I.

A brief history of Microbiology Molds- typically multicellular

o The Early Years of Microbiology organisms that grow as long
filaments that intertwine to make up
Antoni van Leeuwenhoek- a Dutch tailor, merchant, the body of the mold.
and lens grinder, and the man who first discovered
4. Protozoa- single-celled eukaryotes that are
the bacterial world.
similar to animals in their nutritional needs
 Leeuwenhoek’s observations of
and cellular structure.
microbes introduced most types of
Protozoa Greek term for “first animals”
microorganisms to the world. His
- Most protozoa are capable of
discoveries were named and classified
locomotion, own way scientist
by Linnaeus in his taxonomic system.
categorize.
- Pseudopods -extension of a cell
that flow in the direction of
travel.

6 Basic Categories
1. Bacteria- cells lack of nuclei
- Cilia -are numerous short
-genes are not surrounded by a protrusions of a cell that beat
membrane. rhythmically to propel the
protozoan through its
Peptidoglycan – bacterial cell wall environment
is composed of polysaccharide.
-both groups reproduce asexually
between bacteria & archaea.
-Small prokaryotes—bacteria and
archaea—live in a variety of communities and in
most habitats. Even though some cause disease,
- Flagella -extensions of a cell
most are beneficial.
but are fewer, longer, and more
2. Archea whiplike than cilia
3. Fungi- eukaryotic, contains a nucleus
composed of genetic material surrounded by
a distinct membrane.

1
5. Algae -unicellular or multicellular Summary
photosynthetic eukaryotes;
 Relatively large microscopic eukaryotic
fungi include molds and yeasts.
 Animal-like protozoa are single-celled
eukaryotes. Some cause disease.
 Plantlike eukaryotic algae are important
providers of oxygen, serve as food for many
marine animals, and make chemicals used in
- make their own food from microbiological growth media.
carbon dioxide and water using  Parasitic worms, the largest organisms
energy from sunlight. studied by microbiologists, are often visible
- Large algae called seaweeds & without a microscope, although their
kelps, common in the wolrd’s immature stages are microscopic.
ocean.  Viruses, the smallest microbes, are so small
- Manufacturers use gelatinous they can be seen only with an electron
chemicals from the cell walls of microscope.
some large algae as thicken- ers
and emulsifiers in many foods o The Golden Age of Microbiology
and cosmetics.
- Unicelullar algae -common in Redi Experiments (Francesco Redi 1626-1697)
freshwater ponds, streams and
lakes and in the ocean as well. o Demonstrated by a series of experiments that
- Major food of small aquatic and when decaying mean was kept isolated from
marine animals and provide flies, maggots never developed, whereas meat
most of the oxygen as by exposed to flied was soon infested with
product of photosynthesis. maggots.
- Glasslike cell walls of diatoms Needham’s Experiment
provide grit for many polishing
compounds. o Leeuwenhoek discovered microbes and showed
6. Small multicellular animals that they appeared after a few days in freshly
- Parasites & viruses collected rainwater.
Spallanzani’s Experiments (Lazzaro Spallanzani
1729-1799)
o He reported results that contra- dicted
Needham’s findings. Spallanzani boiled
infusions for almost an hour and sealed the vials
by melting their slender necks closed. His
infusions remained clear unless he broke the seal
and exposed the infusion to air, after which they
- Microbiologists also study became cloudy with microorganisms. He
parasitic worms, which range in concluded three things:
size from microscopic forms to
adult tapeworms over 10 meters • Needham either had failed to heat his vials
(approximately 33 feet) in sufficiently to kill all microbes or had not sealed
length. them tightly enough.

2
• Microorganisms exist in the air and can
contaminate experiments.
• Spontaneous generation of microorganisms does
not occur; all living things arise from other living
things.
Pasteur’s Experiment (Louis Pasteur 1822-1895)
o Pasteur’s determination and hard work are
apparent in his investigations of spontaneous
generation. Like Spallanzani, he boiled infusions What causes fermentation?
long enough to kill everything.
First, he observed yeast cells growing and budding in
grape juice and conducted experiments showing that they
arise only from other yeast cells. Then, by sealing some
sterile flasks containing grape juice and yeast and by
leaving others open to the air, he demonstrated that yeast
could grow with or without oxygen; that is, he discovered
that yeasts are facultative anaerobes organisms that can
live with or without oxygen. Finally, by introducing
bacteria and yeast cells into different flasks of sterile
The Scientific Method grape juice, he proved that bacteria ferment grape juice to
produce acids and that yeast cells ferment grape juice to
The debate over spontaneous generation led in part produce alcohol.
to the development of a generalized scientific
method by which questions are answered through
observations of the outcomes of carefully controlled
experiments instead of by conjecture or according to
the opinions of any authority figure. The scientific
method, which provides a framework for conducting
an investigation rather than a rigid set of specific
“rules,” consists of four basic steps (FIGURE 1.13):
o A group of observations leads a scientist to ask a
question about some phenomenon.
o The scientist generates a hypothesis—that is, a
potential answer to the question.
o The scientist designs and conducts an
experiment to test the hypothesis.
o Based on the observed results of the experiment,
the scientist either accepts, rejects, or modifies
the hypothesis.

3
 patients since before dawn. As you enter the room of
your next patient, you observe with frustration and
despair that this case is like hundreds of others you
and your colleagues have attended in the neighbor-
hood over the past month.
A five-year-old boy with a vacant stare lies in bed
listlessly. As you watch, he is suddenly gripped by
severe abdominal cramps, and his gastrointestinal
tract empties in an explosion of watery diarrhea. The
voided fluid is clear, colorless, odor- less, and
streaked with thin flecks of white mucus,
reminiscent of water poured off a pot of cooking
rice. His anxious mother changes his bedclothes as
his father gives him a sip of water, but it is of little
use. With a heavy heart, you confirm the parents’
fear—their child has cholera, and there is nothing
you can do. He will likely die before morning. As
you despondently turn to go, the question that has
haunted you for two months is foremost in your
mind: What causes such a disease?
The third question that propelled the advance of
microbiology concerned disease, defined generally
as any abnormal condition in the body. Prior to the
1800s, disease was attributed to various factors,
including evil spirits, astrological signs, imbalances
in body fluids, and foul vapors. Although the Italian
Pasteur’s discovery that anaerobic bacteria phi-losopher Girolamo Fracastoro (1478–1553)
fermented grape juice into acids suggested a method conjectured as early as 1546 that “germs14 of
for preventing the spoilage of wine. His name contagion” cause disease, the idea that germs might
became a household word when he developed be invisible living organisms awaited
pasteurization, a process of heating the grape juice Leeuwenhoek’s investigations 130 years later.
just enough to kill most contaminating bacteria
without changing the juice’s basic qualities. After Pasteur’s discovery that bacteria are responsible for
pasteurization, wine makers added yeast to ensure spoiling wine led naturally to his hypothesis in 1857
that alcohol fermentation occurred. Pasteur thus that microorganisms are also responsible for
began the field of industrial microbiology (or diseases. This idea came to be known as the germ
biotechnology), in which microbes are intentionally theory of disease. Because a particular dis- ease is
used to manufacture products (TABLE 1.1) Today, typically accompanied by the same symptoms in all
pasteurization is used routinely on milk to eliminate affected individuals, early investigators suspected
pathogens that cause such diseases as bovine that diseases such as cholera, tuberculosis, and
tuberculosis and brucellosis; it is also used to anthrax are each caused by a specific germ, called a
eliminate pathogens in juices and other beverages. pathogen.15 Today, we know that some diseases are
genetic and that allergic reactions and environ-
What causes disease? mental toxins cause others, so the germ theory
applies only to infectious16 diseases.
You are a physician in London, and it is August
1854. It is past midnight, and you have been visiting

4
Just as Pasteur was the chief investigator in 2. The agent must be isolated and grown outside the
disproving spontaneous generation and determining host.
the cause of fermentation, so Robert Koch (1843– 3. When the agent is introduced to a healthy,
1910) dominated etiology17 (dis- ease causation) susceptible host, the host should get the disease.
4. The same agent must be found in the diseased
experimental host.
Koch’s Experiment We use the term suspected causative agent
because it is merely “suspected” until the postulates
Koch and his colleagues are also responsible for have been fulfilled, and “agent” can refer to any
many other advances in laboratory microbiology, fungus, protozoan, bacterium, virus, or other
including the following: pathogen. There are practical and ethical limits in
• Simple staining techniques for bacterial cells and the application of Koch’s postulates, but in almost
flagella every case they must be satisfied before the cause of
• The first photomicrograph of bacteria an infectious disease is proven.
• The first photograph of bacteria in diseased tissue
• Techniques for estimating the number of bacteria Gram’s Stain
in a solution based on the number of colonies that The first of Koch’s postulates demands that the
form after inoculation onto a solid surface suspected agent be found in every case of a given
• The use of steam to sterilize growth media disease, which presupposes that minute microbes
• The use of Petri19 dishes to hold solid growth can be seen and identified.
media Though Koch reported a simple staining technique
• Laboratory techniques such as transferring bacte- in 1877, the Danish scientist Hans Christian Gram
ria between media using a metal wire that has been (1853–1938) developed a more important staining
heat-sterilized in a flame technique in 1884. His procedure, which involves
• Elucidation of bacteria as distinct species the application of a series of dyes, leaves some
microbes purple and others pink. We now label the
Koch’s Postulates purple cells as Gram positive and the pink ones as
Gram negative, and we use the Gram procedure to
After discovering the anthrax bacterium, Koch separate bacteria into these two large groups.
continued to search for disease agents. In two pivotal
scientific publications in 1882 and 1884, he
announced that the cause of tuberculosis was a rod-
shaped bacterium, Mycobacterium tuberculosis (mī
′kō- bak-tēr′ē-ŭm too-ber-kyū-lō′sis). In 1905, he
received the Nobel Prize in Physiology or Medicine
for this work.
In his publications on tuberculosis, Koch
elucidated a series of steps that must be taken to
prove the cause of any infectious disease. These
steps, now known as Koch’s postulates, are one of
his important contributions to microbiology. His
postu- lates (which we discuss in more detail in
Chapter 14) are the following:
1. The suspected causative agent must be found in
every case of the disease and be absent from healthy
hosts. How can we prevent Infection & Disease?

5
Healthcare-associated infections (HAI), formerly founder of antiseptic surgery, and opened new fields
called nosocomial20 infections, were rampant. For of research into antisepsis and disinfection.
example, surgical patients frequently succumbed to
gangrene acquired while under their doctor’s care, Nightingale and Nursing
and many women who gave birth in hospitals died Florence Nightingale (1820-1910)
from puerperal21 fever. Six health care practitioners introduced cleanliness and other anti- septic
who were especially instrumental in changing health techniques into nursing practice. She was
care delivery methods were Ignaz Semmelweis, instrumental in setting standards of hygiene that
Joseph Lister, Florence Nightingale, John Snow, saved innumerable lives during the Crimean War of
Edward Jenner, and Paul Ehrlich. 1854–1856.
- The founder of modern nursing, she was
influential in introducing antiseptic
technique into nursing practice.

Snow and Epidemiology

John Snow (1813-1858)
also played a key role in setting standards for good
public hygiene to prevent the spread of infectious
diseases. Snow had been studying the propagation of
cholera and suspected that the disease was spread by
a contaminating agent in water.
- His study was the foundation for two
branches of microbiology—infection control
and epidemiology,23 which is the study of
the occurrence, distribution, and spread of
disease in humans.

Semmelweis & Handwashing Jenner’s Vaccine

Ignaz Semmelweis (1818–1865) Edward Jenner (1749-1823)
He was a physician on the obstet- ric ward of a tested the hypothesis that a mild disease called
teaching hospital in Vienna cowpox provided protection against potentially fatal
Lister’s Antiseptic Technique smallpox.
Shortly after Semmelweis was rejected in Vienna, - Jenner reported similar results from addi-
tional experiments, demonstrating the
the English physician Joseph Lister (1827–1912)
validity of the procedure he named
modified and advanced the idea of antisepsis in
vaccination after Vaccinia virus,25 the virus
health care settings. As a surgeon, Lister was aware
that causes cowpox.
of the dreadful consequences that resulted from the
- Jenner began the field of immunology—the
infection of wounds. Therefore, he began spraying
study of the body’s defenses against
wounds, surgical incisions, and dressings with
pathogens.
carbolic acid (phenol), a chemical that had
previously proven effective in reducing odor and
Enrlich’s “Magic Bullets”
decay in sewage. Like Semmelweis, he initially met
Paul Ehrlich (1854–1915)
with some resistance, but when he showed that it
To investigate this idea, Ehrlich undertook an
reduced deaths among his patients by two-thirds, his
exhaustive survey of chemicals to find a “magic
method was accepted into common practice. In this
bullet” that would destroy pathogens while
manner, Lister vindicated Semmelweis, became the
remaining nontoxic to humans.

