School Science Lessons
Topic 16a Chemistry of natural products
2009-11-12
Please send comments to: J.Elfick@uq.edu.au
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See: IUPAC, Nomenclature of Organic Chemistry (website)
See: IUPAC Gold Book (website)
Table of contents
16.3.0 Chemistry of natural products
16.3.1 Aliphatic products
16.3.1.1 Carbohydrates
16.3.4.0 Aromatics, aromatic compounds, benzene derivatives, ring systems, arenes: benzene, toluene, naphthalene
16.3.4.1 Benzofuranoids, benzopyranoids
16.3.6.0 Proteins, peptides, amino acids
16.3.6.2 Amines and alkaloids
16.3.6.3 Glycoproteins
16.3.6.4 Alkaloids produced by plants from amino acids
16.4.1 Vitamins
16.10.0 Breakdown large molecules to smaller molecules
16.14.0 Dioxins
Topic 19 Chemical reactions in the home, composition of food, cooking
Appendix 7: Prefixes and suffixes
9.3.11.0 Food, food tests
16.3.1 Aliphatic products
16.3.1.1 Carbohydrates
16.3.1.1a Sugars
9.140 Tests for simple sugars, reducing sugars, Fehling's test
12.18.5.1a Dehydration of sugar by sulfuric acid
16.3.1.3 Monosaccharides
16.3.1.3.1 Left-handed and right-handed structural forms, D and L sugars
16.3.1.4.0 Disaccharides
16.3.1.4.1 Trisaccharides
16.3.1.4.2 Tetrasaccharides
16.3.1.4.3 Polysaccharides
16.3.1.4a Reducing sugars and nonreducing sugars
16.3.1.4.1 Reducing sugars and nonreducing sugars
16.3.1.5 Starches, amylum, glycogen
16.3.1.6 Cellulose, hemicellulose
16.3.1.7 Chitin
16.3.1.8 Pectin
16.3.2.1 Cyclitols, inositols, myo-innositol
16.3.2.2 Carbohydrate acids, D-gluconic acid, D-glucuronic acid
16.3.2.3 Alditols, polyhydric alcohols, mannitol
16.3.2.4 Glycosaminoglycans (mucopolysaccharides) glucosamines
16.3.2.5 Phenolic compounds
16.3.2.6 Glycosides
16.3.2.6.1 Glucoside
16.3.2.7 Polyketides, polyketide antibiotics, aflotoxins
16.3.2.8 Nucleosides, nucleic acids, DNA (deoxyribonucleic acid) RNA (ribonucleac acid)
4.4.01 Structure of DNA and RNA
16.3.2.9 Polysaccharide gums
16.3.3.0 Lipids, fats and oils, fatty acids, glycerides
15.1 Fatty acids in coconut oil and other oils
16.3.3.0.1 Phospholipids (phosphoglycerides)
16.3.3.0.2 Fixed oils
16.3.3.0.3 Essential oils, volatile oils, ethereal oils
16.3.6.4 Alkaloids produced by plants from amino acids
16.3.3.0.4 Lipids
16.3.3.0.5 Glycerides, esters of glycerol
16.3.3.0.6 Fatty acids
16.3.3.1 Waxes
16.3.4.0 Aromatic compounds, benzene derivatives, ring systems, arenes: benzene, toluene, naphthalene
16.3.4.0a Aryl groups
16.3.4.0b Aramids
16.3.4.0.1 Aromatic hydrocarbons, e.g. benzene (C6H6)
16.3.4.0.2 Aromatic nitro compounds, e.g. nitrobenzene (C6H5NO2)
16.3.4.0.3 Lactams (-NH(CO-), e.g. caprolactam (6-hexanelactam) (C6H11NO)
16.3.4.0.4 Aromatic amines, anilides, e.g. phenylamine (aniline, amino benzene) (C6H5NH2)
16.3.4.0.5 Diazo compounds
16.3.4.0.5a Barbiturates
16.3.4.0.5b Benzodiazepines
16.3.4.0.6 Aromatic halogen compounds, aryl halide, halogenarenes, e.g. benzyl chloride (C6H5COCl)
16.3.4.0.7 Aromatic sulfonic acids, e.g. benzene sulfonic acid (C6H5SO2OH) sodium benzene sulfonate
16.1.3.2 Phenols, group: (OH-C), in a benzene ring, phenol = (C6H5O6)
16.3.4.0.9 Aromatic alcohols, e.g. phenyl methanol (benzyl alcohol) (C6H5CH2OH)
16.3.4.0.10 Aromatic aldehydes and ketones, e.g. benzaldehyde (C6H5CHO) acetophenone
16.3.4.0.11 Aromatic acids and their derivatives, e.g. benzoic acid (C6H5COOH)
16.8.1 Reactions of benzene
16.8.2 Prepare ferric tannate with tea leaves
16.8.3 Extraction of caffeine and benzoic acid from soft drinks, e.g. cola and lemonade
3.33.0 Food tests
3.99 Gases from wood
9.127 Elements in foods
9.128 Heat different foods
9.129 Hydrolysis of starch by dilute hydrochloric acid
9.130 Hydrolysis of starch by salivary amylase (ptyalin)
9.131 Hydrolysis of sucrose by dilute acids
12.18.5.1a Dehydration of sugar by sulfuric acid
9.132 Iodine test for starch in parts of plants
9.133 Tests for aldehydes in solution, Fehling's test
9.177 Iodine test for starch in potato tuber cells
9.134 Solubility of carbohydrates in water, vitamin C (ascorbic acid)
9.135 Iodine test for cellulose
9.136 Solubility test for cellulose
9.137 Tests for fats and oils, paper test, Sudan (III) test, solubility test, osmic acid test
9.138 Tests for nitrogen compounds in food, soda lime test
9.139 Tests for proteins, biuret reaction, Millon's reagent, xanthoproteic reaction
9.140 Tests for reducing sugars and aldehydes, test for simple sugars, Fehling's test
9.141 Tests for reducing sugars, Benedict's test for reducing sugars, urine test
9.142 Tests for starch, Fehling's test for starch
9.143 Tests for vitamin C (L-ascorbic acid)
9.144 Tests for wood
9.182 Tests for glucose and starch with "Testape"
16.3.1.6 Tests for wood, hemicellulose, lignin,
16.4.5 Tests for fats, proportion of fats in foods
16.7.15 Commercially available test reagents
16.7.16 Artificial sweeteners
16.9.1 Burn carbohydrates, fats and proteins
16.9.2 Heat food with copper (II) oxide
2.34 Three kinds of food (Primary)
16.10.0 Breakdown large molecules to smaller molecules
16.10.1 Breakdown starch to sugars, hydrolysis of starch, iodine test, Fehling's test
16.10.2 Breakdown of sugar with yeast
16.10.4 Prepare wood gas and wood tar
16.10.4.1 Distil wood (destructive distillation)
10.6.3 Distil crude oil and collect the fractions
19.2.0 Composition of food, vitamins, minerals
19.2.1.8 Omega-3 fatty acids
19.2.1.9 Free radicals
19.2.1.10 Margarine
19.4.3 Margarine label
19.2.1.11 Coconut oil
19.2.1.12 Fish oils
19.2.1.13 Ice-cream
19.1.1.14 Chocolate
16.3.3.1 Waxes
16.3.4.1 Benzofuranoids, benzopyranoids
16.3.4.1a Benzofuranoids, benzopyranoids
16.3.4.1b Earth smells, rain smells and cut grass smells, geosmin
16.3.4.2 Flavonoids, betaines, flavones, anthocyanin, flavonols, flavanones, flavans, chalcones
16.3.4.3 Tannins (kinotannic acid) plant polyphenols, phenolic polymers: polyphenols galloyl ester, vescalagins
16.3.4.4 Lignans, plant phenols
16.3.4.5 Five member heterocycles
