By: Mohamed Elebs Microbiology

General Microbiology
 Chapter (1)
Introduction to Microbiology
❖ Definitions:
o Microbiology is the science that deals with tiny organisms or
microbes that cannot be seen by the naked eye.
o Medical microbiology is a branch of medicine that study
microorganisms of medical importance. It is concerned with
diagnosis, treatment and prevention of infectious diseases.
o Bacteriology: the study of bacteria.
o Virology: the study of viruses.
o Mycology: the study of fungi.
o Immunology: the study of the immune system (immune
cells, organs and immune response).
o Parasitology: the study of the parasites.

❖ Why we study microbiology:

1) Microorganisms have major impacts on human health as
they cause a lot of diseases or even be death.
2) Microorganisms share in maintaining the balance of nature
as they are involved in the flow of energy and food through
photosynthesis and decomposition processes.
3) Microorganisms are essential to many human activities; as
baker's yeast, cheese, genetic engineering, extraction of
antibiotics, ...etc.
4) Microbiology provides insights into life processes in all forms
of life as bacterium can be used as a model organism
because it has simple structure and reproduces quickly.
 ❖ Historical background:

Louis Pasteur Robert Koch

•He discovered the relationship between microbes and •He was the first to use germ theory of disease (i.e. a
disease immunity, and antimicrobial drugs. certain microorganism is responsible for a certain
•He showed that microbes are responsible for disease).
fermentation (conversation of sugar to alcohol) and •He developed a series of criteria around this known
spoilage of food. as the Koch's postulates.
•He demonstrated that these spoilage bacteria could •Koch's Postulates:
be killed by high heat for short time "pasteurization". •1) The pathogen must be present in all cases of the
•He also designed vaccines against several diseases disease.
such as anthrax, fowl cholera and rabies. •2) The pathogen can be isolated from the diseased
host and grown in culture.
•3) The pathogen from the pure culture must cause
the same disease when inoculated into a healthy,
susceptible laboratory animal.
•4) The pathogen must be re-isolated from the new
host and shown to be the same as the originally
inoculated pathogen.

❖ The Microbial World:

o The microbial world is composed of commensal, pathogenic and
opportunistic microorganisms.
o Most microbes are capable of growth and existence as single
organism or together with others.
o They are widely distributed in nature.
o Mostly they are beneficial, few species cause harmful effects and
disease in human & animals.
o Microbes that cause infectious diseases belong to five major
groups of organisms:
 Bacteria: prokaryotic cells.
 Viruses: obligate intracellular parasite (Noncellular or acellular).
 Fungi: Eukaryotic cells.
 Parasites which include protozoa and helminths: Eukaryotic
cells.
❖ General properties of microorganisms
a) Microscopic sizes; nearly all microorganisms cannot be seen by
naked eye.
b) Most of them are unicellular.
c) Simpler structural organization than higher plants and animals.
d) High capacity for rapid adaptability.
e) High rate of reproduction.
f) High and rapid biochemical activity.
g) Each cell contains total capacity for self-sufficiency and
reproduction.

❖ Classification of microorganisms:
o Prokaryote: in that class the cell lacking a true nucleus structure
(primitive nucleus).
o Eukaryote: in that class the cell possessing a membrane-enclosed
nucleus (true nucleus) and usually other organelles.

❖ Comparison of the prokaryotic and eukaryotic cell:

Comparison point Prokaryote Eukaryote

Examples Bacteria, Archaea Fungi, Protozoa, plants

Size Generally small Usually larger

Nuclear membrane Absent Present

Nucleolus Absent Present

Linear, several
Single circular not
DNA complexed with histones
chromosomes, usually
complexed with histones

Membranous
Absent Several present
organelles
Present in plants, algae,
peptidoglycan (Bacteria),
fungi, usually
Cell wall glycoprotein (Archaea)
polysaccharide but absent
except mycoplasma.
in animals, most protozoa.

Cytoplasmic Usually lacks sterols, Sterols usually present, but

membrane hopanoids may be present hopanoids are absent

80S except for ribosomes

Ribosomes 70S
of mitochondria (70S)

Reproduction simple binary fission meiosis and mitosis

 ❖ Morphology of prokaryotes (shapes of bacteria):
Cocci Bacilli Vibrios Spirochetes Spirilla Coccobacilli
spherical or ovoid cylindrical or small slightly Flexable, coiled, Flexable, coiled,
curved rods. corkscrew, motile Ex: influenza
in shape. stick-like bacteria motile organism
organism
Cocci in It may arranged Motile with single
pairs>>diplococci in: flagellum at one progress by: rapid
ex: meningocooci. end. body movements
•chains>>as
streptobacillus
Rapid darting Divided into three
Cocci in chains>> species
motility. main groups:
streptococci •Branching
chains>>as •Treponemes.
ex: streptococcus
pyogens. lactobacilli. Ex: vibrio cholera •Borreliae.
•Mass •Leptospires.
together>>as
Cocci in irregular Mycobacterium
groups>> leprae.
staphytococci •Resembling
ex: staph..aureus. chinese
letters>>as
C.diphtheria.

❖ Classification of bacteria:
1) Filamentous bacteria: Streptomyces (antibiotic producers).
2) True bacteria:
 Cocci: Gram positive: Staphylococcus, Streptococcus.
Gram negative: Neisseria.
 Bacilli: Gram positive: Bacillus, Clostridum, Corynebacterium.
Gram negative: Enterobacteriaceae (E-coli), Brucella.
3) Spirochetes: Slender flexible spiral bacteria.
as Borrelia, Treponema, Leptospira.
4) Mycoplasma: The Smallest bacteria that lack of a rigid cell wall.
5) Rickettsiae and Chlamydiae: they act as intracellular parasites.

❖ Reproduction of bacteria:
o Bacteria reproduce mainly by binary fission. Apparently, after a
cell matures a septum is laid in its middle dividing it into 2 cells
that are copies of the mother cell.
 Chapter (2)
Prokaryotic Cell Structure
❖ Prokaryotes have major structures:
o Cell Wall
o Cytoplasmic (cell or plasma) membrane
o Ribosomes
o Inclusions
o Nucleoid
❖ Prokaryotes have minor structures:
o Capsule
o Flagella
➢ Function:
 Protection.
 More Resistance.

Cell Structures and Function

I. Cytoplasmic (cell or plasma) Membrane

❖ The Structure:
1) phospholipid bilayer with polar (hydrophilic, glycerol) and
nonpolar (hydrophobic, hydrocarbon chain) ends.
2) Protein molecules which may be Integral protein or Peripheral
protein.
❖ Functions:
1) It is the critical permeability barrier or semi permeable
membrane that is responsible for the regulation material flow in
and out of cell by diffusion.
2) lon pumps: to maintain a membrane potential.
3) Secretion of extracellular enzymes (hydrolytic exoenzymes) to
digest large molecules.
4) Bearing the proteins, receptors and enzymes involved in active
transport of nutrients and various metabolic processes.
 5) Endocytosis and exocytosis (only in Eukaryotes)
• Endocytosis is the movement of material into cell by
engulfment. Phagocytosis is a type of endocytosis.
• Exocytosis is the movement of material out of the cell (the
reverse of endocytosis)

II. Structures outside the Cytoplasmic

Membrane
A. Cell wall:
o Bacterial cell wall is a rigid layer surrounds cytoplasmic
membrane of all bacteria (except mycoplasma).

