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Appendix A
The Metric System
▲ TABLE A-1 Metric Measures and English Equivalents
English
Equivalent
Symbol
Linear Measure
1,000 meters
km
0.62137 mile
100m
m
39.37 inches
1/10 meter
101m dm
3.937 inches
1 centimeter
1/100 meter
102m
0.3937 inch
1 millimeter
1/1,000 meter
103m mm
1 decimeter
1 micrometer 1/1,000,000
(or micron)
meter
1 nanometer
1/1,000,000,000
meter
Measures of Capacity
(For Fluids and Gases)
1 liter
1 milliliter
1/1,000 liter
cm
106m m
(or )
English
equivalents
infrequently
used
109m nm
1 cubic
decimeter
1/1,000
cubic meter
1/1,000,000
cubic meter
l
1.0567 U.S.
liquid quarts
1/100,000,000
cubic meter
Chicken egg
1 mm
ml
100 µm
10 µm
Plant and
animal cells
Nucleus
m3
Most bacteria
dm3
Mitochondrion
1 m
cm3 ml
1 milliliter (ml)
1 cubic
millimeter
0.1 m
Length of some
nerve and
muscle cells
Frog egg
1 liter (1)
1 cubic
centimeter
1m
1 cm
volume of 1 g of
water at standard
temperature and
pressure (stp)
Measures of Volume
1 cubic meter
Human height
100 nm
mm3
Electron microscope
1 kilometer
1 meter
10 m
103m
Light microscope
Measure
Unaided eye
Unit
Mycoplasmas
(smallest bacteria)
Viruses
Ribosomes
Measures of Mass
1 kilogram
1,000 grams
kg
2.2046
pounds
1 gram
g
15.432
grains
10 nm
1 milligram
1/1,000 gram
mg
1 microgram
1/1,000,000 gram
g (or mcg)
Proteins
LIpids
1 nm
Small
molecules
0.01 grain
(about)
0.1 nm
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A-2
APPENDIX A
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Appendix B
A Review of Chemical Principles
By Spencer Seager, Weber State College, and Lauralee Sherwood
CHEMICAL LEVEL OF
ORGANIZATION IN THE BODY
Proton
Matter is anything that occupies space and has mass, including all living and nonliving things in the universe. Mass is the
amount of matter in an object. Weight, in contrast, is the effect of gravity on that mass. The more gravity exerted on a
mass, the greater the weight of the mass. An astronaut has the
same mass whether on Earth or in space but is weightless in
the zero gravity of space.
Neutron
Nucleus
Electron
❚ Atoms
All matter is made up of tiny particles called atoms. These particles are too small to be seen individually, even with the most
powerful electron microscopes available today.
Even though extremely small, atoms consist of three types
of even smaller subatomic particles. Different types of atoms
vary in the number of these various subatomic particles they
contain. Protons and neutrons are particles of nearly identical mass, with protons carrying a positive charge and neutrons
having no charge. Electrons have a much smaller mass than
protons and neutrons and are negatively charged. An atom
consists of two regions—a dense, central nucleus made of protons and neutrons surrounded by a three-dimensional electron
cloud, where electrons move rapidly around the nucleus in orbitals (● Figure B-1). The magnitude of the charge of a proton
exactly matches that of an electron, but it is opposite in sign,
being positive. In all atoms, the number of protons in the nucleus is equal to the number of electrons moving around the
nucleus, so their charges balance and the atoms are neutral.
❚ Elements and atomic symbols
A pure substance composed of only one type of atom is called
an element. A pure sample of the element carbon contains
only carbon atoms, even though the atoms might be arranged
in the form of diamond or in the form of graphite (pencil
“lead”). Each element is designated by an atomic symbol, a
one- or two-letter chemical shorthand for the element’s name.
Usually these symbols are easy to follow, because they are derived from the English name for the element. Thus H stands
for hydrogen, C for carbon, and O for oxygen. In a few cases,
● FIGURE B-1
The atom
The atom consists of two regions. The central nucleus contains
protons and neutrons and makes up 99.9% of the mass. Surrounding
the nucleus is the electron cloud, where the electrons move rapidly
around the nucleus. (Figure not drawn to scale.)
the atomic symbol is based on the element’s Latin name—for
example, Na for sodium (natrium in Latin) and K for potassium (kalium). Of the 109 known elements, 26 are normally
found in the body. Four elements—oxygen, carbon, hydrogen,
and nitrogen—compose 96% of the body’s mass.
❚ Compounds and molecules
Pure substances composed of more than one type of atom are
known as compounds. Pure water, for example, is a compound that contains atoms of hydrogen and atoms of oxygen
in a 2-to-1 ratio, regardless of whether the water is in the form
of liquid, solid (ice), or vapor (steam). A molecule is the smallest unit of a pure substance that has the properties of that substance and is capable of a stable, independent existence. For
example, a molecule of water consists of two atoms of hydrogen and one atom of oxygen, held together by chemical bonds.
❚ Atomic number
Exactly what are we talking about when we refer to a “type” of
atom? That is, what makes carbon, hydrogen, and oxygen
atoms different? The answer is the number of protons in the
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nucleus. Regardless of where they are found, all hydrogen
atoms have one proton in the nucleus, all carbon atoms have
six, and all oxygen atoms have eight. Of course, these numbers
also represent the number of electrons moving around each
nucleus, because the number of electrons and number of protons in an atom are equal. The number of protons in the nucleus of an atom of an element is called the atomic number
of the element.
CHEMICAL BONDS
Because all matter is made up of atoms, atoms must somehow
be held together to form matter. The forces holding atoms together are called chemical bonds. Not all chemical bonds are
formed in the same way, but all involve the electrons of atoms.
Whether one atom will bond with another depends on the number and arrangement of its electrons. An atom’s electrons are
arranged in electron shells, to which we now turn our attention.
❚ Atomic weight
As expected, tiny atoms have tiny masses. For example, the actual mass of a hydrogen atom is 1.67 1024 g, that of a carbon atom is 1.99 1023 g, and that of an oxygen atom is
2.66 1023g. These very small numbers are inconvenient
to work with in calculations, so a system of relative masses has
been developed. These relative masses simply compare the actual masses of the atoms with each other. Suppose the actual
masses of two people were determined to be 45.50 kg and
113.75 kg. Their relative masses are determined by dividing
each mass by the smaller mass of the two: 45.50/45.50 1.00,
and 113.75/45.50 2.50. Thus the relative masses of the two
people are 1.00 and 2.50; these numbers simply express the
fact that the mass of the heavier person is 2.50 times that of
the other person. The relative masses of atoms are called atomic
masses, or atomic weights, and are given in atomic mass units
(amu). In this system, hydrogen atoms, the least massive of all
atoms, have an atomic weight of 1.01 amu. The atomic weight
of carbon atoms is 12.01 amu, and that of oxygen atoms is
16.00 amu. Thus, oxygen atoms have a mass about 16 times
that of hydrogen atoms. ▲ Table B-1 gives the atomic weights
and some other characteristics of the elements that are most
important physiologically.
▲ TABLE B-1
❚ Electron shells
Electrons tend to move around the nucleus in a specific pattern. The orbitals, or pathways traveled by electrons around
the nucleus, are arranged in an orderly series of concentric
layers known as electron shells, which consecutively surround
the nucleus. Each electron shell can hold a specific number
of electrons. The first (innermost) shell closest to the nucleus
can contain a maximum of only 2 electrons, no matter what
the element is. The second shell can hold a total of 8 more
electrons. The third shell can hold a maximum of 18 electrons.
As the number of electrons increases with increasing atomic
number, still more electrons occupy successive shells, each at
a greater distance from the nucleus. Each successive shell
from the nucleus has a higher energy level. Because the negatively charged electrons are attracted to the positively charged
nucleus, it takes more energy for an electron to overcome the
nuclear attraction and orbit farther from the nucleus. Thus the
first electron shell has the lowest energy level and the outermost shell of an atom has the highest energy level.
In general, electrons belong to the lowest energy shell possible, up to the maximum capacity of each shell. For example,
hydrogen atoms have only 1 electron, so it is in the first shell.
Helium atoms have 2 electrons, which are both in the first shell
and fill it. Carbon atoms have 6 electrons, 2 in the first shell
and 4 in the second shell, whereas the 8 electrons of oxygen
are arranged with 2 in the first shell and 6 in the second shell.
Characteristics of Selected Elements
Name and
Symbol
Number of
Protons
Atomic
Number
Atomic
Weight (amu)
Hydrogen (H)
1
1
1.01
Carbon (C)
6
6
12.01
Nitrogen (N)
7
7
14.01
Oxygen (O)
8
8
16.00
Sodium (Na)
11
11
22.99
Magnesium (Mg)
12
12
24.31
Phosphorus (P)
15
15
30.97
Sulfur (S)
16
16
32.06
Chlorine (Cl)
17
17
35.45
Potassium (K)
19
19
39.10
Calcium (Ca)
20
20
40.08
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APPENDIX B
❚ Bonding characteristics of an atom; valence
Atoms tend to undergo processes that result in a filled outermost electron shell. Thus the electrons of the outer or higherenergy shell determine the bonding characteristics of an atom
and its ability to interact with other atoms. Atoms that have a
vacancy in their outermost shell tend to either give up, accept,
or share electrons with other atoms (whichever is most favorable energetically) so that all participating atoms have filled
outer shells. For example, an atom that has only one electron
in its outermost shell may empty this shell so its remaining
shells are completely full. By contrast, another atom that lacks
only one electron in its outer shell may acquire the deficient
electron from the first atom to fill all its shells to the maximum.
The number of electrons an atom loses, gains, or shares to
achieve a filled outer shell is known as the atom’s valence. A
chemical bond is the force of attraction that holds participating atoms together as a result of an interaction between their
outermost electrons.
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Na
Cl
Na+
Cl–
Sodium atom
Chlorine atom
Sodium ion
Chloride ion
Sodium chloride (NaCl)
● FIGURE B-2
Ions and ionic bonds
Sodium (Na) and chlorine (Cl) atoms both have partially filled outermost shells. Therefore, sodium
tends to give up its lone electron in the outer shell to chlorine, thus filling chlorine’s outer shell. As
a result, sodium becomes a positively charged ion, and chlorine becomes a negatively charged ion
known as chloride. The oppositely charged ions attract each other, forming an ionic bond.
Consider sodium atoms (Na) and chlorine atoms (Cl)
(● Figure B-2). Sodium atoms have 11 electrons: 2 in the first
shell, 8 in the second shell, and 1 in the third shell. Chlorine
atoms have 17 electrons: 2 in the first shell, 8 in the second shell,
and 7 in the third shell. Because 8 electrons are required to fill
the second and third shells, sodium atoms have 1 electron more
than is needed to provide a filled second shell, whereas chlorine
atoms have 1 less electron than is needed to fill the third shell.
Each sodium atom can lose an electron to a chlorine atom,
leaving each sodium with 10 electrons, 8 of which are in the
second shell, which is full and is now the outer shell occupied
by electrons. By accepting 1 electron, each chlorine atom now
has a total of 18 electrons, with 8 of them in the third, or outer,
shell, which is now full.
hold Na and Cl together in the compound sodium chloride, NaCl, which is common table salt. A sample of sodium
chloride actually contains sodium and chloride ions in a threedimensional geometric arrangement called a crystal lattice.
The ions of opposite charge occupy alternate sites within the
lattice (● Figure B-3).
