plant metabolism

image from paper: Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments: A systems biological analysis


Enzymes (the proteins that speed up chemical reactions in cells without being used up in the reactions) regulate just about every

metabolic activity. In biochemical reactions, one or more specific enzymes are associated with the myriad forms of energy con- version that take place within cells. In some cases, these enzymes help build molecules that store energy in chemical bonds through a process called anabolism. Use of this energy to perform work often requires chemical bonds to be broken through catabolism. Most reactions of photosynthesis are anabolic because they involve construction of molecules that are stored for energy, whereas reactions in cellular respiration (referred to as “respiration” in the text) are generally catabolic, since in per- forming work, they release energy held in chemical bonds. Photosynthesis builds organic compounds by combining carbon di- oxide and water, forming carbohydrates. Respiration, on the other hand, breaks down those carbohydrates, producing carbon dioxide and water, which may be used once again in photosynthesis. As we will see in the sections to follow, this photosynthe- sis-respiration cycle is keyed by an enzyme complex that splits water molecules and releases electrons that function, at least temporarily, in storing biochemical energy. These electrons transfer energy from one form to another through oxidation- reduction reactions.

Introduction to metabolism: anabolism and catabolism | Khan Academy


Playlist-Enzymes/ Photosynthesis/respiration

Oxidation-Reduction Reactions

The processes of both photosynthesis and respiration include many oxidation-reduction reactions. Oxidation is the loss of one or more electrons; it involves removal of electrons from a compound. Reduction is the gain of one or more electrons; it involves the addition of electrons to a compound. In most oxidation-reduction reactions, oxidation of one compound is cou- pled with reduction of another compound catalyzed by the same enzyme or enzyme complex. When an electron is removed, a proton may follow, with the result that a hydrogen atom is often removed during oxidation and added during reduction. Oxy- gen is usually the oxidizing agent (i.e., the final acceptor of the electron), but oxidations can occur without oxygen being in- volved.

Krebs Cycle & Oxidative Phosphorylation

Krebs / citric acid cycle | Cellular respiration

Oxidation and reduction | Redox reactions and electrochemistry | Chemistry

Oxidation and reduction review from biological point-of-view | Biomolecules


The Essence of Photosynthesis

The energy-storing process of photosynthesis takes place in chloroplasts and other parts of green organisms in the pres- ence of light. The light energy stored in a simple sugar molecule is produced from carbon dioxide (CO2) present in the air and water (H2O) absorbed by the plant. When the carbon dioxide and water (H2O) are combined and ultimately a sugar molecule (C6H12O6, glucose) is produced in a chloroplast, oxygen gas (O2) is released as a by-product. The oxygen diffuses out into the atmosphere. The overall process can be depicted by the equation that follows. The equation should not, however, be taken literally because there are many intermediate steps to the process, and glucose is not the immediate first product of photosyn- thesis.


6CO2 + 12H2O + light energy chlorophyll carbon     water     enzymes

C6H12O6    +   6O2    + 6H2O


glucose            oxygen          water

Photosynthesis takes place in chloroplasts (see Figs. 3.4 and 3.11) or in cells with membranes in which chlorophyll is embedded. The principals in the process are carbon dioxide, water, light, and chlorophyll; a brief examination of each fol- lows.

Carbon Dioxide


Less than 1% of all the water absorbed by plants is used in photosynthesis; most of the remainder is transpired or incorporated into cytoplasm, vacuoles, and other materials. The water used is the source of electrons involved in photosynthesis, and the oxygen released is a by-product, even though carbon dioxide also contains oxygen. This has been demonstrated by conducting photosynthetic experiments using either carbon dioxide or water containing isotopes of oxygen. When the isotope is used only in the water, it appears in the oxygen gas released. If, however, it is used only in the carbon dioxide, it is confined to the sugar and water produced and never appears in the oxygen gas, demonstrating clearly that the water is the sole source of the oxygen released.

If water is in short supply, it may indirectly become a limiting factor in photosynthesis; under such circumstances, the stomata usually close and sharply reduce the carbon dioxide supply.


Light that is too intense may change the way in which some of a cell’s metabolism takes place. For example, higher light intensities and temperatures may change the ratio of carbon dioxide to oxygen in the interiors of leaves, which, in turn, may accelerate photorespiration (discussed on p. 177). Photorespiration is typically considered to be a wasteful process that uses oxygen and releases carbon dioxide, although it may help some plants to survive under adverse conditions. It differs from common aerobic respiration in its chemical pathways.

Photooxidation, which involves the destruction (“bleaching”) of chlorophyll by light, may also occur. High light intensities may cause chlorophyll molecules to go to a different excited state. The energy released from the excited chlorophyll is passed to oxygen molecules, which become highly reactive and bleach the chlorophyll. In the fall, photooxidation plays a significant role in the breakdown of chlorophyll in leaves, resulting in the autumn colors discussed in Chapter 7. High light intensities may also cause an increase in transpiration, resulting in the closing of stomata. A sharp reduction in the available carbon dioxide supply inevitably follows.


There are several different types of chlorophyll molecules, all of which contain one atom of magnesium. They are very simi- lar in structure to the heme of hemoglobin, the iron–containing red pigment that transports oxygen in blood. Each molecule has a long lipid tail, which anchors the chlorophyll molecule in the lipid layers of the thylakoid membranes (Fig. 10.4).

Chloroplasts of most plants contain two major kinds of chlorophyll associated with the thylakoid membranes. Chloro- phyll a is blue-green in color and has the formula C55H72MgN4O5. Chlorophyll b is yellow-green in color and has the formula C55H70MgN4O6. Usually, a chloroplast has about three times more chlorophyll a than b. The more chlorophyll a there is in a cell, the brighter green the cell and the tissue of which it is a part appear to be. When a molecule of chlorophyll b absorbs light, it transfers the energy to a -molecule of chlorophyll a. Chlorophyll b, then, makes it possible for photosynthesis to take place over a broader spectrum of light than would be possible with chlorophyll a alone (see Fig. 10.7).

Other such pigments include carotenoids (yellowish to orange pigments), phycobilins (blue or red pigments found in cyanobacteria and red algae), and several other types of chlorophyll. Chlorophylls c, d, and possibly e take the place of chlo- rophyll b in certain algae, and several other photosynthetic pigments are found in bacteria. The various chlorophylls are all closely related and differ from one another only slightly in the structure of their molecules.

In chloroplasts, about 250 to 400 pigment molecules are grouped as a light-harvesting complex called a photosynthetic unit, with countless numbers of these units in each granum. Two types of these photosynthetic units function together in the chloroplasts of green plants, bringing about the first phase of photosynthesis, the light-dependent reactions, which are dis- cussed in the next section, “Introduction to the Major Steps of Photosynthesis.”


What are Electrons and Excitation?


Electrons and photons: absorption and transmission of light

Photoelectric effect | Electronic structure of atoms | Chemistry | Khan Academy

Leaf Pigments and Light



Photo-excitation of Chlorophyll


Introduction to the Major Steps of Photosynthesis

The process of photosynthesis takes place in two series of steps called the light-dependent reactions and the light- independent reactions. Although the light-independent reactions use products of the light-dependent reactions, both proc- esses occur simultaneously.

The Light-Dependent Reactions

The light-dependent reactions are the first major steps in the conversion of light energy to biochemical energy. The reactions are initiated when units of light energy (photons) strike chlorophyll molecules embedded in the thylakoid membranes of chloroplasts.

Our knowledge of the light-dependent reactions essentially began in the 1930s in England through a discovery by Robin Hill, a biochemist. He found that a solution of fragmented and whole chloroplasts, isolated from leaves that had been ground up and centrifuged, could briefly produce oxygen if an electron acceptor was present to receive electrons from water. In 1951, it was shown that NADP (nicotin-amide adenine dinucleotide phosphate), which is derived from the B vitamin niacin, was a natural electron acceptor in this reaction. In honor of its discoverer, the process became known as the Hill reaction.

During the light-dependent reactions,

  1. water molecules are split apart, producing electrons and hydrogen ions, and oxygen gas is released;
  2. the electrons from the split water molecules are passed along an electron transport system;
  3. energy-storing ATP molecules are produced;
  4. some hydrogen from the split water molecules is involved in the reduction of NADP to form NADPH (reduced nicoti- namide adenine dinucleotide phosphate), which carries hydrogen and is used in the second phase of photosynthesis, the light-independent reactions.

Conceptual overview of light dependent reactions

Light-Harvesting: The Antenna Complex

Photosynthesis Splitting H2O to O2 in Light Dependent Reactions 10 6 2018

PhotosynthesisView full playlist


plant videos 3 physiology

ps 1 – light harvesting

ps 2 – electron transport

ps 3 – reaction centers

The Light-Independent Reactions

The light-independent reactions (or carbon-fixing and reducing reactions) complete the conversion of light energy to chemi- cal energy in the form of ATP and NADPH. Some scientists refer to the light-independent reactions as the dark reactions because they don’t directly require light, but darkness has nothing to do with their functioning. In fact, even though light is not directly required in the same sense as it is for the light-dependent reactions, light is nevertheless required for the activa- tion of the enzymes involved, and the processes normally can occur only in daylight.

The light-independent reactions are a series of reactions that take place outside of the grana in the stroma of the chloro- plast (see page 40), if the products of the light-dependent reactions are available. They may initially proceed in different ways, depending on the particular kind of plant involved, but they all go through the Calvin cycle, discovered and elucidated by Dr. Melvin Calvin of the University of California. In 1961, Calvin received a Nobel Prize for unraveling how this most widespread type of light-independent reactions takes place.

In this cycle, carbon dioxide (CO2) from the air is combined with a 5-carbon sugar (RuBP, ribulose bisphosphate), and then the combined molecules are converted, through several steps, to sugars, such as glucose (C6H12O6). Energy and electrons involved in these steps are furnished by the ATP molecules and NADPH produced during the light-dependent reactions. Some of the sugars that are produced during the light-independent reactions are recycled, while others are stored as starch or

other polysaccharides (simple sugars strung together in chains). A summary of simplified photosynthetic reactions is shown in Figure 10.5. More detailed diagrams of the light-dependent and light-independent reactions are shown in Figures 10.8, 10.9, and 10.12.

Two molecules of a 3-carbon sugar compound (3PGA—an abbreviation of 3-phosphoglyceric acid) are shown as the first stable substance produced when carbon dioxide from the air and RuBP are combined and then converted during the light-independent reactions (Fig. 10.5). Some grasses and also many plants of arid regions fix carbon differently. They pro- duce a 4-carbon acid as the first product, followed by the Calvin cycle. This 4-carbon pathway is discussed, along with an- other variation found mostly in desert plants, in the next section, “A Closer Look at Photosynthesis.”

3. A Closer Look at Photosynthesis

A great deal has been learned about photosynthesis since 1772 when Joseph Priestly (1733–1804), a naturalist in England, re- ceived a medal for demonstrating that a sprig of mint “restored” oxygen so that a mouse could live in air that had been used up by a burning candle. Seven years later, Jan Ingen-Housz (1730–1799) of Holland, who visited England to treat the royal family for smallpox, carefully repeated Priestly’s demonstrations. He showed that the air was restored only when green parts of plants were receiving sunlight.

In 1782, Jean Senebier (1742–1809), a Swiss pastor, discovered that the photosynthetic process required carbon dioxide, and in 1796, Ingen-Housz showed that carbon went into the nutrition of the plant. The final component of the overall photo- synthetic reaction was explained in 1804 by another Swiss, Nicholas Theodore de Saussure (1767–1845), who showed that water was involved in the process.

A little current information about the details of photosynthesis is given in the following modest amplification of the pre- ceding section, “Introduction to the Major Steps of Photosynthesis.” Those who wish more information are referred to the reading list at the end of the chapter.

The Light-Dependent Reactions Reexamined

As noted earlier, light has characteristics of both waves and particles. Sir Isaac Newton, while experimenting with a prism over 300 years ago, produced a spectrum of colors from visible white light and postulated that light consisted of a series of discrete particles he called “corpuscles.”

Newton’s theory only partially explained light phenomena, however, and by the middle of the 19th century, James Max- well and others showed that light and all other parts of the extensive electromagnetic spectrum travel in waves.

By the late 1800s, with the discovery that a photoelectric effect can be produced in all metals, the wave theory also be- came inadequate to explain certain attributes of light. When a metal is exposed to radiation of a critical wavelength, it be- comes positively charged because the radiation forces electrons out of the metal atoms. The ability of light to force electrons from metal atoms depends on its particular wavelength—its energy content—and not on its intensity or brightness. The shorter the wavelength, the greater the energy, and vice versa.

In 1905, Albert Einstein proposed that the photoelectric effect results from discrete particles of light energy he called photons. In 1921, he received the Nobel Prize in physics for this work. Both waves and particles (photons) are today almost universally recognized as aspects of light. The energy (quantum) of a photon is not the same for all kinds of light; those of longer wavelengths have lower energy, and those of shorter wavelengths have proportionately higher energy.

Chlorophylls, the principal pigments of photosynthetic systems, absorb light primarily in the violet to blue and also in the red wavelengths; they reflect green wavelengths, which is why leaves appear green. This was first ingeniously demonstrated in 1882 by T. W. Engelmann. He focused a tiny spectrum of light on a filament (single row of cells) of Spirogyra, a freshwater alga. The alga had been mounted in a drop of water on a microscope slide containing bacteria that move toward an oxygen source. As shown in Fig. 10.6, the bacteria assembled in greatest numbers along the algal filament in the blue and red portions of the spectrum, demonstrating that oxygen production is directly related to the light the chlorophyll absorbs. An analysis using living material is called a bioassay. Information gained from bioassays often is significant.

Each pigment has its own distinctive pattern of light absorption, which is referred to as the pigment’s absorption spec- trum (Fig. 10.7). When a pigment absorbs light, the energy levels of some of the pigment’s electrons are raised. When this occurs, the energy may be emitted immediately as light (a phenomenon called fluorescence). In chlorophyll, the emitted light is characteristically in the red part of the visible light spectrum, so an extract of chlorophyll placed in light (especially ultra- violet or blue light) will appear red. The absorbed energy may also be emitted as light after a delay (a phenomenon called phosphorescence); it may otherwise be converted to heat. The most important use of the absorbed energy, however, is its storage in chemical bonds for photosynthesis.

Photosystems The two types of photosynthetic units present in most chloroplasts make up photosystems known as photo- system I and photosystem II (Fig. 10.8). Photosystem II received its “II” designation because it was discovered after photo- system I, but we know now that the events of photosynthesis that take place in photosystem II come before those of photosys- tem I.

While both photosystems produce ATP, only organisms that have photosystems I and II can produce NADPH and oxy-

gen as a consequence of electron flow. It is likely that evolutionary events led to organisms that possess both photosystems. At least 2.8 billion years ago, photosynthetic forms of bacteria (cyanobacteria) are believed to have evolved from primitive bacteria with the development of chlorophyll a and photosystem II. As a consequence of the oxygen-generating steps in pho- tosystem II that have evolved, humans and other organisms are dependent upon photosynthetic organisms that generate oxy- gen in the air we breathe today. Since photosynthetic organisms can generate oxygen from water, this very process in the future could be exploited to sustain human life during space travel and colonization of other planets.

Each photosynthetic unit of photosystem I consists of 200 or more molecules of chlorophyll a, small amounts of chloro- phyll b, carotenoid pigment with protein attached, and a special reaction-center molecule of chlorophyll called P700. Although all pigments in a photosystem can absorb photons, the reaction-center molecule is the only one that can actually use the light energy. The remaining photosystem pigments are called antenna pigments because together they function somewhat like an antenna in gathering and passing light energy to the reaction-center molecule (see Fig. 10.9). There are also iron-sulfur pro- teins that are the primary electron acceptors for photosystem I (i.e., iron-sulfur proteins first receive electrons from P700).

A photosynthetic unit of photosystem II consists of chlorophyll a, b-carotene (the precursor of vitamin A) attached to protein, a little chlorophyll b, and a reaction–center molecule of chlorophyll a; these special molecules are called P680.

The letter P stands for pigment and the numbers 700 and 680 of the reaction-center molecules of chlorophyll a refer to peaks in the absorption spectra of light with wavelengths of 700 and 680 nanometers, respectively. These peaks differ slightly from those of the otherwise identical chlorophyll a molecules of the photosynthetic units. A primary electron acceptor called pheophytin (or Pheo) is also present in photosystem II. One reaction-center molecule was found by Johann Deisenhofer and Hartmot Michel of Germany to have over 10,000 atoms. They received a Nobel Prize in 1988 for their work in determining the atomic structure.

Water-Splitting (Photolysis) When photons of light are absorbed by P680 molecules of a photosystem II reaction center (located near the inner surface of a thylakoid membrane), the light energy boosts electrons to a higher energy level. This is referred to as exciting electrons. Excited electrons are unstable and can rapidly revert back to their lower energy level, releasing absorbed en- ergy, perhaps as heat. However, during photosynthesis, the excited electrons are passed to an acceptor molecule, called pheo- phytin, at the beginning of an electron transport system.

From pheophytin, electrons are shuttled to another acceptor, PQ (plastoquinone), within the thylakoid membrane.4 PQ is mo- bile and moves through the lipid bilayer toward the inner side of the thylakoid membrane, unloading electrons to the cytochromes that are next in line. Electrons extracted from water by a manganese-containing oxygen-evolving complex (OEC) replace the elec- trons lost by the P680 molecule. It has been suggested that there is an oxidation-reduction system, usually designated Z, operating between water and P680. Transfer of electrons from Z to P680 reoxidizes Z and prepares it for accepting additional electrons from the OEC. Recent investigations indicate that for each two water molecules that are split, one molecule of oxygen is produced, along with four protons and four electrons.

This metabolic pathway eventually evolved in photosynthetic bacteria (cyanobacteria). The abundance of water, as an electron source, probably facilitated the mechanism that generated oxygen as a by-product of photosynthesis. This process increased the sup- ply of oxygen in earth’s atmosphere and made it possible for energy-efficient aerobic respiration to evolve.

Electron Flow and Photophospho-rylation The high-energy acceptor molecule PQ releases electrons that originated from photosystem II to an electron transport system, which functions something like a downhill bucket brigade. This electron transport system consists of iron-containing pigments called cytochromes and other electron transfer molecules, plus plastocyanin—a pro- tein that contains copper. When electrons pass along the electron transport system and protons subsequently move across the thy- lakoid membrane by chemiosmosis (see next section, “Chemiosmosis”), ATP molecules are formed from ADP in the process of – photophosphorylation.

A somewhat similar series of events occurs in photosystem I. When photons of light are absorbed by P700 molecules in a photo- synthetic unit, the energy excites electrons, which are transferred to an iron-sulfur acceptor molecule -designated Fe-S. This then passes electrons to another iron-sulfur acceptor molecule, Fd (ferredoxin), which, in turn, releases them to a carrier molecule desig- nated as FAD (flavin adenine dinucleotide). FAD contains flavoprotein, which assists in the reduction of NADP to NADPH. The electrons removed from the P700 molecule are replaced by electrons from photosystem II via the electron transport system outlined previously. This overall movement of electrons from water to photosystem II to photosystem I to NADP is called noncyclic electron flow, because it goes in one direction only. The production of ATP that correspondingly occurs is designated as noncyclic photophos- phorylation.

Photosystem I can also work independently of photosystem II. When it does, the electrons boosted from P700 reaction-center molecules (of photosystem I) are passed from ferredoxin to plastoquinone (instead of NADPH) and back into the reaction center of photosystem I. This process is cyclic electron flow. ATP generated by cyclic electron flow is called cyclic photophosphoryla- tion, but water molecules are not split and neither NADPH nor oxygen are produced in this process.

Chemiosmosis The oxygen-evolving complex on the inside of a thylakoid membrane catalyzes the splitting of water molecules, producing protons and electrons, as well as oxygen gas. These electrons used to replenish those excited in chlorophyll are then trans- ferred in bucket-brigade fashion through an electron transport system, ultimately reducing NADP to NADPH. As electrons travel through this transport system, additional protons move from the stroma to the inside of the thylakoid membrane in specific oxidation- reduction reactions when electrons pass from photosystem II to PQ. These protons join with the protons from the split water mole-

cules and thereby contribute to an accumulation of four protons toward the inside of the thylakoid membrane (an area also known as the thylakoid lumen).

Although some protons are used in the production of NADPH on the stroma side of the thylakoid membrane, there is still a net accumulation of protons in the thylakoid lumen from the splitting of water molecules and electron transport. This establishes a proton gradient, giving special proteins in the thylakiod membrane the potential for moving protons from the thylakoid lumen back to the stroma. Movement of protons across the membrane is thought to be a source of energy for the synthesis of ATP. The action has been described as similar to the movement of molecules during osmosis and has been called chemiosmosis, or the Mitchell theory, after its author, Peter Mitchell. In this concept, protons move across a thylakoid membrane through protein channels called ATPase. With the proton movement, ADP and phosphate (P) combine, producing ATP (Fig. 10.9). This chemiosmotic mechanism for connecting electron flow with conversion of ADP to ATP is essentially the same as that of oxida- tive phosphorylation in mitochondria (see Fig. 10.14), except that in mitochondria, oxygen (instead of NADP) is the terminal electron acceptor.

The Light-Independent Reactions Reexamined

We have seen how synthesis of ATP and NADPH is set in motion during the light-dependent reactions. Both of these substances play key roles in the synthesis of carbohydrate from carbon dioxide from the atmosphere, which during the light-independent re- actions reaches the interior of chlor-enchyma tissues via stomata. As indicated earlier, the light-independent reactions are really a whole series of reactions, each mediated by an enzyme in this major phase of photosynthesis.

The light-independent reactions take place in the stroma of the chloroplasts and, as long as the products of the light- dependent reactions are present, they do not directly need light in the same sense that the light-dependent reactions do. How- ever, they normally take place only during daylight hours because some of the enzymes involved in the light-independent reactions require light for their activation or conversion to a form in which they can actively catalyze steps of the light- independent reactions.

The Calvin Cycle The heart of the light-independent reactions is the Calvin cycle, during which carbon dioxide is fixed and converted to carbohydrate. The carbohydrate produced during these reactions facilitates growth, including the develop- ment of leaves, stems, roots, flowers, and other plant structures. From an ecological standpoint, this process is essential be- cause it is the main biosynthetic pathway through which carbon enters the web of life. As discussed next, the Calvin cycle, or photosynthetic carbon reduction (PCR) pathway (Fig. 10.10), runs in five main steps:

  1. Six molecules of carbon dioxide (CO2) from the air combine with six molecules of ribulose 1,5-bisphosphate (RuBP, the 5- carbon sugar continually being formed while photosynthesis is occurring), with the aid of the enzyme rubisco (RuBP car- boxylase/oxygenase).5
  2. The resulting six 6-carbon unstable complexes are immediately split into twelve 3-carbon molecules known as 3- phosphoglyceric acid (3PGA), the first stable compound formed in photosynthesis.
  3. The NADPH (which has been temporarily holding the hydrogen and electrons released during the light-dependent reac- tions) and ATP (also from the light-dependent reactions) supply energy and electrons that chemically reduce the 3PGA to twelve molecules of glyceraldehyde 3-phosphate (GA3P, 3-carbon sugar phosphate).
  4. Ten of the twelve glyceraldehyde 3-phosphate molecules are restructured, using another six ATPs, and become six 5- carbon molecules of RuBP, the sugar with which the Calvin cycle was initiated.
  5. This leaves a net gain of two GA3P molecules, which can contribute either to an increase in the carbohydrate content of the plant (glucose, starch, cellulose, or related substances) or can be used in pathways that lead to the net gain of lipids and amino acids.

Since rubisco catalyzes formation of the 3-carbon compound 3PGA as the first isolated product in these light– independent reactions, plants demonstrating this process are called C3 plants. However, as indicated by its name, the enzyme RuBP carboxylase/oxygenase has the potential to fix both CO2 through its carboxylase activity described by the Calvin cycle and O2 through its oxygenase activity. The oxygenase activity of rubisco makes C3 plants vulnerable to a process called photorespiration.

Photorespiration While the carboxylase activity of rubisco ultimately results in accumulation of carbohydrates, this same enzyme can exhibit an oxygenase activity that catalyzes combination of oxygen with RuBP and a subsequent pathway that releases carbon dioxide. This photorespiration may be interpreted as a wasteful process that competes with the carbon-fixing role of photosynthesis. However, the oxygenase activity of rubisco responsible for photorespiration is not necessarily an omi- nous alternative because it provides a salvage pathway to allow C3 plants to survive under hot, dry conditions. Evidence sug- gests that photorespiration helps to dissipate ATP and accumulated electrons from the light reactions, thereby preventing photooxidative damage.

Factors that determine the extent of this photorespiration in C3 plants include temperature, CO2:O2 ratio, and kinetic prop- erties of rubisco. Hot and dry climates generally promote photorespiration because stomata are closed under these conditions,

leading to a decreased CO2:O2 ratio within the leaf and near rubisco complexes. Oxygen gas can accumulate from photolysis in a leaf with closed stomata and photorespiration is more likely to occur, particularly when the carbon dioxide concentration drops roughly below 50 parts per million. When temperatures are cooler and moisture is present, the stomata are more likely to open, which leads to an increased CO2:O2 ratio. Under milder climatic conditions, C3 plants are more efficient at fixing carbon dioxide.

Photorespiration requires cooperation among chloroplasts, peroxisomes, and mitochondria to facilitate shuttling of in- termediates along the photorespiratory pathway. The products of photorespiration are the 2-carbon phosphoglycolic acid, which is processed to some extent in peroxisomes and eventually released as carbon dioxide in mitochondria, and the 3- carbon phosphoglyceric acid that can reenter the Calvin cycle. No ATP is produced by photorespiration.

