Chapter 2
THE MOLECULAR COMPOSITION
OF PLANT CELLS
Organisms are made of matter.
Matter is anything that takes up space (volume) and has mass.
Mass is different from weight although it is often used interchangeably.
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Mass is the amount of matter an object has.
Weight is the pull of gravity on the mass of an object.
Elements are the simplest substances. They cannot be broken down into simpler substances by
chemical reactions.
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All matter is made of elements.
There are 92 naturally occurring elements.
Elements are designated by a symbol of one or two letters, e.g. C for carbon; Na for
sodium.
A compound is a substance consisting of two or more elements combined in a fixed ratio.
About 25 elements are essential to life.
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C, O, H and N make about 96% of living matter.
Ca, P, K, S, Na, Cl and Mg make about 4% of the organism's weight.
Trace elements are required in extremely small amounts, e.g. B, Cu, Mn, Mo, Se, etc.
ORGANIC MOLECULES
Small molecules have unique properties arising from the orderly arrangement of its atoms.
The major groups of biologically important molecules are carbohydrates, lipids, proteins and
nucleic acids.
Usually they are very large containing thousands of atoms: macromolecules.
Macromolecules are giant molecules formed by the union (bonding) of smaller molecules. They
consist of hundreds of thousands of atoms. This is another level of biological organization.
CARBOHYDRATES
Most macromolecules are polymers. These are long chains formed by linking small organic
molecules called monomers.
Polymerization is the linking together of monomers to form polymers.
Carbohydrates include sugars and their polymers.
Carbohydrates contain carbon hydrogen and oxygen in a ratio of 1:2:1 or [CH2O]n.
Monosaccharides are simple sugars.
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They serve as sources of energy and carbon atoms.
 Normally containing 3 to 7 carbon atoms.
 A hydroxyl group is bonded to each carbon except one.
 That carbon is double bonded to an oxygen atom forming a carbonyl group; depending
on the position of the carbonyl group, the sugar is an aldehyde (aldose sugars) or a ketone
(ketose sugars).
 Both the carbonyl group and the hydroxyl groups are hydrophilic and make
monosaccharides readily soluble in water.
 Glucose is an aldose and fructose a ketose. Most sugar names end in -ose.
Dissaccharides are made of two monosaccharide units.
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Two monosaccharide rings joined by a glycosidic linkage, a covalent bond formed
between two monosaccharides by a dehydration reactions.
They can be split by the addition of water, a reaction called hydrolysis.
Hydrolysis reactions yield energy.
Linking two glucose monomers forms maltose, and sucrose is formed by linking one
glucose and one fructose. Glucose linked to galactose produces lactose, the sugar in milk.
Polysaccharides.
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Repeating chains of monosaccharides.
Single long chain or branched chain.
They function either as energy storage material or as building blocks of cellular
structures.
Some important polysaccharides:
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Starch is made entirely of glucose and is the main storage carbohydrate of plants:  1-4
linkages; this arrangement makes the starch molecule helical.
 Amylose is the simplest form of starch; it is unbranched and helical.
 Amylopectin is a branched form with 1-6 linkages at the branch point.
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Glycogen is made of glucose and is the storage carbohydrate of animals:  1-4 linkages.
 The glycogen molecule contains more branches than the amylopectin molecules.
 It is also the common storage polysaccharide of fungi, prokaryotes and animals.
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Fructan is the principal storage polysaccharide in the leaves and stems of grains (wheat,
rye and barley).
 It is a polymer of fructose.
Polysaccharides must be hydrolyzed into mono and disaccharides before they can be transported
through the living system and used as a source of energy.
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Cellulose is also made of glucose monomers and is a structural carbohydrate:  1-4
linkages.
 The angles of the bonds of the  1-4 linkages make every other glucose monomer
"upside down."
 Cellulose molecules are straight and never branched.
 Its hydroxyl groups are free to form hydrogen bonds with those of adjacent
molecules.
 In plant cell walls, cellulose molecules form minute cables called microfibrils.
 Wood is about 50% cellulose, and cotton is almost pure cellulose.
 Very few organisms can digest cellulose, e.g. fungi, protozoans and certain
prokaryotes.
 Very few animals can digest cellulose, e.g. silverfish. In most cases cellulose passes
through the digestive tract and is eliminated in the feces.
The glucose molecule is a chain of six carbons but when in solution it forms a ring.
There are two possible ways of forming the ring known as the alpha-glucose and the betaglucose.
Starch and glycogen are made of alpha-glucose; cellulose of beta-glucose subunits.
