All cells have:

1. Cell or plasma membrane (separates the cell from the outer environment)

2. Genetic material (DNA)

3. Cytoplasm.

 I.                 TWO GENERAL TYPES OF CELLS:

A.     Prokaryotic ("before nucleus") - a cell lacking a membrane-bound nucleus &

membrane-bound organelles (ex. bacteria); these cells do have some organelles,
but they are not membrane-bound; all prokaryotic cells have a cell wall, its
primary component being peptidoglycan; prokaryotic cells are much smaller than
eukaryotic cells (about 10 times smaller); their small size allows them to grow
faster & multiply more rapidly than eukaryotic cells (they have a higher surface
area to volume ratio than larger cells; thus, because they are small, they can
easily meet their modest nutritional needs and grow rapidly). This group
includes all bacteria.

B.      Eukaryotic ("true nucleus") - a cell having a membrane-bound nucleus &

membrane-bound organelles (“little organs” – specialized structures that
perform specific functions within the cell); evolved about 2 million years after
the prokaryotes; cell walls are sometimes present, but they are composed of
cellulose or chitin; organisms with eukaryotic cells include fungi, algae, protozoa,
plants, & animals.

It is important to know the differences between prokaryotic and eukaryotic cells; allows
us to control disease-causing bacteria without harming our own cells.

II. PROKARYOTIC CELL STRUCTURE

 A. Appendages

1.    Pili - straight hairlike appendages; they are usually short; all gram negative
bacteria have pili; function is to attach bacteria to other bacteria, other cells,
or other surfaces (not for locomotion):

a.     sex pili allow one bacterial cell to adhere to another (cells can actually
 exchange genetic material through the pili - this is the closest bacteria
get to sexual reproduction!); called conjugation.

b.    other types of pili attach bacteria to plant or animal cells to maintain
themselves in a favorable environment; if pili have been lost (maybe due
to a mutation) in disease-causing bacteria, the bacteria will not be able to
establish an infection.

2.    Flagella (singular – flagellum) - long, thin structures that extend outward from
the surface of the envelope; function is locomotion - bacteria with flagella are
motile; flagella rotate to propel the bacterium. Bacteria can have 1, 2, or many
flagella (ex. of a bacteria with many flagella – Salmonella).

3.    Axial Filaments - bundles of flagella which wrap around the cell body between
the cell wall and the outer membrane; together they form a helical bulge that
moves like a corkscrew as the entrapped flagella turn & propel the cell; found
only in one type of bacteria called the spirochetes; this unique form of
movement is well suited to the viscous environment (mud & mucous) where the
bacteria is generally found. Ex. of bacteria with a.f. – Treponema (causes
syphilis) and Borrelia (causes Lyme disease).

B. Cell Envelope (layers from outside to inside) (BE ABLE TO DIAGRAM!)

1.    Glycocalyx - found in most bacteria; slimy or gummy substance that becomes
the outermost layer of the cell envelope; a thick glycocalyx is often called a
capsule; a thin glycocalyx is often called a slime layer; functions:

a.      protection from drying out

b.      helps a cell adhere to a surface where conditions are favorable for
growth

c.     provide protection against phagocytosis (engulfment & destruction by

cells such as white blood cells) - a slippery glycocalyx makes it difficult
for the phagocyte to grab hold of the bacterium.
2.    Outer Membrane - primarily found in gram negative bacteria (ex. E. coli,
Salmonella, Shigella, Pseudomonas, Proteus, Neisseria gonorrhoeae ); composed
of a bilayer membrane; the inner layer is composed of phospholipids; the outer
layer is composed of lipopolysaccharides (LPS’s), a compound that's not found in
any other living organism!; part of the LPS is hydrophobic, part is hydrophilic;
most molecules are transported across the outer membrane and into the cell
through special proteins called porins; these porins create small pores or
channels in the outer membrane that allow molecules to diffuse in; function of
the outer membrane is mainly protection - because of the outer membrane,
gram negative bacteria are generally more resistant than gram positive bacteria
to many toxic compounds, including antibiotics (antibiotics are too large to
diffuse through the porins).