6
 - By 1908, he had discovered a chemical  The investigations of Semmelweis, Lister,
active against the causative agent of syphilis, Nightingale, and Snow are the foundations
though the arsenic-based drug can have on which infection control, including control
serious side effects in humans. His of healthcare-associated infections (HAI), or
discoveries began the branch of medical nosocomial infections, and epidemiology are
microbiology known as chemotherapy built.
 Jenner’s use of a cowpox-based vaccine for
In summary, the Golden Age of Microbiology was a preventing smallpox began the field of
time when researchers proved that living things immunology. Pasteur significantly advanced
come from other living things, that microorganisms the field.
can cause fermentation and dis- ease, and that  Ehrlich’s search for “magic bullets”—
certain procedures and chemicals can limit, pre- chemicals that differentially kill
vent, and cure infectious diseases. These discoveries microorganisms—laid the foundations for
were made by scientists who applied the scientific the field of chemotherapy.
method to biological investigation, and they led to
an explosion of knowledge in a number of scientific
disciplines o The Modern Age of Microbiology
SUMMARY
Microorganisms played a significant role in the
 The study of the Golden Age of development of these disciplines because
Microbiology includes a look at the men microorganisms are relatively easy to grow, take up
who proposed or refuted the theory of a little space and are available by trillions.
spontaneous generation: Aristotle, Redi,
Needham, Spallanzani, and Pasteur (the
Father of Microbiology). The scientific
What are basic chemical reactions of life?
method that emerged then remains the
accepted sequence of study today. Biochemistry is the study of metabolism—that is,
 The study of fermentation by Pasteur and the chemical reactions that occur in living
Buchner led to the discovery of anaerobic organisms. Biochemistry began with Pasteur’s work
bacteria, to the fields of industrial micro- on fermentation by yeast and bacteria and with
biology (biotechnology) and biochemistry, Buchner’s discovery of enzymes in yeast extract, but
and to the study of metabolism. by the early 1900s, many scientists thought that the
 Koch, Pasteur, and others proved that metabolic reactions of microbes had little to do with
pathogens cause infectious diseases, an idea the metabolism of plants and animals.
that is known as the germ theory of disease.
Eti- ology is the study of the causation of In contrast, microbiologists Albert Kluyver (1888–
diseases. 1956) and his student C. B. van Niel (1897–1985)
 Koch initiated careful microbiological proposed that basic bio- chemical reactions are
laboratory techniques in his search for shared by all living things, that these reactions are
disease agents. Koch’s postulates, the logical relatively few in number, and that their primary
steps he followed to prove the cause of an feature is the transfer of electrons and hydrogen
infectious disease, remain an important part ions.
of microbiology today. Basic biochemical research has many practical
 The procedure for the Gram stain was applications, including the following:
developed in the 1880s and is still used to
differentiate bacteria into two categories: • The design of herbicides and pesticides that are
Gram positive and Gram negative. specific in their action and have no long-term
adverse effects on the environment.

7
• The diagnosis of illnesses and the monitoring of a Streptococcus pneumoniae (strep-tō-kok′ŭs nū mō
patient’s responses to treatment. For example, physi- ′nē-ī), - Oswald Avery (1877–1955), Colin MacLeod
cians routinely monitor liver disease by measuring (1909–1972), and Maclyn McCarty (1911–2005)
blood levels of certain enzymes and products of liver deter- mined that genes are contained in molecules
metabolism. of DNA.
• The treatment of metabolic diseases. One example Neurospora crassa (noo-ros′pōr-ă kras′ă) - In 1958,
is treating phenylketonuria, a disease resulting from George Beadle (1903–1989) and Edward Tatum
the inability to properly metabolize the amino acid (1909–1975), working with the bread mold
phenyl- alanine, by eliminating foods containing
phenylalanine from the diet.
• The design of drugs to treat leukemia, gout,
bacterial infections, malaria, herpes, AIDS, asthma,
and heart attacks.

Molecular Biology
Molecular biology combines aspects of
biochemistry, cell biology, and genetics to explain
cell function at the molecular level. Molecular
How do genes work?
biologists are particularly concerned with genome
Microbial Genetics sequencing.

8
Recombinant DNA Technology
Molecular biology is applied in recombinant DNA
technology, commonly called genetic engineering,
which was first developed using microbial models.
Gene Therapy
Gene therapy, a process that involves inserting a
missing gene or repairing a defective one in human
cells.
SUMMARY
Microbiology in the modern age has focused on
answering ques- tions regarding biochemistry, which
is the study of metabolism; microbial genetics,
which is the study of inheritance in microor-
ganisms; and molecular biology, which involves
investigations of cell function at the molecular level.
2. Scientists have applied knowledge from basic
research to answer questions in recombinant DNA
technology and gene therapy.
3. The study of microorganisms in their natural
environment is environmental microbiology.
4. The discovery of chemicals in the blood that are
active against specific pathogens advanced
immunology and began the field of serology.
5. Advancements in chemotherapy were made in
the 1900s with the discovery of numerous
substances, such as penicillin and sulfa drugs, that
inhibit pathogens.

9
 Cells: OVERVIEW
I. Cell Structure and Function
In the 1800s, two German biologists, Theodor
Processes of Life Schwann (1810–1882) and Matthias Schleiden
(1804–1881), developed the theory that all living
Biologists agree that all living things share at least things are composed of cells.
four processes of life: growth, reproduc- tion, - Cells are living entities, surrounded by a
responsiveness, and metabolism. membrane, that are capable of growing,
• Growth. Living things can grow; that is, reproducing, responding, and metabolizing.
they can increase in size. The smallest living things are single-celled
microorganisms.
• Reproduction. Organisms normally have - All cells may be described as either
the ability to reproduce themselves. Reproduction prokaryotes (prō-kar′ē-ōts) or eukaryotes
means that they increase in number, producing more (yū-kar′ē-ōts).
organisms organized like them- selves. Reproduction
may be accomplished asexually (alone) or sexually
with gametes (sex cells). Note that reproduction is
an increase in number, whereas growth is an
increase in size. Growth and reproduction often
occur simultaneously.
• Responsiveness. All living things respond
to their environment. They have the ability to change
themselves in reaction to changing conditions
around or within them. Many organisms also have
the ability to move toward or away from
Prokaryotes- is that they can read their DNA genetic
environmental stimuli—a response called taxis.
code and simultaneously make proteins—a typical
• Metabolism. Metabolism can be defined as prokaryote does not have a membrane surrounding
the ability of organisms to take in nutrients from its genetic material. In other words, a typical
outside themselves and use the nutrients in a series prokaryote does not have a nucleus
of controlled chemical reactions to provide the Eukaryotes- have a membrane called a nuclear
energy and structures needed to grow, reproduce, envelope surrounding their DNA, forming a nucleus
and be responsive. Metabolism is a unique process which sets eukaryotes in domain Eukarya. Indeed,
of living things; nonliving things cannot metabolize. the term eukaryote comes from Greek words
Cells store metabolic energy in the chemical bonds meaning “true nucleus.”
or adenosine triphosphate (ă-den′ō-sēn trī-fos External Structures of Bacterial Cells
′fāt),or ATP. In bacteria, these features include glycocalyces,
flagella, fimbriae, and pili.

Glycocalyces - This substance is known as a

glycocalyx (plural: glycocalyces), which literally
means “sweet cup.”
- Capsule -When the glycocalyx of a
bacterium is composed of organized
repeating units of organic chemicals firmly
attached to the cell’s surface
Prokaryotic & Eukaryotic

10
 - Slime layer – a loose, water-soluble Flagellin- A bacterial flagellum is composed of
glycocalyx many identical globular molecules of a protein.
- Protects cells from drying (desiccation) and
play a role in the ability of pathogens to
survive and cause disease.
- slime layers are often sticky and provide one
means for bacteria to attach to surfaces as
biofilms,
- Bacteria in a dental biofilm can produce acid
and cause dental caries (cavities).
Ex. Streptococcus pneumoniae (strep- tō-kok′ŭs
nū-mō′nē-ī) and Klebsiella pneumoniae
(kleb-sē-el′ă nū-mō′nē-ī) -enable these
prokaryotes to avoid destruction by defensive
cells in the respiratory tract and to cause
pneumonia.

Flagella- (singular: flagellum) are long structures

that extend beyond the surface of a cell and its
Arrangement
glycocalyx and propel the cell through its
Bacteria may have one of several flagellar
environment.
arrangements.
Structure:
Bacterial flagella are composed of three parts: a
filament, a hook, and a basal body

 filament is a long hollow shaft, about 20 nm

in diameter, that extends out of the cell into
its environment. No membrane covers a
filament.
A filament is a long hollow shaft, about 20 nm in
diameter, that extends out of the cell into its
environment. No membrane covers a filament.

11
 Rotation of endoflagella evidently causes the axial
filament to rotate around the cell, causing the
spirochete to “corkscrew” through its medium.
Treponema pallidum (trep-ō-nē′mă pal′li-dŭm), the
agent of syphilis, and Borrelia burgdorferi (bō-rē′lē-
ă burg-dōr′fer-ē), the cause of Lyme disease, are
Ex. flagella that cover the surface of the cell are
notable spirochetes. Some scientists think that the
termed peritrichous; in contrast, polar flagella
corkscrew motility of these pathogens allows them
are only at the ends. Other bacteria have tufts of
to invade human tissues.
polar flagella.
Some spiral-shaped bacteria, called spirochetes (spī
FUNCTION
′rō-kēts),3 have flagella at both ends that spiral
Bacteria move with a series of “runs” interrupted by
tightly around the cell instead of protruding into the
“tumbles.” Counterclockwise flagellar rotation
surrounding medium. These flagella, called
produces movements of a cell in a single direction
endoflagella, form an axial filament that wraps
for some time; this is called a run. If more than one
around the cell between its cytoplasmic membrane
flagellum is present, the flagella align and rotate
and an outer membrane.
together as a bundle. Runs are interrupted by brief,
abrupt, random changes in direction called tumbles.
Tumbles result from clockwise flagellar rotation
where each flagellum rotates independently.

12
 slimy masses of microbes adhering to a
substrate and to one another by means of
fimbriae and glycocalyces.

Movement in response to a stimulus is

termed taxis. Stimuli are often either light
(phototaxis) or a chemical (chemotaxis). Movement
toward a favorable stimulus is positive taxis,
whereas movement away from an unfavorable
stimulus is negative taxis. For example, movement
toward a nutrient would be positive chemotaxis.

A special type of fimbria is a pilus (pī´lus; plural:

pili, pī´lī), also called a conjugation pilus. Pili are
usually longer than other fimbriae but shorter than
flagella. Typically, only one to a few pili are present
per cell in bacteria that have them. Cells use pili to
transfer DNA from one cell to the other via a process
termed conjugation.

Bacterial Cell Walls

Neisseria gonorrhoeae (nī-se′rē-ă go-nor-rē′ī), which

causes gonorrhea. – example of bacterium with
fimbriae.
Pathogens must be able to adhere to their hosts if
they are to survive and cause disease. This bacterium
is able to colonize the mucous mem- brane of the
reproductive tract by attaching with fimbriae.
Neisseria cells that lack fimbriae are nonpathogenic.
Some fimbriae carry enzymes that render soluble, The cells of most prokaryotes are surrounded by a
toxic metal ions into insoluble, nontoxic forms. cell wall that provides structure and shape to the cell
 Fimbrae also serve an important and protects it from osmotic forces (described
function in biofilms, three-dimensional shortly). In addition, a cell wall assists some cells in

13
attaching to other cells or in resisting anti- microbial
drugs. Note that animal cells do not have cell walls,
a difference that plays a key role in treatment of
many bacterial diseases with certain types of
antibiotics. For example, penicil- lin attacks the cell
wall of bacteria but is harmless to human cells,
because the latter lack walls.
Cell walls give bacterial cells characteristic
shapes. Spherical cells, called cocci (kok′sī), may
appear in various arrangements, including singly or
in chains (streptococci), clusters (staphylo- cocci), or
cuboidal packets (sarcinae, sar′si-nī) (FIGURE
3.13), depending on the planes of cell division. Rod-
shaped cells, called bacilli (bă-sil′ī), typically appear
singly or in chains.
Bacterial cell walls are composed of
peptidoglycan (pep′ti- dō-glī′kan), a meshlike
complex polysaccharide. Peptidoglycan in turn is
Gram-Positive Bacterial Cell Walls
composed of two types of regularly alternat- ing
sugar molecules, called N-acetylglucosamine (NAG)
Gram-positive bacterial cell walls have a relatively
and N-acetylmuramic acid (NAM), which are
thick layer of peptidoglycan that also contains
structurally similar to glucose (FIGURE 3.14).
unique chemicals called teichoic acids (tī-kō′ik).
Millions of NAG and NAM molecules are
Some teichoic acids are covalently linked to lipids,
covalently linked in chains in which NAG and NAM
forming lipoteichoic acids that anchor the
alter- nate. These chains are the “glycan” portions of
peptidoglycan to the cytoplasmic membrane of the
peptidoglycan.
cell.
Chains of NAG and NAM are attached to
Ex. species of Mycobacterium (mī′kō-bak-tēr′ē-ŭm),
other NAG-NAM chains by crossbridges of four
which include the causative agents of tuberculosis
amino acids (tetrapeptides) between neighboring
and leprosy, have walls with up to 60% mycolic
NAMs. FIGURE 3.15 illustrates one possible
acid, a waxy lipid.
configuration. Such peptide crossbridges are the
- Mycolic acid helps these cells survive
“peptido” portion of peptidoglycan. Depending on
desiccation (drying out) and makes them
the bacterium, tetrapeptide bridges are either bonded
difficult to stain with regular water-based
to one another or held together by short connecting
dyes.
chains of other amino acids, as shown in. Gram-Negative Bacterial Cell Walls
Peptidoglycan covers the entire surface of a cell,
which must insert millions of new NAG and NAM Gram-negative cell walls have only a thin layer of
subunits if it is to grow and divide. peptidoglycan outside the cytoplasmic membrane,
Scientists describe two basic types of but outside the peptidoglycan there is another, outer
bacterial cell walls as Gram-positive cell walls or membrane
Gram-negative cell walls. They distinguish Gram- 2 different layers
positive and Gram-negative cells by the use of the The inner leaflet of the outer membrane is composed
Gram staining procedure (described in Chapter 4), of phospholipids and proteins, but the outer leaflet is
which was invented long before the structure and made of lipopolysaccharide (LPS). Integral proteins
chemical nature of bacterial cell walls were known. called porins form channels through both leaflets of
the outer membrane, allowing midsized molecules

