topic16a

Topic 16a Organic chemistry, hydrocarbons, food tests, biochemistry
Classification of hydrocarbons and plant products
Updated 2008-09-27
Please send comments to: J.Elfick@uq.edu.au
See also: Interesting websites
See also: History of this document

This page is based on:
1. G. P. Moss, P. A. S. Smith and D. Tavernier, Pure and Applied Chemistry, 67, 1307-1375 (1995) [Copyright IUPAC]
http://.chem.qmul.ac.uk/iupac/class/
2. Dictionary of Natural Products
http://.chemnetbase.com/introductions/dnp.pdf

Table of contents
16.3.0 Chemistry of natural products
Table of contents
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
16.11.0 Organic chemistry terms
16.14.0 Dioxins
Topic 19 Chemical reactions in the home, composition of food, cooking
Appendix 7: Prefixes and suffixes

16.3.1 Aliphatic products
16.3.1.1 Carbohydrates
9.140 Tests for reducing sugars and aldehydes, test for simple sugars, Fehling's test
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 Disaccharides
16.3.1.5 Starches, amylum, glycogen
16.3.1.6 Cellulose, hemicellulose, lignin, test for wood
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)
16.3.2.8.1 Structure of DNA
16.3.2.9 Polysaccharide gums
16.3.3.0 Lipids, fats and oils, fatty acids, glycerides
16.3.3.0.1 Phospholipids (phosphoglycerides)
16.3.3.1 Waxes

16.3.4.0 Aromatics, aromatic compounds, benzene derivatives, ring systems, arenes: benzene, toluene, naphthalene
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
16.3.4.0.8 Phenols, e.g. phenol (carbolic acid) (C₆H₅OH)
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, iodine test
9.143 Tests for vitamin C (L-ascorbic acid)
9.144 Tests for wood
9.182 Tests for glucose and starch with "Testape"
16.4.5 Tests for 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
16.9.3 Foods, test for nitrogen compounds, soda lime test
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
19.2.1.11 Coconut oil
19.2.1.12 Fish oils
19.2.1.13 Ice-cream

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, terpenoids, terpinenes, carotenoids, 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
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

16.3.6.2 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 C_n(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.
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.
Monosaccharides can be 3C trioses, 4C tetroses, 5C pentoses 6C hexoses etc. and also may be
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 dihydroxyacetone 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 C_3nH_6nO_3n. 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-, 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 all have formula C₆H₁₂O₆. The stereoisomers are: glucose, galactose, fructose (3C triose, 4C tetrose, 5C pentose, 6C hexose, etc.)
Aldoses
An aldose has the aldehyde group, -CHO. The simplest aldose is glyceraldehyde, CHOCHOHCH₂OH. The aldehyde group is at C1. Other aldoses include D-glucose, D-talose, D-galactose, D-mannose, D-galactose, D-altrose, D-idose, D-xylose, D-lyxose, D-arabinose, D-ribose, DS-allose, D-threose, D-erythrose.
Ketoses
A ketose has the ketone group, -CO-. The simplest ketose is dihydroxyacetone, CH₂OHCOCH₂OH. The carbonyl group is at C2. Other ketoses include D-lyxohexulose (tagotose) D-hexulose (sorbose) D-arabinohexulose (fructose) D-robohexulose (psicose) D-threpentulose (xylulose) D-erythropentulose (ribulose) D-glycerotetrulose (erythrulose).

16.3.1.3.1 Left-handed and right-handed structural forms, D- 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 Disaccharides
See diagram 16.3.1.4a: Maltose molecule | See diagram 16.3.1.4b: Lactose molecule | See diagram 16.3.1.4c: Sucrose
Sucrose (glucose + fructose) lactose (glucose + galactose) maltose (glucose + glucose): Non-reducing sugars: fructose-glucoside sucrose, glucose-glucoside trehalose. Reducing sugars: maltose, lactose.

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, 40-60 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, lignin, test for wood
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 in shells of arthropods, 2-acetamido-2-deoxyglucose

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.

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.

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) (K-strophanthin and ouabain or G-strophanthin from Strophanthus)
Salicin glucoside digitonin, digitoxin