More about LPS’s – These compounds are endotoxins and are only released when
the bacteria die and their cell walls are broken down. Endotoxins cause fever
and dilate blood vessels (drop in blood pressure results). Killing the bacteria
may increase the concentrations of this toxin!

3.    The Cell Wall - The structure described below is found in all eubacteria
except the mycoplasmas (these bacteria lack a cell wall); in archaeobacteria, the
cell walls are composed of a different type of peptidoglycan or protein & some
do not have cell walls. In gram negative bacteria, the cell wall lies just inside
the periplasm; in gram positive bacteria, it lies just inside the glycocalyx, if one
exists.

a. Structure & Composition of Cell Wall in Eubacteria

1.) The chief component is peptidoglycan.

2.) Peptidoglycan is composed of long chains of polysaccharides

(glycan) cross-linked by short proteins (peptides).

3.) When linked together these chains create the single rigid mesh-
like molecule that forms the bacterial cell wall (resembles a chain
link fence!)

4.) A major difference between G(+) & G(-) bacterial cell walls:

a.) G(-): peptidoglycan mesh is only one layer thick.

 b.) G(+): peptidoglycan wall is many layers thick.

b.    Cell Wall Function – In many cases, the cell wall is very porous and does
not regulate the transport of substances into the cell. Two major
functions of the cell wall are maintaining shape and withstanding turgor
pressure. Both are discussed below.

1.) Cell Shape - one fxn. of the cell wall is to confer shape on the
bacterium; most bacteria fall into one of these general groups.
However, some bacteria have irregular shapes. Even bacteria of
the same kind or within the same culture sometimes vary in size
and shape (especially in aging cultures).

a.) cocci (singular - coccus) - spherical

b.) bacilli (singular - bacillus) - rod-shaped

c.) spirilli (singular - spirillum) - spiral-shaped

d.)   vibrio - comma-shaped

In addition to these characteristic cell shapes, cells can also be

found in distinctive groups of cells: pairs, chains, tetrads (cubes),
grape-like clusters, etc.

2.) Withstanding Turgor pressure – A cell's turgor pressure is the

internal pressure from its contents. Ordinarily, a bacterium is in
a hypotonic solution (a more dilute solution that has less solute
and more water than the inside of the bacterium) and water tries
to move from a high water concentration to a low water
concentration; that is, water tries to move inside the bacterium
(see tonicity under osmosis later in the handout). Without the
cell wall, the water would continue to more inside the cell, and the
cell would lyse or burst; the cell wall withstands turgor pressure,
 so that the cell does not lyse.

Action of some antibiotics (ex. penicillin) - Bacteria produce

enzymes that reseal breaks in the peptidoglycan cell wall that
occur during normal growth and division; penicillin binds to these
enzymes, inactivating the enzymes so that the breaks cannot be
resealed. The bacteria then lyse.

Lysozyme, an enzyme found in tears, digests (breaks down)

peptidoglycan.

c.     Mycoplasmas - group of bacteria that lack a cell wall; they avoid lysis
from turgor pressure by maintaining a nearly equal pressure between
their cytoplasm and their external environment by actively pumping
sodium ions out of the cell; additionally, their cell membranes are
strengthened because they contain cholesterol, a lipid found in
eukaryotic cell membranes.

4.    Periplasm - used to be called a space, because of the way it looked in electron
micrographs; found between the cell membrane and the peptidoglycan cell wall;
therefore, only found in gram negative cells; composed of a gelatinous material
containing proteins; one function of these proteins is that break down certain
nutrients into smaller molecules that can pass through the cell membrane.

5.    Plasma or Cell Membrane - membrane that encloses the cytoplasm of any cell;
major function is to contain the cytoplasm and to transport and regulate what
comes in and what goes out of the cell. Many prokaryotic cell membranes are
similar to eukaryotic cell membranes. Its structure is referred to as the Fluid
Mosaic Model, because the structure behaves more like a fluid than a solid.
Contains:

Membrane Lipids: (composed primarily of phospholipid molecules)

a.)  phospholipid bilayer (hydrophobic fatty acid tails & hydrophilic

phosphate heads)
  Membrane Proteins: (proteins float in the fluid lipid bilayer)

a.)              Integral proteins - inserted in the bilayer; mainly involved in

transport.

1.) carrier proteins - bind to specific substances & transport

them across the cell membrane.