14
such as glucose to move freely across the outer
membrane.
LPS is a union of lipid with sugar. The lipid
portion of LPS, known as lipid A, can be toxic. The
erroneous idea that lipid A is inside Gram-negative
cells led to the use of the term endotoxin5 for LPS.
Dead Gram-negative cells release lipid A when the
outer membrane disintegrates. This is medically
important because lipid A may trigger fever,
vasodilation, inflammation, shock, and blood  Tell me why?
clotting in humans. Killing large numbers of Gram- The smallest free-living microbe—the bacterium
negative bacteria with antimicrobial drugs within a Mycoplasma—is nonmotile. Why is it alive, even
short time period releases large amounts of lipid A, though it cannot move?
which might threaten the patient more than the live
bacteria; thus, any internal infection by Gram-
negative bacteria is cause for concern.
The outer membrane of a Gram-negative
cell can also be an impediment to the treatment of
disease. For example, the outer membrane may
prevent the movement of penicillin to the underlying
peptidoglycan, thus rendering this drug ineffectual
against many Gram-negative pathogens.
Prokaryotic and Eukaryotic Cells: An Overview
Chapter 3 Cell and Function • Prokaryotes
• Include bacteria and archaea
Processes of Life • Have a simple structure
 Growth • Lack nucleus
• Lack various membrane-bound
 Reproduction
internal structures
 Responsiveness
• Are typically 1.0 µm in diameter or
 Metabolism
smaller

 Eukaryotes
• Have nucleus

15
 • Have internal membrane-bound • Composed of organized repeating units
organelles of organic chemicals
• Are typically 10–100 µm in diameter • Firmly attached to cell surface
• Have more complex structure • May prevent bacteria from being
• Include algae, protozoa, fungi, animals, recognized by host
and plants • Slime layer
• Loosely attached to cell surface
• Water soluble
• Sticky layer allows prokaryotes to attach
to surfaces as biofilms

Flagella
• Are responsible for movement
• Have long structures that extend beyond cell
surface
• Are not present on all bacteria
Structure
• Composed of filament, hook, and basal body
• Basal body anchors the filament and hook to cell
wall
Function
 Tell Me Why • Rotation propels bacterium through environment
• In 1985, an Israeli scientist discovered a • Rotation reversible; can be counterclockwise or
single-celled microbe, Epulopiscium clockwise
fishelsoni. This organism is visible with the • Bacteria move in response to stimuli (taxis)
naked eye. Why did the scientist think • Runs
Epulopiscium was eukaryotic? • Tumbles
• What discovery revealed that the
microbe is really a giant bacterium?

External Structures of Bacterial Cells

Glycocalyx
• Gelatinous, sticky substance surrounding the
outside of the cell
• Composed of polysaccharides, polypeptides, or
both
Two Types of Glycocalyces
• Capsule

16
 • Shorter than flagella
• Serve an important function in biofilms
Pili
• Special type of fimbria
• Also known as conjugation pili
• Longer than fimbriae but shorter than
flagella
• Bacteria typically have only one or two
per cell
• Transfer DNA from one cell to another
(conjugation)

 Tell Me Why
• Why is a pilus a type of fimbria, but a flagellum
is not?

Bacterial Cell Walls

• Provide structure and shape and protect cell
from osmotic forces
• Assist some cells in attaching to other cells or in
resisting antimicrobial drugs
• Can target cell wall of bacteria with antibiotics
• Give bacterial cells characteristic shapes
• Composed of peptidoglycan
• Scientists describe two basic types of bacterial
cell walls
• Gram-positive and Gram-negative

Fimbriae and Pili

Fimbriae
• Sticky, bristlelike projections
• Used by bacteria to adhere to one another
and to substances in environment

17
 Prokaryotic Cell Walls
• Gram-Negative Bacterial Cell Walls
• Have only a thin layer of peptidoglycan
• Bilayer membrane outside the peptidoglycan
contains phospholipids, proteins, and
lipopolysaccharide (LPS)
• Lipid A portion of LPS can cause fever,
vasodilation, inflammation, shock, and
blood clotting
• May impede the treatment of disease
• Appear pink following Gram staining procedure

Bacteria Without Cell Walls

• A few bacteria lack cell walls
• Often mistaken for viruses because of small size
and lack of cell wall
• Have other features of prokaryotic cells, such as
ribosomes

Gram-Positive Bacterial Cell Walls Tell Me Why

• Relatively thick layer of peptidoglycan • Why is the microbe illustrated in Figure 3.2 more
• Contain unique polyalcohols called teichoic acids likely a Gram-positive bacterium than a Gram-
• Appear purple following Gram staining negative one?
procedure
• Presence of up to 60% mycolic acid in acid-fast Bacterial Cytoplasmic Membranes
bacteria helps cells survive desiccation • Structure
• Referred to as phospholipid bilayer
• Composed of lipids and associated
proteins
• Integral proteins
• Peripheral proteins
• Fluid mosaic model describes current
understanding of membrane structure

18
Bacterial Cytoplasmic Membranes
Function
• Control passage of substances into and out of the
cell
• Energy storage
• Harvest light energy in photosynthetic bacteria
• Selectively permeable
• Naturally impermeable to most substances
• Proteins allow substances to cross membrane
• Maintain concentration and electrical gradient

Function
• Active processes
• Active transport
• Group translocation
• Substance is chemically modified
during transport

Function
• Passive processes
• Diffusion
• Facilitated diffusion
• Osmosis

19
  Tell Me Why • Many antibacterial drugs act on bacterial
• E. coli grown in a hypertonic solution turns on a ribosomes without affecting larger
gene to synthesize a protein that transports eukaryotic ribosomes
potassium into the cell. Why?
Nonmembranous Organelles
• Cytoskeleton
• Composed of three or four types of
protein fibers
Cytoplasm of Bacteria • Can play different roles in the cell
• Cytosol • Cell division
• Liquid portion of cytoplasm • Cell shape
• Mostly water • Segregation of DNA molecules
• Contains cell's DNA in region called the • Movement through the
nucleoid environment
• Inclusions
• May include reserve deposits of  Tell Me Why
chemicals • The 2001 bioterrorist anthrax attack in the U.S.
• Endospores involved Bacillus anthracis. Why is B. anthracis able
• Unique structures produced by some to survive in mail?
bacteria
• Defensive strategy against unfavorable
conditions
• Vegetative cells transform into
endospores when nutrients are limited External Structures of Archaea
• Resistant to extreme conditions such as • Glycocalyces
heat, radiation, chemicals • Function in the formation of biofilms
• Adhere cells to one another and
inanimate objects
• Flagella
• Consist of basal body, hook, and
filament
• Numerous differences from bacterial
flagella
• Fimbriae and Hami
• Many archaea have fimbriae
• Some make fimbria-like structures
called hami
• Function to attach archaea to surfaces
Cytoplasm of Prokaryotes
Non membranous Organelles
• Ribosomes
• Sites of protein synthesis
• Composed of polypeptides and ribosomal
RNA
• 70S ribosome composed of smaller 30S
and 50S subunits

20
  Tell Me Why  Tell Me Why
• Why do scientists consider bacterial and archaeal • Why do some scientists consider archaea, which
flagella to be analogous rather than evolutionary are prokaryotic, more closely related to eukaryotes
relations? than they are to bacteria?

External Structure of Eukaryotic Cells

Archaeal Cell Walls and Cytoplasmic Membranes • Glycocalyces
• Most archaea have cell walls • Not as organized as prokaryotic capsules
• Do not have peptidoglycan • Help anchor animal cells to each other
• Contain variety of specialized • Strengthen cell surface
polysaccharides and proteins • Provide protection against dehydration
• All archaea have cytoplasmic membranes • Function in cell-to-cell recognition and
• Maintain electrical and chemical communication
gradients
• Control import and export of substances  Tell Me Why
from the cell • Why are eukaryotic glycocalyces covalently
bound to cytoplasmic membranes, and why don't
eukaryotes with cell walls have glycocalyces?

 Tell Me Why
• Why did scientists in the 19th and early 20th
centuries think that archaea were bacteria? Eukaryotic Cell Walls and Cytoplasmic
Membranes
• Fungi, algae, plants, and some protozoa have cell
Cytoplasm of Archaea walls
• Archaeal cytoplasm similar to bacterial • Composed of various polysaccharides
cytoplasm • Cellulose is found in plant cell walls
• 70S ribosomes • Fungal cell walls are composed of
• Fibrous cytoskeleton cellulose, chitin, and/or glucomannan
• Circular DNA • Algal cell walls are composed of a
• Archaeal cytoplasm also differs from bacterial variety of polysaccharides
cytoplasm All eukaryotic cells have cytoplasmic membrane
• Different ribosomal proteins • Are a fluid mosaic of phospholipids and proteins
• Different metabolic enzymes to make • Contain steroid lipids to help maintain fluidity
RNA • Contain regions of lipids and proteins called
• Genetic code more similar to that of membrane rafts
eukaryotes • Localize signaling, protein sorting, and
movement
• Control movement into and out of cell

21
 • Also used to move substances past the
surface of the cell

 Tell Me Why
• Many antimicrobial drugs target bacterial cell
walls. Why aren't there many drugs that act against
bacterial cytoplasmic membranes?

Cytoplasm of Eukaryotes
• Flagella • Other Nonmembranous Organelles
• Structure and arrangement • Ribosomes
• Differ structurally and functionally from • Larger than prokaryotic ribosomes (80S
prokaryotic flagella versus 70S)
• Within the cytoplasmic • Composed of 60S and 40S subunits
membrane • Cytoskeleton
• Shaft composed of tubulin • Extensive network of fibers and tubules
arranged to form microtubules • Anchors organelles
• Filaments anchored to cell by basal body; • Produces basic shape of the cell
no hook • Made up of tubulin microtubules, actin
• May be single or multiple; generally microfilaments, and intermediate filaments
found at one pole of cell
• Function
• Do not rotate but undulate rhythmically

• Centrioles and centrosome

• Centrioles are composed of nine triplets
of microtubules
• Cilia • Located in region of cytoplasm
• Shorter and more numerous than flagella called centrosome
• Coordinated beating propels cells • Not found in all eukaryotic cells
through their environment

22
 • Centrosomes play a role in mitosis, • Functions as transport system
cytokinesis, and formation of flagella and • Two forms
cilia • Smooth endoplasmic reticulum
(SER)
• Rough endoplasmic reticulum
(RER)

• Golgi body
• Receives, processes, and packages large
molecules for export from cell
• Package’s molecules in secretory vesicles
that fuse with cytoplasmic membrane
Membranous Organelles • Composed of flattened hollow sacs
• Nucleus surrounded by phospholipid bilayer
• Often largest organelle in cell • Not in all eukaryotic cells
• Contains most of the cell's DNA
• Semiliquid portion is called nucleoplasm
• Contains chromatin
• RNA synthesized in nucleoli present in
nucleoplasm
• Surrounded by nuclear envelope
• Contains nuclear pores

• Membranous Organelles
• Lysosomes, peroxisomes, vacuoles, and
vesicles
• Store and transfer chemicals within cells
• Endoplasmic reticulum • May store nutrients in cell
• Netlike arrangement of flattened, hollow • Lysosomes contain catabolic enzymes
tubules continuous with nuclear envelope

23
 • Peroxisomes contain enzymes that • Chloroplasts
degrade poisonous wastes • Light-harvesting structures found in
photosynthetic eukaryotes
• Use light energy to produce ATP
• Have two phospholipid bilayer
membranes and DNA
• Have 70S ribosomes
• Eukaryotes formed from union of small
aerobic prokaryotes with larger anaerobic
prokaryotes
• Smaller prokaryotes became internal
parasites
• Parasites lost ability to exist
independently
• Larger cell became dependent on
parasites for metabolism
• Aerobic prokaryotes evolved into
mitochondria
• Similar scenario for origin of
chloroplasts
• Theory is not universally accepted

• Mitochondria
• Have two membranes composed of
phospholipid bilayer
• Produce most of cell's ATP
• Interior matrix contains 70S ribosomes  Tell Me Why
and circular molecule of DNA • Colchicine is a drug that inhibits microtubule
formation. Why does colchicine inhibit
phagocytosis, movement of organelles within the
cell, and formation of flagella and cilia?

Important topics
• Difference among cilia, flagella, pili, fimberia,
pseudopodia.
• Structure and function of peptidoglycan, lipid A,
mycolic acid.
• Differences between gram positive and gram-
negative bacteria.