❚ Covalent bonds
It is not favorable, energywise, for an atom to give up or accept
more than three electrons. Neverthless, carbon atoms, which
● FIGURE B-3
❚ Ions; ionic bonds
Recall that atoms are electrically neutral because they have an
identical number of positively charged protons and negatively
charged electrons. As a result of giving up and accepting electrons, the sodium atoms and chlorine atoms have achieved
filled outer shells, but now each atom is unbalanced electrically. Although each sodium now has 10 electrons, it still has
11 protons in the nucleus and a net electrical charge, or valence, of 1. Similarly, each chlorine now has 18 electrons,
but only 17 protons. Thus each chlorine has a 1 charge.
Such charged atoms are called ions. Positively charged ions
are called cations; negatively charged ions are called anions.
As a helpful hint to keep these terms straight, imagine the “t”
in cation as standing for a “” sign and the first “n” in anion
as standing for “negative.”
Note that both a cation and anion are formed whenever
an electron is transferred from one atom to another. Because
opposite charges attract, sodium ions (Na) and charged chlorine atoms, now called chloride ions (Cl), are attracted toward each other. This electrical attraction that holds cations
and anions together is known as an ionic bond. Ionic bonds
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Crystal lattice for sodium chloride (table salt)
Cl–
Na+
Na+
Cl–
Cl–
Na+
Na+
Cl–
Na+
Cl–
Cl–
Na+
Na+
Na+
Cl–
Cl–
Na+
Cl–
Na+
Na+
Cl–
Cl–
Cl–
Cl–
Na+
Na+
Cl–
A Review of Chemical Principles
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have four electrons in their outer shell, form compounds. They
do so by another bonding mechanism, covalent bonding. Atoms
that would have to lose or gain four or more electrons to achieve
outer-shell stability usually bond by sharing electrons. Shared
electrons actually orbit around both atoms. Thus a carbon
atom can share its four outer electrons with the four electrons
of four hydrogen atoms, as shown in Equation B-1, where the
outer-shell electrons are shown as dots around the symbol of
each atom. (The resulting compound is methane, CH4, a gas
made up of individual CH4 molecules.)
Shared
electron pairs
H
C 4H → HCH
H
Shared
electron pairs
● FIGURE B-4
A covalent bond
A covalent bond is formed when atoms that share a pair of electrons are both attracted toward the
shared pair.
Molecular formula
H2
Hydrogen
H
(a)
O2
Oxygen
Structural formula
with covalent bond
Atomic structure
H
H
H
O
O
Covalent
bond
O
O
(b)
O
H
O
H
H
Each electron that is shared by two atoms is
counted toward the number of electrons
needed to fill the outer shell of each atom.
Thus each carbon atom shares four pairs, or
eight electrons, and so has eight in its outer
shell. Each hydrogen shares one pair, or two
electrons, and so has a filled outer shell. (Remember, hydrogen atoms need only two electrons to complete their outer shell, which is
the first shell.) The sharing of a pair of electrons by atoms binds them together by means
of a covalent bond (● Figure B-4). Covalent
bonds are the strongest of chemical bonds;
that is, they are the hardest to break.
Covalent bonds also form between some
identical atoms. For example, two hydrogen
atoms can complete their outer shells by sharing one electron pair made from the single
electrons of each atom, as shown in Equation B-2:
H H → HH
Eq. B-2
Thus hydrogen gas consists of individual H2
molecules (● Figure B-4a). (A subscript following a chemical symbol indicates the number of that type of atom present in the
molecule.) Several other nonmetallic elements also exist as molecules, because covalent bonds form between identical atoms;
oxygen (O2) is an example (● Figure B-4b).
Often, an atom can form covalent bonds
with more than one atom. One of the most
familiar examples is water (H2O), consisting
of two hydrogen atoms each forming a single
covalent bond with one oxygen atom (● Figure B-4c). Equation B-3 represents the formation of water’s covalent bonds:
H
H2O
Water
Covalent
bond
(c)
APPENDIX B
O → HO
H
H
Eq. B-3
The water molecule is sometimes represented as
H
A-6
Eq. B-1
H O

H
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where the nonshared electron pairs are not shown and the covalent bonds, or shared pairs, are represented by dashes.
❚ Nonpolar and polar molecules
The electrons between two atoms in a covalent bond are not
always shared equally. When the atoms sharing an electron
pair are identical, such as two oxygen atoms, the electrons are
attracted equally by both atoms and so are shared equally. The
result is a nonpolar molecule. The term nonpolar implies no
difference at the two ends (two “poles”) of the bond. Because
both atoms within the molecule exert the same pull on the
shared electrons, each shared electron spends the same amount
of time orbiting each atom. Thus both atoms remain electrically neutral in a nonpolar molecule such as O2.
When the sharing atoms are not identical, unequal sharing of electrons occurs, because atoms of different elements
do not exert the same pull on shared electrons. For example,
an oxygen atom strongly attracts electrons when it is bonded to
other atoms. A polar molecule results from the unequal sharing of electrons between different types of atoms covalently
bonded together. The water molecule is a good example of a
polar molecule. The oxygen atom pulls the shared electrons
more strongly than do the hydrogen atoms within each of the
two covalent bonds. Consequently, the electron of each hydrogen atom tends to spend more time away orbiting around the
oxygen atom than at home around the hydrogen atom. Because
of this nonuniform distribution of electrons, the oxygen side of
the water molecule where the shared electrons spend more
time is slightly negative, and the two hydrogens that are visited
less frequently by the electrons are slightly more positive
(● Figure B-5). Note that the entire water molecule has the
same number of electrons as it has protons, and so as a whole
has no net charge. This is unlike ions, which have an electron
excess or deficit. Polar molecules have a balanced number of
protons and electrons but an unequal distribution of the shared
electrons among the atoms making up the molecule.
❚ Hydrogen bonds
Polar molecules are attracted to other polar molecules. In water,
for example, an attraction exists between the positive hydrogen ends of some molecules and the negative oxygen ends of
others. Hydrogen is not a part of all polar molecules, but when
it is covalently bonded to an atom that strongly attracts electrons to form a covalent molecule, the attraction of the positive (hydrogen) end of the polar molecule to the negative end
of another polar molecule is called a hydrogen bond (● Figure B-6). Thus, the polar attractions of water molecules to each
other are an example of hydrogen bonding.
CHEMICAL REACTIONS
Processes in which chemical bonds are broken and/or formed
are called chemical reactions. Reactions are represented by
equations in which the reacting substances (reactants) are typically written on the left, the newly produced substances (products) are written on the right, and an arrow meaning “yields”
points from the reactants to the products. These conventions
are illustrated in Equation B-4:
AB r CD
Reactants Products
Eq. B-4
❚ Balanced equations
A chemical equation is a “chemical bookkeeping” ledger that
describes what happens in a reaction. By the law of conservation of mass, the total mass of all materials entering a reaction
equals the total mass of all the products. Thus, the total number of atoms of each element must always be the same on the
left and right sides of the equation, because no atoms are lost.
Such equations in which the same number of atoms of each
● FIGURE B-6
A hydrogen bond
● FIGURE B-5
A polar molecule
A water molecule is an example of a polar molecule, in which the
distribution of shared electrons is not uniform. Because the oxygen atom pulls the shared electrons more strongly than the hydrogen atoms do, the oxygen side of the molecule is slightly negatively
charged, and the hydrogen sides are slightly positively charged.
Slightly negative
charge
A hydrogen bond is formed by the attraction of a positively charged
hydrogen end of a polar molecule to the negatively charged end of
another polar molecule.
( )
( )
( )
O
O
H
H
H
H
O
( )
( )
H
H
( )
O
O
O
H
Dotted lines
represent
hydrogen bonds
( )
( )
( )
OO
H
( )
H
Slightly positive charge
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( )
( )
( )
H
H
( )
( )
Polar covalent
bond
O
O
( )
( )
H
( )
A Review of Chemical Principles
A-7
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type appear on both sides are called balanced equations.
When writing a balanced equation, the number preceding a
chemical symbol designates the number of independent (unjoined) atoms, ions, or molecules of that type, whereas a number written as a subscript following a chemical symbol denotes
the number of a particular atom within a molecule. The absence of a number indicates “one” of that particular chemical.
Let’s look at a specific example, the oxidation of glucose (the
sugar that cells use as fuel), as shown in Equation B-5:
C6H12O6 6O2 r 6CO2 6H2O
Glucose Oxygen Carbon Water
dioxide
Eq. B-5
According to this equation, 1 molecule of glucose reacts with
6 molecules of oxygen to produce 6 molecules of carbon dioxide and 6 molecules of water. Note the following balance in
this reaction:
• 6 carbon atoms on the left (in 1 glucose molecule) and
6 carbon atoms on the right (in 6 carbon dioxide molecules)
• 12 hydrogen atoms on the left (in 1 glucose molecule)
and 12 on the right (in 6 water molecules, each containing
2 hydrogen atoms)
• 18 oxygen atoms on the left (6 in 1 glucose molecule
plus 12 more in the 6 oxygen molecules) and 18 on the right
(12 in 6 carbon dioxide molecules, each containing 2 oxygen
atoms, and 6 more in the 6 water molecules, each containing
1 oxygen atom)
❚ Reversible and irreversible reactions
Under appropriate conditions, the products of a reaction can
be changed back to the reactants. For example, carbon dioxide gas dissolves in and reacts with water to form carbonic acid,
H2CO3:
CO2 H2O r H2CO3
Eq. B-6
Carbonic acid is not very stable, however, and as soon as some
is formed, part of it decomposes to give carbon dioxide and water:
H2CO3 r CO2 H2O
Eq. B-7
Reactions that go in both directions are called reversible reactions. They are usually represented by double arrows pointing
in both directions:
CO2 H2O A H2CO3
Eq. B-8
Theoretically, every reaction is reversible. Often, however, conditions are such that a reaction, for all practical purposes, goes
only in one direction; such a reaction is called irreversible. For
example, an irreversible reaction takes place when an explosion occurs, because the products do not remain in the vicinity of the reaction site to get together to react.
❚ Catalysts; enzymes
The rates (speeds) of chemical reactions are influenced by a
number of factors, of which catalysts are one of the most important. A catalyst is a “helper” molecule that speeds up a reA-8
APPENDIX B
action without being used up in the reaction. Living organisms
use catalysts known as enzymes. These enzymes exert amazing influence on the rates of chemical reactions that take place
in the organisms. Reactions that take weeks or even months
to occur under normal laboratory conditions take place in seconds under the influence of enzymes in the body. One of the
fastest-acting enzymes is carbonic anhydrase, which catalyzes
the reaction between carbon dioxide and water to form carbonic
acid. This reaction is important in the transport of carbon dioxide from tissue cells, where it is produced metabolically, to the
lungs, where it is excreted. The equation for the reaction was
shown in Equation B-6. Each molecule of carbonic anhydrase
catalyzes the conversion of 36 million CO2 molecules per minute! Enzymes are important in essentially every chemical reaction that takes place in living organisms.
MOLECULAR AND FORMULA
WEIGHT AND THE MOLE
Because molecules are made up of atoms, the relative mass of
a molecule is simply the sum of the relative masses (atomic
weights) of the atoms found in the molecule. The relative masses
of molecules are called molecular masses or molecular weights.
The molecular weight of water, H2O, is thus the sum of the
atomic weights of two hydrogen atoms and one oxygen atom,
or 1.01 amu 1.01 amu 16.00 amu 18.02 amu.
Not all compounds exist in the form of molecules. Ionically bonded substances such as sodium chloride consist of
three-dimensional arrangements of sodium ions (Na) and
chloride ions (Cl) in a 1-to-1 ratio. The formulas for ionic compounds reflect only the ratio of the ions in the compound and
should not be interpreted in terms of molecules. Thus the formula for sodium chloride, NaCl, indicates that the ions combine in a 1-to-1 ratio. It is convenient to apply the concept of
relative masses to ionic compounds even though they do not
exist as molecules. The formula weight for such compounds
is defined as the sum of the atomic weights of the atoms found
in the formula. Thus the formula weight of NaCl is equal to
the sum of the atomic weights of one sodium atom and one
chlorine atom, or 22.99 amu 35.45 amu 58.44 amu.
