Biochemistry: The Chemical Reactions of Living Cells

1977 Pages·2003·59.96 MB·English

by  David E. Metzler

Table of Contents
Volume 1
Chapter 1. The Scene of Action 1
Chapter 2. Amino Acids, Peptides, and Proteins 39
Chapter 3. Determining Structures and Analyzing Cells 95
Chapter 4. Sugars, Polysaccharides, and Glycoproteins 161
Chapter 5. The Nucleic Acids 199
Chapter 6. Thermodynamics and Biochemical Equilibria 281
Chapter 7. How Macromolecules Associate 325
Chapter 8. Lipids, Membranes, and Cell Coats 379
Chapter 9. Enzymes: The Catalysts of Cells 455
Chapter 10. An Introduction to Metabolism 505
Chapter 11. The Regulation of Enzymatic Activity and Metabolism 535
Chapter 12. Transferring Groups by Displacement Reactions 589
Chapter 13. Enzymatic Addition, Elimination, Condensation,
and Isomerization: Roles for Enolate and Carbocation
Intermediates 677
Chapter 14. Coenzymes: Nature’s Special Reagents 719
Chapter 15. Coenzymes of Oxidation – Reduction Reactions 765
Chapter 16. Transition Metals in Catalysis and Electron Transport 837
Table of Contents
Volume 2
Chapter 17. The Organization of Metabolism 938
Chapter 18. Electron Transport, Oxidative Phosphorylation,
and Hydroxylation 1012
Chapter 19. The Chemistry of Movement 1088
Chapter 20. Some Pathways of Carbohydrate Metabolism 1128
Chapter 21. Specific Aspects of Lipid Metabolism 1180
Chapter 22. Polyprenyl (Isoprenoid) Compounds 1226
Chapter 23. Light and Life1272
Chapter 24. The Metabolism of Nitrogen and Amino Acids 1358
Chapter 25. Metabolism of Aromatic Compounds and Nucleic
Acid Bases1420
Chapter 26. Biochemical Genetics1472
Chapter 27. Organization, Replication, Transposition, and Repair
of DNA 1528
Chapter 28. The Transcription of Genes 1602
Chapter 29. Ribosomes and the Synthesis of Proteins 1668
Chapter 30. Chemical Communication Between Cells1740
Chapter 31. Biochemical Defense Mechanisms1830
Chapter 32. Growth and Development 1878
Front matter Vol 2 10 2/14/03, 3:03 PM
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
Contents
2 A. The Simplest Living Things Boxes
3 1. Escherichia coli 2 Box 1-A About Measurements
3 2. The Bacterial Genome 4 Box 1-B Relative Molecular Mass, M, and Daltons
r
5 3. Ribonucleic Acids (RNA) and the Transcription 9 Box 1-C In the Beginning
and Translation of Genetic Information 16 Box 1-D Inherited Metabolic Diseases
5 4. Membranes and Cell Walls 25 Box 1-E Errors, Misconceptions, and Speculation
6 5. Flagella and Pili 32 Box 1-F About the References
6 6. Classification and Evolution of Bacteria
8 7. Nutrition and Growth of Bacteria Tables
9 8. Photosynthetic and Nitrogen-Fixing Prokaryotes 7 Table 1-1 A Systematic Classification Scheme for
11 B. Eukaryotic Cells Bacteria
11 1. The Nucleus 11 Table 1-2 Approximate Sizes of Some Cells
11 2. The Plasma Membrane 12 Table 1-3 Haploid Genome Sizes for Several
12 3. Vacuoles, Endocytosis, and Lysosomes Organisms
13 4. The Endoplasmic Reticulum and Golgi Membranes 31 Table 1-4 Approximate Composition of
14 5. Mitochondria, Plastids, and Peroxisomes Metabolically Active Cells and Tissues
15 6. Centrioles, Cilia, Flagella, and Microtubules
15 7. Cell Coats, Walls, and Shells
15 C. Inheritance, Metabolic Variation, and Evolution of
Eukaryotes
17 1. A Changing Genome
17 2. Genetic Recombination, Sex, and Chromosomes
18 3. Haploid and Diploid Phases
18 D. Survey of the Protists
18 1. Protozoa
20 2. Fungi
20 3. Algae
23 E. The Variety of Animal Forms
23 1. Major Groups of Multicellular Animals
25 2. Cell Types and Tissues
26 Tissues
26 Blood cells
26 Cell culture
26 3. Communication
28 Cell contacts and junctions
29 Cell recognition
29 F. Higher Plants and Plant Tissues
30 G. The Chemical Composition of Cells
34 References
36 Study Questions
1
1
The Scene of Action
This book is about the chemistry of living cells synthesize compounds that the human body requires
with special emphasis on the trillions of cells that make but cannot make. Microorganisms cause decay of
up your own body. Every aspect of life depends upon organic matter and convert it into forms usable by
the chemical makeup of cells and on the chemical plants. This book deals with the chemical reactions
properties of the remarkable molecules found within occurring in all of these organisms. We’ll look at
the cells. The information presented here will give strange and unusual reactions, along with those meta-
the reader a solid foundation for understanding not bolic sequences common to most living things.