24
• Endo vs. exotoxin • Various types of light and electron microscopes
• Special bacteria such as mycoplasma and
mycobacterium • General Principles of Microscopy
• Structure and function of chloroplast, • Wavelength of radiation
mitochondria, peroxysome, lysosome • Magnification
• Definition of epidemiology, biotechnology, • Resolution
molecular biology, nosocomial infection • Contrast
• Transportation across the cell membrane and cell
wall, such as simple diffusion, facilitated diffusion,
endocytosis, exocytosis

Chapter 4 Microscopy, Staining and

Classification

Microscopy and Staining: Overview

Units of Measurement
 Tell Me Why
• Why do scientists use metric rather than English
units?
• General Principles of Microscopy
• Contrast
• Differences in intensity between two
Microscopy objects or between an object and its
• Microscopy: the use of light or electrons to background
magnify objects • Important in determining resolution
• Science of microscopy begun by Antoni van • Staining increases contrast
Leeuwenhoek

25
 • Use of light that is in phase increases • Specimen appears light against dark
contrast background
• Light Microscopy • Increases contrast and enables
• Bright-field microscopes observation of more details
• Simple
• Contain a single magnifying lens • Light Microscopy
• Similar to magnifying glass • Phase microscopes
• Leeuwenhoek used simple microscope to • Used to examine living
observe microorganisms organisms or specimens that would
• Bright-field microscopes be damaged/altered by attaching
• Compound them to slides or staining
• Series of lenses for magnification • Light rays in phase produce
• Light passes through specimen brighter image, whereas light rays
into objective lens out of phase produce darker image
• Oil immersion lens increases • Contrast is created because light
resolution waves are out of phase
• Have one or two ocular lenses • Two types
• Total magnification = • Phase-contrast microscope
magnification of objective lens x • Differential interference contrast
magnification of ocular lens microscope
• Most have condenser lens (direct
light through specimen)

• Fluorescent microscopes
• Direct UV light source at
specimen
• Specimen radiates energy back as
a longer, visible wavelength
• UV light increases resolution and
contrast
• Some cells are naturally
fluorescent; others must be stained
• Dark-field microscopes • Used in immunofluorescence to
• Best for observing pale objects identify pathogens and to make
• Only light rays scattered by specimen visible a variety of proteins
enter objective lens

26
 • Electron Microscopy
• Light microscopes cannot resolve
structures closer than 200 nm
• Electron microscopes have greater
resolving power and magnification
• Magnifies objects 10,000x to 100,000x
• Detailed views of bacteria, viruses,
internal cellular structures, molecules, and
large atoms
• Two types
• Transmission electron
microscopes
• Scanning electron microscopes

• Confocal microscopes
• Use UV lasers to illuminate
fluorescent chemicals in a single
plane
• Resolution increased because
emitted light passes through pinhole
aperture
• Each image is "optical slice"
through specimen
• Computer constructs 3-D image
from digitized images

27
• Probe Microscopy Staining
• Magnifies more than 100 million times • Most microorganisms are difficult to view by
• Two types bright- field microscopy
• Scanning tunneling microscopes • Coloring specimen with stain increases contrast
• Atomic force microscopes and resolution
• Scanning tunneling microscopes • Specimens must be prepared for staining
• Passes metallic probe above
specimen surface
• Measures the electron flow
(tunneling current) to and from the
probe and the specimen's surface
• Atomic force microscopes
• Passes probe lightly on the
specimen surface
• Deflection of laser beam
translated into atomic topography

• Principles of Staining
• Dyes used as stains are usually salts
• Chromophore is the colored portion of
the dye
• Acidic dyes stain alkaline structures
• Basic dyes stain acidic structures
• More common because most cells are
negatively charged
• Simple stains—composed of single dye
• Differential stains—use more than one dye
• Gram stain
• Acid-fast stain
• Endospore stain
• Histological stains
• Special stains—reveal specific structures
• Negative (capsule) stain
• Flagellar stain

 Tell Me Why
• Why is magnification high but color absent in an
unretouched electron micrograph?

28
 • Staining for Electron Microscopy
• Chemicals containing heavy metals are
used for transmission electron microscopy
• Stains may bind molecules in specimens
or the background

• Differential Stains
• Histological stains  Tell Me Why
• Two common stains used for histological • Why is a Gram-negative bacterium colorless but
specimens a Gram-positive bacterium purple after it is rinsed
• Gomori methenamine silver with decolorizer?
(GMS) stain
• Hematoxylin and eosin (HE)
stain

29
 • Domains
Classification and Identification of • Carl Woese compared nucleotide
Microorganisms sequences of rRNA subunits
• Taxonomy consists of classification, • Proposal of three domains as determined
nomenclature, and identification by ribosomal nucleotide sequences
• Organize large amounts of information about • Eukarya, Bacteria, and Archaea
organisms • Cells in the three domains also differ
• Make predictions based on knowledge of similar with respect to many other characteristics
organisms
• Taxonomic and Identifying Characteristics
• Linnaeus and Taxonomic Categories • Physical characteristics
• Current taxonomy system began with • Biochemical tests
Carolus Linnaeus • Serological tests
• His system classified organisms based on • Phage typing
characteristics in common • Analysis of nucleic acids
• Grouped organisms that can successfully
interbreed into categories called species
• Used binomial nomenclature
• Linnaeus proposed only two kingdoms
• Later taxonomic approach based on five
kingdoms
• Animalia, Plantae, Fungi, Protista, and
Prokaryotae
• Linnaeus's goal was to classify
organisms in order to catalog them
• Modern goal is to understand
relationships among organisms
• Goal of modern taxonomy is to reflect
phylogenetic hierarchy
• Greater emphasis on comparisons of
organisms' genetic material led to proposal
to add domain

• Physical characteristics
• Can often be used to identify microorganisms
• Protozoa, fungi, algae, and parasitic worms can
often be identified based only on their morphology
• Some bacterial colonies have distinct appearance
used for identification

30
 • Prokaryotic taxonomy now includes the G
+ C content of an organism's DNA

• Serological tests
• Serology—study of serum (liquid portion
of blood after clotting factors removed) • Taxonomic Keys
• Many microorganisms are antigenic • Dichotomous keys
• Trigger immune response that produces • Series of paired statements where only
antibodies one of two "either/or" choices applies to any
• Serum is an important source of particular organism
antibodies • Key directs user to another pair of
• Antibodies can be isolated and bind to the statements or provides name of organism
antigens that triggered their production
 Tell Me Why
• Why didn't Linnaeus create taxonomic
groups for viruses?

Chapter 5 Microbial Metabolism

Basic Chemical Reactions Underlying

Metabolism
• Metabolism
• Collection of controlled biochemical reactions
that take place within a microbe
• Ultimate function of metabolism is to reproduce
• Phage typing the organism
• Bacteriophage (phage)—virus that infects
bacteria • Metabolic Processes Guided by Eight
• Phages are specific for the host they Statements
infect • Every cell acquires nutrients
• Phage typing is based on this specificity • Metabolism requires energy from light
or catabolism of nutrients
• Analysis of nucleic acids • Energy is stored in adenosine
• Nucleic acid sequence can be used to triphosphate (ATP)
classify and identify microbes • Cells catabolize nutrients to form
precursor metabolites

31
 • Precursor metabolites, energy from
ATP, and enzymes are used in anabolic
reactions
• Enzymes plus ATP form
macromolecules
• Cells grow by assembling
macromolecules
• Cells reproduce once they have doubled
in size

• Catabolism and Anabolism

• Two major classes of metabolic reactions
• Catabolic pathways
• Break larger molecules into
smaller products
• Exergonic (release energy)
• Anabolic pathways
• Synthesize large molecules from
the smaller products of catabolism • ATP Production and Energy Storage
• Endergonic (require more energy • Organisms release energy from nutrients
than they release) • Can be concentrated and stored in
high-energy phosphate bonds (ATP)
• Phosphorylation – inorganic phosphate
is added to substrate
• Cells phosphorylate ADP to ATP in
three ways
• Substrate-level phosphorylation
• Oxidative phosphorylation
• Photophosphorylation
• Anabolic pathways use some energy of
ATP by breaking a phosphate bond

The Roles of Enzymes in Metabolism

• Enzymes are organic catalysts
• Oxidation and Reduction Reactions • Increase likelihood of a reaction
• Transfer of electrons from an electron
donor to an electron acceptor • Naming and classifying enzymes
• Reactions always occur simultaneously • Six categories of enzymes based on mode of
• Cells use electron carriers to carry action
electrons (often in H atoms) • Hydrolases
• Three important electron carriers • Isomerases
• Nicotinamide adenine • Ligases or polymerases
dinucleotide (NAD+) • Lyases
• Nicotinamide adenine • Oxidoreductases
dinucleotide phosphate (NADP+) • Transferases
• Flavin adenine dinucleotide
(FAD)

32
• The makeup of enzymes
• Many protein enzymes are complete in
themselves
• Apoenzymes are inactive if not bound to
nonprotein cofactors (inorganic ions or
coenzymes)
• Binding of apoenzyme and its cofactor(s)
yields holoenzyme
• Some are RNA molecules called
ribozymes

• Enzyme activity
• Many factors influence the rate of
enzymatic reactions
• Temperature
• pH
• Enzyme and substrate concentrations
• Presence of inhibitors
• Inhibitors block an enzyme's
active site
• Do not denature enzymes
• Three types

 Tell Me Why
• How can oxidation take place in an anaerobic
environment, that is, without oxygen?

33
 • Glucose is catabolized by two processes
• Cellular respiration
• Fermentation

• Glycolysis
• Occurs in cytoplasm of most cells
• Involves splitting of a six-carbon glucose
into two three- carbon sugar molecules
• Substrate-level phosphorylation – direct
transfer of phosphate between two substrates
• Net gain of two ATP molecules, two
molecules of NADH, and precursor
metabolite pyruvic acid
Divided into three stages involving 10 total
steps
• Energy-investment stage
• Lysis stage
• Energy-conserving stage

• Cellular Respiration
Carbohydrate Catabolism • Resultant pyruvic acid is completely
• Many organisms oxidize carbohydrates as oxidized to produce ATP by series of redox
primary energy source for anabolic reactions reactions
• Glucose is most common carbohydrate used

34
• Three stages of cellular respiration The Krebs cycle
1. Synthesis of acetyl-CoA • Results in
2. Krebs cycle • Two molecules of ATP
3. Final series of redox reaction • Two molecules of FADH2
(electron transport chain) • Six molecules of NADH
• Synthesis of acetyl-CoA • Four molecules of CO2
• Results in
• Two molecules of acetyl-CoA
• Two molecules of CO2
• Two molecules of NADH
• The Krebs cycle
• Great amount of energy remains
in bonds of acetyl-CoA
• Transfers much of this energy to
coenzymes NAD+ and FAD
• Occurs in cytosol of prokaryotes • Electron transport
and in matrix of mitochondria in • Most significant production of ATP
eukaryotes occurs from series of redox reactions known
• Six types of reactions in Krebs cycle as an electron transport chain (ETC)
• Anabolism of citric acid • Series of carrier molecules that pass
• Isomerization electrons from one to another to final
• Redox reactions electron acceptor
• Decarboxylations • Energy from electrons is used to pump
• Substrate-level phosphorylation protons (H+) across the membrane,
• Hydration reaction establishing a proton gradient
• Located in cristae of eukaryotes and in
cytoplasmic membrane of prokaryotes
• Four categories of carrier molecules
• Flavoproteins
• Ubiquinones
• Metal-containing proteins
• Cytochromes
• Aerobic respiration: oxygen serves as
final electron acceptor
• Anaerobic respiration: molecule other
than oxygen serves as final electron acceptor

35
• Chemiosmosis • Partial oxidation of sugar (or
• Use of ion gradients to generate ATP other metabolites) to release energy
• Cells use energy released in redox using an organic molecule from
reactions of ETC to create proton gradient within the cell as final electron
• Protons flow down electrochemical acceptor
gradient through ATP synthases that
phosphorylate ADP to ATP
• Called oxidative phosphorylation because
proton gradient is created by oxidation of
components of ETC
• Total of ~34 ATP molecules formed from
one molecule of glucose
• Alternatives to Glycolysis
• Yield fewer molecules of ATP than does
glycolysis
• Reduce coenzymes and yield different
metabolites needed in anabolic pathways
• Two pathways
• Pentose phosphate pathway
• Entner-Doudoroff pathway

 Tell Me Why
• Why do electrons carried by NADH allow for
production of 50% more ATP molecules than do
• Fermentation electrons carried by FADH2?
• Sometimes cells cannot completely
oxidize glucose by cellular respiration
• Cells require constant source of NAD+
• Cannot be obtained simply by
using glycolysis and Krebs cycle
• Fermentation pathways provide cells
with alternative source of NAD+

36
Other Catabolic Pathways
• Lipids and proteins contain energy in
their chemical bonds
• Can be converted into precursor
metabolites
• Serve as substrates in glycolysis and the
Krebs cycle

Chemica
ls and Structures
• Chlorophylls
• Type of pigment molecule that
photosynthetic organisms use to capture
light energy
• Composed of hydrocarbon tail attached to
light-absorbing active site centered on
magnesium ion
• Active sites are structurally
similar to cytochrome molecules in
ETC
• Structural differences cause absorption at
different wavelengths
• Photosystems
• Arrangement of molecules of chlorophyll
and other pigments to form light-harvesting
matrices
• Embedded in cellular membranes called
thylakoids
• In prokaryotes – invagination of
cytoplasmic membrane
• In eukaryotes – formed from inner
Photosynthesis
membrane of chloroplasts
• Many organisms synthesize their own
• Arranged in stacks called grana
organic molecules from inorganic carbon
• Stroma is space between outer membrane
dioxide
of granum and thylakoid membrane
• Most of these organisms capture light
energy and use it to synthesize
carbohydrates from CO2 and H2O by a
process called photosynthesis

37
• Two types of photosystems
• Photosystem I (PS I)
• Photosystem II (PS II)
• Photosystems absorb light energy and use redox
reactions to store energy in the form of ATP and • Light-Independent Reactions
NADPH • Do not require light directly
• Light-dependent reactions depend on light energy • Use ATP and NADPH generated by
• Light-independent reactions synthesize glucose light-dependent reactions
from carbon dioxide and water • Key reaction is carbon fixation by
Calvin-Benson cycle
• Light-Dependent Reactions • Three steps
• As electrons move down the chain, their • Fixation of CO2
energy is used to pump protons across the • Reduction
membrane • Regeneration of RuBP
• Photophosphorylation uses proton
motive force to generate ATP
• Photophosphorylation can be cyclic or
noncyclic

 Tell Me Why
• An uninformed student describes the Calvin-
Benson cycle as "cellular respiration in reverse."
Why is this student incorrect?

