Chapter 2.

The Chemistry of Living Matter

Matter is made up of elements, substances that cannot be broken down by ordinary chemical
means into simpler particles. Each element is a collection of a particular kind of discrete particle
matter called the atom. An atom is the smallest unit of an element that retains the chemical
properties of that element.
Subatomic Particles. Atoms are made up of even smaller, subatomic particles: the proton, the
neutron, and the electron. Protons have positive charges, electrons are negatively charged, and
neutrons are neutral.
Each element has a different number of protons. The atomic number is a count of the number
of protons in the elemental atom. Oxygen, for example, has 8 protons therefore its atomic number is
8. Carbon has 6. Hydrogen has 1. Nitrogen has 7.
Generally, atoms have approximately the same number of protons, neutrons, and electrons.
Each proton or neutron has a mass of about 1.7x10-24 gram. For convenience, this mass is defined as
1 atomic mass or 1 Dalton. The mass of an electron is about 1/2000 that of a proton, so it is often
disregarded when considering atomic mass. The protons and neutrons form the nucleus while
electrons travel at the speed of light orbiting the nucleus. The atomic mass of an element is the
number of protons plus neutrons in each nucleus.
Isotopes. Atoms with the same number of protons but different number of neutrons are called
isotopes. Two isotopes of ordinary hydrogen (1 proton, 0 neutrons) are deuterium (1 proton, 1
neutron) and tritium (1 proton, 2 neutrons). Isotopes share the same atomic number but differ in
atomic mass, the sum of the atom’s protons and neutrons. Thus, all hydrogen isotopes have the
atomic number 1, but atomic masses of 1, 2, and 3, respectively. Isotopes with their extra neutrons
are often unstable and undergo radioactive decay at typical and predictable rates, giving off
subatomic nuclear particles until they reach stability. Tritium, with a half-life of 12.5 years, is very
useful in biological research as a radioactive tag that allows hydrogen-containing compounds to be
traced through metabolic pathways.
Ions. Atoms with the same number of protons but different number of electrons form ions.
NaCl (sodium chloride, table salt) when in water, dissolves and separates into its constituent ions,
Na+ and Cl-. The Na ion is positively charged because one of its electrons has been “kidnapped” by
the Cl ion. Na+ then, has 11 protons, 11 neutrons, and only 10 electrons. Cl - on the other hand, has
17 protons, 17 neutrons, but 18 electrons, making it negatively charged. Positively charged ions are
called cations and negatively charged ions are called anions.
Chemical Bonds. Following the octet rule, the innermost shell, or the lowest quantum level,
for any atom never contains more than two electrons. Each shell external to this innermost shell
may contain up to eight electrons. The number of electrons in the outermost shell determines the
combining power (valence) of an atom. If the outermost shell contains eight electrons, (or in the
case of He, 2 electrons in the outermost shell) the atom will be unable to bond with any other atom
and the element is said to be inert.
Atoms with less than eight electrons in the outermost shell form bonds with other atoms to
saturate this shell. There are three major kinds of chemical bonds: covalent bonds, ionic bonds, and
hydrogen bonds. Covalent bonds involve the sharing of electrons. Two atoms, each lacking an
electron in their outermost shells, will fill up the vacancies by sharing a pair of electrons. Ionic
bonds involve the transfer of electrons from one atom to another so the atom either loses or gains
electrons. Hydrogen bonds form relatively weaker bonds between polar molecules or polarized
side groups of non-polar molecules. They are important in maintaining the shape of macromolecules
aiding in the performance of their biological functions.
A molecule consists of two or more atoms joined by bonds. The atoms composing a molecule
may be the same (O2, H2) or different (H2O, CH4). A molecule composed of different atoms is called
a compound.

Cl Cl Cl2
Fig. 2.1. Covalent bonds. Two atoms of chlorine form covalent bonds to produce chlorine gas.

Na Cl NaCl
Fig. 2.2. Ionic bonds. Atoms of sodium and chlorine form ionic bonds to produce salt.

