INTRODUCTION TO MICROBIOLOGY

Prof.Dr.Tanju Kadir
 Microbiology is defined as "the study of organisms that are
too small to be seen with naked eye.
 Microbiology can be broken down into several
branches of focus:
food and dairy,
public health,
agriculture,
industry,
immunology
and medical microbiology.


 Microorganisms


 Microorganisms are small organisms, generally smaller than

human eye can detect.

 They can be found in every ecosystem and in close

association with human.

 A very small minority of microorganisms are primary

pathogens. These are capable of infecting individuals and
causing disease.


 Infectious agents are divide into two groups:

1. Non-cells
a. Prion
b. Viroid
c. Virus

2. Cell ones
a. Prokaryotes
(For example, Bacteria)
b. Eukaryotes
Protozoa
Helminths
Fungus (Molds and Yeasts)
On the other hands, microorganisms play a critical role in
human survival. The normal commensal population of
microbes (Microbiome of our body):

• participates in the metabolism of food products,

• provides essential growth factors,
• protects against infections with highly virulent
microorganisms,
• and stimulates the immune response.
In the absence of these organisms, life as we know
it would be impossible.
 Celullar Organization of Organisms

With the exception of the viruses, viroids and prions, microorganisms are
classified as
- Eukaryotic (“eu” = true + “karyos” = nucleus) protists, which consist
of the protozoa, fungi, and algae other than blue-green algae.
- Prokaryotes (“pro” = before + “karyos” = nucleus), which consist of
the bacteria and blue-green algae.
 Eucaryotic cells are structurally more complex than
procaryotic cells, containing

- a true nucleus surrounded by

a nuclear membrane,
- endoplasmic reticulum,
- mitochondria,
- lysosomes, cell membrane,
- may (fungi and algae) or may not (protozoa trophozoites)
contain cell wall.
- can be either unicellular or multicellular.
 Prokaryotic cells are smaller and generally less complex
than eukaryotic cells.

- they are unicellular,

- have neither a well-defined nucleus nor nuclear membrane,

- reproduces through binary fission,

- contain (with one exception) a cell wall of unique chemical

composition.

- other components like; endoplasmic reticulum, mitochondria,

and lysosomes are not found.

 Bacteria

• Bacteria are the most abundant organisms on earth, found

everywhere; air, water, soil, rocks.

 • The human body is initiated by thousands of different bacterial

species (Humans contain 1014 bacterial cells, 1013 human cells;
mostly in large intestine).
A bacterial cell has 4 essential structural components:
- a nucleoid
(or chromosome),
- ribosomes,
- cell membrane,
- cell wall,

and particular structures, which are may or may not be

part of the cell . These are capsule, flagella, pili and spores
 Viruses


 • Viruses are not cells.

 • They are the smallest infectious particles, ranging in

diameter from 18 to almost 300 nm.

 • They comprise a nucleic acid core (either DNA or RNA but

not both) surrounded by a protein coat named capsid.
• Some viruses have an
envelope, made of lipid
and usually derived from
the host cell in which they
grow.
• Viruses are obligate intracellular parasites which requires to
live within a cell in its host.
Specific viruses attack specific types of human or animal
cells.
• There is a special class of virus that attacks bacteria. These
are the bacteriophages.
 Fungi
 • In contrast to bacteria, the cellular structure of fungi is
more complex.

 These are eukaryotic organisms that contain a well-defined

nucleus, mitochondria, Golgy bodies, and endoplasmic
reticulum.

 • There are two major morphological forms of fungi :

- Yeasts
Yeasts are round, unicellular
and multiply by budding or by
fission
Exm; Candida
- Moulds, are multicellular fungi composed of long filaments
called hyphae.
Mould hyphae may be aseptate (without septa) or septate
(with septa).
Multiply by sexual and asexual ways
The masses of hyphae are known as the mycelium
- Dimorphic fungi

Dimorphic fungi are fungi that have a yeast phase and a mold
(filamentous) phase depending on environmental conditions.
Many pathogenic fungi are dimorphic,
- usually the yeast form occurring in tissues
- and the filamentous form in the environment or on culture
at 25°C.
 Parasites


 • Parasites are the most complex microbes.

 • All parasites are classified as eukaryotic, some are unicellular

and others are multicellular.

 • They range in size from tiny protozoa as small as 1 to 2 µm in

diameter (the size of many bacteria) to helminths that can
measure up to 10 m in length.
• Many protozoa are free living, but others cause serious
infections.
• Protozoa can infect any human tissue, and are the cause of a
variety of diseases.
• They spread using a variety of strategies.
• Some produce cysts to survive outside the body.
• Helminths are multicellular worms, which classified as

nematodes (roundworms),

cestodes (tapeworms)

and trematodes (flukes).