❖ Structure of Cell Wall:

 The bacterial cell wall is composed of peptidoglycan (murein or
mucopeptide) that is composed of Long chains of polysaccharide
(alternating strands of N-acetyl muramic acid "NAM"& N-acetyl
glucosamine "NAG") linked with short peptides (amino acid
chains).
 The rigidity is achieved by the cross-linking reactions which is
Catalyzed by transpeptidase and decarboxy-peptidase enzymes.

The bacterial cell Long chains of

wall polysaccharide
short peptides
(amino acid chains)
(layer of peptidoglycan) "NAM"&"NAG"
 Classification of bacteria into Gram-positive and
Gram-negative is based on the differences in their
cell wall structure:

Gram positive bacteria Gram negative bacteria

The Cell wall is more complex, it is

The cell wall is formed of many layers
formed of 1-2 layers of peptidoglycan
of peptidoglycan (60-80% of the wall)
(5-10 % of the wall)

Teichoic acids are acidic Outer membrane (unique to gram-

polysaccharides that may be involved negative bacteria) is
in binding substances to cell surface lipopolysaccharides (LPS). It is
or act as phosphate storage pierced by "porins" (protein
molecule. channels important for the transport
of hydrophilic molecule.
Cell wall carries important virulence
factors "Antigens" as
polysaccharides, protein as M protein Because of the outer membrane, the
of streptococci & R protein of Gram negative bacteria are more
staphylococci. prominent than Gram positive ones
in human infection. Also, it prevents
molecules > 800 Dalton (such as
antibiotics) to go through the cell
wall. This accounts for the high
antibiotic resistance of gram
negative bacteria.

❖ Function of cell wall:

• It is responsible for rigidity & shapes of bacteria.
• It is osmotically insensitive, to protects bacteria from bursting in
hypotonic solutions.
• It is porous / permeable to LMW molecules.
• It contains major antigenic determinants as LPS of gram-negative
bacteria and teichoic acid of gram-positive bacteria.
 B. GIycocalyx (capsule and slime layers)
C. Flagella and Cilia
D. Pili (singular = pilus) or fimbriae

GIycocalyx Flagella and Cilia Pili

Structure Structure Structure

•Glycocalyx is a gelatinous layer lies •Bacterial flagella are thread-like, long, •pili are short, hair like projections
external to cell wall. helical appendages. extend from bacterial surface.
•It is composed of glycoprotein- •They are composed of protein called •They are composed of protein (Pilin).
polysaccharide covering. flagellin. •They are thinner and shorter than
•lt is amorphous. •They are attached to cell wall and flagella.
•It is not usually stained by gram stain cytoplasmic membrane by basal body. •They found mainly on surface of many
so it appears as unstained halo •They are found in Gram positive & G-ve bacilli.
around the organism. Gram negative bacteria
•glycocalyx exists as either a capsule or
slime layer. Types of pili
•If the glycocalyx is not tightly bound Distribution of flagella on •Common (ordinary) pili: cover surface
to the cell, it is rererred to as slime bacteria (Types of flagella) and responsible for adhesion.
Iayer. • F or sex pilus: is responsible for
•monotrichous (single polar flagellum).
conjugation and involved in mating. It
•lophotrichous (multiple polar flagella). is found on the donor cells to transfer
Function •Amphitrichous (multiple non-polar). DNA from donor cell to recipient.
•peritrichous (flagella distributed over
•It protects against dehydration and the entire cell).
loss of nutrients.
•Glycocalyx layer may also play a role
in resistance to desiccation. Pili also act as receptor sites for phages
Function (to transfer phage DNA from virus to cell)
•It acts as pathogenic factor in some
bacteria. •They are the organs of motility in all
•It acts as antiphagocytic activity motile bacteria.
because it prevents phagocytosis by •It carries flagellar or H antigen.
white blood cells.
•Dental plaque is a slime layer formed
by bacteria in the mouth.
 III. Structures inside the Cell
(Internal structure)

Mesosome Cytoplasmic inclusions The Nucleoid (nuclear body)

"Inclusion granules or Reserve materials"

•It is convoluted "coiled" invaginations They are nutritional storage granules •Prokaryotes do not have true nuclei
of cytoplasmic membrane. to be used latter such as: instead the region occupied by
•It is involved in DNA segregation during •Poly-beta-hydroxybutyric acid (PHB); chromosomes is called nucleoid
cell division. a lipid. region.
•It acts as an anchor to bind and pull •Volutin granules (storage form of •Bacterial chromosomes are composed
apart daughter chromosomes during complexed inorganic polyphosphate). of a double-stranded DNA helix in the
cell division. form of a single circular
•Starch/ or Glycogen (polysaccharides).
•It shares in active transport of solutes. macromolecule that is not
surrounded by nuclear membrane.
•Bacterial chromosomes aren't
associated with histones or other
proteins.
•DNA undergoes semi-conservative
bidirectional replication, from fixed
point.

Plasmids Ribosomes Bacterial Spores

(endospores)

•Plasmids are small circular, extra- •They are ribonucleoprotein granules •Spores are small, dense, metabolically
chromosomal DNA molecules that distributed throughout the cytoplasm. inactive, non- reproductive structures,
code variable number of genes. •They are composed of rRNA produced by certain gram positive
•Bacteria may have none or several (ribosomal RNA) and protein. bacteria as Bacillus & Clostridium.
plasmids. •They are site of protein synthesis. •They are a highly resistant resting
•They contain supplemental genetic •The sedimentation coefficient of phase of bacteria.
information as mating capabilities, prokaryotic ribosome is 70S and •The spore core contains high
antibiotic resistance or toxic metal ribosomes composed of 50S and 30S concentration of Calcium dipicolonate,
tolerance. subunits. which is thought to stabilize the DNA.
•They permit survival of bacterium •while the eukaryotic ribosome is 80S Dipicolinic acid is responsible for the
under unfavorable conditions. and ribosomes composed of 60S and heat resistance of the spore, and
•They can be used in genetic 40S subunits. calcium aids in resistance to heat and
engineering because they are easy to oxidizing agents.
•Note: Why sedimentation coefficient
manipulate and can have genetic isn't additive? Because when two •Sporulation: means vegetative state is
information from other sources. particles bind together there is converted to dormant state or spore
inevitable loss of surface area. under unfavourable environmental
conditions. This usually takes 6-8
hours.
•Germination: means the return of
endospore to its vegetative state by
disruption of the outer coat. This
usually takes about 90 minutes.

