Chapter 2:
The Chemical Level of
Organization
Copyright 2009, John Wiley & Sons, Inc.
Introduction
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Since chemicals compose your body and all
body activities are chemical in nature, it is
important to become familiar with the
language and fundamental concepts of
chemistry.
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How Matter is Organized
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Chemical Elements
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All forms of matter are composed of chemical
elements which are substances that cannot be
split into simpler substances by ordinary chemical
means.
Elements are given letter abbreviations called
chemical symbols.
Trace elements are present in tiny amounts
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Structure of Atoms
Units of matter of all chemical elements are
called atoms. An element is a quantity of
matter composed of atoms of the same type.
Atoms contain:
 Nucleus: protons (p+) & neutrons (neutral
charge)
 Electrons (e-) surround the nucleus as a
cloud (electron shells are designated regions
of the cloud)
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2 Representations of the Structure of an
Atom
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Atomic Number and Mass Number
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Atomic number is number of protons in the
nucleus.
Mass number is the sum of its protons and
neutrons.
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Atomic Mass
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Mass is measured as a dalton (atomic mass
unit)
Neutron has mass of 1.008 daltons
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proton has mass of 1.007 daltons
electron has mass of 0.0005 dalton
Atomic mass (atomic weight)of an element
is close to the mass number of its most
abundant isotope.
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Atomic Number and Mass Number
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Atomic Mass
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The atomic mass, also called the atomic weight,
of an element is the average mass of all its
naturally occurring isotopes and reflects the
relative abundance of isotopes with different mass
numbers.
The mass of a single atom is slightly less than the
sum of the masses of its neutrons, protons, and
electrons because some mass (less than1%) was
lost when the atom’s components came together
to form an atom.
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Ions, Molecules, & Compounds
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Ions
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an atom that gave up or gained an electron
written with its chemical symbol and (+) or (-)
Molecule
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atoms that share electrons
written as molecular formula showing the
number of atoms of each element (H2O)
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Free Radicals
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A free radical is an electrically charged atom or group
of atoms with an unpaired electron in its outermost
shell
Unstable and highly reactive; can become stable
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by giving up an electron
taking an electron from another molecule
Antioxidants are substances that inactivate oxygen-derived
free radicals
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Chemical Bonds
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The atoms of a molecule are held together by
forces of attraction called chemical bonds.
The likelihood that an atom will form a
chemical bond with another atom depends on
the number of electrons in its outermost shell,
also called the valence shell.
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Ionic Bonds
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When an atom loses or gains a valence
electron, ions are formed (Figure 2.4a).
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Positively and negatively charged ions are
attracted to one another.
Cations are positively charged ions that have
given up one or more electrons (they are electron
donors).
Anions are negatively charged ions that have
picked up one or more electrons that another
atom has lost (they are electron acceptors).
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The Ionic Bond Formation
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Covalent Bonds
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Covalent bonds are formed by the atoms of molecules
sharing one, two, or three pairs of their valence
electrons.
 Covalent bonds are common and are the strongest
chemical bonds in the body.
 Single, double, or triple covalent bonds are formed by
sharing one,two, or three pairs of electrons,
respectively.
Covalent bonds may be nonpolar or polar.
 In a nonpolar covalent bond, atoms share the
electrons equally; one atom does not attract the
shared electrons more strongly than the other atom
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Polar Covalent Bonds
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Unequal sharing of electrons between atoms. In
a water molecule, oxygen attracts the hydrogen
electrons more strongly

Oxygen has greater electronegativity as indicated by
the negative Greek delta sign.
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Hydrogen Bonds
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Approximately 5% as strong as covalent
bonds
Useful in establishing links between
molecules or between distant parts of a
very large molecule
Large 3-D molecules are
often held together by a
large number of hydrogen
bonds.
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Hydrogen Bonds
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are weak
intermolecular bonds;
they serve as links
between molecules.
help determine threedimensional shape
give water
considerable cohesion
which creates a very
high surface tension
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Chemical Reactions
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New bonds form and/or old bonds are broken.
Metabolism is “the sum of all the chemical
reactions in the body.”
Law of conservation of energy: energy cannot be
created or destroyed.
The total mass of reactants equals the total mass
of the products.
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Forms of Energy and Chemical
Reactions
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Energy is the capacity to do work.