16.3.5.0 Porphyrins, pyrroles, polypyrroles, tetrapyrroles, haemes (haems, hemes) terpenoids, retinoids
16.3.5.1 Terpenes, monoterpenes, terpinenes, sesquiterpenes, diterpenes, sesterterpenes, triterpenes, tetraterpenes, terpenoids, oleoresins
16.3.5.2 Tetrapyrroles, porphyrins (haem, heme) chlorophyll, legheamoglobin, phycobiliproteins, phycobilins, phytochromes, polyvinyl pyrrolidene
16.3.5.3 Steroids, sterols, steroid alcohols
16.3.6.0 Proteins, peptides, amino acids
16.3.6.0.1 Structural forms of proteins
16.3.6.0.2 Fibrous proteins and globular proteins, collagen, peptides and polypeptides
16.3.6.0.3 Prions, "Mad cow disease"
16.3.6.1 Amino acids
16.3.6.1.1 Amino acid nomenclature
16.3.6.1.2 Table of the 20 alpha amino acids
16.3.6.1.3 Methanoic acid (formic acid) ionization reaction
16.3.6.1.4 Ethanoic acid (acetic acid) ionization reaction
16.3.6.1.5 Propanoic acid (propionic acid) ionization reaction
16.3.6.1.6 Butanoic acid (butyric acid)
16.3.6.1.7 Pentanoic acid (valeric acid)
16.3.6.1.8 Butanedioic acid (succinic acid)
16.3.6.2 Amines and alkaloids
16.3.6.3 Glycoproteins
16.3.6.4 Alkaloids produced by plants from amino acids
16.3.5.1 Terpenes
16.3.5.1.1 Monoterpenes, C10 (2 isoprene units) (C10H16)
16.3.5.1.2 Terpinenes (C10H16)
16.3.5.1.3 Sesquiterpenes C15 (3 isoprene units) C15H24
16.3.5.1.4 Diterpenes C20 (4 isoprene units) C20H32
16.3.5.1.5 Sesterterpenes, C25 (5 isoprene units)
16.3.5.1.6 Triterpenes C30 (6 isoprene units) steroids and sterols
16.3.5.1.8 Tetraterpenes C40 (8 isoprene units) C40H56
16.3.5.1.9 Terpenoids
16.3.5.1.10 Oleoresins "gums"
16.3.5.2 Tetrapyrroles
16.3.5.2.1 Tetrapyrroles
16.3.5.2.2 Porphyrins
16.3.5.2.3 Chlorophyll a and chlorophyll b
16.3.5.2.4 Legheamoglobin
16.3.5.2.5 Phycobiliproteins, Anabaena azollae, the water fern Azolla.
16.3.5.2.6 Phycobilins, phycocyanin, phycoerythrin
16.3.5.2.7 Phytochromes
16.3.5.2.8 Polyvinyl pyrrolidene, povidone, PVP-iodine complex
16.3.6.2 Amines and alkaloids
1.1.0A Pyridine-piperidine group
1.2.0A Tropane group, tropine group
1.2.1A Pyrrolizidine group
1.3.0A Isoquinoline group
1.4.0A Quinolizidine group
1.5.0A Quinoline group
1.6.0A Phenethylamine group
1.7.0A Indole group
1.8.0A Indolizidine group
1.9.0A Steroidal group
1.10.0A Purine group
1.11.0A Thiazole group
1.12.0A Capsaicin group
1.13.0A Ephedrine group
1.14.0A Muscarine group
16.4.1 Vitamins
Previously, vitamins ("vita amines") were erroneously thought to contain amines.
16.4.1.1a Vitamin A
16.4.1.2 Vitamin B1
16.4.1.3 Vitamin C (ascorbic acid)
16.4.1.4 Vitamin D
16.4.1.5 Vitamin E
16.3.1 Aliphatic products
Aliphatic compounds describes all organic compounds that are not aromatic compounds, i.e. cyclic. They are alkanes or alkenes or alkynes or derivatives of them. They include complicated chemical compounds, e.g. seriochemicals sex tannins (attractants, pheromes) ticks: 2,6-dichlorophenol, butterfly: 7-dodecenyl acetate, human: 5 alpha-androst-16-en-3-one.
16.3.1.1 Carbohydrates
Monosaccharides, aldoses and ketoses, disaccharides, oligosaccharides, polysaccharides, chitin, branch chain sugars
Carbohydrates were at first compounds such as aldoses and ketoses, with the stoichiometric formula Cn(H2O)n, so "hydrates of carbon". Nowadays, carbohydrates include monosaccharides, oligosaccharides and polysaccharides, and substances made 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.
16.3.1.1a Sugars
The term sugars generally refers to monosaccharides and lower oligosaccharides. Monosaccharides cannot be split into smaller molecules by using dilute acids. They cannot be hydrolysed to simpler compounds.
1. aldoses with an aldehyde group, -CHO, i.e. a carbonyl, group, C=O, with a hydrogen atom attached to the the carbon atom, e.g. glucose, or
2. ketoses with a ketone group, e.g. fructose.
A ketone group is a carbonyl group, C=O, with two single bonds to other carbon atoms. Monosaccharides can have a straight chain form or ring form. Polysaccharides are compounds with more than ten monosaccharides linked by glycosidic bonds, usually between C1 on one sugar and C4 on the other sugar by removal of a water molecule, i.e. a condensation reaction.
A ketose is a sugar containing one ketone group per molecule. The triose has 3 carbon atoms. The tetrose erythrulose has 4 carbon atoms. The pentoses ribulose and xylulose have 5 carbon atoms. The hexoses psicose, sorbose and tagatose have 6 carbon atoms. An aldose is a sugar containing one aldehyde group per molecule and has the chemical formula C3nH6nO3n. The triose glyceraldehyde has 3 carbon atoms. The tetroses erythrose and threose have 4 carbon atoms. The pentoses ribose, arabinose, xylose, lyxose have 5 carbon atoms. The hexoses allose, altrose, glucose, mannose, gulose, idose, galactose, talose have 6 carbon atoms.
16.3.1.3 Monosaccharides
See diagram 16.3.1.3a: Monosaccharides, D-sugars, L-sugars | See diagram 16.3.1.3b: Glucose molecule | See diagram 16.3.1.3Cch: Galactose | See diagram 16.3.1.3d: Fructose | See diagram 16.3.2.8.2: Ribose, deoxyribose, nucleotide
Monosaccharides contain a single sugar unit, e.g. glucose, fructose
Classification:
1. Number of C atoms:
2. Aldose or ketose
Aldose contains aldehyde group (-CHO) at C1, e.g. glyceraldehyde, (CHOCHOHCH2OH), the simplest aldose
Ketose, contains ketone group (-CO-) at C2, e.g. dihydroxyacetone, (CH2OHCOCH2OH), the simplest ketose
No. C Atoms
 Aldose
.
 Ketose
.
3 C
triose
 glyceraldehyde
.
 dihydroxyacetone
.
4 C tetrose
 erythrose,
threose		 erythrulose
.
5 C pentose
 arabinose, lyxose,
ribose, xylose		 ribulose,
xylulose
6 C hexose
 allose, altrose, galactose, glucose, gulose, idose, mannose, talose fructose, psicose, sorbose, tagatose
16.3.1.3.1 Left-handed and right-handed structural forms, D-sugars and L-sugars
See diagram 16.3.1.3a: 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. The cyclic form is shown by a Haworth projection, invented by W. N. Haworth. 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 upo in the Haworth projection for D-sugars, and down for L-sugars.