Other Anabolic Pathways

• Anabolic reactions are synthesis reactions
requiring energy and a source of precursor
metabolites
• Energy derived from ATP from catabolic
reactions
• Many anabolic pathways are the reverse
of catabolic pathways
• Reactions that can proceed in either direction are
amphibol

38
 Integration and Regulation of Metabolic
Function
• Cells synthesize or degrade channel and
transport proteins
• Cells often synthesize enzymes only
when substrate is available
• Cells catabolize the more energy-
efficient choice if two energy sources are
available
• Cells synthesize metabolites they need,
cease synthesis if metabolite is available
• Eukaryotic cells isolate enzymes of
different metabolic pathways within
membrane-bounded organelles
• Cells use allosteric sites on enzymes to
control activity of enzymes
• Feedback inhibition slows/stops anabolic
pathways when product is in abundance
• Cells regulate amphibolic pathways by
requiring different coenzymes for each
pathway

• Two types of regulatory mechanisms

• Control of gene expression
• Cells control amount and timing
of protein (enzyme) production
• Control of metabolic expression
• Cells control activity of proteins
(enzymes) once produced

 Tell Me Why
• Why is nitrogen required for the production of
amino acids by amination?

39
Important topics • Sources of carbon, energy, and electrons
• Chloroplast • Organisms classified into two groups
– Structure – Function based on source of electrons
• Photosynthesis vs. Calvin-Benson cycle • Organotrophs — heterotrophs
• Gluconeogenesis acquire electrons from same organic
• ETC (Electron Transport Chain) molecules that provide them carbon
• Lithotrophs — autrotrophs
acquire electrons from inorganic
Chapter 6 Microbial Nutrition & Growth molecules

Growth Requirements • Oxygen requirements

• Microbial Growth • Oxygen is essential for obligate aerobes
• Increase in a population of microbes • Oxygen is deadly for obligate anaerobes
• Due to reproduction of individual microbes • How can this be true?
• Results in discrete colony or biofilm • Toxic forms of oxygen are highly
• Colony — aggregation of cells arising reactive and excellent oxidizing
from single parent cell agents
• Biofilm — collection of microbes living • Resulting oxidation causes
on a surface in a complex community irreparable damage to cells
• Organisms use a variety of nutrients for their
energy needs and to build organic molecules and
cellular structures
• Most common nutrients contain necessary
elements such as carbon, oxygen, nitrogen, and
hydrogen
• Microbes obtain nutrients from variety of sources

• Nutrients: Chemical and Energy Requirements

• Sources of carbon, energy, and electrons
• Organisms classified into two groups based on • Four toxic forms of oxygen
source of carbon • Singlet oxygen — molecular
• Autotrophs oxygen with electrons in higher
• Heterotrophs energy state
• Organisms classified into two groups based on • Superoxide radicals — form from
source of energy the incomplete reduction of O2
• Chemotrophs • Peroxide anion — formed during
• Phototrophs reactions catalyzed by superoxide
dismutase
• Hydroxyl radical — result from
ionizing radiation and incomplete
reduction of hydrogen peroxide
• Oxygen requirements
• Aerobes
• Anaerobes
• Facultative anaerobes
• Aerotolerant anaerobes
• Microaerophiles

40
 Physical Requirements
• Temperature
• Temperature affects three-
dimensional structure of proteins
• Lipid-containing membranes of
cells and organelles are temperature
sensitive
• If too low, membranes become
rigid and fragile
• If too high, membranes become
• Nitrogen requirements too fluid
• Anabolism often ceases because • pH
of insufficient nitrogen • Organisms are sensitive to
• Nitrogen acquired from organic changes in acidity
and inorganic nutrients • H+ and OH– interfere with H
• All cells recycle nitrogen from bonding
amino acids and nucleotides • Neutrophiles grow best in a
• Nitrogen fixation by certain narrow range around neutral pH
bacteria is essential to life on Earth • Acidophiles grow best in acidic
habitats
• Other chemical requirements • Many microbes produce acidic
• Phosphorus waste products that can accumulate
• Sulfur and inhibit their growth
• Trace elements • Alkalinophiles live in alkaline
• Required only in small soils and water
amounts
• Growth factors
• Necessary organic
chemicals that cannot be
synthesized by certain
organisms

41
 Associations and Biofilms
• Organisms live in association with
different species
• Antagonistic relationships — a microbe
harms another organism
• Synergistic relationships — members of
an association receive benefits that exceed
those that would result if each lived by itself
• Symbiotic relationships — organisms
• Physical effects of water become interdependent and rarely live
• Microbes require water to dissolve outside the relationship
enzymes and nutrients
• Water is important reactant in many • Biofilms
metabolic reactions • Complex relationships among numerous
• Most cells die in absence of water microorganisms
• Some have cell walls that retain • Form on surfaces, medical devices,
water mucous membranes of digestive system
• Endospores and cysts cease most • Form as a result of quorum
metabolic activity sensing
• Two physical effects of water • Many microorganisms more harmful as
• Osmotic pressure part of a biofilm
• Hydrostatic pressure • Dental plaque is a biofilm that can lead to
• Osmotic pressure cavities
• Pressure exerted on a • Scientists seeking ways to prevent biofilm
semipermeable membrane by a formation
solution containing solutes that
cannot freely cross membrane
• Hypotonic solutions have lower solute
concentrations
• Cell placed in hypotonic solution
swells
• Hypertonic solutions have greater solute
concentrations  Tell Me Why
• Cell placed in hypertonic • Why should cardiac nurses and
solution shrivels respiratory therapists care about biofilms?
• Restricts organisms to certain
environments
• Obligate and facultative Culturing Microorganisms
halophiles • Inoculum introduced into nutrients called
• Hydrostatic pressure media
• Water exerts pressure in proportion to its • Inocula obtained from various
depth sources
• Barophiles live under extreme pressure • Environmental specimens
• Their membranes and enzymes depend on • Clinical specimens
pressure to maintain their three-dimensional, • Stored specimens
functional shape • Culture

42
 • Act of cultivating • Can individually pick single cell of some
microorganisms or the large microorganisms and use to establish a
microorganisms that are cultivated culture

• Culture Media
• Majority of prokaryotes have not been
grown in culture medium
• Nutrient broth is common medium
• Agar is a common addition to many
media
• Complex polysaccharide derived
from certain red algae
• Produces a solid surface for
• Obtaining Pure Cultures colonial growth
• Pure cultures are composed of cells • Most microbes cannot digest agar
arising from a single progenitor • Six types of general culture media
• Progenitor is termed a colony- o Defined media
forming unit (CFU) o Complex media
• Aseptic technique prevents o Selective media
contamination of sterile substances or o Differential media
objects o Anaerobic media
• Two common isolation techniques o Transport media
• Streak plates
• Pour plates
• Other isolation techniques
• Some fungi are isolated with
streak and pour plates
• Protozoa and motile unicellular
algae are isolated through dilution of
broth cultures

43
 • Enrichment media
• Use of a selective medium to
increase the numbers of a chosen
microbe to observable levels
• May require a series of cultures
to enrich for the desired microbe
• Cold enrichment used to enrich a
culture with cold- tolerant species
• Defined media
• Medium in which the exact
chemical composition is known
• Fastidious organisms require the
addition of a large number of
growth factors

• Complex media
• Exact chemical composition is
unknown
• Contain nutrients released by
partial digestion of yeast, beef, soy,
or proteins
• Support growth of wide variety of
microorganisms
• Used to culture organisms with
unknown nutritional needs

44
 • Techniques developed for culturing
microorganisms
• Animal and cell culture
• Used when artificial media are
inadequate
• Required for growth of viruses
and other obligate intracellular
parasite
• Techniques developed for culturing
microorganisms
• Low-oxygen culture
• Many organisms prefer
intermediate oxygen levels
• Anaerobic media • Carbon dioxide incubators mimic
• Obligate anaerobes must be the environment of many body
cultured in the absence of free tissues
oxygen • Candle jars are a low cost
• Reducing media contain alternative
compounds that combine with free • Ideal for the growth of
oxygen and remove it from the capnophiles — microbes that grow
medium best in high carbon dioxide levels
• Petri plates are incubated in
anaerobic culture vessels • Preserving Cultures
• Sealable containers that • Refrigeration
contain reducing chemicals • Stores for short periods
of time
• Deep-freezing
• Stores for years
• Lyophilization
• Stores for decades

 Tell Me Why
• Why do clinical laboratory scientists keep many
different kinds of culture media on hand?

• Transport media
• Used by hospital personnel to
ensure clinical specimens are not
contaminated and to protect people
from infection
• Rapid transport of samples is
important

• Special Culture Techniques

45
Growth of Microbial Populations

• Generation Time
• Time required for a bacterial cell to grow
and divide
• Dependent on chemical and physical
conditions

• Continuous Culture in a Chemostat

• Chemostat is used to maintain a
microbial population in a particular phase of
growth
• Open system
• Requires addition of fresh medium and
removal of old medium
• Allows the study of microbial
populations in steady but low nutrient levels
• Used in several industrial settings

46
• Measuring Microbial Reproduction
• Direct methods not requiring incubation
• Microscopic counts
• Count microorganisms directly
through a microscope
• Suitable for stained prokaryotes
and large eukaryotes

•
Direct methods not requiring incubation
• Electronic counters
• Coulter counters
• Counts cells as they interrupt an electrical
current flowing in front of an electronic
detector
• Flow cytometry
• A light-sensitive detector records
changes in light transmission as
cells pass through a tube
• Direct methods requiring incubation
• Serial dilution and viable plate
counts
• Membrane filtration
• Most probable number

47
• Measuring Microbial Growth
• Indirect methods
• Turbidity Chapter 7 Microbial Genetics

The Structure and Replication of Genomes

• Genetics
• Study of inheritance and inheritable traits
as expressed in an organism's genetic
material
• Genome
• The entire genetic complement of an
organism
• Includes its genes and nucleotide
sequences

• Indirect methods
• Metabolic activity
• Using changes in nutrient
utilization, waste production, or pH
to estimate number of cells in a
culture
• Dry weight
• Organisms are filtered from
media, dried, and weighed
• Genetic methods
• Isolate DNA sequences of
unculturable prokaryotes • Prokaryotic chromosomes
• Main portion of DNA, along with
 Tell Me Why associated proteins and RNA
• Students transfer some "gunk" from a two-week- • Prokaryotic cells are haploid (single
old bacterial culture into new media. Why shouldn't chromosome copy)
they be surprised when this "death-phase" sample • Typical chromosome is circular molecule
grows? of DNA in nucleoid

Important Topics
• Growth in microbiology
• Stages of microbial growth
• Classification of microorganisms based on carbon
and energy source
• Different extremophile archaea (halophile,
thermophile, …)
• Plasmids
• Small molecules of DNA that replicate
independently
• Not essential for normal metabolism,
growth, or reproduction
• Can confer survival advantages

48
Chapter 9 Controlling Microbial Growth in the • Extreme heat or
Environment certain chemicals
denature proteins
• Chemicals, radiation,
and heat can alter or
destroy nucleic acids
• Produce fatal mutants
• Halt protein synthesis
through action on
RNA

• Tell Me Why
• Why does milk
eventually go "bad"
despite being
pasteurized?