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Kinetic energy is the energy associated with
matter in motion.
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Potential energy is energy stored by matter
due to its position.
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Energy Transfer in Chemical
Reactions
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An exergonic reaction is one in which the bond being
broken has more energy than the one formed so that
extra energy is released, usually as heat (occurs during
catabolism of food molecules).
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An endergonic reaction is just the opposite and thus
requires that energy be added, usually from a molecule
called ATP, to form a bond, as in bonding amino acid
molecules together to form proteins.
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Activation Energy
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Factors that Cause a Collision and
Chemical Reaction
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Concentration
Temperature
Catalysts are chemical compounds that speed up chemical reactions
by lowering the activation energy needed for a reaction to occur.
A catalyst does not alter the difference in potential energy between
the reactants and products. It only lowers the amount of energy
needed to get the reaction started.
 A catalyst helps to properly orient the colliding particles of matter
so that a reaction can occur at a lower collision speed.
 The catalyst itself is unchanged at the end of the reaction; it is
often re-used many times.
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Catalysts and chemical reactions
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Types of Chemical Reactions
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Synthesis reactions -- Anabolism
Decomposition reactions-- Catabolism
Exchange reactions
Reversible reactions
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Inorganic Compounds and Solutes
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Inorganic compounds usually lack carbon
and are simple molecules; whereas organic
compounds always contain carbon and
hydrogen, usually contain oxygen, and
always have covalent bonds.
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Water
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Is the most important and abundant inorganic
compound in all living systems.
Water’s most important property is polarity, the
uneven sharing of valence electrons
Enables reactants to collide to form products
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Polar Water Molecules
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Water as a Solvent
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In a solution the solvent dissolves the solute.
Substances which contain polar covalent
bonds and dissolve in water are hydrophilic,
while substances which contain non polar
covalent bonds are hydrophobic.
The polarity of water and its bent shape allow
it to interact with several neighboring ions or
molecules.
Water’s role as a solvent makes it essential
for health and survival.
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High Heat Capacity of Water
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Water has a high heat capacity.
It can absorb or release a relatively large amount of heat
with only a modest change in its own temperature.
This property is due to the large number of hydrogen
ions in water.
Heat of vaporization is also high
 Which is the amount of heat needed to change from
liquid to gas
 evaporation of water from the skin removes large
amount of heat
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3 Common Mixtures
A mixture is a combination of elements or compounds that are
physically blended together but are not bound by chemical bonds.
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Solution: a substance called the solvent dissolves
another substance called the solute. Usually there is
more solvent than solute in a solution.
A colloid differs from a solution mainly on the basis of
the size of its particles with the particles in the colloid
being large enough to scatter light (for example, the
protein in milk).
Suspension: the suspended material may mix with the
liquid or suspending medium for some time, but it will
eventually settle out.
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Dissociation of Acids, Bases, and
Salts
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Concept of pH
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pH scale runs from 0 to 14 (concentration of H+
in moles/liter)
pH of 7 is neutral
(distilled water -- concentration of OH- and H+ are
equal)
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pH below 7 is acidic ([H+] > [OH-]).
pH above 7 is alkaline ([H+] < [OH-]).
pH is a logarithmic scale
Example: a change of two or three pH units
pH of 1 contains 10x10=100 more H+ than pH of 3
pH of 8 contains 10x10x10=1000 more H+ than pH of 11
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The pH Scale
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Maintaining pH: Buffer Systems
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The pH values of different parts of the body
are maintained fairly constant by buffer
systems, which usually consist of a weak acid
and a weak base.
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Carbon and Its Functional Groups
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Many functional groups can attach to carbon skeleton
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esters, amino, carboxyl, phosphate groups
Very large molecules are called macromolecules (or
“polymers” if all the monomer subunits are similar)
Isomers have the same molecular formulas but
different structures (glucose & fructose are both
C6H12O6)
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Carbohydrates
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Carbohydrates provide most of the energy needed for
life and include sugars, starches, glycogen, and
cellulose.
Some carbohydrates are converted to other substances
which are used to build structures and to generate ATP.
Other carbohydrates function as food reserves.
Carbohydrates are divided into three major groups
based on their size: monosaccharides, disaccharides,
and polysaccharides
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Monosaccharides
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Disaccharides
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Combining 2 monosaccharides by dehydration
synthesis releases a water molecule.