D-glucose can have alpha or beta forms, depending on the position of the hydroxyl group attached to C1, down in the alpha form and up in the beta form.
Most monosaccharoides 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 alpha-D-fructofuranose, -OH on C2 is down, and beta-D-fructofuranose, -OH on C2 is up.
16.3.1.4.0 Disaccharides, trisaccharides, tetrasaccharides, polysaccharides
See diagram 16.3.1.4a: Maltose molecule | See diagram 16.3.1.4b: Lactose molecule | See diagram 16.3.1.4c: Sucrose
Disaccharides contain two sugar units, e.g. sucrose (glucose + fructose), lactose (milk sugar, glucose + galactose), maltose (malt sugar, glucose + glucose)
16.3.1.4.1 Trisaccharides
Raffinose (triose: fructose + galactose + glucose) (C18H32O16), melezitose, maltotriose (amylotriose)
16.3.1.4.2 Tetrasaccharides
See diagram 16.3.1.4.2: Stachyose, acarbose
Acarbose (C25H43NO18) anti-diabetic drug
Stachyose (tetrose: fructose + galactose + glucose + galactose, i.e. raffinose + galactose) (C24H42O21) in green beans
16.3.1.4.3 Polysaccharides
Glycogen, Starch (Amylose, Amylopectin), Cellulose, Dextrin (C18H32O16), Beta-glucan (cellotriose, beta-D-glucan, glucan, C18H32O16)
Fructans
The molecules are linked by glycosidic bonds. Fructans occur in onion, asparagus, wheat.
1. Inulin - linear fructan
2. Levan - linear fructan
3. Graminan - branched fructan
16.3.1.4a Reducing sugars and nonreducing sugars
See 9.141: Benedict's test for reducing sugars
Reducing sugars: glucose, fructose, glyceraldehyde, lactose, arabinose (C5H10O5), turanose (C12H22O11), maltose.
Non-reducing sugars: Sucrose, trehalose (diglucose)
16.3.1.5 Starches, amylum, glycogen
See diagram 16.3.1.5a: Starch, amylose
(amylum) (amylose, soluble starch, many glucose units) (amylopectin, insoluble starch, 40 to 60 branched glucose units). Glycogen in animals. (Starch, amylum = amylose + amylopectin) (Glycogen = 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 beta-amylase, C6H10O5 that forms a complex with iodine: (beta-amylase)p (I-) (I2)r(H2O)s [where r < p < s].
16.3.1.6 Cellulose, hemicellulose
See diagram 16.3.1.6a: Cellulose, three glucose molecules linked to form cellulose
Cellulose is 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.
16.3.1.7 Chitin
See diagram 16.3.1.7a: 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,
16.3.1.8 Pectin
Pectin, high molecular weight, cements adjacent plant cells, dissolved by pectinase in ripening fruit, forms gel and thickening agent glycogen, chitin
16.3.2.1 Cyclitols, inositols, myo-innositol
16.3.2.2 Carbohydrate acids, D-gluconic acid, CH2(OH)(CHOH)4COOH, produced by fungi, D-glucuronic acid, OC6H9O6, in gums, forms glucuronides
16.3.2.3 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.
16.3.2.4 Glycosaminoglycans (mucopolysaccharides) glucosamines
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 osteoarthitis.
Heparin, Chondroitin sulfate, Hyaluronan, Heparan sulfate, Dermatan sulfate, Keratan sulfate
16.3.2.5 Phenolic compounds
Phenolic compounds: citronella, clove oil, coumarin (1,2-benzopyrone, C9H6O2) dicoumarin, eucalyptol, ubiquinone, urushiol, vanillin.
Phenolic polymers: tannins, lignin.
Flavours: eugenol (olive), cinnamaldehyde, (cinnamon, cassia), anethole (anise), thymol (thyme), carvacuol (oregano), estragola (tarragon), vanillin (vanilla)
16.3.2.6 Glycosides
Glycosides, antho pigments, resveratol, aminoglycosides, saponin glycosides, steroidal glycosides, mustard oil glycosides, cyanogenetic glycosides amygdalin, nightshade glycosides, cardiac glycosides: strophanthins, K-strophanthin, digoxin, ouabain (G-strophanthin) salicin glucoside digitonin, digitoxin, betacyanin (betalain) (Bougainvillea pigment)
16.3.2.6.1 A glucoside is a glycoside with a glucose sugar component.
Glycoside, glucoside: sugar + non-carbohydrate R, e.g. glucose + terpene, glucose + phenolic compound
Saponin glycosides, form soapy foam (from Chlorogalum)
Steroidal glycosides (sugar + steroid) (from Asclepias)
Mustard oil glycosides (from Brassica)
Cyanogenetic glycosides amygdalin (from apricot pits) salicin (from willow bark, Salix)
Nightshade glycosides: solanine (from Solanum)
Cardiac glycosides: (from oleander, Nerium) (digoxin, digitoxin from foxglove, Digitalis purpurea) (K-strophanthin and ouabain or G-strophanthin from Strophanthus)
Salicin glucoside digitonin, digitoxin
The cyanogenic glucoside linamarin occurs in the cells of cassava (Manihot esculanta) linseed (flax, Linum usitatissimum) and Lotus japonica.
The flavonoid glucoside icariin, C33H40O15, occurs in horny goat weed, Epimedium grandiflora, Berberidaceae, and is said to be an oriental aphrodisiac.
16.3.2.7 Polyketides, polyketide antibiotics, aflotoxins
Polyketides, polyketide antibiotics, streptomyces metabolites, erythromycin, linear tetracyclines, macrolides and lactones, erythromycin polyenes, nystatin, polyether antibiotics, aflotoxins, beta-lactams
Lactones are components of coconut aroma and peach aroma, e.g. octalactone.
16.3.2.8 Nucleosides, nucleic acids, DNA (deoxyribonucleic acid) RNA (ribonucleac acid)
Nucleosides, nucleic acids, nitrogenous bases: adenine, guanine, cytosine, thymine DNA, RNA, deoxy-D-ribose, D-ribose
See diagram 16.3.2.8: Nucleic acid, See diagram 16.21.10: Purines, See diagram 16.21.13: Pyrimidines
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. Nucleic acids do several functions in living cells, e.g., the storage of genetic information and its transfer from one generation to the next 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). RNA (ribonucleic acid) contains D-ribose, whereas DNA contains 2-deoxy-D-ribose as the sugar component. 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). 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. An oligonucleotide is a long linear sequences of nucleotides.
16.3.2.9 Polysaccharide gums
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 sugar).
2. Phycocolloids: (alginates, algin, from kelp, Laminaria and Macrocystis) (carrageenan from red algae, Irish moss, Chondrus crispus) (agar from red algae, Gelidium and Gracilaria).
16.3.3.0 Lipids, fats and oils, fatty acids, glycerides
See diagram 16.4.3: 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)
16.3.3.0.1 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, egg yolk, is used as a natural emulsifier.
2. Sphingolipids in plant and animal cell membranes. It is a fat molecule with a phosphate group (PO4) replacing the third fatty acid. glycerol-3-phosphate + 2-monacyl glycerol --> triacyl glycerol + phospholipids. Sphingolipids: sphingenine, cerebrosides, sphingomyelin.
16.3.3.0.4 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.
16.3.3.0.5 Glycerides, esters 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 omega end. Whether the fatty acid is an omega-6 fatty acid or an omega-3 fatty acid depends on the position of the first double bond.
