Bacteriology Introduction
Assistant Prof. Dr. Karreema Amine AL-Khafajii
Babylon University, College of Medicine, Department of Microbiology.
Cells in our World come in two basic types; prokaryotic(has no nucleous) and eukaryotic
(has nucleous). and the main difference between them are;
Differences between Prokaryotic cells and Eukaryotic cells
Prokaryotic Cells
They are very minute in size.
Nuclear region (nucleoid) is not
enveloped by a nuclear membrane.
Eukaryotic Cells
They are comparatively larger in size.
Nucleus is surrounded by a double
membrane layer.
More than one chromosome are
present.
Nucleolus is present.
Membrane bound organelles are
present.
Single chromosome present.
Nucleolus is absent.
Membrane bound organelles are
absent.
Multiplication of cell is by fission or
budding.
Cell Walls preset, which are
chemically complex.
Cell type is usually unicellular.
Cell size is 1-10μm
Example: Bacteria, archaea
Cell division by mitosis or meiosis.
Cell walls seen in only plant cells,
which are chemically simpler.
Usually multicellular cells.
Cell size 10 - 100µm.
Example: animal cells and plant cells.
Prokaryotes

Prokaryotic cells are the smallest, simplest and most abundant cells on Earth.

Most prokaryotes range in size from 1-10 micrometers (µm).

Prokaryotes include bacteria and archaea (ancient bacteria)
Prokaryotes lack a nucleus and complex organelles.
Bacteria are classified and named based upon their genetic structure,
physical structure, and metabolism.


Bacterial Shapes & Arrangements
Prokaryotes (bacteria) are smaller (1-10 micrometers, um) than Eukaryotic cells and
can be distinguished by the lack of a membrane-bound nucleus. Prokaryotic cells
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have 3 major shapes: cocci, bacilli or spirilla. Bacterial cells can be arranged in different
groups or patterns. These cells can be arranged singly, in pairs (diplo), groups of 4
(tetrads), chains (strepto), clusters (staphylo), packets of 8 or 16 (sarcinae), or hinged
together (palisades).
Prokaryotic Cell Structure
In general speech , Bacteria cell structure can be divided into 3 parts: external
(appendages & coverings), cell envelope (cell wall and membranes), and internal
organelles. The external structures of a bacterial cell include appendages for movement
(flagella) and adhesion (pili, fimbriae, and glycocalyx) to surfaces. Bacterial cells
contain: circular chromosome(s), ribosomes (protein synthesis), and internal storage
compartments for nutrients or survival.
1. External structures (appendages & coverings): flagella, fimbriae, sex pilus
and glycocalyx
2. Cell envelope: cell membrane, peptidoglycan cell wall or ad an outer lipid
membrane (only found in Gram-negative cells)
3. Internal Structures: Cytoplasm, nucleoid, bacterial chromosome, plasmid,
ribosomes, and storage granules
External Structures
The external structures of a bacterial cell include appendages for movement
(flagella) and adhesion (pili, fimbriae, and glycocalyx) to surfaces.
Fimbria and (pili): are interchangeable terms used to designate short, hair-like
structures on the surfaces of bactetial cells. Like flagella, they are compose of
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protein (called pilin). Fimbriae are shorter and stiffer than flagella, and slightly
smaller in diameter. There are two types of pili:
common pili(often called Fimbriae): are usually involved in specific adherence
(attachment) of bacteria to surfaces in nature. In medical situation they are major
determinants of bacterial virulence. Second type is called;
A sex pilus is a long, rigid tube made of protein called, pilin. Most bacteria
reproduce asexually through a process called binary fission. However, some
bacteria use the sex pilus or pili (plural) to "mate" with other bacterial cells.
During conjugation (sexual reproduction), bacteria use the sex pilus to transfer
genetic material between the two cells (see photo
below).
Flagella (flagellum-singular) are long, hair-like
appendages attached to the cell surface , function like propellers to allow
bacteria to swim and move. The diameter of a prokaryotic (bacteria), flagellum is
about 20 nanometers, well-below the resolving power of the light microscope.
The flagellar filament is rotated by a motor apparatus in the plasma membrane
allowing the cell to swim in fluid environments. About half of the bacilli and all the
spiral and curved bacteria are motile by means of flagella. Very few cocci are
motile, which reflect their adaptation to dry environments and their lack of
hydrodynamic design. The number and arrangement of flagella on a bacterial
cell can vary. Flagella can have one of the following arrangements:
 axial filament, where the flagellum is located INSIDE the bacterial cell giving the
bacteria cell a "corkscrew" appearance (found in spirochetes such as Treponema
*monotrichous, where there is 1 flagellum located at one 1 end of the cell
.*lophotrichous, where there are small tufts of flagella located at 1 end of the cell
. *amphitrichous, where there are flagella on both ends of the cell.
