Table Of ContentThe Scene of Action 1
Amino Acids, Peptides, and Proteins 39
Determining Structures and Analyzing Cells 95
Sugars, Polysaccharides, and Glycoproteins 161
The Nucleic Acids 199
Thermodynamics and Biochemical Equilibria 281
How Macromolecules Associate 325
Lipids, Membranes, and Cell Coats 379
Enzymes: The Catalysts of Cells 455
An Introduction to Metabolism 505
The Regulation of Enzymatic Activity and Metabolism 535
Transferring Groups by Displacement Reactions 589
Enzymatic Addition, Elimination, Condensation,
and Isomerization: Roles for Enolate and Carbocation
Intermediates 677
Coenzymes: Nature’s Special Reagents 719
Coenzymes of Oxidation – Reduction Reactions 765
Transition Metals in Catalysis and Electron Transport 837
Chapter 1.
Chapter 2.
Chapter 3.
Chapter 4.
Chapter 5.
Chapter 6.
Chapter 7.
Chapter 8.
Chapter 9.
Chapter 10.
Chapter 11.
Chapter 12.
Chapter 13.
Chapter 14.
Chapter 15.
Chapter 16.
Table of Contents
Volume 1
Chapter 17.
Chapter 18.
Chapter 19.
Chapter 20.
Chapter 21.
Chapter 22.
Chapter 23.
Chapter 24.
Chapter 25.
Chapter 26.
Chapter 27.
Chapter 28.
Chapter 29.
Chapter 30.
Chapter 31.
Chapter 32.
The Organization of Metabolism 938
Electron Transport, Oxidative Phosphorylation,
and Hydroxylation 1012
The Chemistry of Movement 1088
Some Pathways of Carbohydrate Metabolism 1128
Specific Aspects of Lipid Metabolism 1180
Polyprenyl (Isoprenoid) Compounds 1226
Light and Life
1272
The Metabolism of Nitrogen and Amino Acids 1358
Metabolism of Aromatic Compounds and Nucleic
Acid Bases
1420
Biochemical Genetics
1472
Organization, Replication, Transposition, and Repair
of DNA 1528
The Transcription of Genes 1602
Ribosomes and the Synthesis of Proteins 1668
Chemical Communication Between Cells
1740
Biochemical Defense Mechanisms
1830
Growth and Development 1878
Table of Contents
Volume 2
Front matter Vol 2
2/14/03, 3:03 PM
10
Contents
A. The Simplest Living Things
1. Escherichia coli
2. The Bacterial Genome
3. Ribonucleic Acids (RNA) and the Transcription
and Translation of Genetic Information
4. Membranes and Cell Walls
5. Flagella and Pili
6. Classification and Evolution of Bacteria
7. Nutrition and Growth of Bacteria
8. Photosynthetic and Nitrogen-Fixing Prokaryotes
B. Eukaryotic Cells
1. The Nucleus
2. The Plasma Membrane
3. Vacuoles, Endocytosis, and Lysosomes
4. The Endoplasmic Reticulum and Golgi Membranes
5. Mitochondria, Plastids, and Peroxisomes
6. Centrioles, Cilia, Flagella, and Microtubules
7. Cell Coats, Walls, and Shells
C. Inheritance, Metabolic Variation, and Evolution of
Eukaryotes
1. A Changing Genome
2. Genetic Recombination, Sex, and Chromosomes
3. Haploid and Diploid Phases
D. Survey of the Protists
1. Protozoa
2. Fungi
3. Algae
E. The Variety of Animal Forms
1. Major Groups of Multicellular Animals
2. Cell Types and Tissues
Tissues
Blood cells
Cell culture
3. Communication
Cell contacts and junctions
Cell recognition
F. Higher Plants and Plant Tissues
G. The Chemical Composition of Cells
References
Study Questions
Boxes
Box 1-A
About Measurements
Box 1-B
Relative Molecular Mass, Mr, and Daltons
Box 1-C
In the Beginning
Box 1-D
Inherited Metabolic Diseases
Box 1-E
Errors, Misconceptions, and Speculation
Box 1-F
About the References
Tables
Table 1-1
A Systematic Classification Scheme for
Bacteria
Table 1-2
Approximate Sizes of Some Cells
Table 1-3
Haploid Genome Sizes for Several
Organisms
Table 1-4
Approximate Composition of
Metabolically Active Cells and Tissues
2
4
9
16
25
32
7
11
12
31
2
3
3
5
5
6
6
8
9
11
11
11
12
13
14
15
15
15
17
17
18
18
18
20
20
23
23
25
26
26
26
26
28
29
29
30
34
36
Left: Cells of the pathogenic O157:H7 strain of Escherichia coli attached to the surface epithelium of the
cecum of a neonatal piglet. Electron-dense filaments (presumably polymerized actin) in the host
cytoplasm can be seen subjacent to attached bacteria. The bacteria have effaced most micro-villi but
some remain between the bacterial cells. Courtesy of Evelyn A. Dean-Nystrom, National Animal