Fig. 2.3. Hydrogen bonds. Four water molecules bonded by hydrogen bonds (dotted line)

Acids, Bases, and Salts. The hydrogen ion H+ is one of the most important ions in living
organisms. The hydrogen atom contains a single electron. When this electron is completely
transferred to another atom (not just shared with another as in covalent bonds), only the hydrogen
nucleus (essentially a single proton) remains. Any compound that releases H+ ions (protons) when
dissolved in solution is called an acid. An acid is classified as strong or weak depending on the
extent to which the acid molecule is dissociated in solution. Examples of strong acids that dissociate
completely in water are hydrochloric acid (HCl) and nitric acid (HNO3). Weak acids such as
carbonic acid (H2CO3) dissociate only slightly. A base, or alkali, is a compound that releases OH-
ions or accepts hydrogen ions in solution. Examples are caustic soda (NaOH) and ammonia water
(NH4OH) which are common household chemicals. Acids and bases, when concentrated, are severe
irritants and will burn the skin and the delicate covering of the eyes and mouth.
A salt is a compound resulting from the chemical interaction of an acid and a base. For
example, common salt, sodium chloride (NaCl), is formed by the interaction of hydrochloric acid
(HCl) and sodium hydroxide (NaOH). In water, the HCl dissociates into H+ and Cl- ions, the
hydroxide reacts with H+ to form water and Na+ and Cl- remain as a dissolved form of salt. This
reaction is shown in the following equation:
HCl + NaOH  NaCl + H 2O

8
 acid base salt water
Water. Water is the predominant chemical component of living organisms. It makes up from 60
– 90% of the protoplasm. Its unique physical properties, which include the ability to solvate a wide
range of organic and inorganic molecules, derive from water’s dipolar structure and exceptional
capacity for forming hydrogen bonds. An excellent nucleophile, water is a reactant or product in
many metabolic reactions. Water has a slight propensity to dissociate into hydroxide ions and
protons.
A water molecule is an irregular, slightly skewed tetrahedron with oxygen at its center. The two
hydrogen atoms and the unshared electrons of the remaining orbitals occupy the corners of the
tetrahedron. Water is a dipole, a molecule with electrical charge distributed asymmetrically about its
structure. The strongly electronegative oxygen atom pulls electrons away from the hydrogen nuclei,
leaving them with partial positive charge while its two unshared electron pairs constitute a region of
local negative charge. This enables water to dissolve large quantities of charged compounds such as
salts.