*peritrichous, where there a several flagella
dispersed around the surface of the cell.

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Bacterial capsule
The cell capsule is a very large structure of some prokaryotic cells, such as
bacterial cells. It is a layer that lies outside the cell wall of bacteria. It is a well
organized layer, not easily washed off, and it can be the cause of various
diseases. When the amorphous viscid secretion (that makes up the capsule)
diffuses into the surrounding medium and remains as a loose undemarcated
secretion, it is known as slime layer.
Composition ;It usually consists of polysaccharides, but can be composed of
other materials (e.g., polypeptide in B. anthracis). Because most capsules are
water soluble , they are difficult to stain using standard stains because most
stains do not adhere to the capsule. For examination under the microscope, the
bacteria and their background are stained darker than the capsule, which doesn't
stain. When viewed, bacterial cells as well as the surface they are on, are stained
dark, while the capsule remains pale or colorless and appears as a ring around
the cell.
Function :(1)The capsule is considered a virulence
factor because it mediates adherence of cells to the surface of the host. (2) it
enhances the ability of bacteria to cause disease (e.g. prevents phagocytosis).
The capsule can protect cells from engulfment by eukaryotic cells, such as
macrophages. (3) Capsules also contain water which protects bacteria
against desiccation.(4) They also exclude bacterial viruses and
most hydrophobic toxic materials such as detergents. There are 14 different
capsule types, which each impart their own specific antigenicity .Immunity to one
capsule type does not result in immunity to the other types. .
Diversity :The capsule is found most commonly among Gram-negative bacteria:
However, some Gram-positive bacteria may also have a capsule
Glycocalyx: the surface of bacteria is covered with a sticky coating called a
glycocalyx. The glycocalyx is composed of polysaccharides (sugars) and
proteins. The bacterial glycocalyx has 2 forms, a rigid capsule and a loose
slime layer. Capsules are found on many pathogenic (disease-causing)
bacteria including, Streptococcus pneumoniae, which causes a respiratory
infection of the lungs. The glycocalyx has several functions including:
protection, attachment to surfaces, and formation of
biofilms.
A biofilm: is a living layer of bacteria that is attached to
a surface. For example, biofilms are commonly found in
showers, toilets, catheters, medical equipment, and even
in your mouth! Dental plaque is an example of a biofilm
commonly found in humans. The glycocalyx helps
protect the bacteria cell by preventing immune cells from
attaching to it and destroying it through phagocytosis.
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Biofilms can have serious medical implications, because once they form on
surfaces, they are difficult to eliminate. They can form on damaged tissues,
teeth, and medical devices (catheters, artificial hip joints, IUDs).
Bacterial Cell Wall
The bacterial cell wall surrounds and protects the fragile cell or plasma
membrane, much like a bicycle tire protects the inner tube. The cell wall
provides protection and structural support for the cell. It also determines the
shape of the bacterial cell. The bacterial cell wall contains peptidoglycan, which
is made from long glycan (sugar) chains cross-linked (held together) by peptides,
much like a chain-link fence. There are 2 types of glycan chains that make up
peptidoglycan: N-acetyl glucosamine (NAG) and N-acetyl muramic acid
(NAM).
Gram-Positive, Gram-Negative and Acid-Fast Bacteria
Bacteria can be classified into 3 groups based on differences in the
thickness or composition of the cell wall structure: Gram-positive, Gramnegative, and Acid-fast.
The Gram stain is a technique used to distinguish between Gram-positive cells
that have a thick layer of peptidoglycan and stain purple and Gram-negative
cells which have a thin layer of peptidoglycyan and stain pink.
The Gram-positive cell wall consists of a thick (20-80nm) layer of
peptidoglycan. This thick layer is porous making the cell wall absorbent like a
sponge. The Gram-positive cell wall also contains teichoic acid, which
functions in cell wall maintenance and gives the cell surface an acidic (-) charge.