As you have seen, chemical reactions can be represented
by equations and discussed in terms of numbers of molecules,
atoms, and ions reacting with each other. To carry out reactions
in the laboratory, however, a scientist cannot count out numbers of reactant particles but instead must be able to weigh out
the correct amount of each reactant. Using the mole concept
makes this task possible. A mole (abbreviated mol) of a pure
element or compound is the amount of material contained in
a sample of the pure substance that has a mass in grams equal
to the substance’s atomic weight (for elements) or the molecular weight or formula weight (for compounds). Thus 1 mole of
potassium, K, would be a sample of the element with a mass
of 39.10 g. Similarly, a mole of H2O would have a mass of
18.02 g, and a mole of NaCl would be a sample with a mass of
58.44 g.
The fact that atomic weights, molecular weights, and formula weights are relative masses leads to a fundamental char-
2373_BC_Sherwood App 4/14/03 4:12 PM Page A-9
acteristic of moles. One mole of oxygen atoms has a mass of
16.00 g, and 1 mole of hydrogen atoms has a mass of 1.01 g.
Thus the ratio of the masses of 1 mole of each element is
16.00/1.01, the same as the ratio of the atomic weights for the
two elements. Recall that these atomic weights compare the
relative masses of oxygen and hydrogen. Accordingly, the number of oxygen atoms present in 16 grams of oxygen (1 mole of
oxygen) is the same as the number of hydrogen atoms present
in 1.01 grams of hydrogen. Therefore, 1 mole of oxygen contains exactly the same number of oxygen atoms as the number
of hydrogen atoms in 1 mole of hydrogen. Thus, it is possible
and sometimes useful to think of a mole as a specific number
of particles. This number, called Avogadro’s number, is equal
to 6.02 1023.
SOLUTIONS, COLLOIDS,
AND SUSPENSIONS
In contrast to a compound, a mixture consists of two or more
types of elements or molecules physically blended together
(intermixed) instead of being linked by chemical bonds. A compound has very different properties from the individual elements of which it is composed. For example, the solid, white
NaCl (table salt) crystals you use to flavor your food are very
different from either sodium (a silvery white metal) or chlorine
(a poisonous yellow-green gas found in bleach). By comparison, each component of a mixture retains its own chemical
properties. If you mix salt and sugar together, each retains its
own distinct taste and other individual properties. The constituents of a compound can only be separated by chemical
means—bond breakage. By contrast, the components of a mixture can be separated by physical means, such as filtration or
evaporation. The most common mixtures in the body are mixtures of water and various other substances. These mixtures
are categorized as solutions, colloids, or suspensions, depending
on the size and nature of the substance mixed with water.
❚ Solutions
Most chemical reactions in the body take place between reactants that have dissolved to form solutions. Solutions are homogenous mixtures containing a relatively large amount of
one substance called the solvent (the dissolving medium) and
smaller amounts of one or more substances called solutes (the
dissolved particles). Salt water, for example, contains mostly
water, which is thus the solvent, and a smaller amount of salt,
which is the solute. Water is the solvent in most solutions found
in the human body.
Cl is broken down, and the individual ions are separated and
distributed uniformly throughout the solution. These mobile,
charged ions conduct electricity through the solution. Solutes
that form ions in solution and conduct electricity are called
electrolytes. Some very polar covalent molecules also behave
this way. When sugar dissolves, however, individual covalently
bonded sugar molecules leave the solid and become uniformly
distributed throughout the solution. These uncharged molecules
cannot conduct a current. Solutes that do not form conductive
solutions are called nonelectrolytes.
❚ Measures of concentration
The amount of solute dissolved in a specific amount of solution can vary. For example, a salt–water solution might contain 1 g of salt in 100 ml of solution, or it could contain 10 g
of salt in 100 ml of solution. Both solutions are salt–water solutions, but they have different concentrations of solute. The
concentration of a solution indicates the relationship between
the amount of solute and the amount of solution. Concentrations can be given in a number of different units.
Molarity
Concentrations given in terms of molarity (M) give the number of moles of solute in exactly 1 liter of solution. Thus a half
molar (0.5 M) solution of NaCl would contain one-half mole,
or 29.22 g, of NaCl in each liter of solution.
Normality
When the solute is an electrolyte, it is sometimes useful to express the concentration of the solution in a unit that gives information about the amount of ionic charge in the solution.
This is done by expressing concentration in terms of normality (N). The normality of a solution gives the number of equivalents of solute in exactly 1 liter of solution. An equivalent of
an electrolyte is the amount that produces 1 mole of positive
(or negative) charges when it dissolves. The number of equivalents of an electrolyte can be calculated by multiplying the
number of moles of electrolyte by the total number of positive
charges produced when one formula unit of the electrolyte dissolves. Consider NaCl and calcium chloride (CaCl2) as examples. The ionization reactions for one formula unit of each
solute are:
NaCl r Na Cl
Eq. B-9
CaCl2 r Ca2 2Cl
Eq. B-10
Thus 1 mole of NaCl produces 1 mole of positive charges (Na)
and so contains 1 equivalent:
(1 mole NaCl)(1) 1 equivalent
❚ Electrolytes; nonelectrolytes
When ionic solutes are dissolved in water to form solutions, the
resulting solution will conduct electricity. This is not true for
most covalently bonded solutes. For example, a salt–water solution conducts electricity, but a sugar–water solution does
not. When salt dissolves in water, the solid lattice of Na and
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where the number 1 used to multiply the 1 mole of NaCl
came from the 1 charge on Na.
One mole of CaCl2 produces 1 mole of Ca2, which is
2 moles of positive charge. Thus 1 mole of CaCl2 contains 2
equivalents:
(1 mole CaCl2)(2) 2 equivalents
A Review of Chemical Principles
A-9
2373_BC_Sherwood App 4/14/03 4:12 PM Page A-10
where the number 2 used in the multiplication came from the
2 charge on Ca2.
If two solutions were made such that one contained 1 mole
of NaCl per liter and the other contained 1 mole of CaCl2 per
liter, the NaCl solution would contain 1 equivalent of solute per liter and would be 1 normal (1 N). The CaCl2 solution would contain 2 equivalents of solute per liter and would
be 2 normal (2 N).
Osmolarity
Another expression of concentration frequently used in physiology is osmolarity (osm), which indicates the total number of
solute particles in a liter of solution instead of the relative
weights of the specific solutes. The osmolarity of a solution is
the product of M and n, where n is the number of moles of
solute particles obtained when 1 mole of solute dissolves. Because nonelectrolytes such as glucose do not dissociate in solution, n 1 and the osmolarity (n times M) is equal to the
molarity of the solution. For electrolyte solutions, the osmolarity exceeds the molarity by a factor equal to the number of
ions produced on dissociation of each molecule in solution.
For example, because a NaCl molecule dissociates into two
ions, Na and Cl, the osmolarity of a 1 M solution of NaCl
is 2 1 M 2 osm.
❚ Colloids and suspensions
In solutions, solute particles are ions or small molecules. By contrast, the particles in colloids and suspensions are much larger
than ions or small molecules. In colloids and suspensions,
these particles are known as dispersed-phase particles instead
of solutes. When the dispersed-phase particles are no more than
about 100 times the size of the largest solute particles found in
a solution, the mixture is called a colloid. The dispersed-phase
particles of colloids generally do not settle out. All dispersedphase particles of colloids carry electrical charges of the same
sign. Thus they repel each other. The constant buffeting from
these collisions keeps the particles from settling. The most
abundant colloids in the body are small functional proteins that
are dispersed in the body fluids. An example is the colloidal dispersion of the plasma proteins in the blood (see p. 392).
When dispersed-phase particles are larger than those in
colloids, if the mixture is left undisturbed the particles will settle out because of the force of gravity. Such mixtures are usually
called suspensions. The major example of a suspension in the
body is the mixture of blood cells suspended in the plasma. The
constant movement of blood as it circulates through the blood
vessels keeps the blood cells rather evenly dispersed within the
plasma. However, if a blood sample is placed in a test tube and
treated to prevent clotting, the heavier blood cells gradually
settle to the bottom of the tube.
INORGANIC AND ORGANIC CHEMICALS
Chemicals are commonly classified into two categories: inorganic and organic. The original criterion used for this classification was the origin of the chemicals. Those that came from
A-10
APPENDIX B
living or once-living sources were organic, and those that came
from other sources were inorganic. Today the basis for classification is the element carbon. Organic chemicals are generally
those that contain carbon. All others are classified as inorganic.
A few carbon-containing chemicals are also classified as inorganic; the most common are pure carbon in the form of diamond and graphite, carbon dioxide (CO2), carbon monoxide
(CO), carbonates such as limestone (CaCO3), and bicarbonates such as baking soda (NaHCO3).
The unique ability of carbon atoms to bond to each other
and form networks of carbon atoms results in an interesting
fact. Even though organic chemicals all contain carbon, millions of these compounds have been identified. Some were
isolated from natural plant or animal sources, and many have
been synthesized in laboratories. Inorganic chemicals include
all the other 108 elements and their compounds. The number
of known inorganic chemicals made up of all these other elements is estimated to be about 250,000, compared to millions
of organic compounds made up predominantly of carbon.
❚ Monomers and polymers
Another result of carbon’s ability to bond to itself is the large
size of some organic molecules. Molecules classified as organic
range in size from methane, CH4, a small, simple molecule
with one carbon atom, to molecules such as DNA that contain
as many as a million carbon atoms. Organic molecules that are
essential for life are called biological molecules, or biomolecules for short. Some biomolecules are rather small organic
compounds, including simple sugars, fatty acids, amino acids,
and nucleotides. These small, single units, known as monomers
(meaning “single unit”), are subunits, or building blocks, for
the synthesis of larger biomolecules, including complex carbohydrates, lipids, proteins, and nucleic acids, respectively. These
larger organic molecules are called polymers (meaning “many
units”), reflecting the fact that they are made by the bonding
together of a number of smaller monomers. For example, starch
is formed by linking many glucose molecules together. Very
large organic polymers are often referred to as macromolecules,
reflecting their large size (macro means “large”). Macromolecules include many naturally occurring molecules, such as
DNA and structural proteins, as well as many molecules that
are synthetically produced, such as synthetic textiles (for example, nylon) and plastics.
ACIDS, BASES, AND SALTS
Acids, bases, and salts may be inorganic or organic compounds.
Acids and bases are chemical opposites, and salts are produced
when acids and bases react with each other. In 1887, Swedish
chemist Svante Arrhenius proposed a theory defining acids and
bases. He said that an acid is any substance that will dissociate,
or break apart, when dissolved in water and in the process release a hydrogen ion, H. Similarly, bases are substances that
dissociate when dissolved in water and in the process release a
hydroxyl ion, OH. Hydrogen chloride (HCl) and sodium hydroxide (NaOH) are examples of Arrhenius acids and bases;
2373_BC_Sherwood App 4/14/03 4:12 PM Page A-11
their dissociations in water are represented in Equations B-11
and B-12, respectively:
HCl r H Cl
Eq. B-11
NaOH r Na OH
Eq. B-12
Note that the hydrogen ion is a bare proton, the nucleus of a
hydrogen atom. Also note that both HCl and NaOH would
behave as electrolytes.