The 4-Carbon Pathway Sugar cane, corn, sorghum, and at least 1,000 other species of tropical grasses or arid region plants sub- ject to high temperature stresses have a distinctive leaf -anatomy called Kranz anatomy (Fig. 10.11). Kranz anatomy leaves have two forms of chloroplasts. In the bundle sheath cells surrounding the veins, there are large chloroplasts, often with few to no grana. The large chloroplasts have numerous starch grains, and the grana, when present, are poorly developed. The chloroplasts of the mesophyll cells are much smaller, usually lack starch grains, and have well-developed grana.

Plants with Kranz anatomy produce a 4-carbon compound, oxaloacetic acid, instead of the 3-carbon 3–phosphoglyceric acid during the initial steps of the light-independent reactions. Oxaloacetic acid is produced when a 3-carbon compound, phosphoenolpyruvate (PEP), and carbon dioxide are combined in mesophyll cells with the aid of a different carbon-fixing enzyme, PEP carboxylase. Depending on the species, the oxaloacetic acid may then be converted to aspartic, malic, or other acids. PEP carboxylase is not sensitive to oxygen and, hence, has a greater enzyme affinity for carbon dioxide, so there is no photorespiratory loss of carbon dioxide captured in the organic acids. The carbon dioxide is transported to the bundle sheath cells where it is released and enters the normal Calvin cycle just as in C3 plants. The carbon dioxide concentration can be kept high in relation to the oxygen concentration in the bundle sheath cells, thereby keeping the reaction of rubisco with oxygen very low (Fig. 10.12).

Because the PEP system produces 4-carbon compounds, plants having this system are called 4-carbon, or C4, plants, to distinguish them from plants that have only the 3-carbon, or C3, system. Besides Kranz anatomy, C4 plants have other charac- teristic features:

  1. High concentrations of PEP carboxylase are found in the mesophyll cells. This is significant because PEP carboxylase allows the conversion of carbon dioxide to carbohydrate at much lower concentrations than does rubisco (found only in the bundle sheath cells), the corresponding enzyme in the Calvin cycle.
  2. The optimum temperatures for C4 photosynthesis are much higher than those for C3 photosynthesis, allowing C4 plants to thrive under conditions that would adversely affect C3 plants.

Obviously, the C4 pathway furnishes carbon dioxide to the Calvin cycle in a more roundabout way than does the C3 path- way, but the advantage of this extra pathway is a major reduction of photorespiration in C4 plants. Also, in C4 plants, the C4 pathway in the mesophyll cells results in carbon dioxide being picked up even at low concentrations (via the enzyme PEP car- boxylase) and in carbon dioxide being concentrated in the bundle sheath, where the Calvin cycle takes place almost exclusively. The Calvin cycle enzyme, rubisco, will catalyze the reaction in which RuBP will react with carbon dioxide rather than oxygen. Consequently, C4 plants, which typically photosynthesize at higher temperatures, have photosynthetic rates that are two to three times higher than those of C3 plants. However, at lower temperatures, C3 photosynthesis is more efficient than that of C4 plants because the cost of photorespiration at those temperatures is usually less than the two extra ATPs required for the C4 pathway.

CAM Photosynthesis Crassulacean acid metabolism (CAM) photosynthesis is found in plants of about 30 families, includ- ing cacti, stonecrops, orchids, bromeliads, and other succulents that are often stressed by limited availability of water. A few succulents do not have CAM photosynthesis, however, and several nonsucculent plants do. Many CAM plants are facultative C3 plants that can switch to C3 photosynthesis during the day after a good rain or when night temperatures are high. Plants with CAM photosynthesis typically do not have a well-defined palisade mesophyll in the leaves, and, in contrast to the chloroplasts of the bundle sheath cells of C4 plants, those of CAM photosynthesis plants resemble the mesophyll cell chloro- plasts of C3 plants.

CAM photosynthesis is similar to C4 photosynthesis in that 4-carbon compounds are produced during the light–independent reactions. In these plants, however, the organic acids (mainly malic acid) accumulate at night and break down during the day, re- leasing carbon dioxide. The enzyme PEP carboxylase is responsible for converting the carbon dioxide plus PEP to organic acids at night when the stomata are open. During daylight, the organic acids diffuse out of the cell vacuoles in which they are stored and are converted back to carbon dioxide for use in the Calvin cycle. A much larger amount of carbon dioxide can be converted to carbohydrate each day than would otherwise be possible, since the stomata of such plants are closed during the day to conserve water. This arrangement allows the plants to function well under conditions of both limited water supply and high light intensity (Fig. 10.13).

Other Significant Processes That Occur in Chloroplasts

In addition to photosynthesis, there are two very important sets of biochemical reactions that take place in chloroplasts (and also in the proplastids of roots).

  1. Sulfates are reduced to sulfide via several steps involving ATP and enzymes. The sulfide is rapidly converted into impor- tant sulfur-containing amino acids, such as methionine and cysteine, which are part of the building blocks for proteins, anthocyanin pigments, chlorophylls, and several other cellular components.
  2. Nitrates are reduced to organic compounds. Initially, the nitrates are reduced to nitrites in the cytoplasm. The nitrites are then transported into chloroplasts (or root proplastids) where, through several enzyme-mediated steps, they are converted to ammonia. The ammonia is then converted to amino groups that are integral parts of several important amino acids such as glutamine and aspartic acid. Glutamine is an important form of nitrogen storage in roots or specialized stems such as those of carrots, beets, and potato tubers.


The solar energy that is converted into biochemical energy by the process of photosynthesis today is stored in various organic compounds such as wood, while coal and oil contain energy originally captured by green organisms in the geological past. If the organic compounds are burned, the energy is released very rapidly in the form of heat and light, and much of the usable energy is lost. Living organisms, however, “burn” their energy-containing compounds in numerous, small, enzyme-controlled steps that release tiny amounts of immediately usable energy. The released energy is usually stored in ATP molecules, which allows the available energy to be used more efficiently and the process to be controlled more precisely.

The Essence of Respiration

Respiration is essentially the release of energy from glucose molecules that are broken down to individual carbon dioxide molecules. The process takes place in all active cells 24 hours a day, regardless of whether or not photosynthesis happens to be occurring simultaneously in the same cells. It is initiated in the cytoplasm and completed in the mitochondria. The energy, stored in chemical bonds containing high-energy electrons, is released from simple sugar molecules that are broken down during a series of steps controlled by enzymes. No oxygen is needed to initiate the process, but in aerobic respiration (the most widespread form of respiration), the process cannot be completed without oxygen gas (O2). The controlled release of energy is the significant event; carbon dioxide (CO2) and water (H2O) are the by-products. Aerobic respiration can be summed up in the following equation, but bear in mind that respiration, like photosynthesis, is a complex process that in- volves many steps not reflected in a simplified equation.

C6H12O6 + 6O2 enzymes 6CO2 + 6H2O + energy glucose                      oxygen   ¾¾®      carbon                     water


Anaerobic respiration and fermentation are two forms of respiration that were probably carried on in the geological past when there was no oxygen in the atmosphere. These forms of respiration are still carried on today by certain bacteria and other organisms in the absence of oxygen gas. Anaerobic respiration and fermentation release less than 6% of the energy re- leased from a molecule of glucose by aerobic respiration. The two forms differ from one another in the manner in which hy- drogen released from the glucose is combined with other substances (see the discussion on p. 183). Fermentation is very im- portant industrially, particularly in the brewing and baking industries. Two well-known forms of fermentation are illustrated by the following equations:

C6H12O6 enzymes 2C2H5OH + 2CO2 + energy (ATP) glucose    õõõã          ethyl                       carbon

alcohol        dioxide

C6H12O6    enzymes 2C3H6O3 + energy (ATP)

glucose õõõã lactic acid

The relatively small amount of energy released during these inefficient forms of respiration is partly stored in two ATP molecules. The actual amount of energy stored is roughly only 29% of the approximately 48 Kcals6 of energy released in anaerobic respiration.

Introduction to the Major Steps of Respiration


In most forms of carbohydrate respiration, the first major phase takes place in the cytoplasm and requires no oxygen gas (O2). This phase, called glycolysis, involves three main steps and several smaller ones, each controlled by an enzyme. During the process, a small amount of energy is released, and some hydrogen atoms are removed from compounds derived from a glu- cose molecule. The essence of this complex series of steps is as follows:

  1. In a series of reactions, the glucose molecule becomes a fructose molecule carrying two phosphates (P).
  2. This sugar (fructose) molecule is split into two 3-carbon fragments called glyceraldehyde 3-phosphate (GA3P).
  3. Some hydrogen, energy, and water are removed from these 3-carbon fragments, leaving pyruvic acid (Fig. 10.14).

Two ATP molecules supply the energy needed to start the process of glycolysis. By the time pyruvic acid has been formed, however, four ATP molecules have been produced from the energy released along the way, for a net gain of two ATP molecules. A great deal of the energy originally in the glucose molecule remains in the pyruvic acid. The hydrogen ions and high-energy electrons released during the process are picked up and temporarily held by an acceptor molecule, NAD (nicotinamide adenine dinucleotide). What happens to them next depends on the kind of respiration involved: aerobic respi- ration, true anaerobic respiration, or fermentation.

Aerobic Respiration

In aerobic respiration (the most common type of respiration), glycolysis is followed by two major stages: the citric acid cycle and electron transport. Both stages occur in the mitochondria and involve many smaller steps, each of which is controlled by enzymes (see Fig. 10.14).

The Citric Acid (Krebs) Cycle The citric acid cycle was originally named the Krebs cycle after Hans Krebs, a British biochemist who received a Nobel Prize in 1953 for his unraveling of many of the complex reactions that take place in respira- tion. The name citric acid cycle, or tricarboxylic acid (TCA) cycle, reflects the important role played by several organic acids during the process.

Before entering the citric acid cycle, which takes place in the fluid matrix located within the compartments formed by the cristae of mitochondria (see Fig. 3.13), carbon dioxide is released from pyruvic acid that was produced by glycolysis. What remains is restructured to a 2-carbon acetyl group. This acetyl group combines with an acceptor molecule called coen- zyme A (CoA). This combination (called acetyl CoA) then enters the citric acid cycle, which is a series of biochemical reac- tions that are catalyzed by enzymes. Little of the energy originally trapped in the glucose molecule is released during glyco- lysis. As the citric acid cycle proceeds, however, high-energy electrons and hydrogen are successively removed. This re- moval takes place from a series of organic acids and, after transfer, ultimately produces compounds such as NADH (re- duced nicotinamide adenine dinucleotide) and FADH2 (reduced flavin adenine dinucleotide), as well as a small amount of ATP. Carbon dioxide is produced as a by-product while the cycle is proceeding.

Electron Transport Much of the energy originally in the glucose molecule now has been transferred to the acceptors NAD and FAD, which became NADH and FADH2, respectively. NADH and FADH2 are electron donors to an electron transport system consisting of special acceptor molecules arranged in a precise sequence on the inner membrane of mitochondria. The electrons flow through a series of carrier molecules, many of which are part of protein complexes, down an energy gradient. Some of these electron carriers also accept protons and release them to the intermembrane space of the mitochondrion. Shut- tling of protons in this way causes a build-up of protons outside the mitochondrial matrix, thereby establishing an electro- chemical gradient. Through the process of chemiosmosis, additional protein complexes couple the transport of protons back into the matrix with phosphorylation of ADP to form ATP. The production of ATP stops if there are no electron donors or electron acceptor oxygen.

The acceptor molecules include iron-containing proteins called cytochromes. Energy is released in small increments at each step along the system, and ATP is produced from ADP and P. As the final step in aerobic respiration (see Fig. 10.14), oxygen acts as the ultimate electron acceptor, producing water as it combines with hydrogen.

By the time the process is complete, the recoverable energy locked in a molecule of glucose has been released and is stored in ATP molecules. This stored energy is then available for use in the synthesis of other molecules and for growth, active transport, and a host of other metabolic processes. Aerobic respiration produces a net gain of 36 ATP molecules from one glucose molecule, using up six molecules of oxygen and producing six molecules of carbon dioxide and a net total of six molecules of water. For each mole (180 grams) of glucose aerobically respired, 686 Kcal of energy is re- leased, with about 39% of it being stored in ATP molecules and the remainder being released as heat.

Anaerobic Respiration and Fermentation

In living organisms, glucose molecules often may undergo glycolysis without enough oxygen being available to complete

aerobic respiration. In such cases, the hydrogen released during glycolysis is simply transferred from the hydrogen acceptor molecules back to the pyruvic acid after it has been formed, creating ethyl alcohol in some organisms, and lactic acid or simi- lar substances in others. A little energy is released during either fermentation or true anaerobic respiration, but most of it re- mains locked up in the alcohol, lactic acid, or other compounds produced.

In true anaerobic respiration, the hydrogen removed from the glucose molecule during glycolysis is combined with an inorganic ion, as, for example, when sulfur bacteria (discussed in Chapter 17) convert sulfate (SO4) to sulfur (S) or another sulfur compound or when certain cellulose bacteria produce methane gas (CH4) by combining the hydrogen with carbon di- oxide.

Oxygen gas is not required to make these compounds, but few organisms can live long without oxygen, and many that carry on fermentation can also respire aerobically. If oxygen becomes available, the remaining energy can be released by further breakdown of these compounds. About 7% of the total energy in a glucose molecule is removed during anaerobic respiration or fermentation. So much of that energy goes into the making of the alcohol or the lactic acid or is dissipated as heat that there is a net gain of only two ATP molecules (compared with 36 ATP molecules produced in aerobic respiration). The forms of anaerobic respiration are adaptive to the organisms that have them in that they recycle NAD and allow glycoly- sis to continue.

Living cells can tolerate only certain concentrations of alcohol. In media in which yeasts are fermenting sugars, for exam- ple, once the alcohol concentration builds up beyond 12%, the cells die and fermentation ceases. This is why most wines have an alcohol concentration of about 12% (24 proof).

Many bacteria carry on both fermentation and true anaerobic respiration simultaneously, making it difficult to distinguish between the two processes. Some texts use the terms anaerobic respiration and fermentation interchangeably to designate respiration occurring in the presence of little or no oxygen gas.

Factors Affecting the Rate of Respiration


Temperature plays a major role in the rate at which the various respiratory reactions occur. For example, when air tempera- tures rise from 20°C (68°F) to 30°C (86°F), the respiration rates of plants double and sometimes even triple. The faster respi- ration occurs, the faster the energy is released from sugar molecules, with an accompanying decrease in weight. In growing plants, this weight loss is more than offset by the production of new sugar by photosynthesis. In harvested fruits, seeds, and vegetables, however, respiration continues without sugar replacement, and some water loss also occurs. Respiring cells con- vert energy stored as starch or sugar primarily to ATP, but much of the energy is lost in the form of heat, with only 39% be- ing stored as ATP. Most fresh foods are kept under refrigeration, not only to lower the respiration rate and retard water loss, but also to dissipate the heat. Keeping the temperatures down is also important to prevent the growth and reproduction of food-spoiling molds and bacteria, which may thrive at warmer temperatures.

Heat inactivates most enzymes at temperatures above 40°C (104°F), but a few organisms, such as various cyanobacteria and algae in the hot springs of Yellowstone National Park and similar places, have adapted in such a way that they are able to thrive at temperatures exceeding 60°C (140°F)—heat that would kill other organisms of comparable size almost instantly.


Water inside the cells and their organelles act as a medium in which the enzymatic reactions can take place. Living cells often have a water content of more than 90%, but the cells of mature seeds may have a water content of less than 10%. When water content becomes this low, respiration does not cease completely, but it continues at a drastically reduced rate, resulting in only very tiny amounts of heat being released and of carbon dioxide being given off. Seeds may remain viable (capable of germinat- ing) for many years if stored under dry conditions. If they come in contact with water, however, they swell by imbibition. Respi- ration rates then increase rapidly. If the wet seeds happen to be in an unrefrigerated storage bin, the temperature may increase to the point of killing the seeds. In fact, if fungi and bacteria begin to grow on the seeds, temperatures from their respiration can become so high that spontaneous combustion can sometimes occur.


If flooding sharply reduces the oxygen supply available to the roots of trees and house plants, their respiration and growth rates may be decreased. They may even die if the condition persists too long. When foods are stored, however, it helps to bring about lower rates of respiration by reducing the oxygen in the storage areas. In fact, it is a common commercial practice to reduce the oxygen present in warehouses where crops are stored. The oxygen content is reduced to as little as 1% to 3% by pumping in nitrogen gas, while maintaining low temperatures and humidity. Oxygen concentration is not reduced below 1% because that can result in an undesirable increase in fermentation.

3. A Closer Look at Respiration

Respiration, like photosynthesis, is a very complex process, and, as with photosynthesis, it is beyond the scope of this book to explore the subject in great detail. The following amplification of information already discussed is modest, and those who wish further information are referred to the reading list at the end of the chapter.

Glycolysis Reexamined

As previously discussed, this initial phase of all forms of respiration brings about the conversion of each 6-carbon glucose molecule to two 3-carbon pyruvic acid molecules via three main steps, each mediated by enzymes. The three main steps are as follows:

  1. Phosphorylation, whereby the 6-carbon sugars receive phosphates
  2. Sugar cleavage, which involves the splitting of 6–carbon fructose into two 3-carbon sugar fragments
  3. Pyruvic acid formation, which involves the oxidation of the sugar fragments

Energy needed to initiate the process is furnished by an ATP molecule, which also furnishes the phosphate group for the phos- phorylation of the sugar glucose to yield glucose 6-phosphate. Another ATP, with the aid of the enzyme fructokinase, yields fruc- tose bisphosphate (fructose 1,6-diphosphate). As a result of the cleavage of the fructose bisphosphate, two different 3-carbon sugars are produced, but ultimately, only two glyceraldehyde 3-phosphate (GA3P) molecules remain. These two 3-carbon sugars are oxi- dized to two 3-carbon acids, and, in the successive production of several of these acids, phosphate groups are removed from the acids. The phosphate groups combine with ADP, producing a net direct gain of two ATP molecules during glycolysis. In addition, hydrogen is removed as GA3P is oxidized. This hydrogen is picked up by the acceptor molecule, NAD, which becomes NADH. Glycolysis, which requires no oxygen gas, is summarized in Figure 10.14.

Transition Step to the Citric Acid (Krebs) Cycle

Before a pyruvic acid molecule enters the citric acid cycle, which takes place in the mitochondria, a molecule of carbon dioxide is removed and a molecule of NADH is produced, leaving an acetyl fragment. The 2-carbon fragment is then bonded to a large mole- cule called coenzyme A. Coenzyme A consists of a combination of the B vitamin pantothenic acid and a nucleotide. Pantothenic acid is one of several B vitamins essential to respiration in both plants and animals; others include thiamine (vitamin B1), niacin, and riboflavin. The bonded acetyl fragment and coenzyme A molecule is referred to as acetyl CoA. The following equation summarizes the fate of the two pyruvic acid molecules following glycolysis and leading to the citric acid cycle:

2 pyruvic acid + 2 CoA + 2 NAD õõõõã 2 acetyl CoA + 2 NADH + 2CO2

In addition to pyruvic acid, fats and amino acids can also be converted to acetyl CoA and enter the process at this point. The NADH molecules donate their hydrogen to an electron transport system (discussed in the section, “Electron Transport and Oxidative Phosphorylation”), and the acetyl CoA enters the citric acid cycle (see Fig. 10.14).

The Citric Acid (Krebs) Cycle Reexamined

In the citric acid cycle, acetyl CoA is first combined with oxaloacetic acid, a 4-carbon compound, producing citric acid, a 6- carbon compound. The citric acid cycle is kept going by oxaloacetic acid, which is produced in small amounts, but is an inter- mediate product rather than a starting substance or an end product of the cycle. As the cycle progresses, a carbon dioxide is removed, producing a 5-carbon compound. Then another carbon dioxide is removed, producing a 4-carbon compound. This 4- carbon compound, through additional steps, is converted back to oxaloacetic acid, the substance with which the cycle began, and the cycle is repeated.

Each full cycle uses up a 2-carbon acetyl group and releases two carbon dioxide molecules while regenerating an ox- aloacetic acid molecule for the next turn of the cycle. Some hydrogen is removed during the process and is picked up by FAD and NAD. One molecule of ATP, three molecules of NADH, and one molecule of FADH2 are produced for each turn of the cycle. The citric acid cycle may be summarized as follows:

oxaloacetic + acetyl + ADP + P + 3 NAD + FAD õõõõã acid         CoA

oxaloacetic + CoA + ATP + 3 NADH + H+ + FADH2 + 2CO2 acid

The hydrogen carried by NAD and FAD can mostly be traced to the acetyl groups and to water molecules added to some compounds in the citric acid cycle. The FAD and FADH2 are now known to be intermediate compounds. Ubiquinol, a com- ponent of the electron transport system, receives electrons from either NADH or FADH2.

Electron Transport and Oxidative Phosphorylation

After completion of the citric acid cycle, the glucose molecule has been totally dismantled, and some of its energy has been transferred to ATP molecules. A considerable portion of the energy was transferred to NAD and FAD when they were used to pick up hydrogen and electrons from the molecules derived from glucose as they were broken down during glycolysis and the citric acid cycle. This energy is released as the hydrogen and electrons are passed along an electron transport system. This sys- tem, like the electron transport system of photosynthesis, functions something like a high-speed bucket brigade in passing along electrons from their source to their destination. Several of the electron carriers in the transport system are cytochromes. They are very specific and, as electrons flow along the system, they can transfer their electrons only to other specific acceptors. When the electrons reach the end of the system, they are picked up by oxygen and combine with hydrogen ions, forming water.

Part of the energy that is released during the movement of electrons along the electron transport system can be used to make ATP in a process called oxidative phosphorylation. If hydrogen ion and electron transport begins with NADH, which was produced inside the mitochondria (i.e., during the conversion of pyruvic acid to acetyl CoA and during the citric acid cycle), enough energy is produced to yield three ATP molecules from each NADH molecule. Similarly, if hydrogen ion and electron transport begins either with FADH2 or with NADH, produced outside the mitochondria (i.e., during glycolysis), two ATP molecules are produced.

The manner in which ATP is produced during the operation of the respiratory electron transport system involves essen- tially the same chemiosmotic concept that was applied earlier to proton movement across thylakoid membranes.

The chemiosmosis theory concerning electron transport and proton movement across membranes was proposed in the 1960s by Peter Mitchell, a British biochemist, and is now widely accepted as the explanation for the movements in both pho- tosynthesis and respiration. In respiration, oxidative phosphorylation is energized by a gradient of protons (H+) that flow by chemiosmosis across the inner membrane of a mitochondrion. Mitchell, who received a Nobel Prize for his work in 1978, surmised that protons are “pumped” from the matrix of the mitochondria to the region between the two membranes (see Fig. 3.13) as electrons flow from their source in NADH molecules along the electron transport system, which is located in the inner membrane. The protons are believed to “diffuse” back into the matrix via channels provided by an enzyme complex known as the F1 particle (an ATPase), releasing energy that is used to synthesize ATP.

If we retrace our steps through the entire process of aerobic respiration, we find that glycolysis yields four -molecules of ATP and two molecules of NADH (from which more molecules of ATP are formed), for a total of eight ATP from the con- version of glucose to two pyruvic acid molecules. Two ATP are used in the process, however, leaving a net gain of six ATP.

When two pyruvic acid molecules are converted to two acetyl CoA in the mitochondria, two more NADH molecules (which will generate six molecules of ATP) are produced. The two acetyl CoA molecules metabolized in the citric acid cycle yield two molecules of ATP, two molecules of FADH2 (from which four ATP are formed), and six molecules of NADH (which cause the formation of 18 molecules of ATP), making a citric acid cycle total of 24 ATP. A grand total of 36 ATP is produced for the aerobic respiration of one glucose molecule (Table 10.1). The 36 ATP molecules represent about 39% of the energy originally present in the glucose molecule. The remaining energy is lost as heat or is unavailable. Aerobic respiration is still about 18 times more efficient than anaerobic respiration.

A condensed comparison between photosynthesis and respiration is shown in Table 10.2.


While photosynthesis and respiration are the main processes through which plants grow, develop, reproduce, and survive, there are many additional processes that contribute toward these activities. Most of these use intermediate steps, but they could not function without photosynthesis and respiration. Some of the essential compounds produced from additional path- ways include sugar phosphates and nucleotides, nucleic acids, amino acids, proteins, chlorophylls, cytochromes, carotenoids, fatty acids, oils, and waxes.

Metabolic processes not required for normal growth and development are generally referred to as secondary metabolism. Although not essential, many of the products from secondary metabolism enable plants to survive and persist under special conditions. These products provide the plant with unique colors, aromas, poisons, and other compounds that may attract or deter other organisms or give them a competitive edge in nature. Humans have exploited many secondary compounds from plants for medicinal, culinary, or other purposes. It has been estimated that 50,000 to 100,000 such compounds exist in plants with only a few thousand of these thus far having been identified. Secondary metabolic products may be derived from modi- fication of amino acids and related compounds to produce alkaloids or through specialized conversions such as the shikimic acid pathway (phenolics) and mevalonic acid pathway (terpenoids). Examples of these compounds are shown in Table 10.3. Lignin, which is a component of secondary cell walls, is, for example, synthesized through the shikimic acid pathway. Be- cause it is hard to digest and is toxic to some predators, it protects plants from herbivorous animals.