 Viroids
Viroids are plant pathogens that consist of a small, single-
stranded, circular RNA without the protein coat that is typical
for viruses,
Viroids do not manufacture any proteins, so they replicate
only withen the host cells.
Human diseases caused by viroids have yet to be identified.
 Prions
A prion is a type of protein that can cause disease in animals
and humans by triggering normally healthy proteins in the brain
to fold abnormally.
They are simply proteins, devoid of any genetic material.
Once a misfolded prion enters a healthy person – potentially by
eating infected food – it converts correctly-folded proteins into
the disease-associated form.
Prions cause
- Bovine Spongiform Encephalopathy in cattle;
- scrapie in sheep and goats;
- and Creutzfeldt-Jakob disease in humans.
 BACTERIOLOGY

Bacterial Morphology and Structure

Bacteria, the smallest cells, are clearly visible under the

light microscope at 900-1000 x utilizing the oil immersion
abjective.
Those that either colonize or infect humans ranges from 0.2
to 10 µm (1 mm = 1000 µm) in diameter.
Some bacteria, such as Rickettsia, Chlamydia, and
Mycoplasma are small (are only 0.1 to 0.2 µm in diameter) as
some viruses.
 Bacteria are found in three forms:

• Cocci (or coccus).

Round or oval bacteria measuring about 0.5 - 1.0μm in
diameter.
Cocci bacteria can exist
-singly (monococci),
-in pairs (diplococci),
-in chains (stereptococci),
-in clusters (staphylococci),
-in tetrad
-or in cubes consisting of eight cells (as sarsina .)
• Bacilli (or bacillus for a single cell)
Are rod shaped bacteria.
Bacilli may be long with square-cut ends (Bacillus anthracis),
filamentous, curved (vibrios), have a series of turns or twists
(spiral=spirochet) or long with pointed ends (fusiform).
Coccobacilli or Coccobacillus
(Şort rod shaped)

Is a type of bacteria with a

shape intermediate between cocci
and bacilli.
 Bacterial Ultrastructure

• Most bacteria have an outer, rigid cell wall. This provides

shape and support.

• Lining the inside of the cell wall is a cytoplasmic membrane.
• The content inside the cell is called "cytoplasm.“ This
contains
the ribosomes (for protein synthesis),
the nucleic material (concentrated genetic material),
and plasmids
• Some bacteria
- have long, whip-like structures called "flagella“ that they
use for movement.
- Some have pili used for attachment and sexual
transmission.
• Many bacteria are surrounded by polysaccharide material
referred to as the glycocalyx. This is referred to as either a
capsule or a slime layer.
 A. Cell Envelope

Cell Wall

• The cell wall is a constituent of all bacteria, except members

of the genus Mycoplasma.
• A wall located outside the cell membrane
- provides the cell support,
- and protection against mechanical stress or damage from
osmotic rupture and lysis.
• Inasmuch as mammalian cells lack cell walls, antimicrobial
agents that inhibit cell wall synthesis (e.g., penicillin) will have
sellective activity gainst bacteria.
 The primary structure of the cell wall is peptidoglycan (syn:
murein, mucopeptide), which lies closest to the cytoplasmic
membrane.
• Peptidoglycan structure composed of
a. Repeating molecules of the (sugars) polysaccharides
- N-acetyl glucosamine (NAG)
- N-acetyl muramic acid (NAM),
b. Tetrapeptide - links the two polysaccharide backbones,
forming a peptidoglycan subunit.
• On the basis of cell wall structure and staining with the
Gram stain method there are two types of bacteria
- Gram positive bacteria
- Gram negative
• Gram stain reaction named after Christian Gram, who
developed the staining protocol in 1884.
• The Gram stain procedure distinguishes between Gram
positive and Gram negative groups by coloring these cells pink
or purple.
- Gram-positive bacteria have cell walls that contain thick
layers of peptidoglycan (90% of cell wall). These stain purple.
- Gram-negative bacteria have walls with thin layers of
peptidoglycan (10% of wall), and high lipid content. These stain
pink.
 Cell Wal of Gram Positive
Bacteria
• The cell walls of Gram-positive (G+) bacteria are thick,
compact, and almost exclusively peptidoglycan, comprising up
to 50% (40 – 90%) of cell wall material.
Most Gram positive cell walls contain additional substances
such as teichoic acid
 There are two types of
teichoic acid,
- wall teichoic acid (linked
to peptidoglycan)
- and lipoteichoic acid
(linked to membrane).
 Some Gram positive bacteria may lack wall teichoic acid but
all contain lipoteichoic acid.
The teichoic acid constitutes major antigens of cells that
possess them.
Some bacteria have cell wall specific polysaccharides
(usually called C polysaccharides).
Several Gram-positive bacteria have surface proteins that
are acts as virulence factors
1. Protein M of the group A streptococci
2. Protein A of Staphylococcus aureus
 Gram Negative Bacteria