only the chemical basis of life but also the revolution- Each one of the thousands of chemical reactions
ary developments in molecular biology, biochemical of metabolism is catalyzed by an enzyme. Most of
genetics, medicine, and agriculture which dominate these enzymes are proteins, but others are made from
today’s scientific news and which will play an increas- RNA (ribonucleic acid). In both cases enzymes are
ingly important role in our lives. very large molecules with precise three-dimensional
The first theme of the book is biomolecular structures. Thestudy of the properties of enzymes
structure. We’ll look carefully at the complex struc- and of enzymatic catalysis is a third theme of the
tures of proteins, carbohydrates, RNA, DNA, and book. Not only are the chemical mechanisms by
many other substances. We’ll not only examine in- which enzymes act of interest but also enzymes are
depth their molecular architecture but also study the often targets for useful drugs. Incorrectly formed en-
chemical properties that make life possible. zymes can result in serious diseases.
A second theme is metabolism, the unceasing, The sequences of the amino acids in the chains
complex network of thousands of chemical reactions from which proteins are constructed are encoded in
by which cells grow and reproduce, take up foods and the nucleotide sequences of DNA (deoxyribonucleic
excrete wastes, move, and communicate with each acid). The coding sequence for a protein in the DNA
other. Within cells we have a steady state, a condi- is found in the structural gene for that protein. The
tion in which the complex chemical constituents of RNA enzymes are also encoded by DNA genes. A
cells are continuously being synthesized in one series fourth major theme of the book deals with the nature
of reactions and degraded in another. The result is a of the genetic code used in DNAand with the pro-
marvelous system of self-renewal or “turnover” of cesses by which cells read and interpret the code. It
tissues. We’ll examine the chemical reactions involved also includes study of the methods by which thousands
in these processes as well as the ways in which they of genes have been mapped to specific positions in
are controlled. We will consider both the reaction chromosomes, isolated, cloned, and sequenced.
sequences and the techniques such as cloning of genes, A large number of proteins present in the outer
isotopic labeling, X-ray diffraction, and nuclear mag- surfaces of cells serve as receptors that receive chemi-
netic resonance spectroscopy, which are used today to cal messages and other signals from outside the cell.
study metabolism. The receptors, which are sometimes enzymes, respond
Human beings are surrounded by many other living by generating internal signals that control metabolism
creatures whose activities are important to us. Photo- and cell growth. Such molecular signaling is another
synthetic organisms obtain energy from sunlight and major area of contemporary biochemistry.
2 Chapter 1. The Scene of Action
Biologists have described over a million species, biological approach. These molecular biologists also
and several millions of others probably exist.1 Many emphasize structure and function but may have a goal
of these organisms have very specialized ways of life. of understanding biological relationships more than
However, they all have much chemistry in common. chemical details. Biophysics, a closely related science,
The same 20 amino acids can be isolated from proteins encompasses the application of physical and mathe-
of plants, animals, and microorganisms. Formation of matical tools to the study of life.