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

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)
The "true oils", "fixed oils" make a permanent greasy mark on paper. They are glycerides of fatty acids. They do not volatilize on heating without decomposition. They harden on exposure to the air. Examples of true oils includes glycerides linseed oil and walnut oil. By contrast, the "essential oils" do volatilize on heating without decomposition to form distinctive scents. They do not harden on exposure to the air. They are volatile mixtures of mainly terpenes. esters, aliphatic and aromatic esters, phenolics and substituted hydrocarbons formed in plant oil glands. They cause plant odours, some of which can be distilled to form perfumes, and substances that deter insects and herbivores from damage or grazing. Examples of essential oils include citrus oils, rose oil, jasmine oil, and oil of cloves.
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.
Glycerides are common biological substances made from esters of glycerol (propane-1,2,3-triol) with fatty acids:
1. triglycerides,
2. 1,2- or 1,3-diglycerides,
3. 1- or 2-monoglycerides.
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. 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.
Useful oils: linseed oil, flax (Linum usitatissimum) mustard oil (Brassica campestris) canola oil (Brassica napus) corn oil (Zea mays) soybean oil (Glycine max) peanut oil (Arachis hypogea) cottonseed oil (Gossypium) safflower oil (Carthamus tinctorius) sunflower oil (Helianthus annuus) sesame oil (Sesamum indicum) coconut oil (Cocos nucifera) palm oil (Elaeis guineensis) castor oil (Ricinus communis) tung oil (Aleurites fordii) candlenut oil (Aleurites moluccana) linseed oil (Linum usitatissimum) castor oil (Ricinis communis)
Fatty acids have trivial and systemic names, e.g. palmitic acid (hexadecanoic acid) oleic acid (cis-09-octodecanoic acid)
Fatty acids in plants occur as 1. esters of glycerol or other hydroxy compound 2. amides of long chain amines, e.g. sphingenine.
Saturated fatty acids, e.g. palmitic acid (hexadecanoic acid) and stearic acid (octadecanoic acid).
Unsaturated fatty acids, e.g. mono-unsaturated fatty acid oleic acid, olive oil form the olive tree Olea europea.
Polyunsaturated fatty acids are essential fatty acids, e.g. linoleic acid, linolenic acid, and arachidonic acid.
The products called "natural oils" are not necessarily unsaturated fats.
The complex lipids are esters of long chain fatty acids, e.g. glycerides, glycolipids, phospholipids, waxes.
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.
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.

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.

16.3.3.1 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, C_25-27H_51-55(C=O)OC_30-32H_61-65] 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
Having planar ring-type groups usually composed of carbon atoms, e.g. benzene, naphthalene, with alternating double and single bonds. (Aryl group: hydrogen removed from an aromatic compound, e.g. benzene - hydrogen atom = phenyl group C₆H₅^-). (Aramid: Aromatic polyamide, e.g. Kevlar, Nomex. Also, aliphatic polyamide, e.g. nylon). 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.

16.3.4.0.1 Aromatic hydrocarbons, e.g. benzene (C₆H₆)
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).

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)
Bromobenzene, iodobenzene, chlorobenzene, DDT (BHC, benzene hexachloride, lindane) chlorothanil, and the insecticide DDT (C₆H₄Cl)₂CH-CCl₃[Former name: dichlorodiphenyltrichloroethane, New IUPAC name: 1,1,1-trichloro-2,2-bis (4-chlorophenyl)ethane.] Cyclodienes: chlordane, aldrin, dieldrin, heptachlor, endosulfan
See also: 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

16.3.4.0.7 Aromatic sulfonic acids, e.g. benzene sulfonic acid (C₆H₅SO₂OH) sodium benzene sulfonate

16.3.4.0.8 Phenols, e.g. phenol (carbolic acid) (C₆H₅OH)
Phenols, e.g. phenol (carbolic acid) (C₆H₅OH) (hydroxyl group -OH connected to a carbon atom in a benzene ring, benzene-OH, hydroxybenzenes) 2-napthol (beta-napthol, napthalen-2-ol) C₁₀H₇OH, cresols (monomethylphenols) epoxy compounds, e.g. 1,2-epoxypropane

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)
See diagram 16.3.4.11: Acetyl salicyclic acid (aspirin) 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
Benzofuranoids, benzopyranoids, coumarin (1,2-benzopyrone) (C₉H₆O₂)

