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16a Chemistry of natural products
Table of contents Aliphatic compounds, acyclic / cyclic, saturated / unsaturated carbon compounds Aromatic compounds, arenes, benzene derivatives Carboxylic acids and fatty acids Terpenes, monoterpenes, terpinenes, oleoresins Tetrapyrroles, porphyrins, (haem, heme), chlorophyll, phytochromes Aliphatic products Alditols, polyhydric alcohols, mannitol Carbohydrate acids, D-gluconic acid, D-glucuronic acid Carbohydrates Carboxylic acids and fatty acids Cellulose, hemicellulose Chitin Cyclitols, inositol Disaccharides Glycosaminoglycans (mucopolysaccharides), glucosamines Glycosides Betanin Glucosides Glycerides, esterification of glycerol Lecithins Lipids, fats and oils, fatty acids, glycerides Monosaccharides Monosaccharides, Left-handed / right-handed structural forms, D and L sugars Nucleosides, nucleic acids, DNA, RNA Pectin, Aspergillus japonicus Phenolic compounds Polyketides, polyketide antibiotics Polysaccharide gums, gums, phycocolloids Reducing sugars / non-reducing sugars Phospholipids, (phosphoglycerides) Polysaccharides Starches, amylum, glycogen Sugars
Aldose sugars
Ketose sugars
RuBisCO Trisaccharides Tetrasaccharides Waxes Aromatic compounds, arenes, benzene derivatives Anthocyanins Aramids
"Kevlar" Aromatic aldehydes and ketones, e.g. benzaldehyde Aromatic amines, anilides, e.g. phenylamine Aromatic alcohols, e.g. phenyl methanol, (benzyl alcohol) Aromatic halogen compounds, e.g. benzyl chloride Aromatic hydrocarbons, e.g. benzene, anthracene Aromatic nitro compounds, e.g. nitrobenzene Aromatic sulfonic acids, e.g. benzene sulfonic acid Aryl groups
16.9.20 Bergamottin
16.8.1 Reactions of benzene, C6H6 Barbiturates (depressants) Benzodiazepines (tranquillizers) Benzofuranoids, benzopyranoids
Bergamottin Diazo compounds Five member heterocycles Flavonoids, (Bioflavonoids), plant polyphenols Flavonols, (flavan-3-ols) Geosmin, Earth smells, rain smells and cut grass smells Lactams (-NH(CO-), e.g. caprolactam Lignans, plant phenols Parabens Pyridine Tannins, (kinotannic acid), plant polyphenols Carboxylic acids and fatty acids, (carboxyl group -COOH), (aliphatic monocarboxylic acids) Carboxylic acids and fatty acids α-hydroxy acids Aromatic carboxylic acids and derivatives, e.g. benzoic acid, salicyclic acid Dicarboxylic acids Keto acids, acetoacetic acid, pyruvic acid Perfluorooctanoic acid Saturated carboxylic acids Tricarboxylic acids Unsaturated fatty acids Terpenes, monoterpenes, terpinenes, oleoresins Carotenes Terpenes Isoprene units, (C5H8) Hemiterpenes, (one isoprene unit), (C5H8) Monoterpenes, (two isoprene units), (C10H16)
Thymol Terpinenes, (cyclic terpenes), (C10H16) Sesquiterpenes C15, (three isoprene units), (C15H24) Geosmin Diterpenes, (four isoprene units), (C20H32) Sesterterpenes, C25, (five isoprene units) Triterpenes C30, (six isoprene units),  (C30H48) Tetraterpenes C40, (eight isoprene units), C40H56, carotenoid pigments Polyterpenes, (thousands of isoprene units)
3.85.0 Rubber, latex Steroids, sterols, steroid alcohols, natural steroids Terpenoids Xanthophylls Tetrapyrroles, porphyrins, (haem, heme), chlorophyll, phytochromes Tetrapyrroles, related compounds Photosynthetic pigments, chlorophyll a and chlorophyll b Legheamoglobin Phycobilins, phycocyanin, phycoerythrin Phycobiliproteins, Anabaena azollae, water fern, (Azolla) Phytochromes Polyvinyl pyrrolidene, povidone, PVP-iodine complex Porphyrins

3.85.0 Rubber, latex
23.6.4 Heat and cool rubber bands, rubber band heat engine
23.6.2 Latex plants
23.6.1 Natural rubber
23.6.3 Negative thermal expansion (NTE) of rubber, entropy Polyterpenes, (thousands of isoprene units)
23.6.5 Stretch rubber bands Carbohydrates
Carbohydrates were compounds such as aldoses and ketoses, stoichiometric formula Cn(H2O)n, so "hydrates of carbon".
Nowadays, carbohydrates include monosaccharides, oligosaccharides and polysaccharides, and substances from monosaccharides,
1. by reduction of the carbonyl group, >C=O, (alditols),
2. by oxidation of one or more terminal groups to carboxylic acids, e.g. ethanoic acid, CH3COOH,
3. by replacement of hydroxy groups by a hydrogen atom, an amino group, thiol group or other groups, and derivatives of these
compounds. Sugars
See diagram Glucose and fructose, straight chain forms
Sugars are simple carbohydrates, one or more monosaccharide units, soluble in water, optically active, sweet to taste and fermentable.
However, the term "sugar" generally refers to monosaccharides and lower oligosaccharides.
"Reducing sugars" reduce copper (II) to copper (I) salts in Fehling's solution or other test solutions, show presence of aldehyde group.
Monosaccharides have a straight chain form or ring form, cannot be split into smaller molecules using dilute acids, cannot be hydrolysed
to simpler compounds.
Polysaccharides have more than ten monosaccharides linked by glycosidic bonds, between C1 on one sugar and C4 on other sugar by
removal of water molecule, i.e. a condensation reaction.
An aldose has aldehyde group, -CHO, i.e. a carbonyl, group, C=O, with a hydrogen atom attached to the carbon atom, e.g. glucose.
Aldose sugars
An aldose sugar is also an aldehyde which contains one aldehyde group per molecule, chemical formula Cn(H2O)n.
Aldose sugars include the following:
1. Glyceraldehyde HO-CH2-CHO
2. Tetrose sugars: erythrose, threose,
3. Pentose sugars:  ribose, arabinose, xylose, lyxose
4. Hexose sugars: allose, altrose, glucose, mannose, gulose, idose, galactose, talose.
Ketose sugars
A ketone group is a carbonyl group, C=O, with two single bonds to other carbon atoms.
A ketose sugar contains one ketone group per molecule, e.g. fructose, CH2OHCHOHCHOHCHOHC=OCH2OH
Ketose sugars include the following:
1. Fructose, C6H12O6, fruit sugar, high fructose corn syrup
Commercial: D-(-)-Fructose, D-Levulose, Fruit sugar
2. Glycerone, C3H6O3, dihydroxyacetone, simplest ketose sugar, triose, stains skin brown but no increase in melanin so used in
sunless tanning, fake sun tan.
Commercial: Dihydroxyacetone, 1,3-Dihydroxy-2-propanone, DHA, Glycerone
3. Ribulose, C5H10O5, pentose, artificial sweetener but not very sweet
Commercial: L-Ribulose, L-Adonose, also D-Ribulose
RuBisCO, C5H12O11P2,  ribulose-1-5 biphosphate carboxylase oxygenase, the most abundant enzyme for first step in carbon
fixation by plants.
Commercial: RuBisCO, powder from spinach
4. Xyulose, C5H10O5, pentose, not used as commercial sweetener
Commercial: D-Xylulose, D-threo-Pentulose, faint yellow syrup Monosaccharides
| See diagram Aldose: D-glyceraldehyde, L-glyceraldehyde, Ketose: dihydroxyacetone
| See diagram Aldose sugar: Glucose
| See diagram Aldose sugar: Galactose
| See diagram Ketose sugar: Fructose
| See diagram Aldose sugar: Ribose, deoxyribose, nucleotide
Monosaccharides, Cx(H2O)y, where x = 1 or 2 or 3,. contain a single sugar unit, e.g. glucose, fructose.
So they cannot be hydrolysed to simpler sugars.

Classification: of monosaccharides
1. Classification by number of carbon atoms
Triose, 3 carbon atoms, C3H6O3, dihydroxyacetone, glyceraldehyde
Tetrose, 4 carbon atoms, C4H8O4, e.g. erythrose, threose, erythrulose
Pentose, 5 carbon atoms, C5H10O5, e.g. arabinose, lyxose, ribose, xylulose
Hexose, 6 carbon atoms, C6H12O6, e.g. allose, altrose, glucose, mannose, gulose, idose, galactose, talose