Postion of spores
•Terminal endospore.
•Equatorial (Central).
•Subterminal.
•Free spores.
 Chapter (3)
Bacterial Growth and Metabolism
❖ Introduction:
o In order to grow in nature or in the laboratory, a
bacterium must have an energy source, a source of
carbon and other required nutrients, and a permissive
range of physical conditions such as O2 concentration,
temperature, and PH.
o Bacteria take nutrient molecules, degrade them to
generate energy and smaller molecules then, use the
energy produced to reassemble these small molecules to
meet their own needs. This very basic process is known
as metabolism.
❖ Bacterial growth:
o If a small number of bacteria are inoculated into liquid
nutrient medium then the bacteria are counted at
frequent intervals and the results plotted, a
characteristic growth curve is obtained.
o This bacterial growth curve includes four phases:

2. Log or 3. Stationary 4. Death (decline)

1. Lag phase
exponential phase phase phase
•Bacteria are preparing for •Bacterial reproduction •As the nutrients in the •As nutrients exhaustion
reproduction synthesizing occurs at maximal rate for media are exhausted and and toxic metabolites
DNA and various enzymes specific growth conditions. toxic metabolites accumulation continue, the
needed for cell division. •Cell population count accumulate the rate of death rate exceeds the
•No increase in cell numbers. increases exponentially growth decrease. multiplication rate.
with time. •The number of dying •Total number of viable cells
cellsequals that of newly decreases exponentially
formed cells so the number with time.
of living bacteria remains
constant (No increase in
bacterial cell counts).
•Growth rate exactly
equabto death rate.
❖ Bacterial metabolism:
o Metabolism is the sum of all biochemical reactions of the cell as:
 Catabolism: substrate breakdown and conversation into
usable energy.
 Anabolism: synthesis of cellular constituents (cell wall,
proteins, fatty acids, nucleic acids).

o Metabolism has two components:

 Energy that is needed for biosynthesis processes and
maintenance of organism.
 Carbon which is used for biosynthesis of macromolecules
(CHO, proteins, ...).
o The four major mechanisms for generating metabolic energy
include:
 Aerobic respiration (oxidation): it is the form of respiration
which uses oxygen. It can be summarized by this equation:
 glucose + oxygen → carbon dioxide + water (+ energy in
the form of ATP).
 Anaerobic respiration: it is a type of respiration that does not
use oxygen. It is used when there is not enough oxygen. It can
be summarized by the following equation: glucose » lactic
acid (+ energy released).
 Fermentation: it is a metabolic process that consumes
(breakdown) sugar, in the absence of oxygen, giving organic
acids, gases, and heat. Fermentation is different from
anaerobic respiration as it does not use the electron transport
chain.
 Photosynthesis (transform light energy into chemical energy):
it is a process by which organisms convert light energy into
chemical energy to be used later.
❖ Bacterial nutrients:
a. An autotrophic "self-feeding" bacteria
 These are bacteria that can utilize simple substances present
in its surroundings to produces complex organic compounds
(such as CHO, fats, and proteins), using energy from light
(Phototrophs) or chemical reactions (Chemotrophs).
  These bacteria are free living, non-parasitic of no medical
importance.
b. Heterotrophic bacteria
 They require complex preformed organic compounds as
sugar, proteins, ..etc. which are derived from animal or plant
sources.
 All bacteria of medical importance are heterotrophs.
 They use light (photoheterotroph) or inorganic compounds
(chemoheterotroph) as a source of energy.

❖ Environmental factors (optional requirement for bacterial

growth):
o Temperature.
o Oxygen requirements.
o Water availability.
o Acidity and pH (hydrogen ion concentration).

Oxygen
Temperature Water availability Acidity and PH
requirements
•Optimal growth •Bacteria can be divided •Water is the solvent in •pH of a solution describes
temperature: is the into (according to their O2 which the molecules of life the hydrogen ion
temperature at which the requirement): are dissolved, and the concentration.
highest rate of •a) Obligate aerobes availability of water is •Microbial growth rates
reproduction (shortest (E.coli): grow only in therefore a critical factor influenced by pH because
generation time) occurs. presence of O2 that affects the growth of of nature of proteins;
(respiratory metabolism). all cells. enzymes normally inactive
•Bacteria can be classificd •b) Obligate anaerobes (e.g at very low pH values.
according to their optimal Clostridium perfringens) •The availability of water •Acidophiles are bacteria
growth temperature into: grow only in absence of for a cell depends upon its restricted to growth at low
•(1) Psychrophiles grow in O2 (fermentation or presence in the pH values (<5) (e.g.
temperatures < 20oC. anaerobic respiration). atmosphere (relative Lactobacillus and
•c) Facultative anaerobes: humidity) or its presence in Acentobacter).
•(2) Mesophiles grow near solution (water).
37oC (the body grow in either the •Alkaliplhiles are bacteria
temperature) e.g. E. coli. presence or the absence restricted to growth at high
of oxygen but better pH (as pH 10-11 for Bacillus
•(3) Thermophiles grow at
growth occurs in presence sp.., pH for Vibrio).
higher temperatures (45-
of O2.
70oC) e.g Thermus
aquaticus. •d) Microaerophilic (e.g
H.pylori): requires small
•(4) Extreme thermophiles
concentration of O2, less
or hyperthermophiles
than that present in the
grow at higher
air as they are poisoned
temperatures around
by high concentrations of
100oC, as some Archaea.
oxygen.
•e) Aerotolerant
anaerobes grow in either
the presence or the
absence of oxygen but
better growth occurs in
absence of O2 because
these organisms can only
ferment.
 Chapter (4)
Bacterial Genetics & Genetic Variation
❖ Introduction:
o Genetic is the discipline that deals with the mechanism by which
traits are passed from one organism to another and how they
are expressed.
o Nucleic Acids (DNA, RNA) are among the most important
biological macro-molecules. They function in encoding,
transmitting and expressing genetic information. In other words,
genetic information is transferred through the nucleic acid
sequence, or the order of nucleotides within a DNA or RNA
molecule.
❖ Structure of nucleic acids:
o Nucleic acids are composed of nucleotides linked together by
covalent bonds.
o Each nucleotide has three components: a 5-carbon sugar
(monosaccharides), a phosphate group, and nitrogenous base.
 If the sugar is deoxyribose, the polymer is DNA
(deoxyribonucleic acid).
 If the sugar is ribose, the polymer is RNA (ribonucleic acid).
o The phosphate group links the monosaccharides of each
nucleotide to form the nucleic acid.