Sugars produced through photosynthesis may undergo many transformations. Some sugars are used directly in respiration, but others not needed for that purpose may be transformed into lipids, proteins, or other carbohydrates. Among the most im- portant carbohydrates produced from simple sugars are sucrose, starch, and cellulose. Much of the organic matter produced through photosynthesis is eventually used in the building of protoplasm and cell walls. This conversion process is called as- similation.

When photosynthesis is taking place, sugar may be produced faster than it can be used or transported away to other parts of the plant. When this happens, the excess sugar may be converted to large, insoluble molecules, such as starch or oils, tem- porarily stored in the chloroplasts and then later changed back to a soluble form that is transported to other cells. The conver- sion of starch and other insoluble carbohydrates to soluble forms is called digestion (Fig. 10.15). The process is nearly al- ways one of hydrolysis, in which water is taken up and, with the aid of enzymes, the links of the chains of simple sugars that comprise the molecules of starch and similar carbohydrates are broken by the addition of water. The disaccharide malt sugar (maltose), for example, is transformed to two molecules of glucose, with the aid of an enzyme (maltase), by the addition of one molecule of water, as follows:


C12H22O11 + H2O   maltase   2C6H12O6

maltose water (enzyme) glucose

Fats are broken down to their component fatty acids and glycerol, and proteins are digested to their amino acid building blocks in similar fashion. Digestion is carried on in any cell where there may be stored food, with very little energy being released in the process. In animals, special digestive organs also play a role in digestion, but plants have no such additional “help” in the process. In both plants and animals, digestion within cells is similar and is a normal part of metabolism.

Except in insect-trapping plants, digestion takes place within plant cells where the carbohydrates, fats, or proteins are stored, while in animals, digestion usually occurs outside of the cells in the digestive tract. Apart from the location, the proc- ess is essentially similar in plants and animals.


  1. Enzymes catalyze reactions of metabolism. Many of these include oxidation-reduction reactions. Oxidation is loss of electrons; reduction is gain of electrons.
  2. Photosynthesis is an anabolic process that combines carbon dioxide and water in the presence of light with the aid of chlo- rophyll; oxygen is a by-product. All life depends on photosynthesis, which takes place in chloroplasts.
  3. Carbon dioxide constitutes 0.037% of the atmosphere, but the percentage has been rising in recent years. Increased car- bon dioxide levels have potential to elevate global temperatures through the “greenhouse effect.”
  4. Chlorophyll b and carotenoids are antenna pigments that direct light energy to chlorophyll a. Photosynthetic units con- taining chlorophylls and accessory pigments absorb units of light energy, become excited, and pass this energy to accep- tors during the light-dependent reactions of photosynthesis.
  5. During the light-dependent reactions of photosynthesis, which occur in thylakoid membranes of chloroplasts, water molecules are split, and oxygen gas is released. Hydrogen ions and electrons are released from water and transferred to produce NADPH and ATP.
  6. The two types of photosynthetic units present in most chloroplasts are photosystems I and II. The events that take place in photosystem II come before those of photosystem I. Each photosystem has a reaction-center molecule of chlorophyll a that boosts electrons to a higher energy level when it is excited by light energy.
  7. Photosystem II boosts electron excitation to a level that, when it encounters photosystem I, has the potential to reduce NADP to NADPH through noncyclic electron flow. Photosystem I, by itself, can cycle electrons for generation of ATP. Electron transport while the photosystems are operating and proton movement across thylakoid membranes are both in- volved in ATP production.
  8. The light-independent reactions occur through a series of reactions known as the Calvin cycle, which takes place in the stroma of chloroplasts. In the first step, carbon dioxide is combined with RuBP through catalytic action of the enzyme rubisco to form two molecules of the 3-carbon compound, GA3P. The ATP and NADPH from the light-dependent reac- tions furnish energy to eventually convert GA3P to 6-carbon carbohydrates. This cycle also regenerates RuBP to enable continued carbon fixation.
  9. In the light-independent reactions of C4 plants, 4-carbon oxaloacetic acid is initially produced instead of 3-carbon PGA. In the leaf mesophyll of C4 plants, there are large chloroplasts, which contain rubisco in the bundle sheaths, and small

chloroplasts, which contain higher concentrations of PEP carboxylase that facilitate the conversion of carbon dioxide to carbohydrate at much lower concentrations than is possible in C3 plants.

  1. CAM photosynthesis occurs in succulent plants whose stomata are closed and admit little CO2 during the day. Regular photosynthesis occurs as the 4-carbon compounds that accumulate at night are converted back to carbon dioxide during the day.
  2. Respiration is a catabolic process that takes place in the cytoplasm and mitochondria of cells. The energy is released, with the aid of enzymes, from simple sugar and organic acid molecules.
  3. In aerobic respiration, stored energy release requires oxygen; CO2 and water are by-products of the process.
  4. Anaerobic respiration and fermentation do not require oxygen gas, and much less energy is released. The remaining energy is in the ethyl alcohol, lactic acid, or other such substances produced. Some released energy is stored in ATP molecules. Temperature, available water, and environmental oxygen affect respiration rates.
  5. Glycolysis, which occurs in the cytoplasm, requires no molecular oxygen; two phosphates are added to a 6-carbon sugar molecule, and the prepared molecule is split into two 3-carbon sugars (GA3P). Some hydrogen, energy, and water are removed from the GA3P, producing pyruvic acid. There is a net gain of two ATP molecules. Hydrogen ions and elec- trons released during glycolysis are picked up by NAD, which becomes NADH.
  6. In aerobic respiration, which occurs in the mitochondria, pyruvic acid loses some CO2, is restructured, and becomes ace- tyl CoA. Energy, CO2, and hydrogen are removed from the acetyl CoA in the citric acid cycle, which involves enzyme- catalyzed reactions of a series of organic acids.
  7. NADH passes the hydrogen gained during glycolysis and the citric acid cycle along an electron transport system; small increments of energy are released and partially stored in ATP molecules, and the hydrogen is combined with oxygen gas, forming water in the final step of aerobic respiration.
  8. Hydrogen removed from glucose during glycolysis is combined with an inorganic ion in anaerobic respiration. The hy- drogen is combined with the pyruvic acid or one of its derivatives in fermentation. Both processes occur in the absence of oxygen gas, with only about 7% of the total energy in the glucose molecule being released, for a net gain of two ATP molecules.
  9. Two molecules of NADH and two ATP molecules are gained during glycolysis when two 3-carbon pyruvic acid mole- cules are produced from a single glucose molecule. Another molecule of NADH is produced when the pyruvic acid molecule is restructured and becomes acetyl CoA prior to entry into the citric acid cycle.
  10. In the citric acid cycle, acetyl CoA combines with 4-carbon oxaloacetic acid, producing first a 6-carbon compound, next a 5-carbon compound, and then several 4-carbon compounds. The last 4-carbon compound is oxaloacetic acid. Two CO2 molecules are also released during this process.
  11. Some hydrogen removed during the citric acid cycle is picked up by FAD and NAD; one molecule of ATP, three mole- cules of NADH, and one molecule of FADH2 are produced during one complete cycle. Energy associated with electrons and/or with hydrogen picked up by NAD and FAD is gradually released as the electrons are passed along the electron transport system; some of this energy is transferred to ATP molecules during oxidative phosphorylation.
  12. Energy used in ATP synthesis during oxidative phosphor-ylation is believed to be derived from a gradient of protons formed across the inner membrane of a mitochondrion, while electrons are moving in the electron transport system by chemiosmosis.
  13. Altogether, 38 ATP molecules are produced during the complete aerobic respiration of one glucose molecule; two are used to prime the process, so there is a net gain of 36 ATP molecules.
  14. In addition to photosynthesis and respiration, other metabolic pathways are required for growth, development, reproduc- tion, and survival. Essential products of additional pathways include nucleotides, proteins, chlorophylls, and fatty acids. Secondary metabolites include alkaloids, phenolics, and terpenoids.
  15. Conversion of sugar produced by photosynthesis to fats, proteins, complex carbohydrates, and other substances is termed assimilation. Digestion takes place within plant cells with the aid of enzymes. During digestion, large insoluble mole- cules are broken down by hydrolysis to smaller soluble forms that can be transported to other parts of the plant.

plant nutrients

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UF-nutrition-Chapter 1 Introduction Course Text-1.pdf
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UF-nutrition-Chapter 2a Supplying Fertilizer Course Text-1.pdf
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plant nutrients


plant biology

Plant Cell Biology

Plant Cell Physiology

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Plant and Soil Science Texts
Introduction to Botany (Shipunov) Botany.pdf
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nutrient table

N P K, C M S, I M Z, C B M.



Uptake form

Mobility in Plant
Mobility in Soil
Acid Deficiency
Alkaline Deficiency
gas and water C, H, O
Carbon, Hydrogen, Oxygen
Carbon © 50% dry weight  present in all macromolecules CO2, H2CO3
 Carbonic acid
Hydrogen (H) h2o is >80% plant weight part of many organic compounds and also forms water Hydron H+, OHHydroxide , H2O        
Oxygen (O)   necessary for cellular respiration; plants use oxygen to store energy in the form of ATP. O2 oxygen gas        


C M S , (Ca Mg S)

N, P, K    Ca Mg S
Nitrogen, Phosporous, Potassium ;
Calcium, Magnesium, Sulfur
Nitrogen (N) 4.00% A component of chlorophyll, nucleic acids, proteins, and
NO3Nitrate,  NH4+ ammonium ion,
also see Urea CH4N2O , and Ammonium nitrate (NH4NO3)
  Mobile as NO3, immobile as NH4+ y Volatilization Urea
Phosphorus 0.50% Required to store and transport energy HPO42- Hydrogen phosphate,
H2PO4 Dihydrogen phosphate
  Immobile y y
Potassium 4.00% Acts as a osmotic regulator in water absorption and loss
by the plant.
K+     y  
Calcium 1.00% Cell structure, secondary plant hormone Ca2+, see also Lime
calcium carbonate (CaCO3).
Magnesium 0.50% Central ion in the chlorophyll molecule Mg2+   Immobile y  
Sulfur 0.50% A component of nucleic acids and proteins SO4 sulfate ion     y  

I M Z , ( Fe Mn Z)

C B M ,  (Cu B Mo)

Fe, Mn, Zn ; Cu, B, Mo
Iron, Manganese, Zinc, Copper, Boron, Molybdenum
Iron 200 ppm Required for chlorophyll synthesis and
energy transferring pathways
Fe2+, Fe3+ Low Immobile   y
Manganese 200 ppm Required for chlorophyll production
and energy transferring pathways
Mn2+ Low     y
Zinc 30 ppm Activates enzymes Zn2+ Low Immobile   y
Copper 10 ppm Involved in respiration and oxidation/reduction reactions Cu2+ Low Immobile   y
Boron 60 ppm cell division and differentiation of young tissue H3BO3Boric Acid,
Low     y
Molybdenum 1 ppm Involved in nitrogen metabolism MoO4Molybdate Low   y  



Sodium 500 ppm Osmotic regulator Na+     10−3 g mg milligram
Chlorine 0.10% Required for photosynthesis Cl     103 g kg kilogram
Silicon 0.05-0.15% Pathogen defense, drought and heat tolerance H4SiO4     10−6 g µg microgram (mcg)
Cobalt     Co2+ Low   1 ppm =  1/1,000,000 =0.000001 = 0.0001%
= 1 mg/kg
Nickel     Ni2+    

Refrences –

Nutrient Uptake in Plants, Smart Fertilizer

Soil analysis: key to nutrient management planning, PDA

The most commonly found nutrient deficiency and toxicity symptoms are presented in the table below:

NutrientDeficiency SymptomsToxicity Symptoms
Nitrogen (N)Stunted growth and restricted growth of lateral shoots. Plants express general chlorosis of the entire plant to light green and yellowing of older leaves which proceeds to younger leaves. Older leaves become necrotic and defoliate earlyPlants are stunted, deep green in color, and secondary shoot development is poor. High N causes vegetative bud formation instead of reproductive bud formation. Ammonium toxicity can cause roots to turn brown, with necrotic root tips; reduce plant growth; necrotic lesions occur on stem and leaves; vascular browning occurs in stems and roots.
Phosphorus (P)Stunted growth. Purplish coloration of older leaves in some plants. Dark green coloration with tips of leaves dying. Delayed maturity, Poor fruit and seed development.Excess P in the plant can cause iron and zinc deficiencies.     
Potassium (K)Leaf margins turn chlorotic and then necrotic.  Tip and marginal burn starting on mature leaves.  Lower leaves turn yellow.  Weak stalks and plant lodge easily.  Slow growth. High amounts of K can cause calcium (Ca), magnesium (Mg) and N deficiencies.  
Magnesium (Mg)Interveinal chlorosis on older leaves which proceeds to the younger leaves as the deficiency becomes more severe.  The chlorotic interveinal yellow patches usually occur toward the center of the leaf with the margins being the last to turn yellow.   Curling of leaves upward along margins.  High Mg can cause Ca deficiency. 
Calcium (Ca)Light green color on uneven chlorosis of young leaves.  Brown or black scorching of new leaf tips and die-back of growing points.  Growing points of stems and roots cease to develop.  Poor root growth and roots short and thickened. High Ca can cause Mg or Boron (B) deficiencies. 
Sulfur (S)Uniform chlorosis first appearing on new leaves.  
Iron (Fe)Interveinal chlorosis of new leaves followed by complete chlorosis and or bleaching of new leaves.  Stunted growth. 
Zinc (Zn)Interveinal chlorosis of new leaves with some green next to veins.  Short internodes and small leaves.  Rosetting or whirling of leaves.  
Manganese (Mn)Interveinal chlorosis of new leaves with some green next to veins and later with grey or tan necrotic spots in chlorotic areas.  
Copper (Cu)Interveinal chlorosis of new leaves with tips and edges green, followed by veinal chlorosis.  Leaves at the top of the plant wilt easily followed by chlorotic and necrotic areas in the leaves.  Dieback of terminal shoots in trees.  
Boron (B)Death of terminal buds, causing lateral buds to develop and producing a ‘witches broom’ effect. Symptoms develop as a yellow-tinted band around the leaf margins.  The chlorotic zone becomes necrotic and gray, while the major portion of the leaf remains green. 
Molybdenum (Mo) Older leaves show interveinal chlorotic blotches, become cupped and thickened.  Chlorosis continues upward to younger leaves as deficiency progresses.  

Diagnosing Nutrient Deficiencies

EC and pH

pH and ECsymptomscorrections
High salts ECSmall, thick, and dark colored leaves. Lower leaves may turn yellow and brown, especially on the leaf margins. Plants become stunted.   Roots are less vigorous, may have brown leaves, and are likely to become diseased.The solution to high salt levels is usually to “leach out” (apply excess water to wash through the container) the growing medium or potting mix (termed the “root substrate” throughout this book).
Low EC ( see specific nutrient deficiency)“chlorosis” (yellowing, resulting from lack of the green chlorophyll pigment that is essential for photosynthesis). These symptoms can be seen on this geraniu   Nitrogen, phosphorus, and other nutrients are being moved out of its lower leaves to provide N and P to the growing points. The plant is essentially cannibalizing itself, because it cannot get nutrients from the roots.   Growth and flowering can be greatly reduced    The solution to low fertilizer levels is simply to apply more fertilizer. However, it is important to diagnose that nutrient levels are indeed low using an onsite soil test method and checking EC is below the adequate range
Substrate pH is too high (alkaline, pH values above 7 are “basic”)  e.g. Iron Symptoms to look for with iron deficiency at high pH:    Chlorosis either in the entire leaf or between the darker leaf veins (“interveinal chlorosis”)     Symptoms show up first in young leaves, in contrast to an overall low nutrient level, which may be in all or older leaves.   With sensitive plants such as the calibrachoa above, growth is severely stunted and growing points turn white and even necrotic (the tissue dies).Reduce excess limestone, or alkaline water, nitrate fertilizer’s basic effects.   To correct a high pH problem, a combination of acid fertilizer (containing ammonium or urea nitrogen) and adding acid into the irrigation water to remove alkalinity can usually drop substrate-pH.   Drenches (irrigations applied to the root substrate) with additional iron in a highly soluble form are also very effective at corr
Substrate pH is too low (acidity)Mn and Fe toxicity (over availability)   Chlorotic (yellow) or necrotic (brown and dead) spots or leaf margins in older leaves,   In marigold, the symptoms appear as brown sandy-colored spots in older leaves  The most common causes of a drop in substratepH are insufficient limestone, a fertilizer high in ammonium or urea nitrogen, which has an acidic reaction. Some plant species  such as geranium also tend to drop substrate-pH. An application of a liming material such as flowable limestone or potassium bicarbonate, and a change to a basic nitrate fertilizer are needed to raise substrate-pH


Calcareous SoilsPlant Nutrition
Cation and Anion Exchange Capacityplant videos 1 chemistry
Chemistry pHplant videos 2
Fertilizer Chemistryplant videos 3 physiology
greenhouse techplant water and transport
MicronutrientsSoil and Roots
nutrient tablesoil science
Plant Cell Biologyspring-lake
Plant Cell PhysiologyStylistics
plant nutrients

Table 1. Soil-borne elements essential for plant growth, the form occurring in the soil and taken up by the plant, and their relative soil mobility.
Element (symbol)Form taken up by the plantMobility in the soil
Nitrogen (N)(NH4)+ Ammonium form
(NO3) Nitrate form
Somewhat immobile
Phosphorous (P)(H2PO4) Dihydrogen phosphate, (HPO4)-2,  Hydrogenphosphate PO-3  phosphate anionImmobile
Potassium (K)K+Somewhat mobile
Calcium (Ca)Ca+Somewhat mobile
Magnesium (Mg)Mg+2Somewhat mobile
Sulfur (S)(SO4)-2 sulfateMobile
Chlorine (Cl)ClMobile
Iron (Fe)Fe+2Immobile
Boron (B)(BO3)Mobile
Manganese (Mn)Mn+2Immobile
Zinc (Z)Zn+2Immobile
Molybdenum (Mo)(MoO4)Mobile
Mn, ZnLet’s talk about manganese (MN) and zinc (Zn)
Manganese Deficiency in Palms – Ask IFAS
Manganese (Mn) and Zinc (Zn) for Citrus Trees

Manganese Fertility in Soybean Production
Zinc Deficiencies and Fertilization in Corn Production

mosaic Resources Zn, and Mn
Troubleshooting Magnesium Deficiencies in Corn
Sulfur Fertility for Crop Production
Mosaic Resources S

Sulfur Amendments to Lower Soil pH – UF/IFAS Extension ..

Iron (Fe) and Copper (Cu) for Citrus Trees – Ask IFAS
Iron (Fe) Nutrition of Plants – University of Florida

Iron Chlorosis
Management of Soybeans on Soils Prone to Iron Deficiency Chlorosis
Soil Fertility – Base Saturation and Cation Exchange Capacity
Environmental Fates, Nutrient Demands, and Efficient Nitrogen Fertility Programs
mosaic Micronutrients

UF/IFAS Standardized Fertilization Recommendations for …
Basics of Soybean Fertility

Phosphorus and Potassium Fertility for Corn and Soybean
Molybdenum Fertility in Crop Production
Molybdenum (Mo) and Nickel (Ni) for Citrus Trees

Growing Pomegranates in Florida … – University of Florida
Guide to Olive Tree Nutrition in Florida –
Develop Your Own Florida Olive IPM … – University of Florida

Soil and Roots

Clay and CEC


Molecular FormulaAl2H2O12Si4
silicon tetrahedron
aluminum octahedron
clay layers
Montmorillonite structure

The basic structural unit of montmorillonite mineral consists of one alumina sheet sandwiched between two silica sheets. The oxygen atoms at the tip of each silica sheet combine with the OH ions of both sides of the alumina sheet by hydrogen bond. As the bond is fairly strong, the basic structural unit of montmorillonite mineral is also stable. The thickness of the basic structural unit of montmorillonite is 9.2 Å.

Montmorillonite mineral is formed by stacking of several structural units one over the other. The interface between the two structural units during this stacking is through the silica sheet of one structural unit and the silica sheet of the other unit.

This bond is by van der Waals’ forces, which is rather weak. In dry condition, the van der Waals’ forces are rather strong so that it is difficult to break a dry lump of montmorillonite clay. However, water can easily enter between the layers, often dividing the montmorillonite particle into indi­vidual structural units.

One characteristic of van der Waals’ forces is that their magnitude decreases rapidly with distance. As water enters between the structural units, the distance between them increases, causing reduction in attractive forces. Thus, a montmorillonite clay particle is stable as long as it is dry but breaks into individual struc­tural units in the presence of water.


Cation Exchange:

cation exchange CEC 1
CEC clay

In a near neutral soil, calcium remains adsorbed on colloidal particle. Hydrogen ion (H+ ) generated as organic and mineral acids formed due to decomposition of organic matter. In colloid, hydrogen ion is adsorbed more strongly than is the calcium (Ca++). The reaction takes place rapidly and the interchange of calcium and hydrogen is Chemically equivalent.

This phenomenon of the exchange of cations between soil and salt solution is known as Cation exchange or Base exchange and the cations that take part in this reaction are called exchangeable cations. Cation exchange reactions are reversible.

Hence, if some form of limestone or other basic calcium compound is applied to an acid soil, the reverse of the replacement just given above occurs. The active calcium ions replace the hydrogen and other cations by mass action. As a result, the clay becomes higher in exchangeable calcium and lower in adsorbed hydrogen and aluminium.

If a soil is treated with a liberal application of a fertilizer containing potassium chloride, following reaction may occur: ; then:

Some of the added potassium pushes its way into the colloidal complex and forces out equivalent quantities of calcium, hydrogen and other elements (e.g., M) which appear in the soil solution. The adsorption of the added potassiumis  largely in an available condition. Hence, cation exchange is an important consideration for making already present nutrients in soils available to plants. Cation exchange also makes available the nutrients, applied in commercial fertilizers.

Cation Exchange Capacity (C.E.C.):

The cation exchange capacity of a soil represents the capacity of the colloidal complex to exchange all its cations with the cations of the electrolyte solution (surrounding liquid). It also represents the total cation adsorbing capacity of a soil. Cation exchange in most soils increases with pH. At a very low pH value, C.E.C. is higher and at high pH, C.E.C. is relatively lower.



The soil is a complex physical, chemical, and biological substrate. It is a heterogeneous material containing solid, liquid, and gaseous phases (see Chapter 4). All of these phases interact with mineral elements. The inorganic particles of the solid phase provide a reservoir of potassium, calcium, magnesium, and iron. Also associated with this solid phase are organic compounds containing nitrogen, phosphorus, and sulfur, among other elements. The liquid phase of the soil constitutes the soil solution, which contains dissolved mineral ions and serves as the medium for ion movement to the root surface. Gases such as oxygen, carbon dioxide, and nitrogen are dissolved in the soil solution, but in roots gases are exchanged predominantly through the air gaps between soil particles. From a biological perspective, soil constitutes a diverse ecosystem in which plant roots and microorganisms compete strongly for mineral nutrients. In spite of this competition, roots and microorganisms can form alliances for their mutual benefit (symbioses, singular symbiosis). In this section we will discuss the importance of soil properties, root structure, and mycorrhizal symbiotic relationships to plant mineral nutrition. Chapter 12 addresses symbiotic relationships with nitrogen-fixing bacteria.

Negatively Charged Soil Particles Affect the Adsorption of Mineral Nutrients

 Soil particles, both inorganic and organic, have predominantly negative charges on their surfaces. Many inorganic soil particles are crystal lattices that are tetrahedral arrangements of the cationic forms of aluminum and silicon (Al3+ and Si4+) bound to oxygen atoms, thus forming aluminates and silicates. When cations of lesser charge replace Al3+ and Si4+, inorganic soil particles become negatively charged. Organic soil particles originate from the products of the microbial decomposition of dead plants, animals, and microorganisms. The negative surface charges of organic particles result from the dissociation of hydrogen ions from the carboxylic acid and phenolic groups present in this component of the soil. Most of the world’s soil particles, however, are inorganic.  Inorganic soils are categorized by particle size:

Gravel has particles larger than 2 mm.

• Coarse sand has particles between 0.2 and 2 mm.

Fine sand has particles between 0.02 and 0.2 mm.

 • Silt has particles between 0.002 and 0.02 mm.

 • Clay has particles smaller than 0.002 mm (see Table 4.1).

The silicate-containing clay materials are further divided into three major groups—kaolinite, illite, and montmorillonite— based on differences in their structure and physical properties (Table 5.5). The kaolinite group is generally found in well-weathered soils; the montmorillonite and illite groups are found in less weathered soils. Mineral cations such as ammonium (NH4 +) and potassium (K+) adsorb to the negative surface charges of inorganic and organic soil particles. This cation adsorption is an important factor in soil fertility. Mineral cations adsorbed on the surface of soil particles are not easily lost when the soil is leached by water, and they provide a nutrient reserve available to plant roots. Mineral nutrients adsorbed in this way can be replaced by other cations in a process known as cation exchange (Figure 5.5). The degree to which a soil can adsorb and exchange ions is termed its cation exchange capacity (CEC) and is highly dependent on the soil type. A soil with higher cation exchange capacity generally has a larger reserve of mineral nutrients. Mineral anions such as nitrate (NO3 –) and chloride (Cl–) tend to be repelled by the negative charge on the surface of soil particles and remain dissolved in the soil solution. Thus the anion exchange capacity of most agricultural soils is small compared to the cation exchange capacity. Among anions, nitrate remains mobile in the soil solution, where it is susceptible to leaching by water moving through the soil. Phosphate ions (H2PO2 –) may bind to soil particles containing aluminum or iron because the positively charged iron and aluminum ions (Fe2+, Fe3+, and Al3+) have hydroxyl (OH–) groups that exchange with phosphate. As a result, phosphate can be tightly bound, and its mobility and availability in soil can limit plant growth. Sulfate (SO4 2–) in the presence of calcium (Ca2+) forms gypsum (CaSO4). Gypsum is only slightly soluble, but it releases sufficient sulfate to support plant growth.