• The cell wall of Gram-negative bacteria are thinner, less

compact, and more complex in their chemical composition.

a. Consist of a relatively thin layer of peptidoglycan,

comprising 5-10% of cell wall material.

b. Lipoprotein . Stabilizes the outer membrane

c. Periplasmic space, is the the space between the inner

and outer membranes. Contains
- lipoproteins,
- digestive enzymes
- and other transport proteins
 d. Outer membrane is phospholipid bilayer, structurally
similar to cytoplasmic membrane.
The outer membranes contain several important porins,
which specifically allow transport of solutes.
 Porins are proteins contain channels that vary in
size.They are responsible for the passage of molecules and
ions into and out of the Gram-negative bacteria.
They may contribute to the relatively high resistence of
Gram- negative organisms to certain antimicrobial agents.
 e. Lipopolysaccharide (syn: endotoxin) consists of

- Lipid A: When Gram negative bacteria is killed, it is released

and it acts as endotoxin.
- Core-polysaccharides: It provides stability to the structure of
outer membrane.
- O-polysaccharides: They act as somatic (O) antigen.
 A few medically important bacteria have an unusual cell
wall (contain lipids, called mycolic acids) resulting in their
inability to be Gram staines.
These bacteria resist decolourisation with both acids and
alcohol, and are known as acid-alcohol fast bacteria.
This is a property of mycobacteria. These include
Mycobacterium tuberculosis, the cause of tuberculosis.
 Protoplast, Spheroplast and L forms:
When bacteria are treated with enzymes that hydrolyze the
cell wall (e.g. lysozyme) or antibiotics that inhibit cell wall
synthesis (penicillin), wall-less bacteria are often produced.
 Such a treatment of bacteria in osmotically protective medium
liberates;
- protoplasts from Gram positive bacteria
- and spheroplasts from Gram negative bacteria.
Spheroplasts retain the outer membrane.
However, if such cells can grow and divide, they are called L
forms
 Glycocalyx

• Many bacterial cells have a coat of glycocalyx that covers the

outer surface.
• The glycocalyx is sticky substance composed of
polysaccharides (long chains of sugars) and/or polypeptides.
• These substances produced in the cytoplasm and secreted
to the outside of the cell and surrounded the cell wall.
• If the molecules are loosely attached to the cell wall, the
glycocalyx is referred to as slime layer.
Allows the bacteria to adhere firmly to various structures,
e.g., oral mucosa, teeth, heart valves and catheters.
'Coagulase-negative' staphylococci live on the skin, and
some bacteria produce a slime that enables them to stick to
plastics. These bacteria cause infections associated with
implanted plastic medical devices.
 • If the molecules are tightly adhered to the cell wall, the
glycocalyx is referred to as capsule. The capsule is important
because:
• It hinders or inhibits phagocytosis
• It helps in laboratory identification of organisms.
• İts polysaccharaide are used as antigens in certain
vaccines.
 In the staining of capsulated bacteria by ink or nigrosin
dyes, the capsules exclude the dye and appear as clear halos
surrounding the bacterial cells.
This is the Quellung reaction
 Cytoplasmic Membrane

• The cytoplasmic membrane is a thin, ductile, and elastic

membrane that encloses the cytoplasm.
Composed mostly of proteins and lipoproteins embedded in
a phospholipid bilayer.

• Functions of cytoplasmic membranes are :

1. Highly selective barrier,

- allows the cell to take up chemicals and nutrients needed
for survival
- keeping the vital cell components separated from the
environment.
2. Electron transport and oxidative phosphorylation, take
place within the membrane of aerobic bacterial species.