2. Classification by whether aldose or ketose
Aldose contains aldehyde group, (-CHO), at C1, monosaccharide bonded to an aldehyde chain, Cn(H2O)n, e.g. glyceraldehyde,
(CHOCHOHCH2OH), the simplest aldose
Ketose, contains ketone group, (-CO-), at C2, monosaccharide sugar containing a ketone group or compound derived from a ketone,
e.g. dihydroxyacetone, (CH2OHCOCH2OH), the simplest ketose
Table Aldoses and ketoseszzz
No. C Atoms
Aldose, contains aldehyde group
Ketose, contains ketone group
3 C triose
4 C tetrose
erythrose, threose
5 C pentose
arabinose, lyxose, ribose, xylose ribulose, xylulose
6 C hexose
allose, altrose, galactose, glucose, gulose, idose, mannose, talose fructose, psicose, sorbose, tagatose Left-handed and right-handed structural forms, D-sugars and L-sugars
See diagram Monosaccharides, D-sugar and L-sugar
The Fischer projection formula invented by Emil Fischer, (1852 - 1919), allows the three-dimensional sugar and amino acid molecules
be represented by two-dimensional diagrams on the page.
Horizontal lines show groups projecting above the plane of the page towards you.
Vertical lines show groups projecting below the plane of the page away from you.
So D-glyceraldehyde has the hydroxyl group on C2 on the right and L-glyceraldehyde has the hydroxyl group on C2 on the left,
(Latin: dextro = right, laevo = left).
For all other carbohydrates, if the carbon atom farthest from the aldehyde or ketone group has the same arrangement as
D-glyceraldehyde, hydroxyl on the right of C2, then the compound is a D-sugar.
Similarly, if this "remote carbon atom" has the same arrangement as L-glyceraldehyde, the compound is an L-sugar.
However, monosaccharides exist mainly as cyclic forms, not the aldo-forms or keto-forms.
See diagram Fischer projection and Haworth projection of glucose
The cyclic structure of monosaccharides is shown by a "Haworth projection", invented by W. N. Haworth, 1813-1950, England.
The oxygen atom is at the upper right and the carbon atoms are arranged clockwise with C1 at the far right.
The hydroxyl groups on the right in the Fischer projection are down in the Haworth projection, so the hydroxyl groups on the left in
the Fischer projection are up in the Haworth projection.
The terminal -CH2OH group is up in the Haworth projection for D-sugars, and down for L-sugars.
D-glucose can have α-or β-forms, depending on the position of the hydroxyl group attached to C1, down in the α-form and up in the
Most monosaccharides have a ring cycle of six atoms, one oxygen atom and five carbon atoms, called the pyranose form.
A ring cycle of 5 atoms, one oxygen atom and four carbon atoms is called a furanose form.
So D-fructose can exist as α-D-fructofuranose, -OH on C2 is down, and β-D-fructofuranose, -OH on C2 is up.
Glucose, Commercial: "D-(+)-Glucose, dextrose"
Fructose, D form, but laevorotatory, so "L-fructose", Commercial: "D-(-)-Fructose, D-Levulose, Fruit sugar" Disaccharides, trisaccharides, tetrasaccharides, polysaccharides
| See diagram Maltose molecule
| See diagram Lactose molecule
| See diagram Sucrose molecule
Disaccharides contain two sugar units:
sucrose = (glucose + fructose),
lactose = (milk sugar, glucose + galactose),
maltose = (malt sugar, glucose + glucose). Trisaccharides
Raffinose, (triose: fructose + galactose + glucose), (C18H32O16),
Also, melezitose, maltotriose, (amylotriose) Tetrasaccharides
See diagram Stachyose, acarbose
Acarbose, (C25H43NO18), anti-diabetic drug
Stachyose, (tetrose: fructose + galactose + glucose + galactose, i.e. raffinose + galactose), (C24H42O21), in green beans Polysaccharides, glycans
Polysaccharides are long carbohydrate molecules consisting of repeated monomer units joined together in a chain by glycosidic bonds
and contain linked monosaccharide units, (C6H10O5)n
1. Homopolysaccharides, homoglycans, contain the same type of monomer unit
2. Glucosans, (from glucose)
Starch, amylopectin glucosan + amylose sugar
Glycogen, glucose residues
Cellulose, D-glucose units
2. Fructans, (from fructose)
Inulin, D-fructose, in artichokes
2. Galactans, (from galactose)
1. Heteropolysaccharides, heteroglycans, contain different type of monomer r units
Acidic, mucopolysaccharides, glycosaminoglycans long unbranched polysaccharides, repeating disaccharide units
Chondroitin sulfate
Keratan sulfate
Hyaluronic acid
Dextran, Modified polysaccharide
Chitin, (C8H13O5N)n, is a polymer of the monosaccharide derivative of glucose, N-acetylglucosamine, in fungi cell walls, arthropod
exoskeletons, e.g. crabs, insect exoskeleton, mollusc radula, cephalopod beak, e.g. squid.
Similar structure to cellulose and keratin
Used as a binder in dyes, adhesives, fabrics and dissolving surgical thread.
Pectin is a polysaccharide that forms the primary cell walls of many terrestrial plants.
Pectin has various uses in the food industry as it acts as a gelling agent for jams and jellies.
It is also used as a food thickening agent and stabilizer in juices, milk.
Arabinoxylans is a polysaccharide found in the primary and secondary cell wall of plants i.e. wood and also in the cereal grains.
It is a combination of arabinose and xylose.
β-glucan, (cellotriose, β-D-glucan, glucan, C18H32O16),  D-(+)-cellotriose, glucopyranosyl
Oligosaccharides raffinose, stachyose and verbascose are present in significant quantities in legume seeds Starches, amylum, glycogen
See diagram Starch, amylose,
(amylum), (amylose, soluble starch, many glucose units), (amylopectin, insoluble starch, 40 to 60 branched glucose units).
(Starch, amylum = amylose + amylopectin)
Glycogen in animals.,
Glycogen, α-1,4- and α-1,6-glucan, unbranched glucose polymer similar to amylopectin
Inulin = D-fructose units, from Helianthus)
Boil cut potato in water then let cool.
Filter the solution to separate the soluble amylase from the insoluble amylopectin of the starch grains.
Add tincture of iodine to the filtered starch solution.
An intense blue colour occurs.
The solution contains β-amylase, C6H10O5 that forms a complex with iodine: (β-amylase)p, (I-), (I2)r(H2O)s [where r < p < s]. Cellulose, hemicellulose
See diagram Cellulose, three glucose molecules linked to form cellulose
See diagram Cellulose
See diagram Linamarin
See diagram Cyanohydrin
Cellulose is a long unbranched glucose polymer.
Cellulose in plant cell walls, hemicellulose in some plant endosperm to form vegetable ivory.
Gun-cotton was prepared by saturating cotton or cellulose material in nitric acid and sulfuric acid to produce a highly explosive material. Chitin
See diagram Chitin
Chitin, (C8H33O5N)n, is an insoluble nitrogenous polysaccharide, contains chains of N-acetylglucosamine in support structure of
invertebrates and fungi, e.g. shells of arthropods. Pectin, Aspergillus japonicus
Pectin, poly-D-galacturonic acid methyl ester, from apple and citrus peel, is a heterosaccharide component of terrestrial plant cell walls.
It is used as a substrate to identify, differentiate and characterized pectinases.
Pectin is used to study its degradation by pectinolytic bacteria.
Pectin has high molecular weight, cements adjacent plant cells, and is dissolved by pectinase in ripening fruit.
It is sold as a white-brown powder and is used to form gels and as thickening agents.
Galactouronic acid, C6H10O7, is a component of pectins.
Pectinase, polygalacturonase, catalyzes hydrolysis in pectin
Pectinesterase, pectin methylesterase, catalyzes hydrolysis of methyl esters of pectin --> pectate + methanol
Pectolyase from Aspergillus japonicus plant cell culture, catalyzes breakdown of methyl esters --> oligosaccharides Cyclitols, inositol
Cyclitols are cycloalkanes containing one hydroxyl group on each of three or more ring atoms, e.g. Inositol, cyclohexane,
cyclohexane-1,2,3,4,5,6-hexol, C6H12O6,  prescribed for some medical conditions, but should not be taken as a "vitamin supplement"
to the diet.
Inositol is in eggs:  22.15
Commercial: myo-Inositol, 1,2,3,4,5,6-Hexahydroxycyclohexane, meso-Inositol, C6H12O6 Carbohydrate acids
D-gluconic acid, CH2(OH)(CHOH)4COOH, produced by fungi
D-glucuronic acid, C6H10O7, in gums, forms glucuronides
d-gluconic acid, d-glucuronic acid, food additive E574, anti-caking agent, sequestrant
Commercial: D-Glucuronic acid, Glucodiuronic acid, C6H10O7 Alditols, polyhydric alcohols, mannitol
General formula: HOCH2[CH(OH)]nCH2OH,
Mannitol CH2OH(CHOH)4CH2OH, from mannose or fructose, sugar in fungi and brown algae, food sweetener.
Commercial: D-Mannitol, Mannite, C6H14O6 Glycosaminoglycans, (mucopolysaccharides), glucosamines
16.3.0 Amines and alkaloids
Glycosaminoglycans, (mucopolysaccharides), glucosamines, dermatan sulfate, chondroitin, hyaluronic acid, heparin, keratin sulfate.
Glucosamine is converted to glycosamineglycans.
Glucosamine hydrochloride and glucosamine sulfate may repair cartilage and alleviate osteoarthritis.
Commercial: D-(+)-Glucosamine hydrochloride, C6H13NO5. HCl
Heparin, Chondroitin sulfate, Hyaluronan, Heparan sulfate, Dermatan sulfate, Keratan sulfate
Commercial: Heparin sodium salt from porcine intestinal mucosa, anticoagulant Phenolic compounds
Phenolic compounds: citronella, clove oil, dicoumarin, eucalyptol, ubiquinone, urushiol, vanillin
Catechol, C6H4(OH)2, 1,2-dihydroxybenzene, colourless crystalline phenol, harmful, irritant, pyrocatechol, powder, C6H4-1,2-(OH)2
Urushiol, mixture of catechol molecules substituted with different alkyl chains, in poison ivy, used in lacquer ware, causes allergic
reactions in people handling mango leaves and stems
Citronella grass, Cymbopogon citratus, Poaceae
Phenolic polymers: tannins, lignin
Flavours: eugenol, (olive, cinnamon), cinnamaldehyde, (cinnamon, cassia), anethole, (anise), thymol, (thyme), carvacuol, (oregano),
estragola, (tarragon), vanillin, (vanilla)
Polyphenols, e.g. hydrolysable tannins Glycosides
A compound formed from a simple sugar and another compound by replacement of a hydroxyl group in the sugar molecule.
A glycoside is a natural compound linked to sugar other than glucose.
A glycoside has a sugar combined with a non-carbohydrate organic molecule.
Any compound that contains a constituent sugar, in which the hydroxyl group attached to the first carbon is substituted by an alcoholic,
phenolic, or other group.
They are named specifically for the sugar contained, such as glucoside (glucose), pentoside (pentose), fructoside (fructose), etc.
Upon hydrolysis, a sugar and non sugar component (aglycone) are formed.

