Principles of Plant Physiology
The field of plant physiology includes the study of all the internal activities of plants. They include the chemical and physical processes associated with life as they occur in plants. This includes studying them at many levels of scale of size and time. At the smallest scale are molecular interactions of photosynthesis and internal diffusion of water, minerals, and nutrients. At the other end are the processes of plant development, seasonality, dormancy, and reproductive control. Major sub disciplines of plant physiology include phytochemistry (the study of the biochemistry of plants) and phytopathology, the study of disease in plants. The scope of plant physiology as a discipline has been divided into several major areas of research. Some of these have already been described in earlier chapters at a basic level where as lesson 17 onwards are more advanced and won’t be covered again here.
The 5 key areas of plant physiology.

• Phytochemistry
• Cellular Interactions
• Molecular and Cell Biology
• Plant Morphology
• Environmental Interactions
  Phytochemistry is the study of the chemical reactions that take part in a plant which includes how they function and survive. Plants produce a wide array of chemical compounds not found in other organisms. Photosynthesis requires a large array of pigments, enzymes, and other compounds to function. Because they cannot move, plants must also defend themselves chemically from herbivores, pathogens and competition from other plants. They do this by producing toxins and foul tasting or smelling chemicals. Other compounds defend plants against disease, permit survival during drought, and prepare plants for dormancy, while other compounds are used to attract pollinators or herbivores to spread ripe seeds.
• 
  Despite the underlying similarity of all molecules within living organisms, plants produce a vast array of chemical compounds with unique properties which they use to cope with their environment. Pigments are used by plants to absorb or detect light, and are extracted by humans for use in dyes. Other plant products may be used for the manufacture of commercially important rubber or biofuel. The most celebrated compounds from plants are those which have served human activity in the forms of pharmaceuticals, such as salicylic acid from which aspirin is made, morphine, and digoxin. Drug companies spend billions of dollars each year researching plant compounds for potential medicinal benefits.
• 
  Constituent elements are required by plants in the forms of macronutrients and micronutrients. Some nutrients, are required in large quantities to survive and are known as macronutrients, where the prefix macro; large, refers to the quantity needed, not the size of the nutrient particles themselves. Those nutrients required in smaller quantities are referred to as micronutrients. Such micronutrients are usually absorbed as ions dissolved in water taken from the soil, though carnivorous plants acquire some of their micronutrients from captured prey. Still some nutrients are required in even smaller quantities and these are known as the trace nutrients and are essential for the plants health and defence mechanisms.

Pigments:
Pigments are among the most important molecules for the healthy functions which are carried out in a plant. Plant pigments include a variety of different kinds of molecules which all have specific functions within the plant. These include chlorophyll, porphyrins, carotenoids, and anthocyanins. All biological pigments selectively absorb certain wavelengths of light while reflecting others. The light that is absorbed may be used by the plant to power chemical reactions, while those wavelengths which are reflected determine the color the pigment appears to the eye of humans and of particular insects, birds or mammals.
Porphyrin is the primary pigment in plants; it is a porphyrin that absorbs red and blue wavelengths of light while reflecting green. It is the presence and relative abundance of chlorophyll that gives plants their green colour. All land plants and green algae possess two forms of this pigment known as chlorophyll a and chlorophyll b.

Kelps, diatoms, and other photosynthetic heterokonts contain chlorophyll c instead of b while red algae possess “chlorophyll “a and d”. All chlorophylls serve as the primary collectors in plants and transfer the energy to the reaction center molecules to fuel photosynthesis. (See Chapter 8.)

Carotenoids are the red, orange, or yellow tetraterpenoids. They function as accessory pigments in plants, helping to fuel photosynthesis by gathering wavelengths of light not readily absorbed by chlorophyll. The most familiar carotenoids are carotene the orange pigment which is so abundantly found in carrots and in the red new growth of plants prior to the formation of chloophyll.

Carotene are found in Lutein are found in Lycopene in Elaeocarpus eumundi, Aceratium ferrugineum and Solanum corifolium Immature leaves. fruits. fruits. Anthocyanins (Anthos means a flowers and Cyan means blue thus blue flower”) These water soluble flavonoid pigments that appear deep reddish-purple, deep reddish-blue, purple to blue, according to pH. They occur in all tissues of higher plants, providing the deeper green color in leaves, stems, roots, flowers, and fruits, though not always in sufficient quantities to be noticeable. Anthocyanins are most visible in the petals of flowers, where they may make up as much as 30mm of the dry weight of the tissue. They are also responsible for the purple color seen on the underside of tropical shade plants such as Alpinia caerulea. In these plants, the anthocyanin catches light that has passed through the leaf and reflects it back towards regions bearing chlorophyll, in order to maximize the use of available light. Anthocyanin also play an important role in attracting both diurnal and nocturnal pollinators as the colours offer strong contrasts in flower and fruit colouration under different light wave lengths.