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- A. The Simplest Living Things
isms. Thus, there is a unity of life and we can study
metabolism as the entirety of chemical transformations The simplest organisms are the bacteria.2–5 Their
going on in all living things. However, the differences cells are called prokaryotic (or procaryotic) because
among species are also impressive. Each species has no membrane-enclosed nucleus is present. Cells of all
its own gene for almost every protein. other organisms contain nuclei separated from the
When the enzyme that catalyzes a particular meta- cytoplasm by membranes. They are called eukaryotic.
bolic reaction is isolated from a number of different While viruses (Chapter 5) are sometimes regarded as
organisms, it is usually found to have similar proper- living beings, these amazing parasitic objects are not
ties and a similar mechanism of catalysis, regardless of complete organisms and have little or no metabolism of
the source. However, the exact sequence of amino acids their own. The smallest bacteria are the mycoplasmas.6–8
in the enzyme will be almost unique to the organism They do not have the rigid cell wall characteristic of
that produced it. When the three-dimensional struc- most bacteria. For this reason they are easily deformed
tures are compared it is found that differences between and often pass through filters designed to stop bacteria.
species often affect only the peripheral parts of an They are nutritionally fussy and are usually, if not
enzyme molecule. The interior structure of the protein, always, parasitic. Some live harmlessly in mucous
including the catalytic machinery, is highly conserved. membranes of people, but others cause diseases.
However, the surface regions, which often interact with
other macromolecules, vary greatly. Such interactions
help to control metabolism and may account for many
BOX 1-A ABOUT MEASUREMENTS
differences in the metabolism among living beings.
Variations in protein structures are not limited to
differences between species. Individuals differ from In 1960 the International General Conference
one another. Serious genetic diseases sometimes result on Weights and Measures adopted an improved
from the replacement of a single amino acid unit in a form of the metric system, The International
protein by a different amino acid. Genetic deviations System of Units (SI). The units of mass, length,
from the “normal” structure of a protein result from and time are the kilogram (kg), meter (m), and
mutations. Many mutations, whether they occurred second (s). The following prefixes are used for
initially in our own cells or in those of our ancestors, fractions and multiples:
are detrimental.
However, such mutations also account for variation 10–18,atto (a) 10–6,micro ((cid:1)) 109,giga (G)
among individuals of a species and allow for evolution. 10–15,femto (f) 10–3,milli (m) 1012, tera (T)
The chemical nature and consequences of mutations 10–12,pico (p) 103,kilo (k) 1015,peta (P)
and their significance to health, medicine, and agricul- 10–9,nano (n) 106,mega (M) 1018,exa (E)
ture are dealt with throughout the book. We now have
reliable methods for inducing in the laboratory muta- There is an inconsistency in that the prefixes are
tions at any specific place in a protein sequence and applied to the gram (g) rather than to the basic
also for synthesizing new DNA sequences. These unit, the kilogram.
techniques of genetic engineering have given bio- SI units have been used throughout the book
chemists the ability to modify protein structures freely, whenever possible. There are no feet, microns,
to create entirely new proteins, and to provide a basis miles, or tons. Molecular dimensions are given
for the rapidly developing field of genetic therapy. uniformly in nanometers rather than in angstrom
It should be clear from this introduction that units (Å; 1Å = 0.1 nm). Likewise the calorie and
biochemistry deals with virtually every aspect of life. kilocalorie have been replaced by the SI unit of
The distinguishing feature of the science is that it energy, the joule (J; 1 calorie = 4.184 J).
approaches biological questions in terms of the under- Throughout the book frequent use is made of
lying chemistry. The term molecular biology is often the following symbols:
regarded as synonymous with biochemistry. ,“approximately equal to”
However, some scientists use it to imply a more ~,“approximately” or “about”
A. The Simplest Living Things 3
For example, Mycoplasma pneumoniae is responsible for proteins, but there is room for a total of only about
primary atypical pneumonia. 50,000 protein molecules. Several types of RNA as
Cells of mycoplasmas sometimes grow as filaments well as many smaller molecules are also present.
but are often spherical and as small as 0.3 micrometer Although we don’t know what minimum quantities
(µm) in diameter. Their outer surface consists of a thin of proteins, DNA, and other materials are needed to
cell membrane about 8 nanometers (nm) thick. This make a living cell, it is clear that they must all fit into
membrane encloses the cytoplasm, a fluid material the tiny cell of the mycoplasma.