Different glycosides
1. Aminoglycoside, (amikacin hydrate, C22H43N5O13.xH2O, broad spectrum antibiotic)
2. Amygdalin glycoside, C20H27NO11, in almonds, Prunus dulcis
3. Anthocyanins, C15H11O +, (glucosides of anthocyanidins), red, blue and purple flavonoids, in cell sap, natural antioxidants,
(blueberry, boysenberry, black raspberry, black currant pigments), (cyanidin chloride, C15H11ClO6)
4. Anthraquinone, C14H8O2, derivatives include alizarin and compounds in senna, rhubarb, cascara, alizarin
5. Cardiac glycosides, (digoxin, C41H64O14, Digitalis purpurea, for heart disease ), (from oleander, Nerium),
(Ouabagenin, C23H34O8, G-Strophanthidin)
6. Mustard oil glycosides, glucosinolates, from Brassica, (phenethyl glucosinolate potassium salt, C15H20NO9S2K)
7. Nightshade glycosides, (solanine in Solanum nigrum), ( α-Solanine from potato sprouts, C45H73NO15)
8. Saponins, foaming glycosides, in soapwort plant Saponaria, alfalfa Medicago sativa, chickpeas Cicer arietinum, horse chestnut
Aesculus hippocastanum, triterpenoid aglycone in liquorice plant Glycyrrhiza glabra. wavy-leafed soap plant Chlorogalum
, soap bark tree Quillaja saponaria (bark has sapogenin content 10 %, harmful, irritant).
9. Steroidal glycosides, (sugar + steroid), (from roots of Asclepias curassavica ), (steroid glycoside H.g.-12 from Hoodia gordonii) Betanin
Betanin, C24H26N2O13, is cyanogenic glycoside (betacyanin) betanidin-5-O- b-glycoside, beetroot red dye, the red
glycosidic food dye E162 obtained from beets, Beta vulgaris Swiss chard, Opuntia ficus-indica cactus,  Amaranthus spinosus
leaves, Bougainvillea glabra floral bracts.
Betanin is not broken down in the body so can cause temporary red urine, (beeturia and red faeces), and cause distress in people who
think they are suffering haematuria, (blood in the urine).
Commercial: Betanin, Red beef extract diluted with dextrin, C24H26N2O13, Glucosides
A glucoside is a glycoside with a glucose sugar component, a glycoside that yield glucose upon hydrolysis.
Glucosides are natural compounds linked to glucose.
Glycoside, glucoside: sugar + non-carbohydrate R, e.g. glucose + terpene, glucose + phenolic compound
1. Salicin glucoside, C13H18O7, alcoholic β-glucoside, similar to aspirin, acetylsalicylic acid, from white willow bark, Salix, (digitonin,
digitoxin, βcyanin)
2. Stilbenoid glucoside, C20H22O8, (piceid, from grape juice and Picea sitchensis and Polygonum cuspidatum, Japanese knotweed)
3. Cyanogenic glucosides, (amygdalin glucoside, from apricot pits, C20H27NO11), (linamarin glucoside, C10H17NO6, from cassava,
Manihot esculanta), from linseed, flax, Linum usitatissimum, and Lotus japonica.)
4. Flavonoid glucoside, icariin, C33H40O15, occurs in horny goat weed, Epimedium grandiflora, Berberidaceae, and is said to be an
oriental aphrodisiac.
5. Resveratrol glucoside, C14H12O3, antioxidant and free radical, synthesis in seeds of transgenic oilseed rape (Brassica napus),
(produced from Japanese knotweed, piceid) Polyketides, polyketide antibiotics Lactones
Molecules having more than two carbonyl groups connected by single carbon atoms.
Occur in some bacteria and fungi, e.g. Aspergillus.
They have antibiotic, anticancer, cholesterol-lowering, immunosuppressive effects, e.g. erythromycin, lovastatin.
They include polyketide antibiotics, streptomyces metabolites, erythromycin, linear tetracyclines, macrolides and lactones,
erythromycin polyenes, nystatin, polyether antibiotics, β-lactams, aflatoxins.
Commercial: Erythromycin, E-Mycin, Erythrocin, C37H67NO13, white powder
Lactones are components of coconut aroma and peach aroma, e.g. octalactone.
Commercial: Y-Octalactone, 4-Hydroxy octanoic acid, C8H14O2 Nucleosides, nucleic acids, DNA, RNA
| See diagram Nucleic acid
| See diagram 16.21.10: Purines
| See diagram 16.21.13: Pyrimidines
1. Nucleic acids are macromolecules from the nuclei of cells, composed of nucleotide units, and can be hydrolysed into pyrimidine or
purine bases, adenine, cytosine, guanine, thymine, uracil, D-ribose or 2-deoxy-D-ribose, and phosphoric acid.
2. Nucleic acids do several functions in living cells, e.g., the storage of genetic information and its transfer from one generation to the next
3. DNA, (deoxyribonucleic acid), the expression of this information in protein synthesis, (mRNA, tRNA), and may act as functional
components of subcellular units such as ribosomes, (rRNA).
4. RNA, (ribonucleic acid), contains D-ribose, whereas DNA contains 2-deoxy-D-ribose as the sugar component.
5. A nucleoside is a compound in which a purine or pyrimidine base is bound via a N-atom to C-1 replacing the hydroxy group of
either 2-deoxy-D-ribose or of D-ribose, but without any phosphate groups.
Nucleosides include adenosine, guanosine, cytidine, and uridine, (which contain ribose), and deoxyadenosine, deoxyguanosine,
deoxycytidine and thymidine, (which contain deoxyribose).
6. A nucleotide is a nucleoside in which the primary hydroxy group of either 2-deoxy-D-ribose or of D-ribose is esterified by
orthophosphoric acid.
7. An oligonucleotide is a long linear sequences of nucleotides. Polysaccharide gums, gums, phycocolloids
Food stabilizers and thickeners:
1. Gums: (guar gum from Cyamopsis), (gum tragacanth from Astragalus, locoweed), (locust bean gum from carob, Certonia),
(gum arabic from Acacia senegal), (gum karyaya from Sterculia), (gum ghatti from Anogeissus), (xanthan gum from fermented corn
2. Phycocolloids: (alginates, algin, from kelp, Laminaria and Macrocystis), (carrageenan from red algae, Irish moss, Chondrus
), (agar from red algae, Gelidium and Gracilaria). Lipids, fats and oils, fatty acids, glycerides
Fatty acids are aliphatic monocarboxylic acids.
See diagram Esterification of glycerol to form fatty acids, fats
See diagram 16.3.3: Lipids, cephalins, glycerides, (triglycerides), glycolipids, lecithins, (choline), phosphoglycerides, prostaglandins
See diagram 19.2.1: Oleic acid, stearic acid, linoleic acid, (cis and trans)
See diagram Fat molecules
See diagram Tristearin
See diagram Human fat molecule Phospholipids, (phosphoglycerides)
Phospholipids form when hydroxyl groups form esters with phosphate groups.
They occur as two groups:
1. Phosphoglycerides, e.g. lecithin in cell membranes and in bile.
Phosphatidyl choline, (formerly lecithin), phosphatide with organic base choline, in biological membranes, e.g. egg yolk, is used as a
natural emulsifier.
Egg yolk phospholipids (EYPL) are used as carriers for lipophilic drugs and are a major ingredient of lipid microspheres.
2. Sphingolipids in plant and animal cell membranes.
It is a fat molecule with a phosphate group, replacing the third fatty acid.
glycerol-3-phosphate + 2-monacyl glycerol --> triacyl glycerol + phospholipids.
Sphingolipids: sphingenine, cerebrosides, sphingomyelin. Lecithins
Lecithins, diacylphosphatidylcholine, esters of glycerol and choline with fatty acids and H3PO4, in cell membranes.
The lecithin group, (phosphatidylcholine group) are yellow-brown fatty phospholipids in egg yolks and plasma membranes of plant
and animal cells.
They are used as emulsifiers in commercial foods, and cosmetics. Lipids
Lipids are biological substances that are soluble in nonpolar solvents:
1. saponification lipids, e.g. glycerides, (fats and oils), and phospholipids,
2. non-saponification lipids, e.g. steroids.
Lipids refers to the oils, fats and waxes found in living organisms.
Lipids are insoluble in water but soluble in inorganic solvents, e.g. chloroform.
The simple lipids do not contain fatty acids, e.g. steroids, terpenes.
The complex lipids are esters of long chain fatty acids, e.g. glycerides, glycolipids, phospholipids, waxes. Glycerides, esterification of glycerol
Glycerides are common biological substances made from esters of glycerol, (propane-1,2,3-triol), with fatty acids:
1. triglycerides,
2. 1,2-diglycerides or 1,3-diglycerides,
3. 1-monoglycerides or 2-monoglycerides.
The fats and oils found in living organisms are mainly triglycerides:
1. Monoglycerols, (monoglycerides), e.g. 1-monoacyl glycerol, 2-monoacyl glycerol,
2. Diglycerols, (diglycerides), e.g. 1,2-diacyl glycerol, 1,3-diacyl glycerol,
3. Triglycerols, (triglycerides), (fats, main storage lipids), e.g. triacyl glycerol.
Glycerides, glycerine esters, are fatty acid esters of glycerol, (HOCH2CH(OH)CH2OH).
Esters can form at one, two or three of the hydroxyl groups to form monoglycerides, diglycerides and triglycerides.
Esterification of glycerol
Plant oils are usually triglyceride molecules, esters, composed of a 3C alcohol, glycerol, + 18C or 16C fatty acids containing 12C to 24C.
The number of carbon atoms is counted from the end of the molecule with the carboxylic acid group, COOH.
The position of the first double bond is counted from the other end, the methyl or ω end.
Whether the fatty acid is an ω-6 fatty acid or an ω-3 fatty acid depends on the position of the first double bond. Carboxylic acids and fatty acids
Carboxylic acids contain the carboxyl group, carbonyl: -COOH, e.g. ethanoic acid (acetic acid) CH3COOH, so the general formula
The carbonyl group, (carboxy) is -COOH.
The group of saturated and unsaturated aliphatic carboxylic acids are called fatty acids and are found as esters in fats and oils.
Lower carbon fatty acids are corrosive liquids with strong odour and are soluble in water.
Higher carbon fatty acids are oily liquids with unpleasant smell and are only slightly soluble in water.
Fatty acids from C10 onwards are usually solids and are insoluble in water.
The poly unsaturated fatty acids linoleic acid, linolenic acid and arachidonic acids are essential fatty acids in the diet to prevent
atheroma ("hardening of the arteries"), and synthesize prostaglandins.
Saturate fatty acids with no double bonds are linked to the development of atheroma.
Fatty acids in plants occur as esters of glycerol or other hydroxy compound, or amides of long chain amines, e.g. sphingenine.
Fatty acids have trivial and systemic names and the molecule may be saturated, (no double bonds), or unsaturated, (one or more
double bonds).
The products called "natural oils" are not necessarily unsaturated fats. Saturated carboxylic acids
Arachidic acid, (icosanoic acid), CH3(CH2)18COOH, (in peanut oil)
Benzoic acid, C6H5COOH, benzenecarboxylic acid, phenylformic acid, harmful if ingested
Butyric acid, butanoic acid, C3H7COOH, CH3(CH2)2COOH, in rancid butter
Capric acid, decanoic acid, CH3(CH2)8COOH, (in coconut oil, palm oil, mammal milk)
Caproic acid, (hexanoic acid), CH3(CH2)4COOH, (in goat fat)
Caprylic acid, octanoic acid, CH3(CH2)6COOH, (coconuts, breast milk, in sting of whip scorpions!)
Chloroacetic acid, CH2ClCOOH, (used in chemical reactions)
Decanedioic acid, HOOC(CH2)8COOH, sebacic acid, from castor oil
Dichloroacetic acid, DCA, CHCl2COOH, (in chlorinated drinking water)
Ethanoic acid, CH3COOH, acetic acid, vinegar
Formic acid, CH2O2, HCOOH, methanoic acid, (in insect stings, ants)
Lauric acid, dodecanoic acid, CH3(CH3)10COOH, (in coconut oil, soaps)
Myrstic acid, tetradecanoic acid, CH3(CH3)12COOH, (in nutmeg)
Oxalic acid, C2H2O4.2H2O, HO2CCOOH, ethanedioic acid, (in rhubarb, Oxalis)
Palmitic acid, CH3(CH2)14CO2H, hexadecanoic acid, (palm oil, coconut oil, most animals / plants)
Proprionic acid, propanoic acid, CH3CH2COOH, (stored grains preservative)
Stearic acid, octadecanoic acid, CH3(CH2)16COOH, (in fats, soaps, waxes)
Trichloroacetic acid, C2HCl3O2,CCl3COOH, Highly toxic, (used in chemical reactions)
Trifluoroacetic acid, CF3COOH, corrosive, (used in chemical reactions)
Valeric acid, (pentanoic acid), CH3(CH2)3COOH, (valerian herb) Dicarboxylic Acids
Adipic acid, hexanedioic acid, HOOC(CH2)4COOH
Aldaric acid, HOOC-(CHOH)n-COOH
Fumaric acid, butenedioic acid, HCOOHC:CHCOOH } isomers
Maleic acid, butenedioic acid, HCOOHC:CHCOOH } isomers
Malic acid, 2-hydroxybutanedioic acid, HOOCCH(OH)CH2.COOH
Malonic acid, propanedioic acid, HOOCCH2COOH
Oxalic acid, ethanedioic acid, (COOH)2
Oxaloacetic acid, HO2CCH2COCO2H (in Kreb's cycle)
Succinic acid, butanedioic acid, (CH2)2(COOH)2
Tartaric acid, 2,3-dihydroxybutanedioic acid, (CHOH)2(COOH)2 Tricarboxylic acids
16.9.5 Citric acid cycle, Krebs cycle
Citric acid, HOOCCH2C(OH)(COOH)CH2COOH (in Kreb's cycle, plant and animal cells)
Isocitric acid, C6H8O7 Unsaturated fatty acids ,(have double bond =)
Acrylic acid, (2-propenoic acid), CH2=CHCOOH
α-linoleic acid, CH3(CH2)CH=CH(CH2)CH=CH(CH2)CH=CH(CH2)7COOH, polyunsaturated fatty acid
Linoleic acid, CH3(CH2)4CH=CHCH2CH=CH(CH2)7COOH, polyunsaturated fatty acid
Oleic acid, cis-octadec-9-enoic acid, cis-09-octodecanoic acid, CH3(CH2)7CH=CH(CH2)7COOH, mono-unsaturated fatty acid
See: Models, biochemistry, Oleic acid, C18H34O2, 1 molecule, (photograph), "Scientrific", (commercial website)
Oleic acid, C17H33COOH, CH3(CH2)7CHCH(CH2)7COOH, octadec-8-enoic acid, colourless viscous liquid, red oil, m.p. 14oC
Palmitoleic CH3(CH2)5CH=CH(CH2)7COOH Perfluorooctanoic acid
Perfluorooctanoic acid, (PFOA), C8HF15O2, a surfactant, is used to make non-stick cookware, e.g. PTFE, ("Teflon"), and
stain-resistant footwear and clothing.
It persists in the environment and is toxic to animals may be a carcinogen. α-hydroxy acids
Naturally occurring carboxylic acid, hydroxyl group on the carbon adjacent to the carboxyl group.
Use in skin care.
See diagram Alpha hydroxy acids
Citric acid, HOOCCH2C(OH)(COOH)CH2COOH, citric fruits
Glyceric acid, C3H6O4, 2,3-Dihydroxypropanoic acid
Glycolic acid, Hydroxyacetic acid, HOCH2COOH, sugar cane, sugar beet
Lactic acid, L-(+)-Lactic acid , 2-Hydroxypropionic acid, Sarcolactic acid, C3H6O3, sour milk
Malic acid, HOOCCH(OH)CH2.COOH, green apple sour taste, grapes
Mandelic acid, C6H5CH(OH)CO2H, bitter almond
Tartaric acid, L-(+)-Tartaric acid, L-Threaric acid, C4H6O6, HO2CCH(OH)CH(OH)CO2H, leavening agent Keto acids
Acetoacetic acid, diacetic acid, C4H6O3, CH3COCH2COOH
Pyruvic acid, C3H4O3, CH3COCOOH, metabolism of proteins and carbohydrates, release of energy Waxes
Waxes are fatty acid esters of high molecular weight alcohols, i.e. lipids with a long chain alcohol + more than 3 fatty acids.
Solid at room temperature, harder, more brittle and less greasy than fats at the same temperature.
Waxes are found in skin, fur feathers, and outer layers of leaves and fruits as follows:
Fats and oils that are fatty acid esters of the trialcohol glycerol.
Waxes are esters of long chain C16 and above alcohols, (with one hydroxyl group), and long chain C18 and above fatty acids.
Natural waxes are mixtures of esters and some hydrocarbons.
Beeswax [C30H61(C=O)OC15H31, C25-27H51-55(C=O)OC30-32H61-65] comes from the cells of the honeycomb and contains esters
of C16 and C28 acids with C30 and C32 alcohols + mainly C31 hydrocarbons.
Beeswax is used in furniture polishes.