Disease Center, USDA, Agricultural Research Service, Ames, IA. Center: Many unicellular organisms
such as these Vorticella inhabit wet and moist environments throughout the biosphere. Invertebrates
have evolved as long as humans and have complex specializations such as the contractile stem of these
protozoa. Courtesy of Ralph Buchsbaum. Right: Although 97% of animals are invertebrates, ~ 3%
of the several million known species have backbones. Giraffe: © M. P. Kahl, Photo Researchers
1
This book is about the chemistry of living cells
with special emphasis on the trillions of cells that make
up your own body. Every aspect of life depends upon
the chemical makeup of cells and on the chemical
properties of the remarkable molecules found within
the cells. The information presented here will give
the reader a solid foundation for understanding not
only the chemical basis of life but also the revolution-
ary developments in molecular biology, biochemical
genetics, medicine, and agriculture which dominate
today’s scientific news and which will play an increas-
ingly important role in our lives.
The first theme of the book is biomolecular
structure. We’ll look carefully at the complex struc-
tures of proteins, carbohydrates, RNA, DNA, and
many other substances. We’ll not only examine in-
depth their molecular architecture but also study the
chemical properties that make life possible.
A second theme is metabolism, the unceasing,
complex network of thousands of chemical reactions
by which cells grow and reproduce, take up foods and
excrete wastes, move, and communicate with each
other. Within cells we have a steady state, a condi-
tion in which the complex chemical constituents of
cells are continuously being synthesized in one series
of reactions and degraded in another. The result is a
marvelous system of self-renewal or “turnover” of
tissues. We’ll examine the chemical reactions involved
in these processes as well as the ways in which they
are controlled. We will consider both the reaction
sequences and the techniques such as cloning of genes,
isotopic labeling, X-ray diffraction, and nuclear mag-
netic resonance spectroscopy, which are used today to
study metabolism.
Human beings are surrounded by many other living
creatures whose activities are important to us. Photo-
synthetic organisms obtain energy from sunlight and
synthesize compounds that the human body requires
but cannot make. Microorganisms cause decay of
organic matter and convert it into forms usable by
plants. This book deals with the chemical reactions
occurring in all of these organisms. We’ll look at
strange and unusual reactions, along with those meta-
bolic sequences common to most living things.
Each one of the thousands of chemical reactions
of metabolism is catalyzed by an enzyme. Most of
these enzymes are proteins, but others are made from
RNA (ribonucleic acid). In both cases enzymes are
very large molecules with precise three-dimensional
structures. The study of the properties of enzymes
and of enzymatic catalysis is a third theme of the
book. Not only are the chemical mechanisms by
which enzymes act of interest but also enzymes are
often targets for useful drugs. Incorrectly formed en-
zymes can result in serious diseases.
The sequences of the amino acids in the chains
from which proteins are constructed are encoded in
the nucleotide sequences of DNA (deoxyribonucleic
acid). The coding sequence for a protein in the DNA
is found in the structural gene for that protein. The
RNA enzymes are also encoded by DNA genes. A
fourth major theme of the book deals with the nature
of the genetic code used in DNA and with the pro-
cesses by which cells read and interpret the code. It
also includes study of the methods by which thousands
of genes have been mapped to specific positions in
chromosomes, isolated, cloned, and sequenced.
A large number of proteins present in the outer
surfaces of cells serve as receptors that receive chemi-
cal messages and other signals from outside the cell.