Arrhenius did not know that free hydrogen ions cannot
exist in water. They covalently bond to water molecules to form
hydronium ions, as shown in Equation B-13:
H O H → HO H 

Eq. B-13
H
H
In 1923, Johannes Brønsted in Denmark and Thomas
Lowry in England proposed an acid–base theory that took this
behavior into account. They defined an acid as any hydrogencontaining substance that donates a proton (hydrogen ion) to
another substance (an acid is a proton donor) and a base as any
substance that accepts a proton (a base is a proton acceptor).
According to these definitions, the acidic behavior of HCl given
in Equation B-11 is rewritten as shown in Equation B-14:
HCl H2O A H3O Cl
Eq. B-14
Note that this reaction is reversible, and the hydronium
ion is represented as H3O. In Equation B-14, the HCl acts as
an acid in the forward (left-to-right) reaction, whereas water acts
as a base. In the reverse reaction (right-to-left), the hydronium
ion gives up a proton and thus is an acid, whereas the chloride
ion, Cl, accepts the proton and so is a base. It is still a common practice to use equations such as B-11 to simplify the representation of the dissociation of an acid, even though scientists recognize that equations like B-14 are more correct.
❚ Neutralization reactions
At room temperature, inorganic salts are crystalline solids that
contain the positive ion (cation) of an Arrhenius base such as
NaOH and the negative ion (anion) of an acid such as HCl.
Salts can be produced by mixing solutions of appropriate acids
and bases, allowing a neutralization reaction to occur. In neutralization reactions, the acid and base react to form a salt and
water. Most salts that form are water soluble and can be recovered by evaporating the water. Equation B-15 is a neutralization reaction:
HCl NaOH r NaCl H2O
Eq. B-15
When acids or bases are used as solutes in solutions, the
concentrations can be expressed as normalities just as they
were earlier for salts. An equivalent of acid is the amount that
gives up 1 mole of H in solution. Thus, 1 mole of HCl is also
1 equivalent, but 1 mole of H2SO4 is 2 equivalents. Bases are
described in a similar way, but an equivalent is the amount of
base that gives 1 mole of OH.
See Chapter 15 for a discussion of acid–base balance in
the body.
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FUNCTIONAL GROUPS
OF ORGANIC MOLECULES
Organic molecules consist of carbon and one or more additional elements covalently bonded to one another in “Tinker
Toy” fashion. The simplest organic molecules, hydrocarbons,
such as methane and petroleum products, have only hydrogen
atoms attached to a carbon backbone of varying lengths. All
biomolecules always have additional elements besides hydrogen added to the carbon backbone. The carbon backbone forms
the stable portion of most biomolecules. Other atoms covalently bonded to the carbon backbone, either alone or in clusters, form what is termed functional groups. All organic compounds can be classified according to the functional group or
groups they contain. Functional groups are specific combinations of atoms that generally react in the same way, regardless
of the number of carbon atoms in the molecule to which they
are attached. For example, all aldehydes contain a functional
group that contains one carbon atom, one oxygen atom, and
one hydrogen atom covalently bonded in a specific way:
O

( C H)
The carbon atom in an aldehyde group forms a single covalent bond with the hydrogen atom and a double bond (a bond
in which two covalent bonds are formed between the same
atoms, designated by a double line between the atoms) with
the oxygen atom. The aldehyde group is attached to the rest of
the molecule by a single covalent bond extending to the left
of the carbon atom. Most reactions of aldehydes involve this
group, so most aldehyde reactions are the same regardless of
the size and nature of the rest of the molecule to which the
aldehyde group is attached. Reactions of physiological importance often occur between two functional groups or between
one functional group and a small molecule such as water.
CARBOHYDRATES
Carbohydrates are organic compounds of tremendous biological and commercial importance. They are widely distributed
in nature and include such familiar substances as starch, table
sugar, and cellulose. Carbohydrates have five important functions in living organisms: they provide energy, they serve as a
stored form of chemical energy, they provide dietary fiber, they
supply carbon atoms for the synthesis of cell components, and
they form part of the structural elements of some cells.
❚ Chemical composition of carbohydrates
Carbohydrates contain carbon, hydrogen, and oxygen. They
acquired their name because most of them contain these three
elements in an atomic ratio of one carbon to two hydrogens to
one oxygen. This ratio suggests that the general formula is
CH2O and that the compounds are simply carbon hydrates
(“watered” carbons), or carbohydrates. It is now known that
they are not hydrates of carbon, but the name persists. All carA Review of Chemical Principles
A-11
2373_BC_Sherwood App 4/14/03 4:12 PM Page A-12
bohydrates have a large number of functional groups per molecule. The most common functional groups in carbohydrates
are alcohol, ketone and aldehyde—
O
O


( OH), ( C ), ( C H)
Alcohol Ketone Aldehyde
—or functional groups formed by reactions between pairs of
these three.
❚ Types of carbohydrates
The simplest carbohydrates are simple sugars, also called
monosaccharides. As their name indicates, they consist of
single units called saccharides (mono means “one”). The molecular structure of glucose, an important monosaccharide, is
shown in ● Figure B-7a. In solution, most glucose molecules
assume the ring form shown in ● Figure B-7b. Other common
monosaccharides are fructose, galactose, and ribose.
Disaccharides are sugars formed by linking two monosaccharide molecules together through a covalent bond (di means
“two”). Some common examples of disaccharides are sucrose
(common table sugar) and lactose (milk sugar). Sucrose molecules are formed from one glucose and one fructose molecule.
Lactose molecules each contain one glucose and one galactose unit.
Because of the many functional groups on carbohydrate
molecules, large numbers of simple carbohydrate molecules
are able to bond together and form long chains and branched
networks. The resultant substances are called polysaccharides,
a name that indicates that they contain many saccharide units
(poly means “many”). Three common polysaccharides made
up entirely of glucose units are glycogen, starch, and cellulose.
• Glycogen is a storage carbohydrate found in animals. It
is a highly branched polysaccharide that averages a branch
every eight to twelve glucose units. The structure of glycogen
is represented in ● Figure B-8, where each circle represents
one glucose unit.
• Starch, a storage carbohydrate of plants, consists of two
fractions, amylose and amylopectin. Amylose consists of long,
essentially unbranched chains of glucose units. Amylopectin
is a highly branched network of glucose units averaging 24 to
30 glucose units per branch. Thus it is less highly branched than
glycogen.
• Cellulose, a structural carbohydrate of plants, exists in
the form of long, unbranched chains of glucose units. The
bonding between the glucose units of cellulose is slightly different from the bonding between the glucose units of glycogen and starch. Humans have digestive enzymes that catalyze
the breaking (hydrolysis) of the glucose-to-glucose bonds in
starch but lack the necessary enzymes to hydrolyze cellulose
glucose-to-glucose bonds. Thus starch is a food for humans,
but cellulose is not. Cellulose is the indigestible fiber in our diets.
LIPIDS
Lipids are a diverse group of organic molecules made up of
substances with widely different compositions and molecular
structures. Unlike carbohydrates, which are classified on the
basis of their molecular structure, substances are classified as
lipids on the basis of their solubility. Lipids are insoluble in
water but soluble in nonpolar solvents such as alcohol. Thus,
lipids are the waxy, greasy, or oily compounds found in plants
and animals. Lipids repel water, a useful characteristic of the
protective wax coatings found on some plants. Fats and oils are
energy-rich and have relatively low densities. These properties
account for the use of fats and oils as stored energy in plants
and animals. Still other lipids occur as structural components,
especially in cellular membranes. The oily plasma membrane
that surrounds each cell serves as a barrier that separates the
intracellular contents from the surrounding extracellular fluid
(see p. 25, p. 57, and p. 60).
❚ Simple lipids
Simple lipids contain just two types of components, fatty acids
and alcohols. Fatty acid molecules consist of a hydrocarbon
chain with a carboxylic acid functional group ( COOH) on
● FIGURE B-7
Forms of glucose
● FIGURE B-8
(a) Chain. (b) Ring.
H
A simplified representation
of glycogen
O
Each circle represents a
glucose molecule.
C
CH2OH
H
C
OH
HO
C
H
H
C
OH
H
C
OH
CH2OH
(a)
A-12
APPENDIX B
H
C
HO
C
O
H
OH
H
C
C
H
OH
(b)
H
C
OH
2373_BC_Sherwood App 4/14/03 4:12 PM Page A-13
the end. The hydrocarbon chain can be
O
O
of variable length, but natural fatty acids
always contain an even number of carHO
C
(CH2)14CH3
(CH2)7CH
CH2
O
C
CH(CH2)7CH3
bon atoms. The hydrocarbon chain can
O
CH2
OH
Fatty acid
also contain one or more double bonds
(saturated)
between carbon atoms. Fatty acids with
(CH2)14CH3
CH
O
C
CH
OH
no double bonds are called saturated fatty
O
acids, whereas those with double bonds
CH2
OH
are called unsaturated fatty acids. The
(CH2)16CH3
CH2
O
C
O
Glycerol
more double bonds present, the higher
the degree of unsaturation. Saturated fatty
HO
C
(CH2)7CH
CH(CH2)7CH3
Triglyceride
acids predominate in dietary animal products (for example, meat, eggs, and dairy
Fatty acid
products), whereas unsaturated fatty acids
(unsaturated)
are more prevalent in plant products (for
example, grains, vegetables, and fruits).
● FIGURE B-9
Consumption of a greater proportion of
Triglyceride components and structure
saturated than unsaturated fatty acids is
linked with a higher incidence of cardiovascular disease (see p. 337).
acetone. Excess ketone bodies are produced during diabetes
The most common alcohol found in simple lipids is glycmellitus, a condition in which most cells resort to using fatty
erol (glycerin), a three-carbon alcohol that has three alcohol
acids as an energy source because the cells are unable to take
functional groups ( OH).
up adequate amounts of glucose in the face of inadequate inSimple lipids called fats and oils are formed by a reaction
sulin action (see p. 726).
between the carboxylic acid group of three fatty acids and the
three alcohol groups of glycerol. The resulting lipid is an Eshaped molecule called a triglyceride. Such lipids are classified as fats or oils on the basis of their melting points. Fats are
❚ Complex lipids
solids at room temperature, whereas oils are liquids. Their meltComplex lipids contain more than two types of components.
ing points depend on the degree of unsaturation of the fatty
The different complex lipids usually contain three or more of
acids of the triglyceride. The melting point goes down with inthe following components: glycerol, fatty acids, a phosphate
creasing degree of unsaturation. Thus oils contain more ungroup, an alcohol other than glycerol, and a carbohydrate.
saturated fatty acids than do fats. Examples of the components
Those that contain phosphate are called phospholipids. ● Figof fats and oils and a typical triglyceride molecule are shown
ure B-10 contains representations of a few complex lipids; it
in ● Figure B-9.
When triglycerides form, a molecule of water is released
emphasizes the components but does not give details of the
as each fatty acid reacts with glycerol. Adipose tissue in the body
molecular structures.
contains triglycerides. When the body uses adipose tissue as
Steroids are lipids that have a unique structural feature
an energy source, the triglycerides react with water to release
consisting of a fused carbon ring system containing three
free fatty acids into the blood. The fatty acids can be used as
six-membered rings and a single five-membered ring (● Figan immediate energy source by many organs. In the liver, free
ure B-11). Different steroids possess this characteristic ring
fatty acids are converted into compounds called ketone bodies.
structure but have different functional groups and carbon chains
Two of the ketone bodies are acids, and one is the ketone called
attached.
G
l
y
c
e
r
o
l
Fatty acid
Fatty acid
Phosphate
S
p
h
i
n
g
o
s
i
n
e
Fatty acid
Phosphate
S
p
h
i
n
g
o
s
i
n
e
● FIGURE B-10
Examples of complex lipids
Fatty acid
(a) A phosphoglyceride.
(b) A sphingolipid (sphingosine is an alcohol).
(c) A glycolipid.