Candelilla wax, food additive E902, glazing agent, emollient, (Euphorbia antisyphilitica, E. cerifera, Euphorbiaceae), milkweed,
spurge, poisonous, unpleasant milky sap.
It is yellow-brown, hard, brittle, aromatic, and opaque to translucent, glazing agent E902, in chewing gum.

Carnauba wax comes from the leaves of the Brazilian wax palm, Coperniciaprunifera, (C. cerifera), Arecaceae.
It contains esters of the C32 and C34 alcohols and C24 and C28 fatty acids.
This wax is harder and more impervious than beeswax.
Carnauba wax, glazing agent, E903, used to wax fruit, in cosmetics.

Cetyl palmitate [(CH3(CH2)13CH2(C=O)O(CH2)15CH3)] [C15H31COO-C16H33] is a component of spermaceti wax in sperm
whale oil.

Jojoba oil, Simmondsia chinensis, Simmondsiaceae, mainly wax esters, in cosmetics, seed is toxic and indigestible
 Meadow foam oil, (Limnanthes alba), Family Geometridea

Wool wax, wool grease, degras, from the scouring of wool contains fatty acid esters of cholesterol, lanosterol and fatty alcohols.
It forms as semi-solid emulsion in water that is purified to make lanolin. Aromatics, aromatic compounds
Aromatics, aromatic compounds, benzene derivatives, ring systems, arenes: benzene, toluene, naphthalene
See diagram Acridine, anthracene, anthroquinone, cinnoline, naphthalene, naphthol, quinoline
See diagram 16.8.0: Acetylsalicyclic acid, (aspirin), benzene, benzoic acid, naphthalene
See diagram Single substitution, more than single substitution
See diagram Heterocyclic compounds: pyridine, (2-aminopyridine, 3-bromopyridine, 3-nitropyridine, nicotinic acid ),
(azines: piperidine, pyridinium chloride), pyrylium ion, (quinoline, isoquinoline, 5-nitroquinoline), (pyrimidines: cytisine, thymine, uracil),
(diazines: pyrazine, pyridazine, pyrimidine)
Aromatics have planar ring-type groups usually composed of carbon atoms, at least one benzene ring in the molecule, e.g. benzene,
naphthalene, with alternating double and single bonds.
Extensive localization occurs because some electrons in the molecule are free to move from one atom to another.
The term "aromatic" was used to describe the smell of some compounds later were found to contain benzene or fused benzene rings in
the structure.
It includes arenes and their substitution products, e.g. benzene, naphthalene, toluene, and aromatic heterocyclic structures, e.g. thiophene. Aryl groups
Groups derived from arenes by removal of a hydrogen atom from a ring carbon atom.
Usually, groups having hydrogen removed from an aromatic compound, e.g. (benzene - hydrogen atom = phenyl group, C6H5). Aramids
Aramids are aromatic polyamides, e.g. "Kevlar", "Nomex".
Aramid fibres are made by spinning liquid crystal aramid polymers to long chain polymer molecules with remarkable strength.
The polymer chains are linked laterally by hydrogen bonds, used in rope and textile high performance fibres.
"Kevlar", a synthetic fibre with of high-tensile strength, is used as a reinforcing material for the rubber in motor vehicle tyres. Aromatic hydrocarbons, arenes
See diagram 16.8.1: Benzene compounds, anthracene
Aromatic hydrocarbons, e.g. Benzene, (C6H6), also in some countries: petrol, pentane-hexane mixture, petroleum spirit.
Benzene is the simplest aromatic compound. As it is toxic and carcinogenic, it should not be used in schools.
Aromatic hydrocarbons, arenes, alkylbenzenes, e.g. benzene C6H6, toluene C6H5CH3, [xylene (dimethylbenzene) (CH3)2C6H4],
[styrene, (phenylethene), (C6H5CH=CH2)], naphthalene C10H8, anthracenen C14H10, cyclohexane C6H12.
Anthracene, C14H10, paranaphthalene, anthracin, anthracene oil, Irritant, harmful if ingested, Very Hazardous, Toxic Aromatic nitro compounds
Aromatic nitro compounds, e.g. Nitrobenzene, oil of mirhan, (C6H5NO2) Lactams
Lactams, (-NH(CO-), e.g. caprolactam, (6-hexanelactam), (C6H11NO)
See diagram Lactams, penicillin G, amoxicillin
Lactams in part of a ring, cyclic amides, amino group + carboxylic acid group --> amide linkage, e.g. caprolactam, (6-hexanelactam),
(C6H11NO), to make nylon, 4-aminobutanoic acid lactam, (β lactam 4C ring, γ-lactam 5C ring, δ-lactam 6C ring), e.g. the pyrimidine
base uracil, β-lactam antibiotics, e.g. penicillin, also: caprolactam, (C6H11NO), also: lactones, (cyclic esters), e.g. 4-hydroxybutanoic
acid lactone CH2CH2CH2OC=O, γ-butyrolactone, GBL, C4H6O2. Aromatic amines
Aromatic amines, anilides, e.g. phenylamine, (aniline, amino benzene), (C6H5NH2)
(phenylammonium ion, anilinium ion C6H5NH3+), benzylamine, diphenylamine, methylaniline, triphenylamine, dimethylaniline, acetanilide,
quinoline, (C9H7N). Diazo compounds
Diazo compounds, (2 linked nitrogen compounds), e.g. methyl orange, (dimethyl-aminoazobenzene sulfonic acid),
(diazonium ion: C6H5N2+, C6H5N+N), diazonium salts [(RNN+)Cl-], e.g., methyl orange, (dimethyl-aminoazobenzene sulfonic acid),
[(CH2)2NC6H4N=NC6H4SO2O-Na+] benzene diazonium chloride, chrysoidine azo compounds, (-N-N-), (diazonium ion + benzene
ring) Barbiturates (central nervous system depressants)
See diagram Amylobarbital, barbital, pentobarbital, phenobarbital, quinalbarbital, sodium phenytoin, thiopental
barbiturates were formerly used as sedatives and hypnotics.
Barbituric acid is formed by condensing urea with diethyl malonate, an ester from apples.
Barbituric acid derivatives include the following:
1. Barbital (US), barbitone, C8H12N2O3, "Veronal", formerly used or attempted used by would-be suicides)
2. Phenobarbital (US), phenobarbitone, C12H12N2O3, "Luminal", sedative and hypnotic, an anticonvulsant drug used to treat epilepsy.
Phenobarbital causes side effects, e.g. sedation, depression and agitation,  so it may be replaced by phenytoin, C15H12N2O2, in the
anti-epileptic drug sodium phenytoin, "Dilantin".
3. Sodium thiopental, C11H17N2NaO2S,  ("Sodium Pentathol", thiopentone sodium, "Trapanal"), "truth drug", is a short acting
barbiturate general anaesthetic, used to start anaesthesia, e.g. for caesarian section operation.
It causes unconsciousness in seconds. Benzodiazepines (tranquillizers, sedatives, hypnotics)
See diagram Diazepam (Valium), oxazepam (Serax), nitrazepam (Mogadon), chlordiazepoxide (Librium), flunitrazepam
Benzodiazepines assist the neurotransmitter γ-aminobutyric acid to treat anxiety, insomnia, seizures, and preparation for medical
procedures. Aromatic halogen compounds
Aromatic halogen compounds, aryl halide, halogenarenes, e.g. benzyl chloride, (C6H5COCl)
See diagram DDT, methoxychlor, Synergists: piperonyl butoxide
See diagram 16.13.3: Benzene hexachloride, chlorothalanil, DCPA, dalapon
See diagram 16.13.4: Aldrin, chlordane, dieldrin, endosulfan, heptachlor
16.7.2 Dalapon
Bromobenzene, iodobenzene, chlorobenzene, (BHC, benzene hexachloride, lindane), chlorothanil
Cyclodienes: chlordane, aldrin, dieldrin, heptachlor, endosulfan
DDT insecticide: (ClC6H4Cl)2CH(CCl3), (Former name: dichlorodiphenyltrichloroethane), ( New IUPAC name:
1,1,1-trichloro-2,2-bis, (4-chlorophenyl)ethane.)! Aromatic sulfonic acids
Aromatic sulfonic acids, e.g. benzene sulfonic acid, (C6H5SO2OH), sodium benzene sulfonate Aromatic alcohols
Aromatic alcohols, e.g. phenyl methanol, (benzyl alcohol), (C6H5CH2OH), Aromatic aldehydes and ketones
Benison, C14H12O2, 2-Hydroxy-2-phenylacetophenone, 2-Hydroxy-1,2-Diphenylethanone, desyl alcohol, bitter almond oil
Benzaldehyde, benzenecarbaldehyde, benzene aldehyde, C6H5CHO, almond kernel flavouring, camphor is synthesized from
benzaldehyde in a condensation reaction.
See diagram 16.8.1 Aromatic acids
Aromatic acids and their derivatives, e.g. benzoic acid, (C6H5COOH)
See diagram Acetyl salicyclic acid, (aspirin), | See diagram Benzoic acid, caffeine, paracetamol, phenacetin
e.g. benzoic acid, (C6H5COOH), benzoyl chloride, (C6H5COCl), salicyclic acid, (1-hydroxybenzoic acid), (HOC6H4COOH),
aspirin, acetyl salicyclic acid, (2-acetoxy benzoic acid), [C6H4(OCOCH3)COOH] alcohol detergent, aromatic detergent, weed killer
2:4-dichlorophenoxyacetic acid, shikimic acid [C6H6(OH)3COOH]
Acetyl salicyclic acid is hydrolysed with hydrochloric acid to salicylic acid and acetic acid.
Sometimes old bottles of aspirin have a vinegar (acetic acid) smell because of this reaction. Parabens
Parabens get their name from their origin as esters of parahydroxybenzoic acid., Parabens, HO.C6H4.CO.O-R, where R = alkyl group
See diagram Parabens
See Preservatives, food additives: E214 to E219
Parabens are esters of para-hydroxybenzoic acid and are used commonly as preservatives in cosmetics and food.
However, some parabens may cause allergic reactions in some people and affect DNA.
Some parabens are said to imitate oestrogen and are suspected of causing cancer, but there is no evidence that they are carcinogenic.
However, in Australia, some skin care products are labelled "Paraben free" because of this suspicion.
Propyl paraben, propyl 4-hydroxybenzoate, "Nipagin A", E216, is a natural subsonic but is usually manufactured for use as a food
preservative against fungi and as a cosmetics industry preservative.
Methyl paraben, methyl 4-hydroxybenzoate, "Nipagin B", E218, CH3(C6H4(OH)COO, is used as anti-fungal agent in hair gels and
similar products, it occurs in blueberries
Ethyl paraben, ethyl 4-hydroxybenzoate, E214, is used as a food preservative. Pyridine
Pyridine, (pyridino), C5H5N, monodentate ligand
Pyridine, C5H5N, has a penetrating offensive odour and in some countries it is added to methylated spirit to deter ingestion. Benzofuranoids, benzopyranoids
See diagram Coumarin, furan, bergamottin | See diagram Bergamottin, lovastatin, atorvastatin
Benzofuranoids: (furan C4H4O), (benzofuran, coumarone, C8H6O, 2,3-benzofuran), (benzodifuran), (isobenzofuran)
Benzofuranoid derivatives used as anti-inflammatory constituents from Eupatorium cannabinum.
Benzopyranoids: (pyran, C5H6O, oxime, 2H pyran, 4H pyran), (1-benzopyrans), (3,4-dihydro-2H-1-benzopyran, chroman),
4-chromanone, C9H8O2), (chromone, C9H6O2), (2-chromeme), (3-chromeme), (flavone, C15H10O2), (flavanone C15H12O2),
(fisetin flovanol C15H10O6.nH2O), (coumarin, C9H6O2)
Benzopyrans, chromenes, have a benzene ring + heterocyclic pyran ring, C5H6O.
Coumarin, warfarin, (C9H6O2, 1,2-benzopyrone, 1-benzopyran-2-one), in perfumes, (from tonka bean Dipterix odorata, Aloe vera,
Artemisia vulgaris), (used to make warfarin, C19H16O4, a medical anticoagulant and rat poison, e.g. "Ratsac".)