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sucrose = glucose & fructose
maltose = glucose & glucose
lactose = glucose & galactose (lactose intolerance)
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Polysaccharides
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Polysaccharides are the
largest carbohydrates and
may contain hundreds of
monosaccharides.
The principal
polysaccharide in the
human body is glycogen,
which is stored in the liver
or skeletal muscles.
When blood sugar level
drops, the liver hydrolyzes
glycogen to yield glucose
which is released from the
liver into the blood
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Lipids
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Lipids, like carbohydrates, contain carbon,
hydrogen, and oxygen; but unlike carbohydrates,
they do not have a 2:1 ratio of hydrogen to oxygen.
They have few polar covalent bonds
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hydrophobic
mostly insoluble in polar solvents such as water
combines with proteins (lipoproteins) for transport in blood
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Triglycerides
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Triglycerides are the most plentiful lipids in
the body and provide protection, insulation,
and energy (both immediate and stored).
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At room temperature, triglycerides may be either
solid (fats) or liquid (oils).
Triglycerides provide more than twice as much
energy per gram as either carbohydrates or
proteins.
Triglyceride storage is virtually unlimited.
Excess dietary carbohydrates, proteins, fats, and
oils will be deposited in adipose tissue as
triglycerides.
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Triglycerides
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Phospholipids
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Phospholipids are important membrane
components.
They are amphipathic, with both polar and
nonpolar regions
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a polar head
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a phosphate group (PO4-3) & glycerol molecule
forms hydrogen bonds with water
2 nonpolar fatty acid tails
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interact only with lipids
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Steroids
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Steroids have four rings of carbon atoms
Steroids include
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sex hormone
bile salts
some vitamins
cholesterol, with cholesterol serving as an
important component of cell membranes and as
starting material for synthesizing other steroids.
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Four Ring Structure of Steroids
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Proteins
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Constructed from combinations of 20 amino acids.
 dipeptides formed from 2 amino acids joined by a
covalent bond called a peptide bond
 polypeptides chains formed from 10 to 2000 amino
acids.
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Formation of a Dipeptide Bond
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Dipeptides formed from 2 amino acids joined by a
covalent bond called a peptide bond
 dehydration synthesis
Polypeptides chains contain 10 to 2000 amino acids.
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Levels of Structural Organization
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Levels of structural organization include
 primary
 secondary
 tertiary
 quaternary
The resulting shape of the protein greatly influences its
ability to recognize and bind to other molecules.
Denaturation of a protein by a hostile environment
causes loss of its characteristic shape and function.
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Enzymes (usually proteins)
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Catalysts in living cells are called enzymes.
Enzymes are highly specific in terms of the
“substrate” with which they react.
Enzymes are subject to variety of cellular
controls.
Enzymes speed up chemical reactions by
increasing frequency of collisions, lowering
the activation energy and properly orienting
the colliding molecules.
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How and Enzyme Works
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DNA and RNA
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Nucleic acids are huge organic molecules that contain
carbon, hydrogen, oxygen, nitrogen, and phosphorus.
Deoxyribonucleic acid (DNA) forms the genetic code
inside each cell and thereby regulates most of the
activities that take place in our cells throughout a
lifetime.
Ribonucleic acid (RNA) relays instructions from the
genes in the cell’s nucleus to guide each cell’s assembly
of amino acids into proteins by the ribosomes.
The basic units of nucleic acids are nucleotides,
composed of a nitrogenous base, a pentose, sugar, and
a phosphate group.
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RNA Structure
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Differs from DNA
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single stranded
ribose sugar not deoxyribose sugar
uracil nitrogenous base replaces thymine
Types of RNA within the cell, each with
a specific function
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messenger RNA
ribosomal RNA
transfer RNA
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Adenosine Triphosphate (ATP)
Temporary
molecular storage of
energy as it is being
transferred from
exergonic catabolic
reactions to cellular
activities
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Formation & Usage of ATP
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Hydrolysis of ATP (removal of terminal
phosphate group by enzyme -- ATPase)
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releases energy
leaves ADP (adenosine diphosphate)
Synthesis of ATP
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enzyme ATP synthase catalyzes the addition of
the terminal phosphate group to ADP
energy from 1 glucose molecule is used during
both anaerobic and aerobic respiration to
create 36 to 38 molecules of ATP
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End of Chapter 2
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