16.3.3.0.6 Fatty acids
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).
Caprylic acid, octanoic acid, CH3(CH2)6COOH, saturated fatty acid, in sting of whip scorpions
Capric acid, decanoic acid, CH3(CH2)8COOH, saturated fatty acid
Lauric acid, dodecanoic acid, CH3(CH2)10COOH, saturated fatty acid
Myrstic acid, tetradecanoic acid, CH3(CH3)12COOH, saturated fatty acid
Palmitic acid, hexadecanoic acid, CH3(CH2)14COOH, saturated fatty acid
Stearic acid, octadecanoic acid, CH3(CH2)16COOH, saturated fatty acid
Oleic acid, cis-octadec-9-enoic acid, cis-09-octodecanoic acid, CH3(CH2)7CH=CH(CH2)7COOH, mono-unsaturated fatty acid
Linoleic acid, CH3(CH2)4CH=CHCH2CH=CH(CH2)7COOH, polyunsaturated fatty acid
Alpha linoleic acid, CH3(CH2)CH=CH(CH2)CH=CH(CH2)CH=CH(CH2)7COOH, polyunsaturated fatty acid
The products called "natural oils" are not necessarily unsaturated fats.
16.3.3.1 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:
1. 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.
2. 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.
3. Carnauba wax comes from the leaves of the Brazilian wax palm Copernicia prunifera (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.
4. 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.
5. Jojoba oil (Simmondsia chinensis)
6. Candelilla wax (Euphorbia antisyphilitica) milkweed, spurge, poisonous, unpleasant milky sap
7. Meadow foam oil (Limnanthes alba) Family Geometridea
8. Cetyl palmitate [(CH3(CH2)13CH2(C=O)O(CH2)15CH3)] [C15H31COO-C16H33] is a component of spermaceti wax in sperm whale oil.
16.3.4.0 Aromatics, aromatic compounds, benzene derivatives, ring systems, arenes: benzene, toluene, naphthalene
See diagram 16.3.4.0: 6-member cyclic compounds
See diagram 16.8.0: Acetylsalicyclic acid (aspirin) anthracene, benzene, benzoic acid, naphthalene, toluene (methyl benzene, methylbenzene)
See diagram 16.3.4.1: Aromatic names
See diagram 16.3.4.4: Heterocyclic compounds: cytosine, piperidine (pyridine, 2-aminopyridine, 3-bromopyridine, 3-nitropyridine,) pyridinium chloride, pyrimidine, pyrylium ion (quinoline, isoquinoline, 5-nitroquinoline) thymine, uracil
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. 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 and pyridine.
16.3.4.0a Aryl groups have hydrogen removed from an aromatic compound, e.g. (benzene - hydrogen atom = phenyl group, C6H5).
16.3.4.0b Aramids are aromatic polyamides, e.g. Kevlar, Nomex. Also, aliphatic polyamides, e.g. nylon.  Aramid fibres are made by spinning liquid crystal aramid polymers. The polymer chains are linked laterally by hydrogen bonds, used in rope and textile high performance fibres.
16.3.4.0.1 Aromatic hydrocarbons, e.g. benzene (C6H6)
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 (phenyl ethene) (C6H5CH=CH2) naphthalene (C10H8) anthracene (C14H10) cyclohexane (C6H12)
16.3.4.0.2 Aromatic nitro compounds, e.g. nitrobenzene (C6H5NO2)
16.3.4.0.3 Lactams (-NH(CO-), e.g. caprolactam (6-hexanelactam) (C6H11NO)
See diagram 16.3.4.3: 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 (beta lactam 4C ring, gamma lactam 5C ring, delta lactam 6C ring), e.g. the pyrimidine base uracil, beta-lactam antibiotics, e.g. penicillin, also: caprolactam (C6H11NO) also: lactones (cyclic esters), e.g. 4-hydroxybutanoic acid lactone CH2CH2CH2OC=O, gamma-butyrolactone, GBL, C4H6O2.
16.3.4.0.4 Aromatic amines, anilides, e.g. phenylamine (aniline, amino benzene) (C6H5NH2)
(phenylammonium ion, anilinium ion C6H5NH3+) benzylamine, diphenylamine, methylaniline, triphenylamine, dimethylaniline, acetanilide, quinoline (C9H7N)
Magenta is a brilliant red aniline dye derived from coal tar.
16.3.4.0.5 Diazo compounds
Diazo compounds (2 linked nitrogen compounds), e.g. methyl orange (dimethyl-aminoazobenzene sulfonic acid)
(diazonium ion: C6H5N2+, C6H5N+=--N) diazonium salts [(RN=--N+)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)
16.3.4.0.5a Barbiturates
See diagram 16.3.4.0.5a: Barbiturates
Barbituric acid is formed by condensing urea with diethyl malonate, an ester from apples. Barbituric acid derivatives include barbital (Veronal) and phenobarbital (Luminal) an anticonvulsant drug used to treat epilepsy. Phenobarbital causes side effects, e.g. sedation, depression and agitation so to some extent it has been replaced by phenytoin [C15H12N2O2, 5,5-diphenyl-2,4-imidazolidinedione] in the anti-epileptic drug sodium phenytoin (Dilantin).
16.3.4.0.5b Benzodiazepines
See diagram 16.3.4.0.5b: Benzodiazepones
Examples of Benzodiazepines: diazepam (Valium) oxazepam (Serax) nitrazepam (Mogadon) chlordiazepoxide (Librium) flunitrazepam (Rohypnol).
16.3.4.0.6 Aromatic halogen compounds, aryl halide, halogenarenes, e.g. benzyl chloride (C6H5COCl)
See: 13.4.0: Chlorine, DDT
See diagram 16.3.4.0.6: DDT, methoxychlor, Synergists: piperonyl butoxide
See diagram 16.13.3.3: Benzene hexachloride, chlorothalanil, DCPA, dalapon
See diagram 16.13.3.4: aldrin, chlordane, dieldrin, endosulfan, heptachlor
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.)
16.3.4.0.7 Aromatic sulfonic acids, e.g. benzene sulfonic acid (C6H5SO2OH) sodium benzene sulfonate
16.3.4.0.9 Aromatic alcohols, e.g. phenyl methanol (benzyl alcohol) (C6H5CH2OH)
16.3.4.0.10 Aromatic aldehydes and ketones, e.g. benzaldehyde (C6H5CHO) acetophenone
See diagram 16.3.4.11: Benzoin
Benzoin, C14H12O2, 2-Hydroxy-2-phenylacetophenone, 2-Hydroxy-1,2-Diphenylethanone, desyl alcohol, bitter almond oil camphor is synthesized from benzaldehyde in a condensation reaction.
16.3.4.0.11 Aromatic acids and their derivatives, e.g. benzoic acid (C6H5COOH)
See diagram 16.3.4.11: Acetyl salicyclic acid (aspirin) | See diagram 16.3.4.12: 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, weedkiller 2:4-dichlorophenoxyacetic acid, shikimic acid [C6H6(OH)3COOH]
16.3.4.1a Benzofuranoids, benzopyranoids
See diagram 16.3.4.12: Coumarin, coumarone
See: Coumarin
Benzofuranoids, benzopyranoids,
Coumarin (1,2-benzopyrone), C9H6O2
Benzfuran, coumarone, C8H6O, crystal
16.3.4.1b Earth smells, rain smells and cut grass smells, geosmin
See diagram 16.3.4.1: Coumarin, isocoumarin, cycloalkyls, geosmin
A filamentous 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 (trans-1, 10-dimethyl-trans-9-decalol). The smell occurs after you have breathed in tiny particles of soil containing the bacteria. 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. 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. Some people say they can smell ozone in the smell after rain and this may be true after severe lightning from thunder storms.