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 break down 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 also 16.1.1.2.1: Dienes, isoprene units
Terpenes, found mostly plants and may be isolated as a water-insoluble oil through distillation. Terpenes are unsaturated hydrocarbons formed by the polymerization of 5-carbon isoprene units [2-methylbuta-1,3-diene, CH₂=C(CH₃)CH=CH₂ (C₅H₈)] that consists of a four carbon chain and a one carbon branch at C2. Different structural forms are called isomers. 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). Terpenes have linked isoprene units that. occur in natural rubber.
Isoprenoids are compounds derived from isoprene, often showing repeated occurrence of isoprene units.
Terpenes are subdivided as follows:
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.
C10 Monoterpenes (2 isoprenes) (C₁₀H₁₆) e.g. alpha pinene in turpentine, alpha thujene, beta-linene, camphor C₁₀H₁₆O, citronellal C₁₀H₁₈O (aldehyde) citronellol, eucalyptol, geraniol, menthol in peppermint oil, myrcene,
Anethole, 4-Propenylanisole, C₁₀H₁₂O, CH₃CH=CHC₆H₄OCH_3, 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, from Pimpinella anisum, is used in absinthe, anisette (anis) arak, champurrado (atole de anis) ouzo, pastis, Pernod, raki, sambuca and some root beers.
C15 Sesquiterpenes (3 isoprenes) C₁₅H₂₄, e.g. abscisic acid, caryophyllene, curcumene, eugenol [C₆H₃(OH)(OCH₃)(CH₂CH=CH₂)] (in oil of cloves and cinnamon leaf oil) farasene, farnesol (in citronella, neroli, 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)
C20 Diterpenes (4 isoprenes) C₂₀H₃₂, in resins, pine turpentine, distil essential oils, e.g. 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)
C25 Sesterterpenes (5 isoprenes) insect waxes, fungi, rarely occurs, e.g. geranylfarnesol, ceroplastol
C30 Triterpenes (6 isoprenes) steroids and sterols, e.g. squalene (in shark liver oil) cephalosporin, gonane, hopane, diplotene, lupeole
C40 Tetraterpenes (8 isoprenes) C₄₀H₅₆, e.g.
Caroteins: gamma carotene, alpha carotene, beta carotene, lycopene, phytoene
Xanthophylls: lutein, zeaxanthin, cantaxanthin, from fruit and vegetables
Terpenes are found in the following
1. Essential oils that are monoterpenes and sesquiterpenes volatile at room temperature, e.g. eucalyptol, citronella (citrus oils) and eugenol (oil of cloves).
2. Herbs and spices containing terpinene oil.
3. Perfumes that contain aromatic terpenes, and resins, 20-carbon diterpenes and 30-carbon triterpenes.
4. Lutein and zeaxanthin are the only xanthophylls found in human serum. Fucoxanthin is found in brown algae

Terpenoids are natural products and related compounds derived from isoprene units, e.g. carotenoid pigments, chlorophyll a (C₅₅H₇₂O₅N₄Mg) chorophyll b (C₅₅H₇₀O₆N₄Mg) plant growth substances abscisic acid and gibberellic acid, gibberellins
Terpineme is cyclic terpene, e.g. alpha-terpinene
Terpenoids contain oxygen in various functional groups and are subdivided: C10 monoterpenoids, C15 sesquiterpenoids, C20 diterpenoids, C25 sesterterpenoids, C30 triterpenoids, C40 tetraterpenoids.

Carotenoids are tetraterpenoids derived from the acyclic parent-carotene (I). Carotenoids includes carotenes and xanthophylls, the oxygenated carotenes.
Carotenes are hydrocarbon carotenoids, a subclass of tetraterpenes and C5n polyterpenes.
Iridoids are cyclic monoterpenoids having the iridane skeleton (1-isopropyl-2,3-dimethylcyclopentane)
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.

Oleoresins "gums" include the following:
1. oleoresins 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 similsr to that of glass.
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 from resinous excretions of the lac insect (Tachardia lacca)
5. amber 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, e.g. beta-carotene (C₄₀H₅₆) precursor of the anti-oxidant vitamin A (C₂₀H₂₈O) retinol, astaxanthin in the red pigment of exoskeletons of lobsters and in egg yolks, zeaxanthin that causes yellow colour of corn (maize) kernels (Zea mays) and lycopene in red tomato, alpha carotene and beta carotene in carrot roots and ripe tomato fruits.
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 wormwood (Artemisia absinthium) that was 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
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).
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.
3. Chlorophyll a C₅₅H₇₂O₅N₄Mg and chlorophyll b C₅₅H₇₀O₆N₄Mg are magnesium porphyrins. Invertebrates with green blood have copper porphyrins.
4. Legheamoglobin occurs in nitrogen-fixing bacteria in the root nodules of legumes.
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.
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.
7. Phytochromes are phycobilin-protein pigments involved in floral induction. activated by the length of day, hours of darkness.
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 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).

16.3.6.0.0 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
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 cystine 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 16.3.0a: Cystine
2. Proteins lose their structure and coagulate when heated above 50^oC, 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.

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 diagram 16.3.6.0a
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
1. Amino acids with aliphatic R-groups, e.g. glycine, alanine, valine, leucine, isoleucine
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, asparagine, glutamic acid, glutamine
See diagram 16.3.6.0b:
5. Basic amino acids: arginine, lysine, histidine
Amino acids with aromatic rings: phenylalanine, tyrosine, tryptophan.
6. 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
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
19. Tyrosine, Tyr, 2-Amino-3-(4-hydroxyphenyl)-propanoic acid
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 - 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:
n-valeric acid, pentanoic acid, CH₃(CH₂)COOH, a colourless liquid used in perfume.
iso-valeric acid, 3-methyl butanoic acid, (CH3)2=CHCH2COOH,
methylethylacetic acid, 2-methyl bytanoic acid(CH3)(C2H5)CHCOOH,
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
See also: 16.3.6.4 Alkaloids produced by plants from amino acids | See diagram 14.10: nicotine, morphine, codein, heroin, methadone, pethidine | See diagram 16.20.0: nicotine, strychnine, cocaine cocaine (C₁₇H₂₁ON₄) coniine, heroin, morphine, LSD, quinine, caffeine, theobromine, theophylline | See diagram 16.21.7: mescaline, serotonin, psilocybin, ergine, LSD (tropane, dopamine) | 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: (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: Indole, tryptophan, tryptamine, serotonin, lysergic acid, LSD
(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 also: 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, amine alkaloids: (colchicine from crocus, Colchicum, 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
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 damages 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.