The selection of Microbial control methods

• Ideally, agents should be
• Inexpensive
• Fast-acting
• Stable during storage
• Capable of controlling microbial
growth while being harmless to
humans, animals, and objects
Plot of microbial death rate • Factors Affecting the Efficacy of
Antimicrobial Methods
Basic Principles of Microbial Control • Site to be treated
• Action of Antimicrobial Agents • Harsh chemicals and
• Alteration of cell walls and membranes extreme heat cannot be used
• Cell wall maintains integrity of cell on humans, animals, and
• When damaged, effects of fragile objects
osmosis cause cells to burst • Method of microbial control
• Cytoplasmic membrane contains based on site of medical
cytoplasm and controls passage of procedure
chemicals into and out of cell
• When damaged, cellular
contents leak out
• Nonenveloped viruses can better
tolerate harsh conditions
• Damage to proteins and nucleic
acids
• Protein function depends on 3-D
shape

49
 • Handling microbes that do not
cause disease in humans
• Biosafety Level 2 (BSL-2)
• Handling moderately hazardous
agents
• Biosafety Level 3 (BSL-3)
• All manipulations of microbes
done in safety cabinets
• Biosafety Level 4 (BSL-4)
• Handling microbes that cause
severe or fatal disease
• Lab space is isolated, and
personnel wear protective suits
• Factors Affecting the Efficacy of
Antimicrobial Methods
• Relative susceptibility of microorganisms
• Germicide classification • Tell Me Why
• High-level germicides • Why are BSL-4
• Kill all pathogens, suits
including pressurized?
endospores Why not just
• Intermediate-level wear tough
germicides regular suits?
• Kill fungal spores,
protozoan cysts,
viruses, and
pathogenic bacteria
• Low-level germicides Physical Methods of Microbial Control
• Kill vegetative Heat-Related Methods
bacteria, fungi, • Effects of high temperatures
protozoa, and some • Denature proteins
viruses • Interfere with integrity of
cytoplasmic membrane and cell
wall
• Disrupt structure and function of
nucleic acids
• Thermal death point
• Lowest temperature that kills all
cells in broth in 10 min
• Thermal death time
• Time to sterilize volume of
liquid at set temperature
The selection of microbial control methods
Biosafety Levels
• Four levels of safety in labs dealing with
pathogens
• Biosafety Level 1 (BSL-1)

50
 • Moist heat
• Used to disinfect, sanitize,
sterilize, and pasteurize
• Denatures proteins and destroys
cytoplasmic membranes
• More effective than dry heat
• Methods of microbial control using
moist heat
• Boiling
• Autoclaving
• Pasteurization
• Ultrahigh-temperature
sterilization
• Boiling
• Kills vegetative cells of bacteria
and fungi, protozoan
trophozoites, and most viruses
• Boiling time is critical
• Different elevations
require different boiling
times
• Endospores, protozoan cysts,
and some viruses can survive
boiling
• Moist heat
• Autoclaving
• Pressure applied to boiling
water prevents steam from
escaping
• Boiling temperature
increases as pressure
increases • Pasteurization
• Autoclave conditions: • Used for milk, ice cream,
121ºC, 15 psi, 15 minutes yogurt, and fruit juices
• Not sterilization
• Heat-tolerant microbes
survive
• Pasteurization of milk
• Batch method

51
 • Flash pasteurization
• Ultrahigh-temperature
pasteurization
• Ultrahigh-temperature sterilization
• 140ºC for 1 to 3 seconds,
then rapid cooling
• Treated liquids can be
stored at room temperature

• Dry heat
• Used for materials that cannot be
sterilized with moist heat
• Denatures proteins and oxidizes
metabolic and structural chemicals
• Requires higher temperatures for
longer time than moist heat
• Incineration is ultimate means of
sterilization
Refrigeration and Freezing
• Decrease microbial metabolism, growth,
and reproduction
• Chemical reactions occur more
slowly at low temperatures
• Liquid water not available
• Refrigeration halts growth of most
pathogens
• Some microbes can multiply in
refrigerated foods
• Slow freezing is more effective than
quick freezing
• Organisms vary in susceptibility to
freezing

Desiccation and Lyophilization

• Desiccation (drying) inhibits growth as a
result of removal of water
• Lyophilization (freeze-drying) is used
Osmotic Pressure
for long-term preservation of microbial
• High concentrations of salt or sugar in foods
cultures
to inhibit growth
• Prevents formation of
damaging ice crystals

52
• Cells in hypertonic solution of salt or sugar
lose water
• Fungi have greater ability than bacteria to
survive hypertonic environments
Radiation
• Two types of radiation
• Particulate radiation
• High-speed subatomic
particles freed from their
atoms
• Electromagnetic radiation
• Energy without mass • Nonionizing radiation
traveling in waves at the • Wavelengths greater than 1 nm
speed of light • Excites electrons, causing them
• The shorter the wavelength, to make new covalent bonds
the more energy the wave • Affects 3-D structure of
carries proteins and nucleic
• All types of radiation are described acids
as either ionizing or nonionizing • UV light causes pyrimidine
• Based on the effects to dimers in DNA
chemicals within cells • UV light does not penetrate well
• Ionizing radiation • Suitable for disinfecting air,
• Wavelengths shorter than 1 nm transparent fluids, and surfaces
• Electron beams, gamma of objects
ray, some X rays
• Ejects electrons from atoms to
create ions
• Ions disrupt hydrogen bonding,
oxidize double covalent bonds,
and create hydroxyl radicals
• Ions denature other
molecules (DNA)
• Electron beams effective at
killing microbes but do not
penetrate well
• Gamma rays penetrate well but
require hours to kill microbes
• X rays require long time to kill
microbes
• Not practical for
• Tell Me Why
microbial control
• Why are Bacillus endospores used
as sterility indicators (see Figure
9.8)?

Chemical Methods of Microbial Control

53
 • Affect microbes' cell walls, cytoplasmic
membranes, proteins, or DNA
• Effect varies with differing environmental
conditions
• Often more effective against enveloped
viruses and vegetative cells of bacteria,
fungi, and protozoa
• Oxidizing Agents
• Phenol and Phenolics
• Peroxides, ozone, and peracetic acid
• Denature proteins and disrupt cell
• Kill by oxidation of microbial
membranes
enzymes
• Effective in presence of organic matter
• High-level disinfectants and
• Remain active for prolonged time
antiseptics
• Commonly used in health care settings,
• Hydrogen peroxide can disinfect
labs, and homes
and sterilize surfaces
• Have disagreeable odor and possible
• Not useful for treating open
side effects
wounds because of catalase
activity
• Ozone treatment of drinking water
• Peracetic acid is effective sporicide
used to sterilize equipment
Surfactants
• "Surface active" chemicals
• Reduce surface tension of solvents
• Soaps and detergents
• Alcohols • Soaps have hydrophilic and
• Intermediate-level disinfectants hydrophobic ends
• Denature proteins and disrupt • Good degerming agents but
cytoplasmic membranes not antimicrobial
• More effective than soap in removing • Detergents are positively charged
bacteria from hands organic surfactants
• Swabbing skin with alcohol prior to • Quaternary ammonium
injection removes most microbes compounds (quats)
• Halogens • Low-level
• Include iodine, chlorine, bromine, and disinfectants
fluorine • Disrupt cellular
• Intermediate-level antimicrobial membranesIdeal for
chemicals many medical and
• Damage proteins by denaturation industrial
• Widely used in numerous applications applications
• Iodine tablets, iodophores,
chlorine treatment, bleach, • Heavy Metals
chloramines, bromine • Heavy-metal ions denature proteins
disinfection, and the addition of • Low-level bacteriostatic and
fluoride to water and toothpastes fungistatic agents

54
 • 1% silver nitrate once commonly • Prionzyme can remove
used to prevent blindness caused by prions on medical
N. gonorrhoeae instruments
• Thimerosal used to preserve • Antimicrobials
vaccines • Antibiotics and semisynthetic and
• Copper controls algal growth synthetic chemicals
• Typically are used to treat disease
• Some are used for antimicrobial
control outside the body

• Aldehydes
• Compounds containing terminal –
CHO groups
• Cross-link functional groups to
denature proteins and inactivate
nucleic acids
• Glutaraldehyde disinfects and
sterilizes
• Formalin used in embalming and in
disinfection of rooms and • Methods for Evaluating Disinfectants and
instruments Antiseptics
• Gaseous Agents • Phenol coefficient
• Microbicidal and sporicidal gases • Evaluates efficacy of
used in closed chambers to sterilize disinfectants and antiseptics
items • Compares to phenol an
• Denature proteins and DNA by agent's ability to control
cross-linking functional groups microbes
• Used in hospitals and dental offices • Greater than 1.0 indicates
• Disadvantages agent is more effective than
• Can be hazardous to people phenol
• Often highly explosive • Has been replaced by newer
• Extremely poisonous methods
• Potentially carcinogenic • Use-dilution test
• Enzymes • Metal cylinders dipped into
• Antimicrobial enzymes act against broth cultures of bacteria
microorganisms • Contaminated cylinder
• Human tears contain lysozyme immersed into dilution of
• Digests peptidoglycan cell disinfectant
wall of bacteria • Cylinders removed, washed,
• Uses of enzymes to control and placed into tube of
microbes in the environment medium
• Lysozyme is used to reduce • Most effective agents
the number of bacteria in entirely prevent growth at
cheese highest dilution

55
 • Current standard test in the
U.S.
• New standard procedure Chapter 10 Controlling Microbial Growth in the
being developed Body: Antimicrobial Drugs
• Kelsey-Sykes capacity test
• Alternative assessment The History of Antimicrobial Agents
approved by the European • Drugs
Union • Chemicals that affect physiology in
• Bacterial suspensions added any manner
to the chemical being tested • Chemotherapeutic agents
• Samples removed at • Drugs that act against diseases
predetermined times and • Antimicrobial agents
incubated • Drugs that treat infections
• Lack of bacterial
reproduction reveals • Paul Ehrlich
minimum time required for • "Magic bullets"
the disinfectant to be • Arsenic compounds that
effective killed microbes
• In-use test • Alexander Fleming
• Swabs taken from objects • Penicillin released from Penicillium
before and after application • Gerhard Domagk
of disinfectant or antiseptic • Discovered sulfanilamide
• Swabs inoculated into • Selman Waksman
growth medium and • Antibiotics
incubated • Antimicrobial agents
• Medium monitored for produced naturally by
growth organisms
• Accurate determination of • Semisynthetics
proper strength and • Chemically altered antibiotics that
application procedure for are more effective, longer lasting,
each specific situation or easier to administer than naturally
• Development of Resistant Microbes occurring ones
• Little evidence that products • Synthetics
containing antiseptic and • Antimicrobials that are completely
disinfecting chemicals add to human synthesized in a lab
or animal health
• Use of such products promotes
development of resistant microbes

• Tell Me Why
• Many chemical disinfectants and
antiseptics act by denaturing
proteins. Why does denaturation kill
cells?

56
 Chemotherapeutic Agents: Modes of Action

Inhibition of Cell Wall Synthesis

• Inhibition of synthesis of bacterial walls
• Most common agents prevent cross-
linkage of NAM subunits
• Beta-lactams are most prominent in
this group
• Functional groups are beta-
lactam rings
• Beta-lactams bind to
enzymes that cross-link
NAM subunits
• Bacteria have weakened cell walls
and eventually lyse
• Tell Me Why
• Why aren't antibiotics effective
against the common cold?

Mechanisms of Antimicrobial Action

• Successful chemotherapy requires selective
toxicity
• Antibacterial drugs constitute largest
number and diversity of antimicrobial
agents
• Fewer drugs to treat eukaryotic infections
• Antiviral drugs limited

• Inhibition of synthesis of bacterial walls

Semisynthetic derivatives of beta-
lactams
More stable in acidic
environments
More readily absorbed
Less susceptible to deactivation
More active against more types
of bacteria

57
 Inhibition of Cell Wall Synthesis • Disruption of Cytoplasmic Membranes
Inhibition of synthesis of bacterial walls Some drugs form channel through cytoplasmic
Vancomycin and cycloserine membrane and damage its integrity
Interfere with particular Amphotericin B attaches to ergosterol in fungal
bridges that link NAM membranes
subunits in many Gram- Humans somewhat susceptible because cholesterol
positive bacteria is similar to ergosterol
• Bacitracin Bacteria lack sterols; not susceptible
Blocks transport of
NAG and NAM from
cytoplasm
• Isoniazid and ethambutol
Disrupt mycolic acid
formation in
mycobacterial species
• Inhibition of synthesis of bacterial walls
• Prevent bacteria from increasing
amount of peptidoglycan
• Have no effect on existing
peptidoglycan layer • Disruption of Cytoplasmic Membranes
• Effective only for growing cells Azoles and allylamines inhibit
• Inhibition of synthesis of fungal walls ergosterol synthesis
• Fungal cells are composed of Polymyxin disrupts cytoplasmic
various polysaccharides not found membranes of Gram-negative bacteria
in mammalian cells Toxic to human kidneys
• Echinocandins inhibit the enzyme Pyrazinamide only disrupts transport
that synthesizes glucan across the cytoplasmic membrane of
Inhibition of Protein Synthesis Mycobacterium tuberculosis
• Prokaryotic ribosomes are 70S (30S and • Some antiparasitic drugs act against
50S) cytoplasmic membranes
• Eukaryotic ribosomes are 80S (40S and • Inhibition of Metabolic Pathways
60S) Antimetabolic agents can be effective when
• Drugs can selectively target translation pathogen and host metabolic processes differ
• Mitochondria of animals and humans Atovaquone interferes with electron transport in
contain 70S ribosomes protozoa and fungi
• Can be harmful • Heavy metals inactivate enzymes
• Agents that disrupt tubulin
polymerization and glucose uptake
by many protozoa and parasitic
worms
• Drugs block activation of viruses
• Metabolic antagonists
• Antiviral agents can target unique
aspects of viral metabolism
• Amantadine, rimantadine,
and weak organic bases
prevent viral uncoating

58
 • Protease inhibitors interfere with an Act against an enzyme HIV uses in its replication
enzyme that HIV needs in its cycle
replication cycle Do not harm people because humans lack reverse
transcriptase
• Inhibition of Nucleic Acid Synthesis
• Several drugs block DNA • Prevention of Virus Attachment and
replication or RNA transcription Entry
• Drugs often affect both eukaryotic • Attachment antagonists block viral
and prokaryotic cells attachment or receptor proteins
• Not normally used to treat infections • New area of antimicrobial drug
• Used primarily in research and development
perhaps to slow cancer cell
replication • Tell Me Why
• Some antimicrobial drugs are
harmful to humans. Why can
physicians safely use such drugs
despite the potential danger?