The receptors, which are sometimes enzymes, respond
by generating internal signals that control metabolism
and cell growth. Such molecular signaling is another
major area of contemporary biochemistry.
The Scene of Action
1
2
Chapter 1. The Scene of Action
BOX 1-A ABOUT MEASUREMENTS
Biologists have described over a million species,
and several millions of others probably exist.1 Many
of these organisms have very specialized ways of life.
However, they all have much chemistry in common.
The same 20 amino acids can be isolated from proteins
of plants, animals, and microorganisms. Formation of
lactic acid in both bacteria and human muscle requires
the same enzymes. Except for some small variations,
the genetic code is universal—the same for all organ-
isms. Thus, there is a unity of life and we can study
metabolism as the entirety of chemical transformations
going on in all living things. However, the differences
among species are also impressive. Each species has
its own gene for almost every protein.
When the enzyme that catalyzes a particular meta-
bolic reaction is isolated from a number of different
organisms, it is usually found to have similar proper-
ties and a similar mechanism of catalysis, regardless of
the source. However, the exact sequence of amino acids
in the enzyme will be almost unique to the organism
that produced it. When the three-dimensional struc-
tures are compared it is found that differences between
species often affect only the peripheral parts of an
enzyme molecule. The interior structure of the protein,
including the catalytic machinery, is highly conserved.
However, the surface regions, which often interact with
other macromolecules, vary greatly. Such interactions
help to control metabolism and may account for many
differences in the metabolism among living beings.
Variations in protein structures are not limited to
differences between species. Individuals differ from
one another. Serious genetic diseases sometimes result
from the replacement of a single amino acid unit in a
protein by a different amino acid. Genetic deviations
from the “normal” structure of a protein result from
mutations. Many mutations, whether they occurred
initially in our own cells or in those of our ancestors,
are detrimental.
However, such mutations also account for variation
among individuals of a species and allow for evolution.
The chemical nature and consequences of mutations
and their significance to health, medicine, and agricul-
ture are dealt with throughout the book. We now have
reliable methods for inducing in the laboratory muta-
tions at any specific place in a protein sequence and
also for synthesizing new DNA sequences. These
techniques of genetic engineering have given bio-
chemists the ability to modify protein structures freely,
to create entirely new proteins, and to provide a basis
for the rapidly developing field of genetic therapy.
It should be clear from this introduction that
biochemistry deals with virtually every aspect of life.
The distinguishing feature of the science is that it
approaches biological questions in terms of the under-
lying chemistry. The term molecular biology is often
regarded as synonymous with biochemistry.
However, some scientists use it to imply a more
biological approach. These molecular biologists also
emphasize structure and function but may have a goal
of understanding biological relationships more than
chemical details. Biophysics, a closely related science,
encompasses the application of physical and mathe-
matical tools to the study of life.
A. The Simplest Living Things
The simplest organisms are the bacteria.2–5 Their
cells are called prokaryotic (or procaryotic) because
no membrane-enclosed nucleus is present. Cells of all
other organisms contain nuclei separated from the
cytoplasm by membranes. They are called eukaryotic.
While viruses (Chapter 5) are sometimes regarded as
living beings, these amazing parasitic objects are not
complete organisms and have little or no metabolism of
their own. The smallest bacteria are the mycoplasmas.6–8
They do not have the rigid cell wall characteristic of
most bacteria. For this reason they are easily deformed
and often pass through filters designed to stop bacteria.
They are nutritionally fussy and are usually, if not
always, parasitic. Some live harmlessly in mucous
membranes of people, but others cause diseases.
In 1960 the International General Conference
on Weights and Measures adopted an improved
form of the metric system, The International
System of Units (SI). The units of mass, length,
and time are the kilogram (kg), meter (m), and
second (s). The following prefixes are used for
fractions and multiples:
10–18, atto (a)
10–6, micro (�)
109, giga (G)
10–15, femto (f)
10–3, milli (m)
1012, tera (T)
10–12, pico (p)
103, kilo (k)
1015, peta (P)
10–9, nano (n)
106, mega (M)
1018, exa (E)
There is an inconsistency in that the prefixes are
applied to the gram (g) rather than to the basic
unit, the kilogram.
