They require the supply of high-energy ATP and NADPH molecules that are produced during the light reactions. The hydrogen ions and electrons generated during the light reactions, reduce CO₂ from air to produce organic molecules in the form of simple sugars, here shown as a carbohydrate unit (CH₂O), leading to the formation of glucose, C₆H₁₂O₆ (eqn (1.8)).

These reactions also produce the NADP⁺ and ADP required for the light reactions in a cycle of the reactions.

Plants pick up carbon dioxide through their stomata, the tiny openings at the underside of leaves and sometimes on stems. But, at the same time, water is lost in large quantities through the stomata. Therefore, plants that grow in hot climates need special adaptations to reduce water loss.

Most plants follow the so-called C₃ pathway. Their products of the Calvin cycle are organic three-carbon molecules that serve as starting materials for the synthesis of glucose, with six carbons. C₃ plants tend to grow well in areas where sunlight intensity is moderate, temperatures are not extreme, carbon dioxide concentrations are adequate, and ground water is plentiful.

Many plants that originate from hot climates have evolved somewhat different photosynthetic pathways that allow them to keep their stomata closed or partially closed during the hot daytime hours. This cuts down on water loss, but it also inhibits uptake of CO₂. In C₄ plants, the CO₂ from air is incorporated or fixed into four-carbon compounds that are then transported into a different part of the cell where the compounds break down to release CO₂ ready to be used in the Calvin cycle. Stomata can be partially closed as a supply of CO₂ is available in this fixed form, and less water is lost from the plants. C₄ plants include many grasses (Figure 1.25a) as well as sugar cane and corn (Figure 1.25b), which are also in the grass family. CAM plants (for crassulacean acid metabolism) evolved a similar adaptation to hot and dry climates. Their stomata are open during the cooler night time only, and carbon dioxide is fixed during the night by storing it as a four-carbon acid. The CO₂ is released during the day into the cell, entering the Calvin cycle. The CAM pathway allows stomata to remain shut during the day, reducing loss of water. Therefore, it is especially common in plants adapted to hot and arid conditions, like in cacti (Figure 1.25c) or agaves.

Let us examine the photosynthetic pigment chlorophyll more closely. The chemical structure of chlorophyll a 1.1 is shown in Figure 1.26. It is a highly complex molecule. The following descriptions will explain how to read such structures.

The lines and double lines in the line structure in Figure 1.26a represent covalent bonds between carbon atoms. Assume a carbon atom in every corner, at every intersection, and at every end of a bond. As each carbon atom needs to have four bonds, mentally attach hydrogen atoms until the four required bonds are obtained. Elements other than carbon and hydrogen, like oxygen (O, shown in red in Figure 1.26b) or nitrogen (N, shown in blue) are always written out, and so is the magnesium atom (shown in green) in the center of the chlorophyll molecule. A special type of bond, called a coordinate covalent bond, between magnesium and the nitrogen atoms is shown as broken lines. If we count all the atoms correctly and summarize them, we get the molecular formula: For chlorophyll a it is C₅₅H₇₂O₅N₄Mg, which is a complex molecule.

The simple line structure (Figure 1.26a) shows the pattern of single bonds alternating with double bonds well. This pattern is known as conjugated double bonds. It is found in all colorful organic pigments. The space-filling model of the molecule in Figure 1.26b displays the flat, ring-like structure, called the porphyrin ring. In its center is a magnesium atom. Bonds between metal atoms and organic molecules further intensify the absorption of light within the human visible range. Note also the long “tail” attached to the molecule, called the phytyl group. It consists of carbon and hydrogen atoms only. This makes chlorophyll water-insoluble, but soluble in nonpolar media like fats and oils.

A pigment is generally a chemical compound that absorbs a section of the electromagnetic spectrum of sunlight (Figure 1.27) and reflects or transmits the nonabsorbed portion. The segment of sunlight that is visible to humans is roughly between the wavelengths of 400 and 750 nanometers (a nanometer, or nm, is 0.000000001 meters or 10⁻⁹ m). When a plant pigment absorbs a portion of this visible segment and reflects or transmits the nonabsorbed portion between 400 and 750 nm, then we see a colored plant part.

Chlorophyll a, the main photosynthetic pigment, absorbs wavelengths in the red and blue regions of the spectrum (Figure 1.28) and reflects a combination of wavelengths that looks green to us. Other types of chlorophylls, like chlorophyll b, absorb different wavelengths and therefore have slightly different colors. Together with pigments like the carotenoids, they act as accessory pigments. They extend the spectrum of absorbed light energy for plants. Accessory pigments, like the carotenoids, also serve to protect chlorophyll from an overload of electrons.