DNA RNA

•It stores the genetic information of the organism. •It is single-stranded (except in some viruses).
•It is a double helix molecule (except in some viruses). •It converts the genetic information (carried in the DNA)
•It is composed of : into proteins in order to carry out the biological functions
•(1) Two sugar-phosphate backbone. of the organism.
•(2) Four bases: two pyrimidine bases (cytosine and •It contains the same bases as in DNA except that uracil
thymine) and two purine bases (guanine and adenine) replaces thymine (uracil has the same structure as
held together by hydrogen bonds: thymine except that it lacks a methyl group).
•Adenine-thymine: two hydrogen bonds. •There are three main types of RNA:
•Guanine-cytosine: three hydrogen bonds. •Messenger RNA (mRNA)
•Carries information from DNA in the nucleus to
ribosomes in the cytoplasm.
•Ribosomal RNA (rRNA)
•Combines with protein to form ribosomes.
•Transfer RNA (tRNA)
•Transfers amino acid to ribosomes to help build
proteins.
❖ Proteins:
o Transcription and translation of nucleic acids gives proteins that
are responsible for all functions of the cell.
o Proteins are composed of long chains of amino acids linked by
peptide bonds.
o There are twenty amino acids (a.a.) normally found in protein
macromolecules.
o Each a.a. has carboxyl and amino groups that remain in the same
position in all amino acids.
o Amino acids are linked together by binding of the carboxyl
carbon of one a.a. to the nitrogen of the next a.a. forming
peptide bond.
o Differences between amino acids are in the "R" groups attached
to the alpha carbon. These "R" groups establish the chemical
properties of the amino acid (and protein) molecules.

Bacterial Genetics
❖ Introduction:
o It is the study of the mechanisms of heritable information in
bacteria, their chromosomes, plasmids, transposons and phages.
It is probably the fastest growing branch of microbiology.
Interpretation of chemical structure of DNA has quickly leads to
an understanding of how the cell functions at a molecular level.
o Genetic information that is contained within the (genome) and
has the potential for being expressed is the genotype (not all the
genotype is expressed).
o Expression of genetic information is the phenotype (apparent
characteristics) of an organism.
o A gene is a segment of DNA that carries in its nucleotide
sequence the genetic information for a specific biochemical or
physiological property.
o Most bacterial genes are carried on the chromosome & they are
essential for bacterial growth. Additional genes are present in
plasmids & they are associated with specialized functions as
antibiotic resistance, toxin production or some surface antigens.
❖ Bacterial DNA is present in:
o Chromosome: Haploid, circular molecule of ds-DNA in nucleoid
region.
Replication is semi-conservative: i.e. produce two copies that
each contained one of the original strands and one new strand.
No histons (proteins around which DNA coils).
o Plasmid: Small, circular, extrachromosomal DNAs. It is not
usually essential for cellular survival. It is most commonly found
in gram-negative bacteria.
o Transposonable elements: genetic units capable of mediating
their own transfer from site to another on chromosome or
between chromosome and plasmid. They include insertion
sequence elements (which code enzymes for their own
transposition) and transposones (segment of DNA containing
genes).
o Bacteriophages which are viruses that infect bacteria. The word
PHAGE (as in phagocytosis) means "to eat". Bacteriophages are
very common in environment.
o Sequencing of bacterial genomes has revealed that phage
genome elements are an important source of sequence diversity
and can potentially influence pathogenicity and the evolution of
bacteria.

❖ Application of bacteriophages:
o Bacteriophages and animal cell viruses have many similarities, so
phages can be used as model systems for animal cell viruses to
study steps of the viral life cycle and to understand the
mechanisms by which bacterial genes can be transferred from
one bacterium to another.
o Bacteriophages can be used as clonning vector.
o Whole phage can be used as antimicrobial agents for eliminating
multidrug resistant bacteria.
 Genetic Variation
❖ Causes:
o The great diversity seen in different microorganisms is
due to two major factors:
1) The difference in DNA nucleotides' sequences that code
for different proteins. Different proteins result in
organisms with different properties.
2) The expression of genetic information that organisms
possess is regulated so that genes are turned off and on
depending on the particular environment.

❖ Alterations in genetic information:

o Genomes change by a variety of mechanisms including:
1) Mutation i.e. change in gene sequence or DNA sequence.
2) Gene transfer which occurs either within individual cell
(transposition) or between different cells.
3) Plasmids (extrachromosomal elements) provide
additional site for storage of genetic information.

I. Mutations
o They are heritable changes in the sequence of nucleotide
bases that alter the genome and introduce variability into
the gene pool.
o This may or may not have an effect on the phenotype
(physically manifested properties) of the organism.
 ❖ Mutations in the structure of genes can be classified as:

Point mutations Framshit mutation

•It is the exchange of a single nucleotide.

•These changes are called transitions or •It is exchange in more than one nucleotide.
trans-versions.
•The most common is the exchanges of
purine with purine (A« »G) or pyrimidine
with pyrimidine (C« »T). Types
•It is often caused by chemicals or •Insertions
malfunction of DNA replication. •It means add one or more extra
•It can be reversed by another point nucleotides into the DNA.
mutation. •They are usually caused by transposable
elements.
•Insertions can be reversed by excision of
Types the transposable element.
•Deletions
•Silent mutations: codes for the same amino
acid. •This means removal of one or more
nucleotides from the DNA.
•Missense mutations: codes for a different
amino acid. •Like insertions, these mutations can alter
the reading frame of the gene.
•Nonsense mutations: codes for a stop
codon. •They are irreversible.

II. Gene Transfer in Prokaryotes

o Gene transfer occurs either within individual cell (transposition)
or between different-cells.
o Successful gene transfer should be followed by recombination.

Gene transfer occurs between different cells

through:

a) Transformation: involves release of DNA into environment by

cell lysis followed by its direct uptake by the recipient cell.

b) Electroporation (transfection) is the application of an electrical

current across a cell membrane resulting in temporary "pore" formation
enabling the uptake of exogenous molecules found in the medium to either
cytoplasm (transient transfection) or into nucleus (stable transfection).

c) Transduction: involves transfer of (DNA) from donor to

recipient by bacteriophage.

d) Conjugation (Mating): involves plasmid mediated transfer by

direct wall to wall contact.
 Chapter (5)
Antimicrobial agents & Chemotherapeutic agents
& Antibiotics
❖ Definition:
o chemical agents that are used to treat diseases. It must kill
pathogenic (irreversible) microorganisms (bacteriocidal) or
inhibit (reversible) their growth (bacteriostatic) while damaging
host as little as possible.

❖ Selective toxicity:
o The ability of drug to target sites that are relative specific to
microorganism, essential to survival of microorganism.
o N.B: Penicillin inhibits bacterial cell wall peptidoglycan synthesis,
has little effect on host cells because they lack cell walls, TI is
high.