Picture of the Gram positive cell wall
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The Gram-Negative Cell Wall consists of thin (1-3nm) layer of
peptidoglycan. Because the Gram-negative cell wall is so thin, these bacterial
cells require an extra layer of protection, called the outer membrane. The outer
membrane consists of a phospholipid membrane, similar to the cell or plasma
membrane. This membrane has tiny holes or openings called porins. Porins
block the entrance of harmful chemicals and antibiotics, making Gram-negative
bacteria much more difficult to treat than Gram-positive cells.In many
antibiotic resistant bacteria, these porins are connected to drug pumps, which
pump out any drugs or harmful chemicals that enter through the porins. Attached
to the outer membrane is is a highly-branched fatty sugar called
lipopolysaccharide (LPS). LPS acts as an endotoxin because it induces fever
and shock in the human host.
The importance of LPS:
1-LPS is the major component of the outer membrane of Gram-negative bacteria,
contributing greatly to the structural integrity of the bacteria, and protecting the
membrane from certain kinds of chemical attack.2- LPS also increases the
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negative charge of the cell membrane and helps stabilize the overall membrane
structure. 3- It is of crucial importance to gram-negative bacteria, whose death
results if it is mutated or removed. LPS is an endotoxin, and induces a strong
response from normal animal immune systems. It has also been implicated in
non-pathogenic aspects of bacterial ecology, including 4-surface adhesion,
5- bacteriophage sensitivity, and 6- interactions with predators such as amoebae.
LPS acts as the prototypical endotoxin because it binds
the CD14/TLR4/MD2 receptor complex, which promotes the secretion of proinflammatory cytokines in many cell types, but especially in macrophages and B
cells. In Immunology, the term "LPS challenge" refers to the process of exposing
a subject to an LPS that may act as a toxin.
LPS is also an exogenous pyrogen (external fever-inducing substance).
Being of crucial importance to gram-negative bacteria, these molecules make
candidate targets for new antimicrobial agents.
It comprises three parts: 1-O antigen (or O polysaccharide)
2-Core oligosaccharide
O-antigen
3- Lipid A
A repetitive glycan polymer contained within an LPS is referred to as the
O antigen, O polysaccharide, or O side-chain of the bacteria. The O antigen is
attached to the core oligosaccharide, and comprises the outermost domain of the
LPS molecule. The composition of the O chain varies from strain to strain. For
example, there are over 160 different O antigen structures produced by
different E. coli strains. The presence or absence of O chains determines
whether the LPS is considered rough or smooth. Full-length O-chains would
render the LPS smooth, whereas the absence or reduction of O-chains would
make the LPS rough. Bacteria with rough LPS usually have more penetrable cell
membranes to hydrophobic antibiotics, since a rough LPS is more hydrophobic.
O antigen is exposed on the very outer surface of the bacterial cell, and, as a
consequence, is a target for recognition by host antibodies.
Core oligosaccharide
The Core domain always contains an oligosaccharide component that attaches
directly to lipid A and commonly contains sugars such as heptose and 3-deoxyD-mannooctulosonic Acid (also known as KDO, keto-deoxyoctulosonate). The
LPS Cores of many bacteria also contain non-carbohydrate components, such as
phosphate, amino acids, and ethanolamine substitutents.
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Lipid A: Lipid A is, in normal circumstances,
a phosphorylated glucosamine disaccharide decorated with multiple fatty acids.
These hydrophobic fatty acid chains anchor the LPS into the bacterial
membrane, and the rest of the LPS projects from the cell surface. The lipid A
domain is responsible for much of the toxicity of Gram-negative bacteria. When
bacterial cells are lysed by the immune system, fragments of membrane
containing lipid A are released into the circulation, causing fever, diarrhea, and
possible fatal endotoxic shock (also called septic shock). The Lipid A moiety is a
very conserved component of the LPS.
Gram negative bacteria cell wall , the LPS continents.
‫مهم جدا‬the differentiation between Gram positive and gram negativebacterial cell
wall
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In a Gram stain test, bacteria are washed with a decolorizing solution after
being dyed with crystal violet. On adding a counterstain such as safranin or
fuchsine after washing, Gram-negative bacteria are stained red or pink while
Gram-positive bacteria retain their crystal violet dye. This is due to the difference
in the structure of their bacterial cell wall. Gram-positive bacteria do not have an
outer cell membrane found in Gram-negative bacteria. The cell wall of Grampositive bacteriais high in peptidoglycan which is responsible for retaining the
crystal violet dye.
Acid-Fast Bacteria
Acid-fast bacteria contain a waxy substance called mycolic acid and a small
amount of peptidoglyan. Due to their waxy cell wall, these bacteria are highly
resistant to staining and treatment. Mycobacterium tuberculosis , the causative
agent of TB, is one example of a bacterial cell with an acid-fast cell wall. These
bacteria must be heated and treated with an acid-alcohol in order to stain them in
the lab (See image below).