Clinical Considerations in Prescribing

Antimicrobial Drugs

• Ideal Antimicrobial Agent

• Nucleotide or nucleoside analogs Readily available
• Interfere with function of nucleic Inexpensive
acids Chemically stable
• Distort shapes of nucleic acid Easily administered
molecules and prevent further Nontoxic and nonallergenic
replication, transcription, or Selectively toxic against wide range of pathogens
translation • Spectrum of Action
• Most often used against viruses Number of different pathogens a drug acts against
• Effective against rapidly dividing • Narrow-spectrum: effective
cancer cells against few organisms
• Broad-spectrum: effective
against many organisms
• May allow for
secondary or
superinfections to
develop
• Killing of normal
flora reduces
microbial
antagonism

• Quinolones and fluoroquinolones

Act against prokaryotic DNA gyrase
• Inhibitors of RNA polymerase
• Reverse transcriptase inhibitors

59
 Intramuscular administration delivers drug via
• Effectiveness needle into muscle
Efficacy of antimicrobials assessed by a variety of Intravenous administration delivers drug directly to
tests bloodstream
Diffusion susceptibility test Must know how antimicrobial agent will be
Minimum inhibitory concentration test distributed to infected tissues
Minimum bactericidal concentration test
• Safety
and Side
Effects
Toxicity
Cause of many
adverse reactions
is poorly
understood
Drugs may be
toxic to kidneys, liver, or nerves
Consideration needed when prescribing drugs to
pregnant women
Therapeutic index is the ratio of the dose of a drug
that can be tolerated to the drug's effective dose
• Use drug within its
therapeutic range

Allergies
Allergic reactions are rare but may be life
threatening
Anaphylactic shock
Disruption of normal microbiota
May result in secondary infections
Overgrowth of normal flora, causing superinfections
Of greatest concern for hospitalized patients

• Tell Me Why
• Routes of Administration Why don't physicians invariably prescribe the
Topical application of drug for external infections antimicrobial with the largest zone of inhibition?
Oral route requires no needles and is self-
administered Resistance to Antimicrobial Drugs

60
 • The Development of Resistance in Maintain high concentration of drug in patient for
Populations sufficient time
Some pathogens are naturally resistant Inhibit the pathogen so immune system can
Bacteria acquire resistance in two ways eliminate
New mutations of chromosomal genes Use antimicrobial agents in combination
Acquisition of R plasmids via transformation, Synergism versus antagonism
transduction, and conjugation. Use antimicrobials only when necessary
Develop new variations of existing drugs
Second-generation drugs
Third-generation drugs
Search for new antibiotics, semisynthetics, and
synthetics
Bacteriocins
Design drugs complementary to the shape of
• Mechanisms of Resistance microbial proteins to inhibit them
• At least seven mechanisms of microbial
resistance exist
Produce enzyme that destroys or deactivates drug
Slow or prevent entry of drug into the cell
Alter target of drug so it binds less effectively
Alter their own metabolic chemistry
Pump antimicrobial drug out of the cell before it can
act
Bacteria in biofilms can resist antimicrobials
Mycobacterium tuberculosis produces MfpA protein
Binds DNA gyrase, preventing the binding of • Tell Me Why
fluoroquinolone drugs Why is it incorrect to say that an individual
bacterium develops resistance in response to an
antibiotic?

Important topics
• Multiple Resistance and Cross Resistance • Beta lactam antibiotics
Pathogen can acquire resistance to more than one • Tetracyclines
drug • Antibiotics that disrupt cytoplasmic
Common when R plasmids exchanged membrane
Develop in hospitals and nursing homes • E test, MIC, MBC
Constant use of drugs eliminates sensitive cells
Multi-drug-resistant pathogens are resistant to at
least three antimicrobial agents
Cross resistance to similar drugs may develop
• Retarding Resistance

61
Chapter 11 Characterizing and Classifying
Prokaryotes

General Characteristics of Prokaryotic Organisms

• Prokaryotes
Most numerous and diverse group of cellular
microbes
Thrive in various habitats
Only a few are capable of colonizing humans and
causing disease

• Endospores
Produced by Gram-positive bacteria
Bacillus and Clostridium
• Each vegetative cell transforms into one
endospore
• Each endospore germinates to form one
vegetative cell
• Defensive strategy against unfavorable
conditions
• Endospores are often difficult to kill
Concern to food processors,
health care professionals, and
governments

• Reproduction of Prokaryotic Cells

62
 • All reproduce asexually • Epulopiscium and its relatives have unique
• Several different methods method of reproduction
Binary fission (most common) • Live offspring emerge from the
Snapping division body of the dead mother cell
Reproductive spores (viviparity)
Budding • First noted case of viviparous
Viviparity behavior in prokaryotic world

Arrangements of Prokaryotic Cells

• Result from two aspects of division during
binary fission
Planes in which cells divide
Separation of daughter cells

Reproduction of Prokaryotic Cells

63
 Survey of Archaea
• Common features
Lack true peptidoglycan
Cell membrane lipids have branched hydrocarbon
chains
AUG codon codes for methionine
• Two phyla: Crenarchaeota, Euryarchaeota
• Reproduce by binary fission, budding, or
fragmentation
• Are cocci, bacilli, spirals, or pleomorphic
• Not known to cause disease

• Tell Me Why
Why does binary fission produce chains of cocci in
some species but clusters of cocci in other species?

Modern Prokaryotic Classification

• Currently based on genetic relatedness of
rRNA sequences
• Three domains
Archaea
Bacteria
Eukarya
• Bergey's Manual of Systematic Bacteriology
provides prokaryotic classification scheme

• Tell Me Why • Extremophiles

Why are taxonomic names and Require extreme conditions to survive
categories in our current taxonomic Temperature, pH, and/or salinity
scheme different from those in 1990? Prominent members are thermophiles and halophiles
• Thermophiles
DNA, RNA, cytoplasmic membranes, and proteins
do not function properly below 45ºC
Hyperthermophiles – require temperatures over 80ºC
Two representative genera
• Geogemma
Pyrodictium
Thermophilic enzymes are used for research and
industrial applications
Recombinant DNA technologies

64
Additives in laundry detergents • Produced ~10 trillion tons of methane
buried on ocean floor
• Digest sludge during sewage treatment

• Tell Me Why
Why did scientists formerly think archaea were a
type of bacteria?

Survey of Bacteria
• Deeply Branching and Phototrophic
Bacteria
Deeply branching bacteria
• Halophiles Scientists believe these organisms are similar to
• Inhabit extremely saline habitats earliest bacteria
• Depend on greater than 9% NaCl to Autotrophic
maintain integrity of cell walls Live in habitats similar to those thought to exist on
• Many contain red or orange early Earth
pigments Aquifex
May protect from sunlight Considered to represent earliest branch of bacteria
Most studied – Halobacterium salinarium Deinococcus
• Halobacterium salinarium Has outer membrane similar to Gram-negatives but
• Most studied halophile stains Gram-positive
• Photoheterotroph Phototrophic bacteria
• Lacks photosynthetic pigments Phototrophs that contain photosynthetic lamellae
Uses bacteriorhodopsins to establish proton gradient Autotrophic
Divided into five groups based on pigments and
source of electrons for photosynthesis
Blue-green bacteria (cyanobacteria)
Green sulfur bacteria
Green nonsulfur bacteria
Purple sulfur bacteria
Purple nonsulfur bacteria

• Methanogens
Largest group of archaea
Convert carbon dioxide, hydrogen gas,
and organic acids to methane gas
• Convert organic wastes in pond, lake,
and ocean sediments to methane
• Some live in colons of animals
One of primary sources of
environmental methane

65
 • Produce toxins that
cause diseases in
humans
• Endospores survive
harsh conditions
Related microbes include Epulopiscium, sulfate-
reducing microbes, and Selenomonas
Mycoplasmas
Facultative or obligate anaerobes
Lack cell walls
Smallest free-living cells
Colonize mucous membranes of the respiratory and
urinary tracts of animals

• Low G + C Gram-Positive Bacteria

Other low G + C bacilli and cocci
Bacillus
Endospore-forming aerobes
and facultative anaerobes
Many common in soil
Bacillus thuringiensis toxin
is used by farmers and
gardeners as an insecticide
• Bacillus anthracis causes
anthrax
• Low G + C Gram-Positive Bacteria • Other species synthesize
G + C content below 50% antibiotics
Have similar 16S rRNA sequences
Classified in phylum Firmicutes
Rod-shaped, obligate anaerobes
Clostridia
Rod-shaped, obligate anaerobes
Important in medicine and industry

66
 • High G + C Gram-Positive Bacteria
• Corynebacterium
Pleomorphic aerobes and facultative anaerobes
Produces metachromatic granules
• Mycobacterium
Aerobic rods that sometimes form filaments
Slow growth, partly due to mycolic acid in its cell
walls
Some species are pathogens of animals and humans
• Actinomycetes
Form branching filaments resembling fungi
Cause disease primarily in immunocompromised
patients
• Other low G + C bacilli and cocci Important genera include Actinomyces, Nocardia,
Listeria Streptomyces
Contaminates milk and meat • Actinomycetes
products Actinomyces
Capable of reproducing under Normally present in oral cavity and throats of
refrigeration humans
Survives inside phagocytic Nocardia
white blood cells Soil- and water-dwelling aerobes
Rarely causes disease in adults Can degrade a variety of pollutants
In pregnant women, can kill the Streptomyces
fetus if crosses the placenta Recycles nutrients in the soil
• Lactobacillus Produces most of the important antibiotics
Grows in the human mouth, stomach, intestinal tract,
and vagina
Rarely causes disease
Inhibits the growth of pathogens within the body
Used in the production of various foods
• Streptococcus and Enterococcus
Cause numerous diseases
Various strains of multi-drug-resistant streptococci
• Staphylococcus
One of the most common inhabitants of humans
Produces toxins and enzymes that contribute to
Disease • Gram-Negative Proteobacteria
Largest and most diverse group of bacteria
Five classes of proteobacteria
Alphaproteobacteria
Betaproteobacteria
Gammaproteobacteria
Deltaproteobacteria
Epsilonproteobacteria
• Alphaproteobacteria
Often capable of growing at low nutrient levels
Some species have extensions called prosthecae

67
Used for attachment and nutrient absorption Do not generate oxygen during photosynthesis
Nitrogen fixers • Pathogenic alphaproteobacteria
Two genera important to agriculture Rickettsia
Grow in association with the roots of plants Transmitted through
Azospirillum bite of an arthropod
Produces chemicals that aid in nutrient uptake Causes several human
Rhizobium diseases
Produces ammonia, which aids in plant growth Brucella
Causes brucellosis
Survives phagocytosis
by white blood cells
Other alphaproteobacteria
Important in industry and the
environment
Acetobacter and Gluconobacter
are used in vinegar production
Caulobacter inhabits nutrient-
poor waters
Agrobacterium plasmid useful
for genetic manipulation of
plant

• Gram-Negative Proteobacteria
Alphaproteobacteria
Nitrogen fixers
Rhodopseudomonas palustris
Reduces hydrogen to hydrogen gas (H2)
Potential for use as a biofuel
Nitrifying bacteria
Oxidation of nitrogenous compounds provides
electrons
Important in the environment and agriculture
Convert reduced nitrogenous compounds into nitrate
(nitrification)
Nitrobacter
• Alphaproteobacteria
Purple nonsulfur phototrophs
Grow at the bottom of lakes and ponds
Use bacteriochlorophylls to harvest light energy

68
 • Divided into subgroups
• Purple sulfur bacteria
• Intracellular pathogens
• Methane oxidizers
• Glycolytic facultative
anaerobes
• Pseudomonads
• Purple sulfur bacteria
• Obligate anaerobes
• Oxidize hydrogen sulfide to sulfur
• Found in sulfur-rich zones in lakes,
bogs, and oceans

• Betaproteobacteria
Pathogenic betaproteobacteria
Neisseria
Inhabits mucous
membranes of mammals
Causes numerous
diseases
Bordetella
Causes pertussis
Burkholderia
Colonizes moist
environmental surfaces
and respiratory
passages of cystic
fibrosis patients

• Other betaproteobacteria
• Thiobacillus
• Recycles sulfur in the • Gammaproteobacteria
environment • Intracellular pathogens
• Zoogloea Legionella
• Form flocs that assist in the Causes Legionnaires' disease
treatment of sewage Coxiella
• Sphaerotilus Causes Q fever
• Flocs impede flow of waste Both pathogens survive within white blood cells
in treatment plants Methane oxidizers
• Use methane as a carbon and energy source
• Gram-Negative Proteobacteria Inhabit anaerobic environments
• Gammaproteobacteria Digest methane within local environment before it
• Largest and most diverse can
class of proteobacteria impact climate

69
 Glycolytic facultative anaerobes • Epsilonproteobacteria
Largest group of Campylobacter
gammaproteobacteria Causes blood poisoning and intestinal inflammation
Catabolize carbohydrates by Helicobacter
glycolysis and the pentose Causes ulcers
phosphate pathway
Divided into three families

• Gram-Negative Proteobacteria
Gammaproteobacteria
Pseudomonads
Break down numerous
organic compounds
Important pathogens of
humans and animals
Pseudomonas
causes infections of
the urinary tract,
ear, and lung
• Azotobacter and Azomonas
are nonpathogenic solid
dwelling pseudomonads

• Other Gram-Negative Bacteria

• Chlamydias
Grow intracellularly in
mammals, birds, and
some invertebrates
• Deltaproteobacteria
Some are smaller than
Desulfovibrio
viruses
Recycles sulfur in the
Most common sexually
environment
transmitted bacteria in
Contributes to the
the United States
corrosion of iron pipes
• Spirochetes
Bdellovibrio
Motile bacteria that move in a corkscrew motion
Destroys other Gram-
Have diverse metabolism and habitats
negative bacteria
Treponema and Borrelia both cause disease in
Myxobacteria
humans
Produce differentiated
reproductive structures
• Bacteroids

70
Bacteroides
Inhabits digestive tracts of humans and animals
Some species cause infections
Cytophaga Important topics
Aquatic, gliding bacteria • Archaea characteristics
Important in the degradation of raw sewage • Endospore former bacteria (clostridia,
bacillus) and their related
diseases
• Mycoplasma
• Streptococcus
• Staphylococcus
• Helicobacter
• STD causing bacteria
• Prosthecae
• Lipid A

Tell Me Why
Why are bacteria all in the same domain (Bacteria)
despite their widely divergent oxygen tolerance,
sizes, shapes, and nutritional requirements?