Most nonacid soils contain substantial amounts of calcium; consequently, sulfate mobility in these soils is low, so sulfate is not highly susceptible to leaching.

clay mineral structure

Soil pH Affects Nutrient Availability, Soil Microbes, and Root Growth

Hydrogen ion concentration (pH) is an important property of soils because it affects the growth of plant roots and soil microorganisms. Root growth is generally favored in slightly acidic soils, at pH values between 5.5 and 6.5. Fungi generally predominate in acidic soils; bacteria become more prevalent in alkaline soils. Soil pH determines the availability of soil nutrients (see Figure 5.4). Acidity promotes the weathering of rocks that releases K+, Mg2+, Ca2+, and Mn2+ and increases the solubility of carbonates, sulfates, and phosphates. Increasing the solubility of nutrients facilitates their availability to roots. Major factors that lower the soil pH are the decomposition of organic matter and the amount of rainfall. Carbon dioxide is produced as a result of the decomposition of organic material and equilibrates with soil water in the following reaction: CO2 + H2O ~ H+ + HCO3 – This reaction releases hydrogen ions (H+), lowering the pH of the soil. Microbial decomposition of organic material also produces ammonia and hydrogen sulfide that can be oxidized in the soil to form the strong acids nitric acid (HNO3) and sulfuric acid (H2SO4), respectively. Hydrogen ions also displace K+, Mg2+, Ca2+, and Mn2+ from the cation exchange complex in a soil. Leaching then may remove these ions from the upper soil layers, leaving a more acid soil. By contrast, the weathering of rock in arid regions releases K+, Mg2+, Ca2+, and Mn2+ to the soil, but because of the low rainfall, these ions do not leach from the upper soil layers, and the soil remains alkaline.

5-8 rootapical
5-9 nutrient depletion
root fungi
t fungi 2

Excess Minerals in the Soil Limit Plant Growth

 When excess minerals are present in the soil, the soil is said to be saline, and plant growth may be restricted if these mineral ions reach levels that limit water availability or exceed the adequate zone for a particular nutrient (see Chapter 25). Sodium chloride and sodium sulfate are the most common salts in saline soils. Excess minerals in soils can be a major problem in arid and semiarid regions because rainfall is insufficient to leach the mineral ions from the soil layers near the surface. Irrigated agriculture fosters soil salinization if insufficient water is applied to leach the salt below the rooting zone. Irrigation water can contain 100 to 1000 g of minerals per cubic meter. An average crop requires about 4000 m3 of water per acre. Consequently, 400 to 4000 kg of minerals may be added to the soil per crop (Marschner 1995). In saline soil, plants encounter salt stress. Whereas many plants are affected adversely by the presence of relatively low levels of salt, other plants can survive high levels (salt-tolerant plants) or even thrive (halophytes) under such conditions. The mechanisms by which plants tolerate salinity are complex (see Chapter 25), involving molecular synthesis, enzyme induction, and membrane transport. In some species, excess minerals are not taken up; in others, minerals are taken up but excreted from the plant by salt glands associated with the leaves. To prevent toxic buildup of mineral ions in the cytosol, many plants may sequester them in the vacuole (Stewart and Ahmad 1983). Efforts are under way to bestow salt tolerance on salt-sensitive crop species using both classic plant breeding and molecular biology (Hasegawa et al. 2000). Another important problem with excess minerals is the accumulation of heavy metals in the soil, which can cause severe toxicity in plants as well as humans . Heavy metals include zinc, copper, cobalt, nickel, mercury, lead, cadmium, silver, and chromium (Berry and Wallace 1981).

Plants Develop Extensive Root Systems

The ability of plants to obtain both water and mineral nutrients from the soil is related to their capacity to develop an extensive root system. In the late 1930s, H. J. Dittmer examined the root system of a single winter rye plant after 16 weeks of growth and estimated that the plant had 13 × 106 primary and lateral root axes, extending more than 500 km in length and providing 200 m2 of surface area (Dittmer 1937). This plant also had more than 1010 root hairs, providing another 300 m2 of surface area  the desert, the roots of mesquite (genus Prosopis) may extend down more than 50 m to reach groundwater. Annual crop plants have roots that usually grow between 0.1 and 2.0 m in depth and extend laterally to distances of 0.3 to 1.0 m. In orchards, the major root systems of trees planted 1 m apart reach a total length of 12 to 18 km per tree. The annual production of roots in natural ecosystems may easily surpass that of shoots, so in many respects, the aboveground portions of a plant represent only “the tip of an iceberg.” Plant roots may grow continuously throughout the year. Their proliferation, however, depends on the availability of water and minerals in the immediate microenvironment surrounding the root, the so-called rhizosphere. If the rhizosphere is poor in nutrients or too dry, root growth is slow. As rhizosphere conditions improve, root growth increases. If fertilization and irrigation provide abundant nutrients and water, root growth may not keep pace with shoot growth. Plant growth under such conditions becomes carbohydrate limited, and a relatively small root system meets the nutrient needs of the whole plant (Bloom et al. 1993). Roots growing below the soil surface are studied by special techniques

oots 1
roots by species differ

Root Systems Differ in Form but Are Based on Common Structures

The form of the root system differs greatly among plant species. In monocots, root development starts with the emergence of three to six primary (or seminal) root axes from the germinating seed. With further growth, the plant extends new adventitious roots, called nodal roots or brace roots. Over time, the primary and nodal root axes grow and branch extensively to form a complex fibrous root system (Figure 5.6). In fibrous root systems, all the roots generally have the same diameter (except where environmental conditions or pathogenic interactions modify the root structure), so it is difficult to distinguish a main root axis. In contrast to monocots, dicots develop root systems with a main single root axis, called a taproot, which may thicken as a result of secondary cambial activity. From this main root axis, lateral roots develop to form an extensively branched root system (Figure 5.7). The development of the root system in both monocots and dicots depends on the activity of the root apical meristem and the production of lateral root meristems. Figure 5.8 shows a generalized diagram of the apical region of a plant root and identifies the three zones of activity: meristematic, elongation, and maturation. In the meristematic zone, cells divide both in the direction of the root base to form cells that will differentiate into the tissues of the functional root and in the direction of the root apex to form the root cap. The root cap protects the delicate meristematic cells as the root moves through the soil. It also secretes a gelatinous material called mucigel, which commonly surrounds the root tip. The precise function of the mucigel is uncertain, but it has been suggested that it lubricates the penetration of the root through the soil, protects the root apex from desiccation, promotes the transfer of nutrients to the root, or affects the interaction between roots and soil microorganisms (Russell 1977). The root cap is central to the perception of gravity, the signal that directs the growth of roots downward. This process is termed the gravitropic response (see Chapter 19). Cell division at the root apex proper is relatively slow; thus this region is called the quiescent center. After a few generations of slow cell divisions, root cells displaced from the apex by about 0.1 mm begin to divide more rapidly. Cell division again tapers off at about 0.4 mm from the apex, and the cells expand equally in all directions. The elongation zone begins 0.7 to 1.5 mm from the apex (see Figure 5.8). In this zone, cells elongate rapidly and undergo a final round of divisions to produce a central ring of cells called the endodermis. The walls of this endodermal cell layer become thickened, and suberin (see Chapter 13) deposited on the radial walls forms the Casparian strip, a hydrophobic structure that prevents the apoplastic movement of water or solutes across the root (see Figure 4.3). The endodermis divides the root into two regions: the cortex toward the outside and the stele toward the inside. The stele contains the vascular elements of the root: the phloem, which transports metabolites from the shoot to the root, and the xylem, which transports water and solutes to the shoot.

Phloem develops more rapidly than xylem, attesting to the fact that phloem function is critical near the root apex. Large quantities of carbohydrates must flow through the phloem to the growing apical zones in order to support cell division and elongation. Carbohydrates provide rapidly growing cells with an energy source and with the carbon skeletons required to synthesize organic compounds. Sixcarbon sugars (hexoses) also function as osmotically active solutes in the root tissue. At the root apex, where the phloem is not yet developed, carbohydrate movement depends on symplastic diffusion and is relatively slow  (Bret-Harte and Silk 1994). The low rates of cell division in the quiescent center may result from the fact that insufficient carbohydrates reach this centrally located region or that this area is kept in an oxidized state   Root hairs, with their large surface area for absorption of water and solutes, first appear in the maturation zone (see Figure 5.8), and it is here that the xylem develops the capacity to translocate substantial quantities of water and solutes to the shoot. 

Different Areas of the Root Absorb Different Mineral Ions

The precise point of entry of minerals into the root system has been a topic of considerable interest. Some researchers have claimed that nutrients are absorbed only at the apical regions of the root axes or branches (Bar-Yosef et al. 1972); others claim that nutrients are absorbed over the entire root surface (Nye and Tinker 1977). Experimental evidence supports both possibilities, depending on the plant species and the nutrient being investigated: • Root absorption of calcium in barley appears to be restricted to the apical region. • Iron may be taken up either at the apical region, as in barley (Clarkson 1985), or over the entire root surface, as in corn (Kashirad et al. 1973). • Potassium, nitrate, ammonium, and phosphate can be absorbed freely at all locations of the root surface (Clarkson 1985), but in corn the elongation zone has the maximum rates of potassium accumulation (Sharp et al. 1990) and nitrate absorption (Taylor and Bloom 1998). • In corn and rice, the root apex absorbs ammonium more rapidly than the elongation zone does (Colmer and Bloom 1998). • In several species, root hairs are the most active in phosphate absorption (Fohse et al. 1991). The high rates of nutrient absorption in the apical root zones result from the strong demand for nutrients in these tissues and the relatively high nutrient availability in the soil surrounding them. For example, cell elongation depends on the accumulation of solutes such as potassium, chloride, and nitrate to increase the osmotic pressure within the cell (see Chapter 15). Ammonium is the preferred nitrogen source to support cell division in the meristem because meristematic tissues are often carbohydrate limited, and the assimilation of ammonium consumes less energy than that of nitrate (see Chapter 12). The root apex and root hairs grow into fresh soil, where nutrients have not yet been depleted. Within the soil, nutrients can move to the root surface both by bulk flow and by diffusion (see Chapter 3). In bulk flow, nutrients are carried by water moving through the soil toward the root. The amount of nutrient provided to the root by bulk flow depends on the rate of water flow through the soil toward the plant, which depends on transpiration rates and on nutrient levels in the soil solution. When both the rate of water flow and the concentrations of nutrients in the soil solution are high, bulk flow can play an important role in nutrient supply. In diffusion, mineral nutrients move from a region of higher concentration to a region of lower concentration. Nutrient uptake by the roots lowers the concentration of nutrients at the root surface, generating concentration gradients in the soil solution surrounding the root. Diffusion of nutrients down their concentration gradient and bulk flow resulting from transpiration can increase nutrient availability at the root surface. When absorption of nutrients by the roots is high and the nutrient concentration in the soil is low, bulk flow can supply only a small fraction of the total nutrient requirement (Mengel and Kirkby 1987). Under these conditions, diffusion rates limit the movement of nutrients to the root surface. When diffusion is too slow to maintain high nutrient concentrations near the root, a nutrient depletion zone forms adjacent to the root surface (Figure 5.9). This zone extends from about 0.2 to 2.0 mm from the root surface, depending on the mobility of the nutrient in the soil. The formation of a depletion zone tells us something important about mineral nutrition: Because roots deplete the mineral supply in the rhizosphere, their effectiveness in mining minerals from the soil is determined not only by the rate at which they can remove nutrients from the soil solution, but by their continuous growth. Without growth, roots would rapidly deplete the soil adjacent to their surface. Optimal nutrient acquisition therefore depends both on the capacity for nutrient uptake and on the ability of the root system to grow into fresh soil.

Mycorrhizal Fungi Facilitate Nutrient Uptake by Roots

Our discussion thus far has centered on the direct acquisition of mineral elements by the root, but this process may be modified by the association of mycorrhizal fungi with the root system. Mycorrhizae (singular mycorrhiza, from the Greek words for “fungus” and “root”) are not unusual; in fact, they are widespread under natural conditions. Much of the world’s vegetation appears to have roots associated  with mycorrhizal fungi: 83% of dicots, 79% of monocots, and all gymnosperms regularly form mycorrhizal associations (Wilcox 1991). On the other hand, plants from the families Cruciferae (cabbage), Chenopodiaceae (spinach), and Proteaceae (macadamia nuts), as well as aquatic plants, rarely if ever have mycorrhizae. Mycorrhizae are absent from roots in very dry, saline, or flooded soils, or where soil fertility is extreme, either high or low. In particular, plants grown under hydroponics and young, rapidly growing crop plants seldom have mycorrhizae. Mycorrhizal fungi are composed of fine, tubular filaments called hyphae (singular hypha). The mass of hyphae that forms the body of the fungus is called the mycelium (plural mycelia). There are two major classes of mycorrhizal fungi: ectotrophic mycorrhizae and vesicular-arbuscular mycorrhizae (Smith et al. 1997). Minor classes of mycorrhizal fungi include the ericaceous and orchidaceous mycorrhizae, which may have limited importance in terms of mineral nutrient uptake. Ectotrophic mycorrhizal fungi typically show a thick sheath, or “mantle,” of fungal mycelium around the roots, and some of the mycelium penetrates between the cortical cells (Figure 5.10). The cortical cells themselves are not penetrated by the fungal hyphae but instead are surrounded by a network of hyphae called the Hartig net. Often the amount of fungal mycelium is so extensive that its total  mass is comparable to that of the roots themselves. The fungal mycelium also extends into the soil, away from this compact mantle, where it forms individual hyphae or strands containing fruiting bodies. The capacity of the root system to absorb nutrients is improved by the presence of external fungal hyphae that are much finer than plant roots and can reach beyond the areas of nutrient-depleted soil near the roots (Clarkson 1985). Ectotrophic mycorrhizal fungi infect exclusively tree species, including gymnosperms and woody angiosperms. Unlike the ectotrophic mycorrhizal fungi, vesiculararbuscular mycorrhizal fungi do not produce a compact mantle of fungal mycelium around the root. Instead, the hyphae grow in a less dense arrangement, both within the root itself and extending outward from the root into the surrounding soil (Figure 5.11). After entering the root through either the epidermis or a root hair, the hyphae not only extend through the regions between cells but also penetrate individual cells of the cortex. Within the cells, the hyphae can form oval structures called vesicles and branched structures called arbuscules. The arbuscules appear to be sites of nutrient transfer between the fungus and the host plant.  Outside the root, the external mycelium can extend several centimeters away from the root and may contain spore-bearing structures. Unlike the ectotrophic mycorrhizae, vesicular-arbuscular mycorrhizae make up only a small mass of fungal material, which is unlikely to exceed 10% of the root weight. Vesicular-arbuscular mycorrhizae are found in association with the roots of most species of herbaceous angiosperms (Smith et al. 1997). The association of vesicular-arbuscular mycorrhizae with plant roots facilitates the uptake of phosphorus and trace metals such as zinc and copper. By extending beyond the depletion zone for phosphorus around the root, the external mycelium improves phosphorus absorption. Calculations show that a root associated with mycorrhizal fungi can transport phosphate at a rate more than four times higher than that of a root not associated with mycorrhizae (Nye and Tinker 1977). The external mycelium of the ectotrophic mycorrhizae can also absorb phosphate and make it available to the plant. In addition, it has been suggested that ectotrophic mycorrhizae proliferate in the organic litter of the soil and hydrolyze organic phosphorus for transfer to the root (Smith et al. 1997).

Nutrients Move from the Mycorrhizal Fungi to the Root Cells

Little is known about the mechanism by which the mineral nutrients absorbed by mycorrhizal fungi are transferred to the cells of plant roots. With ectotrophic mycorrhizae, inorganic phosphate may simply diffuse from the hyphae in the Hartig net and be absorbed by the root cortical cells. With vesicular-arbuscular mycorrhizae, the situation may be more complex. Nutrients may diffuse from intact arbuscules to root cortical cells. Alternatively, because some root arbuscules are continually degenerating while new ones are forming, degenerating arbuscules may release their internal contents to the host root cells. A key factor in the extent of mycorrhizal association with the plant root is the nutritional status of the host plant. Moderate deficiency of a nutrient such as phosphorus tends to promote infection, whereas plants with abundant nutrients tend to suppress mycorrhizal infection. Mycorrhizal association in well-fertilized soils may shift from a symbiotic relationship to a parasitic one in that the fungus still obtains carbohydrates from the host plant, but the host plant no longer benefits from improved nutrient uptake efficiency. Under such conditions, the host plant may treat mycorrhizal fungi as it does other pathogens (Brundrett 1991; Marschner 1995).  


  The soil is a complex substrate—physically, chemically, and biologically. The size of soil particles and the cation exchange capacity of the soil determine the extent to which a soil provides a reservoir for water and nutrients. Soil pH also has a large influence on the availability of mineral elements to plants. If mineral elements, especially sodium or heavy metals, are present in excess in the soil, plant growth may be adversely affected. Certain plants are able to tolerate excess mineral elements, and a few species—for example, halophytes in the case of sodium—grow under these extreme conditions. To obtain nutrients from the soil, plants develop extensive root systems. Roots have a relatively simple structure with radial symmetry and few differentiated cell types. Roots continually deplete the nutrients from the immediate soil around them, and such a simple structure may permit rapid growth into fresh soil. Plant roots often form associations with mycorrhizal fungi. The fine hyphae of mycorrhizae extend the reach of roots into the surrounding soil and facilitate the acquisition of mineral elements, particularly those like phosphorus that are relatively immobile in the soil. In return, plants provide carbohydrates to the mycorrhizae. Plants tend to suppress mycorrhizal associations under conditions of high nutrient availability.  

Plant Nutrition


Only certain elements have been determined to be essential for plant growth. An essential element is defined as one whose absence prevents a plant from completing its life cycle (Arnon and Stout 1939) or one that has a clear physiological role (Epstein 1999). If plants are given these essential elements, as well as energy from sunlight, they can synthesize all the compounds they need for normal growth. Table 5.1 lists the elements that are considered to be essential for most, if not all, higher plants. The first three elements—hydrogen, carbon, and oxygen—are not considered mineral nutrients because they are obtained primarily from water or carbon dioxide.

Essential mineral elements are usually classified as macronutrients or micronutrients, according to their relative concentration in plant tissue. In some cases, the differences in tissue content of macronutrients and micronutrients are not as great as those indicated in Table 5.1. For example, some plant tissues, such as the leaf mesophyll, have almost as much iron or manganese as they do sulfur or magnesium. Many elements often are present in concentrations greater than the plant’s minimum requirements.

Some researchers have argued that a classification into macronutrients and micronutrients is difficult to justify physiologically. Mengel and Kirkby (1987) have proposed that the essential elements be classified instead according to their biochemical role and physiological function. Table 5.2 shows such a classification, in which plant nutrients have been divided into four basic groups:

  1. The first group of essential elements forms the organic (carbon  carbon) compounds of the plant. Plants assimilate these nutrients via biochemical reactions involving oxidation and reduction.
  2. The second group is important in energy storage reactions or in maintaining structural integrity. Elements in this group are often present in plant tissues as phosphate, borate, and silicate esters in which the elemental group is bound to the hydroxyl group of an organic molecule (i.e., sugar–phosphate).
  3. The third group is present in plant tissue as either free ions or ions bound to substances such as the pectic acids present in the plant cell wall. Of particular importance are their roles as enzyme cofactors and in the regulation of osmotic potentials.
  4. The fourth group has important roles in reactions involving electron transfer.

Naturally occurring elements, other than those listed in Table 5.1, can also accumulate in plant tissues. For example, aluminum is not considered to be an essential element, but plants commonly contain from 0.1 to 500 ppm aluminum, and addition of low levels of aluminum to a nutrient solution may stimulate plant growth  Many species in the genera Astragalus, Xylorhiza, and Stanleya accumulate selenium, although plants have not been shown to have a specific requirement for this element.

Cobalt is part of cobalamin (vitamin B12 and its derivatives), a component of several enzymes in nitrogen-fixing microorganisms. Thus cobalt deficiency blocks the development and function of nitrogen-fixing nodules. Nonetheless, plants that do not fix nitrogen, as well as nitrogen-fixing plants that are supplied with ammonium or nitrate, do not require cobalt. Crop plants normally contain only relatively small amounts of nonessential elements.

 Special Techniques Are Used in Nutritional Studies

 To demonstrate that an element is essential requires that plants be grown under experimental conditions in which only the element under investigation is absent. Such conditions are extremely difficult to achieve with plants grown in a complex medium such as soil. In the nineteenth century, several researchers, including Nicolas-Théodore de Saussure, Julius von Sachs, Jean-Baptiste-Joseph-Dieudonné Boussingault, and Wilhelm Knop, approached this problem by growing plants with their roots immersed in a nutrient solution containing only inorganic salts. Their demonstration that plants could grow normally with no soil or organic matter proved unequivocally that plants can fulfill all their needs from only inorganic elements and sunlight. The technique of growing plants with their roots immersed in nutrient solution without soil is called solution culture or hydroponics (Gericke 1937). Successful hydroponic culture (Figure 5.1A) requires a large volume of nutrient solution or frequent adjustment of the nutrient solution to prevent nutrient uptake by roots from producing radical changes in nutrient concentrations and pH of the medium. Asufficient supply of oxygen to the root system—also critical—may be achieved by vigorous bubbling of air through the medium. Hydroponics is used in the commercial production of many greenhouse crops. In one form of commercial hydroponic culture, plants are grown in a supporting material such as sand, gravel, vermiculite, or expanded clay (i.e., kitty litter). Nutrient solutions are then flushed through the supporting material, and old solutions are removed by leaching. In another form of hydroponic culture, plant roots lie on the surface of a trough, and nutrient solutions flow in a thin layer along the trough over the roots (Cooper 1979, Asher and Edwards 1983). This nutrient film growth system ensures that the roots receive an ample supply of oxygen (Figure 5.1B). Another alternative, which has sometimes been heralded as the medium of the future, is to grow the plants aeroponically (Weathers and Zobel 1992). In this technique, plants are grown with their roots suspended in air while being sprayed continuously with a nutrient solution (Figure 5.1C). This approach provides easy manipulation of the gaseous environment around the root, but it requires higher levels of nutrients than hydroponic culture does to sustain rapid plant growth. For this reason and other technical difficulties, the use of aeroponics is not widespread.

TABLE 5.1 Adequate tissue levels of elements that may be required by plants
  Chemical Element                                symbolConcentration in dry matter (% or ppm) aRelative number of atoms with respect to molybdenum
Obtained from water or carbon dioxide  
Obtained from the soil  

Identifying nutrient deficiency symptoms in field crops

Nutrient Solutions Can Sustain Rapid Plant Growth Over

the years, many formulations have been used for nutrient solutions. Early formulations developed by Knop in Germany included only KNO3, Ca(NO3)2, KH2PO4, MgSO4, and an iron salt. At the time this nutrient solution was believed to contain all the minerals required by the plant, but these experiments were carried out with chemicals that were contaminated with other elements that are now known to be essential (such as boron or molybdenum). Table 5.3 shows a more modern formulation for a nutrient solution. This formulation is called a modified Hoagland solution, named after Dennis R. Hoagland, a researcher who was prominent in the development of modern mineral nutrition research in the United States

A modified Hoagland solution contains all of the known mineral elements needed for rapid plant growth. The concentrations of these elements are set at the highest possible levels without producing toxicity symptoms or salinity stress and thus may be several orders of magnitude higher than those found in the soil around plant roots. For example, whereas phosphorus is present in the soil solution at concentrations normally less than 0.06 ppm, here it is offered at 62 ppm (Epstein 1972). Such high initial levels permit plants to be grown in a medium for extended periods without replenishment of the nutrients. Many researchers, however, dilute their nutrient solutions severalfold and replenish them frequently to minimize fluctuations of nutrient concentration in the medium and in plant tissue.

Another important property of the modified Hoagland formulation is that nitrogen is supplied as both ammonium (NH4 +) and nitrate (NO3 –). Supplying nitrogen in a balanced mixture of cations and anions tends to reduce the rapid rise in the pH of the medium that is commonly observed when the nitrogen is supplied solely as nitrate anion (Asher and Edwards 1983). Even when the pH of the medium is kept neutral, most plants grow better if they have access to both NH4 + and NO3 – because absorption and assimilation of the two nitrogen forms promotes cation–anion balance within the plant (Raven and Smith 1976; Bloom 1994).