The type of subunit has a profound effect on the three dimensional structure of the
polysaccharide.
As a result, cellulose is not acted on by enzymes that breakdown glycogen and starch.
The hydroxyl groups that project from both sides of the cellulose molecule form hydrogen bonds
with neighboring hydroxyl groups of adjacent molecules, resulting in microfibrils made up of
cross-linked parallel cellulose molecules.
In plant cell walls, the cellulose microfibrils are embedded in a matrix of two other complex
branched polysaccharides, hemicellulose and pectin.
 Hemicellulose forms hydrogen bonds with the cellulose microfibrils.
 Pectin is the major component of the middle lamella, a layer of intercellular material
that cements the cell walls of adjacent cells.
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Chitin is a polysaccharide used by arthropods in building the exoskeleton.
 The chitin monomer is a glucose-like molecule called N-acetylglucosamine in which
an OH group is replaced by a chain of R–NHCOCH3 group.
 When it becomes encrusted with calcium carbonate, it becomes hard.
 Chitin is also found in the cell wall of fungi, insects, spiders, crustaceans and other
animals.
LIPIDS
Some plants store energy in the form of oils, especially in fruits and seeds.
Fats and oils contain a higher proportion of energy-rich hydrogen-carbon bonds than
carbohydrates and, as a consequence, contain more chemical energy.
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On the average, fats yield 9.1 kcal per gram of fat that is oxidized to release energy,
compared with 3.8 kcal per gram of carbohydrate and 3.1 kcal per gram of protein.
Lipids are diverse group of compounds made mostly of carbon and hydrogen, with a few oxygen
atoms found mainly in functional groups.
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Hydrophobic molecules: water repellent.
They are made mostly of hydrocarbons.
Soluble in nonpolar solvents.
For energy storage, hormones, structure of cell membrane.
Neutral fats, phospholipids, steroids, waxes, carotenoids and other pigments.
1. Storage lipids
Fats are large molecules made from smaller molecules linked together by dehydration reactions.
Neutral fats are made of glycerol and three fatty acids.
Glycerol is a 3-carbon alcohol.
Fatty acids are long unbranched hydrocarbon chain with a carboxyl group (COOH) at one end.
The carbon skeleton of the fatty acid usually has 16 to 18 carbon atoms.
At one end there is a carboxyl group that gives these molecules the name of fatty acids.
The nonpolar C–H is the reason for the hydrophobic properties of the hydrocarbons.
When a fatty acid combines with a glycerol molecule a molecule of water is removed and an
ester linkage is formed.
The fatty acids in a fat molecule may or may not be the same.
Triglyceride (triacylglycerol) is a synonym for fat.
Saturated fats have a maximum number of hydrogen atoms in the chain, and are usually are
solid at room temperature, e.g. lard, blubber and butter.
Unsaturated fats have double bonds between some of the carbon atoms and have less than the
maximum number of hydrogen atoms.
Unsaturated fats have bends in the chains that prevent the aligning with the adjacent chain and
prevent the van der Waals forces from acting. They are usually liquid at room temperature, e.g.
vegetable oils.
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Unsaturated fats are found primarily in plants.
Fats store at least twice as much energy as starch.
Humans and mammals store their fat in the adipose tissue of the body. This tissue serves as a
reservoir of energy, as an insulator, and cushions internal organs.
2. Structural lipids
Phospholipids are major components of cell membranes.
Phospholipids differ from fats in having only two fatty acids instead of three and a phosphate
group with a small additional molecule attached to the third carbon of glycerol instead of a
hydroxyl group.
The hydrocarbon chains are hydrophobic but the phosphate group and its attached organic
molecule (e.g. choline, lecithin) are hydrophilic (affinity for water).
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Amphipathic molecule.
Phospholipids form micelles and bilayers or double layers in aqueous solutions.
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A micelle is a droplet formed by phospholipid molecules arranged with their hydrophilic
heads facing out toward the water medium, and their hydrophobic tails facing inward away
from the water.
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Bilayers are double membranes. In a bilayer, the heads face toward the aqueous solution and
the tails point to the interior of the membrane.
Lipids that form barriers to water loss
Cutin and suberin are important lipid components of the cell wall.
They form a matrix in which waxes are embedded.
Waxes are complex lipids made of many fatty acids linked to a long-chain alcohol.
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Hydrophobic: the most water repellent of the lipids.
Coating of fruits and leaves, beeswax, earwax, etc.
The combination of cutin, suberin and waxes form a barrier that help prevent the loss of water
and other molecules from the plant surface.