❖ Degree of selective toxicity can be expressed in terms of:

1) Therapeutic dose: drug level required for treatment.
2) Toxic dose: drug level at which agent become toxic to host.
3) Therapeutic index: ratio between toxic dose and therapeutic
dose.
 The larger (TI) the safer the drug, better chemotherapeutic
agent, higher selective toxicity.
 Drug A
- Therapeutic dose = 5mg
- Toxic dose = 50mg
- TI = 50÷5 = 10
‫ اضعاف الجرعه المعالجه يعنى لو مريض عاوز ينتحر‬10 ‫الجرعه القاتله تساوى‬ -
. ‫ حبايات مثال‬10 ‫ياخد‬
 Drug B
- Therapeutic dose= 5mg
- Toxic dose= 15mg
- TI = 15÷5 = 3
‫ اضعاف الجرعه المعالجه يعنى لو مريض عاوز ينتحر‬3 ‫الجرعه القاتله تساوى‬ -
. ‫ حبايات مثال‬3 ‫ياخد‬
 . (TI) ‫ كل ما زاد‬, ‫ كل ما كان الدواء آمن‬-

❖ An ideal antibiotic should be:

o Water soluble.
o Stable in blood stream.
o Easily taken up by cells.

❖ An ideal antibiotic shouldn't be:

o Toxic.
o Carcinogenic.
o Allergenic.
o Mutagenic.
o Teratogenic.

❖ Spectrum of antibiotics:
o Wide spectrum = broad spectrum
 They are active against broad spectrum of bacteria either
gram +ve or gram -ve e.g. ciprofloxacin, amikacin.
o Narrow spectrum:
 They are active against limited number of microorganisms
e.g. penicillin G, erythromycin.
o Specific spectrum:
 They are used for one or two microorganisms e.g. viomycin
and cycloserine are used only for TB.

❖ Classification of antibiotics according to mode of action:

1) Antibiotics act on bacterial cell wall.
2) Antibiotics act on protein synthesis.
3) Antibiotics act on chromosome function.
4) Antibiotics act on cytoplasmic membrane.
5) Folate antagonism.
❖ Cell wall synthesis:
o Cytoplasmic stage
 Synthesis NAG, NAM, 5 amino acids.
o Membrane stage (Transfer)
 Transfer peptidoglycan unit from cytosol to membrane by lipid
carrier.
o Extracellular stage (cross linking)
 Peptidoglycan units linked together by peptide bond.
 Transpeptidase enzyme: responsible for linking of newly
synthesized peptidoglycan with the existing one.
 D- carboxypeptidase enzyme: responsible for removing of
D- Alanine from pentapeptide of newly formed glycan strand.
 N.B: These two enzymes are called penicillin binding protein or
penicillin sensitive enzymes.

❖ Antibiotics act on cell wall:

o Structure of cell wall:
 Peptidoglycan units linked together by peptide bond.
 Peptidoglycan
NAM + NAG
 5 amino acids which are:
L- Ala
D- Glu
L- lys
D- Ala
D- Ala
o Antibiotics that inhibit cell wall:

β-lactams Non β-lactam

penicillin & cephalosporines D- cycloserine

•act at cross linking stage. •Act at cytoplasmic stage.
•They act on transpeptidase and •Used to treat TB ( mycobacteria).
D-carboxypeptidase enzymes, and inhibit •It bears a structural resemblance to D- alanine it
cross linking, so inhibit cell wall synthesis. bind instead of it and inhibit cell wall synthesis.

Vancomycin
•Act at transfer stage.
•Attach to last amino acid and prevent lipid
carier from transferring peptidoglycan to
outside, so prevent cell wall synthesis.
•Due to high molecular weight compound
shows poor penetration to gram negative and
only have useful activity aganist gram positive.
❖ Protein synthesis occur in 3 stages:
o Initiation.
o Elongation.
o Termination.

❖ Antibiotics that inhibit protein synthesis:

1) Aminoglycosides: prevent initiation of protein synthesis,
interfere selectivity of 30 subunits of ribosomes.
2) Tetracyclines: 30s-Initiation.
3) chloramphenicol: 50s -Elongation.
4) Erythromycin: 50s-Elongation.
5) Lincomycin & clindamycin: 50s-Elongation.
6) oxazolidine: initiation, disrupt translation of mRNA
 N.B: linezolid: act on gram positive bacteria.
7) fusidic acid: doesn't act on ribosome but one elongation factor.

❖ Antibiotics that act on chromosomes function:

1) Lopoisomerase = DNA gyrase enzyme
 It is unique to bacteria.
 Responsible for supercoiling of DNA.
 If we stop the action of this enzyme supercoiling won't occur
(negative supercoiling).
 Damage of DNA gyrase is irreversible due to absence of DNA
repair system.
2) RNA polymerase: responsible for transcription of mRNA from
DNA.

❖ Antibiotics that act on chromosomes function:

1) Quinolone carboxylic acids
 E.g. ciprofloxacin & norfloxacin
 Inhibit on DNA gyrase enzyme and inhibit replication

2) Metronidazole & nitrofurantoin

 Damage DNA / breakage of DNA.
 It is active against anaerobic bacteria.
  resistance to metronidazole doesn't occur because the action of
these antimicrobial agents is thought to be due to unstable
metabolites produced by reduction of bacteria after uptake.
 It isn't the active form, but it's metabolite.
3) Rifampicin
 Used to treat TB.
 Side effects: red urine.
 Inhibit action of RNA polymerase enzyme.
 Before initiation step.

❖ Folate antagonists:
o Folate is important in formation of nucleotide nitrogenous base
o Human source of folate is from diet, not formed inside body
o Bacteria synthesis folate by itself.

❖ Synthesis of folate in bacteria:

❖ Antibiotics that inhibit folate synthesis:

1) Sulfonamides: inhibit synthetase enzyme.
2) Trimethoprim: inhibit reductase enzyme.
❖ Difference between bactericidal and bacteriostatic:
o Bactericidal antibiotics: kill pathogen.
o Bacteriostatic antibiotics: inhibit bacterial growth.
 N.B: Don't give bacteriostatic antibiotics to
immunocompromised patients.

❖ Types (classification) of Antibiotic:

o Bacteriostatic antibiotics
a) Tetracycline.
b) Macrolides.
c) Chloramphenicol.
d) Glycopeptide antibiotic.

1) β-lactam antibiotics
 Bactericidal.
 Inhibit cell wall synthesis.
 Safe in pregnancy.
 Examples:
1. Penicillins
 Penicillin G, methicillin, oxacillin, Amoxicillin
2. Cephalosporines
 First generation
cefalexin, cefadroxil
 Second generation
cefaclor, cefuroxime
 Third generation
cefixime, ceftriaxone, cefotaxime, cefoperaxone
 Fourth generation
Cefepime - fifth generation Ceftobiprole, ceftaroline
3. Clavams
 B- lactamase inhibitor.
 Has no antibacterial action, not antibiotic.
 Must be used in combination.
 It's a combination of clavulanic acid with amoxycillin
this is known as Augmentin.
2) Tetracycline antibiotics
 Bacteriostatic
 Inhibit protein synthesis
 Broad spectrum
 Examples:
 Tetracycline & Doxycycline
 N.B: Tetracycline act on gram positive & gram-negative
bacteria except (ps. aeruginosa).
 Ps. Aeruginosa: gram negative bacteria target
immunocompromised patients, patients with burns
Treatment: car-penicillin.
 Doxycycline: treatment of acne.