Bergamottin, C21H22O4, oil of bergamot, is a furanocoumarin, (furan ring C4H4O + coumarin), from Citrus bergamia, bergamot
orange, (in Earl Grey tea).
The bergamottin in grapefruit interferes with the action of drugs, e.g. atorvastatin, ("Lipitor", to lower bad cholesterol), by blocking the
action of enzymes in the small intestine to increase the amount of drug absorbed and the action of fexofenadine, ("Allegra", allergy
medicine, runny nose), by blocking the action of transporters to decrease the amount of drug to target cells. Geosmin, Earth smells, rain smells, cut grass smells
See diagram Coumarin, isocoumarin, cycloalkyls, geosmin
1. The degraded sesquiterpene geosmin, C12H22O, causes the smell of moist soil, produced by Streptomycesis species,
Streptomyces antibioticus and Streptomyces coelicolor and blue-green algae.
The "earth smell", "rain smell" noticed after rain and in wet rugby dressing rooms, causes the earthy taste of beetroot, and "off tastes"
in water and wine.
Blue-green algae in water can also produce geosmin.
In Australia, when heavy rain occurs after a long period of dry weather, a bad taste, "off taste", may develop in the drinking water
caused by the high concentration of geosmin washed into water supply dams.
Actinomycetes bacteria grows in damp soil but produces survival spores during hot weather.
During the first rainfall, wind suspends the spores in the air as an aerosol causing the "after the rain smell" from geosmin, C12H22O,
The smell occurs after you have breathed in tiny particles of soil containing the bacteria.
Another explanation for the after rain smell is that volatile chemicals in the air spaces between soil particles are washed out by the rain
and become relatively concentrated just above the soil.
Some people call the earth smell "petrichor" and say that is caused by plant oils that become adsorbed to clay minerals to produce an
argillaceous odour.
Some people say they can smell ozone in the smell after rain and this may be true after severe lightning from thunder storms.
2. Geosmin also causes the earthy taste of beetroot and off-flavours in wine and drinking water.
It can be isolated from Streptomyces antibioticus.
Also, Streptomyces coelicolor may be involved in producing the smell.
3. Geosmins are also produced by blue-green algae and anaerobic bacteria when they die.
Geosmins may cause the muddy smell of fish, e.g. catfish, carp and mullet.
Geosmins breakdown in acid solutions so fish is generally eaten with lemon juice.
4. The sweet smell of new mown hay is because of a coumarin from cut clover, e.g. white clover, (Melilotus alba), when a glucosidase
reacts with glycosylated cinnamic acid to produce hydroxycinnamic acid that esterifies to form coumarin.
Newly cut grass produces a variety of volatile organic compounds depending on the species of the grass and when it is cut during its
life cycle.
The compounds include methanol, ethanol, acetaldehyde, acetone, butane, 1,8-cineole, aldehydes of hexanoic acid, (caproic acid,
CH3(CH2)4COOH), and so-called hexenyl compounds.
These emitted compounds may be a significant proportion of atmospheric pollution emitted during motorized grass cutting and grazing. Flavonoids, (Bioflavonoids), plant polyphenols
See diagram Flavonoids, (apigenin-7-monoglucoside), flavones, riboflavin, anthicyanin
More than 6,000 bioflavonoids,
Bioflavonoids have vasodilating actions, antioxidant, anti-allergenic, anti-inflammatory and antiviral properties.
They cause the colour, flavour and aroma for many foods and are found in fruits and vegetables, tea, red wine, cacao and some nuts.
Chemists and the food industry do not have the same classification of the flavonoids - bioflavonoids group.
Flavonoids, isoflavonoids and neoflavonoids are natural products, derived from flavone, derivatives --> flavanones and flavanols
Flavonoids are 3-ring phenolic compounds with a double benzene ring with OH groups attached to a 3rd benzene ring by a single
bond, (flavonoid - sugar = aglycone)
Flavanoids include the following:
1. Apigenin, (4,5,7-trihydroxyflavone), from parsley, C15H10O5
2. Baicalin, in leaves of Scutellaria lateriflora (blue skullcap) and Scutellaria galericulata (common skullcap) leaves, glucuronide of
baicalein, in Chinese medicinal herb Huang-chin (Scutellaria baicalensis) to treat cancer, C21H18O11
3. Catechin, flavanol, from green tea, cocoa, vinegar, C15H14O6
4. Catechin gallate, from green tea, C22H18O10
5. Epicatechin, from green tea, cocoa, kola nut, peach, C15H14O6
6. Genistein, from Glycine max (soybean), C15H10O5
7. Naringin, from citrus fruit, C27H32O
8. Theaflavins, (theaflavin and theaflavin gallates), from black tea Anthocyanins
Anthocyanins, plant pigments, glycosides, hydrolysis --> coloured aglycons, deep red anthocyanidins become tannins.
Anthocyanidins include cyanidin, delphinidin, malvidin, pelargonidin, peonidin.
Anthocyanins in fruits and vegetables:.
apples, berries, currants, eggplant, grapes, pears, plums, cabbage, radishes, red onions.
Anthocyanins in nuts: e.g. hazelnuts, pecans, pistachios, in red wine. Flavonols, (flavan-3-ols), yellow
Flavonols include isorhamnetin, kaempferol, myricetin and quercetin.
In fruits and vegetables, e.g. apples, apricots, blueberries, blackberries, arugula, asparagus.
In green and oolong tea, cocoa, red wine.
Quercetin (C15H10O7), also called flavone, is the most active of the flavonoids, and many medicinal plants with a high quercetin content.
Has anti-inflammatory activity by inhibiting release of histamine and has antioxidant activity.
Rutin, (C27H30O16), citrus flavonoid glycoside, rutin hydrate, C27H30O16.xH2O, quercetin-3-rutinoside hydrate, vitamin P hydrate
Apigenin and luteolin in fruits and vegetables, e.g. peppers, olives, artichokes, celery, onions and parsley.
Flavan-3-ols include catechins, epicatechins, theaflavins and thearubigins.
In fruits and vegetables, e.g. apples, apricots, berries, cherries, grapes, nectarines, peaches, pears, plums, Swiss chard.
In nuts, e.g. almonds, cashews, hazelnuts, pecans and pistachios.
In green, black and oolong teas, cacao, red and white wine.

3. Flavanols, catechin, (C15H14O6), colourless monomer, (isomer epicatechin)

4. Flavanones, usually glycosylated to form flavanone glycosides, e.g. butin, (C15H12O5), in seeds of Vernonia anthelmintica.
Flavonones include eriodictyol, hesperetin, naringenin.
In citrus fruits, e.g. kumquats, lemons, limes, grapefruits, oranges and tangerines.
In artichokes.
In red and white wine.