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- 1. Escherichia coli
tutes the bacterial chromosome. Besides the DNA
there may be, in a small spherical mycoplasma, about The biochemist’s best friend is Escherichia coli, an
1000 particles ~20 nm in diameter, the ribosomes. ordinarily harmless inhabitant of our intestinal tract.
These ribosomes are the centers of protein synthesis. This bacterium is easy to grow in the laboratory and
Included in the cytoplasm are many different kinds of 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
A pilus. Some E. coli are covered with rod ~2 µm long and 0.8 µm in diameter
0.5µm hundreds of pili of various lengths with a volume of ~1 µm3 and a density
of ~1.1 g/cm3. The mass is ~1 x 10–12 g,
Cell membrane, ~8 nm i.e., 1 picogram (pg) or ~0.7 x 1012
daltons (Da) (see Box 1-B).4 It is about
Cell wall, ~10 nm
100 times bigger than the smallest
mycoplasma but the internal structure,
E. coli
~0.8× 0.8 × 2.0µm as revealed by the electron microscope,
Ribosomes resembles that of a mycoplasma.
~20 nm diameter Each cell of E. coli contains from
DNA, 1.4 mm long.
Only 1% of the total one to four identical DNA molecules,
Ribosomes attached is drawn here depending upon how fast the cell is
to thread of mRNA growing, and ~15,000–30,000 ribosomes.
Other particles that are sometimes seen
Some strains of E. coli within bacteria include food stores such
have flagella—as many
as fat droplets and granules (Fig. 1-3).
as 8, but often fewer
13–14 nm diameter The granules often consist of poly-(cid:1)-
hydroxybutyric acid10 accounting
for up to 25% of the weight of Bacillus
megaterium. Polymetaphosphate, a
highly polymerized phosphoric acid,
The lengths of the flagella
is sometimes stored in “metachromatic
vary but are often ~4× longer
than the cell proper granules.” In addition, there may be
Bdellovibrio, a parasite that lives droplets of a separate aqueous phase,
withinE. coli [see picture by J.C. known as vacuoles.
Sheathed
Burnham, T. Hashimoto, and S.F.
flagellum,
Conti,J. Bacteriol.96, 1366 (1968)]
28 nm
2. The Bacterial Genome
The genetic instructions for a cell
are found in the DNA molecules. All
DNA is derived from four different
A small kinds of monomers, which we call
mycoplasma
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-
Figure 1-1 Escherichia coli and some smaller bacteria.
sages in the DNA are in the form of
4 Chapter 1. The Scene of Action
sequences of nucleotides. These sequences usually Assume that a typical protein molecule consists of
consist of a series of code “words” or codons. Each a folded chain of 400 amino acids. Its structural gene
codon is composed of three successive nucleotides and will therefore be a sequence of 1200 nucleotide pairs.
specifies which one of the 20 different kinds of amino Allowing a few more nucleotides to form spacer regions
acids will be used at a particular location in a protein. between genes we can take ~1300 as the number of
The sequence of codons in the DNA tells a cell how to nucleotide pairs in a typical bacterial gene. However,
order the amino acids for construction of its many some genes may be longer and some may be much
different proteins. 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-
1µm 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 (M) is 0.385 x 109 (See Box 1-B for
r
definitions of dalton and M). The DNA of E.coli is
r
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
Figure 1-2 Transmission electron micrograph of a dividing
cell of Escherichia coli O157:H7 attached to the intestinal that accounts for their appearance in the electron micro-
epithelium of a neonatal calf. These bacteria, which are able scope as dense aggregates called nucleoids, which
to efface the intestinal microvilli, form characteristic attach- occupy about one-fifth of the cell volume (Fig. 1-4).