2.) channel proteins - proteins with a channel through which

small, water soluble substances move across the cell
membrane.

b.) Peripheral proteins - usually attached to membrane surface; some

are enzymes; some are involved in the electron transport chain
and/or photosynthesis others are involved in the changes in cell
shape that occur during cell division.

Note: Archaeobacteria Cell Membranes - there are different kinds of

bonds in the phospholipid molecules that link the lipids (tails) to the glycerol
molecule (head); these bonds are stronger and may help these bacteria
survive extreme temperature and pH.

Cell Membrane Invaginations - the cell membrane sometimes invaginates or

folds back on itself, forming structures that extend into the cytoplasm;
since prokaryotic cells lack organelles, these invaginations provide increased
surface area for peripheral proteins (enzymes) to catalyze chemical
reactions.

C. Cytoplasm - matrix composed primarily of water (90%) & proteins. Contains the
following:

1.    Nucleoid - or nuclear region is a mass of DNA; well defined, although it is not
surrounded by a membrane; most of a bacterium's DNA is arranged in a single
circular molecule called a chromosome; some bacteria also contains smaller
circular DNA molecules called plasmids.
 

2.    Ribosomes - site of protein synthesis; prokaryotic ribosomes are smaller than
eukaryotic ribosomes. Antibiotics such as tetracycline, erythromycin, and
streptomycin can specifically target bacterial ribosomes & not harm the host's
eukaryotic ribosomes.

3.    Endospores - extremely hardy, resting (non-growing) structures that some

bacteria, principally G(+), produce through the process of sporulation when
nutrients are exhausted; when favorable conditions return, endospores
germinate to produce new vegetative cells, which grow & reproduce; they are
able to withstand harsh environmental conditions because they contain so little
water and high concentrations of calcium and dipicolinic acid; when favorable
conditions return, the spore germinates into a new vegetative cell.

Some of endospore-producing bacteria are pathogenic to humans. Ex. Clostridium tetani

causes tetanus (other species of this genus cause botulism and gas gangrene). Bacillus is
another genus of bacteria that forms spores. This set of notes goes with the Bacterial unit.

Intro. To Taxonomy & The Classification of the Bacteria

 I. Principles of Biological Classification

Organisms are classified into any particular group because they have certain common
characteristics. Classification of organisms 1.) establishes the criteria for identifying
organisms; 2.) it arranges related organisms into groups based on shared
characteristics; and 3.) it provides important information on how organisms evolved.

A classification system based on collecting individuals into groups and groups into
progressively more inclusive and broader groups is called a hierarchical scheme of
classification. A basic principle of taxonomy is that members of higher-level groups
share fewer characteristics than those in lower-level groups. For example, humans
have backbones like all other vertebrates, but they share fewer characteristics with
fish and birds than with other mammals. Likewise, nearly all bacteria have a cell wall,
but in some the wall is G(+) and in others it is G (-).
 

Taxonomy is the science of classifying organisms.

A Swedish biologist names Carolus Linnaeus devised a taxonomic scheme that was both
practical and adaptable to expanding information. The Linnaean scheme remains the
basis for biological classification today in 2 regards: 1.) we continue to group
organisms hierarchically, & 2.) we use his nomenclature

Species defined: groups of actually or potentially interbreeding natural populations

which are reproductively isolated from other such groups. Bacteria, with their variety
of forms of genetic exchange, do not fit this definition neatly. Microbiologists use the
term “species,” more as a category of convenience (bacteria are grouped based on
similarities), existing more in the human mind than in the natural world.

The Linnaean scheme uses the following hierarchical classification scheme:

Kingdom

Phylum (division)

Class

Order

Family

Genus

Specific epithet

  

Example: Humans Example: Treponema pallidum (causes syphilis)

Kingdom – Animalia Kingdom Monera (Prokaryotae)

 Phylum – Chordata Phylum Gracilicutes

[Subphylum - Vertebrata]

Class – Mammalia Class Scotobacteria

Order – Primates Order Spirochaetales

Family – Hominidae Family Spriochaetaceae

Genus – Homo Genus Treponema

Species - Homo sapiens Species – Treponema pallidum

II. Binomial Nomenclature

Linnaeus introduced a binomial nomenclature (each organism is designated by 2
names). The first name is the organism’s genus designation & the second is its
specific epithet. Together, the 2 constitute the species name. The species name
is always latinized and underlined or italicized. The genus designation is capitalized,
but the specific epithet is not. Thus, the proper designation for humans is Homo
sapiens (or Homo sapiens ). By convention, the genus designation can be replaced
with an initial if the complete genus name has been used recently enough to avoid
possible confusion. For example, the bacterium Staphylococcus aureus becomes S.
aureus . All eukaryotes & prokaryotes are named this way. Viruses are not!