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.
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.
16.3.4.2 Flavonoids, betaines, flavones, anthocyanin, flavonols, flavanones, flavans, chalcones
See diagram 16.3.4.2: Flavonoids (apigenin-7-monoglucoside) flavones, riboflavin, anthicyanin
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):
1. Anthocyanins
2. Flavonols, e.g. quercetin
3. Flavones, e.g. anthocyanidin
4. Glucoflavonoids
5. Bioflavonoids, e.g. catechin (C15H14O6) isoflavones, proanthocyanidin, rotenone, pisatin, isoflavan, catechin (C15H14O6) pisatin, proanthocyanidins [brazilin (C16H14O5) from Caesalpinia, "Brazil wood" originally "bresel wood"] [haematoxylin, logwood (C16H14O6) from Haematoxylum] orcein, vulpinic acid, taxol, urushiol (pentadecyl-catechol) (phytoalexins: resveratrol, psoralen) (flavone alkaloids: ficine, vochysine).
16.3.4.3 Tannins (kinotannic acid) plant polyphenols, phenolic polymers: polyphenols, galloyl ester, vescalagins
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).
16.3.4.4 Lignans, plant phenols
Lignans: (from degradation of lignin) plant phenols, dihydroguaiaretic acid, hinokinin, podophyllotaxin
16.3.4.5 Five member heterocycles
Heterocyclic molecules have different atoms in the ring: furan C4H4O, thiephene C4H4S, pyrrole (CH)4NH, thiazole C3SNH3, saccharin C7H5NO3S, histamine C5H9N3, indole C8H7N, proline (amino acid, pyrrolidine-2-carboxylic acid) (CH2)3NHCHCOOH, immidazole C3N2H4
See diagram 16.3.4.5: 5-member heterocycles | See diagram 14.05: Histamine, major tranquillizers, tricyclic anti-depressants
16.3.5.0 Polycyclic aromatics: (quinones) naphthoquinone, binaphthyl
See diagram 16.3.5.0: Quinones
16.3.5.1 Terpenes, terpenoids, terpinenes, carotenoids, oleoresins
See diagram 16.1.1.2.2: Isoprene | See 16.1.1.2.2: Dienes, isoprene units
(limonene, pinene, camphene, cadinene, caryophyllene, cedrene, dipentene, phellandrene, terpinene, sabinene, myrcene)
1. 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 odors derived from pine trees or citrus fruit, e.g. a-pinene, d-limonene, and turpentine (a mixture of terpenes). Terpenes are volatile organic compounds (VOCs) and are flammable or combustible.
2. Terpenes are found in the following
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
3. 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.
4. Terpenes are subdivided as follows:
4.1 C5 Hemiterpenes (1 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.
16.3.5.1.1 Monoterpenes, C10 (2 isoprene units) (C10H16)
Monoterpenes include alpha pinene in turpentine (pine needles flavour), alpha thujene, beta-linene, camphor C10H16O, citronellal C10H18O (aldehyde) citronellol, eucalyptol, geraniol (rose flavour), menthol (peppermint flavour), myrcene,
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.
Thymol, Topical antifungal Thymus vulgaris (thyme), Origanum vulgare contains thymol, C10H14O
16.3.5.1.2 Terpinenes (C10H16)
Terpinenes are cyclic terpenes and occur as three isomers:
1. Alpha-terpinene is an oil with a lemon smell. It occurs in cardamom, coriander, marjoram
2. Beta-terpinene occurs in oil of savin
3. Gamma-terpinene occurs in coriander, cumin, lemon, samphire
It can be formed from the action of alcoholic sulfuric acid solution on pinene from turpentine.
16.3.5.1.3 Sesquiterpenes C15 (3 isoprene units) C15H24
abscisic acid
caryophyllene
chamazulene (chamomile oil)
curcumene
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,
gossypol,
humulene,
huratoxin,
myrrh,
nerolidol (in neroli, ginger, jasmine, lavender, tea tree and lemon grass)
oleoresin
turpentine
zingiberene (in ginger)
16.3.5.1.4 Diterpenes C20 (4 isoprene units) C20H32, in resins, pine turpentine, distilled essential oils
casbene (disease resistance)
crocin (in saffron)
cembrene
dehydroleucodine (medicine from Artemisia douglasiana)
gibberellins (phytohormones and germination) gibberellin A1 (stem elongation)
podocarpic acid (disease resistance)
retinol (vitamin A activity)
taxadiene, taxol (in yew tree bark, anticancer)
trisporic acid (fungal hormones)
16.3.5.1.5 Sesterterpenes, C25 (5 isoprene units) insect waxes, fungi
geranylfarnesol
ceroplastol
16.3.5.1.6 Triterpenes C30 (6 isoprene units) steroids and sterols
Saponins are toxic glycosides forming frothy colloidal solutions in water when agitated in water. Although they cause breakdown of red blood cells some saponinns have been discovered in traditional medicines, e.g. in the Maesa balansae plant in VietNam used to treat leishmaniasis. Saponinns occur in the horse chestnut, Aesculus hippocastanum. One triterpene saponin has formula C30H48O4.
Tio test for saponins add ground plant material to test-tub eof water, heat to boiling, stopper and shake and note presence of stable froth.
sterols (steroids)
squalene (in shark liver oil)
cephalosporin
gonane
hopane
diplotene
lupeole
16.3.5.1.8 Tetraterpenes C40 (8 isoprene units) C40H56
Caroteins: gamma carotene, alpha carotene, beta carotene, lycopene, phytoene
Xanthophylls: lutein, zeaxanthin, cantaxanthin, from fruit and vegetables
16.3.5.1.9 Terpenoids
Terpenoids are terpenes modified by oxidation or rearrangement of the carbon skeleton. Terpenoids are natural products and related compounds derived from isoprene units. They ontain oxygen in various functional groups and are subdivided as follows :
2.1 C10 Monoterpenoids
Iridoids are cyclic monoterpenoids having the iridane skeleton (1-isopropyl-2,3-dimethylcyclopentane)
2.2 C15 Sesquiterpenoids
2.3 C20 Diterpenoids
2.4 C25 Sesterterpenoids
2.5 C30 Triterpenoids
Steroids, sterols
2.6 C40 Tetraterpenoids.
Carotenoid pigments are tetraterpenoids derived from the acyclic parent-carotene (I). Carotenoids include the following
Carotenes, e.g. beta-carotene in carrot roots, lycopene in tomato fruit. Carotenes can be digested to form vitamin A.
xanthophylls, the oxygenated carotenes.
Carotenes are hydrocarbon carotenoids, a subclass of tetraterpenes and C5n polyterpenes.
Retinoids are oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene. Retinoids are not carotenoids.
Photosynthetic pigments, chlorophyll pigments: chlorophyll a (C55H72O5N4Mg) chorophyll b (C55H70O6N4Mg)
Plant growth substances abscisic acid and gibberellic acid, gibberellins.
Antioxidants
16.3.5.1.10 Oleoresins "gums"
1. Oleoresins come from gymnosperm trees from the nonvolatile diterpene residue called rosin.
2. Balsams, hard varnishes and fragrant perfumes have oleoresins containing volatile essential oils and nonvolatile resins, e.g. "Canada balsam", natural turpentine (Abies balsamea) used in microscopy because the refractive index is similar to the refractive index of glass.