SI units have been used throughout the book
whenever possible. There are no feet, microns,
miles, or tons. Molecular dimensions are given
uniformly in nanometers rather than in angstrom
units (Å; 1Å = 0.1 nm). Likewise the calorie and
kilocalorie have been replaced by the SI unit of
energy, the joule (J; 1 calorie = 4.184 J).
Throughout the book frequent use is made of
the following symbols:
, “appr oximately equal to”
~, “approximately” or “about”
3
For example, Mycoplasma pneumoniae is responsible for
primary atypical pneumonia.
Cells of mycoplasmas sometimes grow as filaments
but are often spherical and as small as 0.3 micrometer
(µm) in diameter. Their outer surface consists of a thin
cell membrane about 8 nanometers (nm) thick. This
membrane encloses the cytoplasm, a fluid material
containing many dissolved substances as well as sub-
microscopic particles. At the center of each cell is a
single, highly folded molecule of DNA, which consti-
tutes the bacterial chromosome. Besides the DNA
there may be, in a small spherical mycoplasma, about
1000 particles ~20 nm in diameter, the ribosomes.
These ribosomes are the centers of protein synthesis.
Included in the cytoplasm are many different kinds of
A pilus. Some E. coli are covered with
hundreds of pili of various lengths
Cell membrane, ~8 nm
Cell wall, ~10 nm
E. coli
~0.8 × 0.8 × 2.0 µm
DNA, 1.4 mm long.
Only 1% of the total
is drawn here
13–14 nm diameter
The lengths of the flagella
vary but are often ~4× longer
than the cell proper
Sheathed
flagellum,
28 nm
A small
mycoplasma
Some strains of E. coli
have flagella—as many
as 8, but often fewer
Ribosomes attached
to thread of mRNA
Ribosomes
~20 nm diameter
0.5 µm
Bdellovibrio, a parasite that lives
within E. coli [see picture by J.C.
Burnham, T. Hashimoto, and S.F.
Conti, J. Bacteriol. 96, 1366 (1968)]
Figure 1-1 Escherichia coli and some smaller bacteria.
proteins, but there is room for a total of only about
50,000 protein molecules. Several types of RNA as
well as many smaller molecules are also present.
Although we don’t know what minimum quantities
of proteins, DNA, and other materials are needed to
make a living cell, it is clear that they must all fit into
the tiny cell of the mycoplasma.
1. Escherichia coli
The biochemist’s best friend is Escherichia coli, an
ordinarily harmless inhabitant of our intestinal tract.
This bacterium is easy to grow in the laboratory and
has become the best understood organism at the mo-
lecular level.4,9 It may be regarded as a
typical true bacterium or eubacterium.
The cell of E. coli (Figs. 1-1, 1-2) is a
rod ~2 µm long and 0.8 µm in diameter
with a volume of ~1 µm3 and a density
of ~1.1 g/cm3. The mass is ~1 x 10–12 g,
i.e., 1 picogram (pg) or ~0.7 x 1012
daltons (Da) (see Box 1-B).4 It is about
100 times bigger than the smallest
mycoplasma but the internal structure,
as revealed by the electron microscope,
resembles that of a mycoplasma.
Each cell of E. coli contains from
one to four identical DNA molecules,
depending upon how fast the cell is
growing, and ~15,000–30,000 ribosomes.
Other particles that are sometimes seen
within bacteria include food stores such
as fat droplets and granules (Fig. 1-3).
The granules often consist of poly-�-
hydroxybutyric acid10 accounting
for up to 25% of the weight of Bacillus
megaterium. Polymetaphosphate, a
highly polymerized phosphoric acid,
is sometimes stored in “metachromatic
granules.” In addition, there may be
droplets of a separate aqueous phase,
known as vacuoles.
2. The Bacterial Genome
The genetic instructions for a cell
are found in the DNA molecules. All
DNA is derived from four different
kinds of monomers, which we call
nucleotides. DNA molecules are
double-stranded: two polymer chains
are coiled together, their nucleotide
units being associated as nucleotide
pairs (see Fig. 5-7). The genetic mes-
sages in the DNA are in the form of
A. The Simplest Living Things
4
Chapter 1. The Scene of Action
sequences of nucleotides. These sequences usually
consist of a series of code “words” or codons. Each
codon is composed of three successive nucleotides and
specifies which one of the 20 different kinds of amino
acids will be used at a particular location in a protein.