III. Artificial & Natural Systems of Classification

 

1.    Artificial - the Linnaean scheme; he grouped organisms on the basis of visible
similarities, but does not indicate how closely organisms are related.

2.    Natural - based on evolutionary (phylogenetic) relatedness.

IV.           Using a Taxonomic Key

 Biologists often use a taxonomic key to id. organisms according to their
characteristics. The most common kind of key is a dichotomous key, which has
paired statements describing characteristics or organisms. Paired statements
present an “either –or” choice, such that only one statement is true. Each
statement is followed by directions to go to another pair of statements until the
name of the organism finally appears. See example given in class.

  

V.               The Five Kingdom Classification System

No single classification system is completely accepted by all biologists, but one of

the most widely accepted is the five-kingdom system.

Kingdom Monera – prokaryotic; unicellular; most have a cell wall;

reproduction

usually by binary fission; photosynthetic, some chemosynthetic;

acquire nutrients from environment by absorption.

Kingdom Protista – eukaryotes; most are unicellular (some are organized

into colonies); cell wall present in some, absent in others;

reproduction mostly asexual, sometimes sexual; some are
photosynthetic; acquire nutrients from environment by absorption
and ingestion; this group includes the algae (resemble plants), the
protozoa (resemble animals), and the euglenoids (resemble both
plants and animals).

Kingdom Fungi – eukaryotic; unicellular or multicellular; cell wall present;

sexual and asexual reproduction; acquire nutrients by absorption of

organic matter from dead organisms.

Kingdom Plantae – eukaryotic; multicellular; cell wall present; sexual and

asexual reproduction; photosynthetic; acquire nutrients from

environment by absorption.

Kingdom Animalia - eukaryotic; multicellular; no cell wall; primarily sexual

 reproduction; acquire nutrients from environment by ingestion (some
parasites by absorption).

VI.            The Three-Domain Classification System

After the discovery of the archaeobacteria in the 1970’s, scientists suggested that
these organisms represented a third cell type and they proposed another scheme
for the evolution of living things from a universal common ancestor. This common
ancestor gave rise to the archaeobacteria, the urkaryotes, and the eubacteria (true
bacteria). They hypothesized a group of urkaryotes that gave rise to the
eukaryotes directly rather than by way of the prokaryotes. See figure 9.11 on p.
232. In 1990 Woese suggested a new taxonomic category, the domain, to be
erected above the level of kingdom. The three domains Woese proposes are shown
in Figure 9.13 on p. 234. The domain Eukarya contains all those kingdoms of
eukaryotic organism (animals, plants, fungi, and protists). The traditional kingdom
Monera has been divided into 2 domains: the domain Bacteria (true bacteria ) and
the domain Arachaea. The Archaea exhibit many differences from the Bacteria:

       Different cell membrane structure

       Cell wall present, but not composed of peptidoglycan

       First amino acid in proteins not methionine like in other bacteria and
eukaryotes

       DNA Contains histone-like proteins similar to eukaryotes (true bacteria

have no histone proteins)

       Live in only extreme environments (groups include extreme halophiles,

extreme thermoacidophiles, and methanogens)

VII. Classification of Bacteria

The artificial scheme of classification in Bergey's Manual of Systematic
Bacteriology is widely used. Bergey’s Manual disregards evolutionary relationships
because they often group bacteria into assemblages that cannot be easily identified
by standard laboratory procedures. Instead, the manual takes a strictly practical
approach so that it can be used as a comprehensive & quick reference when
accuracy & speed are important, as is often the case in diagnostic labs. Bergey’s
Manual divides bacteria into 4 divisions on the basis of their cell wall [G(+) or G(-)],
 their lack of a cell wall (mycoplasmas), & walls lacking peptidoglycan
(archaeobacteria). Bacteria species in each division are assigned to one or two
sections; sections have no taxonomic standing; they are simply groups of bacteria,
which share certain easily identifiable properties.