A significant problem with nutrient solutions is maintaining the availability of iron. When supplied as an inorganic salt such as FeSO4 or Fe(NO3)2, iron can precipitate out of solution as iron hydroxide. If phosphate salts are present, insoluble iron phosphate will also form. Precipitation of the iron out of solution makes it physically unavailable to the plant, unless iron salts are added at frequent intervals. Earlier researchers approached this problem by adding iron together with citric acid or tartaric acid. Compounds such as these are called chelators because they form soluble complexes with cations such as iron and calcium in which the cation is held by ionic forces, rather than by covalent bonds. Chelated cations thus are physically more available to a plant. More modern nutrient solutions use the chemicals ethylenediaminetetraacetic acid (EDTA) or diethylenetriamine pentaacetic acid (DTPA, or pentetic acid) as chelating agents (Sievers and Bailar 1962). Figure 5.2 shows the structure of DTPA. The fate of the chelation complex during iron uptake by the root cells is not clear; iron may be released from the chelator when it is reduced from Fe3+ to Fe2+ at the root surface. The chelator may then diffuse back into the nutrient (or soil) solution and react with another Fe3+ ion or other metal ions. After uptake, iron is kept soluble by chelation with organic compounds present in plant cells. Citric acid may play a major role in iron chelation and its long-distance transport in the xylem.

Inadequate supply of an essential element results in a nutritional disorder manifested by characteristic deficiency symptoms. In hydroponic culture, withholding of an essential element can be readily correlated with a given set of symptoms for acute deficiencies. Diagnosis of soil-grown plants can be more complex, for the following reasons

  • Both chronic and acute deficiencies of several elements may occur simultaneously.
  • Deficiencies or excessive amounts of one element may induce deficiencies or excessive accumulations of another.
  • Some virus-induced plant diseases may producesymptoms similar to those of nutrient deficiencies.

Nutrient deficiency symptoms in a plant are the expression of metabolic disorders resulting from the insufficient supply of an essential element. These disorders are related to the roles played by essential elements in normal plant metabolism and function. Table 5.2 lists some of the roles of essential elements.

Even though each essential element participates in many different metabolic reactions, some general statements about the functions of essential elements in plant metabolism are possible. In general, the essential elements function in plant structure, metabolic function, and osmoregulation of plant cells. More specific roles may be related to the ability of divalent cations such as calcium or magnesium to modify the permeability of plant membranes. In addition, research continues to reveal specific roles of these elements in plant metabolism; for example, calcium acts as a signal to regulate key enzymes in the cytosol (Hepler and Wayne 1985; Sanders et al. 1999). Thus, most essential elements have multiple roles in plant metabolism.

When relating acute deficiency symptoms to a particular essential element, an important clue is the extent to which an element can be recycled from older to younger leaves. Some elements, such as nitrogen, phosphorus, and potassium, can readily move from leaf to leaf; others, such as boron, iron, and calcium, are relatively immobile in most plant species (Table 5.4). If an essential element is mobile, deficiency symptoms tend to appear first in older leaves. Deficiency of an immobile essential element will become evident first in younger leaves. Although the precise mechanisms of nutrient mobilization are not well understood, plant hormones such as cytokinins appear to be involved (see Chapter 21). In the discussion that follows, we will describe the specific deficiency symptoms and functional roles for the mineral essential elements as they are grouped in Table 5.2.

mobile young leaves

Group 1: Deficiencies in mineral nutrients that are part of carbon compounds.

This first group consists of nitro- gen and sulfur. Nitrogen availability in soils limits plant productivity in most natural and agricultural ecosystems. By contrast, soils generally contain sulfur in excess. Nonetheless, nitrogen and sulfur share the property that their oxidation–reduction states range widely (see Chapter 12). Some of the most energy-intensive reactions in life con- vert the highly oxidized, inorganic forms absorbed from the soil into the highly reduced forms found in organic compounds such as amino acids.


Nitrogen is the mineral element that plants require in greatest amounts. It serves as a constituent of many plant cell components, including amino acids and nucleic acids. Therefore, nitrogen deficiency rapidly inhibits plant growth. If such a deficiency persists, most species show chlorosis (yellowing of the leaves), especially in the older leaves near the base of the plant (for pictures of nitro- gen deficiency and the other mineral deficiencies described in this chapter, see Web Topic 5.1). Under severe nitrogen deficiency, these leaves become completely yellow (or tan) and fall off the plant. Younger leaves may not show these symptoms initially because nitrogen can be mobilized from older leaves. Thus a nitrogen-deficient plant may have light green upper leaves and yellow or tan lower leaves.

When nitrogen deficiency develops slowly, plants may have markedly slender and often woody stems. This wood- iness may be due to a buildup of excess carbohydrates that cannot be used in the synthesis of amino acids or other nitrogen compounds. Carbohydrates not used in nitrogen metabolism may also be used in anthocyanin synthesis, leading to accumulation of that pigment. This condition is revealed as a purple coloration in leaves, petioles, and stems of some nitrogen-deficient plants, such as tomato and certain varieties of corn.


 Sulfur is found in two amino acids and is a con- stituent of several coenzymes and vitamins essential for metabolism. Many of the symptoms of sulfur deficiency are similar to those of nitrogen deficiency, including chlorosis, stunting of growth, and anthocyanin accumulation. This similarity is not surprising, since sulfur and nitrogen are both constituents of proteins. However, the chlorosis caused by sulfur deficiency generally arises initially in mature and young leaves, rather than in the old leaves as in nitrogen deficiency, because unlike nitrogen, sulfur is not easily remobilized to the younger leaves in most species. Nonetheless, in many plant species sulfur chlorosis may occur simultaneously in all leaves or even initially in the older leaves.

Group 2: Deficiencies in mineral nutrients that are impor- tant in energy storage or structural integrity.

This group consists of phosphorus, silicon, and boron. Phosphorus and silicon are found at concentrations within plant tissue that warrant their classification as macronutrients, whereas boron is much less abundant and considered a micronutri- ent. These elements are usually present in plants as ester linkages to a carbon molecule.


 Phosphorus (as phosphate, PO 3–) is an inte- gral component of important compounds of plant cells, including the sugar–phosphate intermediates of respiration and photosynthesis, and the phospholipids that make up plant membranes. It is also a component of nucleotides used in plant energy metabolism (such as ATP) and in DNA and RNA. Characteristic symptoms of phosphorus deficiency include stunted growth in young plants and a dark green coloration of the leaves, which may be mal- formed and contain small spots of dead tissue called necrotic spots

As in nitrogen deficiency, some species may produce excess anthocyanins, giving the leaves a slight purple col- oration. In contrast to nitrogen deficiency, the purple col- oration of phosphorus deficiency is not associated with chlorosis. In fact, the leaves may be a dark greenish purple. Additional symptoms of phosphorus deficiency include the production of slender (but not woody) stems and the death of older leaves. Maturation of the plant may also be delayed.


Only members of the family Equisetaceae—called scouring rushes because at one time their ash, rich in gritty silica, was used to scour pots—require silicon to complete their life cycle. Nonetheless, many other species accumu- late substantial amounts of silicon within their tissues and show enhanced growth and fertility when supplied with adequate amounts of silicon (Epstein 1999).

Plants deficient in silicon are more susceptible to lodg- ing (falling over) and fungal infection. Silicon is deposited primarily in the endoplasmic reticulum, cell walls, and intercellular spaces as hydrated, amorphous silica (SiO2·nH2O). It also forms complexes with polyphenols and thus serves as an alternative to lignin in the reinforcement of cell walls. In addition, silicon can ameliorate the toxicity of many heavy metals.


Although the precise function of boron in plant metabolism is unclear, evidence suggests that it plays roles in cell elongation, nucleic acid synthesis, hormone responses, and membrane function (Shelp 1993). Boron- deficient plants may exhibit a wide variety of symptoms, depending on the species and the age of the plant.

A characteristic symptom is black necrosis of the young leaves and terminal buds. The necrosis of the young leaves occurs primarily at the base of the leaf blade. Stems may be unusually stiff and brittle. Apical dominance may also be lost, causing the plant to become highly branched; how- ever, the terminal apices of the branches soon become necrotic because of inhibition of cell division. Structures such as the fruit, fleshy roots, and tubers may exhibit necro- sis or abnormalities related to the breakdown of internal tissues.

Group 3: Deficiencies in mineral nutrients that remain in ionic form.

This group includes some of the most familiar mineral elements: The macronutrients potassium, calcium, and magnesium, and the micronutrients chlorine, manganese, and sodium. They may be found in solution in the cytosol or vacuoles, or they may be bound electrostati- cally or as ligands to larger carbon-containing compounds.


Potassium, present within plants as the cation K+, plays an important role in regulation of the osmotic potential of plant cells (see Chapters 3 and 6). It also acti- vates many enzymes involved in respiration and photo- synthesis. The first observable symptom of potassium defi- ciency is mottled or marginal chlorosis, which then develops into necrosis primarily at the leaf tips, at the mar- gins, and between veins. In many monocots, these necrotic lesions may initially form at the leaf tips and margins and then extend toward the leaf base.

Because potassium can be mobilized to the younger leaves, these symptoms appear initially on the more mature leaves toward the base of the plant. The leaves may also curl and crinkle. The stems of potassium-deficient plants may be slender and weak, with abnormally short internodal regions. In potassium-deficient corn, the roots may have an increased susceptibility to root-rotting fungi present in the soil, and this susceptibility, together with effects on the stem, results in an increased tendency for the plant to be easily bent to the ground (lodging).


Calcium ions (Ca2+) are used in the synthesis of new cell walls, particularly the middle lamellae that sepa- rate newly divided cells. Calcium is also used in the mitotic spindle during cell division. It is required for the normal functioning of plant membranes and has been implicated as a second messenger for various plant responses to both environmental and hormonal signals (Sanders et al. 1999). In its function as a second messenger, calcium may bind to calmodulin, a protein found in the cytosol of plant cells. The calmodulin–calcium complex regulates many meta- bolic processes.

Characteristic symptoms of calcium deficiency include necrosis of young meristematic regions, such as the tips of roots or young leaves, where cell division and wall forma- tion are most rapid. Necrosis in slowly growing plants may be preceded by a general chlorosis and downward hook- ing of the young leaves. Young leaves may also appear deformed. The root system of a calcium-deficient plant may appear brownish, short, and highly branched. Severe stunting may result if the meristematic regions of the plant die prematurely.


In plant cells, magnesium ions (Mg2+) have a specific role in the activation of enzymes involved in respi- ration, photosynthesis, and the synthesis of DNA and RNA. Magnesium is also a part of the ring structure of the chloro- phyll molecule (see Figure 7.6A). A characteristic symptom of magnesium deficiency is chlorosis between the leaf veins, occurring first in the older leaves because of the mobility of this element. This pattern of chlorosis results because the chlorophyll in the vascular bundles remains unaffected for longer periods than the chlorophyll in the cells between the bundles does. If the deficiency is extensive, the leaves may become yellow or white. An additional symptom of mag- nesium deficiency may be premature leaf abscission.


The element chlorine is found in plants as the chloride ion (Cl–). It is required for the water-splitting reac- tion of photosynthesis through which oxygen is produced (see Chapter 7) (Clarke and Eaton-Rye 2000). In addition, chlorine may be required for cell division in both leaves and roots (Harling et al. 1997). Plants deficient in chlorine develop wilting of the leaf tips followed by general leaf chlorosis and necrosis. The leaves may also exhibit reduced growth. Eventually, the leaves may take on a bronzelike color (“bronzing”). Roots of chlorine-deficient plants may appear stunted and thickened near the root tips.

Chloride ions are very soluble and generally available in soils because seawater is swept into the air by wind and is delivered to soil when it rains. Therefore, chlorine defi- ciency is unknown in plants grown in native or agricultural habitats. Most plants generally absorb chlorine at levels much higher than those required for normal functioning.


Manganese ions (Mn2+) activate several enzymes in plant cells. In particular, decarboxylases and dehydrogenases involved in the tricarboxylic acid (Krebs) cycle are specifically activated by manganese. The best- defined function of manganese is in the photosynthetic reaction through which oxygen is produced from water (Marschner 1995). The major symptom of manganese defi- ciency is intervenous chlorosis associated with the devel- opment of small necrotic spots. This chlorosis may occur on younger or older leaves, depending on plant species and growth rate.


Most species utilizing the C4 and CAM pathways of carbon fixation (see Chapter 8) require sodium ions (Na+). In these plants, sodium appears vital for regenerat- ing phosphoenolpyruvate, the substrate for the first car-boxylation in the C4 and CAM pathways (Johnstone et al. 1988). Under sodium deficiency, these plants exhibit chloro- sis and necrosis, or even fail to form flowers. Many C3 species also benefit from exposure to low levels of sodium ions. Sodium stimulates growth through enhanced cell expansion, and it can partly substitute for potassium as an osmotically active solute.

Group 4: Deficiencies in mineral nutrients that are involved in redox reactions.

This group of five micronu- trients includes the metals iron, zinc, copper, nickel, and molybdenum. All of these can undergo reversible oxidations and reductions (e.g., Fe2+ ~ Fe3+) and have important roles in electron transfer and energy transformation. They are usu- ally found in association with larger molecules such as cytochromes, chlorophyll, and proteins (usually enzymes).


 Iron has an important role as a component of enzymes involved in the transfer of electrons (redox reac- tions), such as cytochromes. In this role, it is reversibly oxi- dized from Fe2+ to Fe3+ during electron transfer. As in mag- nesium deficiency, a characteristic symptom of iron deficiency is intervenous chlorosis. In contrast to magne- sium deficiency symptoms, these symptoms appear ini- tially on the younger leaves because iron cannot be readily mobilized from older leaves. Under conditions of extreme or prolonged deficiency, the veins may also become chlorotic, causing the whole leaf to turn white.

The leaves become chlorotic because iron is required for the synthesis of some of the chlorophyll–protein complexes in the chloroplast. The low mobility of iron is probably due to its precipitation in the older leaves as insoluble oxides or phosphates or to the formation of complexes with phyto- ferritin, an iron-binding protein found in the leaf and other plant parts (Oh et al. 1996). The precipitation of iron dimin- ishes subsequent mobilization of the metal into the phloem for long-distance translocation.


Many enzymes require zinc ions (Zn2+) for their activity, and zinc may be required for chlorophyll biosyn- thesis in some plants. Zinc deficiency is characterized by a reduction in internodal growth, and as a result plants dis- play a rosette habit of growth in which the leaves form a circular cluster radiating at or close to the ground. The leaves may also be small and distorted, with leaf margins having a puckered appearance. These symptoms may result from loss of the capacity to produce sufficient amounts of the auxin indoleacetic acid. In some species (corn, sorghum, beans), the older leaves may become inter- venously chlorotic and then develop white necrotic spots. This chlorosis may be an expression of a zinc requirement for chlorophyll biosynthesis.


Like iron, copper is associated with enzymes involved in redox reactions being reversibly oxidized from Cu+ to Cu2+. An example of such an enzyme is plasto- cyanin, which is involved in electron transfer during the light reactions of photosynthesis (Haehnel 1984). The ini- tial symptom of copper deficiency is the production of dark green leaves, which may contain necrotic spots. The necrotic spots appear first at the tips of the young leaves and then extend toward the leaf base along the margins. The leaves may also be twisted or malformed. Under extreme copper deficiency, leaves may abscise prematurely.


Urease is the only known nickel-containing enzyme in higher plants, although nitrogen-fixing microor- ganisms require nickel for the enzyme that reprocesses some of the hydrogen gas generated during fixation (hydrogen uptake hydrogenase) (see Chapter 12). Nickel- deficient plants accumulate urea in their leaves and, con- sequently, show leaf tip necrosis. Plants grown in soil sel- dom, if ever, show signs of nickel deficiency because the amounts of nickel required are minuscule.


Molybdenum ions (Mo4+ through Mo6+) are components of several enzymes, including nitrate reductase and nitrogenase. Nitrate reductase catalyzes the reduction of nitrate to nitrite during its assimilation by the plant cell; nitrogenase converts nitrogen gas to ammonia in nitrogen-fixing microorganisms (see Chapter 12). The first indication of a molybdenum deficiency is general chloro- sis between veins and necrosis of the older leaves. In some plants, such as cauliflower or broccoli, the leaves may not become necrotic but instead may appear twisted and sub- sequently die (whiptail disease). Flower formation may be prevented, or the flowers may abscise prematurely.

Because molybdenum is involved with both nitrate assimilation and nitrogen fixation, a molybdenum defi- ciency may bring about a nitrogen deficiency if the nitrogen source is primarily nitrate or if the plant depends on sym- biotic nitrogen fixation. Although plants require only small amounts of molybdenum, some soils supply inadequate levels. Small additions of molybdenum to such soils can greatly enhance crop or forage growth at negligible cost.

TABLE 5.3 Composition of a modified Hoagland nutrient solution for growing plants
    Compound  Molecular weightConcentration of stock solutionConcentration of stock solutionVolume of stock solution per liter of final solution    ElementFinal concentration of element
 g mol–1mMg L–1mL mMppm
KNO3 Potassium nitrate  101.101,000101.106.0N16,000224
Ca(NO3)2×4H2O Calcium Nitrate Tetrahydrate  236.161,000236.164.0K6,000235
NH4H2PO4 Ammonium dihydrogen phosphate115.081,000115.082.0Ca4,000160
Heptahydrate, 2O (“Epsom salt”) Epsonite of Magnesium sulfate    S1,00032
KCl74.55251.864 Cl501.77
H3BO3 Boric Acid61.8312.50.773 B250.27
MnSO4×H2O Manganese sulfate monohydrate169.011.00.169  2.0Mn2.00.11
ZnSO4×7H2O Zinc sulfate heptahydrate287.541.00.288 Zn2.00.13
CuSO4×5H2O Copper sulfate pentahydrate249.680.250.062 Cu0.50.03
 161.970.250.040 Mo0.50.05
NaFe DTPA (10% Fe)468.206430.00.3–1.0Fe16.1–53.7 1.00–3.00
NiSO4×6H2O Nickel sulfate hexahydrate  262.860.250.0662.0Ni0.50.03
Na2SiO3×9H2O Sodium metasilicate nonahydrate284.201,000284.201.0Si1,00028
chelate NaCl Iron
Chelates   Several factors reduce the bioavailability of Fe, including high soil pH, high bicarbonate content, plant species (grass species are usually more efficient than other species because they can excrete effective ligands), and abiotic stresses. Plants typically utilize iron as ferrous iron (Fe2+). Ferrous iron can be readily oxidized to the plant-unavailable ferric form (Fe3+) when soil pH is greater than 5.3 (Morgan and Lahav 2007). Iron deficiency often occurs if soil pH is greater than 7.4. Chelated iron can prevent this conversion from Fe2+ to Fe3+.   Applying nutrients such as Fe, Mn, Zn, and Cu directly to the soil is inefficient because in soil solution they are present as positively charged metal ions and will readily react with oxygen and/or negatively charged hydroxide ions (OH-). If they react with oxygen or hydroxide ions, they form new compounds that are not bioavailable to plants. Both oxygen and hydroxide ions are abundant in soil and soilless growth media.   The ligand can protect the micronutrient from oxidization or precipitation. Figure 1 shows examples of the typical iron deficiency symptoms of lychee grown in Homestead, Florida, in which the lychee trees have yellow leaves and small, abnormal fruits. Applying chelated fertilizers is an easy and practical correction method to avoid this nutrient disorder. For example, the oxidized form of iron is ferric (Fe3+), which is not bioavailable to plants and usually forms brown ferric hydroxide precipitation (Fe(OH)3). Ferrous sulfate, which is not a chelated fertilizer, is often used as the iron source. Its solution should be green. If the solution turns brown, the bioavailable form of iron has been oxidized and Fe is therefore unavailable to plants.   Figure 3.  Comparison of foliar applications of chelated Fe, regular iron fertilizers, and no iron fertilization for correcting iron deficiency of lychee (Litchi chinensis, the soapberry family).
Credit: Yuncong Li, UF/IFAS   [Pentetic acid or diethylenetriaminepentaacetic acid (DTPA)] The ligands EDTA, DTPA, and EDDHA are often used in chelated fertilizers (Table 4). Their effectiveness differs significantly. EDDHA chelated Fe is most stable at soil pH greater than 7 (Figure 4, A and B). Chelated fertilizer stability is desired because it means the chelated micronutrient will remain in a bioavailable form for a much longer time period, thus increasing micronutrient use efficiency in vegetable and fruit production. The stability of three typical chelated Fe fertilizers varies at different pH conditions (Figure 4, A). The Y-axis represents the ratio of chelated Fe to total chelate and ranges from 0 to 1.0. A value of 1.0 means the chelate is stable. The X-axis represents soil pH. At 6.0, the ratios for all three chelated Fe fertilizers are 1.0 (stable), but at pH 7.5, only the ratio of EDDTA chelated Fe is 1.0. That of DTPA chelated Fe is only 0.5, and that of EDTA chelated Fe is only 0.025. So, in practice, EDDTA chelated Fe fertilizer is most effective when pH is greater than 7 but most costly. Accordingly, crop yields of these three chelated fertilizers are in this order: FeEDDHA > FeDTPA > FeEDTA (Figure 4, B). See Micronutrient Deficiencies in Citrus: Iron, Zinc, and Manganese ( for effective pH ranges of iron chelates. Table 3 shows the relationship between soil pH and chelated fertilizer requirement. Correction of Fe deficiency depends on individual crop response and many other factors. For instance, for vegetables, the rate is usually 0.4–1 lb. chelated Fe in 100 gal. of water per acre. Deciduous fruits need 0.1–0.2 lb. chelated Fe in 25 gal. of water per acre (Table 5). Foliar application is more effective than soil application. For foliar application, either inorganic or chelated Fe is effective, but for fertigation, chelated Fe should be used. In high pH soil, crops are also vulnerable to Cu deficiency stresses. Chelated Cu is significantly more effective than inorganic Cu. A commonly used copper chelate is Na2CuEDTA, which contains 13% Cu. Natural organic materials have approximately 0.5% Cu (Table 5). In addition to soil pH, Mn is also influenced by aeration, moisture, and organic matter content. Chelated Mn can improve Mn bioavailability. Mn deficiency occurs more often in high pH and dry soil. Similar to other micronutrients, foliar spray is much more effective than soil application. For commercial vegetable production, 0.2–0.5 lb. MnEDTA in 200 gal. of water per acre can effectively correct Mn deficiency (Table 5). Zinc is another micronutrient whose bioavailability is closely associated with soil pH. Crops may be susceptible to Zn deficiency in soil with pH > 7.3. Spraying 0.10–0.14 lb. chelated Zn in 100 gal. of water per acre is effective (Poh et al. 2009). Animal waste and municipal waste also contain Cu, Mn, and Zn micronutrients (Table 5). For more information about micronutrient deficiency in crops, see Plant Tissue Analysis and Interpretation for Vegetable Crops in Florida (,    
TABLE 5.5 Comparison of properties of three major types of silicate clays found in the soil
    PropertyType of clay
Size (µm)0.01–1.00.1–2.00.1–5.0
ShapeIrregular flakesIrregular flakesHexagonal crystals
Water-swelling capacityHighMediumLow
Cation exchange capacity (milliequivalents 100 g-1)80–10015–403–15
TABLE 6.1 Comparison of observed and predicted ion concentrations in pea root tissue
    IonConcentration in external medium (mmol L–1)  Internal concentration (mmol L–1)
K+ Na+ Mg2+ Ca2+ NO – 3 Cl– H2PO – 4 SO 2– 41 1 0.25 1 2 1 1 0.2574 74 1340 5360 0.0272 0.0136 0.0136 0.0000575 8 3 2 28 7 21 19
TABLE 6.2 The vacuolar pH of some hyperacidifying plant species
Fruits  Lime (Citrus aurantifolia) Lemon (Citrus limonia) Cherry (Prunuscerasus) Grapefruit (Citrus paradisi)     Rosette oxalis (Oxalisdeppei) Wax begonia (Begonia semperflorens) Begonia ‘Lucerna’ Oxalis sp. Sorrel (Rumex sp.) Prickly Pear (Opuntia phaeacantha)b 
 0.9 – 1.4
 1.9 – 2.6
 1.4 (6:45A.M.)
 5.5 (4:00 P.M.)


ph availability

Analysis of Plant Tissues Reveals Mineral Deficiencies

Requirements for mineral elements change during the growth and development of a plant. In crop plants, nutri- ent levels at certain stages of growth influence the yield of the economically important tissues (tuber, grain, and so on). To optimize yields, farmers use analyses of nutrient levels in soil and in plant tissue to determine fertilizer schedules.

Soil analysis is the chemical determination of the nutri- ent content in a soil sample from the root zone. As dis- cussed later in the chapter, both the chemistry and the biol- ogy of soils are complex, and the results of soil analyses vary with sampling methods, storage conditions for the samples, and nutrient extraction techniques. Perhaps more important is that a particular soil analysis reflects the lev- els of nutrients potentially available to the plant roots from the soil, but soil analysis does not tell us how much of a particular mineral nutrient the plant actually needs or is able to absorb. This additional information is best deter- mined by plant tissue analysis.

Proper use of plant tissue analysis requires an under- standing of the relationship between plant growth (or yield) and the mineral concentration of plant tissue sam- ples (Bouma 1983). As the data plot in Figure 5.3 shows, when the nutrient concentration in a tissue sample is low, growth is reduced. In this deficiency zone of the curve, an increase in nutrient availability is directly related to an increase in growth or yield. As the nutrient availability con- tinues to increase, a point is reached at which further addi- tion of nutrients is no longer related to increases in growth or yield but is reflected in increased tissue concentrations. This region of the curve is often called the adequate zone. The transition between the deficiency and adequate zones of the curve reveals the critical concentration of the nutrient (see Figure 5.3), which may be defined as the min- imum tissue content of the nutrient that is correlated with maximal growth or yield. As the nutrient concentration of the tissue increases beyond the adequate zone, growth or yield declines because of toxicity (this is the toxic zone).