5. Isoflavones, related to isoflavonoids, phytestrogens and antioxidants, soy isoflavones may prevent breast cancer, only found in legumes.
Isoflavones include genestein and daidzein.
In soybeans, pistachios.

6. Other bioflavonoids include the following:
 proanthocyanidin, rotenone, pisatin, isoflavan, pisatin, proanthocyanidins, orcein, vulpinic acid, taxol, urushiol, (pentadecyl-catechol),
(phytoalexins: resveratrol, psoralen), (flavone alkaloids: ficine, vochysine).
Brazilin, red pigment, (C16H14O5), from Caesalpinia echinata, "Brazil wood" originally "bresel wood", Natural Red 24
Haematoxylin, log wood, (C16H14O6), from Haematoxylum campechianum, logwood tree, Natural Black

7. Classification of flavanoids
Plant secondary metabolites, formerly "Vitamin P"
1. Flavones, from 2-phenylchromen-4-one, e.g.quercetin, rutin).
2. Isoflavonoids, from 3-phenylchromen-4-one
3. Neoflavonoids, from 4-phenylcoumarine.
1. Flavonols
2. Flavan-3-ols (hydroxy derivative of flavone) --> flavanol, (flavonoid in red wine)
3. Flavones, e.g. Baicalin
4. Flavanones --> flavone C15H10O2
5. Flavanonols
6. Flavan-3,4,diol --> anthocyanidins, anthocyanins Tannins
Tannins, (kinotannic acid), plant polyphenols, phenolic polymers: polyphenols, galloyl ester, vescalagins
Tannin, i.e. tannic acid, a polyphenol, is a yellow-brown compound in coffee beans, oak galls, mahogany, tea leaves, tree bark, walnuts.
Reacts with proteins in skins to form leather.
Used as a mordant, inks and dyeing. Tannic acid is not an acid.
Tannins are any group of yellow-brown astringent compounds derived from gallic acid, found in bark and galls, used to convert animal
hide to leather.
Tannins from hemlock, (Tsuga), oak, (Quercus), mangrove, (Rhizophora), wattle, (Acacia), babul, (Acacia sp) chestnut, (Castanea),
quebracho, (Schinopsis), sumacs, (Rhus), canaigre from tanner's dock, (Rumex), E181 Tannic acid, tannins, (from oak trees, tea), (clarifying agent). Lignans, plant phenols
Lignans: (from degradation of lignin), plant phenols, dihydroguaiaretic acid, hinokinin, podophyllotaxin Five member heterocycles
See diagram 5-member heterocycles | See diagram 14.05: Histamine, major tranquillizers, tricyclic anti-depressants
Heterocyclic molecules have different atoms in the ring: furan C4H4O, thiephene C4H4S, pyrrole, (CH)4NH, thiazole C3SNH3,
saccharin C7H5NO3S, histamine C5H9N3, immidazole C3N2H4, indole C8H7N, [proline (CH2)3NHCHCOOH, an amino acid called
yrrolidine-2-carboxylic acid)] Terpenes
Terpenes, monoterpenes, terpinenes, sesquiterpenes, diterpenes, sesterterpenes, triterpenes, tetraterpenes, terpenoids, oleoresins
See diagram Isoprene | See Dienes, isoprene units
(limonene, α-pinene, camphene, cadinene, caryophyllene, cedrene, dipentene, phellandrene, terpinene, sabinene, myrcene)
Terpenes are aromatic volatile hydrocarbons, formula C10H16, usually isoprenoid structure and occurring in essential plant oils.
They are hydrocarbons with of two or more isoprene (C5H8) units joined together.
Terpenes, (isoprenoids), occur mostly in plants and may be isolated as a water-insoluble oil through distillation.
Terpenes contain functional groups, e.g. C=C, OH, C=O and may be acyclic or cyclic.
Phenolic compounds often associated with terpenes contain benzene rings with attached hydroxyl groups, (C-OH).
Some terpenes are organic solvents and cleaning agents with strong characteristic odours derived from pine trees or citrus fruit,
e.g. α-pinene, d-limonene, and turpentine, (a mixture of terpenes).
Terpenes are volatile organic compounds, (VOCs), and are flammable or combustible.
Terpenes may be poisonous and can cause painful rashes, e.g. Manchineel tree, (Hippomane mancinella),  Cicutoxin water hemlock,
(Cicuta douglasii).

1. List of terpenes, molecular formula
Bisabolol C15H26O (-)-α-Bisabolol, from leaves of Hymenocrater yazdianus, Lamiaceae
Camphor, D-Camphor, C10H16O, original source was camphor tree, camphor laurel, Cinnamomum camphora, Lauraceae
trans-Caryophyllene, C15H24, cloves Syzygium aromaticum, hemp Cannabis sativa, rosemary Rosmarinus officinalis, hops, black
1,4-Cineole, C10H18O, in eucalyptus oil, natural monoterpene that inhibits plant growth
1,8-Cineole, C10H18O from Lavandula.
Citral, C10H16O, from Cymbopogon citratus, lemongrass, monoterpenoid
Citronellal, C10H18O, from Citrus depressa, Taiwan mandarin
Citronellol, C10H20O, 3,7-Dimethyl-6-octen-1-ol,
Cymene, C10H14, 4-Isopropyltoluene
Dimethyl-3-octanol, C10H22O, Tetrahydrolinalool
Geraniol, C10H18O
Limonene, C10H16, cyclie terpene, Chinese medicinal herb, used in synthesis of carvone, dissolve polystyrene, insect repellant
Linalool, C10H18O
Menthone, C10H18O
Mercaptomenthone, 8-Mercaptomenthone, C10H18OS
Myrcene, C10H16
Myrtenal, C10H14O, in cumin seed, juniper berry, pepper, peppermint, scotch spearmint.
Pinene, C10H16, from stem of Canarium tramdenanum
Pulegone, C10H16O, in Schizonepeta tenuifalia
Rose oxide, C10H18O
Sabinene hydrate, 4-Thujanol, C10H18O
Terpinene, gamma terpinene, C10H16
Terpineol, C10H18O, α-terpineol, from pine oil
Terpinoline, C10H16, flavour and fragrance agent
Terpinyl acetate, C12H20O2, oleoresin from pine oil
Terpyridine, C15H11N3, tridentate ligand
Verbenone, C10H14O