Plants that do not have chlorophyll in their plant structures need special mechanisms to survive. Read about examples of such plants in Box 1.3.

We are familiar with the vital intake of oxygen during breathing which leads to the breakdown of larger molecules, like sugars and fats, in our metabolism. The process of respiration provides us with energy for all other metabolic processes, and ultimately producing carbon dioxide which we exhale. The intake of oxygen is vital for plants as well. They, too, undergo respiration, which provides them with the energy for all the other metabolic reactions. Respiration is a series of controlled reaction steps that break down larger organic molecules and create high-energy compounds, such as ATP, that then power the biosynthesis of plant molecules.

There are several biochemical pathways, each one with multiple steps, that plants follow during respiration. They start out with glycolysis, the breakdown of sugars. In the presence of a good supply of oxygen, plants (and fungi and animals) undergo aerobic respiration. As carbohydrates are the main compounds that provide energy during respiration, the overall, general (unbalanced) reaction equation for aerobic respiration is shown with glucose (eqn (1.9)):

This equation is a very short version of a series of complex, multistep reactions. In the complete oxidation of reactants, the final products of aerobic respiration are carbon dioxide and water. Note that this is the reverse of photosynthesis. Respiration and photosynthesis are connected and depend on the supply of available reactants. While photosynthesis composes organic molecules of sugars, respiration is the process of producing energy by breaking them down (catabolism). Aerobic respiration produces large amounts of high-energy ATP. Some plants undergo highly increased rates of aerobic respiration at certain stages of plant development and in specific parts of the plant (Box 1.4).

Anaerobic respiration is respiration in the absence of oxygen. In evolutionary terms, it is a much older form of respiration; it was the source of life's energy when oxygen was scarce. These processes produce a lot less energy in the form of ATP than aerobic respiration. Many lower organisms still live by this inefficient process, and higher organisms use it when a supply of oxygen is not available or is very limited. Anaerobic conditions exist when plants are flooded or grow in mud submerged in water. Some plants, like rice, can undergo anaerobic respiration for a while, providing the shoots with just enough energy to grow until they reach above water, thus giving them an advantage over other plants.

Fermentation involves a partial breakdown of sugars in the absence of oxygen. Although carbon dioxide is still one of the products, larger organic molecules are produced as well, as shown in the next examples. The energy produced is much lower than in aerobic respiration.

In alcohol fermentation, plant carbohydrates, like glucose or starch, together with yeast and water, produce CO₂ and ethanol (C₂H₆O) (eqn (1.10)). This process is important in wine making and bread baking. (The CO₂ makes bread rise and for wine CO₂ is produced by yeast as a natural product of fermentation.)

Lactic acid fermentation is another type of fermentation. It is used, e.g. to make sauerkraut by covering shredded white cabbage (Brassica oleracea) with salt.²⁰  Microorganisms, like Lactobacillus spp. and yeasts, induce the breakdown of sugars in cabbage. The fermentation products include lactic acid (C₃H₆O₃), some acetic acid (C₂H₄O₂), small amounts of ethanol, and CO₂.

Photosynthesis introduced organic compounds in the form of simple sugars. In everyday life, the term “organic” is used in connection with a living source, and we talk about organic gardening or organic food. In chemistry the term has a different meaning: Organic chemistry is the chemistry of compounds that contain carbon.^21,22  (There are a few exceptions to this rule: for example, carbonates and CO₂ are not part of organic chemistry.) To this day, several millions of different organic compounds are known. Note that water, H₂O, is not an organic compound. But most compounds in plants are composed of organic molecules.

What leads to such a wealth of different organic compounds? Carbon atoms have the unique ability to link up with other carbon atoms, much more so than any other element. They can form chains of any length with other carbon atoms and rings of many sizes and combinations. Additional carbon atoms may branch off from the main chains or rings, which creates infinite possibilities for potential structures. Methane gas (CH₄), produced in swamps, glucose or grape sugar (C₆H₁₂O₆), the product from photosynthesis, and ethanol, C₂H₆O, that we encountered as a product of fermentation, are all organic compounds. So is aspirin, C₉H₈O₄, the over-the-counter pain killer. A large number of organic compounds known to us are artificial.