3) Rifamycins
 Bactericidal
 Inhibit RNA polymerase enzyme
 Example: Rifampicin
 Treatment of TB
 N.B: TB infect respiratory tract, complications: infect brain
and cross blood brain barrier and get into CFS.
 It's active orally
 It penetrates into cerebrospinal fluid and used in treatment
of TB meningitis.

4) Aminoglycosides
 bactericidal
 Inhibit protein synthesis
 Broad spectrum
 Examples: (GPS TAN)
1. Gentamycin
 It is often administrated in conjunction with
car-penicillin to delay development of resistance.
2. Paromomycin
 Treatment of intestinal amoebiasis.
3. Streptomycin
4. Tobramycin
 5. Amikacin
 spray antibiotic, topical
6. Neomycin
 It's poorly absorbed from GIT when given orally, usually
used in the form of lotions & ointments for topical
application against skin and eye infection.

5) Macrolides
 Bacteriostatic
 Inhibit protein synthesis
 Examples:
1. Erythromycin
 Active against gram positive bacteria as Neisseria and
Haemophilus influenzae (respiratory tract) but not
‫ر‬
against Entrobacteriaceae ‫البكتيا المعوية‬
 Treat acne
2. Spiramycin
 used in treatment of toxoplasmosis (cat transmitted
disease) cause abortion in first trimester
 safe in pregnancy
3. Azithromycin, clarithromycin

6) Glycopeptide & lipoglycopeptides antibiotics

o Glycopeptide antibiotics
 Bacteriostatic
 Example:
 Vancomycin (life saving drug)
 Active against gram positive bacteria and not active
against gram negative due to its high molecular weight.
 Treat (MRSA) (mecicillin resistant staphylococcus
aureus).
o Lipoglycopeptides
 Bactericidal
 Inhibit protein synthesis
 Example:
 Telavancin
 7) Chloramphenicol
 Bacteriostatic
 Inhibit protein synthesis
 Broad spectrum
 Treatment of typhoid fever
 Side effects & complications: aplastic anemia
 Contraindicated with children

8) Synthetic antimicrobial agents

o 4-quinolone antibacterial drug
 Bactericidal
 Inhibit DNA gyrase enzyme
 Used in conjunction with b- lactam or Aminoglycosides
when severe neutropenia is present.
 Second generation: Norfloxacin, ciprofloxacin, pefloxacin
 Third generation: Levofloxacin, moxifloxacin
 Fourth generation: Gemifloxacin
o Imidazole derivatives (metronidazole)
 Bactericidal
 Damage DNA
 Inhibit growth of pathogenic protozoa
 Used in dentistry against anaerobic bacteria that cause
abscess
 No resistance

❖ Bacterial Resistance to Antibiotics:

o The spread of drug resistant pathogen is one of the most serious
threats to the successful treatment of microbial disease.
o The antibiotic resistance is the acquired ability of an organism to
resist the effects of an antibiotic to which it is normally
susceptible.
❖ Classification of antibiotics resistance:
A. Inherent Resistance:
o Certain bacteria are more or less resistant to some antibiotics
due to:
1) Impermeability
 Gram-negative bacteria are inherently resistant to a
number of antibiotics that are very effective against
Gram-positive organisms due to the impermeability of
the complex outer layers of cell envelope to these drugs.
2) Lose of Target Structure
 The organism may lack the structure an antibiotic
inhibits.
 Some bacteria, such as Mycoplasma, lack a typical
bacterial cell wall and are resistant to penicillin.
3) Metabolic Inactive Cell
 Most antimicrobial agents are active on replicating cells.
 Mycobacteria survive for many year in tissue yet are
restrained by the host’s defence and do not multiply.
 Such organisms are resistant to treatment.
 When they start to multiply, they are susceptible to
drugs.
4) Existing of Different Metabolic Pathways
 When the antibiotic’s target is an enzyme in certain
metabolic pathway, sometimes the microorganism can
obtain their end-product metabolite by switching to
another metabolic pathway in which the enzymes are not
susceptible to that antibiotic.
5) Conversion of an active drug to non-toxic derivative
 As inactivation of β-lactams Antibiotics by
β-lactamases.
B. Acquired Resistance:
o When a new antibiotic is introduced into clinical practice for
treatment of infections caused by bacteria that are not
inherently resistant to the drug, the majority of infections
respond to the new drug, but after months or years of
continuous use, reports often appear describing treatment
failures caused by infections by strains of bacteria that are
resistant to the drug.
❖ Appropriate solution for the antibiotic resistance
problem:
o Limitation of antibiotics uses.
o Overcome the cross-infection.
o Development of the existing antibiotics or new antibiotics.
o Usage of combination chemotherapy.

❖ Clinical uses of antibiotics:

o The proper choice of antibiotic drug for treatment of
infectious disease requires good knowledge and
information about:
1) The susceptibility of the infecting organism to different
antibiotics.
2) Host factors (immunity, hypersensitivity).
3) Pharmacological factors
• absorption, distribution, metabolism & excretion of the
drug.
4) Antibiotic resistance.
5) Adverse reactions.
6) Super-infection due to the overuse of antibiotics as
occurrence of oral or vaginal candidiasis in patients treated
with broad-spectrum agents such as ampicillin or tetracycline.
7) Antibiotic drug combinations that may result in:
• Synergism: where microbial inhibition is achieved at
concentrations below that for each agent alone.
 The antibiotics in the combination have different
mechanism of action or different structure. e.g.
penicillin and gentamycin.
• Indifference: microbial inhibition is achieved at
concentrations below that for each agent alone. The
antibiotics in the combination have the same mechanism
of action and/or the same structure.
 e.g. Two antibiotics from penicillin family, or penicillin
and cephalosporine.
 • Antagonism: in this case the presence of an antibiotic
interferes with the action of another.
 For example, combination of a bacteriostatic and
bactericidal as Penicillin and tetracycline or
chloramphenicol where penicillin act on growing
organism that require formation of new cell wall while
the bacteriostatic will inhibit the growth and hence
reduce the action of penicillin.

❖ Adverse reactions of antibiotics:

1) Hypersensitivity reactions:
 Fatal anaphylaxis, in which there is widespread tissue
oedema, airway obstruction and cardiovascular collapse. e.g.
penicillin.
 Minor and reversible hypersensitivity reactions such as skin
eruptions and drug fever. e.g. sulfa drugs.
 Cephalosporins should be used with caution in patients
allergic to penicillin since these agents are structurally
related.