How do we identify bacteria?

1.)    We begin with morphological characteristics (shape, arrangement, etc.),

2.)   Rely primarily on physiological characteristics (ability to grow on a selective

medium, metabolic end products, etc.).

3.)   Knowing the source of the bacterium is also important.

4.)   Can also use DNA probes.

THE FOLLOWING IS A LIST OF THE MEDICALLY IMPORTANT MEMBERS OF

SELECTED SECTIONS DEFINED IN BERGEY’S MANUAL OF SYSTEMATIC
BACTERIOLOGY.

I.                 GRAM-NEGATIVE BACTERIA (eubacteria) - have an outer membrane, a

periplasmic space, & a thin peptidoglycan cell wall.

A.   Section 1 - Spirochetes - Distinguished by their corkscrew shape; possess

axial filaments (bundled flagella contained within the periplasm) that enable
them to move through viscous environments (mud, mucous). Some live
harmlessly in our mouths. Ex. of pathogenic species:

Treponema pallidum – syphilis, Borrelia burgdorferi - lyme disease (carried

by ticks) Leptospira - leptospirosis

B.    Section 2 - Aerobic/Microaerophilic, Motile, Helical/Vibrioid Bacteria -

 Helical members are corkscrew shaped, but flagella are ordinary; vibrioid
members are comma-shaped. Ex. of species:

Campylobacter jejuni - major cause of diarrhea

[hint: the jejunum is part of the small intestine]

Helicobacter pylori - cause gastric ulcers in humans

  

C. Section 4 - Aerobic Rods & Cocci - large & diverse group. Ex. of species:

Bordetella pertussis - pertussis (whooping cough)

Neisseria meningitidis - meningococcal meningitis (infection of meninges or

coverings of the brain/spinal cord)

Neisseria gonorrhoeae - gonorrhea

Pseudomonas aeruginosa - important opportunistic pathogen; common cause

of infection in weakened hosts, such as burn victims; another species has
been used to clean up oil spills.

Brucella – brucellosis

Legionella - pneumonia and other respiratory infections.

Francisella - tularemia

D.   Section 5 - Facultatively Anaerobic Rods - Grouped into 3 Families; many can
be distinguished by their characteristic fermentation reactions; includes the
enterics; Examples:

Salmonella typhi - typhoid fever; other species cause food poisoning

Shigella spp. - shigellosis, a form of dysentery

Yersenia pestis - bubonic plague

 Vibrio cholerae - cholera

Escherichia coli - some species cause diarrhea & dysentery; uti’s

Enterobacter cloacae – opportunistic infections

Proteus vulgaris – UTI’s

Vibrio cholerae - cholera

Haemophilus influenzae - upper respiratory infections (epiglottitis, sinusitis,

ear infections), pneumonia, & meningitis.

Zymomonas - alcoholic fermentation; used to make tequilla

Klebsiella pneumoniae - pneumonia; uti’s

E.    Section 6 - Anaerobic Straight, Curved, & Helical Rods - most abundant
microbes in mouth & intestinal tract; Example: Bacteroides gingivalis - causes
gingvivitis & peridontal disease. Other species cause digestive & respiratory
infections,UTI’s, infections of wounds.

F.    Section 9 - The Rickettsias & Chlamydias - Once thought to be viruses

because of small size. Most species are obligate intracellular parasites & can't
be cultivated outside a living host cell. In general, rickettsial pathogens are
transmitted by arthropods (ticks, lice, mites, fleas); chlamydiae are spread
directly from one infected human to another. Chlamydiae alternate between 2
cell types, elementary bodies and vegetative cells. Elementary bodies are tiny,
round structures released when an infected host cell lyses. When phagocytized,
they differentiate into rod-shaped vegetative cells that multiply within the host
cell [This is different from other bacteria which do not invade the host cell!].
They then differentiate into elementary bodies again before the host cell lyses.
Examples:

Rickettsia spp. - typhus (transmitted by body lice & rat fleas), Rocky Mt.