19.2.1.8 Omega-3 fatty acids
Omega-3 is a family of polyunsaturated fatty acids. The parent omega-3-alpha linolenic acid (ALA) is obtained from the diet and is polyunsaturated with 8 carbon atoms and 3 double bonds. The long chain omega-3 fatty acids eicosapentaenoic acid, EPA, and docosahexaenoic acid, DHA, can be synthesized from dietary ALA, but in seems that EPA and DHA should be obtained from the diet containing oily fish and fish oil as well as fortified bread and fruit juice. ALA, EPA and DHA are important role for structural membrane lipids, in nerve tissue and the retina beside a wide range of functions in cells and tissues.

19.2.1.9 Free radicals
A free radical is a molecule carrying an impaired electron. Free radicals are extremely reactive. As free radicals take an electron from the other molecules, they convert these molecules into free radicals or breakdown or alter their chemical structure. Free radicals can damage proteins, sugars, fatty acids and nucleic acids that combine and accumulate as "age pigment". The main free radicals are superoxide radical (SOR) hydroxyl radical (OHR) hydroperoxyl radical (HPR) alkoxyl radical (AR) peroxyl radical (PR) and nitric oxide radical (NOR) Other molecules that are not free radicals, but act much like them, are singlet oxygen, hydrogen peroxide (H₂O₂) and hypochlorous acid (HOCl)The free radicals and non-free radical mimics are called "oxidants" or "reactive oxygen species" (ROS). Free radicals live for only a few seconds because of their extreme reactivity. Free radical damage includes ageing, cancer, heart/artery disease, hypertension, Alzheimer's disease, ageing immune deficiency, cataracts, diabetes, inflammatory disease, and just ageing. Free radicals and oxidants are produced by normal physiological processes and by enzymes that detoxify pollutants. Monosaturated fats, cholesterol, and saturated fats are subject to free radical but polyunsaturated fatty acids are most susceptible. In humans the first line of antioxidant defence are the antioxidant enzymes, e.g. glutathione peroxidase (GPX) and tripeptide glutathione (GSH) help destroy SOR, H₂O₂ and lipid peroxides. Vitamins C and E, and mineral selenium have a major antioxidant role, besides various drugs. Vitamin C may be the most important nutrient antioxidant. Vitamin E is the chief fat-soluble antioxidant, and occurs in all membranes. Alpha-lipoic acid (ALA) is a quasi-vitamin anti-oxidant. It can be made by the body, but also absorbed from diet or supplements.

19.2.1.10 Margarine
See also 19.4.3: Margarine label | Diacetyl, 2,3-butanedione 16.3.3a
Information from a margarine label An example of a legal definition of table margarine is that it is a mixture of edible fats, oils and water prepared in the form of a water in oil emulsion containing < 16% water, < 4% salt and > 8.5 mg of vitamin A and > 55 mu g of vitamin D per kilogram. The term polyunsaturated is permitted where the proportion of cis-methylene interrupted polyunsaturated fatty acids in the margarine is > 49%, the proportion of saturated fatty acids < 20% of the total fatty acids, and the P/S ratio > 2: 1. The total cholesterol content as mg/100 g must appear on the packet. The remaining 40% of the fatty acids can be mono-unsaturated (e.g. oleic acid). A softer margarine that requires constant refrigeration has a P/S ratio 3:1. Table margarine may contain antioxidants, flavouring, e.g. flavour of butter from 3-hydroxy-2-butanone and diacetyl (2,3-butanedione, dimethylglyoxal, C₄H₆O₂) vegetable colouring, e.g. usually carotene, a source of vitamin A, and which gives the colour to butter. Previously margarine contained coconut oil but produces changed to soybean oil because of concern about the high content of saturated fats in coconut oil.