A protective cuticle covers the outer walls of epidermal cells embedded in cutin (cuticular
wax); it is frequently covered with epicuticular wax.
Suberin is a major component of cork cell walls that form the outermost layer of bark.
Suberized cell walls consist of alternating layers of suberin and wax.
3. Functional lipids
Steroids stabilize cell membranes and also function as hormones.
Steroids have their carbon skeleton bent into four fused rings with a carbon chain attached to one
of the rings.
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Three rings have six carbon atoms and one has five carbons.
There are different functional groups attached to the rings.
The length and structure of the chain distinguishes one steroid from another.
The function of steroids depends on the functional groups attached to their carbon rings.
When a hydroxyl group is attached to the carbon-3 position, the steroid is called a sterol.
Sterols are important components of the cell membrane:
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Sitosterol is the most common sterol found in algae and plants.
Ergosterol is common in fungi.
Cholesterol, common in animal cells, is found in trace amounts in plant cells.
PROTEINS
Proteins make more than 50% of the dry weight of most cells. Only plants, with their high
cellulose content, have less than half protein in their dry weight.
Proteins perform a variety of functions in the body: structural support, transport of other
molecules, body defense, signaling between cells, chemical catalysts called enzymes, storage,
and other functions.
Proteins vary in their structure so they can perform specific functions.
In plants, the largest amount of protein is found in certain seeds, in which as much as 40% of
their dry weight may be protein.
Proteins are large complex molecules, polymers of amino acids, joined by peptide bonds. These
polymers are called polypeptides.
A protein is made one or more polypeptides folded and coiled into a specific conformation.
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20 amino acids (AA) involved.
Carbon, hydrogen, oxygen, nitrogen and usually sulfur.
AA contain an amino group, NH2, at one end and a carboxyl group, COOH, at the other
end, both attached to an alpha carbon (α).
AAs have a variable side chain (R group) that determines the specific physical and
chemical properties of each AA.
Bacteria and plants can synthesize all AA. There are a few exceptions.
Animals synthesize some but not all AA. Essential AA must be obtained from the diet.
Summarizing the four variable components of an amino acid: alpha carbon, amino group,
carboxyl group and the side chain.
Two AA combine to form a dipeptide; three form a tripeptide; many form a polypeptide.
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The amino end of one AA joins the carboxyl end of the adjacent AA.
An enzyme catalyzes the dehydration reaction. The resulting covalent bond is called a
peptide bond.
When this process is repeated thousands of times the resulting molecule is called a polypeptide.
Polypeptide chain may contain thousands of AA.
Polypeptide and protein are not synonymous.
Protein Structure
Proteins consist of one or more polypeptide chains twisted into a unique shape.
The function of the protein depends on its ability to bind to another molecule.
Proteins have four levels of organization.
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Primary structure: a unique sequence of AA for each polypeptide chain.
 The sequence of AA is determined by inherited genetic information.
 All proteins of a kind have the same AA sequence, e.g. all lysozyme molecules.
 A change in the sequence of AA is called a mutation.
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Secondary structure results from hydrogen bonds between H and O atoms of the
backbone of the chain resulting in coiling (α helix) or folding (β pleated sheet). The side
chains atoms are not involved in the secondary structure of polypeptides.
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Tertiary structure is the overall shape of the polypeptide due to the interaction among the
side chains, R groups.
 Hydrophobic interactions between side chains usually end up in the interior of the
twisted polypeptide chain while hydrophilic side chains are exposed to the aqueous
solutions.
 Disulfide bridges are formed between the two sulfhydril groups of the AA cysteine.
This strong bonds.
 Van der Waals forces, ionic bonds and hydrogen bonds also contribute to the tertiary
structure of the polypeptide chain.
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Quaternary structure is the relationship among several polypeptide chains of a protein.
These polypeptide chains become aggregated into a functional protein.
 Fibrous proteins have several polypeptides coiled or aligned into rope-like structures.
 Globular proteins are roughly spherical or compact.
The shape of the proteins determines its function.
Chaperonins or chaperone proteins help in the proper folding of proteins but do not specify the
conformation. They protect the polypeptide from denaturing influences in the cytoplasm.
Protein conformation depends also on the physical and chemical conditions of the environment
like salt concentration, temperature, pH, etc.
Changes in any of these conditions can cause the protein to unravel and become denatured.
Proteins become denatured become biologically inactive.
Most proteins probably go through several intermediate stages before achieving its active
conformation.