Carbohydrate
Alcohol
Alcohol
(a)
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(b)
(c)
A Review of Chemical Principles
A-13
2373_BC_Sherwood App 4/14/03 4:12 PM Page A-14
CH2
CH
CH2
CH3
CH2
CH(CH2)3CH
CH2
CH2
CH
CH
CH2
CH2
CH
CH2
CH3
CH3
CH
CH
CH3
CH2
CH3
CH2
CH2
HO
(a)
Cholesterol
CH2OH
C
O
CH3
HO
OH
CH3
O
Cortisol
(b)
● FIGURE B-11
The steroid ring system
● FIGURE B-12
Examples of steroidal compounds
(a) Detailed. (b) Simplified.
Cholesterol, a steroidal alcohol, is the most abundant steroid in the human body. It is a component of cell membranes
and is used by the body to produce other important steroids
that include bile salts, male and female sex hormones, and
adrenocortical hormones. The structures of cholesterol and
cortisol, an important adrenocortical hormone, are given in
● Figure B-12.
PROTEINS
The name protein is derived from the Greek word proteios,
which means “of first importance.” It is certainly an appropriate
term for these very important biological compounds. Proteins
are indispensable components of all living things, where they
play crucial roles in all biological processes. Proteins are the
main structural component of cells, and all chemical reactions
in the body are catalyzed by enzymes, all of which are proteins.
❚ Chemical composition of proteins
Proteins are macromolecules made up of monomers called
amino acids. Hundreds of different amino acids, both natural
and synthetic, are known, but only 20 are commonly found in
natural proteins. From this seemingly limited pool of amino
acids, cells build thousands of different types of proteins, each
with a distinctly different function, much the same way that
composers create a diversity of unique music from a relatively
small number of notes. Different proteins are constructed by
A-14
APPENDIX B
varying the types and numbers of amino acids used and by
varying the order in which they are linked together. Proteins are
not built haphazardly, though, by randomly linking together
amino acids. Every protein in the body is deliberately and precisely synthesized under the direction of the blueprint laid down
in the person’s genes. Thus amino acids are assembled in a specific pattern to produce a given protein to accomplish a particular structural or functional task in the body. (More information about protein synthesis can be found in Appendix C.)
❚ Peptide bonds
Each amino acid molecule has three important parts: an
amino functional group ( NH2), a carboxyl functional group
( COOH), and a characteristic side chain or R group. These
components are shown in ● Figure B-13. Amino acids form long
chains as a result of reactions between the amino group of one
● FIGURE B-13
The general structure of amino acids
Carboxyl group
O
Amino group
H2N
CH
C
OH
R
Side chain (different for each amino acid)
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-15
amino acid and the carboxyl group of another amino acid. This
reaction is illustrated in Equation B-16 in which the components
of the carboxyl group are shown in the expanded form for clarity:
O
O


H2N  CH  C  OH H2N  CH2 C  OH→

CH3 O
O
Eq. B-16
 peptide bond 
H2N CH  C  NH CH2 C  OH H2O

CH3
Notice that after the two molecules react, the ends of the product still have an amino group and a carboxyl group that can
react to extend the chain length. The covalent bond formed
in the reaction is called a peptide bond (● Figure B-14).
On a molecular scale, proteins are immense molecules.
Their size can be illustrated by comparing a glucose molecule to a molecule of hemoglobin, a protein. Glucose has
a molecular weight of 180 amu and a molecular formula of
C6H12O6. Hemoglobin, a relatively small protein, has a molecular weight of 65,000 amu and a molecular formula of
C2952H4664O832N812S8Fe4.
❚ Levels of protein structure
The many atoms in a protein are not arranged in a random
way. In fact, proteins have a high degree of structural organization that plays an important role in their behavior in the body.
Primary structure
The first level of protein structure is called the primary structure. It is simply the order in which amino acids are bonded
● FIGURE B-14
A peptide bond
In forming a peptide bond, the carboxyl group of one amino acid
reacts with the amino group of another amino acid.
R1
H
N
H
C
N
C
OH
H
R2
H
O
H
C
H
O
C
OH
together to form the protein chain. Amino acids are frequently
represented by three-letter abbreviations, such as Gly for glycine and Arg for arginine. When this practice is followed, the
primary structure of a protein can be represented as in ● Figure B-15, which shows part of the primary structure of human
insulin, or as in ● Figure B-16a, which depicts a portion of the
primary structure of hemoglobin.
Secondary structure
The second level of protein structure, called the secondary
structure, results when hydrogen bonding occurs between the
amino hydrogen of one amino acid in the primary chain and
the carboxyl oxygen
O

( C )
of another amino acid in the same or another chain. When the
hydrogen bonding occurs between amino acids in the same
chain, the chain assumes a coiled, helical shape called the
alpha () helix, which is by far the most common secondary
structure found in natural proteins (● Figure B-16b). Other
secondary structures such as the beta () pleated sheet and
random coils also form as a result of hydrogen bonding between amino acids located in different parts of the same chain.
Tertiary and quaternary structure
The third level of structure in proteins is the tertiary structure. It
results when functional groups of the side chains of amino acids
in the protein chain react with each other. Several different types
of interactions are possible, as shown in ● Figure B-17. Tertiary
structures can be visualized by letting a length of wire represent
the chain of amino acids in the primary structure of a protein.
Next imagine that the wire is wound around a pencil to form a
helix, which represents the secondary structure. The pencil is removed, and the helical structure is now folded back on itself or
carefully wadded into a ball. Such folded or spherical structures
represent the tertiary structure of a protein (● Figure B-16c).
All functional proteins exist in at least a tertiary structure.
Sometimes, several polypeptides interact with each other to
form a fourth level of protein structure, the quaternary structure. For example, hemoglobin contains four highly folded
polypeptide chains (the globin portion) (● Figure B-16d). Four
iron-containing heme groups, one tucked within the interior
of each of the folded polypeptide subunits, completes the quaternary structure of hemoglobin (see ● Figure 11-3, p. 394).
❚ Hydrolysis and denaturation
One of the important functions of proteins is to serve as enzymes
that catalyze the many essential chemical reactions of the body.
H
N
H
R1
O
C
C
H
R2
N
C
H
H
Peptide bond
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O
C
OH
● FIGURE B-15
A portion of the primary protein structure of human insulin
Thr—Lys—Pro—Thr—Tyr—Phe—Phe—Gly—Arg— · · · · ·
A Review of Chemical Principles
A-15
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Peptide bonds
Primary
structure
Amino acids
(a)
C
C
H N
C O
H
N
O
N
C
O
H
N
N
C O
C
C
O
O
H
O
H
H
C
Secondary
structure
C
H
N
C
R
N
H
H
C
N
C
H
C
C
H
C
N
C
Alpha
helix
C
O
H
C
N
N
HO
C
C O
C
O
N
R
C
O
N H
C
H
H
N
N
C
C
C
N H
C
C
C O
C
Beta
pleated
sheet
N
C
H
C O
O
H
C
C
H
HO
N H
N H
N
C
C
C
H
C
C O
C
O
Hydrogen
bonds
C
C
O
C
C
C
O
N
O
O
Random
coil
N
R
C
N
R
R
C
C
O
H
(b)
C
O
N
Tertiary
structure
(c)
Quaternary
structure
Hemoglobin molecule
composed of four
highly folded polypeptides
(d)
● FIGURE B-16
Levels of protein structure
Proteins can have four levels of structure. (a) The primary structure is a particular sequence of amino
acids bonded in a chain. (b) At the secondary level, hydrogen bonding occurs between various amino
acids within the chain, causing the chain to assume a particular shape. The most common secondary
protein structure in the body is the alpha helix. (c) The tertiary structure is formed by the folding of
the secondary structure into a functional three-dimensional configuration. (d) Many proteins form a
fourth level of structure composed of several polypeptides, as exemplified by hemoglobin.
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-17
In addition to catalyzing reactions, proteins can undergo reactions themselves. Two of the most important are hydrolysis and denaturation.
Phe
Hydrolysis
Notice that according to Equation B-16, the formation
of peptide bonds releases water molecules. Under appropriate conditions, it is possible to reverse such reactions by adding water to the peptide bonds and breaking them. Hydrolysis (“breakdown by H2O”) reactions
of this type convert large proteins into smaller fragments or even into individual amino acids. Hydrolysis
is the means by which digestive enzymes break down
ingested food into small units that can be absorbed
from the digestive tract lumen into the blood.
Phe
Cys
—S—S—
Cys
Hydrophobic
interactions
Disulfide
bridge
Ser
Asp
—COO –
H3N + —
Salt bridge
Peptide
backbone
(α -helix)
O
H
Lys
O
H
Ser
Hydrogen
bond
Denaturation
● FIGURE B-17
Side chain interactions leading to the tertiary protein structure
Denaturation of proteins occurs when the bonds holding a protein chain in its characteristic tertiary or secondary conformation are broken. When this happens,
the protein chain takes on a random, disorganized conformachain forms specific loops or helices. See Appendix C for furtion. Denaturation can result when proteins are subjected to
ther details.
heating (including when body temperature rises too high; see
p. 655), to extremes of pH (see p. 573), or to treatment with
HIGH-ENERGY BIOMOLECULES
specific chemicals such as alcohol or heavy metal ions. In
some instances, denaturation is accompanied by coagulation
Not all nucleotides are used to construct nucleic acids. One very
or precipitation, as illustrated by the changes that occur in the
important nucleotide—adenosine triphosphate (ATP)—is
white of an egg as it is fried.
used as the body’s primary energy carrier. Certain bonds in ATP
temporarily store energy that is harnessed during the metabolism of foods and make it available to the parts of the cells where
NUCLEIC ACIDS
it is needed to do specific cellular work (see pp.35–42). Let’s
Nucleic acids are high-molecular-weight macromolecules resee how ATP functions in this role. Structurally, ATP is a modsponsible for storing and using genetic information in living
ified RNA (ribose-containing) nucleotide that has adenine as its
cells and passing it on to future generations. These important
base and two additional phosphates bonded in sequence to the
biomolecules are classified into two categories: deoxyribooriginal nucleotide phosphate. Thus adenosine triphosphate,
nucleic acids (DNA) and ribonucleic acids (RNA). DNA is
as the name implies, has a total of three phosphates attached
found primarily in the cell’s nucleus, and RNA is found primarin a string to adenosine, the composite of ribose and adenine
ily in the cytoplasm that surrounds the nucleus.
(● Figure B-18). Attaching these additional phosphates reBoth types of nucleic acid are made up of units called nuquires considerable energy input. The high-energy input used
cleotides, which in turn are composed of three simpler comto create these high-energy phosphate bonds is “stored” in
ponents. Each nucleotide contains an organic nitrogenous
the bonds for later use. Most energy transfers in the body inbase, a sugar, and a phosphate group. The three components are chemically bonded together with the sugar molecule lying between the base and the phosphate. In RNA,
● FIGURE B-18
NH2
the sugar is ribose, whereas in DNA it is deoxyribose.
The structure of ATP
When nucleotides bond together to form nucleic acid
C
N
chains, the bonding is between the phosphate of one nuC
N
HC
cleotide and the sugar of another. Thus, the resulting nuCH
C
cleic acids consist of chains of alternating phosphates and
OH
OH
OH
N
N
Adenosine
sugar molecules, with a base molecule extending out of
HO P O P O P O CH2
O
the chain from each sugar molecule (see ● Figure C-1,
Adenine
p. A-20).
