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Chapter 2.

The Chemistry of Living Matter


Matter is made up of elements, substances which 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 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.
The two atoms both lack electrons in their outer shells. They fill up the vacancies by

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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.

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) 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.
Electrolytes. The combination of water with a chemical compound dissolved in it is
called a solution. A compound that dissociates into anions and cations when dissolved in
water forms a solution which will conduct an electric current. Hence, any chemical
compound which will dissociate into ions in water is called an electrolyte. Electrolytes
are described as strong or weak, depending on how completely ionize. Strong electrolytes
ionize completely; weak electrolytes ionize slightly.
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.

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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 + H2O
acid base salt water
Hydrogen Concentration (pH). pH means “potential hydrogen” where pH indicates
neutrality. Pure water if fully ionized to H+ and OH- would potentially yield a molar
concentration of 107 H+ and 107 OH- (i.e. pH 7). A mildly acidic solution if fully ionized
would yield 106 H+ and 108 OH- and would be designated “pH 6” and so forth.
With few exceptions, living systems do not tolerate strongly acidic or alkaline
conditions, and their vital processes must take place within a range from pH 6 to pH 8.
Saliva has a pH of 6.8. Gastric juice is the most acid substance in the body (pH 1.6). The
pH of human blood must remain between 7.35 to 7.45. If human blood plasma merely
becomes neutral, pH 7, this seemingly harmless deviation actually would represent a life
threatening acidosis. This slightly basic range is zealously guarded by buffers that can
neutralize excess H+ and OH-.
description pH examples
14 NaOH, lye
very basic 13 oven cleaner
12 hair remover
11 ammonia
10 soap, milk of magnesia
weakly basic 9 chlorine bleach, phosphate detergent
8 seawater, egg white
neutral 7 pure water
6 urine, milk, saliva
weakly acidic 5 black coffee, rain water
4 tomatoes, grapes
3 vinegar, wine, soft drinks, beer, orange juice, pickles
2 lemon juice, lime juice
very acidic 1 stomach acid
0 HCl, battery acid
Table 2.1. The pH of some solutions.
Buffers. The hydrogen ion concentration in the extra-cellular fluid (ECF) must be
regulated so that the metabolic reactions within the cells will not be adversely affected by
a constantly changing hydrogen ion concentration (pH) to which they are extremely
sensitive. To maintain pH within physiologic limits, there are certain substances that tend
to compensate for any change in the pH when acids or alkalis are produced in metabolic

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reactions or are added to the body fluids. These are called buffers. A buffer is a mixture of
slightly ionized weak acid and its completely ionized salt. In such a system, added H +
combine with the anion of the salt to form undisassociated acid, and added OH- combines
with H+ to form water. The most important buffers in the blood and other body fluids are
bicarbonates and phosphates. For example, blood contains carbonate buffers made up of
salts sodium and potassium bicarbonate (NaHCO3 and KHCO3) and of the weak carbonic
acid (H2CO3). If a strong acid, such as HCl, enters the blood, the salts of the buffer
convert it to a weak acid which cannot lower the pH as much as HCl can:
NaHCO3 + HCl  NaCl + H2CO3
sodium hydrochloric sodium carbonic
bicarbonate acid chloride acid
On the other hand, if a strong base, such as sodium hydroxide (NaOH) enters the
blood, the carbonic acid will neutralize it:
H2CO3 + NaOH  NaHCO3 + H2O
carbonic sodium sodium
water
acid hydroxide bicarbonate
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 animals, we will mostly be concerned with organic compounds,
that is, compounds that always contain carbon and hydrogen. Four of the most important
organic matters are carbohydrates, proteins, lipids, and nucleic acids.
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
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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.). Fig. 2.5. The molecular structure of
The main role of carbohydrates in the protoplasm is fructose (left) and glucose (right).
to serve as a source of chemical energy.
Monosaccharides are the end product in the digestion of carbohydrates. Over 200 are
known but most important are glucose, fructose, and galactose. Except immediately after
a meal, glucose is the only monosaccharide present in significant quantities in the blood
and interstitial fluids of man and animals. There are two reasons for this:
1. Usually 80% to 100% of the monosaccharides absorbed from the gastrointestinal
tract is glucose, and only rarely is more than 20% of these fructose and galactose
together.
2. Within less than an hour after absorption from the gut, essentially all the fructose
and galactose will have entered the cells and been converted into glucose.
These 3 monosaccharides form disaccharides in the following manner:
- glucose and fructose form sucrose (cane sugar)
- glucose and galactose form lactose (milk sugar)
- glucose and glucose form maltose
The polysaccharide typical in animals is glycogen. It is commonly stored in
vertebrate liver and can be reconverted into glucose for transport by the blood.
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.

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

Most abundant of organic materials in animal protoplasm are the proteins. They
function as enzymes, components of cell membranes, contractile elements of muscle,
hormones, receptors on the cell surface and within the cell, antibodies, buffers, oxygen
carriers (hemoglobin) and oxygen storers (myoglobin), blood constituents (albumin –
most abundant), blood clotting factors, sources of energy, and as important components
of intracellular fabric of connective tissue.

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There are basically 20 amino acids that form all kinds of proteins found in living
things. Ten are classified as essential amino acids, meaning those that cannot be
synthesized in the body and must be supplied in the diet in adequate quantities.
Deficiency will result in a negative nitrogen balance with loss of weight and arrest of
growth. The other ten are classified as non-essential amino acids, meaning they can be
synthesized by the body.
Essential Amino Acids
Phenylalanine arginine isoleucine methionine
valine threonine leucine
tryptophan histidine lysine
Non-essential Amino Acids
alanine glutamine praline cysteine
asparagine glutamic acid serine
aspartic acid glycine tyrosine
Table 2.2. Essential and non-essential amino acids.
Pepsin II and gastricin (pepsin I) are the most important peptic enzymes of the
stomach; they are most active at a pH of 2 to 3 and completely inactive at a pH of 5.
Pepsin is capable of digesting collagen. They break down proteins into proteoses,
peptones and polypeptides. These are then hydrolyzed by pancreatic enzymes trypsin and
chymotrypsin into dipeptides and smaller polypeptides. Dipeptidases and
aminopolypeptidases in the epithelial cells of the small intestine are responsible for the
hydrolysis of peptides into amino acids.
Lipids. Unlike other bio-
logical polymers, lipids are not
defined by specific, repeating,
monomeric subunits. Rather,
they are defined by their water-
repellant property. The only
Fig. 2.7. Glycerol with fatty acid showing reactive site.
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.
Lipids are fats and other related substances. They are insoluble in H2O but soluble in
organic liquids like ether, chloroform, and acetone. Three types of lipids generally exist
in animals: neutral fats, phospholipids, and sterols.
Neutral Fats. Neutral fats (triglycerides) are composed of a glycerol and three
molecules of fatty acids. Neutral fats make up the major fuel of animals.
Phospholipids. Phospholipids (where one of the three fatty acids is replaced by
phosphoric acid and an organic base) is an important component of the molecular
organization of tissues especially membranes (e.g. Lecithin is an important
phospolipid of nerve membrane).
Sterols. Sterols are complex alcohols which have fat-like properties. Cholesterol,
the most common sterol in animal tissue, is a component of cell membranes.
Cholesterol can also undergo rearrangement to form such substances as sex
hormones and bile acids.
Fats are emulsified in the small intestines by bile acids and broken down into
glycerol and fatty acids by enteric and pancreatic lipases.

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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 2.3. 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.

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