71
Chapter 12 Characterizing and Classifying
Eukaryotes

General Characteristics of Eukaryotic Organisms

• Eukaryotic microorganisms
Protozoa
Fungi
Algae
Water molds
Slime molds
• Include both human pathogens and
organisms vital for human life Telophase

Reproduction of Eukaryotes
• More complicated than that in prokaryotes
Eukaryotic DNA is packaged as chromosomes in the
nucleus
Have variety of methods of asexual reproduction
Many reproduce sexually by forming gametes and
zygotes
Algae, fungi, and some protozoa reproduce both • Nuclear division
sexually and asexually Meiosis
Nuclear division that
• Nuclear division partitions chromatids into
Nucleus has one or two complete copies four nuclei
of genome Diploid nuclei produce
Single copy (haploid) haploid daughter nuclei
Most fungi, many algae, Two stages – meiosis I and
some protozoa meiosis II
Two copies (diploid) Each stage has four phases
Other fungi, algae, and Prophase
protozoa Metaphase
• Two types Anaphase
Mitosis Telophase
Meiosis

• Nuclear division
Mitosis
Cell partitions that replicate
DNA equally between two
nuclei
Maintains ploidy of parent
nucleus
Four phases
Prophase
Metaphase
Anaphase

72
General Characteristics of Eukaryotic Organisms
• Reproduction of Eukaryotes
Cytokinesis (cytoplasmic division) Protozoa
Typically occurs simultaneously with telophase of • Diverse group defined by three
mitosis characteristics
In some algae and fungi, is postponed or does not Eukaryotic
occur at all Unicellular
Results in multinucleated cells called coenocytes Lack a cell wall
• Motile by means of cilia, flagella, and/or
pseudopods
• Tell Me Why Except a subgroup: apicomplexans
Why is it incorrect to call mitosis cell division? Distribution of Protozoa
Require moist environments
Most live in ponds, streams, lakes, and oceans

73
 • Critical members of • Binary fission or
plankton schizogony
Others live in moist soil, beach sand, and decaying Few also have sexual reproduction
organic matter • Some become gametocytes
Very few are pathogens that fuse to form diploid
zygotes
• Morphology of Protozoa • Some utilize a process
Great morphological diversity called conjugation
Some have two nuclei
• Macronucleus
• Contains many
copies of the
genome
• Micronucleus
Variety in number and kinds of mitochondria
Some have contractile vacuoles that pump water out
of cells
Different stages in life cycle
• Motile feeding stage called
a trophozoite
• Resting stage called a cyst
• Classification of Protozoa
Classification of protozoa has shifted over the years
Revised and updated based on 18S rRNA sequences
One current scheme groups protozoa into six groups
• Parabasala
• Diplomonadida
• Euglenozoa
• Alveolates
• Rhizaria
• Amoebozoa
Parabasala
• Lack mitochondria
• Have a single nucleus
• Nutrition of Protozoa • Contain Golgi body–like
Most are chemoheterotrophic structure called a parabasal
• Obtain nutrients by body
phagocytizing bacteria, • Important parabasalids
decaying organic matter, • Trichonympha
other protozoa, or the • Trichomonas
tissues of host
Few absorb nutrients from surrounding water
Dinoflagellates and euglenoids are photoautotrophic

• Reproduction of Protozoa
Most reproduce only asexually

74
 • Diplomonadida
Lack mitochondria
Have mitosomes in the cytoplasm
Mitochondrial genes found in the nuclear
chromosomes
Also lack Golgi bodies and peroxisomes
Have two equal-sized nuclei and multiple flagella
Prominent diplomonad
Giardia
• Euglenozoa
Characteristics of both plants and animals • Alveolates
Flagella contain a crystalline rod of unknown Have membrane-bound cavities called alveoli
function Purpose is unknown
Mitochondria have disk-shaped cristae Divided into three subgroups
Two groups Ciliates
Euglenids Apicomplexans
Kinetoplastids Dinoflagellates

• Alveolates
Ciliates
Use cilia to move themselves or water
All are chemoheterotrophs and have two nuclei
Balantidium is the only ciliate pathogenic to humans
Apicomplexans
Chemoheterotrophic pathogens of animals
Complex of organelles allows them to penetrate host
cells
Plasmodium, Cryptosporidium, and Toxoplasma
cause disease in humans

• Euglenozoa
Euglenids
Photoautotrophic, unicellular microbes with
chloroplasts
Historically classified as plants
Kinetoplastids • Alveolates
Have region of mitochondrial DNA called a • Dinoflagellates
kinetoplast Unicellular microbes with photosynthetic pigments
Some kinetoplastids are pathogenic Historically classified as algae
• Trypanoso Large proportion of freshwater and marine plankton
ma Motile dinoflagellates have two flagella
• Leishmania Many dinoflagellates are bioluminescent
Abundance in marine water is one cause of red tides
Some dinoflagellates produce neurotoxins

75
 • Rhizaria
Amoebae are protozoa that
move and feed with pseudopods
Amoebae exhibit little
uniformity
Rhizaria are amoebae with
threadlike pseudopods
Foraminifera
Often live
attached to the
ocean floor
Most are fossil
species
Radiolaria Tell Me Why
Have ornate • Why did early taxonomists categorize such
shells of silica obviously different microorganisms as
Live as part of parabasalids, diplomonads, euglenozoa,
the marine alveolates, rhizaria, and amoebozoa in a
plankton single taxon, Protozoa?

Fungi
• Chemoheterotrophic
• Have cell walls typically composed of chitin
• Do not perform photosynthesis
Lack chlorophyll
• Related to animals

• Amoebozoa • The Significance of Fungi

Amoebae with lobe-shaped pseudopods and no Decompose dead organisms and recycle their
shells nutrients
Includes some human pathogens Help plants absorb water and minerals
Naegleria Used for food, in religious ceremonies, and in
Acanthamoeba manufacture of foods and beverages
Entamoeba Produce antibiotics and other drugs
Slime molds are now classified as amoebozoa Serve as important research tools
Two types 30% cause diseases of plants, animals, and humans
Plasmodial slime molds Can spoil fruit, pickles, jams, and jellies
Cellular slime mold

76
 • Nutrition of Fungi
Acquire nutrients by absorption
Most are saprobes
Some trap and kill microscopic soil-dwelling
nematodes
Haustoria allow some fungi to derive nutrients from
living plants and animals
Most fungi are aerobic
Many yeasts are facultative anaerobes
Reproduction of Fungi
• All have some means of asexual
reproduction involving mitosis and
cytokinesis
• Most also reproduce sexually Classification of Fungi
• Budding and asexual spore formation Division Zygomycota
Yeasts bud in manner similar to prokaryotic budding Division Ascomycota
Some yeasts produce long filament called a Division Basidiomycota
pseudohypha Deuteromycetes
Filamentous fungi produce lightweight spores that • Division Zygomycota
disperse over large distances 1100 known species
• Sexual spore formation Most are saprobes
• Fungal mating types designated as "+" and Others are obligate parasites of insects and other
"–" fungi
• Four basic steps Reproduce asexually via sporangiospores

• Division Zygomycota
Microsporidia
• Once classified as protozoa
• More similar to
zygomycetes by genetic
analysis
• Obligate intracellular
parasites
• Spread as small,
resistant spores
• Nosema parasitic on
insects

77
 • Used as biological
control agent for
grasshoppers
• Several genera cause
disease in
immunocompromised
patients

• Division Basidiomycota
22,000 known species
Mushrooms and other fruiting
bodies of basidiomycetes called
basidiocarps
• Basidiomycetes affect humans
in several ways
Division Ascomycota Most are decomposers
• 32,000 known species that return nutrients to
• Ascomycetes form ascospores the soil
in sacs called asci Many mushrooms
• Also reproduce by produce toxins or
conidiospores hallucinatory chemicals
• Includes most of the fungi that Some cause expensive
spoil food crop damage
• Some infect plants and humans
• Many are beneficial
• Penicillium
• Saccharomyces

78
 • Deuteromycetes
• Heterogeneous collection of fungi
with unknown sexual stages
• Most deuteromycetes belong to the
division Ascomycota based on
rRNA analysis

• Lichens
Partnerships between fungi and photosynthetic
microbes
Fungus provides nutrients, water, and protection
Photosynthetic microbe provides carbohydrates and
oxygen
Abundant throughout the world • Tell Me Why
Grow in almost every habitat Why isn't a fungal dikaryon—with its two haploid
Occur in three basic shapes (n) nuclei—considered diploid?
Foliose, crustose, fruticose
Create soil from weathered rocks
Some lichens provide nitrogen in nutrient-poor
environments
Eaten by many animals Algae
• Simple, eukaryotic phototrophs
• Carry out oxygenic photosynthesis using
chlorophyll a
• Have sexual reproductive structures in
which every cell becomes a gamete
• Differ widely in distribution, morphology,
reproduction, and biochemical traits

• Distribution of Algae
Most are aquatic
Live in the photic zone of freshwater, brackish
water, and saltwater
Have accessory photosynthetic pigments that trap
energy of short-wavelength light
Allows algae to inhabit deep parts of the photic zone
• Morphology of Algae
Can have different morphologies
Unicellular
Colonial
Simple multicellular bodies called thalli

• Reproduction of Algae
Reproduction in unicellular algae
Asexual reproduction involves mitosis followed by
cytokinesis

79
In sexual reproduction, individual gametes form • 18S rRNA
zygotes that undergo meiosis sequences are
Reproduction in multicellular algae similar
Reproduce asexually by fragmentation Most are unicellular and filamentous
Reproduce sexually with alternation of generations • Live in freshwater
Some multicellular forms grow in marine waters
Kingdom Rhodophyta (red algae)
Have the red accessory pigment phycoerythrin
Use the storage molecule glycogen
Cell walls composed of agar or carrageenan
• Both are used as
thickening agents
Nonmotile male gametes called spermatia
Most are marine algae

Phaeophyta (brown algae)

• Classification of Algae Motile gametes have two flagella
Classification is not settled Produce chlorophylls a and c, carotene, and
Classification schemes are based on different xanthophylls
features Most are marine algae
Differences in photosynthetic pigments Use laminarin and oils as food reserves
Storage products Cell walls are composed of cellulose and alginic acid
Cell wall composition • Alginic acid is used
Various groups medically and as a
Division Chlorophyta thickening agent
Kingdom Rhodophyta
Phaeophyta
Chrysophyta

Division Chlorophyta (green algae)

Share numerous characteristics with plants
• Have chlorophylls a
and b
• Use sugar and
starch as food
reserves
• Many have cell
walls of cellulose

80
 Chrysophyta (golden algae, yellow- • Some species are pathogens of crops
green algae, and diatoms) Phytophthora infestans caused the Irish potato
Use chrysolaminarin and oils as famine
storage products
Some lack cell walls; others
have ornate coverings
Most are unicellular or colonial
Diatoms
• Component of marine
phytoplankton
• Major source of the
world's oxygen

• Tell Me Why
Why are water molds more closely related to brown
algae than to true molds?

Other Eukaryotes of Microbiological Interest:

Parasitic Helminths and Vectors
• Parasitic worms have microscopic infective
and diagnostic stages
• Arthropod vectors are animals that carry
pathogens
Mechanical vectors
Biological vectors
• Disease vectors belong to two classes of
arthropod
Arachnida
• Tell Me Why Insecta
Why aren't there large numbers of pathogenic algae? • Arachnids
Adult arachnids have four pairs of legs
Ticks are the most important arachnid vectors
Water Molds • Hard ticks are most
• Differ from fungi in several ways prominent tick vectors
Have tubular cristae in their mitochondria A few mite species transmit rickettsial diseases
Cell walls are of cellulose instead of chitin • Insects
Spores have two flagella Adult insects have three pairs of legs and three body
Have true diploid bodies regions
• Decompose dead animals and return Include
nutrients to the environment • Fleas

81
 • Lice
• Flies
• Mosquitoes
• Most important
arthropod vectors of
disease
• Kissing bugs

Chapter 13 Characterizing and Classifying

• Tell Me Why
viruses, viroids, and prions
Why are large eukaryotes such as mosquitoes and
ticks considered in a microbiology class?
Characteristics of Viruses
• Viruses
Minuscule, acellular, infectious agents having either
DNA or RNA
Important topics
Cause infections of humans, animals, plants, and
• Mitosis and meiosis
bacteria
• Different forms of fungi (mold and yeast)
Cause most of the diseases that plague the
characteristics
industrialized world
• Fungi replication
Cannot carry out any metabolic pathway
• Algae photosynthetic features
Neither grow nor respond to the environment
• Lichens
Cannot reproduce independently
• Division of Basidiomycota
Recruit the cell's metabolic pathways to increase
• Division if Ascomycota
their numbers
• Diatoms
No cytoplasmic membrane, cytosol, organelles
• Ciliates
Have extracellular and intracellular state
• Kelps
• Extracellular state
Called virion
Protein coat (capsid) surrounding nucleic acid
Nucleic acid and capsid, also called nucleocapsid
Some have phospholipid envelope
Outermost layer provides protection and recognition
sites for host cells
• Intracellular state
Capsid removed
Virus exists as nucleic acid

82
83