Enzymes are proteins that catalyze chemical reactions in cells.
NUCLEIC ACIDS
Two classes: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
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Transmit hereditary information.
Determine what the cells manufacture.
Nucleic acids are polymers of nucleotides. They are called polynucleotides.
A nucleotide is made of three parts: an organic molecule called a nitrogenous base, a pentose
sugar (5-C sugar), and a phosphate group.
There are five nitrogenous bases found in nucleic acids.
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Cytosine (C), thymine (T) and uracil (U).
Cytosine is found in both DNA and RNA; thymine is found only in DNA; uracil found only
in RNA.
Adenine (A) and guanine (G).
Both are found in DNA and RNA
Pentose sugars:
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Ribose is found in RNA and deoxyribose in DNA.
They differ in the absence of an oxygen atom on the 2-carbon of deoxyribose molecules.
Deoxy- = without an oxygen.
DNA and RNA play different biological roles.
Encoded in the structure of DNA is the information that programs all the cell's activities.
The DNA molecule contains hundreds of thousands of genes.
Genes determine the polymer sequence of AA in a protein.
Proteins are needed to implement what is in the genetic code, in the DNA.
Nucleic acids are polymers that serve blueprints of proteins.
DNA is the genetic material that organisms inherit from their parents.
Flow of genetic information within the cell.
DNA → mRNA → protein
DNA is located in the nucleus of the cell.
Protein synthesis takes place in organelles called ribosomes found in the cytoplasm of the cell.
Messenger RNA, mRNA, is synthesized in the nucleus following the DNA blueprint and then
moves to the ribosomes with the message of about the protein to be synthesized.
ATP - ADENOSINE TRIPHOSPHATE
ATP is the link between exergonic catabolic reactions and endergonic anabolic reactions.
The structure resembles a nucleotide used in RNA.
The nitrogenous base adenine bonded to a ribose sugar, which in turn is bonded to a chain of
three phosphate groups; only one phosphate is attached to the ribose.
The phosphate bonds are referred to as high-energy bonds and can be broken by hydrolysis thus
releasing energy.
High-energy bonds imply strong bonds but in reality, ATP phosphate bonds are relatively weak
compared to the strong bonds of other organic molecules.
Hydrolysis of ATP: ATP + H2O → ADP + Pi
ΔG = -7.3 kcal/mole (-31 kJ/mole)
7.3 kcal/mole are released in the laboratory under standard conditions (STP: 25°C and 1 atm).
SECONDARY METABOLITES
Primary metabolites are molecules found in plant cells and are necessary for the life of the
plant.
Secondary metabolites are restricted in their distribution, both within the plant and among the
different species of plants.
Secondary metabolites are important in the survival of the plant:
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Many are chemical signals that allow the plant to respond to environmental cues.
Other function in the defense of the plant against herbivores, pathogens or competitors.
Some provide protection against radiation from the sun.
Some aid in pollen and seed dispersal.
Secondary metabolites are produced in specific organs, tissues, or cell types at specific stages of
development.
Phytoalexins are antimicrobial compounds produced only after wounding or after attack by
bacteria or fungi.
Secondary metabolites are stored primarily within the vacuoles.
They are often synthesized in one part of the plant and stored in another.
Their concentration may vary greatly during the 24-hour period.
ALKALOIDS
Alkaloids are alkaline nitrogenous compounds.
Alkaloids are derived from amino acids
Alkaloids are basic - they form water soluble salts. Most alkaloids are well-defined crystalline
substances, which unite with acids to form salts.
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Check source: http://www.friedli.com/herbs/phytochem/alkaloids/alkaloid1.htmlCheck
Nearly 10,000 alkaloids have been isolated and their structures identified.
Morphine was the first alkaloid to be identified, in 1806.
 It is derived from the poppy plant, Papaver somniferum.
 It is used as an analgesic and cough suppressant.
Cocaine comes from coca, Erythroxylum coca.
 From a small tree or shrub indigenous to eastern slope of the Andes in Peru and Bolivia.
 Coca leaves are chewed by people to lessen fatigue and hunger.
 Chewing coca leaves is harmless.
 Cocaine has been used as an anesthetic in eye surgery and as a local anesthetic by
dentists.
Caffeine is a stimulant found in coffee (Coffea arabica), tea (Camelia sinensis), and cocoa
(Theobroma cacao).
 High concentration of caffeine present in the developing seedlings of the coffee plant is
toxic and lethal to insects and fungi.
 Caffeine also inhibits the germination seeds in the vicinity of the seedling. This is called
allelopathy.