2. Terpenes are found in the following substances:
2.1 Essential oils that are monoterpenes and sesquiterpenes volatile at room temperature, e.g. eucalyptol, citronella, (citrus oils), and
eugenol, (oil of cloves).
2.2 Herbs and spices containing terpinene oil.
2.3 Perfumes that contain aromatic terpenes, and resins, 20-carbon diterpenes and 30-carbon triterpenes.
2.4 Lutein and zeaxanthin are the only xanthophylls found in human serum.
Fucoxanthin is found in brown algae. Isoprene units, (C5H8)
Terpenes are unsaturated hydrocarbons formed by the polymerization of 5-carbon isoprene units .
An isoprene unit has a four carbon chain and a one carbon branch at C2.
Different structural forms are called isomers.
Isoprene: [2-methyl-1,3-butadiene], [CH2=C(CH3)CH=CH2], (C5H8)
Isoprenoids are compounds derived from isoprene, often
showing repeated occurrence of isoprene units.
Terpenes have linked isoprene units that occur in natural rubber. Hemiterpenes, (one isoprene unit), (C5H8)
 Prenol hemiterpenoids, prenols are alcohols of general formula H-[CH2C(Me)=CHCH2]nOH
in which the carbon skeleton is composed of one or more isoprene units.
So terpenes can be defined as a class of compounds composed of repeating 5-carbon units of hemiterpenes. Monoterpenes, (two isoprene units), (C10H16)
Monoterpenes, (C10H16), Monoterpenes include α-pinene in turpentine, (pine needles flavour), α-thujene,
β-linene,  camphor C10H16O, citronellal C10H18O, (aldehyde), citronellol, eucalyptol, geraniol, (rose flavour), myrcene, [menthol, (-)
C10H20O, hexahydrothymol, peppermint camphor (a methyl cyclohexanol), (mint flavour, peppermint flavour)].
Anethole, (anise flavour), 4-Propenylanisole,
C10H12O, CH3CH=CHC6H4OCH3, p-methyoxypropenylbenzene, trans-1-Methoxy-4-(1-propenyl)benzene,
trans-1-Methoxy-4-(prop-1-enyl)benzene, isomer estragole, occurs in anise, anise myrtle, fennel, star anise.
Anise, aniseed, oil of aniseed from Pimpinella anisum is used in absinthe, anisette, (anis), arak, champurrado, (atole de anis), ouzo,
pastis, Pernod, raki, sambuca and some root beers.
Thujone, ketone, monoterpene, menthol odour, in oil of wormwood, from (Artemisia absinthium), used in the alcoholic drink absinthe,
Thymol,  C10H14O,  is used as a topical antifungal,  from Thymus vulgaris, (thyme), and  Origanum vulgare. Terpinenes, (cyclic terpenes)
Terpinenes, (C10H16), Terpinenes are cyclic terpenes and occur as three isomers:
1. α-terpinene is an oil with a lemon smell.
It occurs in cardamom, coriander, and marjoram.
2. β-terpinene occurs in oil of savin.
3. γ-terpinene occurs in coriander, cumin, lemon, samphire.
It can be formed from the action of alcoholic sulfuric acid solution on pinene from turpentine. Sesquiterpenes, (three isoprene units)
Sesquiterpenes C15, C15H24 Abscisic acid, C15H20O4
chamazulene, (chamomile oil), curcumene
Eugenol, Clove oil, oil of clove
eugenol [C6H3(OH)(OCH3)(CH2CH=CH2)], (in oil of cloves, cinnamon leaf oil, West Indian Bay oil), farnesene
farnesol, (in citronella, chamomile oil, oil of neroli petate, cyclamen, lemon grass, tuberose, rose, musk, and balsam), frankincense
geosmin, C12H22O, is a degraded sesquiterpene
nerolidol, (in neroli, ginger, jasmine, lavender, tea tree and lemon grass), oleoresin
β-Selinene, in celery oil
turpentine --> rosin
zingiberene, (in ginger) Geosmin
The degraded sesquiterpene geosmin, C12H22O, is produced by Streptomycesis species and blue-green algae, causes the  "earth
smell" after rain. Diterpenes, (four isoprene units), C20H32
Diterpenes, C20H32, have four isoprene units, e.g. steviol C20H30O3, from Stevia rebaudiana, artificial sweetener
Diterpenes C20, (4 isoprene units), C20H32, in resins, pine turpentine, distilled essential oil,
casbene, (disease resistance),
crocin, (in saffron),
cembrene phytol, a building block of the chlorophyll molecule
dehydroleucodine, (medicine from Artemisia douglasiana),
gibberellins, (phytohormones and germination), gibberellin A1, gibberellin plant hormones.(stem elongation),
podocarpic acid, (disease resistance),
retinol, (vitamin A activity),
taxadiene, taxol, (in yew tree bark, anticancer),
trisporic acid, (fungal hormones). Sesterterpenes, (five isoprene units)
Sesterterpenes, C25, insect waxes, fungi products, phytotoxins, geranyl, farnesol, ceroplastol, insect gascardic acid Triterpenes, (six isoprene units), (C30H48)
Triterpenes C30, steroids and sterols
Ambrein, C30H52O, a triterpene alcohol, is the main constituent of ambergris found in the sperm whales or floating on the sea as whale
barf (vomit), whale spit.
It is supposed to protect the intestines of whales from the sharp beaks of cuttlefish.
It was used for food flavouring and in the perfume industry to prevent scent from dissipating too quickly.
Since 1970 the perfume industry has turned to substitutes to protect whales.
It is supposed to be an aphrodisiac.
Saponins are toxic glycosides forming frothy colloidal solutions in water when agitated in water.
Although they cause breakdown of red blood cells some saponins have been discovered in traditional medicines, e.g. in the
Maesa balansae plant in Vietnam used to treat leishmaniasis. Saponins that foam in water occur in the horse chestnut,
Aesculus hippocastanum.
One triterpene saponin has formula C30H48O4.
sterols, (steroids) in animal sex hormones, squalene, (in shark liver oil), cephalosporin, gonane, hopane, diplotene, lupeole
Squalene, in liver oil of sharks
Tests for saponins
Add ground plant material to test-tube of water, heat to boiling, add stopper and shake the test-tube.
Note presence of stable froth. Tetraterpenes, (eight isoprene units), C40H56, carotenoid pigments
Tetraterpenes are terpenes with 8 isoprene subunits, (C40H64) lycopene, α-carotene and β-carotene, their derivatives the tetraterpenoids
are terpenoids of 8 isoprene units, 40 carbon atoms in the skeleton.
Terpenoids, similar to terpenes are the largest group of natural products and are responsible for many scents and flavours, e.g. citral,
menthol, camphor, salvinorin A in Salvia divinorum, and cannabinoids in Cannabis.
Carotenoid pigments are tetraterpenoids derived from the acyclic parent carotene.
They occur in chloroplasts of plants and in some algae.
Carotenoids are divided into 1. Carotenes, hydrocarbons only that contain no oxygen, and 2. Xanthophylls, that contain oxygen,yellow
pigments in the leaves of most plants.
Carotenoids absorb blue light.
Carotenoid pigments are tetraterpenoids derived from the acyclic parent carotene. They occur in chloroplasts of plants and in some algae.
Carotenoids are yellow, orange, or red fat-soluble plant and animal pigments,with molecular formula C40H56.
Many tropical fruits can be considered a reservoir of bioactive substances with a special interest due to their possible health-promoting
The interest in carotenoids from a nutritional standpoint has recently greatly increased, because of their alleged important health benefits,
perhaps as antioxidants.
Carotenoid pigments are usually red, orange, or yellow, e.g. carotene in carrots.
Carotenoids have two six-carbon rings connected by a chain of carbon atoms.
They do not dissolve in water and are attached to cell membranes.
Carotenoids are called accessory pigments because they pass their absorbed energy from sunlight to chlorophyll.
The accessory pigment fucoxanthin is the brown pigment in brown algae and diatoms.
Carotenoids include 1. alpha-carotene, beta-carotene, beta-cryptoxanthin, are provitamin A carotenoids, which we can convert to retinol
(vitamin A), 2. lutein, zeaxanthin, and lycopene (in tomatoes).
Lutein and zeaxanthin, (from spinach, kale, and broccoli), are in the retina and lens of the eye. The carotenoid beta-carotene may
decrease sensitivity to the sun. Polyterpenes, (thousands of isoprene units)
Polyterpenes contain thousands of C5H8 isoprene subunits in milky latex sap
5.1 Natural rubber, (C5H8)n, [n = 4,0005,000], (Hevea brasiliensis), and (Ficus elastica)
5.2 Gutta-percha, (Palaquium gutta)
5.3 Chicle polyterpene from the sapodilla tree, (Manilkara zapota), used for chewing gums. Carotenes
Carotenes are hydrocarbon carotenoids, a subclass of tetraterpenes and C5n polyterpenes. Vitamins
1. α-carotene, (C40H56)
2. β-carotene, (C40H56), is a precursor to be digested to form the antioxidant vitamin A, (C20H28O), retinol.
α-carotene and yellow pigment β-carotene are in carrot roots and ripe tomato fruits.
Commercial: β-Carotene, Type I, synthetic, 93% (UV), powder, β,β-Carotene, Provitamin A, C40H56
Commercial: β-Carotene, Type II, synthetic, 95% (HPLC), crystalline, β,β-Carotene, Provitamin A, C40H56
Commercial: β-Carotene, 95%, trans-β-Carotene, Provitamin A, C40H56
Commercial: β-Carotene, 97.0% (UV), β,β-Carotene, Provitamin A, C40H56
3. δ-carotene, (C40H56)
4. Lycopene is a bright red carotene and carotenoid pigment, in ripe tomato, carrots, bell peppers, watermelons, papaya, (C40H56)
E160d Lycopene, (carotenoid), (from tomatoes, pink grapefruit), (colour: red), (may decrease risk of cancer)
Commercial: Lycopene, 90%, from tomato, ψ,ψ-Carotene, "Octamethyl-dotriaconta-tridecaene", C40H56
Lycopene is a antioxidant micronutrient of tomatoes associated with decreased risk for cancer and cardiovascular disease.
It inhibits cholesterol synthesis and enhances low-density lipoprotein degradation.
Plants rich in carotenes
Sweet potato, (red variety), (9,507 μg in 100 g), Kale, (9,226 μg in 100 g), Carrot, (8,285 μg in 100 g), Mustard greens, (6,300 μg
in 100 g), Spinach, (5,626 μg in 100 g), Dried basil, (5,584 μg in 100 g), Butternut squash, (4,570 μg in 100 g), Lettuce, (red leaf
variety), (4,495 μg in 100g). Xanthophylls
1. Astaxanthin is in the red pigment of exoskeletons of lobsters and in egg yolks, (C40H52O4)
2. Canthaxanthin, terpenoid, E161g, (C40H52O2)
3. Flavoxanthin, yellow xanthophyll pigment, E161a, (C40H56O3)
4. Phytoene, (C40H64)
5. Rhodoxanthin, purple xanthophyll pigment, in Taxus baccata, E161f , (C40H50O2)
6. Rubixanthin, natural yellow 27, red-orange xanthophyll pigment, in rose hips, E161d, (C40H56O)
7. Staphyloxanthin, produced Staphylococcus aureus, "golden staph", C51H78O8
8. Violaxanthin, orange xanthophyll pigment, in pansy, E161e, (C40H56O4)
9. Zeaxanthin, most common carotenoid, causes yellow colour of corn, (maize), kernels, (Zea mays), paprika from bell peppers, saffron,
10. Xanthophylls are oxygenated carotenoids, the yellow leaf pigments of leave, synthesized within plastids without need for light for
synthesis, but do absorb some wavelengths not absorbed by chlorophyll, so appear in etiolated leaves and plants with chlorosis nutrient
Astaxanthin in red fish, fruits and vegetables, is an antioxidant that may be anti-inflammatory, prevents Alzheimers disease, cold and
influenza, protect the iris from sunlight and protect skin cells from ultraviolet rays.
Canthaxanthin in algae, lobsters, fish and chanterelle mushrooms is an antioxidant that may protect cells from ultraviolet rays.
It may be an ingredient in sunless tanning products but this can be very dangerous.
Cryptoxanthin in yellow maize, orange and red pumpkins and chillies is an antioxidant that may improve vision and night vision and
bone growth and prevent arthritis.
Deficiency may cause dry skin, and vision problems.
Lutein it in the macula lutea, the oval shaped yellow spot near the centre of the retina, from green vegetables, is an antioxidant that may
help pregnant and lactating women and prevent atherosclerosis and damage from ultraviolet rays.
Consuming too much lutein causes carotenemia, orange skin.
Zeaxanthin from yellow maize, green vegetables.
Also, part of the macula lutea, is an antioxidant that may prevent macular degeneration and cataracts.
Zeaxanthin has a hydroxy function at each end group. Terpenoids
Terpenoids including terpenes, diterpenes, sesquiterpenes and others, have formula (C5H8)n, andmolecules composed of linked
isoprene units.
Terpenoids are terpenes modified by oxidation or rearrangement of the carbon skeleton.
Terpenoids are natural products and related compounds derived from isoprene units.
They contain oxygen in various functional groups and are subdivided as follows:
1. C10 Monoterpenoids
Iridoids are cyclic monoterpenoids having the iridane skeleton, (1-isopropyl-2,3-dimethylcyclopentane)
2. C15 Sesquiterpenoids
3. C20 Diterpenoids
4. C25 Sesterterpenoids
5. C30 Triterpenoids
Steroids, sterols
6. C40 Tetraterpenoids
A terpin, called a crystalline hydrate, C6H10(CH3)3(OH)2, is formed from acidification of alpha pinene.
Terpineols, C10H17OH, are used in lilac perfume. Tetrapyrroles, related compounds
See diagram Bilin, haeme (heme) | See diagram Haeme (heme) | See diagram Tetrapyrroles
Tetrapyrroles are natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to
position 5 of the next pyrrole ring.
Porphyrins are macrocyclic tetrapyrroles, e.g. bilin, (a linear tetrapyrrole).
Tetrapyrroles have the following related compounds: haemin, haematin, haemoglobin, myoglobin, cytochromes, chlorophylls a and b,
bile pigments biliverdin and bilirubin, vitamin B12, bilin, in congenital disease polyphyria, tetrapyrrole derivative DPEP in geological
deposits possibly from chlorophyll, chlorin, (2,3-dihydroporphyrin).
Haeme, (heme), in haemoglobin, globular protein in animals, oxygen carriers
Haeme A, C49H56O6N4Fe, (cytochrome oxidase ligand complex) tetradentate ligand],
Haeme, Constituents of blood: 9.214 Porphyrins
See diagram Porphine | See diagram Porphyrins, porphine | See diagram Porphyrins (IUPAC)
Porphyrins are natural pigments containing a fundamental skeleton of four pyrrole nuclei united through the α-positions by four methine
groups to form a macrocyclic structure.
Porphyrins refers to any of a group of compounds containing the porphyrin structure of four pyrrole rings connected by methine
bridges in a cyclic configuration with usually metal side chains attached, e.g. with iron to form heme, (haeme).
Porphyrin chelates include haeme, in haemoglobin, bonded to iron (II) ion, and chlorophyll bonded to Mg (II) ion.
The heme component of the protein haemoglobin has four iron porphyrins.
Porphyrins occur in iron-containing cytochrome pigments in mitochondria in plants, animals and bacteria.
For oxidative phosphorylation, electron transport system, and ATP production. Photosynthetic pigments, chlorophyll a and chlorophyll b
See diagram: Chlorophyll a and chlorophyll b | See diagram Chlorophyll a
Chlorophyll a C55H72O5N4Mg and chlorophyll b C55H70O6N4Mg are magnesium porphyrins.
Invertebrates with green blood have copper porphyrins.
Colours, food colours, food additives E140 Chlorophylls and chlorophyllins (used to dye oils and wax in medicines and cosmetics)
Chlorophyll pigments are green.
The pigment chlorophyll a, (C55H72O5N4Mg), occurs in in plants, algae, and cyanobacteria.
The pigment chlorophyll b, (C55H70O6N4Mg), occurs only in green algae.
Chlorophyll pigments contain a porphyrin ring with electrons that move freely and be added to the ring or lost from the ring.
During photosynthesis, electrons become more energized by sunlight and can be passed on enable the process of sugar formation.
The pigment chlorophyll C occurs in photosynthetic Chromista and dinoflagellates.
E140 Chlorophylls and chlorophyllins, (colour: olive to dark green), (used to dye oils and wax in medicines and cosmetics)
E141 Copper complexes of chlorophylls and chlorophyllins, (colour: bright green) Legheamoglobin
Legheamoglobin, leghemoglobin, legoglobin) occurs in nitrogen-fixing bacteria in the root nodules of legumes.
It is an oxygen carrier and a hemoprotein, produced by legumes in response to the roots being infected by nitrogen-fixing bacteria,
like hemoglobin, it is red in colour.
The apoprotein is produced by the plant and the heme (an iron atom bound in a porphyrin ring) is also produced by the plant.
It stores enough oxygen to support nodule respiration for a few seconds.
Its function is to help transport oxygen to the respiring symbiotic bacterial cells, analogous to hemoglobin transporting oxygen to
respiring tissues in animals. Phycobiliproteins
Phycobiliproteins occur in cyanobacteria and red algae are composed of water-soluble phycobilin pigments and protein.
N-fixing cyanobacteria such as Anabaena azollae live symbiotically within leaf cavities of the water fern Azolla. Phycobilins
Phycobilins include the blue-green pigment phycocyanin and the red pigment phycoerythrin to enable red algae to be photosynthetically
efficient in deep water where blue light predominates.
Phycobilin pigments are soluble in water-soluble and occur in the cytoplasm and stroma of chloroplast.
They occur only in Cyanobacteria and Rhodophyta.
The blue green pigment phycocyanin occurs in the Cyanobacteria their name.
The red brown pigment phycoerythrin occurs in the red algae.
Phycobilin pigments absorb light energy that is passed on to other processes.
Pycocyanin and phycoerythrin fluoresce are fluorescent. Phytochromes
Phytochromes are phycobilin-protein pigments involved in floral induction.
activated by the length of day, hours of darkness. Polyvinyl pyrrolidene, povidone, PVP
See diagram Povidone, PVP
Polyvinyl pyrrolidene, povidone, PVP, is a water-soluble polymer, E1201, used as a coating or binder in medical tablets,
e.g. povidone-iodine complex (PVD-iodine) in the antiseptic "Betadine", that nowadays has replaced tincture of iodine solution in
medicine. Steroids, sterols, steroid alcohols, natural steroids
| See diagram Steroids
| See diagram Cholesterol, cholic acid, bile salt, estradiol, progesterone, northindrone,
RU 486, (mifepristone), testosterone, androsterone, cortisone
The sterols, (steroid alcohols), androstane steroids, (testosterone), C20 steroids, 19-norpregnane, pregnane steroids, (progesterone).
Steroids are naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially
or completely hydrogenated, and usually with methyl groups at C-10 and C-13, and an alkyl group at C-17.
atural steroids are derived biogenetically from triterpenoids.
Sterols are natural products derived from the steroid skeleton and containing a hydroxy group in the 3 position, closely related to
Steroids have a saturated 4 ring steroid structure.
Steroids include sex hormones, coricosteroid hormones, cardiac glycosides, bile acids, cholesterol lanosterol, (animal sterols),
β-sitosteron, (plant sterol), ergosterol, (fungus sterol), estrogen, cardiac glucosides, diosgenin, androstane, 19-norpregnane,
7-dehydrocholesterol, previtamin D3, ergocalciferol, (vitamin D2), cholecalciferol, (vitamin D3).