To evaluate the relationship between growth and tissue nutrient concentration, researchers grow plants in soil or nutrient solution in which all the nutrients are present in adequate amounts except the nutrient under consideration. At the start of the experiment, the limiting nutrient is added in increasing concentrations to different sets of plants, and the concentrations of the nutrient in specific tis- sues are correlated with a particular measure of growth or yield. Several curves are established for each element, one for each tissue and tissue age.

Because agricultural soils are often limited in the ele- ments nitrogen, phosphorus, and potassium, many farm- ers routinely use, at a minimum, curves for these elements. If a nutrient deficiency is suspected, steps are taken to cor- rect the deficiency before it reduces growth or yield. Plant analysis has proven useful in establishing fertilizer sched- ules that sustain yields and ensure the food quality of many crops.


Many traditional and subsistence farming practices pro- mote the recycling of mineral elements. Crop plants absorb the nutrients from the soil, humans and animals consume locally grown crops, and crop residues and manure from humans and animals return the nutrients to the soil. The main losses of nutrients from such agricultural systems ensue from leaching that carries dissolved ions away with drainage water. In acid soils, leaching may be decreased by the addition of lime—a mix of CaO, CaCO3, and Ca(OH)2—to make the soil more alkaline because many mineral elements form less soluble compounds when the pH is higher than 6 (Figure 5.4).

In the high-production agricultural systems of industrial countries, the unidirectional removal of nutrients from the soil to the crop can become significant because a large por- tion of crop biomass leaves the area of cultivation. Plants synthesize all their components from basic inorganic sub- stances and sunlight, so it is important to restore these lost nutrients to the soil through the addition of fertilizers.

crop yield

Crop Yields Can Be Improved by Addition of Fertilizers

Most chemical fertilizers contain inorganic salts of the macronutrients nitrogen, phosphorus, and potassium (see Table 5.1). Fertilizers that contain only one of these three nutrients are termed straight fertilizers. Some examples of straight fertilizers are superphosphate, ammonium nitrate, and muriate of potash (a source of potassium). Fertilizers that contain two or more mineral nutrients are called com- pound fertilizers or mixed fertilizers, and the numbers on the package label, such as 10-14-10, refer to the effective per- centages of N, P2O5, and K2O, respectively, in the fertilizer.

With long-term agricultural production, consumption of micronutrients can reach a point at which they, too, must be added to the soil as fertilizers. Adding micronutrients to the soil may also be necessary to correct a preexisting defi- ciency. For example, some soils in the United States are

water and oxygen availability, and the type and number of microorganisms present in the soil.

As a consequence, the rate of mineralization is highly variable, and nutrients from organic residues become avail- able to plants over periods that range from days to months to years. The slow rate of mineralization hinders efficient fertilizer use, so farms that rely solely on organic fertilizers may require the addition of substantially more nitrogen or phosphorus and suffer even higher nutrient losses than farms that use chemical fertilizers. Residues from organic fertilizers do improve the physical structure of most soils, enhancing water retention during drought and increasing drainage in wet weather.

TABLE 5.4 Mineral elements classified on the basis of their mobility within a plant and their tendency to retranslocate during deficiencies

Some Mineral Nutrients Can Be Absorbed by Leaves

In addition to nutrients being added to the soil as fertiliz- ers, some mineral nutrients can be applied to the leaves as sprays, in a process known as foliar application, and the leaves can absorb the applied nutrients. In some cases, this method can have agronomic advantages over the applica- tion of nutrients to the soil. Foliar application can reduce the lag time between application and uptake by the plant, which could be important during a phase of rapid growth. It can also circumvent the problem of restricted uptake of a nutrient from the soil. For example, foliar application of mineral nutrients such as iron, manganese, and copper may be more efficient than application through the soil

deficient in boron, copper, zinc, manganese, molybdenum, or iron (Mengel and Kirkby 1987) and can benefit from nutrient supplementation.

Chemicals may also be applied to the soil to modify soil pH. As Figure 5.4 shows, soil pH affects the availability of all mineral nutrients. Addition of lime, as mentioned previ- ously, can raise the pH of acidic soils; addition of elemental sulfur can lower the pH of alkaline soils. In the latter case, microorganisms absorb the sulfur and subsequently release sulfate and hydrogen ions that acidify the soil.

Organic fertilizers, in contrast to chemical fertilizers, originate from the residues of plant or animal life or from natural rock deposits. Plant and animal residues contain many of the nutrient elements in the form of organic com- pounds. Before crop plants can acquire the nutrient ele- ments from these residues, the organic compounds must be broken down, usually by the action of soil microorgan- isms through a process called mineralization. Mineraliza- tion depends on many factors, including temperature,
available to the root system.

Nutrient uptake by plant leaves is most effective when the nutrient solution remains on the leaf as a thin film (Mengel and Kirkby 1987). Production of a thin film often requires that the nutrient solutions be supplemented with surfactant chemicals, such as the detergent Tween 80, that reduce surface tension. Nutrient movement into the plant seems to involve diffusion through the cuticle and uptake by leaf cells. Although uptake through the stomatal pore could provide a pathway into the leaf, the architecture of the pore (see Figures 4.13 and 4.14) largely prevents liquid penetration (Ziegler 1987).

For foliar nutrient application to be successful, damage to the leaves must be minimized. If foliar sprays are applied on a hot day, when evaporation is high, salts may accumulate on the leaf surface and cause burning or scorching. Spraying on cool days or in the evening helps to alleviate this problem. Addition of lime to the spray dimin- ishes the solubility of many nutrients and limits toxicity. Foliar application has proved economically successful mainly with tree crops and vines such as grapes, but it is also used with cereals. Nutrients applied to the leaves could save an orchard or vineyard when soil-applied nutri- ents would be too slow to correct a deficiency. In wheat, nitrogen applied to the leaves during the later stages of growth enhances the protein content of seeds.

symptoms 1
symptoms 2


Plants are autotrophic organisms capable of using the energy from sunlight to synthesize all their components from carbon dioxide, water, and mineral elements. Studies of plant nutrition have shown that specific mineral ele- ments are essential for plant life. These elements are clas- sified as macronutrients or micronutrients, depending on the relative amounts found in plant tissue.

Certain visual symptoms are diagnostic for deficiencies in specific nutrients in higher plants. Nutritional disorders occur because nutrients have key roles in plant metabolism. They serve as components of organic compounds, in energy storage, in plant structures, as enzyme cofactors, and in electron transfer reactions. Mineral nutrition can be studied through the use of hydroponics or aeroponics, which allow the characterization of specific nutrient requirements. Soil and plant tissue analysis can provide information on the nutritional status of the plant–soil sys- tem and can suggest corrective actions to avoid deficien- cies or toxicities.

When crop plants are grown under modern high-pro- duction conditions, substantial amounts of nutrients are removed from the soil. To prevent the development of defi- ciencies, nutrients can be added back to the soil in the form of fertilizers. Fertilizers that provide nutrients in inorganic forms are called chemical fertilizers; those that derive from plant or animal residues are considered organic fertilizers. In both cases, plants absorb the nutrients primarily as inor- ganic ions. Most fertilizers are applied to the soil, but some are sprayed on leaves.

plant water and transport

Calcareous SoilsPlant Nutrition
Cation and Anion Exchange Capacityplant videos 1 chemistry
Chemistry pHplant videos 2
Fertilizer Chemistryplant videos 3 physiology
greenhouse techplant water and transport
MicronutrientsSoil and Roots
nutrient tablesoil science
Plant Cell Biologyspring-lake
Plant Cell PhysiologyStylistics
plant nutrients

Passive Transport


This movement of molecules or ions from a region of higher concentration to a region of lower concentration is called diffusion. Molecules that are moving from a region of higher concentration to a region of lower concentration are said to be moving along a diffusion gradient, while molecules going in the opposite direction are said to be moving against a diffusion gradient. When the molecules, through their random movement, have become distributed throughout the space available, they are considered to be in a state of equilibrium. The rate of diffusion depends on several factors, including tem- perature and the density of the medium through which it is taking place.

Except within the area immediately surrounding the source, unaided diffusion requires a great deal of time because mole- cules and ions are infinitesimally small. Something that is less than a millionth of a millimeter in diameter is going to take a long time to move just 1 millimeter, even though the amount of movement may be great in proportion to the size of the particle concerned. In gases, there is a great deal of space between the molecules and correspondingly less chance of the molecules bumping into each other and thus being slowed down. Accordingly, gas molecules occupy a space that becomes available to them relatively rapidly, while liquids do so more slowly, and solids are slower yet.

  Substances diffuse according to their concentration gradient; within a system, different substances in the medium will each diffuse at different rates according to their individual gradients.After a substance has diffused completely through a space, removing its concentration gradient, molecules will still move around in the space, but there will be no net movement of the number of molecules from one area to another, a state known as dynamic equilibrium.Several factors affect the rate of diffusion of a solute including the mass of the solute, the temperature of the environment, the solvent density, and the distance traveled.  
plant diffusion


Solvents are liquids in which substances dissolve. Despite the fact that the cytoplasm of living cells is bounded by membranes, it is now well known that water (a solvent) moves freely from cell to cell. This has led scientists to believe that plasma, vacuolar, and other membranes have tiny holes or spaces in them, even though such holes or spaces are invisible to the instruments pres- ently available. It also has led to the construction of models of such membranes (see Fig. 3.11). Membranes through which dif- ferent substances diffuse at different rates are described as semipermeable. All plant cell membranes appear to be semiperme- able.

In plant cells, osmosis is essentially the diffusion of water through a semipermeable membrane from a region where the water is more concentrated to a region where it is less concentrated. Osmosis ceases if the concentration of water on both sides of the membrane becomes equal.

A demonstration of osmosis can be made by tying a membrane over the mouth of a thistle tube that has been filled with a solution of 10% sugar in water (i.e., the solution consists of 10% sugar and 90% water). Fluid rises in the narrow part of the tube as osmosis occurs when the thistle tube is immersed in water

Although the previous simple definition of osmosis serves our purposes, plant physiologists prefer to define and discuss osmosis more precisely in terms of potentials. It is possible to prevent osmosis by applying pressure. Just enough pressure to prevent fluid from moving as a result of osmosis is referred to as the osmotic potential of the solution. In other words, os- motic potential is the pressure required to prevent osmosis.

Water enters a cell by osmosis until the osmotic potential is balanced by the resistance to expansion of the cell wall. Wa- ter gained by osmosis may keep a cell firm, or turgid, and the turgor pressure that develops against the walls as a result of water entering the vacuole of the cell is called pressure potential.

The release of turgor pressure can be heard each time you bite into a crisp celery stick or the leaf of a young head of let- tuce. When we soak carrot sticks, celery, or lettuce in pure water to make them crisp, we are merely assisting the plant in bringing about an increase in the turgor of the cells.

The water potential of a plant cell is essentially its osmotic potential and pressure potential combined. If we have two ad- jacent cells of different water potentials, water will move from the cell having the higher water potential to the cell having the lower water potential.

Osmosis is the primary means by which water enters plants from their surrounding environment. In land plants, water from the soil enters the cell walls and intercellular spaces of the epidermis and the root hairs and travels along the walls until it reaches the endodermis. Here it crosses the differentially permeable membranes and cytoplasm of the endodermal cells on its way to the xylem. Water flows from the xylem to the leaves, evaporates within the leaf air spaces, and diffuses out (tran- spires) through the stomata into the atmosphere. The movement of water takes place because there is a water potential gradi- ent from relatively high soil water potential to successively lower water potentials in roots, stems, leaves, and the atmosphere.

  Osmosis occurs according to the concentration gradient of water across the membrane, which is inversely proportional to the concentration of solutes.Osmosis occurs until the concentration gradient of water goes to zero or until the hydrostatic pressure of the water balances the osmotic pressure.Osmosis occurs when there is a concentration gradient of a solute within a solution, but the membrane does not allow diffusion of the solute.  
root osmosis


If you place turgid carrot and celery sticks in a 10% solution of salt in water, they soon lose their rigidity and become limp enough to curl around your finger. The water potential inside the carrot cells is greater than the water potential outside, and so diffusion of water out of the cells into the salt solution takes place. If you were to examine such cells with a microscope, you would see that the vacuoles, which are largely water, had disappeared and that the cytoplasm was clumped in the middle of the cell, having shrunken away from the walls. Such cells are said to be plasmolyzed. This loss of water through osmosis, which is accompanied by the shrinkage of protoplasm away from the cell wall, is called plasmolysis . If plasmo- lyzed cells are placed in fresh water before permanent damage is done, water reenters the cell by osmosis, and the cells be- come turgid once more.

  A hypertonic solution contains a higher concentration of solutes compared to another solution. The opposite solution with a lower concentration is known as the hypotonic solution.
  Generally, plants prefer to live in hypotonic environments. In a hypotonic environment, water easily floods plant cells and they can remain turgid, or rigid, due to pressures exerted on their cell walls by the influx of water. The plants use this water potential to give their bodies structure and move water from the roots to the top of the plant. However, many plants have adapted to live in hypertonic environments. Marshes by the sea, mangrove swamps, and other brackish waters contain a much higher salt content than fresh water. The soil becomes saturated with these salts, creating a much higher solute concentration in the soil.   Passive diffusion is the movement of molecules from a higher concentration to a lower concentration.

Osmosis and plasmolysis are two events that occur due to the movement of water molecules. Water is considered as the universal solvent in cells that dissolves polar molecules. The main difference between osmosis and plasmolysis is that osmosis is the movement of water molecules from high water potential to a lower water potential across a semipermeable membrane whereas plasmolysis is the shrinkage of a cell due to the persisting movement of the water molecules out of the cell. Plasma membrane serves as the semipermeable membrane during osmosis. The two types of osmosis are endosmosis and exosmosis. Plasmolysis occurs due to persisting exosmosis.  

Osmosis and plasmolysis


Osmosis is not the only force involved in the absorption of water by plants. Colloidal materials (i.e., materials that contain a permanent suspension of fine particles) and large molecules, such as cellulose and starch, usually develop electrical charges when they are wet. The charged colloids and molecules attract water molecules, which adhere to the internal surfaces of the materials. Because water molecules are polar, they can become both highly adhesive to large organic molecules such as cellu- lose and cohesive with one another. As discussed, polar molecules have slightly different electrical charges at each end due to their asymmetry. This process, known as imbibition, results in the swelling of tissues, whether they are alive or dead, often to several times their original volume. Imbibition is the initial step in the germination of seeds.

Active Transport

Most molecules needed by cells are polar, and those of solutes may set up an electrical gradient across a semi-permeable membrane of a living cell. To pass through the membrane, molecules require special embedded transport proteins (see Fig. 3.7). The transport proteins are believed to occur in two forms: one facilitating the transport of specific ions to the outside of the cell and the other facilitating the transport of specific ions into the cell.

The plants absorb and retain these solutes against a diffusion (or electrical) gradient through the expenditure of energy. This process is called active transport. The precise mechanism of active transport is not fully understood, but recent evi- dence suggests that this process involves an enzyme complex and what has been referred to as a proton pump. The pump in- volves the plasma membrane of plant and fungal cells and sodium and potassium ions in animal cells. Both pumps are ener- gized by special energy-storing ATP molecules.

Mangroves, saltbush, and certain algae thrive in areas where the water or soil contains enough salt to kill most vegeta- tion. Such plants accumulate large amounts of organic solutes, including the carbohydrate mannitol and the amino acid proline. The organic solutes facilitate osmosis, despite the otherwise adverse environment.  The leaves of some mangroves also have salt glands through which they excrete excess salt.


Why do living plants require so much water? Water constitutes about 90% of the weight of young cells. The thousands of enzyme actions and other chemical activities of cells take place in water, and additional, although relatively negligible, amounts are used in the process of photosynthesis. The exposed surfaces of the mesophyll cells within the leaf have to be moist at all times, for it is through this film of water that the carbon dioxide molecules needed for the process of photosynthe- sis enter the cell from the air. Water is also needed for cell turgor, which gives rigidity to herbaceous plants.

Consider also what it must be like in the mesophyll of a flattened leaf that is fully exposed to the midsummer sun in areas where the air temperature soars to well over 38°C (100°F) in the shade. If it were not for the evaporation of water molecules from the moist surfaces, which brings about cooling, and reradiation of energy by the leaf, the intense heat could damage the plant. Sometimes, the transpiration is so rapid that more water is lost than is taken in. The stomata may then close, preventing wilting. The relation and role of abscisic acid in excessive water loss is discussed elsewhere .

How does water travel through the roots from 3 to 6 meters (10 to 20 feet) or more beneath the surface and then up the trunk to the topmost leaves of a tree that is more than 90 meters (300 feet) tall? We know that interconnected tubes of xylem extend throughout the plant, from the young roots up through the stem and branches to the tiny veinlets of the leaves. We also know that the water, following a water potential gradient, gets to the start of this “plumbing system” by osmosis. Water is then raised through the columns apparently by a combination of factors, and the process has been the subject of much debate for the past 200 years

The Cohesion-Tension Theory

Water molecules move partly through cell cytoplasm and partly through spaces between cells; they also move between cellulose fibers in the walls and through spaces in the centers of dead cells. Most water and solutes can travel across the epi- dermis and cortex via the cell walls until they reach the endodermis. There, the water and solutes are forced by Casparian strips to cross the cytoplasm of the endodermal cells on their way to the vessels or tracheids of the xylem.

If significant transpiration is occurring, the roots are likely to grow rapidly toward available water. In corn plants, for ex- ample, the main roots may grow at a rate of more than 6 centimeters (2.3 inches) a day. Solutes, as well as water, may move so rapidly during periods of rapid transpiration that there is little osmosis taking place across the endodermis. Scientists be- lieve that at such times water may be pulled through the roots by bulk flow, which is the passive movement of a liquid from higher to lower water potential.

In summary: “columns” of water molecules are pulled through the plant from roots to leaves, and the abundant water of a normally moist soil supplies these “columns” as the water continues to enter the root by osmosis (see Fig. 9.10); simply put, the difference between the water potentials (water “concentrations”) of two areas (e.g., soil and the air around stomata) generates the force to transport water in a plant.

Figure: -cylinderThe cohesion and adhesion of water in the vessel element helps water move up the vessel without breaking under tension. Adhesion occurs when water molecules are attracted to the walls of the vessel element, which has thick walls with lignin, a stiff substance. Cohesion occurs when water molecules are attracted to each other. This is due to hydrogen bonds, which form between the partially negative oxygen of one molecule and the partially positive hydrogen of another molecule. Hydrogen bonds are a strong intermolecular force. As some water molecules move up the vessel element, they pull other water molecules with them. Water molecules move up the xylem (in one direction). 

Figure-tree: The cohesion–tension theory is shown. Evaporation from the mesophyll cells produces a negative water potential gradient that causes water to move upwards from the roots through the xylem. Water potential is measured in megapascals (MPa), which is a measure of pressure. Water potential decreases from the root cells (-0.2 MPa) to the stem (-0.6 MPa) to the leaf at the tip of a tree (-1.5 MPa) to the atmosphere (-100 MPa). Transpiration draws water from the leaf. The water leaves the tube-shaped xylem and enters the air space between mesophyll cells. Finally, it exits through the stoma. Cohesion and adhesion draw water up the xylem. Negative water potential draws water into the root. Water moves from the spaces between soil particles into the root hairs, and into the xylem of the root.
cohesion tension figure 1
tree cohesion tension 2


Two guard cells and an opening called the stoma (plural: stomata) comprise the stomatal apparatus. These stomatal appara- tuses, which often occupy 1% or more of the surface area of a leaf, regulate transpiration and gas exchange. Control of tran- spiration is, however, strongly influenced by the water-vapor concentration of the atmo-sphere. The guard cells bordering each stoma have relatively elastic walls with radially oriented microfibrils, making them analogous to pairs of sausage- shaped balloons joined at each end, each with a row of rubber bands around it. The part of the wall adjacent to the hole itself is considerably thicker than the remainder of the wall . This thickness allows each stoma to be opened and closed by means of changes in the turgor of the guard cells. The stoma is closed when turgor pressure is low and open when turgor pressure is high. Changes in turgor pressures in the guard cells, which contain chloroplasts, take place when they are exposed to changes in light intensity, carbon dioxide concentration, or water concentration.

Changes in turgor pressure take place when osmosis and active transport between the guard cells and other epidermal cells bring about shifts in solute concentrations. While photosynthesis is occurring in the guard cells, they expend energy to acquire potassium ions from adjacent epidermal cells, leading to the opening of the stomata. When photosynthesis is not oc- curring in the guard cells, the potassium ions leave, and the stomata close. With an increase in potassium ions, the water po- tential in the guard cells is lowered, and the osmosis that takes place as a result brings in water that makes the cells turgid. The departure of potassium ions also results in water leaving, making the cells less turgid and causing the stomata to close (see Fig. 9.13).

Stomata will close passively whenever water stress occurs, but there is evidence that the hormone abscisic acid is pro- duced in leaves subject to water stress and that this hormone causes membrane leakages, which induce a loss of potassium ions from the guard cells and cause them to deflate.

The stomata of most plants are open during the day and closed at night. However, the stomata of a number of desert plants are open only at night when there is less water stress on the plants. This conserves water but makes carbon dioxide needed for photosynthesis inaccessible during the day. Such plants convert the carbon dioxide available at night to organic acids, which are stored in cell vacuoles. The organic acids are then converted back to carbon dioxide during the day when photosynthesis occurs . A specialized form of photosynthesis called CAM photosynthesis uses the carbon dioxide released from the organic acids. CAM photosynthesis is discussed .

Other desert plants have their stomata recessed below the surface of the leaf or stem in small chambers. These chambers, called stomatal crypts, often are partially filled with epidermal hairs, which further reduce water loss by slowing down air movement. Similar recessed stomata are found in the leaves of pine trees, which have little water available to them in winter when the soil is frozen (see Fig. 7.12). A few tropical plants that occur in damp, humid areas (e.g., ruellias; see also Fig. 4.13B) have stomata that are raised above the surface of the leaf, while plants of wet habitats generally lack stomata on submerged surfaces.

Although light and carbon dioxide concentration affect transpiration rates, several other factors play at least an indirect role. For example, air currents speed up transpiration as they sweep away water molecules emerging from stomata. Humidity plays an inverse but direct role in transpiration rates: high humidity reduces transpiration, and low humidity accelerates it. Temperature also plays a role in the movement of water molecules out of a leaf. The transpiration rate of a leaf at 30°C (86°F), for example, is about twice as great as it is for the same leaf at 20°C (68°F). The various adaptive modifica- tions of leaves and their surfaces and the availability of water to the roots also may play important roles in influencing the amount of water transpired. Leaf modifications are discussed.

If a cool night follows a warm, humid day, water droplets may be produced through structures called hydathodes at the tips of veins of the leaves of some herbaceous plants. This loss of water in liquid form is called guttation. Miner- als absorbed at night are pumped into the intercellular spaces surrounding the vessels and tracheids of the xylem. As a result, the water potential of the xylem elements is lowered, and water moves into them from the surrounding cells. In the absence of transpiration at night, the pressure in the xylem elements builds to the point of forcing liquid water out of the hydathodes in the leaves. Although the droplets resemble dew, the two should not be confused. Dew is water that is condensed from the air, while guttation water is literally forced out of the plant by root pressure. As the sun strikes the droplets in the morning, they dry up, leaving a residue of salts and organic substances, one of which is used in the manufacture of commercial flavor enhancers (e.g., the monosodium glutamate in products such as Accent®). In the tropics, the amount of water produced by guttation can be considerable. In taro plants, used by the Polynesians to make poi, a single leaf may overnight produce as much as a cupful (about 240 milliliters) of water through guttation.


One of the most important functions of water in the plant involves the translocation (transportation) of food substances in solution by the phloem, a process that has only recently come to be better understood. Many of the studies that led to our pre- sent knowledge of the subject used aphids (small, sucking insects) and organic compounds designed as radioactive tracers.

Most aphids feed on phloem by inserting their tiny, tubelike mouthparts (stylets) through the leaf or stem tissues until a sieve tube is reached and punctured. The turgor pressure of the sieve tube then forces the fluid present in the tube through the aphid’s digestive tract, and it emerges at the rear as a droplet of “honeydew.” In some studies, research workers anesthetized feeding aphids and cut their stylets so that much of the tiny tube remained where it had been inserted. Fluid exuded (some- times for many hours) from the cut stylets and was then collected and analyzed .

Carbon dioxide, a basic raw material of photosynthesis, can be synthesized with radioactive carbon. By exposing a pho- tosynthesizing leaf to radioactive carbon dioxide, the pathway of manufactured food substances can be traced. The radioac- tive substances produce on photographic film an image corresponding to the food pathway. Data obtained from such studies reveal that food substances in solution are confined entirely to the sieve tubes while they are being transported. At one time, it was believed that ordinary diffusion and cyclosis were responsible for the movement of the sub- stances from one sieve tube member to the next, but it is now known that the substances move through the phloem at ap- proximately 100 centimeters (almost 40 inches) per hour—far too rapid a movement to be accounted for by diffusion and cyclosis alone.