H
H
O
O
O
H
H
The chains of nucleic acid assume structural features
somewhat like those found in proteins. DNA occurs in the
Phosphate groups
HO
OH
form of two chains that mutually coil around one another
to form the well-known double helix. Some RNA occurs
Ribose
Triphosphate
in essentially straight chains, whereas in other types the
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A Review of Chemical Principles
A-17
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-18
volve ATP’s terminal phosphate bond. When energy is needed,
the third phosphate is cleaved off by hydrolysis, yielding adenosine diphosphate (ADP) and an inorganic phosphate (Pi) and
releasing energy in the process (Equation B-17):
ATP r ADP Pi energy for use by cell Eq. B-17
Why use ATP as an energy currency that cells can cash in
by splitting of the high-energy phosphate bonds as needed?
Why not just directly use the energy released during the oxidation of nutrient molecules such as glucose? If all the chemical
energy stored in glucose were to be released at once, most of
the energy would be squandered, because the cell could not
A-18
APPENDIX B
capture much of the energy for immediate use. Instead, the
energy trapped within the glucose bonds is gradually released
and harnessed as cellular “bite-size pieces” in the form of the
high-energy phosphate bonds of ATP.
Under the influence of an enzyme, ATP can be converted
to a cyclic form of adenosine monophosphate, which contains
only one phosphate group, the other two having been cleaved
off. The resultant molecule, called cyclic AMP or cAMP, serves
as an intracellular messenger, affecting the activities of a number of enzymes involved in important reactions in the body (see
p. 67).
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-19
Appendix C
Storage, Replication, and
Expression of Genetic Information
DEOXYRIBONUCLEIC ACID (DNA)
AND CHROMOSOMES
The nucleus of the cell houses deoxyribonucleic acid (DNA),
the genetic blueprint that is unique for each individual.
❚ Functions of DNA
As genetic material, DNA serves two essential functions. First,
it contains “instructions” for assembling the structural and enzymatic proteins of the cell. Cellular enzymes in turn control
the formation of other cellular structures and also determine
the functional activity of the cell by regulating the rate at which
metabolic reactions proceed. The nucleus serves as the cell’s
control center by directly or indirectly controlling almost all cell
activities through the role its DNA plays in governing protein
synthesis. Because cells make up the body, the DNA code determines the structure and the function of the body as a whole.
The DNA an organism possesses not only dictates whether the
organism is a human, a toad, or a pea but also determines the
unique physical and functional characteristics of that individual, all of which ultimately depend on the proteins produced
under DNA control.
Second, by replicating (making copies of itself), DNA perpetuates the genetic blueprint within all new cells formed
within the body and is responsible for passing on genetic information from parents to children. We will first examine the structure of DNA and the coding mechanism it uses, then turn our
attention to the means by which DNA replicates itself and controls protein synthesis.
❚ Structure of DNA
Deoxyribonucleic acid is a huge molecule, composed in humans of millions of nucleotides arranged into two long, paired
strands that spiral around each other to form a double helix.
Each nucleotide has three components: (1) a nitrogenous base,
a ring-shaped organic molecule containing nitrogen; (2) a fivecarbon ring-shaped sugar molecule, which in DNA is deoxyribose; and (3) a phosphate group. Nucleotides are joined end to
end by linkages between the sugar of one nucleotide and the
phosphate group of the adjacent nucleotide to form a long poly-
nucleotide (“many nucleotide”) strand with a sugar–phosphate
backbone and bases projecting out one side (● Figure C-1).
The four different bases in DNA are the double-ringed bases
adenine (A) and guanine (G) and the single-ringed bases
cytosine (C) and thymine (T). The two polynucleotide strands
within a DNA molecule are wrapped around each other and
oriented so that their bases all project to the interior of the helix.
The strands are held together by weak hydrogen bonds formed
between the bases of adjoining strands (● Figure B-6, see
p. A-7). Base pairing is highly specific: Adenine pairs only with
thymine and guanine pairs only with cytosine (● Figure C-2).
Genes
The composition of the repetitive sugar–phosphate backbones
that form the “sides” of the DNA “ladder” is identical for every
molecule of DNA, but the sequence of the linked bases that
form the “rungs” varies among different DNA molecules. The
particular sequence of bases in a DNA molecule serves as “instructions,” or a “code,” that dictates the assembly of amino
acids into a given order for the synthesis of specific polypeptides (chains of amino acids linked by peptide bonds; see
p. A-14). A gene is a stretch of DNA that codes for the synthesis of a particular polypeptide. Polypeptides, in turn, are folded
into a three-dimensional configuration to form a functional
protein. Not all portions of a DNA molecule code for structural or enzymatic proteins. Some stretches of DNA code for
proteins that regulate genes. Other segments appear important
in organizing and packaging DNA within the nucleus. Still
other regions are “nonsense” base sequences that have no apparent significance.
❚ Packaging of DNA into chromosomes
The DNA molecules within each human cell, if lined up end
to end, would extend more than 2 m (2,000,000 mm), yet these
molecules are packed into a nucleus that is only 5 mm in diameter. These molecules are not randomly crammed into the
nucleus but are precisely organized into chromosomes. Each
chromosome consists of a different DNA molecule and contains a unique set of genes.
Somatic (body) cells contain 46 chromosomes (the diploid number), which can be sorted into 23 pairs on the basis
of various distinguishing features. Chromosomes composing a
A-19
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-20
matched pair are termed homologous chromosomes, one member of each pair having been derived from the individual’s maternal parent and the other member from the paternal parent.
Germ (reproductive) cells (that is, sperm and eggs) contain
only one member of each homologous pair for a total of 23
chromosomes (the haploid number). Union of a sperm and
an egg results in a new diploid cell with 46 chromosomes, consisting of a set of 23 chromosomes from the mother and another set of 23 from the father.
● FIGURE C-1
Polynucleotide strand
Sugar–phosphate bonds link adjacent nucleotides
together to form a polynucleotide strand with
bases projecting to one side. The sugar–phosphate
backbone is identical in all polynucleotides, but
the sequence of the bases varies.
O
CH3
N
Thymine
O
O
N
CH2 O
O
Base
N
N
O
N
N
CH2 O
O
N
CH2 O
NH2
P O
O–
O
N
N
N
O
N
CH2 O
O
P O
O–
O
= Sugar-phosphate backbone of polynucleotide strand
A-20
Complementary base pairing serves as the foundation for both
DNA replication and the initial step of protein synthesis. We
will examine the mechanism and significance of complementary base pairing in each of these circumstances, starting with DNA replication.
Phosphate
O
N
O
Guanine
COMPLEMENTARY BASE PAIRING,
REPLICATION, AND TRANSCRIPTION
Nucleotide
Cytosine
O
P O
O–
NH2
P O
O–
NH2
Adenine
The packaging and compression of DNA molecules into
discrete chromosomal units are accomplished in part by nuclear proteins associated with DNA. Two classes of proteins—
histone and nonhistone proteins—bind with DNA. Histones
form bead-shaped bodies that play a key role in packaging DNA
into its chromosomal structure. The nonhistones are believed
to be important in gene regulation. The complex formed between the DNA and its associated proteins is known as chromatin. The long threads of DNA within a chromosome are
wound around histones at regular intervals, thus compressing
a given DNA molecule to about one-sixth its fully extended
length. This “beads-on-a-string” structure is further folded and
supercoiled into higher and higher levels of organization to
further condense DNA into rodlike chromosomes that are readily visible by means of a light microscope during cell division
(● Figure C-3). When the cell is not dividing, the chromosomes
partially “unravel” or decondense to a less compact form of
chromatin that is indistinct under a light microscope but appears as thin strands and clumps with an electron microscope.
The decondensed form of DNA is its working form; that is, it
is the form used as a template for protein assembly. Let us turn
our attention to this working form of DNA in operation.
APPENDIX C
Sugar
❚ DNA replication
During DNA replication, the two decondensed DNA
strands “unzip” as the weak bonds between the paired
bases are enzymatically broken. Then complementary base
pairing takes place: New nucleotides present within the nucleus pair with the exposed bases from each unzipped strand
(● Figure C-4). New adenine-bearing nucleotides pair with
exposed thymine-bearing nucleotides in an old strand, and new
guanine-bearing nucleotides pair with exposed cytosine-bearing
nucleotides in an old strand. This complementary base pairing
is initiated at one end of the two old strands and proceeds in an
orderly fashion to the other end. The new nucleotides attracted
to and thus aligned in a prescribed order by the old nucleotides
are sequentially joined by sugar–phosphate linkages to form two
new strands that are complementary to each of the old strands.
This replication process results in two complete double-stranded
DNA molecules, one strand within each molecule having come
from the original DNA molecule and one strand having been
newly formed by complementary base pairing. These two DNA
molecules are both identical to the original DNA molecule, with
the “missing” strand in each of the original separated strands
having been produced as a result of the imposed pattern of base
pairing. This replication process, which occurs only during
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-21
P
P
S
C
S
G
P
P
S
Base
Phosphate
A
T
S
P
Sugar
P
S
G
C
S
P
Nucleotide
P
S
T
S
A
P
P
S
C
S
G
P
P
S
G
C
S
P
P
S
T
S
A
P
P
S
A
T
S
P
P
(a)
A
= Adenine
T
= Thymine
(b)
G
C
= Guanine
= Sugar–phosphate backbone
= Cytosine
= Hydrogen bonds
● FIGURE C-2
Complementary base pairing in DNA
(a) Two polynucleotide strands held together by weak hydrogen bonds formed between the bases
of adjoining strands—adenine always paired with thymine and guanine always paired with cytosine.
(b) Arrangement of the two bonded polynucleotide strands of a DNA molecule into a double helix.
cell division, is essential for ensuring the perpetuation of the
genetic code in both of the new daughter cells. The duplicate
copies of DNA are separated and evenly distributed to the two
halves of the cell before it divides. We will cover the topic of
cell division in more detail later.
❚ DNA transcription and messenger RNA
At other times, when DNA is not replicating in preparation for
cell division, it serves as a blueprint for dictating cellular protein synthesis. How is this accomplished when DNA is sequestered within the nucleus and protein synthesis is carried
out by ribosomes within the cytoplasm? Several types of another nucleic acid, ribonucleic acid (RNA), serve as the “gobetween.”
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Structure of ribonucleic acid
Ribonucleic acid differs structurally from DNA in three regards:
(1) The five-carbon sugar in RNA is ribose instead of deoxyribose, the only difference between them being the presence in
ribose of a single oxygen atom that is absent in deoxyribose;
(2) RNA contains the closely related base uracil instead of
thymine, with the three other bases being the same as in DNA;
and (3) RNA is single-stranded and not self-replicating.
All RNA molecules are produced in the nucleus using DNA
as a template or mold, then exit the nucleus through openings
in the nuclear membrane known as nuclear pores (see p. 25).
These pores are large enough for passage of RNA molecules
but preclude passage of the much larger DNA molecules.
The DNA instructions for assembling a particular protein
coded in the base sequence of a given gene are “transcribed”
Storage, Replication, and Expression of Genetic Information
A-21
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-22
(a)
DNA
Histone
DNA counterparts in the exposed gene (● Figure C-5).
The same pairing rules apply except that uracil,
the RNA nucleotide substitute for thymine,
pairs with adenine in the exposed DNA nucleotides. As soon as the RNA nucleotides pair with their DNA counterparts,
sugar–phosphate bonds are formed to
join the nucleotides together into a
(b)
single-stranded RNA molecule that is
released from DNA once transcription
is complete. The original conformation
of DNA is then restored. The RNA strand
is much shorter than a DNA strand, because only a one-gene segment of DNA
● FIGURE C-4
Complementary base pairing during DNA replication
During DNA replication, the DNA molecule is unzipped, and each
old strand directs the formation of a new strand; the result is two
identical double-helix DNA molecules.