19.2.1.11 Coconut oil
See also Topic 17: New ways to prepare coconut oil | See also: Coconut Project
Proponents of including coconut oil in the diet claim that In the United States, the commercial interests of the US domestic fats and oils industry and soybean growers were successful at driving down usage of coconut oil by pointing to the high concentration of saturated fats in coconut oil. During concern over increased rates of heart disease the edible oil industry's response at that time was to claim that it was only the saturated fat in the hydrogenated oils which was causing the problem. Not being domestically grown in the US, coconut oil and palm oil industries were not able to defend themselves. However, the proponents for coconut oil say it is rich in short and medium chain fatty acids. Desiccated coconut is about 69% coconut fat. and coconut milk is about 24% fat. About 50% of coconut fat is lauric acid which has antibacterial, antiviral and antiprotozoal functions in food. Also, another one medium chain fatty acid, capric acid, has been added to the list of coconut's antimicrobial components. It is claimed that natural coconut fat in the diet leads to a normalization of body lipids, protects against alcohol damage to the liver, and improves the immune system's anti-inflammatory response and that the medium chain fatty acids and monoglycerides found primarily in coconut oil have tremendous healing power.

19.2.1.12 Fish oils
Fish oils, omega-3 containing eicosapentaenic acid, EPA and docosahexaenoic acid, DHA, are taken as supplements to lower total serum triglycerides and maintain healthy levels of cholesterol.

19.2.1.13 Ice-cream
Ice-cream is a foam preserved by freezing. Under a microscope you can see solid globules of milk fat, air cells, ice crystals, solution of concentrated sugars, salts and suspended milk proteins. The ice crystals were formed by water freezing out of the solution to a point where the lowering of the freezing point caused by the concentration of the remaining solutes in the water corresponds to the freezer temperature. Manufacturers can expand the ice-cream with air to double its volume. Expanded ice-cream feels fluffier and has a warmer taste. Ice-cream containing Less milk fat has bigger ice crystals, coarser texture and colder taste but the addition of emulsifiers and stabilizers can mask these low fat properties but prepare the ice-cream sticky. If not stored at a low enough temperature partial thawing causes the smaller crystals to melt and later refreezing to larger crystals. Ice-cream on the tongue crystallizing out the lactose, milk sugar, which stays on the tongue after the ice has melted leaving a sweet taste.

16.11.0 Organic chemistry terms
alkyd resin: Adhesive and coating resins made from glycerol and unsaturated organic acids. They are rigid cross-linked polymers formed when there are more than two functional groups on linear chain monomers. They are use in paint enamels and making dentures.
alkylation: Replacing a hydrogen on a cyclic compound with an alkyl CH₃ or longer chain group.
ATP, adenosine triphosphate: Molecule that allows extraction of energy from food by cycling between ADP, adenosine diphosphate.
bifunctional: A molecule with two reactive groups.
catenation: Formation of chains of atoms.
citric acid cycle, Krebs cycle: A cycle of reactions in which ADP is recharged to ATP as part of the energy conversion processes in the body.
conjugated: Alternating double and single bonds. Note that polyunsaturated chains have "cis-methylene interrupted" or "skipped" double bonds which are not
denature: The tertiary structure of a protein collapses, denatured, by heating, acid or agitation in air.
epoxy: Oxygen directly linked to two adjacent bonded carbon atoms forming a triangle.
esterification: Forming an ester, reaction of organic acid with an alcohol. Reverse process is ester hydrolysis, saponification, the making of soap from fat.
fume cupboard, fume hood, fume cabinet: Enclosed reinforced cupboard with facilities for chemical reactions and used under negative air pressure.
hydrogenation: Addition of hydrogen to a molecule to convert unsaturated molecules to saturated and reducing double bonds to single bonds.
hydrolysis: Splitting a molecule using a reaction with water.
peptides: amides derived from two or more amino carboxylic acid molecules by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with loss of water. Peptides include structures formed from alpha-amino acids and from any amino carboxylic acid. C = any organyl group
phosphorylation: Adding a phosphate group to a molecule.
racemic: A one-to-one mixture of left handed and right-handed, chiral, forms of the same molecule. Most chemical reactions produce products as racemic mixtures, whereas biological reactions generally produce one or the other form only. R,R" The R designates an undefined organic group, e.g. a hydrocarbon chain. The R it is not necessarily the same as R".
saponify: To prepare soap from fat.
tautomer: When an atom, e.g. hydrogen, moves backwards and forwards between different places on a molecule, the new and original molecules form a tautomeric pair.
sulfonation: Addition of the function group -SO₃H to a molecule.