  1. Molecules and ions are in constant random motion and tend to distribute themselves evenly in the space available to them. They move from a region of higher concentration to a region of lower concentration by simple diffusion along a diffusion gradient; they may also move against a diffusion gradient. Evenly distributed molecules are in a state of equi- librium. Diffusion rates are affected by temperature, molecule size and density, and other factors.
  2. Osmosis is the diffusion of water through a semipermeable membrane. It takes place in response to concentration differ- ences of dissolved substances.
  3. Osmotic pressure or potential is the pressure required to prevent osmosis from taking place. The pressure that develops in a cell as a result of water entering it is called turgor. Water moves from a region of higher water potential (osmotic po- tential and pressure potential combined) to a region of lower water potential when osmosis is occurring. Osmosis is the primary means by which plants obtain water from their environment.
  4. Plasmolysis is the shrinkage of the cytoplasm away from the cell wall as a result of osmosis taking place when the water potential inside the cell is greater than outside.
  5. Imbibition is the attraction and adhesion of water molecules to the internal surfaces of materials; it results in swelling and is the initial step in the germination of seeds.
  6. Active transport is the expenditure of energy by a cell that results in molecules or ions entering or leaving the cell against a diffusion gradient.
  7. Water that enters a plant passes through it and mostly transpires into the atmosphere via stomata. Water retained by the plant is used in photosynthesis and other metabolic activities.
  8. The cohesion-tension theory postulates that water rises through plants because of the adhesion of water molecules to the walls of the capillary-conducting elements of the xylem, cohesion of the water molecules, and tension on the water col- umns created by the pull developed by transpiration.
  9. The translocation of food substances takes place in a water solution, and according to the pressure-flow hypothesis, such substances flow along concentration gradients between their sources and sinks.
  1. Transpiration is regulated by humidity and the stomata, which open and close through changes in turgor pressure of the guard cells. These changes, which involve potassium ions, result from osmosis and active transport between the guard cells and the adjacent epidermal cells.
  2. Aquatic, desert, tropical, and some cold-zone plants have modifications of stomatal apparatuses or specialized forms of photosynthesis that adapt them to their particular environments.
  3. Guttation is the loss of water at night in liquid form through hydathodes at the tips of leaf veins.

Growth phenomena are controlled by both internal and external means and by chemical and physical forces in balance with one another. Besides carbon, hydrogen, and oxygen, 15 other elements are essential to most plants. When any of the essential elements are deficient in the plant, characteristic deficiency symptoms appear

The Pressure-Flow Hypothesis

At present, the most widely accepted theory for movement of substances in the phloem is called the pressure-flow (or mass- flow) hypothesis. According to this theory, food substances in solution (organic solutes) flow from a source, where water en- ters by osmosis (e.g., a food-storage tissue, such as the cortex of a root or rhizome, or a food-producing tissue, such as the mesophyll tissue of a leaf). The water exits at a sink, which is a place where food is utilized, such as the growing tip of a stem or root. Food substances in solution (organic solutes) are moved along concentration gradients between sources and sinks.

First, in a process called phloem-loading, sugar, by means of active transport, enters the sieve tubes of the smallest veinlets. This decreases the water potential in the sieve tubes, and water then enters these phloem cells by osmosis. Tur- gor pressure, which develops as this osmosis occurs, is responsible for driving the fluid through the sieve-tube network toward the sinks.

As the food substances (largely sucrose) in solution are actively removed at the sink, water also exits the sink ends of sieve tubes, and the pressure in these sieve tubes is lowered, causing a mass flow from the higher pressure at the source to the lower pressure at the sink. Most of the water diffuses back to the xylem, where it then returns to the source and is transpired or recirculated. The pressure-flow hypothesis explains how nontoxic dyes applied to leaves or substances entering the sieve tubes, such as viruses introduced by aphids, are carried through the phloem.

phloem translocation
phloem translocation 2
Translocation: Transport from Source to Sink Photosynthates, such as sucrose, are produced in the mesophyll cells of photosynthesizing leaves. From there they are translocated through the phloem to where they are used or stored. Mesophyll cells are connected by cytoplasmic channels called plasmodesmata. Photosynthates move through these channels to reach phloem sieve-tube elements (STEs) in the vascular bundles. From the mesophyll cells, the photosynthates are loaded into the phloem STEs. The sucrose is actively transported against its concentration gradient (a process requiring ATP) into the phloem cells using the electrochemical potential of the proton gradient. This is coupled to the uptake of sucrose with a carrier protein called the sucrose-H+ symporter. Phloem STEs have reduced cytoplasmic contents, and are connected by a sieve plate with pores that allow for pressure-driven bulk flow, or translocation, of phloem sap. Companion cells are associated with STEs. They assist with metabolic activities and produce energy for the STEs.

Figure 19.6.6: Phloem is comprised of cells called sieve-tube elements. Phloem sap travels through perforations called sieve tube plates. Neighboring companion cells carry out metabolic functions for the sieve-tube elements and provide them with energy. Lateral sieve areas connect the sieve-tube elements to the companion cells.


Once in the phloem, the photosynthates are translocated to the closest sink. Phloem sap is an aqueous solution that contains up to 30 percent sugar, minerals, amino acids, and plant growth regulators. The high percentage of sugar decreases Ψs, which decreases the total water potential and causes water to move by osmosis from the adjacent xylem into the phloem tubes, thereby increasing pressure. This increase in total water potential causes the bulk flow of phloem from source to sink (Figure 19.6.7). Sucrose concentration in the sink cells is lower than in the phloem STEs because the sink sucrose has been metabolized for growth, or converted to starch for storage or other polymers, such as cellulose, for structural integrity. Unloading at the sink end of the phloem tube occurs by either diffusion or active transport of sucrose molecules from an area of high concentration to one of low concentration. Water diffuses from the phloem by osmosis and is then transpired or recycled via the xylem back into the phloem sap.  

Figure 19.6.7: Sucrose is actively transported from source cells into companion cells and then into the sieve-tube elements. This reduces the water potential, which causes water to enter the phloem from the xylem. The resulting positive pressure forces the sucrose-water mixture down toward the roots, where sucrose is unloaded. Transpiration causes water to return to the leaves through the xylem vessels.  

Plant Cell Physiology

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Plant Cells Are Surrounded by Rigid Cell Walls

New Cells Are Produced by Dividing Tissues Called Meristems

Three Major Tissue Systems Make Up the Plant Body

  • dermal tissue
    • Cuticle
    • Stomata, guard cells and trichomes
  • ground tissue
    • Parenchyma
    • Collenchyma
    • Sclerenchyma
      • Sclereids
      • Fibers
  • vascular tissue
    • Xylem
      • Vessel members
      • Tracheids
    • Phloem
      • Sieve cells and companion cells
    • Procambium cell development

Biological Membranes Are Phospholipid Bilayers That Contain Proteins

All cells are enclosed in a membrane that serves as their outer boundary, separating the cytoplasm from the exter- nal environment. This plasma membrane (also called plas- malemma) allows the cell to take up and retain certain sub- stances while excluding others. Various transport proteins embedded in the plasma membrane are responsible for this selective traffic of solutes across the membrane. The accu- mulation of ions or molecules in the cytosol through the action of transport proteins consumes metabolic energy. Membranes also delimit the boundaries of the specialized internal organelles of the cell and regulate the fluxes of ions and metabolites into and out of these compartments.

According to the fluid-mosaic model, all biological membranes have the same basic molecular organization. They consist of a double layer (bilayer) of either phospho- lipids or, in the case of chloroplasts, glycosylglycerides, in which proteins are embedded (Figure 1.5A and B). In most membranes, proteins make up about half of the mem- brane’s mass. However, the composition of the lipid com- ponents and the properties of the proteins vary from mem- brane to membrane, conferring on each membrane its unique functional characteristics

Phospholipids. Phospholipids are a class of lipids in which two fatty acids are covalently linked to glycerol, which is covalently linked to a phosphate group. Also attached to this phosphate group is a variable component, called the head group, such as serine, choline, glycerol, or inositol (Figure 1.5C). In contrast to the fatty acids, the head groups are highly polar; consequently, phospholipid mol- ecules display both hydrophilic and hydrophobic proper- ties (i.e., they are amphipathic). The nonpolar hydrocarbon chains of the fatty acids form a region that is exclusively hydrophobic—that is, that excludes water.

Plastid membranes are unique in that their lipid com- ponent consists almost entirely of glycosylglycerides rather than phospholipids. In glycosylglycerides, the polar head group consists of galactose, digalactose, or sulfated galactose, without a phosphate group. The fatty acid chains of phospholipids and glycosyl- glycerides are variable in length, but they usually consist of 14 to 24 carbons. One of the fatty acids is typically saturated (i.e., it contains no double bonds); the other fatty acid chain usually has one or more cis double bonds (i.e., it is unsaturated).

The presence of cis double bonds creates a kink in the chain that prevents tight packing of the phospholipids in the bilayer. As a result, the fluidity of the membrane is increased. The fluidity of the membrane, in turn, plays a critical role in many membrane functions. Membrane flu- idity is also strongly influenced by temperature. Because plants generally cannot regulate their body temperatures, they are often faced with the problem of maintaining mem- brane fluidity under conditions of low temperature, which tends to decrease membrane fluidity. Thus, plant phos- pholipids have a high percentage of unsaturated fatty acids, such as oleic acid (one double bond), linoleic acid (two double bonds) and a-linolenic acid (three double bonds), which increase the fluidity of their membranes.

plant cell membranes


 The proteins associated with the lipid bilayer are of three types: integral, peripheral, and anchored. Inte gral proteins are embedded in the lipid bilayer. Most inte- gral proteins span the entire width of the phospholipid bilayer, so one part of the protein interacts with the outside of the cell, another part interacts with the hydrophobic core of the membrane, and a third part interacts with the inte- rior of the cell, the cytosol. Proteins that serve as ion chan- nels (see Chapter 6) are always integral membrane pro- teins, as are certain receptors that participate in signal transduction pathways (see Chapter 14). Some receptor-like proteins on the outer surface of the plasma membrane rec- ognize and bind tightly to cell wall consituents, effectively cross-linking the membrane to the cell wall.

Peripheral proteins are bound to the membrane surface by noncovalent bonds, such as ionic bonds or hydrogen bonds, and can be dissociated from the membrane with high salt solutions or chaotropic agents, which break ionic and hydrogen bonds, respectively. Peripheral proteins serve a variety of functions in the cell. For example, some are involved in interactions between the plasma membrane and components of the cytoskeleton, such as microtubules and actin microfilaments, which are discussed later in this chapter.

Anchored proteins are bound to the membrane surface via lipid molecules, to which they are covalently attached. These lipids include fatty acids (myristic acid and palmitic acid), prenyl groups derived from the isoprenoid pathway (farnesyl and geranylgeranyl groups), and glycosylphos- phatidylinositol (GPI)-anchored proteins (Figure 1.6) (Buchanan et al. 2000).

membrane proteins

The Nucleus Contains Most of the Genetic Material of the Cell

The nucleus (plural nuclei) is the organelle that contains the genetic information primarily responsible for regulating the metabolism, growth, and differentiation of the cell. Collectively, these genes and their intervening sequences are referred to as the nuclear genome. The size of the nuclear genome in plants is highly variable, ranging from about 1.2 × 108 base pairs for the diminutive dicot Arabidopsis thaliana to 1 × 1011 base pairs for the lily Fritillaria assyriaca.  The  remainder of the genetic information of the cell is contained in the two semiautonomous organelles—the chloroplasts and mitochondria—which we will discuss a little later in this chapter. The nucleus is surrounded by a double membrane called the nuclear envelope (Figure 1.7A). The space between the two membranes of the nuclear envelope is called the perinuclear space, and the two membranes of the nuclear envelope join at sites called nuclear pores (Figure 1.7B).

plant cell nucleus
nuclear pore complex
Nuclear import and export through nuclear pore complexes. An import complex consisting of an NLS-bearing cargo and a nuclear transport receptor (NTR) is formed in the cytoplasm. After translocation through the NPC, Ran-GTP displaces the cargo from the NTR, resulting in nuclear cargo release. This reaction occurs due to the chromatin localization of the Ran guanine nucleotide exchange factor (RanGEF), which is restricted to the nucleus. The NTR–Ran-GTP complex returns to the cytoplasm through the NPC where the Ran GTPase-activating protein (RanGAP1) stimulates GTP hydrolysis, releasing the NTR for another import cycle. Nuclear export cycles require the formation of a trimeric cargo–NTR–Ran-GTP complex in the nucleus. After NPC passage, this complex dissociates due to Ran-GTP hydrolysis, releasing the cargo into the cytoplasm.   Perforating the nuclear boundary – how nuclear pore complexes assemble  

 The nuclear “pore” is actually an elaborate structure composed of more than a hundred different proteins arranged octagonally to form a nuclear pore complex (Figure 1.8). There can be very few to many thousands of nuclear pore complexes on an individual nuclear envelope. The central “plug” of the complex acts as an active (ATPdriven) transporter that facilitates the movement of macromolecules and ribosomal subunits both into and out of the nucleus. (Active transport will be discussed in detail in Chapter 6.) A specific amino acid sequence called the nuclear localization signal is required for a protein to gain entry into the nucleus.  The nucleus is the site of storage and replication of the  chromosomes, composed of DNA and its associated proteins. Collectively, this DNA–protein complex is known  chromatin. The linear length of all the DNA within any plant genome is usually millions of times greater than the diameter of the nucleus in which it is found. To solve the problem of packaging this chromosomal DNA within the  nucleus, segments of the linear double helix of DNA are coiled twice around a solid cylinder of eight histone protein molecules, forming a nucleosome. Nucleosomes are arranged like beads on a string along the length of each chromosome. During mitosis, the chromatin condenses, first by coiling tightly into a 30 nm chromatin fiber, with six nucleosomes per turn, followed by further folding and packing processes that depend on interactions between proteins and nucleic acids (Figure 1.9). At interphase, two types of chromatin are visible: heterochromatin and euchromatin. About 10% of the DNA consists of heterochromatin, a highly compact and transcriptionally inactive form of chromatin. The rest of the DNA consists of euchromatin, the dispersed, transcriptionally active form. Only about 10% of the euchromatin is transcriptionally active at any given time. The remainder exists in an intermediate state of condensation, between heterochromatin and transcriptionally active euchromatin. Nuclei contain a densely granular region, called the nucleolus (plural nucleoli), that is the site of ribosome synthesis (see Figure 1.7A). The nucleolus includes portions of one or more chromosomes where ribosomal RNA (rRNA) genes are clustered to form a structure called the nucleolar organizer. Typical cells have one or more nucleoli per nucleus. Each 80S ribosome is made of a large and a small subunit, and each subunit is a complex aggregate of rRNA and specific proteins. The two subunits exit the nucleus separately, through the nuclear pore, and then unite in the cytoplasm to form a complete ribosome (Figure 1.10A). Ribosomes are the sites of protein synthesis. Protein Synthesis Involves Transcription and Translation The complex process of protein synthesis starts with transcription— the synthesis of an RNA polymer bearing a base  Translation is the process whereby a specific protein is synthesized from amino acids, according to the sequence information encoded by the mRNA. The ribosome travels the entire length of the mRNA and serves as the site for the sequential bonding of amino acids as specified by the base sequence of the mRNA (Figure 1.10B).

MPC nuclear pore complex

The Endoplasmic Reticulum Is a Network of Internal Membranes

 Cells have an elaborate network of internal membranes called the endoplasmic reticulum (ER). The membranes of the ER are typical lipid bilayers with interspersed integral and peripheral proteins. These membranes form flattened or tubular sacs known as cisternae (singular cisterna). Ultrastructural studies have shown that the ER is continuous with the outer membrane of the nuclear envelope. There are two types of ER—smooth and rough (Figure 1.11)—and the two types are interconnected. Rough ER (RER) differs from smooth ER in that it is covered with ribosomes that are actively engaged in protein synthesis; in addition, rough ER tends to be lamellar (a flat sheet composed of two unit membranes), while smooth ER tends to be tubular, although a gradation for each type can be observed in almost any cell. The structural differences between the two forms of ER are accompanied by functional differences. Smooth ER functions as a major site of lipid synthesis and membrane assembly. Rough ER is the site of synthesis of membrane proteins and proteins to be secreted outside the cell or into the vacuoles.

endoplasmic ER
golgi apparatus transport
Transport pathways between the ER and the Golgi complex. COPII vesicles exiting from the ER (shown on the left) carry transport machinery (black), membrane phospholipids (red), membrane cargo proteins (green), fluid (light blue) and captured soluble cargo (dark blue) in the forward direction, as indicated by the colored arrows (1). COPI vesicles (shown on the right) retrieve the machinery to the ER but might be insufficient to also recycle lipids and fluid. This concept is schematically illustrated by the relative lengths of the colored arrows representing COPII-dependent forward transport (1) and COPI-dependent retrograde transport (2). Fluid content of the ER could re-equilibrate with the cytosol (curved light-blue arrows at the bottom of the figure), whereas phospholipids could be returned by Rab6-dependent tubular carriers (arrows, 3). The imbalance of fluid transport between the anterograde and retrograde directions could be responsible for a valve-like system that ensures movement in the forward direction of soluble cargo (light and dark blue arrows, 4). Membrane cargo could be captured into the COPI-independent retrograde carriers more efficiently than fluid could, because of the high surface-to-volume ratio of tubules; this partitioning phenomenon is expected to cause recycling of membrane cargo (green arrow, 3) with a consequent delay in their anterograde transport. Membrane cargo that escapes this recycling phenomenon progresses further through the Golgi (green arrow, 4). Membrane cargo proteins that carry export signals are not represented in this cartoon.   Getting membrane proteins on and off the shuttle bus between the endoplasmic reticulum and the Golgi complex

Secretion of Proteins from Cells Begins with the Rough ER

 Proteins destined for secretion cross the RER membrane and enter the lumen of the ER. This is the first step in the secretion pathway that involves the Golgi body and vesicles that fuse with the plasma membrane. The mechanism of transport across the membrane is complex, involving the ribosomes, the mRNA that codes for the secretory protein, and a special receptor in the ER membrane. All secretory proteins and most integral membrane proteins have been shown to have a hydrophobic sequence of 18 to 30 amino acid residues at the amino-terminal end of the chain. During translation, this hydrophobic leader, called the signal peptide sequence, is recognized by a signal recognition particle (SRP), made up of protein and RNA, which facilitates binding of the free ribosome to SRP receptor proteins (or “docking proteins”) on the ER (see Figure 1.10A). The signal peptide then mediates the transfer of the elongating polypeptide across the ER membrane into the lumen. (In the case of integral membrane proteins, a portion of the completed polypeptide remains embedded in the membrane.) Once inside the lumen of the ER, the signal sequence is cleaved off by a signal peptidase. In some cases, a branched oligosaccharide chain made up of N-acetylglucosamine (GlcNac), mannose (Man), and glucose (Glc), having the stoichiometry GlcNac2Man9Glc3, is attached to the free amino group of a specific asparagine side chain. This carbohydrate assembly is called an N-linked glycan (Faye et al. 1992). The three terminal glucose residues are then removed by specific glucosidases, and the processed glycoprotein (i.e., a protein with covalently attached sugars) is ready for transport to the Golgi apparatus. The so-called N-linked glycoproteins are then transported to the Golgi apparatus via small vesicles. The vesicles move through the cytosol and fuse with cisternae on the cis face of the Golgi apparatus (Figure 1.12). 

 Proteins and Polysaccharides for Secretion Are Processed in the Golgi Apparatus

 The Golgi apparatus (also called Golgi complex) of plant cells is a dynamic structure consisting of one or more stacks of three to ten flattened membrane sacs, or cisternae, and an irregular network of tubules and vesicles called the trans Golgi network (TGN) (see Figure 1.12). Each individual stack is called a Golgi body or dictyosome. As Figure 1.12 shows, the Golgi body has distinct functional regions: The cisternae closest to the plasma membrane are called the trans face, and the cisternae closest to the center of the cell are called the cis face. The medial cisternae are between the trans and cis cisternae. The trans Golgi network is located on the trans face. The entire structure is stabilized by the presence of intercisternal elements, protein crosslinks that hold the cisternae together. Whereas in animal cells Golgi bodies tend to be clustered in one part of the cell and are interconnected via tubules, plant cells contain up to several hundred apparently separate Golgi bodies dispersed throughout the cytoplasm (Driouich et al. 1994). The Golgi apparatus plays a key role in the synthesis and secretion of complex polysaccharides (polymers composed of different types of sugars) and in the assembly of the oligosaccharide side chains of glycoproteins (Driouich et al. 1994). As noted already, the polypeptide chains of future glycoproteins are first synthesized on the rough ER, then transferred across the ER membrane, and glycosylated on the —NH2 groups of asparagine residues. Further modifications of, and additions to, the oligosaccharide side chains are carried out in the Golgi. Glycoproteins destined for secretion reach the Golgi via vesicles that bud off from the RER. The exact pathway of glycoproteins through the plant Golgi apparatus is not yet known. Since there appears to  be no direct membrane continuity between successive cisternae, the contents of one cisterna are transferred to the next cisterna via small vesicles budding off from the margins, as occurs in the Golgi apparatus of animals. In some cases, however, entire cisternae may progress through the Golgi body and emerge from the trans face. Within the lumens of the Golgi cisternae, the glycoproteins are enzymatically modified. Certain sugars, such as mannose, are removed from the oligosaccharide chains, and other sugars are added. In addition to these modifications, glycosylation of the —OH groups of hydroxyproline, serine, threonine, and tyrosine residues (O-linked oligosaccharides) also occurs in the Golgi. After being processed within the Golgi, the glycoproteins leave the organelle in other vesicles, usually from the trans side of the stack. All of this processing appears to confer on each protein a specific tag or marker that specifies the ultimate destination of that protein inside or outside the cell. In plant cells, the Golgi body plays an important role in cell wall formation (see Chapter 15). Noncellulosic cell wall polysaccharides (hemicellulose and pectin) are synthesized, and a variety of glycoproteins, including hydroxyprolinerich glycoproteins, are processed within the Golgi. Secretory vesicles derived from the Golgi carry the polysaccharides and glycoproteins to the plasma membrane, where the vesicles fuse with the plasma membrane and empty their contents into the region of the cell wall. Secretory vesicles may either be smooth or have a protein coat. Vesicles budding from the ER are generally smooth. Most vesicles budding from the Golgi have protein coats of some type. These proteins aid in the budding process during vesicle formation. Vesicles involved in traffic from the ER to the Golgi, between Golgi compartments, and from the Golgi to the TGN have protein coats. Clathrin-coated vesicles (Figure 1.13) are involved in the transport of storage proteins from the Golgi to specialized protein-storing vacuoles. They also participate in endocytosis, the process that brings soluble and membrane-bound proteins into the cell. The

Central Vacuole Contains Water and Solutes

Mature living plant cells contain large, water-filled central vacuoles that can occupy 80 to 90% of the total volume of the cell (see Figure 1.4). Each vacuole is surrounded by a vacuolar membrane, or tonoplast. Many cells also have cytoplasmic strands that run through the vacuole, but each transvacuolar strand is surrounded by the tonoplast.  In meristematic tissue, vacuoles are less prominent, though they are always present as small provacuoles. Provacuoles are produced by the trans Golgi network (see Figure 1.12). As the cell begins to mature, the provacuoles fuse to produce the large central vacuoles that are characteristic of most mature plant cells. In such cells, the cytoplasm is restricted to a thin layer surrounding the vacuole. The vacuole contains water and dissolved inorganic ions, organic acids, sugars, enzymes, and a variety of secondary metabolites (see Chapter 13), which often play roles in plant defense. Active solute accumulation provides the osmotic driving force for water uptake by the vacuole, which is required for plant cell enlargement. The turgor pressure generated by this water uptake provides the structural rigidity needed to keep herbaceous plants upright, since they lack the lignified support tissues of woody plants. Like animal lysosomes, plant vacuoles contain hydrolytic enzymes, including proteases, ribonucleases, and glycosidases. Unlike animal lysosomes, however, plant vacuoles do not participate in the turnover of macromolecules throughout the life of the cell. Instead, their degradative enzymes leak out into the cytosol as the cell undergoes senescence, thereby helping to recycle valuable nutrients to the living portion of the plant. Specialized protein-storing vacuoles, called protein bodies, are abundant in seeds. During germination the storage proteins in the protein bodies are hydrolyzed to amino acids and exported to the cytosol for use in protein synthesis. The hydrolytic enzymes are stored in specialized lytic vacuoles, which fuse with the protein bodies to initiate the breakdown process (Figure 1.14).

physiology chloroplast

Mitochondria and Chloroplasts Are Sites of Energy Conversion

A typical plant cell has two types of energy-producing organelles: mitochondria and chloroplasts. Both types are separated from the cytosol by a double membrane (an  outer and an inner membrane). Mitochondria (singular mitochondrion) are the cellular sites of respiration, a process in which the energy released from sugar metabolism is used for the synthesis of ATP (adenosine triphosphate) from ADP (adenosine diphosphate) and inorganic phosphate (Pi) (see Chapter 11). Mitochondria can vary in shape from spherical to tubular, but they all have a smooth outer membrane and a highly convoluted inner membrane (Figure 1.15). The infoldings of the inner membrane are called cristae (singular crista). The compartment enclosed by the inner membrane, the mitochondrial matrix, contains the enzymes of the pathway of intermediary metabolism called the Krebs cycle. In contrast to the mitochondrial outer membrane and all other membranes in the cell, the inner membrane of a mitochondrion is almost 70% protein and contains some phospholipids that are unique to the organelle (e.g., cardiolipin). The proteins in and on the inner membrane have special enzymatic and transport capacities. The inner membrane is highly impermeable to the passage of H+; that is, it serves as a barrier to the movement of protons. This important feature allows the formation of electrochemical gradients. Dissipation of such gradients by the controlled movement of H+ ions through the transmembrane enzyme ATP synthase is coupled to the phosphorylation of ADP to produce ATP. ATP can then be released to other cellular sites where energy is needed to drive specific reactions. Chloroplasts (Figure 1.16A) belong to another group of double membrane–enclosed organelles called plastids. Chloroplast membranes are rich in glycosylglycerides  Chloroplast membranes contain chlorophyll and its associated proteins and are the sites of photosynthesis. In addition to their inner and outer envelope membranes, chloroplasts possess a third system of membranes called thylakoids. A stack of thylakoids forms a granum (plural grana) (Figure 1.16B). Proteins and pigments (chlorophylls and carotenoids) that function in the photochemical events of photosynthesis are embedded in the thylakoid membrane. The fluid compartment surrounding the thylakoids, called the stroma, is analogous to the matrix of the mitochondrion. Adjacent grana are connected by unstacked membranes called stroma lamellae (singular lamella). The different components of the photosynthetic apparatus are localized in different areas of the grana and the stroma lamellae. The ATP synthases of the chloroplast are located on the thylakoid membranes (Figure 1.16C). During photosynthesis, light-driven electron transfer reactions result in a proton gradient across the thylakoid membrane. As in the mitochondria, ATP is synthesized when the proton gradient is dissipated via the ATP synthase. Plastids that contain high concentrations of carotenoid pigments rather than chlorophyll are called chromoplasts. They are one of the causes of the yellow, orange, or red colors of many fruits and flowers, as well as of autumn leaves (Figure 1.17). Nonpigmented plastids are called leucoplasts. The most important type of leucoplast is the amyloplast, a starchstoring plastid. Amyloplasts are abundant in storage tissues of the shoot and root, and in seeds. Specialized amyloplasts in the root cap also serve as gravity sensors that direct root growth downward into the soil (see Chapter 19).