Nicotine is a stimulant from the tobacco plant, Nicotiana tabacum.
 It is a highly toxic alkaloid.
 Nicotine is synthesized in the roots and transported to the leaves where it is stored in
vacuoles.
 It protects the plant from herbivores and insect.
 It is also synthesized as a result of wounding, possibly acting as a phycoalexin.
Atropine is a cardiac stimulant, pupil dilator for eye examination and an effective antidote for
some nerve gas poisoning.
 It is produced by Atropa belladonna and Hyoscyamus muticus.
TERPENOIDS
Terpenoids are composed of isoprene units.
Terpenoids include essential oils, taxol, rubber, and cardiac glycosides.
Terpenoids or terpenes occur in all plants and are the largest class of secondary metabolites.
About 22,000 terpenes have been described.
Isoprene, C5H8, is the simplest terpenoid.
A plant may synthesize many terpenoids at different locations within the plants for a variety of
purposes and at different times during the course of its development.
Isoprene is a gas that is emitted by the leaves of many plants and is largely responsible for the
bluish haze that hovers over wooded hills and mountains in the summer.
Isoprene is made in chloroplast from carbon dioxide and emitted only in the light.
Isoprene may help stabilize the membrane of chloroplasts.
Monoterpenoids (two isoprene units) and sesquiterpenoids (three isoprene units) are called
essential oils because they are highly volatile and contribute to the fragrance or essence of plants
that produce them.
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Mint produces large quantities of monoterpenoids menthol and menthone.
Essential oils produced by the leaves deter herbivores, protect against fungi or bacteria, while
others are known to be allelopathic.
The terpenoids of flower fragrances attract insect pollinators to the flowers.
The diterpenoid taxol has anti-cancer properties.
Taxol is collected from the bark of the Pacific yew tree, Taxus brevifolia, from needles of the
European yew bush, Taxus baccata and Taxus bushes, as well as yew fungus.
Taxol is now being synthesized in the laboratory.
Rubber is a terpenoid compound containing 400 to more than 100,000 units.
Rubber is obtained commercially from the latex of Hevea brasiliensis.
In Hevea, the latex contains about 40 to 50% rubber.
Cardiac glycosides are poisonous terpenoids that can cause heart attacks.
They are used in medicine to strengthen and slower the heartbeat.
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Foxglove Digitalis is the source of digitoxin and digoxin.
Glycosides produced by members of the milkweed and dogbane families deter
herbivores.
Some terpenoids called carotenoids play a role in photosynthesis.
Others are hormones: gibberellins, abscisic acid.
Some are part of the structure of membranes, sterols, or electron carriers, ubiquinone,
plastoquinone.
PHENOLICS
Phenolics include flavonoids, tannins, lignins and salicylic acid.
Phenolics include a broad range of compounds that have hydroxyl group attached to an aromatic
ring
They universal in the plant kingdom and accumulate in all parts of the plant.
The function of many phenolic compounds is unknown.
Flavonoids include anthocyanins that range in color from red to purple to blue.
Some flavones and flavonols are yellowish or ivory colored pigments.
Colorless flavones and flavonols can change the color of the plant by combining with metal ions
and anthocyanins. This phenomenon is called co-pigmentation.
Flower pigments attract pollinators.
Flavonoids interact with bacteria living in the plant roots, e.g. symbiotic bacteria in the root of
legumes.
Some protect against damage by UV radiation.
Tannins are the most important deterrent to herbivores.
Tannins are stored in the vacuoles of the cells.
Lignins are deposited in the cell wall.
It is the most abundant organic compound on Earth only after cellulose.
Lignins are polymers containing three monomers: p-coumaryl, coniferyl and sinapyl alcohols.
The amount of each monomers differs significantly depending on whether they lignin is from
gymnosperms, woody angiosperms, or grasses.
There is also a great variation of lignin in different organs, tissues, wall fractions and species of
plants.
The major importance of lignin is the strength and stiffness that it provides to the cell wall of
plants.
Lignification is believed to have played a major role in the evolution of terrestrial plants.
Lignification allowed the plants to increase in stature and develop branches.
Lignin waterproofs the cell wall and facilitates the transport of water upward in the xylem
vessels.
Lignin also protects against fungal attack by resisting mechanical penetration.
Salicylic acid is essential for the development of systemic acquired resistance or SAR.
SAR develops in response to a localized attack by pathogenic bacteria, fungi and viruses; as a
result, other parts of the plant are provided with long-lasting protection against the same and
unrelated pathogens.