ments, and secrete shiga toxins, are responsible for ~73,000
illnesses and 60 deaths per year in the U. S.10aAfter embed-
ding, the glutaraldehyde-fixed tissue section was immuno-
stained with goat anti-O157 IgG followed by protein A con-
BOX 1-B RELATIVE MOLECULAR MASS,
jugated to 10-nm gold particles. These are seen around the
M , AND DALTONS
periphery of the cell bound to the O-antigen (see Fig. 8-28). r
Notice the two microvilli of the epithelium. Courtesy of
Evelyn A. Dean-Nystrom, National Animal Disease Center, Atomic and molecular masses are assigned
USDA, Agricultural Research Service, Ames, IA. 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). Thismolecularmass
in daltons is numerically equivalent to the relative
molecular mass (M ) or molecular weight (MW)a
r
and also to the molar mass (g/mol). However, it
1µm is not correct to use the dalton for the unitless
quantityM. Masses of structures such as chro-
r
mosomes, ribosomes, mitochondria, viruses, and
whole cells as well as macromolecules can be
Figure 1-3 A cell of a Spirillum negatively stained with given in daltons.b
phosphotungstic acid. Note the tufts of flagella at the ends,
the rough appearance of the outer surface, the dark granules
a The Union of Pure and Applied Chemistry renamed
of poly-(cid:2)-hydroxybutyric acid and the light-colored gran- molecular weight as relativemolecular mass with the
ules of unknown nature. Courtesy of F. D. Williams, Gail E. symbolM;M = MW.
r r
VanderMolen, and C. F. Amstein. b J. T. Edsall (1970) Nature (London)228, 888.
A. The Simplest Living Things 5
Each bacterial nucleoid contains a complete set of
3. Ribonucleic Acids (RNA) and the
genetic“blueprints” and functions independently.
Transcription and Translation of Genetic
Each nucleoid is haploid, meaning that it contains
Information
only a single complete set of genes. In addition to
their chromosome, bacteria often contain smaller
The genetic information in the DNA is not utilized
DNA molecules known as plasmids. These plasmids
directly by the protein-synthesizing machinery of cells.
also carry genetic information that may be useful to
Instead, molecules of ribonucleic acid (RNA) are syn-
bacteria. For example, they often encode proteins that
thesized according to the instructions encoded in the
confer resistance to antibiotics. The ability to acquire
DNA, a process called transcription. Although they
new genes from plasmids is one mechanism that
differ from DNA significantly in their structure, these
allows bacteria to adapt readily to new environments.12
RNA molecules carry the same coded information as
Plasmids are also used in the laboratory in the cloning
is found in a length of DNA that contains one or a few
of genes and in genetic engineering (Chapter 26).
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
A 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 ribosomalRNA 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
0.25µm 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.
B
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
Figure 1-4 (A) Thin (~60 nm) section of an aquatic gram- and out of the cell. Its outer surface carries receptors
negative bacterium, Aquaspirillum fasciculus. Note the light- for recognition of various materials. The inside surface
colored DNA, the dark ribosomes, the double membrane of bacterial membranes contains enzymes that catalyze
characteristics of gram-negative bacteria (Chapter 8, Section
most of the oxidative metabolism of the cells. Bacterial
E), and the cell wall. In addition, an internal “polar mem-
cell membranes are sometimes folded inward to form
brane” is seen at the end. It may be involved in some way in
internal structures involved in photosynthesis or other
the action of the flagella. (B) A thin section of dividing cell
specialized reactions of metabolism such as oxidation
ofStreptococcus, a gram-positive organism. Note the DNA
(light-stranded material). A portion of a mesosome is seen of ammonia to nitrate.2 InE. coli replication of DNA
in the center and septum can be seen forming between the seems to occur on certain parts of the membrane sur-
cells. Micrographs courtesy of F. D. Williams, Gail E. face, probably under the control of membrane-bound
VanderMolen, and C. F. Amstein. enzymes. The formation of the new membrane which
6 Chapter 1. The Scene of Action
divides multiplying cells proceeds synchronously with
6. Classification and Evolution of Bacteria
the synthesis of DNA.