The sequence of codons in the DNA tells a cell how to
order the amino acids for construction of its many
different proteins.
Figure 1-2 Transmission electron micrograph of a dividing
cell of Escherichia coli O157:H7 attached to the intestinal
epithelium of a neonatal calf. These bacteria, which are able
to efface the intestinal microvilli, form characteristic attach-
ments, and secrete shiga toxins, are responsible for ~73,000
illnesses and 60 deaths per year in the U. S.10a After embed-
ding, the glutaraldehyde-fixed tissue section was immuno-
stained with goat anti-O157 IgG followed by protein A con-
jugated to 10-nm gold particles. These are seen around the
periphery of the cell bound to the O-antigen (see Fig. 8-28).
Notice the two microvilli of the epithelium. Courtesy of
Evelyn A. Dean-Nystrom, National Animal Disease Center,
USDA, Agricultural Research Service, Ames, IA.
Figure 1-3 A cell of a Spirillum negatively stained with
phosphotungstic acid. Note the tufts of flagella at the ends,
the rough appearance of the outer surface, the dark granules
of poly-�-hydroxybutyric acid and the light-colored gran-
ules of unknown nature. Courtesy of F. D. Williams, Gail E.
VanderMolen, and C. F. Amstein.
Assume that a typical protein molecule consists of
a folded chain of 400 amino acids. Its structural gene
will therefore be a sequence of 1200 nucleotide pairs.
Allowing a few more nucleotides to form spacer regions
between genes we can take ~1300 as the number of
nucleotide pairs in a typical bacterial gene. However,
some genes may be longer and some may be much
shorter. The genome is the quantity of DNA that carries
a complete set of genetic instructions for an organism.
In bacteria, the genome is a single chromosome con-
sisting of one double-stranded DNA molecule. Myco-
plasma genitalium is the smallest organism for which
the DNA sequence is known.11 Its genome is a double-
helical DNA circle of 580,070 nucleotide pairs and
appears to contain about 480 genes (an average of ~1200
nucleotides per gene).
The average mass of a nucleotide pair (as the
disodium salt) is 664 Da. It follows that the DNA of
M. genitalium has a mass of ~385 x 106 Da. The relative
molecular mass (Mr) is 0.385 x 109 (See Box 1-B for
definitions of dalton and Mr). The DNA of E. coli is
about seven times larger with a mass of ~2.7 x 109 Da.
It contains ~4.2 x 106 nucleotide pairs and encodes
over 4000 different proteins (see Table 1-3).
Each nucleotide pair contributes 0.34 nm to the
length of the DNA molecule; thus, the total length of
DNA of an E. coli chromosome is 1.4 mm. This is
about 700 times the length of the cell which contains it.
Clearly, the molecules of DNA are highly folded, a fact
that accounts for their appearance in the electron micro-
scope as dense aggregates called nucleoids, which
occupy about one-fifth of the cell volume (Fig. 1-4).
Atomic and molecular masses are assigned
relative to the mass of the carbon isotope, 12C,
whose atomic weight is defined as exactly 12.
The actual mass of a single atom of 12C is defined
as 12 daltons, one dalton being 1.661 x 10–24 g.
The mass of a molecule can be given in daltons
(Da) or kilodaltons (kDa). This molecular mass
in daltons is numerically equivalent to the relative
molecular mass (Mr) or molecular weight (MW)a
and also to the molar mass (g/mol). However, it
is not correct to use the dalton for the unitless
quantity Mr. Masses of structures such as chro-
mosomes, ribosomes, mitochondria, viruses, and
whole cells as well as macromolecules can be
given in daltons.b
a The Union of Pure and Applied Chemistry renamed
molecular weight as relative molecular mass with the
symbol Mr; Mr = MW.
b J. T. Edsall (1970) Nature (London) 228, 888.
BOX 1-B
RELATIVE MOLECULAR MASS,
Mr, AND DALTONS
1 µm
1 µm
5
A. The Simplest Living Things
Each bacterial nucleoid contains a complete set of
genetic “blueprints” and functions independently.