16.3.6.4 Alkaloids produced by plants from amino acids
Botanical Name, Common Name, Alkaloid or Main alkaloid (Use)
Aconitum napellus, monks hood, aconitine
Aesculus chinensis, horse chestnut, escin, aescin
Aloe vera, aloe, aloin, isobarbaloin, aloin, alomicin
Alpinia officinarum, galangal root, galangine
Anadenanthera peregrina, yopa, parica, bufotenine
Anhalonium lewinii, peyote cactus, mescaline
Areca catechu, areca, betel nut, arecoline
Artemisia annua, Artemisia absinthium wormwood, artemisinine
Astragalus, locoweeds, swainsonine, miserotoxin
Atropa belladonna, deadly nightshade, belladonna, atropine, hyoscyamine
Atropa mandrogora, European mandrake, atropine, hyoscyamine, scopolamine
Brugmansia, deadly datura
Buxus microphylla, cyclovirobuxine
Camellia sinensis, green tea, theanine, caffeine
Camptotheca acuminata, camptotheca, camptothecine
Cannabis sativa, cannabis, hemp, THC, tetra hydrocannabinol resin, also cannabis alkaloids
Capsicum frutescens, red pepper, capsaicine
Carthamus tinctoria, carthamus, carthamine
Catharanthus roseus, Madagascar periwinkle, vindoline, catharanthine, vinblastine
Cephaelis ipecacuanha, ipecac, ipecacuanha, emetin
Cephalotaxus fortune, homoharringtonine
Chelidonium majus, celandine, chelerythrine, chelidonine
Cinchona officinalis, cincona,"quina" quinine
Chondodendron tomentosum, cuare, isoquinoline, D-tubocurarine
Cimum gratissimum, basil
Citrus aurantium, synephrine, oxedrine
Claviceps purpurea (Fungus) ergot, ergotamine (d-lysergic acid amide) natural LSD, d-lysergic acid diethylamide
Coffea arabica, coffee plant, caffeine, theobromine
Cola acuminata, kola nut, theobromine, caffeine
Colchicum autumnale, autumn crocus, meadow saffron, colchicine
Conium maculatum, hemlock, coniine
Cordyceps militaris, cordyceps sinensis, adenosine
Cytisus scoparius, Scotch broom, sparteine, cytisine
Datura stromonium, Jimson weed, thorn apple, atropine, scopolamine
Dioscorea villosa, wild yam, diosgenine
Duboisia hopwoodii, pituri, tryptophan
Ephedra bronchodilator, ephedra, pseudoephedrine (isomer of ephedrine)
Ephedra sinica, Ephedra coryi, Chinese ephedra, ephedra, mormon tea, ephedrine
Erigeron breviscapus, breviscapine
Erythrina, coral tree, erythroidine
Erythroxylon, coca shrub, cocaine
Gentiana triflora, Chinese gentian, gentianine alkaloids
Humulus lupinus, hops, lupulin
Huperezia serrata, huperzine
Hydrastis cannadensis, golden seal, berberine, coptisine
Hyoscyamus niger, henbane, scopolamine, hyoscyamine
Hypericum perforatum, St. John's wort, klamath weed, hypericin
Ilex paraguariensis, yerba, mate, caffeine
Ipomea violacea, morning glory, natural LSD
Lophophora williamsii, peyote cactus, mescaline
Lupinus, lupines, lupinine
Lycoris radiata, galanthamine
Macleayae Cordatae, pink plume poppy, sanguinarine, bocconine
Mandragora officinarum, mandrake, atropine, hyoscyamine, scopolamine
Momordica charantia, bitter melon, momordicine
Myristica nutmeg, myristicin
Nelumbo nucifera, lotus, liensinine
Nicotiana tabacum, tobacco plant, nicotine
Oxytropis, locoweeds, swainsonine, miserotoxin
Panax ginseng, ginseng, ginsenosides
Papaver somniferum, opium poppy, codeine, morphine
Paullinia cupana, guarana, caffeine
Phaseolus vulgaris, white kidney bean, phaseolamine
Piper nigrum, piper, piperine
Piper methysticum, kava, kavain
Rauvolfia viridis, Caribbean snakeroot, reserpine
Rhaponticum uniflorum, uniflower, Swiss centaury, polypodine
Ricinus communis, castor bean, ricinine
Sinomenium acutum, sinomenium, sinomenine
Solanum, nightshades, solanidine.
Sophora secundiflora, mescal bean, cytisine.
Sophora flavescens, kuhseng, oxymatrine, matrine
Spartium junceum, Spanish broom, sparteine
Strychnos nux-vomica, strychnine, bucine, poison
Swainsona, Darling pea, swainsonine, swainsonine-N-oxide
Symphytum officinale, comfrey, echinidine
Taxus baccata, English yew, taxine
Theobroma cacao, cocoa, theobromine
Trichocereus pachanoi, Trichocereus peruvianus, San Pedro cactus, mescaline
Uncaria tomentosa, cat's claw, una de gato, seratonin, tryptophan and others
Veratrum, corn lily, false helibore, solanine
Zigadenus venenosus, death camas
Drugs from Plants