23.6.1 Natural rubber
Natural rubber, (C5H8)n, [n = 4,0005,000], (Hevea brasiliensis), and (Ficus elastica)
Polyisoprene, elastomer, diene polymer, natural rubber is mainly cis-1,4-polyisprene, from Hevea brasiliensis, main monomer isoprene,
-CH2=C(CH3)CH=CH2-, 2-methyl-1,3-butadiene, also made synthetically, cis polyisoprene, isoprene rubber.
Gutta-percha is mainly trans-1,4-polyisprene.
1. Natural polymers occur as brittle glassy gums and resins in plants, e.g. conifers, and as polysaccharides, e.g. starch.
Natural rubber, para rubber, hevea rubber obtained from the milky latex sap of Hevea braziliensis, Euphorbiaceae, contains
polyterpenes with linked isoprene units CH2=C(CH3)CH=CH2, [cis-1,4-polyisoprene], in which all the -CH=CH-= groups are cis.

2. The polymer chains in natural rubber are elastic in the sense that the chains can be unravelled without coming apart, i.e. the rubber
can stretch.
Elasticity was improved by cross-linking with sulfur, using the Goodyear process to produce vulcanized rubber.
Stretching aligns the random chains, and temporarily crystallizes and toughens rubber, so that rubber tyres do not form cracks.
Natural rubber is not very elastic in the Hooke's law sense of stress being proportional to strain.
The transisoprene polymer, trans-1,4-polyisoprene, occurs in tropical trees in the latex of Palaquium oblongifolium, Sapotaceae
family,  the same chemical as natural rubber, polyisoprene, but with trans not cis bonding.

3. Test for strength of cross-linkages, add toluene then measure the increase in volume.
Rubber bands are made mostly of natural rubber cured by heat.
Petrol can dissolve the cross-linkages between the polyisoprene molecules to allow water molecules to move in between them and swell
the rubber band.

4. Hard rubber was made by Charles Goodyear and shown at the 1851 exhibition at Crystal Palace, London.
During the vulcanization process, 30-40% sulphur is added to the natural rubber to form a compound with high dielectric power,
high resistance to chemical products, hardness and rigidity up to 50C,
and a bright shiny appearance.
It is processed with extruders then worked on machines or compression moulds to make battery separators, telephone receivers, tyres.

23.6.2 Latex plants
Latex is an emulsion of rubber globules in water, found in latex paints, male latex condom, and latex tubing.
1. Ficus elastica, Indian rubber plant, India rubber tree, [polyterpenes in milky latex sap], Moraceae
2. Hevea braziliensis, natural rubber, para rubber, hevea rubber, [polyterpenes with linked isoprene units, cis-1,4-polyisoprene, in milky
latex sap], Euphorbiaceae
3. Manilkara achras, sapodilla, chiku, chicle polyterpene, Mexico, South America, desert fruit, latex chicle used, chewing gum,
4. Manilkara bidentata, balata, latex used for non-elastic rubber, sticky pulp eaten, Sapotaceae
5. Palaquium oblongifolium, latex called gutta-percha, polymer, natural trans-1.4-polyisoprene, the same chemical as natural rubber,
polyisoprene, but with trans not cis bonding, Sapotaceae.

23.6.3 Negative thermal expansion (NTE) of rubber, entropy,
Negative thermal expansion (NTE) materials contract on heating within certain temperature ranges.
They are not called "thermal contraction" materials.
When the long polymer chains in rubber absorb energy, they adopt a more contorted configuration, reducing the volume of the material,
so a rubber band contracts on heating.
A cooled rubber band, becomes stretchier and expands slightly because the molecules become more organized into a more efficient
stretching shape.
A common explanation of this phenomenon is that the arrangement of long polymer chains in rubber is like a ball of mixed up threads
of string.
By grabbing hold of each end of the tangle and pulling it in opposite directions, the threads of string become more horizontal as the
ball of string is elongated.
So the arrangement of threads becomes more ordered and the entropy of the system becomes lower.
Reduced entropy, more orderly alignment of molecules, causes the rubber band to lose heat.
A stretched rubber band feels hotter as it expands with heat lost in an exothermic process.
A contracting rubber band feels cooler with heat gained in an endothermic process.
The particles making up rubber in its natural state are more disordered than when the rubber is stretched and is under tension.
When tension is removed the rubber contracts back with the particles returning to their initial disordered state.
Entropy is a measure of the amount of disorder in a system, so the entropy of a rubber band increases when it changes from a stretched
state to a natural state.
The change of entropy of a system in a reversible process = the amount of heat absorbed or emitted / absolute temperature of the

23.6.4 Heat and cool rubber bands, rubber band heat engine
See diagram 23.6.4: Test heated rubber bands
1. To demonstrate the effect of heating rubber bands, stretch a rubber band around a wooden box.
Cut out an arrow shape from a piece of cardboard.
Mount the arrow on a pin and then push the pin under the middle of the elastic band.
If the elastic band is heated at the left of the pin, it contracts, pulling the pin towards it and the point of the arrow moves to the right.
2. Rubber band heat engine is a bicycle wheel with rubber bands instead of spokes.
Set up the bicycle wheel vertically.
Rubber contracts on heating so a lamp or a hair dryer placed on one side of the wheel shift the centre of gravity, resulting in rotation.
Cooler rubber spokes move into the irradiated region to repeat the process.
To achieve a smoother rotation the wheel is balanced using small pieces of Plasticine placed around the rim.
3. To make more space in a freezer, you might collect scattered items, e.g. ice lollies,
and put an elastic band around them .
However, after some time the originally stretched elastic band become loose and slacker, than when first applied to the ice lollies at
room temperature.
4. To observe the thermal properties of rubber, hang a 1 kg mass from four rubber bands, so it touches the table.
Heat with a radiant heater for 20 seconds and the mass will lift.
Enclose a rubber tube in a copper cylinder and heat with a Bunsen burner.
The rubber tubing contracts as it is heated.
Stretch and unstretch rubber bands on the lips to feel the changes in temperature.

23.6.5 Stretch rubber bands
1. Stretch a thick rubber bandit (> 0.5 cm wide) quickly against the forehead, lips, or wrist and note the increase in temperature.
Hold it stretched, allow it to cool back to room temperature.
Then let it suddenly contract against the lips to its original length and note the temperature drop.
2. Use a hair dryer to heat a stretched rubber band, e.g. 1 cm wide, with a weight on the end, e.g. 2 kg.
3. Stretch a wide rubber band between the index finger of your two hands.
Let the rubber band touch the lips.
Stretch the rubber band (not so far that it breaks!) then slowly release the tension.
Feel heat in your lips when the rubber band stretches because of friction between the rubber molecules.
The stretched rubber band feels cooler when the tension is released.
4. Hold each end of the rubber band with the fingers of your hands,
press your lips firmly to the middle of the rubber band,
and maintain contact as you quickly stretch the rubber band in opposite directions outward.
Your lips you will feel a sudden heat from the rubber band.
5. Suspend a 100 g weight from a rubber band attached to a clamp stand.
Adjust the height of the 100 g weight until it just touches the table.
Use a vertical ruler to measure the length of the suspended rubber band.
Bring a heat source, e.g. a lighted match or hair dryer close to the middle of the stretched rubber band.
Note that the heated rubber band contracts.