Betalains are red or yellow pigments and like anthocyanins they are water soluble, but unlike anthocyanins they are indole derived compounds synthesized from tyrosine. These pigments are only found in the Caryophyllales; including cactus and amaranthus. They never co-occur in plants with anthocyanins. Betalains are responsible for the deep purple color of beets, and are used commercially as food-coloring agents. Plant physiologists are uncertain of the function that betalains have in plants which possess them, but there is some preliminary evidence that they may have fungicidal properties.

Cellular Interactions includes the study of biological and chemical processes of individual plant cells. Plant cells have a number of features that distinguish them from cells of animals, and which lead to major differences in the way that plant life behaves and responds differently from animal life. For example, plant cells have a thick rigid cell wall which restricts the shape of plant cells and thereby limits the flexibility and mobility of a plant. Plant cells also contain chlorophyll, the green chemical compound that interacts with light in a way that enables plants to manufacture their own nutrients rather than consuming other living or dead things as animals and fungi do. (See Chapter 8 for leaf cell interactions & Chapter 4 for root interactions.)
Molecular and Cell

Biology plant physiology deals with interactions between cells, tissues, and organs within a plant. Different cells and tissues are physically and chemically specialized to perform different functions. Roots and rhizoids function to anchor the plant and absorb minerals from the soil. Stems cells transport the minerals and sugars to different parts of the plant. Leaves catch light in order to manufacture nutrients. For these organs to remain living, and to function minerals that the roots acquire must be transported through the xylem tissues to the leaves, and the nutrients manufactured in the leaves must be transported through the phloem to the stems and roots.
Plant Morphology is the study of how plants control or regulate internal functions. (See the different chapters relating to the morphology of leaves, roots and stems and flowers.) Like animals, plants produce chemicals called hormones which are produced in one part of the plant to signal cells in another part of the plant to respond. Many flowering plants bloom at the appropriate time because of light sensitive compounds that respond to the length of the night, a phenomenon known as photoperiodism. The ripening of fruit and loss of leaves in the winter are controlled in part by the production of the gas ethylene by the plant due to temperature decrease or increase, available soil moisture or photoperiodism.
Environmental Interactions includes the study of plant response to environmental conditions and their variation, a field known as environmental physiology. Stress from water loss, changes in air chemistry, or crowding by other plants can lead to changes in the way a plant functions. These changes may be affected by genetic, chemical, and physical factors.

Signals and regulators:

Arabidopsis thaliana is a small flowering; non problematic weed plant of Australia from northern Europe, that is widely used as a model plant organism in botany and biology. Arabidopsis thaliana is a member of the mustard family (Brassicaceae), which includes the cultivated species of cabbages and radishes. Although not of major agronomic significance itself, Arabidopsis thaliana offers important advantages for basic research in genetics and molecular biology:

• Approximately 115 Mb of the 125 Mb genome has been sequenced and annotated (Nature, 408:796-815; 2000).
• Extensive genetic and physical maps of all 5 chromosomes are available.
• The life cycle is short–about 6 weeks from germination to seed maturation.
• Seed production is prolific and the plant is easily cultivated in restricted space.
• Transformation is efficient utilizing Agrobacterium tumefaciens.
• A large number of mutant lines and genomic resources is available.
• Arabidopsis thaliana is studied by a multinational research community in academia, government and industry.
  Such advantages have made it an easy organism to study the cellular and molecular biology of flowering plants.

Here a common mutation was formed due to environmental conditions where the mutation caused Arabidopsis thaliana to stop responding to auxin and becoming stunted.
Plants also produce hormones and other growth regulators which act to signal a physiological response in their tissues. Compounds like auxin are sensitive to light and trigger growth or development in response to environmental signals.

Plant hormones, known as plant growth regulators (PGRs) or phytohormones, are chemicals that regulate a plant’s growth. Hormones occur in very low concentrations and are produced at specific locations within the plant. They cause altered processes in target cells at the site or other locations. Plants lack specific hormone producing tissues or organs thus are not usually transported to other parts of the plant and production is not limited to specific locations.
Plant hormones even in very small amounts promote and influence the growth, development and differentiation of cells and tissues. They are vitally important to plant growth, affecting the flowering, seed development, dormancy and germination of the seeds. They regulate which tissues grow upwards and which tissues grow downwards, leaf formation and stem growth, fruit development and ripening, as well as leaf abscission and even plant death.

The most important plant hormones are abscissic acid (ABA), auxins, (See chapter 4) ethylene, gibberellins, and cytokinins, though there are many other substances that serve to regulate plant physiology.

Photomorphogenesis:
Morphogenesis is the plant’s sensitivity to light and plays an important role in the control of plant structural development. The use of light to control structural development is called photomorphogenesis, and is dependent upon the presence of specialized photoreceptors, which are chemical pigments capable of absorbing specific wavelengths of light.
Plants use four kinds of photoreceptors: phytochrome, cryptochrome, a UV-B photoreceptor, and protochlorophyllide a.
The first two of these, phytochrome and cryptochrome, are photoreceptor proteins, complex molecular structures formed by joining a protein with a light-sensitive pigment. Cryptochrome is also known as the UV-A photoreceptor, because it absorbs ultraviolet light in the long wave “A” region.
The UV-B receptor is one or more compounds not yet identified with any certainty, though the latest evidence suggests that carotene and or riboflavin are involved.
Protochlorophyllide is a chemical precursor for the manufacturing of chlorophyll.