Ethnobotany & Chemistry
There are over a hundred chemical substances that have been derived from plants for use as drugs and medicines. This is by no means a comprehensive list of all of the plants, names of chemicals, or uses for those chemicals, but it should serve as a useful starting point for further research. For your convenience, I have listed the common name of a plant next to its scientific name. Be advised that common names are very imprecise and often assigned to completely different plants, so use the scientific name when looking for additional information concerning a plant.
Drug/Chemical Action Plant Source
Acetyldigoxin Cardiotonic Digitalis lanata (Grecian foxglove, woolly foxglove)
Adoniside Cardiotonic Adonis vernalis (pheasant's eye, red chamomile)
Aescin Antiinflammatory Aesculus hippocastanum (horse chestnut)
Aesculetin Antidysentery Frazinus rhychophylla
Agrimophol Anthelmintic Agrimonia supatoria
Ajmalicine Treatment for circulatory disorders Rauvolfia sepentina
Allantoin Vulnerary Several plants
Allyl isothiocyanate Rubefacient Brassica nigra (black mustard)
Anabesine Skeletal muscle relaxant Anabasis sphylla
Andrographolide Treatment for baccillary dysentery Andrographis paniculata
Anisodamine Anticholinergic Anisodus tanguticus
Anisodine Anticholinergic Anisodus tanguticus
Arecoline Anthelmintic Areca catechu (betel nut palm)
Asiaticoside Vulnerary Centella asiatica (gotu cola)
Atropine Anticholinergic Atropa belladonna (deadly nightshade)
Benzyl benzoate Scabicide Several plants
Berberine Treatment for bacillary dysentery Berberis vulgaris (common barberry)
Bergenin Antitussive Ardisia japonica (marlberry)
Betulinic acid Anticancerous Betula alba (common birch)
Borneol Antipyretic, analgesic, antiinflammatory Several plants
Bromelain Antiinflammatory, proteolytic Ananas comosus (pineapple)
Caffeine CNS stimulant Camellia sinensis (tea, also coffee, cocoa and other plants)
Camphor Rubefacient Cinnamomum camphora (camphor tree)
Camptothecin Anticancerous Camptotheca acuminata
(+)-Catechin Hemostatic Potentilla fragarioides
Chymopapain Proteolytic, mucolytic Carica papaya (papaya)
Cissampeline Skeletal muscle relaxant Cissampelos pareira (velvet leaf)
Cocaine Local anaesthetic Erythroxylum coca (coca plant)
Codeine Analgesic, antitussive Papaver somniferum (poppy)
Colchiceine amide Antitumor agent Colchicum autumnale (autumn crocus)
Colchicine Antitumor, antigout Colchicum autumnale (autumn crocus)
Convallatoxin Cardiotonic Convallaria majalis (lily-of-the-valley)
Curcumin Choleretic Curcuma longa (turmeric)
Cynarin Choleretic Cynara scolymus (artichoke)
Danthron Laxative Cassia species
Demecolcine Antitumor agent Colchicum autumnale (autumn crocus)
Deserpidine Antihypertensive, tranquilizer Rauvolfia canescens
Deslanoside Cardiotonic Digitalis lanata (Grecian foxglove, woolly foxglove)
L-Dopa Anti-parkinsonism Mucuna species (nescafe, cowage, velvetbean)
Digitalin Cardiotonic Digitalis purpurea (purple foxglove)
Digitoxin Cardiotonic Digitalis purpurea (purple foxglove)
Digoxin Cardiotonic Digitalis purpurea (purple or common foxglove)
Emetine Amoebicide, emetic Cephaelis ipecacuanha
Ephedrine Sympathomimetic, antihistamine Ephedra sinica (ephedra, ma huang)
Etoposide Antitumor agent Podophyllum peltatum (mayapple)
Galanthamine Cholinesterase inhibitor Lycoris squamigera (magic lily, resurrection lily, naked lady)
Gitalin Cardiotonic Digitalis purpurea (purple or common foxglove)
Glaucarubin Amoebicide Simarouba glauca (paradise tree)
Glaucine Antitussive Glaucium flavum (yellow hornpoppy, horned poppy, sea poppy)
Glasiovine Antidepressant Octea glaziovii
Glycyrrhizin Sweetener, treatment for Addison's disease Glycyrrhiza glabra (licorice)
Gossypol Male contraceptive Gossypium species (cotton)
Hemsleyadin Treatment for bacillary dysentery Hemsleya amabilis
Hesperidin Treatment for capillary fragility Citrus species (e.g., oranges)
Hydrastine Hemostatic, astringent Hydrastis canadensis (goldenseal)
Hyoscyamine Anticholinergic Hyoscyamus niger (black henbane, stinking nightshade, henpin)
Irinotecan Anticancer, antitumor agent Camptotheca acuminata