(c)
(d)
● FIGURE C-3
Levels of organization of DNA
(a) Double helix of a DNA molecule. (b) DNA molecule wound around histone
proteins, forming a “beads-on-a-string” structure. (c) Further folding and supercoiling of the DNA–histone complex. (d) Rodlike chromosomes, the most condensed form of DNA, which are visible in the cell’s nucleus during cell division.
into a molecule of messenger RNA
New DNA nucleotide being attached
(mRNA). The segment of the DNA
to growing polynucleotide chain
molecule to be copied uncoils, and
the base pairs separate to expose the
particular sequence of bases in the gene.
In any given gene, only one of the DNA
New complementary strand
strands is used as a template for transcribing RNA, with the copied strand varying for
different genes along the same DNA molecule. The beginning and end of a gene
within a DNA strand are desigOriginal strand
nated by particular base sequences
M=MAdenine
that serve as “start” and “stop”
M=MThymine
signals.
M=MGuanine
Transcription
Transcription is accomplished by
complementary base pairing of
free RNA nucleotides with their
A-22
APPENDIX C
M=MCytosine
M=MSugar–phosphate backbone
of original strand
M=MSugar–phosphate backbone
of new complementary strand
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-23
is transcribed into a single RNA molecule. The length of the
finished RNA transcript varies, depending on the size of the
gene. Within its nucleotide base sequence, this RNA transcript
contains instructions for assembling a particular protein. Note
that the message is coded in a base sequence that is complementary to, not identical to, the original DNA code.
Messenger RNA delivers the final coded message to the
ribosomes for translation into a particular amino acid sequence
to form a given protein. Thus genetic information flows from
DNA (which can replicate itself) through RNA to protein. This
is accomplished first by transcription of the DNA code into a
complementary RNA code, followed by translation of the
RNA code into a specific protein (● Figure C6). In the
next section, you will learn more about the steps in
translation. The structural and functional characteristics of the cell as determined by its protein composition
can be varied, subject to control, depending on which
genes are “switched on” to produce mRNA.
Free nucleotides present in the nucleus cannot be randomly joined together to form either DNA or RNA strands, because the enzymes required to link together the sugar and phosphate components of nucleotides are active only when bound
to DNA. This ensures that DNA, mRNA, and protein assembly occur only according to genetic plan.
RNA nucleotide
Messenger RNA
DNA strand
TRANSLATION AND PROTEIN
SYNTHESIS
Three forms of RNA participate in protein synthesis. Besides
messenger RNA, two other forms of RNA are required for translation of the genetic message into cellular protein: ribosomal
RNA and transfer RNA.
• Messenger RNA carries the coded message
from nuclear DNA to a cytoplasmic ribosome, where
it directs the synthesis of a particular protein.
• Ribosomal RNA (rRNA) is an essential component of ribosomes, the “workbenches” for protein
synthesis (see p. 26). Ribosomal RNA “reads” the
base sequence code of mRNA and translates it into
the appropriate amino-acid sequence during protein
synthesis.
• Transfer RNA (tRNA) transfers the appropriate amino
acids in the cytosol to their designated site in the amino acid
sequence of the protein under construction.
M=MAdenine
M=MThymine
M=MGuanine
M=MCytosine
M=MUracil
M=MSugar–phosphate backbone
● FIGURE C-5
Complementary base pairing during DNA transcription
During DNA transcription, a messenger RNA molecule is formed as RNA
nucleotides are assembled by complementary base pairing at a given segment
of one strand of an unzipped DNA molecule (that is, a gene).
❚ Triplet code; codon
Twenty different amino acids are used to construct proteins,
yet only four different nucleotide bases are used to code for
these twenty amino acids. In the “genetic dictionary,” each different amino acid is specified by a triplet code that consists of
a specific sequence of three bases in the DNA nucleotide chain.
For example, the DNA sequence ACA (adenine, cytosine, adenine) specifies the amino acid cysteine, whereas the sequence
ATA specifies the amino acid tyrosine. Each DNA triplet code
is transcribed into mRNA as a complementary code word, or
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● FIGURE C-6
Flow of genetic information from DNA through RNA to protein by
transcription and translation
Transcription
DNA
Translation
RNA
Protein
Replication
Storage, Replication, and Expression of Genetic Information
A-23
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-24
Large subunit
Amino acid
tRNA
Small subunit
3
2
A
U
U
A C
C
U
G
A
C
U
G
C
U
CG
C
A AA
G
A
Anticodon
1
mRNA
G A
C
A G
U
A C
C
G A U G U
UCC
CG
U
U A
G
AU
G
U A
G
Ribosome
Leader
sequence
First
codon
Second
codon
First ribosomal
binding site
Second ribosomal
binding site
9
7
8
5
G
U A
U
A
G A
CGAUG U C U C
UC
G
6
C
4
A
U
A
GU
G
CG
A
A C
A
Steps 5
through 8
are repeated
A G
G A U G U
UCC
CG
C
U
C
AU
G
U A
G
1
On binding with a messenger RNA (mRNA) molecule, the small ribosomal subunit joins with the large subunit to form a functional ribosome.
2
A transfer RNA (tRNA), charged with its specific amino acid passenger, binds to mNRA by means of complementary base pairing
between the tRNA anticodon and the first mRNA codon positioned in the first ribosomal binding site.
3
Another tRNA molecule attaches to the next codon on mRNA positioned in the second ribosomal binding site.
4
The amino acid from the first tRNA is linked to the amino acid on the second tRNA.
5
The first tRNA detaches.
6
The mRNA molecule shifts forward one codon (a distance of a three-base sequence).
7
Another charged tRNA moves in to attach with the next codon on mRNA, which has now moved into the second ribosomal binding site.
8
The amino acids from the tRNA in the first ribosomal site are linked with the amino acid in the second site.
9
This process continues (that is, steps 5 through 8 are repeated), with the polypeptide chain continuing to grow, until a stop codon is
reached and the polypeptide chain is released.
● FIGURE C-7
Ribosomal assembly and protein translation
A-24
APPENDIX C
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-25
codon, consisting of a sequenced order of the three bases that
pair with the DNA triplet. For example, the DNA triplet code
ATA is transcribed as UAU (uracil, adenine, uracil) in mRNA.
Sixty-four different DNA triplet combinations (and, accordingly, 64 different mRNA codon combinations) are possible using the four different nucleotide bases (43). Of these possible combinations, 61 code for specific amino acids and the
remaining three serve as “stop signals.” A stop signal acts as a
“period” at the end of a “sentence.” The sentence consists of a
series of triplet codes that specify the amino acid sequence in
a particular protein. When the stop codon is reached, ribosomal RNA releases the finished polypeptide product. Because
61 triplet codes each specify a particular amino acid and there
are 20 different amino acids, a given amino acid may be specified by more than one base-triplet combination. For example,
tyrosine is specified by the DNA sequence ATG as well as by
ATA. In addition, one DNA triplet code, TAC (mRNA codon
sequence AUG) functions as a “start signal” in addition to specifying the amino acid methionine. This code marks the place
on mRNA where translation is to begin so that the message is
started at the correct end and thus reads in the right direction.
Interestingly, the same genetic dictionary is used universally; a
given three-base code stands for the same amino acid in all living things, including micro-organisms, plants, and animals.
Amino acid
attaches here
Region of
base pairing
A
C
C
G
C
tRNA
A
U
A
Anticodon
U
A
U
Codon
❚ Ribosomes
A ribosome brings together all components that participate in
protein synthesis—mRNA, tRNA, and amino acids—and provides the enzymes and energy required for linking the amino
acids together. The nature of the protein synthesized by a given
ribosome is determined by the mRNA message that is being
translated. Each mRNA serves as a code for only one particular
polypeptide.
A ribosome is an rRNA-protein structure organized into two
subunits of unequal size. These subunits are brought together
only when a protein is being synthesized (● Figure C-7, step
1 ). During assembly of a ribosome, an mRNA molecule attaches to the smaller of the ribosomal subunits by means of a
leader sequence, a section of mRNA that precedes the start
codon. The small subunit with mRNA attached then binds to
a large subunit to form a complete, functional ribosome.
When the two subunits unite, a groove is formed that accommodates the mRNA molecule as it is being translated.
❚ Transfer RNA and anticodons
Free amino acids in the cytoplasm are not able to “recognize”
and bind directly with their specific codons in mRNA. Transfer RNA is required to bring the appropriate amino acid to its
proper codon. Even though tRNA is single-stranded, as are all
RNA molecules, it is folded back onto itself into a T shape with
looped ends (● Figure C-8). The open-ended stem portion recognizes and binds to a specific amino acid. There are at least
20 different varieties of tRNA, each able to bind with only one
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mRNA
● FIGURE C-8
Structure of a tRNA molecule
The open end of a tRNA molecule attaches to free amino acids. The
anticodon loop of the tRNA molecule attaches to a complementary
mRNA codon.
of the 20 different kinds of amino acids. A tRNA is said to be
“charged” when it is carrying its passenger amino acid. The loop
end of a tRNA opposite the amino-acid binding site contains a
sequence of three exposed bases, known as the anticodon,
which is complementary to the mRNA codon that specifies the
amino acid being carried. Through complementary base pairing, a tRNA can bind with mRNA and insert its amino acid
into the protein under construction only at the site designated
by the codon for the amino acid. For example, the tRNA molecule that binds with tyrosine bears the anticodon AUA, which
can pair only with the mRNA codon UAU, which specifies tyrosine. This dual binding function of tRNA molecules ensures
that the correct amino acids are delivered to mRNA for assembly in the order specified by the genetic code. Transfer RNA can
only bind with mRNA at a ribosome, so protein assembly does
not occur except in the confines of a ribosome.
❚ Steps of protein synthesis
The three steps of protein synthesis are initiation, elongation,
and termination.
Storage, Replication, and Expression of Genetic Information
A-25
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-26
1. Initiation. Protein synthesis is initiated when a charged
tRNA molecule bearing the anticodon specific for the start
codon binds at this site on mRNA (● Figure C-7, step 2 ).
2. Elongation. A second charged tRNA bearing the anticodon specific for the next codon in the mRNA sequence then
occupies the site next to the first tRNA (step 3 ). At any given
time, a ribosome can accommodate only two tRNA molecules
bound to adjacent codons. Through enzymatic action, a peptide bond is formed between the two amino acids that are linked
to the stems of the adjacent tRNA molecules (step 4 ). The
linkage is subsequently broken between the first tRNA and its
amino acid passenger, leaving the second tRNA with a chain
of two amino acids. The uncharged tRNA molecule (the one
minus its amino acid passenger) is released from mRNA (step
5 ). The ribosome then moves along the mRNA molecule by
precisely three bases, a distance of one codon (step 6 ), so that
the tRNA bearing the chain of two amino acids is moved into
the number one ribosomal site for tRNA. Then, an incoming
charged tRNA with a complementary anticodon for the third
codon in the mRNA sequence occupies the number two ribosomal site that was vacated by the second tRNA (step 7 ). The
chain of two amino acids subsequently binds with and is transferred to the third tRNA to form a chain of three amino acids
(step 8 ). Through repetition of this process, amino acids are
subsequently added one at a time to a growing polypeptide
chain in the order designated by the codon sequence as the ribosomal translation machinery moves stepwise along the mRNA
molecule one codon at a time (step 9 ). This process is rapid.
Up to 10 to 15 amino acids can be added per second.
3. Termination. Elongation of the polypeptide chain continues until the ribosome reaches a stop codon in the mRNA
molecule, at which time the polypeptide is released. The polypeptide is then folded and modified into a full-fledged protein.
The ribosomal subunits dissociate and are free to reassemble
into another ribosome for translation of other mRNA molecules.