Each nucleoid is haploid, meaning that it contains
only a single complete set of genes. In addition to
their chromosome, bacteria often contain smaller
DNA molecules known as plasmids. These plasmids
also carry genetic information that may be useful to
bacteria. For example, they often encode proteins that
confer resistance to antibiotics. The ability to acquire
new genes from plasmids is one mechanism that
allows bacteria to adapt readily to new environments.12
Plasmids are also used in the laboratory in the cloning
of genes and in genetic engineering (Chapter 26).
3. Ribonucleic Acids (RNA) and the
Transcription and Translation of Genetic
Information
The genetic information in the DNA is not utilized
directly by the protein-synthesizing machinery of cells.
Instead, molecules of ribonucleic acid (RNA) are syn-
thesized according to the instructions encoded in the
DNA, a process called transcription. Although they
differ from DNA significantly in their structure, these
RNA molecules carry the same coded information as
is found in a length of DNA that contains one or a few
genes. If DNA is regarded as the “master blueprint” of
the cell, molecules of RNA are “secondary blueprints.”
This concept is embodied in the name messenger
RNA (mRNA) which is applied to a small, short-lived
fraction of RNA that carries information specifying
amino acid sequences of proteins. Each molecule of
mRNA carries the genetic message from one or more
genes to the ribosomes where the proteins are made.
Ribosomes are extraordinarily complex little
protein-synthesizing machines. Each ribosome of
E. coli has a mass of 2.7 x 106 Da and contains 65% of
a stable ribosomal RNA and ~35% protein. About
50 different kinds of protein molecules are present as
parts of the ribosomal structure. Working together
with a variety of transfer RNA molecules and enzymes,
the ribosomes are able to read the genetic messages
from mRNA and to accurately assemble any kind of
protein molecule that a gene may specify. This process
is called translation of the genetic message.
4. Membranes and Cell Walls
Like the mycoplasma, the E. coli cell is bounded
by an 8-nm membrane which consists of ~50% protein
and 50% lipid. When “stained” (e.g., with perman-
ganate) for electron microscopy, this single membrane
appears as two very thin (2.0 nm) dark lines separated
by an unstained center band (~3.5 nm) (Fig. 1-4; see
also Fig. 8-4). Single membranes of approximately the
same thickness and staining behavior occur in all cells,
both of bacteria and of eukaryotes.
A cell membrane is much more than just a sack.
It serves to control the passage of small molecules into
and out of the cell. Its outer surface carries receptors
for recognition of various materials. The inside surface
of bacterial membranes contains enzymes that catalyze
most of the oxidative metabolism of the cells. Bacterial
cell membranes are sometimes folded inward to form
internal structures involved in photosynthesis or other
specialized reactions of metabolism such as oxidation
of ammonia to nitrate.2 In E. coli replication of DNA
seems to occur on certain parts of the membrane sur-
face, probably under the control of membrane-bound
enzymes. The formation of the new membrane which
Figure 1-4 (A) Thin (~60 nm) section of an aquatic gram-
negative bacterium, Aquaspirillum fasciculus. Note the light-
colored DNA, the dark ribosomes, the double membrane
characteristics of gram-negative bacteria (Chapter 8, Section
E), and the cell wall. In addition, an internal “polar mem-
brane” is seen at the end. It may be involved in some way in
the action of the flagella. (B) A thin section of dividing cell
of Streptococcus, a gram-positive organism. Note the DNA
(light-stranded material). A portion of a mesosome is seen
in the center and septum can be seen forming between the
cells. Micrographs courtesy of F. D. Williams, Gail E.
VanderMolen, and C. F. Amstein.
B
0.25 µm
A
6
Chapter 1. The Scene of Action
divides multiplying cells proceeds synchronously with
the synthesis of DNA.
A characteristic of true bacteria (eubacteria) is a
rigid cell wall which surrounds the cell membrane.
The 40-nm-thick wall of E. coli is a complex, layered
structure five times thicker than the cell membrane.
Its chemical makeup is considered in Chapter 8. One
of the layers is often referred to as the outer mem-
brane. In some bacteria the wall may be as much as
80 nm thick and may be further surrounded by a thick
capsule or glycocalyx (slime layer).13 The main
function of the wall seems to be to prevent osmotic
swelling and bursting of the bacterial cell when the
surrounding medium is hypotonic.