A characteristic of true bacteria (eubacteria) is a
Bacteria vary greatly in their chemistry and meta-
rigidcell wall which surrounds the cell membrane.
bolism, and it is difficult to classify them in a rational
The 40-nm-thick wall of E. coli is a complex, layered
way. In higher organisms species are often defined as
structure five times thicker than the cell membrane.
forms that cannot interbreed and produce fertile off-
Its chemical makeup is considered in Chapter 8. One
spring, but such a criterion is meaningless for bacteria
of the layers is often referred to as the outer mem-
whose reproduction is largely asexual and which are
brane. In some bacteria the wall may be as much as
able readily to accept “visiting genes” from other
80 nm thick and may be further surrounded by a thick
bacteria.12 The classification into species and genera
capsule or glycocalyx (slime layer).13 The main
is therefore somewhat arbitrary. A currently used
function of the wall seems to be to prevent osmotic
scheme (Table 1-1)20 classifies the prokaryotes into 35
swellingand bursting of the bacterial cell when the
groups on the basis of many characteristics including
surrounding medium is hypotonic.
shape, staining behavior, and chemical activities. Table
If the osmotic pressure of the medium is not too
1-1 also includes genus names of most of the bacteria
low, bacterial cell walls can sometimes be dissolved,
discussed in this book.
leaving living cells bounded only by their membranes.
Bacteria may have the shape of spheres or straight
Suchprotoplasts can be produced by action of the
or curved rods. Some, such as the actinomycetes,
enzyme lysozyme on gram-positive bacteria such as
grow in a branching filamentous form. Words used to
Bacillusmegaterium. Treatment of cells of gram-negative
describe bacteria often refer to these shapes: a coccus
bacteria with penicillin (Box 20-G) produces sphero-
is a sphere, a bacillus a rod, and a vibrio a curved rod
plasts, cells with partially disrupted walls. Sphero-
with a flagellum at one end. A spirillum is screw-
plasts and protoplasts are useful in biochemical studies
shaped. These same words are frequently used to
because substances enter cells more readily when the
name particular genera or families. Other names are
cell wall is absent. Strains of bacteria lacking rigid
derived from some chemical activity of the bacterium
walls are known as L forms.
being described.
Thegram stain provides an important criterion
of classification that depends upon differences in the
5. Flagella and Pili
structure of the cell wall (see Chapter 20). Bacterial
cells are described as gram-positive or gram-negative
Many bacteria swim at speeds of 20–60µm/s, ten
according to their ability to retain the basic dye crystal
or more body lengths per second! Very thin thread-
violet as an iodine complex. This difference distinguishes
likeflagella of diameter 13–20 nm coiled into a helical
two of four large categories of bacteria.20 Most actino-
form are rotated by the world’s smallest “electric
mycetes, the spore-forming bacilli, and most cocci are
motors” to provide the motion.14 While some bacteria
gram-positive, while E. coli, other enterobacteria, and
have a single flagellum, the corkscrew-like Spirillum
pseudomonads are gram-negative. A third category
(Fig. 1-3) synchronously moves tufts of flagella at both
consists of eubacteria that lack cell walls, e.g. the
ends. Some strains of E. coli have no flagella, but
mycoplasma.
others contain as many as eight flagella per cell dis-
Comparisons of amino acid sequences of proteins
tributed over the surface. The flagella stream out
and the nucleotide sequences of DNA and RNA have
behind in a bundle when the bacterium swims. The
provided a new approach to classification of bacteria.21–28
flagella of the helical spirochetes are located inside
Although the origins of life are obscure, we can easily
the outer membrane.15,16
observe that the genome changes with time through
In addition to flagella, extremely thin, long,
mutation and through the enzyme-catalyzed process
straight filaments known as pili or fimbriae (Fig. 1-2)
ofgenetic recombination. The latter gives rise to the
project from the surfaces of many bacteria.14 The “sex
deletion of some nucleotides and the insertion of others
pili” (F pili and I pili) of E. coli have a specific role in
into a DNA chain. When we examine sequences of
sexual conjugation. The similar but more numerous
closely related species, such as E. coli and Salmonella
common pili or fimbriae range in thickness from 3 to
typhimurium, we find that the sequences are very similar.
25 nm and in length from 0.2 to 2 (cid:1)m. Pili are involved
However, they differ greatly from those of many other
in adhesion of bacteria to surrounding materials or to
bacteria. Consider the 23S ribosomal RNA, a molecule
other bacteria and facilitate bacterial infections.17–19
found in the ribosomes of all bacteria. It contains ~3300
A typical E. coli cell has 100–300 pili.5
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