❚ Energy cost of protein synthesis
Protein synthesis is expensive, in terms of energy. Attachment
of each new amino acid to the growing polypeptide chain requires a total investment of splitting four high-energy phosphate bonds—two to charge tRNA with its amino acid, one to
bind tRNA to the ribosomal-mRNA complex, and one to move
the ribosome forward one codon.
❚ Polyribosomes
A number of copies of a given protein can be produced from a
single mRNA molecule before the latter is chemically degraded.
As one ribosome moves forward along the mRNA molecule, a
new ribosome attaches at the starting point on mRNA and also
starts translating the message. Attachment of many ribosomes
to a single mRNA molecule results in a polyribosome. Multiple
copies of the identical protein are produced as each ribosome
moves along and translates the same message (● Figure C-9).
A-26
APPENDIX C
Ribosome
Protein
mRNA
● FIGURE C-9
A polyribosome
A polyribosome is formed by numerous ribosomes simultaneously
translating mRNA.
The released proteins are used within the cytosol, except for
the few that move into the nucleus through the nuclear pores.
Recall that, in contrast to the cytosolic polyribosomes, ribosomes directed to bind with the rough endoplasmic reticulum
(ER) feed their growing polypeptide chains into the ER lumen
(see p. 26). The resultant proteins are subsequently packaged
for export out of the cell or for replacement of membrane components within the cell.
❚ Control of gene activity and
protein transcription
Because each somatic cell in the body has the identical DNA
blueprint, you might assume that they would all produce the
same proteins. This is not the case, however, because different
cell types are able to transcribe different sets of genes and thus
synthesize different sets of structural and enzymatic proteins.
For example, only red blood cells can synthesize hemoglobin,
even though all body cells carry the DNA instructions for hemoglobin synthesis. Only about 7% of the DNA sequences in
a typical cell are ever transcribed into mRNA for ultimate expression as specific proteins.
Control of gene expression involves gene regulatory proteins that activate (“switch on”) or repress (“switch off”) the
genes that code for specific proteins within a given cell. Various DNA segments that do not code for structural and enzymatic proteins code for synthesis of these regulatory proteins.
The molecular mechanisms by which these regulatory genes
in turn are controlled in human cells are only beginning to be
understood. In some instances, regulatory proteins are controlled by gene-signaling factors that bring about differential
gene activity among various cells to accomplish specialized
tasks. The largest group of known gene-signaling factors in
humans is the hormones. Some hormones exert their homeostatic effect by selectively altering the transcription rate of the
genes that code for enzymes that are in turn responsible for
catalyzing the reaction(s) regulated by the hormone. For example, the hormone cortisol promotes the breakdown of fat
stores by stimulating synthesis of the enzyme that catalyzes the
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-27
conversion of stored fat into its component fatty acids. In other
cases, gene action appears to be time specific; that is, certain
genes are expressed only at a certain developmental stage in
the individual. This is especially important during embryonic
development.
CELL DIVISION
Most cells in the human body can reproduce themselves, a process important in growth, replacement, and repair of tissues.
The rate at which cells divide is highly variable. Cells within
the deeper layers of the intestinal lining divide every few days
to replace cells that are continually sloughed off the surface of
the lining into the digestive tract lumen. In this way, the entire
intestinal lining is replaced about every three days (see p. 628).
At the other extreme are nerve cells, which permanently lose
the ability to divide beyond a certain period of fetal growth and
development. Consequently, when nerve cells are lost through
trauma or disease, they cannot be replaced (see p. 5). In between these two extremes are cells that divide infrequently except when needed to replace damaged or destroyed tissue. The
factors that control the rate of cell division remain obscure.
❚ Mitosis
Recall that cell division involves two components: nuclear division and cytoplasmic division (cytokinesis) (see p. 49). Nuclear division in somatic cells is accomplished by mitosis, in
which a complete set of genetic information (that is, a diploid
number of chromosomes) is distributed to each of two new
daughter cells.
A cell capable of dividing alternates between periods of
mitosis and nondivision. The interval of time between cell division is known as interphase. Because mitosis takes less than
an hour to complete, the vast majority of cells in the body at any
given time are in interphase.
Replication of DNA and growth of the cell take place during interphase in preparation for mitosis. Although mitosis is a
continuous process, it displays four distinct phases: prophase,
metaphase, anaphase, and telophase (● Figure C-10).
Prophase
1. Chromatin condenses and becomes microscopically
visible as chromosomes. The condensed duplicate strands
of DNA, known as sister chromatids, remain joined together
within the chromosome at a point called the centromere (● Figure C-11).
2. Cells contain a pair of centrioles, short cylindrical structures that form the mitotic spindle during cell division (see
● Figure 2-1, p. 26). The centriole pair divides, and the daughter centrioles move to opposite ends of the cell, where they assemble between them a mitotic spindle made up of microtubules (see p. 48).
3. The membrane surrounding the nucleus starts to break
down.
www.brookscole.com/biology
Metaphase
1. The nuclear membrane completely disappears.
2. The 46 chromosomes, each consisting of a pair of sister chromatids, align themselves at the midline, or equator, of
the cell. Each chromosome becomes attached to the spindle by
means of several spindle fibers that extend from the centriole
to the centromere of the chromosome.
Anaphase
1. The centromeres split, converting each pair of sister
chromatids into two identical chromosomes, which separate
and move toward opposite poles of the spindle. Motor proteins
are responsible for pulling the chromosomes along the spindle
fibers toward the poles (see p. 46).
2. At the end of anaphase, an identical set of 46 chromosomes is present at each of the poles, for a transient total of 92
chromosomes in the soon-to-be-divided cell.
Telophase
1. The cytoplasm divides through formation and gradual
tightening of an actin contractile ring at the midline of the cell,
thus forming two separate daughter cells, each with a full
diploid set of chromosomes (see ● Figure 2-22a, p. 49).
2. The spindle fibers disassemble.
3. The chromosomes uncoil to their decondensed chromatin form.
4. A nuclear membrane reforms in each new cell.
Cell division is complete with the end of telophase. Each
of the new cells now enters interphase.
❚ Meiosis
Nuclear division in the specialized case of germ cells is accomplished by meiosis, in which only half a set of genetic information (that is, a haploid number of chromosomes) is distributed
to each daughter cell. Meiosis differs from mitosis in several
important regards (● Figure C-10). Specialized diploid germ
cells undergo one chromosome replication followed by two nuclear divisions to produce four haploid germ cells.
Meiosis I
1. During prophase of the first meiotic division, the members of each homologous pair of chromosomes line up side by
side to form a tetrad, which is a group of four sister chromatids
with two identical chromatids within each member of the pair.
2. The process of crossing over occurs during this period,
when the maternal copy and the paternal copy of each chromosome are paired. Crossing over involves a physical exchange
of chromosome material between nonsister chromatids within
a tetrad (● Figure C-12). This process yields new chromosome
combinations, thus contributing to genetic diversity.
3. During metaphase, the 23 tetrads line up at the equator.
4. At anaphase, homologous chromosomes, each consisting of a pair of sister chromatids joined at the centromere, separate and move toward opposite poles. Maternally and pater-
Storage, Replication, and Expression of Genetic Information
A-27
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-28
MITOSIS
Nucleus
Chromatids
DNA replication
Interphase
MEIOSIS
Paired
homologous
chromosomes
DNA replication
Tetrad
Interphase
Prophase I
Metaphase I
Anaphase I
● FIGURE C-10
A comparison of events in mitosis and meiosis
nally derived chromosomes migrate to opposite poles in random assortments of one member of each chromosome pair
without regard for its original derivation. This genetic mixing
provides novel new combinations of chromosomes.
5. During the first telophase, the cell divides into two cells.
Each cell contains 23 chromosomes consisting of two sister
chromatids.
Meiosis II
1. Following a brief interphase in which no further replication occurs, the 23 unpaired chromosomes line up at the
equator, the centromeres split, and the sister chromatids separate for the first time into independent chromosomes that move
to opposite poles.
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APPENDIX C
2. During cytokinesis, each of the daughter cells derived
from the first meiotic division forms two new daughter cells.
The end result is four daughter cells, each containing a haploid
set of chromosomes.
Union of a haploid sperm and haploid egg results in a zygote (fertilized egg) that contains the diploid number of chromosomes. Development of a new multicellular individual from
the zygote is accomplished by mitosis and cell differentiation.
Because DNA is normally faithfully replicated in its entirety
during each mitotic division, all cells in the body possess an
identical aggregate of DNA molecules. Structural and functional variations between different cell types result from differential gene expression.
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-29
Spindle
Prophase
Centriole
Metaphase
Anaphase
Telophase
Diploid
daughter cells
Daughter cells
Telophase I
Prophase II
Metaphase II
Anaphase II
Telophase II
Haploid
daughter cells
❚ Mutations
An estimated 1016 cell divisions take place in the body during
the course of a person’s lifetime to accomplish growth, repair,
and normal cell turnover. Because more than 3 billion nucleotides must be replicated during each cell division, no wonder
“copying errors” occasionally occur. Any change in the DNA
sequence is known as a point (gene) mutation. A point mutation arises when a base is inadvertently substituted, added, or
deleted during the replication process.
When a base is inserted in the wrong position during DNA
replication, the mistake can often be corrected by a built-in
“proofreading” system. Repair enzymes remove the newly repliwww.brookscole.com/biology
cated strand back to the defective segment, at which time normal base pairing resumes to resynthesize a corrected strand.
Not all mistakes can be corrected, however.
Mutations can arise spontaneously by chance alone or
they can be induced by mutagens, which are factors that increase the rate at which mutations take place. Mutagens include various chemical agents as well as ionizing radiation such
as X rays and atomic radiation. Mutagens promote mutations
either by chemically altering the DNA base code through a variety of mechanisms or by interfering with the repair enzymes
so that abnormal base segments cannot be cut out.
Depending on the location and nature of a change in the
genetic code, a given mutation may (1) have no noticeable
effect if it does not alter a critical region of a cellular protein;
Storage, Replication, and Expression of Genetic Information
A-29
2373_BC_Sherwood App 4/14/03 4:13 PM Page A-30
● FIGURE C-11
A scanning electron micrograph of human chromosomes from
a dividing cell
The replicated chromosomes appear as double structures, with identical sister chromatids joined in the middle at a common centromere.
(2) adversely alter cell function if it impairs the function of a
crucial protein; (3) be incompatible with the life of the cell, in
which case the cell dies and the mutation is lost with it; or
(4) in rare cases, prove beneficial if a more efficient structural
or enzymatic protein results. If a mutation occurs in a body
cell (a somatic mutation), the outcome will be reflected as an
alteration in all future copies of the cell in the affected individual, but it will not be perpetuated beyond the life of the individual. If, by contrast, a mutation occurs in a sperm- or eggproducing cell (germ cell mutation), the genetic alteration
may be passed on to succeeding generations.
In most instances, cancer results from multiple somatic
mutations that occur over a course of time within DNA segments known as proto-oncogenes. Proto-oncogenes are normal genes whose coded products are important in the regulation of cell growth and division. These genes have the potential
of becoming overzealous oncogenes (“cancer genes”), which
induce the uncontrolled cell proliferation characteristic of cancer. Proto-oncogenes can become cancer producing as a result
of several sequential mutations in the gene itself or by changes
in adjacent regions that regulate the proto-oncogenes. Less frequently, tumor viruses become incorporated in the DNA blueprint and act as oncogenes.
Centromere
(a)
(b)
(c)
● FIGURE C-12
Crossing over
(a) During prophase I of meiosis, each homologous pair of chromosomes lines up side by side to form a
tetrad. (b) Physical exchange of chromosome material occurs between nonsister chromatids. (c) As a result
of this crossing over, new combinations of genetic material are formed within the chromosomes.
A-30
APPENDIX C