Just a few elements assemble organic compounds: Carbon (always), hydrogen (almost always), oxygen (very commonly), nitrogen (very commonly), phosphorus and sulfur, and a couple of other nonmetals. A few simple bonding rules make it possible to construct organic molecules. Carbon atoms always form a total of four bonds (with double bonds counting as two bonds, triple bonds as three). Hydrogen atoms always form one bond. Oxygen atoms form two bonds, either as two single bonds or as a double bond. Nitrogen atoms form three bonds, in the form of three single bonds, or a single and a double bond, or as a triple bond. Figure 1.31 shows some structures of organic compounds written in different ways. As we progress through this book, organic structures will become increasingly familiar.

It is best to begin drawing organic structures by writing the carbon atoms and connecting them by their bonds. The result is the carbon skeleton or carbon backbone of a molecule. With a bit of practice, the process can be shortened by merely drawing the bonds—leading to so-called line structures—with carbon atoms assumed in each corner, at each intersection, and at each end of a bond. This is especially helpful when drawing larger structures. Hydrogen atoms are often omitted for greater simplicity. We mentally fill in as many hydrogen atoms as are needed to give each carbon atom, or oxygen or nitrogen atom, the correct total number of bonds. Oxygen and nitrogen atoms are always written.

The examples in Figure 1.31 illustrate these rules. Each example shows the molecular formula of a compound, the molecule structures fully written out, and the line structures. We encountered methane 1.2 earlier already. Methane, formed as a product of anaerobic decomposition of plant materials, is used as cooking gas. Ethanol or ethyl alcohol 1.3, the product of fermentation, has the molecular formula of C₂H₆O. So does dimethyl ether 1.4, a nonnatural compound. The larger the molecules are, the more possibilities exist to correctly assemble the atoms in different structures. Compounds with the same molecular formula, but with different structures, are known as isomers. The formation of possible isomers contributes to the large number of different organic compounds.

Groups with atoms other than carbon or hydrogen can be bonded to the carbon skeleton. They frequently contain oxygen or nitrogen atoms. They are functional groups as they determine the chemical properties of a compound. Ethanol 1.3 and dimethyl ether 1.4 have such functional groups. Other functional groups are found in the compounds of cadaverin 1.5 and lactic acid 1.6. Cadaverin is a compound with an unpleasant smell (as its name suggests); it is found e.g. in seeds of legumes. Lactic acid was encountered as one of the compounds responsible for the sourness in sauerkraut. As we progress in our exploration of organic plant compounds, we will become familiar with typical functional groups and with some of their properties. The different functional groups further increase the enormous diversity of organic compounds.

Organic compounds that are composed of carbon and hydrogen only are called hydrocarbons. They serve here as an introduction to understanding organic structures. The term “hydrocarbons” may be familiar from crude oil (petroleum), a complex mixture of hydrocarbons from ancient plant and animal materials, or from gasoline, a mixture of mostly liquid hydrocarbons. The simplest hydrocarbon is methane. We can write a series of hydrocarbons with increasing numbers of carbon atoms, each carbon atom forming four single bonds in a tetrahedral arrangement (see Table 1.3 and Figure 1.32). Note that starting with butane (C₄H₁₀) we can write two isomers for the same molecular formula: butane and isobutane. As the number of carbon atoms in molecules increases, the more isomers are possible. Carbon can easily form double bonds to other carbon atoms, too. There are also hydrocarbons with triple bonds between carbon atoms. The bonding patterns, single or double or triple bonds, determine the shape of the molecules and with this also their chemical and biological behavior. Table 1.3 shows molecular formulas, condensed structures, and line structures of representative hydrocarbons, including some examples of hydrocarbons found in plants. Molecular models, as shown in Figure 1.32, help visualize the three-dimensional shapes of molecules.

Some of the characteristic properties of hydrocarbons can be remembered by reflecting on the properties of crude oil or gasoline: they burn well and do not mix with water. Plants produce numerous, different, hydrocarbon compounds (Table 1.3 and Figure 1.33). Many protective layers of plants, like e.g. plant resins, are to a large extent hydrocarbons; they repel water and help plants cut down on water loss. Some pine trees, like gray or foothill pines (Pinus sabiniana, Figure 1.33a) from western North America, contain resins with considerable amounts of heptane (C₇H₁₆), a hydrocarbon that is also a component of gasoline. These resins are highly flammable mixtures. Hydrocarbons with up to 10 carbon atoms in their molecules evaporate easily as the nonpolar molecules cannot form hydrogen bonds, or other strong bonds, between the molecules. Many plant smells are hydrocarbons that can rapidly evaporate on a warm day.