Fig. 2.4. (a) Water as a polar molecule. (b) Water forming hydration shells around chloride and sodium ions.
Organic Compounds
Of the 92 naturally occurring elements, 16 can be found in living things, and only 4 make up
99% of living matter. These elements are carbon, hydrogen, oxygen, and nitrogen. In the study of
plants, we will mostly be concerned with organic compounds, that is, compounds that always
contain carbon and hydrogen. Five of the most important organic matters found in plants are
carbohydrates, proteins, lipids, nucleic acids, and secondary metabolites.
Carbohydrates. Glucose and other simple sugars (monosaccharides), as well as their
polymers (polysaccharides), are called carbohydrates. Carbohydrates generally contain one oxygen
and 2 hydrogen atoms for every carbon. For example, glucose and fructose consist of six carbon
atoms, 12 hydrogen atoms, and 6 oxygen atoms, and have the formula C6H12O6. Galactose,
mannose, and many other monomers have this same formula, differing only in the arrangement of
the elements. Common carbohydrates having different chemical formulas include ribose, xylose,
arabinose, and ribose (C5H10O5); deoxyribose (C5H10O4); glucuronic acid and galacturonic acid
(C6H12O7); and rhamnose (C6H12O5).
Carbohydrates are synthesized from H2O and CO2 by plants
through photosynthesis (a process on which all life depends
because it is the starting point in the formation of food). They
provide much of the immediate or ultimate food for animals and
are much used by humans (food, fabrics, wood, paper, etc.). The
main role of carbohydrates in the protoplasm is to serve as a
source of chemical energy.
Fig. 2.5. The molecular structure of
Monosaccharides rarely occur as free sugars in plants; fructose (left) and glucose (right).
rather they are usually bound to other kinds of molecules or
linked together into larger carbohydrates. Two monosaccharides form a disaccharide. The most
common disaccharide in plants is sucrose, which is a glucose sugar and a fructose sugar linked
9
together. Sucrose is common table sugar, also called cane sugar or beet sugar. This disaccharide is
the major form of carbohydrate that moves in plants. (Glucose is also called grape sugar, blood
sugar, or dextrose. Fructose is often referred to as fruit sugar because of its abundance in ripening
fruit).
Polysaccharides present in plants may be classified into two types: structural and storage
polysaccharides.
Structural polysaccharides. Polysaccharides that hold cells and organisms together are called
structural polysaccharides. Cellulose is the most abundant structural polysaccharide in plants
and the most abundant polymer on earth. Cellulose polymers are made up of beta-glucose units.
A thousand or more cellulose polymers twist together to form microfibrils. Microfibrils are like
strong, tiny cables. Several microfibrils intertwine to make cellulose fibrils. Layers of fibrils
are cemented together into strong, three-dimensional grids by other kinds of structural
polysaccharides.
Pectins and hemicelluloses are gluey polysaccharides that hold cellulose fibrils together.
Cell wall pectins are mostly polymers of galacturonic acid. Hemicelluloses are not related to
cellulose and are made up of different kinds of monosaccharides. For example, celluloses in
grasses consist mostly of xylose, with lesser amounts of arabinose, galactose, and uronic acids.
In contrast, hemicelluloses in legumes are high in uronic acids, galactose, arabinose, with little
xylose.
Some of the most interesting hemicelluloses may not be structural hemicelluloses at all.
These are usually exuded from stems, roots, leaves, or fruits in a sticky mixture called gum.
(Gums are complex, branched polysaccharides consisting of several kinds of monomers.) For
example, a gum called gum arabic (from Acacia senegal) consists of arabinose, galactose,
glucose, and rhamnose. It is almost everywhere in our daily lives; it is used to stabilize postage-
stamp glue, beer suds, hand lotions, and liquid soaps.
Agar and carrageenan are two commercially important polysaccharides of algae. These
polymers are slimy substances that surround the cellulosic cell walls of certain red algae. Agar
(mostly from Gelidium robustum) is used to make drug capsules, cosmetics, gelatin desserts,
and temporary preservatives. Carrageenan (mostly from Chondrus sp.) is used primarily as
stabilizer in paints and cosmetics, and in foods such as salad dressings and dairy products.
Storage polysaccharides. Starch is the most common storage polysaccharide in plants. It is
composed mostly of two polysaccharides: amylose and amylopectin. Both are polymers of
alpha-glucose. In general, amylose twists into coils, groups of which are surrounded by larger
amylopectin.
Many plants also make inulin instead of or in addition to starch. Inulin is a polymer of
fructose. It is the storage polysaccharide in dahlias (Dahlia sp.), Jerusalem artichoke
(Helianthus tuberosum), globe artichoke (Cynara scolymus), chicory (Cichorium intybus), and
sweet corn. The storage organs of these plants (e.g., tubers of Jerusalem artichoke, kernels of
sweet corn) taste sweet because inulin releases fructose.
Proteins. A protein consists of one or more polypeptides and may also include sugars or other
kinds of small molecules. A polypeptide is a chain of amino acids linked together by carbon-
nitrogen bonds called peptide bonds. They contain C, H, O, N, and usually S.
Ten essential amino acids – those which cannot be synthesized in the ANIMAL body – must be
supplied in the diet in adequate quantities. Deficiency in any of these amino acids will result in a
negative nitrogen balance with loss of weight and arrest of growth. These include: phenylalanine,
10
valine, tryptophan, methionine, arginine, threonine, histidine, isoleucine, leucine, and lysine. Ten
non-essential amino acids – those which can be synthesized by the ANIMAL body – include:

Fig. 2.6. Structural formula of some amino acids. From left: methionine, alanine, tryptophan, and lysine.