Mitochondria and Chloroplasts Are Semiautonomous Organelles

 Both mitochondria and chloroplasts contain their own DNA and protein-synthesizing machinery (ribosomes, transfer RNAs, and other components) and are believed to have evolved from endosymbiotic bacteria. Both plastids and mitochondria divide by fission, and mitochondria can also undergo extensive fusion to form elongated structures or networks.  The DNA of these organelles is in the form of circular chromosomes, similar to those of bacteria and very different from the linear chromosomes in the nucleus. These DNA circles are localized in specific regions of the mitochondrial matrix or plastid stroma called nucleoids. DNA replication in both mitochondria and chloroplasts is independent of DNAreplication in the nucleus. On the other hand, the numbers of these organelles within a given cell type remain approximately constant, suggesting that some aspects of organelle replication are under cellular regulation. The mitochondrial genome of plants consists of about 200 kilobase pairs (200,000 base pairs), a size considerably larger than that of most animal mitochondria. The mitochondria of meristematic cells are typically polyploid; that is, they contain multiple copies of the circular chromosome. However, the number of copies per mitochondrion gradually decreases as cells mature because the mitochondria continue to divide in the absence of DNA synthesis. Most of the proteins encoded by the mitochondrial genome are prokaryotic-type 70S ribosomal proteins and components of the electron transfer system. The majority of mitochondrial proteins, including Krebs cycle enzymes, are encoded by nuclear genes and are imported from the cytosol. The chloroplast genome is smaller than the mitochondrial genome, about 145 kilobase pairs (145,000 base pairs). Whereas mitochondria are polyploid only in the meristems, chloroplasts become polyploid during cell maturation. Thus the average amount of DNA per chloroplast in the plant is much greater than that of the mitochondria. The total amount of DNA from the mitochondria and plastids combined is about one-third of the nuclear genome (Gunning and Steer 1996). Chloroplast DNA encodes rRNA; transfer RNA (tRNA); the large subunit of the enzyme that fixes CO2, ribulose-1,5- bisphosphate carboxylase/oxygenase (rubisco); and several of the proteins that participate in photosynthesis. Nevertheless, the majority of chloroplast proteins, like those of mitochondria, are encoded by nuclear genes, synthesized in the cytosol, and transported to the organelle. Although mitochondria and chloroplasts have their own genomes and can divide independently of the cell, they are characterized as semiautonomous organelles because they depend on the nucleus for the majority of their proteins.

Different Plastid Types Are Interconvertible

Meristem cells contain proplastids, which have few or no internal membranes, no chlorophyll, and an incomplete complement of the enzymes necessary to carry out photosynthesis (Figure 1.18A). In angiosperms and some gymnosperms, chloroplast development from proplastids is triggered by light. Upon illumination, enzymes are formed inside the proplastid or imported from the cytosol, light-absorbing pigments are produced, and membranes proliferate rapidly, giving rise to stroma lamellae and grana stacks (Figure 1.18B). Seeds usually germinate in the soil away from light, and chloroplasts develop only when the young shoot is exposed to light. If seeds are germinated in the dark, the proplastids differentiate into etioplasts, which contain semicrystalline tubular arrays of membrane known as prolamellar bodies (Figure 1.18C). Instead of chlorophyll, the etioplast contains a pale yellow green precursor pigment, protochlorophyll. Within minutes after exposure to light, the etioplast differentiates, converting the prolamellar body into thylakoids and stroma lamellae, and the protochlorophyll into chlorophyll. The maintenance of chloroplast structure depends on the presence of light, and mature chloroplasts can revert to etioplasts during extended periods of darkness. Chloroplasts can be converted to chromoplasts, as in the case of autumn leaves and ripening fruit, and in some cases  Another type of microbody, the glyoxysome, is present in oil-storing seeds. Glyoxysomes contain the glyoxylate cycle enzymes, which help convert stored fatty acids into sugars that can be translocated throughout the young plant to provide energy for growth (see Chapter 11). Because both types of microbodies carry out oxidative reactions, it has been suggested they may have evolved from primitive respiratory organelles that were superseded by mitochondria.

Oleosomes Are Lipid-Storing Organelles

In addition to starch and protein, many plants synthesize and store large quantities of triacylglycerol in the form of oil during seed development. These oils accumulate in organelles called oleosomes, also referred to as lipid bodies or spherosomes (Figure 1.20A). Oleosomes are unique among the organelles in that they are surrounded by a “half–unit membrane”—that is, a phospholipid monolayer—derived from the ER (Harwood 1997). The phospholipids in the half–unit membrane are oriented with their polar head groups toward the aqueous phase and their hydrophobic fatty acid tails facing the lumen, dissolved in the stored lipid. Oleosomes are thought to arise from the deposition of lipids within the bilayer itself (Figure 1.20B). Proteins called oleosins are present in the half–unit membrane (see Figure 1.20B). One of the functions of the oleosins may be to maintain each oleosome as a discrete organelle by preventing fusion. Oleosins may also help other proteins bind to the organelle surface. As noted earlier, during seed germination the lipids in the oleosomes are broken down and converted to sucrose with the help of the glyoxysome. The first step in the process is the hydrolysis of the fatty acid chains from the glycerol backbone by the enzyme lipase. Lipase is tightly associated with the surface of the half–unit membrane and may be attached to the oleosins.


 The cytosol is organized into a three-dimensional network of filamentous proteins called the cytoskeleton. This network provides the spatial organization for the organelles and serves as a scaffolding for the movements of organelles and other cytoskeletal components. It also plays fundamental roles in mitosis, meiosis, cytokinesis, wall deposition, the maintenance of cell shape, and cell differentiation.

physiology microtubule

Plant Cells Contain  Microtubules,Microfilaments, and Intermediate Filaments

filament assembley

 Three types of cytoskeletal elements have been demonstrated in plant cells: microtubules, microfilaments, and intermediate filament–like structures. Each type is filamentous, having a fixed diameter and a variable length, up to many micrometers.  Microtubules and microfilaments are macromolecular assemblies of globular proteins. Microtubules are hollow  cylinders with an outer diameter of 25 nm; they are composed of polymers of the protein tubulin. The tubulin monomer of microtubules is a heterodimer composed of two similar polypeptide chains (á- and â-tubulin), each having an apparent molecular mass of 55,000 daltons (Figure 1.21A). A single microtubule consists of hundreds of thousands of tubulin monomers arranged in 13 columns called protofilaments. Microfilaments are solid, with a diameter of 7 nm; they are composed of a special form of the protein found in muscle: globular actin, or G-actin. Each actin molecule is composed of a single polypeptide with a molecular mass of approximately 42,000 daltons. Amicrofilament consists of two chains of polymerized actin subunits that intertwine in a helical fashion (Figure 1.21B). Intermediate filaments are a diverse group of helically wound fibrous elements, 10 nm in diameter. Intermediate filaments are composed of linear polypeptide monomers of various types. In animal cells, for example, the nuclear lamins are composed of a specific polypeptide monomer, while the keratins, a type of intermediate filament found in the cytoplasm, are composed of a different polypeptide monomer. In animal intermediate filaments, pairs of parallel monomers (i.e., aligned with their —NH2 groups at the same ends) are helically wound around each other in a coiled coil. Two coiled-coil dimers then align in an antiparallel fashion (i.e., with their —NH2 groups at opposite ends) to form a tetrameric unit. The tetrameric units then assemble into the final intermediate filament (Figure 1.22). Although nuclear lamins appear to be present in plant cells, there is as yet no convincing evidence for plant keratin intermediate filaments in the cytosol. As noted earlier, integral proteins cross-link the plasma membrane of plant cells to the rigid cell wall. Such connections to the wall  undoubtedly stabilize the protoplast and help maintain cell shape. The plant cell wall thus serves as a kind of cellular exoskeleton, perhaps obviating the need for keratin-type intermediate filaments for structural support.

Microtubules and Microfilaments Can Assemble and Disassemble

In the cell, actin and tubulin monomers exist as pools of free proteins that are in dynamic equilibrium with the polymerized forms. Polymerization requires energy: ATP is required for microfilament polymerization, GTP (guanosine triphosphate) for microtubule polymerization. The attachments between subunits in the polymer are noncovalent, but they are strong enough to render the structure stable under cellular conditions. Both microtubules and microfilaments are polarized; that is, the two ends are different. In microtubules, the polarity arises from the polarity of the á- and -tubulin heterodimer; in microfilaments, the polarity arises from the polarity of the actin monomer itself. The opposite ends of microtubules and microfilaments are termed plus and minus, and polymerization is more rapid at the positive end. Once formed, microtubules and microfilaments can disassemble. The overall rate of assembly and disassembly of these structures is affected by the relative concentrations of free or assembled subunits. In general, microtubules are more unstable than microfilaments. In animal cells, the half-life of an individual microtubule is about 10 minutes. Thus microtubules are said to exist in a state of dynamic instability. In contrast to microtubules and microfilaments, intermediate filaments lack polarity because of the antiparallel orientation of the dimers that make up the tetramers. In addition, intermediate filaments appear to be much more stable than either microtubules or microfilaments. Although very little is known about intermediate filament–like structures in plant cells, in animal cells nearly all of the intermediate- filament protein exists in the polymerized state. Microtubules Function in Mitosis and Cytokinesis Mitosis is the process by which previously replicated chromosomes are aligned, separated, and distributed in an orderly fashion to daughter cells (Figure 1.23). Microtubules are an integral part of mitosis. Before mitosis begins, microtubules in the cortical (outer) cytoplasm depolymerize, breaking down into their constituent subunits. The subunits then repolymerize before the start of prophase to form the preprophase band (PPB), a ring of microtubules encircling the nucleus (see Figure 1.23C–F). The PPB appears in the region where the future cell wall will form after the completion of mitosis, and it is thought to be involved in regulating the plane of cell division. During prophase, microtubules begin to assemble at two foci on opposite sides of the nucleus, forming the prophase spindle (Figure 1.24). Although not associated with any specific structure, these foci serve the same function as animal cell centrosomes in organizing and assembling microtubules. In early metaphase the nuclear envelope breaks down, the PPB disassembles, and new microtubules polymerize to form the mitotic spindle. In animal cells the spindle microtubules radiate toward each other from two discrete foci at the poles (the centrosomes), resulting in an ellipsoidal, or football-shaped, array of microtubules. The mitotic spindle of plant cells, which lack centrosomes, is more boxlike in shape because the spindle microtubules arise from a diffuse zone consisting of multiple foci at opposite ends of the cell and extend toward the middle in nearly parallel arrays (see Figure 1.24). Some of the microtubules of the spindle apparatus become attached to the chromosomes at their kinetochores, while others remain unattached. The kinetochores are located in the centromeric regions of the chromosomes. Some of the unattached microtubules overlap with microtubules from the opposite polar region in the spindle midzone. Cytokinesis is the process whereby a cell is partitioned into two progeny cells. Cytokinesis usually begins late in mitosis. The precursor of the new wall, the cell plate that Plant Cells 21  forms between incipient daughter cells, is rich in pectins (Figure 1.25). Cell plate formation in higher plants is a multistep process.  Vesicle aggregation in the spindle midzone is organized by the phragmoplast, a complex of microtubules and ER that forms during late anaphase or early telophase from dissociated spindle subunits.

Microfilaments Are Involved in Cytoplasmic Streaming and in Tip Growth

Cytoplasmic streaming is the coordinated movement of particles and organelles through the cytosol in a helical path down one side of a cell and up the other side. Cytoplasmic streaming occurs in most plant cells and has been studied extensively in the giant cells of the green algae Chara and Nitella, in which speeds up to 75 ìm s–1 have been measured. The mechanism of cytoplasmic streaming involves bundles of microfilaments that are arranged parallel to the longitudinal direction of particle movement. The forces necessary for movement may be generated by an interaction of the microfilament protein actin with the protein myosin in a fashion comparable to that of the protein interaction that occurs during muscle contraction in animals. Myosins are proteins that have the ability to hydrolyze ATP to ADP and Pi when activated by binding to an actin microfilament. The energy released by ATP hydrolysis propels myosin molecules along the actin microfilament from the minus end to the plus end. Thus, myosins belong to the general class of motor proteins that drive cytoplasmic streaming and the movements of organelles within the cell. Examples of other motor proteins include the kinesins and dyneins, which drive movements of organelles and other cytoskeletal components along the surfaces of microtubules. Actin microfilaments also participate in the growth of the pollen tube. Upon germination, a pollen grain forms a tubular extension that grows down the style toward the embryo sac. As the tip of the pollen tube extends, new cell wall material is continually deposited to maintain the integrity of the wall. A network of microfilaments appears to guide vesicles containing wall precursors from their site of formation in the Golgi through the cytosol to the site of new wall formation at the tip. Fusion of these vesicles with the plasma membrane deposits wall precursors outside the cell, where they are assembled into wall material.

 Intermediate Filaments Occur in the Cytosol and Nucleus of Plant Cells

 Relatively little is known about plant intermediate filaments. Intermediate filament–like structures have been identified in the cytoplasm of plant cells (Yang et al. 1995), but these may not be based on keratin, as in animal cells, since as yet no plant keratin genes have been found. Nuclear lamins, intermediate filaments of another type that form a dense network on the inner surface of the nuclear membrane, have also been identified in plant cells (Frederick et al. 1992), and genes encoding laminlike proteins are present in the Arabidopsis genome. Presumably, plant lamins perform functions similar to those in animal cells as a structural component of the nuclear envelope.


 The cell division cycle, or cell cycle, is the process by which cells reproduce themselves and their genetic material, the nuclear DNA. The four phases of the cell cycle are designated G1, S, G2, and M (Figure 1.26A).

 Each Phase of the Cell Cycle Has a Specific Set of Biochemical and Cellular Activities

 Nuclear DNA is prepared for replication in G1 by the assembly of a prereplication complex at the origins of replication along the chromatin. DNA is replicated during the S phase, and G2 cells prepare for mitosis. The whole architecture of the cell is altered as cells enter mitosis: The nuclear envelope breaks down, chromatin condenses to form recognizable chromosomes, the mitotic spindle forms, and the replicated chromosomes attach to the spindle fibers. The transition from metaphase to anaphase of mitosis marks a major transition point when the two chromatids of each replicated chromosome, which were held together at their kinetochores, are separated and the daughter chromosomes are pulled to opposite poles by spindle fibers. At a key regulatory point early in G1 of the cell cycle, the cell becomes committed to the initiation of DNA synthesis. In yeasts, this point is called START. Once a cell has passed START, it is irreversibly committed to initiating DNA synthesis and completing the cell cycle through mitosis and cytokinesis. After the cell has completed mitosis, it may initiate another complete cycle (G1 through mitosis), or it may leave the cell cycle and differentiate. This choice is made at the critical G1 point, before the cell begins to replicate its DNA. DNAreplication and mitosis are linked in mammalian cells. Often mammalian cells that have stopped dividing can be stimulated to reenter the cell cycle by a variety of hormones and growth factors. When they do so, they reenter the cell cycle at the critical point in early G1. In contrast, plant cells can leave the cell division cycle either before or after replicating their DNA (i.e., during G1 or G2). As a consequence, whereas most animal cells are diploid (having two sets of chromosomes), plant cells frequently are tetraploid (having four sets of chromosomes), or even polyploid (having many sets of chromosomes), after going through additional cycles of nuclear DNA replication without mitosis.

plamy physiology cell cycle

The Cell Cycle Is Regulated by Protein Kinases

The mechanism regulating the progression of cells through their division cycle is highly conserved in evolution, and plants have retained the basic components of this mechanism (Renaudin et al. 1996). The key enzymes that control the transitions between the different states of the cell cycle, and the entry of nondividing cells into the cell cycle, are the cyclin-dependent protein kinases, or CDKs (Figure 1.26B). Protein kinases are enzymes that phosphorylate proteins using ATP. Most multicellular eukaryotes use several protein kinases that are active in different phases of the cell cycle. All depend on regulatory subunits called cyclins for their activities. The regulated activity of CDKs is essential for the transitions from G1 to S and from G2 to M, and for the entry of nondividing cells into the cell cycle. CDK activity can be regulated in various ways, but two of the most important mechanisms are (1) cyclin synthesis and destruction and (2) the phosphorylation and dephosphorylation of key amino acid residues within the CDK protein. CDKs are inactive unless they are associated  with a cyclin. Most cyclins turn over rapidly. They are synthesized and then actively degraded (using ATP) at specific points in the cell cycle. Cyclins are degraded in the cytosol by a large proteolytic complex called the proteasome. Before being degraded by the proteasome, the cyclins are marked for destruction by the attachment of a small protein called ubiquitin, a process that requires ATP. Ubiquitination is a general mechanism for tagging cellular proteins destined for turnover (see Chapter 14). The transition from G1 to S requires a set of cyclins (known as G1 cyclins) different from those required in the transition from G2 to mitosis, where mitotic cyclins activate the CDKs (see Figure 1.26B). CDKs possess two tyrosine phosphorylation sites: One causes activation of the enzyme; the other causes inactivation. Specific kinases carry out both the stimulatory and the inhibitory phosphorylations. Similarly, protein phosphatases can remove phosphate from CDKs, either stimulating or inhibiting their activity, depending on the position of the phosphate. The addition or removal of phosphate groups from CDKs is highly regulated and an important mechanism for the control of cell cycle progression (see Figure 1.26B). Cyclin inhibitors play an important role in regulating the cell cycle in animals, and probably in plants as well, although little is known about plant cyclin inhibitors. Finally, as we will see later in the book, certain plant hormones are able to regulate the cell cycle by regulating the synthesis of key enzymes in the regulatory pathway.


Plasmodesmata (singular plasmodesma) are tubular extensions of the plasma membrane, 40 to 50 nm in diameter, that traverse the cell wall and connect the cytoplasms of adjacent cells. Because most plant cells are interconnected in this way, their cytoplasms form a continuum referred to as the symplast. Intercellular transport of solutes through plasmodesmata is thus called symplastic transport (see Chapters 4 and 6).  

There Are Two Types of Plasmodesmata: Primary and Secondary

 Primary plasmodesmata form during cytokinesis when Golgi-derived vesicles containing cell wall precursors fuse to form the cell plate (the future middle lamella). Rather than forming a continuous uninterrupted sheet, the newly deposited cell plate is penetrated by numerous pores (Figure 1.27A), where remnants of the spindle apparatus, consisting of ER and microtubules, disrupt vesicle fusion. Further deposition of wall polymers increases the thickness of the two primary cell walls on either side of the middle lamella, generating linear membrane-lined channels (Figure 1.27B). Development of primary plasmodesmata thus provides direct continuity and communication between cells that are clonally related (i.e., derived from the same mother cell). Secondary plasmodesmata form between cells after their cell walls have been deposited. They arise either by evagination of the plasma membrane at the cell surface, or by branching from a primary plasmodesma (Lucas and Wolf 1993). In addition to increasing the communication between cells that are clonally related, secondary plasmodesmata allow symplastic continuity between cells that are not clonally related.

Plasmodesmata Have a Complex Internal Structure

Like nuclear pores, plasmodesmata have a complex internal structure that functions in regulating macromolecular traffic from cell to cell. Each plasmodesma contains a narrow tubule of ER called a desmotubule (see Figure 1.27). The desmotubule is continuous with the ER of the adjacent cells. Thus the symplast joins not only the cytosol of neighboring cells, but the contents of the ER lumens as well. However, it is not clear that the desmotubule actually represents a passage, since there does not appear to be a space between the membranes, which are tightly appressed. Globular proteins are associated with both the desmotubule membrane and the plasma membrane within the pore (see Figure 1.27B). These globular proteins appear to be interconnected by spokelike extensions, dividing the pore into eight to ten microchannels (Ding et al. 1992). Some molecules can pass from cell to cell through plasmodesmata, probably by flowing through the microchannels, although the exact pathway of communication has not been established. By following the movement of fluorescent dye molecules of different sizes through plasmodesmata connecting leaf epidermal cells, Robards and Lucas (1990) determined  the limiting molecular mass for transport to be about 700 to 1000 daltons, equivalent to a molecular size of about 1.5 to 2.0 nm. This is the size exclusion limit, or SEL, of plasmodesmata. If the width of the cytoplasmic sleeve is approximately 5 to 6 nm, how are molecules larger than 2.0 nm excluded? The proteins attached to the plasma membrane and the ER within the plasmodesmata appear to act to restrict the size of molecules that can pass through the pore. As we’ll see in Chapter 16, the SELs of plasmodesmata can be regulated. The mechanism for regulating the SEL is poorly understood, but the localization of both actin and myosin within plasmodesmata, possibly forming the “spoke” extensions (see Figure 1.27B), suggests that they may participate in the process (White et al. 1994; Radford and White 1996). Recent studies have also implicated calcium-dependent protein kinases in the regulation of plasmodesmatal SEL.


 Despite their great diversity in form and size, all plants carry out similar physiological processes. As primary producers, plants convert solar energy to chemical energy. Being nonmotile, plants must grow toward light, and they must have efficient vascular systems for movement of water, mineral nutrients, and photosynthetic products throughout the plant body. Green land plants must also have mechanisms for avoiding desiccation. The major vegetative organ systems of seed plants are the shoot and the root. The shoot consists of two types of organs: stems and leaves. Unlike animal development, plant growth is indeterminate because of the presence of permanent meristem tissue at the shoot and root apices, which gives rise to new tissues and organs during the entire vegetative phase of the life cycle. Lateral meristems (the vascular cambium and the cork cambium) produce growth in girth, or secondary growth. Three major tissue systems are recognized: dermal, ground, and vascular. Each of these tissues contains a variety of cell types specialized for different functions. Plants are eukaryotes and have the typical eukaryotic cell organization, consisting of nucleus and cytoplasm. The nuclear genome directs the growth and development of the organism. The cytoplasm is enclosed by a plasma membrane and contains numerous membrane-enclosed organelles, including plastids, mitochondria, microbodies, oleosomes, and a large central vacuole. Chloroplasts and mitochondria are semiautonomous organelles that contain their own DNA. Nevertheless, most of their proteins are encoded by nuclear DNA and are imported from the cytosol. The cytoskeletal components—microtubules, microfilaments, and intermediate filaments—participate in a variety of processes involving intracellular movements, such as mitosis, cytoplasmic streaming, secretory vesicle transport  transport, cell plate formation, and cellulose microfibril deposition. The process by which cells reproduce is called the cell cycle. The cell cycle consists of the G1, S, G2, and M phases. The transition from one phase to another is regulated by cyclin-dependent protein kinases. The activity of the CDKs is regulated by cyclins and by protein phosphorylation. During cytokinesis, the phragmoplast gives rise to the cell plate in a multistep process that involves vesicle fusion. After cytokinesis, primary cell walls are deposited. The cytosol of adjacent cells is continuous through the cell walls because of the presence of membrane-lined channels called plasmodesmata, which play a role in cell–cell communication-    

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MIT Chemistry

Lecture 8: The Periodic Table and Periodic Trends
Lecture 9: Periodic Table; Ionic and Covalent Bonds
Lecture 10: Introduction to Lewis Structures
Lecture 11: Lewis Structures: Breakdown of the Octet Rule

MIT Biochemistry

Bishop-Introduction to Chemistry

Chapter 3: Chemical Compounds

Section 3.1: Classification of Matter

Section 3.2: Compounds and Chemical Bonds

Section 3.3: Molecular Compounds

Section 3.4: Naming Binary Covalent Compounds

Section 3.5: Ionic Compounds

Chapter 4: An Introduction to Chemical Equations

Section 4.1: Chemical Reactions and Chemical Equations

Section 4.2: Solubility of Ionic Compounds and Precipitation Reactions

Chapter 5: Acids, Bases, and Acid-Base Reactions

Chapter 5: Acids, Bases, and Acid-Base Reactions

Section 5.1: Acids

Sections 5.2 and 5.3: Acid Nomenclature and Summary of Chemical Nomenclature

Section 5.4: Strong and Weak Bases

Section 5.5: pH and Acidic and Basic Solutions

Section 5.6: Arrhenius Acid-Base Reactions

Section 5.7: Brønsted-Lowry Acids and Bases

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