The most studied of the photoreceptors in plants is phytochrome. It is sensitive to light in the red and far red region of the visible spectrum. Many flowering plants use it to regulate the time of flowering based on the length of day and night; photoperiodism, and to set circadian rhythms. It also regulates other responses including the germination of seeds, elongation of seedlings, the size, shape and number of leaves, the synthesis of chlorophyll, and the straightening of the epicotyl or hypocotyl hook of dicot seedlings.

Photoperiodism
Photoperiodismic plants are actually controlled by night length rather than day length.

Many flowering plants use the pigment phytochrome to sense seasonal changes in day length, which they take as signals to flower. This sensitivity to day length is termed photoperiodism. Flowering plants are classified as long day plants, short day plants, or day neutral plants, depending on their particular response to changes in night length.
Long day plants require certain night time lengths shorter than 12 hours to start flowering. These plants are usually noted for flowering in the spring or summer.
Conversely, short day plants require certain uninterrupted night time lengths longer than 12 hours to start flowering. These plants are usually noted for flowering in the late winter to early spring. Note that some flowers may flower 1 or even 2 months after the signal for flowering has been initiated. Experiments have been conducted with short periods of light during the night which has adversely affected the flowering of short day plants.

Day neutral plants do not initiate flowering based on photoperiodism, though some may use temperature sensitivity or vernalization (is when a plant is artificially exposed to a low temperature to enhance seed production or stimulate flowering) as a precursor to flowering instead. Plants make use of the phytochrome system to sense day length or photoperiod. Photoperiodism is utilized by florists and floriculturalists to control and even induce flowering out of season. By using lights at night during the winter Xerochrysum bracteatum can be convinced that it is summer and begin flowering earlier than they would in the wild.

Environmental physiology:
The subdiscipline of environmental physiology is one of the oldest subjects studied in botany. Environmental physiology is the ways in which plants respond to their environment or ecological region. Environmental physiologists examine plant response to physical factors such as radiation including light and ultraviolet radiation, temperature, fire, and wind. (See chapter 4) Of particular importance are water relations which can be measured with the Pressure bomb and the stress of drought or inundation, exchange of gases with the atmosphere, as well as the cycling of nutrients such as nitrogen and carbon.

Tropisms, Thigmotropism and Nastic movements:
Plants may respond both to directional and non directional stimuli. A response to a directional stimulus, such as gravity or sunlight, is called a tropism. A response to a nondirectional stimulus, such as temperature or humidity is a nastic movement and a response to touch is a Thigmotropism. (See chapter 4)
Tropisms in plants are the result of differential cell growth, in which the cells on one side of the plant elongates more than those on the other side, causing the part to bend toward the side with less growth. Among the common tropisms seen in plants is phototropism, the bending of the plant toward a source of light. Phototropism allows the plant to maximize light exposure in plants which require additional light for photosynthesis, or to minimize it in plants subjected to intense light and heat. Geotropism allows the roots of a plant to determine the direction of gravity and grow downwards. Tropisms generally result from an interaction between the environment and production of one or more plant hormones.
Thigmotropism Thigma is Greek for to touch. It is the movement in which a plant moves or grows in response to touch or contact with a stimulus. The most common form is found in climbing vines as their stems bend around an object looking for support. Climbing plants, also develop tendrils that coil around supporting objects. Touched cells produce auxin and transport it to untouched cells. The auxin untouched cells will then elongate faster so cell growth bends away from the auxin cells and around the object it is touching. Others include carnivorous plants which respond to touch on 2 or more hairs and the sensitive plant when the leaves fold and drop in response to being touched by grazing animals.
Nastic Movement is the rapid movement found in some plants like Mimosa pudica which is well known for its rapid plant movement. The leaves close up and droop when touched. They are non directional responses to stimuli like temperature, humidity, light irradiance or touch pressure. The movement can be due to changes in turgor or changes in growth, therefore Potassium ion concentration usually controls such movement in plants and is not auxin related. Nastic movements are independent of the stimulus’s position. The rate or frequency of these responses increases as intensity of the stimulus increases.

Plant disease:
Economically, one of the most important areas of research in environmental physiology is phytopathology, the study of diseases in plants and the manner in which plants resist or cope with infection. Plants are susceptible to diseases organisms including viruses, bacteria, and fungi, as well as physical invasion by insects and roundworms.
Because the biology of plants is different to that of animals, their symptoms and responses are also noticeably different. Abscission is the ability of the plant to simply discard the infected part to prevent the spread of disease.

Plant pathogens have the tendency to spread via spores on air currents, water or are carried by animal vectors. One of the most important advances in the control of plant disease was the discovery of Bordeaux mixture in the nineteenth century. The mixture is the first known fungicide and is a combination of copper sulphate and lime. Application of the mixture served to inhibit the growth of downy mildew which threatened to seriously damage the French wine industry. Bordeaux was also found to be very affective in the control of other fungal diseases especially in the Cucurbitaceae family which includes the commercial cucumbers, pumpkins and bitter melons.

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