alanine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, proline, serine, and
tyrosine. All twenty amino acids may be synthesized by plants.
After cellulose, proteins make up most of the remaining biomass of living plant cells. Proteins
in plants may be classified into 3 categories: structural proteins, storage proteins, and enzymes.
Structural proteins. In addition to containing carbohydrates, cell walls also include from 2%
to 10% protein. Among these proteins are expansins that help cell walls increase their surface
area. Expansins do this by causing slippage between the polysaccharides. This slippage results
from the breakage and formation of hydrogen bonds between the polysaccharides.
The synthesis of extensins is induced when cells are damaged by wounding, infection, or
freezing, suggesting that they somehow help protect or repair damaged cells. Extensins consist
of up to 30% carbohydrate, which make them glycoproteins – “sugar-proteins”.
Structural proteins also occur in all the membranes of a cell, and each kind of membrane
has a different protein composition.
Storage proteins. Storage proteins are mostly stored in seeds and are used as a source of
nutrition for the early development of seedlings. The composition of seed proteins depends on
the plant species. For example, corn produces a storage protein called zein, which consists of
nearly 30 polypeptides that occur in two major subunits and one minor subunit. In comparison,
wheat produces a storage protein called gliadin, which has four major subunits that are made
up of at least 46 polypeptides. The most complex storage proteins may be the glutenins of
wheat, which consist of up to 15 different proteins.
Seed storage proteins in soybeans and cereal grains (oats, rice, wheat, corn, barley) are
especially important because they are a major source of nutrition for humans and cattle.
However, corn and barley are low in the amino acids lysine, threonine, and tryptophan.
Soybean and other legume seeds are deficient in cysteine and methionine, but their lysine
content is adequate.
Seeds of some plants also contain proteins that have undesirable nutritional effects on the
animals that eat them. For example, up to 10% of the protein in many cereal grains inhibit
certain digestive enzymes of animals. These proteins are called protease inhibitors because
they inhibit proteases, the enzymes that digest proteins. The seed proteins of a few plants are
toxic. These include glycoproteins such as ricin D from the castor bean (Ricinus communis)
and abrin from the rosary pea (Abrus precatorius).
Enzymes. Most proteins in a living cell are enzymes which are the catalysts for biochemical
reactions. This means that enzymes speed up reactions without being consumed in the process.
These enzymes catalyze reactions that make or digest cell walls, membranes, storage polymers,
proteins, DNA, RNA, pollen walls, seed coats, chlorophyll, amino acids, and other plant
metabolites.

11
 Enzymes often remain active even after they are removed from the cell. Pure enzymes that
maintain their activity are commercially important. These enzymes include the proteases
papain and chymopapain from papaya
(Carica papaya). Papain digests
muscle tissue of animals, which is
why it is a major ingredient in meat
tenderizers. Chymopapain is a drug
used to treat the slippage of a disk in
the spinal column. It dissolves the
proteinaceous cartilage of which the Fig. 2.7. Glycerol with fatty acid showing reactive site.
disk is made.
Lipids. Unlike other biological polymers, lipids are not defined by specific, repeating,
monomeric subunits. Rather, they are defined by their water-repellant property. The only common
structural theme shared by all lipids is a large proportion of non-polar hydrocarbon groups. These
hydrocarbon groups are often made from polymers of two-carbon compound called acetate.
The major plant lipids with acetate-derived hydrocarbon chains include oils, phospholipids, and
waxes.
Oils. Oils are fats that are liquid at room temperature. A fat is a molecule of glycerol with three
long-chain organic acids called fatty acids, linked to it. The linkage between a fatty acid and a
glycerol is called an acylglyceride linkage. Thus, a fat is a triacylglyceride.
A fatty acid having no carbon-carbon double bonds is saturated. Oils are liquids because
their fatty acids are unsaturated; that is, they have double bonds between one or more pairs of
carbon atoms. Double bonds provide molecular rigidity at sharp angles, which prevents the
molecules from packing tightly into a solid. That is why unsaturated lipids such as corn oil and
peanut oil are liquids at room temperature.
The most common fatty acids in plants are oleic acid (one double bond), linoleic acid (two
double bonds), and linolenic acid (three double bonds). Linoleic and linolenic acids are
essential fatty acids. This means that they are necessary for human growth and development,
but our bodies cannot synthesize them. Seed oils from palms, coconuts, and other tropical
plants contain mostly palmitic acid, which is saturated.
Although triacylglycrides occur in all parts of a plant, they are most abundant in seeds.
Like carbohydrates, seed oils are a form of chemical energy that is harvested when the seed
germinates. Some seeds contain enough oil to be commercially valuable. The best known of
these are cotton, sesame, safflower, sunflower, olive, coconut, peanut, corn, castor bean, and
soybean. Most are used for products such as margarines, shortenings, salad oils, and frying oils;
the rest is used for non-food products such as lubricants, fuels, coatings, and soaps.
Phospholipids. Membranes contain phospholipids which are basically oils where a phosphate
group replaces one of the fatty acids. The phosphate group gives the compound a polar end that
dissolves in water or forms a covalent bond with a membrane protein. This property causes
phospholipids to have a dual solubility, since the phosphate end is water soluble (hydrophilic)
and the fatty end is water-repellent (hydrophobic). Consequently, phospholipids interact with
the polar group of proteins at one end and form an oily matrix at the other. This versatility
enables membranes to control the passage of polar and non-polar substances through them.
Wax and Wax-like Substances. Waxes are complex mixtures of fatty acids linked to long-
chain alcohols. They are usually harder and more water-repellent than other fats. Waxes that