3. Synthesis of cell wall precursors

4. Secretion of enzymes and toxins.

 Mesosomes
• Are intracellular membrane structures, formed by an
invagination of the cytoplasmic membrane.
Mesosomes are absent in eukaryotes.
• They are more frequently seen in Gram-positive than Gram-
negative bacteria.
 Functions of Mesosomes
- Mesosomes are play role in septum formation during cell
division.
- Participate in aerobic respiration but they are not
analogous to mitochondria.
 Flagella

• Flagella are filamentous protein structures (flagellin) that

extends far beyond the cell Wall.
• Flagella is used only for motility by most motile bacteria.
It is guide the bacteria toward nutritional and other
sources.
• Many bacilli (rods) have flagella, but most cocci do not
and are therefore non-motile.
 The flagellum is attached to the cell body by hook and basal
body.
While the hook and basal body are embedded in the cell
envelope, the filament is free.
 Bacteria have four distinct patterns of flagella

• Monotrichous, the most common form, bacterium has one

flagell located at one end of the cell.
• Amphitrichous, bacterium has two flagella, one at each end
of the cell.
• lophotrichous, bacterium has two or more flagella located
at the same end of the cell.
• peritrichous, another common form, in which the entire cell is
surrounded by flagella.
 Fimbriae and Pilus
• Fimbriae (Latin for “fringe”) or pili fine, hair-like filaments,
shorter than flagella, that extend from the cell surface.
• Pilus, found mainly on Gram negative, and some Gram-
positive bacteria.
• They are composed of subunits of protein called pilin.
Both structures are involved in adherence to host cells and
to other bacterial cells.
• Although adherence seems to be the only function of the
fimbriae, pilus are also involved in the transfer of genetic
material from donor bacterium to a recipient bacterium.
 B. Intracellular Structure

The Cytoplasm

• It is a gel-like matrix composed of water, enzymes,

nutrients, wastes, and gases and contains cell structures such
as ribosomes, a chromosome, and plasmids.
 Nuclear Material
or Nucleoid (chromosome)

Bacteria do not have well developed nucleus as Eukaryotic

cells.
It has a single circular coiled of double-stranded DNA
called nucleotide or bacterial chromosome.
 The long of bacterial chromosome is between 1 to 1.4 mm
when unfolded.
The bacterium DNA contains about 2000 gens.
By contrast, human DNA has approximately 100.000 genes.
 Plasmids

Smaller extra-chromosomal DNA molecules, called

plasmids, that can replicate independently, may also be
present.
Plasmids are found both in Gram-negative bacteria and Gram
positive bacteria.
Different types of plasmids can exist in one cell.
They are not usually essential for cellular survival, but they
often provide a selective advantage: many confer resistance
to one or more antibiotics.
 Bacterial Ribosomes

• The cytoplasm has many ribosomes which contain RNA and

proteins, and are involved in protein synthesis.

• More active bacteria contain more ribosomes. Fore
example, Escherichia coli can have anywhere between 7000
and 25,000 ribosomes.
• Bacterial ribosomes are 70S monomers composed of 30S
and 50S subunits in contrast to the 80S monomer mammalian
ribosomes that are made up of 40S and 60S subunits.
- 30S subunit, contains 21 proteins and 16S rRNA.
- 50S subunit, contains 34 proteins, a 23S rRNA and a 5S
rRNA.
 S (Svedburg unit) is used as a measuring unit for
sedimentation speed in an ultracentrifuge.
These difference are the bases of the selective action of some
antibiotics that inhibit bacterial, but not human protein synthesis.
The ribosomes attach to the mRNA and use the sequences
of RNA bases to make proteins according to the "genetic code."
 Granules

• The cytoplasm of some bacteria also contains several types

of granules that serve as storage areas for nutrients and stain
characteristically with certain dyes.
The size of these granules may increase in a favourable
enviroment and decrease when conditions are adverse.
 Endospores

• Some Gram-positive bacteria such as members of the genera

Bacillus and Clostridium (soil bacteria) are spore formers.

• These types of bacteria essentially have two phases to their

life cycle, vegetative (growing) cells and endospores.

• When the living, vegetative cells of these genera are exposed
to harsh environmental conditions (loss of a nutritional
requirement, high temperature, high UV irradiation,
desiccation, chemical damage and enzymatic destruction), they
undergo a process called sporulation and ultimately generate
endospores.
 The endospore is able to survive for long periods of time until
environmental conditions again become favorable for growth.
The endospore then germinates, producing a single
vegetative bacterium.
Spores are called central, terminal or subterminal,
depending on their position in the cell.
 Parts of the Spore
Core - The core is dehydrated cytoplasm containing DNA, ribosomes,
enzymes etc. Everything that is needed to function once returned to the
vegetative state.
Cortex - The cortex is a modified cell wall/peptidoglycan layer that is not as
cross-linked as in a vegetative cell.
Coats - Outside of the cortex are several protein layers that are impermeable
to most chemcials. The coat is responsible for the spores resistance to
chemicals.