2) Drug toxicity:
 It is often dose-related and may affect a variety of organs or
tissues.
 Aminoglycosides are both nephrotoxic and ototoxic.
 Chloramphenicol induces bone marrow suppression and
interferes with the normal maturation of bone marrow stem
cells and its high concentrations may result in a steady fall in
circulating red and white blood cells.
 Sulphonamid or Primaquine cause haemolysis in patients
those deficient in the red cell enzyme glucose-6-phosphate
dehydrogenase.
❖ Antibiotic Policies:
o An antibiotic policy should ensure that the unnecessary use
(i.e. abuse of antibiotics or the absence of clear indications)
should be avoided for many reasons as:
 To prevent the emergence of antibiotic resistance.
 To reduce the coast of antibiotic use.
 To prevent antibiotic toxicity.

❖ Antibiotic Non-Antimicrobial Agents:

o A number of chemicals are rapidly germicidal and can be used to
disinfect surfaces they include:

1) Disinfectant:
 Chemical disinfectants must be capable of making articles
safe from infection, i.e. destroying pathogenic organisms,
which in practice requires rapid bactericidal action.
 They are usually not sporicidal.
 Disinfectants are used to treat inanimate objects and
materials and some are suitable for the treatment of skin and
other body membranes and cavities.
 Examples: Phenols, Alcohols, Halogen.

2) Antiseptic:
 Antiseptics must be capable of preventing sepsis.
 They are used for application to skin and mucous membranes.
 They must be non-toxic.
 Examples: Iodine.
By: Mohamed Elebs Microbiology
Immunology
 Chapter (1)
Host-Parasite Relationship

o Ecosystem is a community of living organisms in conjunction

with the non-living components of their environment (things like
air, water and mineral soil), interacting as a system through
nutrient cycles and energy flows.
o Ecological relationships: are the relationships between
organisms in an ecosystem.
o Symbiosis: is defined as "life together" i.e. the relationships
between two organisms living in an association with one
another.
❖ Types of ecological relationships (symbiosis):
1) MUTUALISM (+/+): mutually beneficial relationship between two
species, as normal bacterial flora and synthesis of vitamins K in
humans.
2) COMMENSALISM (+/0): relationship between two species in
which one gets benefit and the other is not affected, neither
negatively nor positively, as microbial flora living on skin.
3) PARASITISM (+/-): relationship between two species in which
one gets benefits (parasite) and the other (host) is harmed; as
pathogenic infection.

Infection and Disease

o Infection is defined as invasion and multiplication of pathogenic
microorganisms in a body part or tissue.
It may progress to tissue injury and overt disease or not.
❖ Steps of infection:
1) Entry of the parasite into the host: The most frequent portals
of entry are the respiratory tract, gastrointestinal tract, skin
and/or mucous membranes.
2) Establishment and multiplication of the parasite: Denotes the
ability of microorganism to adhere and colonize body surfaces
 to avoid the leaching out effect of body secretions or the
peristaltic movement of the intestine. Adhesion and
colonization are favored by pili on the surface of the
microorganism.

o Disease means tissue injury and manifestations following

infection. It is an abnormal condition of body function(s) or
structure that is considered to be harmful to the infected
individual (host).
o Contagious disease (communicable; infectious): means disease
that is easily or rapidly transmitted from one host to another.
o Morbidity means illness while Mortality means death.
o Epidemiology means the incidence and prevalence of the
disease. It can be:
• Endemic: i.e. usually present or prevalent in a population or
geographic area at all times.
• Epidemic: i.e. occurs suddenly in large number beyond
normal expectancy.
• Pandemic: i.e. a widespread epidemic occurs widely tin many
regions, countries, continents or globally.

❖ Types of micro-organisms:
1) Commensal which is harmless microorganism as the normal
microbial flora found on skin and mucous membranes.
2) Opportunistic (potential pathogen) which is a usually harmless
microorganism but becomes pathogenic under favourable
conditions (immune-compromised rands hosts) causing an
opportunistic infection.
3) True Pathogen: is any microorganism capable of causing disease;
an infecting agent. These pathogens must infect a host in order
to survive.
4) Saprobe: a microbe that lives on dead or decaying organic
matter.
❖ Properties of true pathogen:
1) Infectivity: it is the ability of a microorganism to cause infection
(i.e. has a portal of entry to the host, can grow and multiply
within the host).
2) Pathogenicity: it is the ability of a microorganism to cause
disease in another organism, namely the host for the pathogen.
This capacity to initiate disease depends on its number, growth
phase and virulence factors.
3) Virulence: it is the degree of pathogenicity of the organism
which depends on the ability to produce toxins and/or enzymes
and its invasiveness.

❖ Virulence factors:
• They are structures or molecules produced by pathogens
(bacteria, viruses, fungi and protozoa) that help
micro-organism to overcome the body defence mechanisms
and promote establishment and maintenance of disease.
• Determinants of Virulence are the overall characteristics that
allow a given bacterium to produce disease.

❖ Examples of virulence factors:

1) Specific attachment & entry factors.
2) Enzymes.
3) Capsules.
4) Exotoxins.
5) Endotoxins.
 Specific attachment &
Enzymes Capsules
entry factors

•Pathogen must be able to bind to •Many bacteria have specific enzymes •Many pathogens have capsules as
some receptor molecule on cell that allow them to penetrate host pneumococci that inhibit
surfaces. tissues as Collagenase, produced by phagocytosis, prevent quick disposal
Clostridium perfringens, degrade of bacterium by WBCS.
collagen present in connective tissue
(25% of body's protein) and allow
•Pili are used by some bacteria to penetration into tissues.
attach selectively to certain tissues. •Loss of capsule typically causes loss of
infectivity.

•Some pathogens secrete Leukocidins

that specifically kill WBCS.

•Staphylococcus. aureus produces

Coagulase enzyme that coagulates
blood.

Exotoxins Endotoxins

•Most exotoxins are proteins, secreted from cell, often •Endotoxins (as LPS, lipopolysaccharide) are integral parts
damaging tissues at some distance. of Gram-negative outer membrane.
•Very potent, very toxic even at low concentration.
•Often coded by plasmid DNA (E. coli) or lysogenic phage •Unlike Exotoxins, they are typically heat resistant, active
DNA (botulism, diphtheria). only in sizable amounts, and remain bound to cells.
•Almost always inactivated by heat.
•Most are good antigens when inactive, can make toxoids •Mechanism of action is very diverse, including fever,
(antigens without poison activity) = strong immune decrease in iron, inflammation, blood clotting, reduced
response. sugar in blood, etc. Most important clinical problems are
fever and shock.