12
 comprise the outermost layer (cuticle) of leaves, fruits, and herbaceous stems are called
epicuticular waxes. Waxes embedded in the cuticle are called cuticular waxes. The structures
of different waxes vary depending on the plants that produce them.
Cuticular wax is also associated with cutin, another waxy substance, which makes up most
of the cuticle in stems. A similar substance, called suberin, occurs in cork cells in bark and in
the same cells of underground plant parts. Cutin and suberin differ mainly in the kinds of fatty
acids they contain, but both function as barriers to water loss.
Nucleic Acids. The most complex biological polymers are nucleic acids. The two most
common nucleic acids are deoxyribonucleic acids and ribonucleic acids. DNA and RNA are
polymers made up of repeated units called nucleotides; nucleotides are composed of: a sugar, a
nitrogenous base, and a phosphate group.

DNA RNA
Sugar Deoxyribose Ribose
Nitrogenous base
Purine Adenine (A) Adenine (A)
Guanine (G) Guanine (G)
Pyrimidine Cytosine (C) Cytosine (C)
Thymine (T) Uracil (U)
Table 2.1. Differences between molecules of DNA and RNA.
Nucleic acids are unique because they can replicate themselves. Furthermore, DNA can make
RNA, which guides the assembly of proteins. Nucleic acids form the molecular foundation for
every living organism.
Secondary Metabolites. Plants make a variety of less widely distributed compounds such as
morphine, nicotine, menthol, and rubber. These compounds are the products of secondary
metabolism, which is the metabolism of chemicals that occur irregularly or rarely among plants and
that have no known general metabolic role in cells. Most occur in plants in combination with one or
more sugars. Such combination molecules are called glycosides. Suggested roles of these
metabolites are ecological. For example, some of these metabolites are brightly colored pigments
that attract insects for pollination. Others are toxic, protecting the plants from attacks by hungry
insects or invasion from pathogenic microbes. Three of the largest classes of secondary metabolites
are alkaloids, terpenoids, and phenolics.
Alkaloids. Alkaloids generally include alkaline substances that contain nitrogen as part of a
ring structure. They produce dramatic physiological effects in humans and other animals and
are often bitter. More than 6500 are known.
Terpenoids. Although considered secondary metabolites, terpenoids include some compounds
that have clear roles in plants. Some are plant hormones (abscisic acid and gibberellins) that
regulate plant growth and development while others maintain membrane function (sterols) and
are involved in the photosynthetic process (beta-carotene). These substances often are volatile
and have strong odors.
Phenolics. The diversity of phenolics is remarkable. Some phenolics are the red and blue
pigments of flowers (anthocyanins), while others are colorless except in UV light. Some are
sold in health shops as a supplement to vitamin C (flavanoids). Some are used in tanning

13
 leather and used to make dry wine (tannins). Lignin, perhaps the most significant phenolic, is a
major structural component of wood.
Other secondary metabolites besides these three exist. Many are familiar to us as the unique
flavors and odors of common edible plants or the colors of garden flowers.
Alkaloids
Compound Example Source Comment
Coniine Poison Hemlock nerve toxin; poison used to kill Socrates
Strychnine Strychnine tree potent nerve stimulant and convulsant
Tubocurarine Curare tree used as muscle relaxant during surgery, component of arrow
poisons
Morphine Opium poppy main painkiller used worldwide
Codeine Opium poppy cough suppressant
Atropine Belladonna used in eye exams to dilate pupils and antidote to nerve gas
Vincristine Madagascar Periwinkle main treatment for certain kinds of leukemia
Quinine Quinine tree bitter flavor of tonic in gin and tonic, prevents malaria
Amygladin Apricot seeds releases cyanide; may be active ingredient in unapproved
cancer drug

Terpenoids
Compound Example Source Comment
Menthol Eucalyptus tree strong aroma, used in cough medicines
Camphor Camphor tree component of disinfectants
Nepetalactone Catnip very attractive to cats
Digitalin Purple Foxglove cardiotonic used to stimulate heart action
Oleandrin Oleander heart poison (similar to digitalin)
Rubber Rubber tree component of rubber tires

Phenolics
Compound Example Source Comment
Myristicin Nutmeg main flavor of the spice
Salicin Willow tree folk medicine against headacche and fever, precursor of
aspirin
Rutin Buckwheat common "bioflavanoid" sold in nutrition stores

14