Kaibic acud Ascaricide Digenea simplex (wireweed)
Kawain Tranquilizer Piper methysticum (kava kava)
Kheltin Bronchodilator Ammi visaga
Lanatosides A, B, C Cardiotonic Digitalis lanata (Grecian foxglove, woolly foxglove)
Lapachol Anticancer, antitumor Tabebuia species (trumpet tree)
a-Lobeline Smoking deterrant, respiratory stimulant Lobelia inflata (Indian tobacco)
Menthol Rubefacient Mentha species (mint)
Methyl salicylate Rubefacient Gaultheria procumbens (wintergreen)
Monocrotaline Topical antitumor agent Crotalaria sessiliflora
Morphine Analgesic Papaver somniferum (poppy)
Neoandrographolide Treatment of dysentery Andrographis paniculata
Nicotine Insecticide Nicotiana tabacum (tobacco)
Nordihydroguaiaretic acid Antioxidant Larrea divaricata (creosote bush)
Noscapine Antitussive Papaver somniferum (poppy)
Ouabain Cardiotonic Strophanthus gratus (ouabain tree)
Pachycarpine Oxytocic Sophora pschycarpa
Palmatine Antipyretic, detoxicant Coptis japonica (Chinese goldenthread, goldthread, Huang-Lia)
Papain Proteolytic, mucolytic Carica papaya (papaya)
Papavarine Smooth muscle relaxant Papaver somniferum (opium poppy, common poppy)
Phyllodulcin Sweetener Hydrangea macrophylla (bigleaf hydrangea, French hydrangea)
Physostigmine Cholinesterase inhibitor Physostigma venenosum (Calabar bean)
Picrotoxin Analeptic Anamirta cocculus (fish berry)
Pilocarpine Parasympathomimetic Pilocarpus jaborandi (jaborandi, Indian hemp)
Pinitol Expectorant Several plants (e.g., bougainvillea)
Podophyllotoxin Antitumor, anticancer agent Podophyllum peltatum (mayapple)
Protoveratrines A, B Antihypertensives Veratrum album (white false hellebore)
Pseudoephredrine Sympathomimetic Ephedra sinica (ephedra, ma huang)
nor-pseudoephedrine Sympathomimetic Ephedra sinica (ephedra, ma huang)
Quinidine Antiarrhythmic Cinchona ledgeriana (quinine tree)
Quinine Antimalarial, antipyretic Cinchona ledgeriana (quinine tree)
Qulsqualic acid Anthelmintic Quisqualis indica (Rangoon creeper, drunken sailor)
Rescinnamine Antihypertensive, tranquilizer Rauvolfia serpentina
Reserpine Antihypertensive, tranquilizer Rauvolfia serpentina
Rhomitoxin Antihypertensive, tranquilizer Rhododendron molle (rhododendron)
Rorifone Antitussive Rorippa indica
Rotenone Piscicide, Insecticide Lonchocarpus nicou
Rotundine Analagesic, sedative, traquilizer Stephania sinica
Rutin Treatment for capillary fragility Citrus species (e.g., orange, grapefruit)
Salicin Analgesic Salix alba (white willow)
Sanguinarine Dental plaque inhibitor Sanguinaria canadensis (bloodroot)
Santonin Ascaricide Artemisia maritma (wormwood)
Scillarin A Cardiotonic Urginea maritima (squill)
Scopolamine Sedative Datura species (e.g., Jimsonweed)
Sennosides A, B Laxative Cassia species (cinnamon)
Silymarin Antihepatotoxic Silybum marianum (milk thistle)
Sparteine Oxytocic Cytisus scoparius (scotch broom)
Stevioside Sweetener Stevia rebaudiana (stevia)
Strychnine CNS stimulant Strychnos nux-vomica (poison nut tree)
Taxol Antitumor agent Taxus brevifolia (Pacific yew)
Teniposide Antitumor agent Podophyllum peltatum (mayapple or mandrake)
a-Tetrahydrocannabinol (THC) Antiemetic, decreases occular tension Cannabis sativa (marijuana)
Tetrahydropalmatine Analgesic, sedative, tranquilizer Corydalis ambigua
Tetrandrine Antihypertensive Stephania tetrandra
Theobromine Diuretic, vasodilator Theobroma cacao (cocoa)
Theophylline Diuretic, bronchodilator Theobroma cacao and others (cocoa, tea)
Thymol Topical antifungal Thymus vulgaris (thyme)
Topotecan Antitumor, anticancer agent Camptotheca acuminata
Trichosanthin Abortifacient Trichosanthes kirilowii (snake gourd)
Tubocurarine Skeletal muscle relaxant Chondodendron tomentosum (curare vine)
Valapotriates Sedative Valeriana officinalis (valerian)
Vasicine Cerebral stimulant Vinca minor (periwinkle)
Vinblastine Antitumor, Antileukemic agent Catharanthus roseus (Madagascar periwinkle)
Vincristine Antitumor, Antileukemic agent Catharanthus roseus (Madagascar periwinkle)
Yohimbine Aphrodisiac Pausinystalia yohimbe (yohimbe)
Yuanhuacine Abortifacient Daphne genkwa (lilac)
Yuanhuadine Abortifacient Daphne genkwa (lilac)