Hydrocarbons with double bonds are very common in plants. The simplest one is ethene (C₂H₄₎, also known as ethylene. It is a gas that acts as a ripening hormone in plants. If unripe tomatoes or avocadoes are placed in a plastic bag, the ethylene gas formed by the fruits accumulates and hastens the ripening process. Lemons (Figure 1.33b) contain limonene (C₁₀H₁₆), a hydrocarbon with a ring structure, in their peel. Limonene gives lemons their typical smell. We will encounter hydrocarbons again as colorful pigments, like β-carotene, and in the form of rubber particles in milky plant saps. A couple of hydrocarbons with triple bonds are also known from plants, e.g. from dahlias (Dahlia spp., Figure 1.33c) where they provide protection by repelling insects.

As hydrocarbons are important sources of fuels for humans, deciduous plants that grow rapidly and produce a high load of hydrocarbons are of great interest as potential sources for renewable energy and have been keenly researched.

This chapter on basic plant chemistry reviewed key concepts as an introduction to organic plant compounds.

Elements compose all compounds. Just a few elements, mainly carbon, hydrogen, oxygen, and nitrogen, and a few others compose organic molecules. Mineral ions frequently serve as catalysts in plant reactions, facilitating the processes that compose organic plant compounds, all at ambient temperature and mostly in an aqueous environment. Plants, like all living things on Earth, are to a large extent aqueous systems. This means that the properties of water, like the balance (or imbalance) of hydrogen and hydroxide ions in plant saps, greatly affect plant life. What needs to be efficiently transported in plants, has to be reasonably soluble in water. Water-insoluble compounds, on the other hand, often have protective functions. Nutrients for plants are provided by the soils they grow in, with the exception of carbon dioxide which comes from air.

Photosynthesis delivers the basic sugars needed for the biosynthesis of all other organic plant compounds. Respiration, the breakdown of sugars, provides the energy for reactions in plants. An introduction to the structures of organic compounds included some simple rules that allow composing organic structures. They are a preparation for understanding and evaluating the basic families of organic compounds that are found in all living organisms—namely sugars, fats, and amino acids—that we will encounter in Chapter 2. Keep in mind that plants are capable of making these basic organic molecules from soils and air, while animals and humans need to ingest them through a plant-related diet.

There are many excellent texts that provide additional background information on chemistry, plant biology, and plant ecology.

Some examples are:

• P. Atkins, Atkins’ Molecules, Cambridge University Press, Cambridge, 2nd edn, 2003.

• R. Cooper and J. Deakin, Botanical Miracles: Chemistry of Plants that Changed the World, CRC Taylor and Francis, Boca Raton, FL, 2016.

• J. E. McMurry, D. S. Ballantine, C. A. Hoeger and V. E. Peterson, Fundamentals of General, Organic, and Biological Chemistry, Pearson Education Inc., USA, 8th edn, 2017.

• K. C. Timberlake, General, Organic, and Biological Chemistry, Pearson Education Inc., USA, 13th edn, 2017.

• M. S. Silberberg and P. Amateis, Chemistry, the Molecular Nature of Matter and Change, McGraw-Hill, New York, NY, 8th edn, 2018.

• N. J. Tro, Chemistry, A Molecular Approach, Pearson Education Inc., USA, 4th edn, 2017.

• J. R. Hanson, Chemistry in the Garden, The Royal Society of Chemistry, Cambridge, 2007.

• R. F. Evert and S. E. Eichhorn, Raven Biology of Plants, Bedford, Freeman & Worth Publishing Group, LLC. c/o Macmillan, New York, NY, 8th edn, 2013.

• L. A. Urry, M. L. Cain, S. A. Wasserman, P. V. Minorsky and J. B. Reece, Campbell Biology, Pearson Education Inc., New York, NY, 11th edn, 2017.

• J. B. Harborne, Introduction to Ecological Biochemistry, Academic Press, London, 4th edn, 1993.

• D. L. Nelson and M. M. Cox, Lehninger Principles of Biochemistry, W. H. Freeman, New York, NY, 7th edn, 2017.

• C. Bowsher, M. Sterr and A. Tobin, Plant Biochemistry, Garland Science, New York, NY, 2008.

• For reference on organic structures:

• The Merck Index: An Encyclopedia of Chemicals, Drugs, and Biologicals, ed. M. J. O'Neil, The Royal Society of Chemistry, Cambridge, UK, 15th edn, 2013.

The end-chapter references include books on general and specific topics, as well as review and journal articles, and a few relevant websites. While some referenced materials are in-depth texts, others are for popular reading.