See 2.4: Canada balsam
3. Incenses containing strong-scented oleoresins, e.g. frankincense (Boswellia carteri), myrrh (Commiphora abyssinica).
4. "Natural lacquer" (Toxicodendron vernicifluum) poison ivy (Toxicodendron. radicans) and shellac form from resinous excretions of the lac insect (Tachardia lacca).
5. Amber is made of nonvolatile terpenes from subterranean deposits of resin from pine trees, a yellow, translucent, fossilized vegetable resin. (Hymenaea courbaril).
6. Phenolic resins of hashish the pure resin of marijuana (Cannabis sativa) contain volatile monoterpenes and sesquiterpenes + phenolic cannabinoids, e.g. psychoactive delta-tetrahydrocannabinol (THC) an alcohol.
6. Polyterpenes containing thousands of C5H8 isoprene subunits in milky latex sap, e.g. natural rubber (Hevea brasiliensis) and (Ficus elastica) gutta-percha (Palaquium gutta) chicle polyterpene from the sapodilla tree (Manilkara zapota) used for chewing gums.
8. Diterpenes, e.g. gibberellin plant hormones.
9. Triterpenes include saponins that foam in water and sterols (steroids) for animal sex hormones.
10. Carotenoid tetraterpenes with 8 isoprene subunits
10.1 Beta-carotene (C40H56) is precursor of the anti-oxidant vitamin A (C20H28O) retinol. Alpha carotene and beta carotene are in carrot roots and ripe tomato fruits.
10.2 Astaxanthin is in the red pigment of exoskeletons of lobsters and in egg yolks
10.3 Zeaxanthin causes yellow colour of corn (maize) kernels (Zea mays).
10.4 Lycopene is in red tomato.
11. Terpenes may be poisonous and can cause painful rashes, e.g. manchineel tree (Hippomane mancinella). cicutoxin water hemlock (Cicuta douglasii) and the terpenoid compound thujone in oil of wormwood (Artemisia absinthium) used in the alcoholic drink absinthe.
16.3.5.2 Tetrapyrroles, porphyrins (haem, heme) chlorophyll, legheamoglobin, phycobiliproteins, phycobilins, phytochromes, polyvinyl pyrrolidene (povidone, PVP)
See diagram 16.3.5.2: Porphyrins (porphines) chlorophyll a, haeme (heme) bilin
16.3.5.2.1 Tetrapyrroles have the following related compounds: haemin, haematin, haemoglobin, myoglobin, cytochromes, chlorophylls a and b, bile pigments biliverdin and bilirubin, vitamin B12, bilin, uro"gen I in congenital disease polyphyria, tetrapyrrole derivative DPEP in geological deposits possibly from chlorophyll, chlorin (2,3-dihydroporphyrin).
16.3.5.2.2 Porphyrins refers to any of a group of compounds containing the porphin 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). 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.
16.3.5.2.3 Chlorophyll a C55H72O5N4Mg and chlorophyll b C55H70O6N4Mg are magnesium porphyrins. Invertebrates with green blood have copper porphyrins.
16.3.5.2.4 Legheamoglobin occurs in nitrogen-fixing bacteria in the root nodules of legumes.
16.3.5.2.5 Phycobiliproteins 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.
16.3.5.2.6 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.
16.3.5.2.7 Phytochromes are phycobilin-protein pigments involved in floral induction. activated by the length of day, hours of darkness.
16.3.5.2.8 Polyvinyl pyrrolidene, povidone, PVP, is a water-soluble polymer, E1201, used as a coating or binder in medical tablets, e.g. PVP-iodine complex in the antiseptic "Betadine", that nowadays has replaced tincture of iodine solution in medicine.
16.3.5.3 Steroids, sterols, steroid alcohols
See diagram 19.2.1.7: Steroids | See diagram 16.3.5.3: 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.
Natural 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 cholestan-3-ol. Steroids have a saturated 4 ring steroid structure. Steroids include sex hormones, coricosteroid hormones, cardiac glycosides, bile acids, cholesterol lanosterol (animal sterols) beta-sitosteron (plant sterol) ergosterol (fungus sterol) estrogen, cardiac glucosides, diosgenin, androstane, 19-norpregnane, 7-dehydrocholesterol, previtamin D3, ergocalciferol (vitamin D2) cholecalciferol (vitamin D3).
16.3.6.0 Proteins, peptides, amino acids
Proteins, peptides, amino acids are used to make:
1. Structural proteins for the body and its organs and tissues
2. Enzymes for catalysts in biochemical reactions
3. Hormones, e.g. insulin to regulate the blood sugar level
4. Antibodies to protect from viruses and bacteria
5. Intermediates in complex reactions, e.g. ornithine [H2NCH2CH2CH2CH(NH2)COOH]
16.3.6.0.1 Structural forms of proteins:
1. Primary proteins with a straight chain of amino acids
2. Secondary proteins with a helical coil of amino acids stabilized by hydrogen bonds
3. Tertiary proteins with folding and looping of a coiled polypeptide stabilized by hydrogen bonds
4. Quaternary proteins with four joined tertiary proteins, e.g. haemoglobin.
Amino acids are water-soluble organic compounds and are the primary products of nitrogen anabolism in plants. Amino acids use peptide bonds to join and form short chain peptides and long chain polypeptides, e.g. proteins. Only 20 of the hundred plant amino acids known, the primary protein amino acids, are used by all organisms in the formation of peptides and proteins. However, animals cannot synthesize all 20 amino acids.
16.3.6.0.2 Fibrous proteins and globular proteins, collagen, peptides and polypeptides
1. Fibrous proteins are usually insoluble in water and form long coiled strands, e.g. keratin, collagen, actin, myosin, fibrin. Collagen is an insoluble fibrous protein in connective tissue, e.g. tendons, skin, bone. Keratin contains the cysteine molecule formed by oxidation between sulfhydryl groups, -SH, of 2 cysteine molecules to form disulfide bonds, -S-S-, for strong proteins as in hair. Globular proteins are usually water-soluble, e.g. enzymes, antibodies, haemoglobin, casein, albumin, insulin
See diagram 16.3.6.0.1: Cysteine
2. Proteins lose their structure and coagulate when heated above 50oC, or are acted on by acids or alkalis, e.g. egg white. Such proteins lose their biological function, i.e. become denatured. Peptides and polypeptides are polymers of the 20 alpha amino acids are listed below. Other amino acids with special functions occur in the mammal body free or in combined states, i.e. not associated with peptides or proteins. Some alpha amino acids listed below have functions other than forming peptides and proteins, e.g. tyrosine is used to form thyroid hormones.
3. Peptides are formed when two amino acids are joined, peptide bond, polypeptide, protein is a large polypeptide.
16.3.6.0.3 Prions, "Mad cow disease"
Prions are proteins with an abnormal tertiary structure that may force normal proteins to fold abnormally and destroy brain tissue. They may be transmitted by eating infected brain tissue in animal feed or humans to cause diseases called spongiform encephalopathies, e.g. scrapie in sheep and BSE (Bovine Spongiform Encephalopathy) in cows, Mad Cow Disease, CJD (Creutzfeldt-Jacob Disease) and Kuru, Alpers Syndrome, laughing disease in humans.
16.3.6.1.0 Amino acids
See: Peptide Guide, by Oleg Larin, Postgraduate Student (D. Mendeleev University of Chemical Technology of Russia).
Most amino acids have the structure R-CH(NH2)COOH, with R = hydrogen or an organic group, aliphatic, aromatic or heterocyclic. The alpha amino acids in peptides and proteins, except proline, have a carboxylic acid group (-COOH) an amino group (-NH2, H3N+-) with these groups attached to the same carbon atom, the alpha carbon atom, and R-group, an organic group or H, that distinguishes one amino acid from another.