Spotted Fever (transmitted by ticks)

 Coxiella – Q fever

Chlamydia trachomatis - trachoma, sexually transmissible nongonococcal

urethritis or NGU.

Chlamydia psittaci - ornithosis (parrot fever) (a respiratory disease)

II.             MYCOPLASMAS (eubacteria) - Section 10 - All lack a rigid cell wall. To maintain
turgor pressure: 1.) their cell membrane contain sterols to add strength (sterols
are also found in eukaryotic cell membranes), and 2.) they maintain their cytoplasm
at the same pressure as their external environment by actively pumping sodium ion
out of the cell. All are parasites of humans, animals, or plants. Almost all are
obligate fermenters (they ferment even in the presence of oxygen). Their colonies
have a distinctive fried egg appearance. They have various shapes, but when growth
conditions are suboptimal, they become distorted, forming long strands that
resemble fungi (thus accounting for the name myco , which means "fungus"). Their
wall-less structure allows them to squeeze through even the tiny pores in filters
used to sterilize liquids. Mycoplasma pneumoniae - common cold & primary atypical
pneumonia (walking pneumonia)

III.         GRAM-POSITIVE BACTERIA (eubacteria) - lack an outer membrane & a

periplasmic space; have a thick peptidoglycan cell wall.

A. Section 12 - Cocci - large group. Some examples:

Micrococcus spp. - normal inhabitant of human skin; often contaminants on

agar plates.

Staphylococcus spp. - normal inhabitant of human skin; many species

produce

carotenoid pigments, giving colonies characteristic yellow & orange

colors

Staphylococcus aureus - major human pathogen; can infect almost any tissue
 in the body; causes impetigo, pneumonia, food poisoning; causes many
nosocomial (hospital-acquired) infections.

Streptococcus - S. pyogenes causes strep throat, scarlet fever, rheumatic

fever, endocarditis; S. pneumoniae causes life-threatening

pneumococcal pneumonia & meningitis; S. mutans causes dental plaque.

B.    Section 13 - Endospore-Forming Rods & Cocci - These bacteria are the most
heat-resistant living things; they are used as an index of sterilization; location
of endospore can be used to distinguish species. Some examples:

  

Clostridium spp. - all strict anaerobes, inhabiting soil & mud; C. tetani causes

tetanus (fatal rigid paralysis); C. perfringens causes gas gangrene &

food poisoning, C. difficile causes iatrogenic (medically induced)
diarrhea when antibiotics upset the normal balance of intestinal
microbes; C. botulinum causes botulism (food poisoning); some species
are harmless.

Bacillus spp. - aerobes, some facultative anaerobes; B. anthracis - causes

anthrax; B. cereus causes food poisoning.

C.    Section 14 - Nonsporing Rods - Listeria monocytogenes – food poisoning

(listeriosis); in young, old, & immunocompromised patients it can cause a form of
meningitis.

D.   Section 15 - Irregular Nonsporing Rods - Members have irregular shapes

(branched, club-shaped, etc.); shapes can change with growth phase of culture.

Propionibacterium acnes - causes acne

Corynebacterium diptheriae - causes diphtheria.

 

IV.            MYCOBACTERIUM (Section 16) - have a waxy outer layer composed of

polysaccharides & mycolic acids; protects against hostile environments & affects
staining; identified by the acid-fast stain procedure; Examples: Mycobacterium
tuberculosis - causes tuberculosis; Mycobacterium leprae - causes leprosy

V. OTHER SECTIONS

A.   Section 27 - Actinomycetes with Multiocular Sporangia - Bacteria in this

group grow as mycelia, masses of branching filamentous cells that resemble a
mycelial fungus. They form spores within a multiocular sporangium, a many-
chambered swelling at the end of a filament. Dermatophilus spp. infects
animals & sometimes human skin.

B.    Section 29 - Streptomyces & Related Genera - These bacteria are also
actinomycetes. Abundant in most soils (important in breakdown of organic
matter). Odor of freshly turned soil comes from volatile compounds produced
by these bacteria. Colonies have pastel colors, soil-like odor, & are hard & stick
into agar. Members of this genus produce most of antibiotics in current us