If the osmotic pressure of the medium is not too
low, bacterial cell walls can sometimes be dissolved,
leaving living cells bounded only by their membranes.
Such protoplasts can be produced by action of the
enzyme lysozyme on gram-positive bacteria such as
Bacillus megaterium. Treatment of cells of gram-negative
bacteria with penicillin (Box 20-G) produces sphero-
plasts, cells with partially disrupted walls. Sphero-
plasts and protoplasts are useful in biochemical studies
because substances enter cells more readily when the
cell wall is absent. Strains of bacteria lacking rigid
walls are known as L forms.
5. Flagella and Pili
Many bacteria swim at speeds of 20–60 µm/s, ten
or more body lengths per second! Very thin thread-
like flagella of diameter 13–20 nm coiled into a helical
form are rotated by the world’s smallest “electric
motors” to provide the motion.14 While some bacteria
have a single flagellum, the corkscrew-like Spirillum
(Fig. 1-3) synchronously moves tufts of flagella at both
ends. Some strains of E. coli have no flagella, but
others contain as many as eight flagella per cell dis-
tributed over the surface. The flagella stream out
behind in a bundle when the bacterium swims. The
flagella of the helical spirochetes are located inside
the outer membrane.15,16
In addition to flagella, extremely thin, long,
straight filaments known as pili or fimbriae (Fig. 1-2)
project from the surfaces of many bacteria.14 The “sex
pili” (F pili and I pili) of E. coli have a specific role in
sexual conjugation. The similar but more numerous
common pili or fimbriae range in thickness from 3 to
25 nm and in length from 0.2 to 2 �m. Pili are involved
in adhesion of bacteria to surrounding materials or to
other bacteria and facilitate bacterial infections.17–19
A typical E. coli cell has 100–300 pili.5
6. Classification and Evolution of Bacteria
Bacteria vary greatly in their chemistry and meta-
bolism, and it is difficult to classify them in a rational
way. In higher organisms species are often defined as
forms that cannot interbreed and produce fertile off-
spring, but such a criterion is meaningless for bacteria
whose reproduction is largely asexual and which are
able readily to accept “visiting genes” from other
bacteria.12 The classification into species and genera
is therefore somewhat arbitrary. A currently used
scheme (Table 1-1)20 classifies the prokaryotes into 35
groups on the basis of many characteristics including
shape, staining behavior, and chemical activities. Table
1-1 also includes genus names of most of the bacteria
discussed in this book.
Bacteria may have the shape of spheres or straight
or curved rods. Some, such as the actinomycetes,
grow in a branching filamentous form. Words used to
describe bacteria often refer to these shapes: a coccus
is a sphere, a bacillus a rod, and a vibrio a curved rod
with a flagellum at one end. A spirillum is screw-
shaped. These same words are frequently used to
name particular genera or families. Other names are
derived from some chemical activity of the bacterium
being described.
The gram stain provides an important criterion
of classification that depends upon differences in the
structure of the cell wall (see Chapter 20). Bacterial
cells are described as gram-positive or gram-negative
according to their ability to retain the basic dye crystal
violet as an iodine complex. This difference distinguishes
two of four large categories of bacteria.20 Most actino-
mycetes, the spore-forming bacilli, and most cocci are
gram-positive, while E. coli, other enterobacteria, and
pseudomonads are gram-negative. A third category
consists of eubacteria that lack cell walls, e.g. the
mycoplasma.
Comparisons of amino acid sequences of proteins
and the nucleotide sequences of DNA and RNA have
provided a new approach to classification of bacteria.21–28
Although the origins of life are obscure, we can easily
observe that the genome changes with time through
mutation and through the enzyme-catalyzed process
of genetic recombination. The latter gives rise to the
deletion of some nucleotides and the insertion of others
into a DNA chain. When we examine sequences of
closely related species, such as E. coli and Salmonella
typhimurium, we find that the sequences are very similar.
However, they differ greatly from those of many other
bacteria. Consider the 23S ribosomal RNA, a molecule
found in the ribosomes of all bacteria. It contains ~3300
nucleotides in a single highly folded chain. The basic
structure is highly conserved but between any two
species of bacteria there are many nucleotide substitu-
tions caused by mutations as well as deletions and
insertions. By asking what is the minimum number of