Types of amino acids
See diagram 16.3.6.0.1: Amino acids, Types 1 to 4
1. Amino acids with aliphatic R-groups, e.g. alanine, glycine, isoleucine, leucine, valine
2. Non-aromatic amino acids with hydroxyl R-groups, e.g. serine, threonine
3. Amino acids with sulfur-containing R-groups, e.g. cysteine, methionine
4. Acidic amino acids and their amides, e.g. aspartic acid 2-aminopentanedioic acid, asparagine, glutamic acid, glutamine
See diagram 16.3.6.0.2: Amino acids, Types 5 and 6 and 7, and imino acid proline
5. Basic amino acids: arginine, lysine, histidine
6. Amino acids with aromatic rings: phenylalanine, tyrosine, tryptophan.
7. Imino acids: proline
16.3.6.1.1 Amino acid nomenclature
The table below contains the trivial name of the L or D or DL-amino acid, e.g. Alanine, the IUPAC 3-letter code, e.g. Ala, the systematic name, e.g. 2-Aminopropanoic acid, and the formula, e.g. CH3-CH(NH2)-COOH. The ten essential amino acids, marked with *, must be in the diet because they cannot be synthesized. Also, plant proteins may not contain sufficient lysine and tryptophan in the diets of strict vegetarians.
Carboxylic acids (fatty acids) R-(COOH)n, contain the group -CO.OH, i.e. -COOH, carbonyl group attached to a hydroxyl group, are weak acids. An anion formed from carboxylic acid is called a carboxylate.
Methanoic acid (formic acid) HCOOH
Ethanoic acid (acetic acid) CH3COOH
Propanoic acid (propionic acid) CH3CH2COOH
Butanoic acid (butyric acid) C3H7COOH
Pentanoic acid (valeric acid) CH3(CH2)COOH
Butanedioic acid (succinic acid) (CH2)2(COOH)2
The symbol Asx denotes Asp or Asn.
Numbering of carbon atoms
In acyclic amino acids, the carbon atom of the carboxyl group next to the carbon atom carrying the amino group is numbered 1.
The carbon atoms in proline are numbered as in pyrrolidine, the nitrogen atom being numbered 1, and proceeding towards the carboxyl group.
The carbon atoms in the aromatic rings of phenylalanine, tyrosine and tryptophan are numbered as in systematic nomenclature, with 1 (or 3 for tryptophan) designating the carbon atom bearing the aliphatic chain.
16.3.6.1.2 Table of the 20 alpha amino acids
* = essential amino acid, must be in the diet
1. Alanine, Ala, 2-aminopropanoic acid, CH3-CH(NH2)-COOH
2. Arginine*, Arg, 2-amino-5-guanidinopentanoic acid, H2N-C(=NH)-NH-[CH2]3-CH(NH2)-COOH
3. Asparagine, Asn, 2-amino-3-carbamoylpropanoic acid, H2N-CO-CH2-CH(NH2)-COOH
4. Aspartic acid, Asp, 2-aminobutanedioic acid, HOOC-CH2-CH(NH2)-COOH
5. Cysteine, Cys, 2-amino-3-mercaptopropanoic acid, HS-CH2-CH(NH2)-COOH
6. Glutamic acid, Glu, 2-aminopentanedioic acid, HC5H8NO4, HOOC-[CH2]2-CH(NH2)-COOH
7. Glutamine, Gln, 2-amino-4-carbamoylbutanoic acid, H2N-CO-[CH2]2-CH(NH2)-COOH
8. Glycine, Gly, aminoethanoic acid, CH2(NH2)-COOH
9. Histidine*, His, 2-amino-3-(1H-imidazol-4-yl)-propanoic acid
10. Isoleucine*, Ile, 2-amino-3-methylpentanoic acid, C2H5-CH(CH3)-CH(NH2)-COOH
11. Leucine*, Leu, 2-amino-4-methylpentanoic acid, (CH3)2CH-CH2-CH(NH2)-COOH
12. Lysine*, Lys, 2,6-Diaminohexanoic acid, H2N-[CH2]4-CH(NH2)-COOH
13. Methionine*, Met, 2-amino-4-(methylthio)butanoic acid, CH3-S-[CH2]2-CH(NH2)-COOH
14. Phenylalanine*, Phe, 2-amino-3-phenylpropanoic acid, C6H5-CH2-CH(NH2)-COOH
15. Proline, Pro, Pyrrolidine-2-carboxylic acid
16. Serine, Ser, amino-3-hydroxypropanoic acid, HO-CH2-CH(NH2)-COOH
17. Threonine*, Thr, 2-amino-3-hydroxybutanoicacid, CH3-CH(OH)-CH(NH2)-COOH
18. Tryptophan*, Trp, 2-amino-3-(lH-indol-3-yl)-propanoic acid, C11H12N2O2
19. Tyrosine, Tyr, 2-amino-3-(4-hydroxyphenyl)-propanoic acid, C9H11NO3
20. Valine*, Val, 2-amino-3-methylbutanoic acid, (CH3)2CH-CH(NH2)-COOH
16.3.6.1.3 Methanoic acid (formic acid) ionization reaction
Formic acid, HCOOH, is a colourless, corrosive liquid with a pungent odour, prepared by passing carbon monoxide and steam under pressure over a hot catalyst.
Ionization reaction, Ka = 1.8 X 10-4
HCOOH + H2O <--> H3O+ + HCOO-
16.3.6.1.4 Ethanoic acid (acetic acid) ionization reaction
Ethanoic acid, CH3COOH, is prepared by destructive distillation of wood, oxidation of ethanol and is synthesised from ethyne((acetylene). Acetic acid is a weak acid and is used as a preservative. Vinegar, prepared by fermentation of fruit juices, e.g. grape juice and cider, contains 3 to 6 % acetic acid.
Ionization reaction, Ka = 1.76 X 10-5
CH3COOH + H2O <--> H3O+ + CH3COO-
16.3.6.1.5 Propanoic acid (propionic acid) ionization reaction
Naturally occurring, colourless, pungent fatty acid. Sodium and calcium salts are used to inhibit mould in animal feed and bread, e.g. in bread, calcium propionate, food additive E282, preservative, anti fungal mould inhibitor
Ionization reaction, Ka = 1.34 X 10-5
CH3CH2COOH <--> H3O+ + CH3CH2COO-
The anions, CH3CH2COO-, are called propionates (propanoates).
16.3.6.1.6 Butanoic acid (butyric acid)
Butanoic acids, C3H7COOH, are in the form of two isomers, normal butyric acid (n-butyric acid) and iso-butyric acid. The n-butyric acid is a thick liquid with the rancid odour and occurs in rancid butter and human sweat. It is used to make flavour and perfume esters. It is a weak acid, Ka = 1.5 X 10-5.
16.3.6.1.7 Pentanoic acid (valeric acid)
Valeric acids are in the form of four isomers:
1. n-valeric acid, pentanoic acid, CH3(CH2)COOH, a colourless liquid used in perfume.
2. iso-valeric acid, 3-methyl butanoic acid, (CH3)2=CHCH2COOH,
3. methylethylacetic acid, 2-methyl bytanoic acid(CH3)(C2H5)CHCOOH,
4. pivalic acid, 2,2-dimetyl propanoic acid, (CH3)3CCOOH.