Another type of bacteria with an unusual cell wall is Mycoplasma pneumoniae.
This bacteria attaches to the epithelial cells in the lungs, causing pneumonia.
The cell wall of this bacteria contains large amounts of sterols (rigid lipids),
which make it difficult to treat. Due to the waxy content of their cell wall, these
bacteria are pleiomorphic and vary in shape from long and filamentous to
round.
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Cell or Plasma Membrane
The cell or plasma membrane is a thin, fragile membrane located just beneath
the bacterial cell wall. The plasma membrane consists of a phospholipid
bilayer that contains negatively-charged phosphate heads that are hydrophilic
and hydrophobic lipid tails that are insoluble in water. The plasma membrane
also contains proteins that aid in the transport of materials into and out of the cell.
The plasma membrane is selectively permeable, which allows it to regulate
the flow of materials into and out of the cytoplasm. Materials that dissolve in
lipids (fat soluble) pass between phospholipids. Materials that cannot dissolve in
lipids must pass through the transport proteins.
The plasma membrane is often targeted and disrupted by detergents and
antibiotics.
Picture shows the plasma membrane
Internal Structures
Inside the flexible plasma membrane is the cytoplasm or "guts" of the cell. The
cytoplasm is a gelatin-like substance made of water, protein , carbohydrates and
salt. The other internal structures, such as the nucleoid, plasmid, ribosomes,
storage granules, and endospores are suspended in the cytoplasm.
Bacterial Chromosome & Nucleoid Region
Like all prokaryotes, bacteria do not have a nucleus. Instead, the bacterial
chromosome is found floating within a dense region of the cytoplasm called the
nucleoid region. Unlike humans, bacteria only have 1 or at most a few
chromosomes, which are tightly-coiled, circular pieces of DNA that contain all of
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the information required for survival. In addition to the bacterial chromosome,
some bacteria also contain plasmids. Plasmids are small, circular pieces of
DNA that are not required for survival. Plasmids are transferred between
bacterial cells during conjugation via the sex pilus. Plasmids carry genes
(information) for antibiotic resistance. They also allow bacteria to produce a sex
pilus for sexual reproduction
(conjugation).
Ribosomes
Although bacteria lack many of the complex organelles found in Eukaryotic cells,
they do contain up to 10,000 ribosomes per cell. Ribosomes consist of 2 subunits
(50S/30S) or parts that resemble a hamburger bun. The large subunit (top of
the bun) is made of ribosomal RNA (rRNA) and has the molecular size of 50
Svedberg units (50S). The smaller subunit (bottom of the bun) has a size of
30S. These subunits join together to form a protein factory where messenger
RNA (mRNA) is translated into long chains of amino acids to form proteins.
Storage Granules
Bacteria use granules to store minerals and nutrients (lipids, carbohydrates,
phosphates, sulfur or metals) for the cell to use when needed.
Endospores
Some
bacteria have the ability to produce endospores.
Endospores are an internal storage compartment
that
consists of 3 layers of protection: peptidoglycan,
calcium (dipicolinic acid) and keratin.
Endospores provide long-term storage and
protection of the genetic material when moisture
and
nutrients are not available. Sporulation, or the
formation of an endospore, occurs when nutrients
and moisture are low. This process takes about 6-8 hours and begins with
duplication of the bacterial chromosome. During the process of sporulation, the
duplicated chromosome is sealed inside 3 thick layers of protection. Once
moisture and nutrients return, the endospore quickly uncoats during a process
called germination.
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Endospores are highly resistant to conditions that would kill most bacteria. They
can withstand extremely high and low temperatures, pH, treatment with
chemicals, and exposure to ultraviolet (UV) radiation. Endospores can survive
these extreme conditions for up to 250 million years! This makes endosporeforming bacteria the very difficult to treat. Not all bacteria are able to form
endospores. Bacillus anthracis (anthrax), Clostridium botulinum (botulism) and
Clostridium tetani (tetanus) are examples of endospore-forming.
Methods of Bacterial Identification
Bacteria are classified based upon: cell wall structure, aerobes vs. anaerobes,
shape, genetic structure .
-Macroscopic morphology (appearance of bacterial colonies on petri dish.
-Microscopic morphology (bacterial shape & arrangement under the
microscope).-Physiological / biochemical characteristics (metabolism:
aerobes vs anaerobes).-Chemical analysis (cell wall composition). -Serological
analysis (antibodies).-Genetic & molecular analysis (DNA & rRNA sequence).
Good luck
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