16.3.6.1.8 Butanedioic acid (succinic acid)
Butanedioic acid, HCOOHC:CHCOOH is in two colourless crystalline forms, the cis from is maleic acid and the trans form is is fumaric acid. They are used to make synthetic alkyd thermoset resins. It occurs in sugar cane juice, castor oil plant and animal tissues as an intermediate stage of the Krebs cycle.
16.3.6.2 Amines and alkaloids
See16.3.6.4: Alkaloids produced by plants from amino acids
See diagram 16.20.0: Nicotine, strychnine, cocaine (C17H21ON4) coniine, heroin, morphine, LSD, quinine, caffeine, theobromine, theophylline
See diagram 16.21.7: Mescaline, dopamine, psilocybin, serotonin, ergine, LSD, tropane
See diagram 16.21.8: Tryptamine, THC, Tetrahydrocannabinol, marijuana
Amines are organic derivative of ammonia, NH3, where one, two or three hydrogen atoms are replaced by alkyl groups as a primary amine, secondary amine or tertiary amine, e.g. trimethylamine CH3NCH3CH3. Amines are weak bases that form ammonium salts that are more soluble in water than the original amine, e.g. cough medicine may contain the cough suppressants dextramethorphan hydrobromide or the decongestant, expectorant, pseudoephidrine hydrochloride and ephedrine. Alkaloids have the properties of amines and are natural bitter, alkaline, nitrogenous compounds, nitrogenous organic bases in plants They usually contain one or more N and a heterocyclic ring structure. The names of alkaloids usually end in "ine". Their function is probably to defend against grazing animals or being eaten by insects. Many alkaloids are plant metabolic by-products derived from amino acids. more than 10 000 different alkaloids may exist in over 300 plant families. Alkaloids often contain one or more phenolic or indole rings, usually with a nitrogen atom in the ring. The term alkaloid was first used to describe chemical bases from plants used in medicines, but now there is no exact definition of alkaloid. Some classifications of alkaloids are based on structure and some on origin.
Alkaloids
1.1.0A Pyridine-piperidine group: (single carbon ring with one nitrogen atom) arecaidine, coniine, guvacine, nicotine, pilocarpine, piperine, sparteine, trigonelline
1.2.0A Tropane group, tropine group
See diagram 16.20.0: Cocaine
(methylated nitrogen atom, N-CH3) 5-hydroxytryptamine, atropine (from Atropa belladonna) cocaine, C17H21ON4 (from coca, Erythroxylum) conotoxin, decaline, ecgonine, hygrine, hyoscyamine, novocain, pelletierine, scopolamine ("truth drug") tetramine, tetrodoxin
1.2.1A Pyrrolizidine group: e.g. retronecine a 2,4-D, 2,4,5-Th
1.3.0A Isoquinoline group: (2 carbon rings one containing a nitrogen atom) (morphine, codeine and thebane from opium poppy, Papaver somniferum) (D-tubocurarine from curare, Chondodendron) berberine, diacetylmorphine, hydrastine, narceine, narcotine, papaverine, podophyllotoxin, reticuline, heroin vinblastine, vincristine
1.4.0A Quinolizidine group: (2 carbon rings with one nitrogen atom) (cytisine from Cytisus and Sophora and Agave for tequila) erythroidine (lupinine from Lupinus) sparteine
1.5.0A Quinoline group: (2 rings containing one nitrogen atom) (quinine from Cinchona) echinopsone, atabrine, brucine, cevadine, chloroquine, primaquine, veratrine
1.6.0A Phenethylamine group:
See diagram 16.21.6: anthocyanin, catechin, catechol, mescaline, tyrosine, DOPA (dihydroxyphenylalanine) | See diagram 14.03: Amphetamine, epidephrine
e.g. DOPA (dihydroxyphenylalanine) catecholamines [CH4(OH)2= catechol ring], e.g. dopamine (3-hydroxy tyramine) adrenaline (epinephrine) noradrenaline (norepinephrine) substituted phenethylamines, e.g. catecholamine ether, guaiacol (HOC6H4OCH3, 2-hydroxyphenol, 1,2-hydroxybenzene)
1.7.0A Indole group: (double ring containing an indole group)
See diagram 16.21.8: THC, tetrahydrocannibinol, tryptophan, Ecstasy, methylenedioxymethamphetamine, MDMA
(ergine, d-lysergic amide, from ergot fungus, Claviceps) LSD.(lysergic acid diethylamide) LSA d-lysergic acid diethylamide, bufotenine (5-hydroxydimethyltryptamine) DMT, ergine, MDMA (ecstasy), mescaline, methamphetamine, NMT, psilocybin (reserpine from Rauwolfia) serotonin, strychnine, tryptamine (vinblastine and vincristine from Catharanthus) (strychnine from Strychnos nux-vomica) (podophyllotoxin from may apple, Podophyllum)
1.8.0A Indolizidine group: (2 rings including an indole ring) (swainsonine from Swainsona and locoweed, stagger weed Astragalus)
1.9.0A Steroidal group: (2 rings containing one nitrogen atom + 4 carbon ring steroid) solanidine (from Solanum) triterpene, zygadenine
1.10.0A Purine group: (double carbon ring containing 4 nitrogen atom)
See diagram 16.21.0: Purines, purine, uric acid adenine, guanine, caffeine, theobromine, theophylline
1.11.0A Thiazole group: (single carbon ring containing one nitrogen atom and one sulfur atom)
See diagram 16.21.11: Thiazole, thiamin (vitamin B) penicillin basic structure
1.12.0A Capsaicin group: capsaicin from Capsicum chilli
See: Capsaicin | See diagram 16.21.12: Capsaicin
Capsaicin is used as a topical counter-irritant analgesic cream for osteoarthritic pain in adults only, e.g. "Axsain"
1.13.0A Ephedrine group
See diagram 16.20.0: Colchicine
Amine alkaloids: (colchicine, C22H25O6N, from autumn crocus, Colchicum autumnale, mitosis spindle poison) (ephedrine from Ephedra) (pseudoephedrine, isomer of ephedrine) (mescaline from cactus species, e.g. Trichocereus) bufotenine, ficin, papain, bromelain
1.14.0A Muscarine group: (one carbon ring and one nitrogen atom) muscarine, muscimol (muscimole) from agaric mushroom Amanita
16.3.6.3 Glycoproteins
Glycoproteins are complex polypeptides + polysaccharides chains. They are involved in cell recognition in T-cells, blood cell antigens, antibodies and pollen recognition. Immunotoxins are conjugated proteins monoclonal antibodies with an attached lectin protein. Lectins called haemagglutinins occur in red kidney beans and may cause intestinal problems when eaten if the beans are not first soaked and cooked thoroughly.
16.14.0 Dioxins
See diagram 16.14.0: Dioxins
The term dioxins generally refers to a series of chlorinated dioxins, e.g. 2,3,7,8-tetracholorodibenzo-p-dioxin (2,3,7,8-TCDD) by-product of manufacture of herbicide 2,4,5-T and occurred in the Agent Orange defoliant used in the Vietnam War. They are chlorinated hydrocarbon compounds called dibenzo-p-dioxins. They are very toxic and persist in the environment for long periods. They are produced during incineration of wastes and are a contaminant in chemical manufacturing processes. They interfere with the action of hormones and the genetic system even in very small concentrations. They accumulate in the fat cells but are not metabolized. They damage the immune system, leading to increased susceptibility to infectious disease. When chemicals and plastics are manufactured or burned, dioxin may be produced as a by-product and dumped into landfill. Landfill gas may include dioxins which may spread into the community if landfill gas, mainly methane is burned as a source of energy. An important source of dioxins is from burning polyvinyl chloride in incinerators.