•Typical scenario: Gram -ve bacteria (e.g. E. coli,

Examples Pseudomonas) enter body via clinical procedure
•Diphtheria toxin: (improperly sterilized kidney dialysis, catheter, etc.), cause
sudden decrease in blood pressure (hypotension) →"septic
•from Corynebacterium diphtheriae.
shock" and could be lethal.
•Enters cell, inactivates elongation factor needed for
protein synthesis → cell gradually loses ability to make
proteins.
•Botulinum toxin:
• a neurotoxin (attacks nervous system) from Clostridium
botulinum.
•Most potent toxin known since 1 gram could kill 10
million people.
•Toxin interferes with synaptic transmission at
nerve/muscle junctions which in turns leads to flaccid
paralysis.
•Occurs most typically in canned foods that are not
cooked long enough.
•Tetanus toxin:
•another neurotoxin from Clostridium tetanus.
•Blocks synaptic transmission to inhibitory neurons
needed to relax one muscle when the other in paired
muscle contracts, leads to rigid paralysis.
 ❖ comparison between exotoxins and endotoxins

Exotoxins Endotoxins

Excreted by living cells Integral part of cell wall of G-ve bacteria

Produced mainly by G+ve and some G-ve

bacteria Found in G-ve bacteria only

Polypeptides Lipopolysaccharide

Relatively heat unstable & rapidly destroyed by Relatively heat stable

heat > 60 °C

Highly immunogenic weakly immunogenic

Can be used in vaccines Cannot be used in vaccines

Highly toxic less toxic

Bind to specific receptors on host cells No need to specific receptors on host cells

Don't produce fever usually produce fever

 Chapter (2)
Immune response (Immunity)
❖ Definitions:
o Immunology
 It is a science that examines the structure and function of the
immune system.
 It is the study of the organs, cells, and molecules responsible
for the recognition and disposal of foreign substances.
o An immune system
 It is a collection of mechanisms within an organism that
protects against disease by identifying and killing pathogens
and tumor cells.
 It detects a wide of agents, from viruses to parasitic worms,
and needs to distinguish them from variety the organism's
own healthy cells and tissues in order to function properly.
o Immunity
 It is concerned with the recognition and disposal of
foreign or "non-self" material that enters the body.

❖ The immune system is divided into two functional

divisions:

The immune system

Natural Adaptive
(innate or non-specific) (acquired or specific)
immune response. immune response.
I. Innate (non-specific or natural) immunity:
o Definition of innate immunity  It refers to the basic
resistance to disease that a species possesses or the first
line of defense against infection.
 It provides an immediate, but non-specific response
against pathogens.
o However, if pathogens successfully evade the innate
response, the adaptive immunity will be activated.
This immune response is then retained after the
pathogen has been eliminated, in the form of an
immunological memory, and allows the adaptive
immune system to mount faster and stronger attacks
each time this pathogen is encountered.
o The characteristics of the innate immune response
include the following:
 Acts immediately as the first line of defense against
infectious agents.
 Responses are Broad-Spectrum (non-specific).
 There is no memory or lasting protective immunity.
 Such mechanisms are present since birth.

❖ Mechanisms of innate immunity:

1) Anatomic & mechanical barriers.
2) Physiologic barriers.
3) Chemical barriers.
4) Phagocytic barriers.
5) Inflammatory barriers.
Anatomic & Mechanical
Physiologic barriers Chemical barriers
barriers

include include include

•Skin: •Temperature: •Fatty acids and bacteriocins
•(physical barrier, low pH due to •normal body temperature inhibits produced by normal flora inhibit the
lactic and fatty acids). growth of most microorganisms. growth of many pathogens.
•Epidermis: •HCL and protein-digesting enzymes
•Thin outer layer containing tightly •pH: as pepsin in stomach.
packed epidermal cells and keratin •low pH of stomach, skin & vagina •Lysozymes (hydrolytic enzyme)
(water-proofing) completely (inhibits microbial growth). found in saliva, lacrimal fluid and
renewed every 15-30 days. mucous secretions are able to
•Dermis: cleave the peptidoglycan layer of
the bacterial cell wall
•Thicker inner layer contains
sebaceous glands associated with •Interferons:
hair follicles produce sebum which •group of proteins produced by cells
consists of lactic and fatty acids following viral infection. Secreted
maintaining a pH 3-5. by the cells, and then binds to
•Mucous membranes nearby cells and induces
mechanisms which inhibit viral
•(ciliated epithelial cells) gastro-
replication.
intestinal, urogenital, respiratory
tracts collectively represent huge •Complement:
surface area. •a group of serum proteins that
•Cilia circulate in an inactive state.
•sweep dust and bacteria away •These proteins can be activated by
from lower respiratory passages. a variety of specific and non-
specific immunologic mechanisms
•Coughing/ sneezing.
that convert the inactive form into
•Tears & urination. active enzymes.
•The activated complement
components participate in a
controlled enzymatic cascade that
results in membrane-damaging
reactions which destroy pathogenic
organisms by formation of a
membrane attack complex (MAC).
 Phagocytic barrier Inflammatort barrier
(Phagocytosis) (Inflammation)

Definition Definition
•Phagocytosis means ingestion of particulate material •It is the tissue response to injury is triggered whenever
including whole pathogenic microorganisms. body tissues are injured.

Types of Phagocytic cells Cardinal signs of acute inflammation

•Professional phagocytes: •Redness
•macrophages, monocytes, neutrophils & dendritic cells. •Heat
•Non-professional phagocytes: •Swelling
•fibroblasts and epithelial cells. •Pain.

Steps of phagocytosis
•(i) Chemotaxis:
•movement of leukocytes towards the site of infection
due to chemical stimulus.
•(ii) Binding:
•phagocytes adhere to foreign particles or
microorganism.
•(iii) Engulfment:
•ingestion of the microbe by the pseudopodia forming
phagosome.
•(iv) Phagosome:
•fuse with intracellular lysosome
(contain digestive enzymes) forming phagolysosome.
•(v) Intracellular Killing of foreign particles:
•Through oxygen radicals (i.e. superoxide or hydrogen
peroxide) and nitrogen radicals (nitric oxide).
• Then Processed antigen are extruded outside the cell
by exocytosis.
•This is required to activate the acquired immunity i.e.
this step is a link between innate and adaptive
immunity.
II. Adaptive (Acquired or specific) immunity:

➢ Main characters of adaptive immunity:

 Antigenic specificity.
 Diversity.
 Immunologic memory.
 Self/non self-recognition.

➢ Functionally, adaptive immunity includes:

 Primary immune response (IR): it develops against an
antigen within five or six days after the initial
exposure to that antigen.
 Secondary immune response: it develops with
re-exposure to the same antigen in the future. It is
mainly due to presence of memory cells. It is
characterized by being faster, stronger & more
effective in neutralizing & clearing pathogen than the
primary IR.

➢ comparison between primary & secondary

immune response:
 ➢ Main components of adaptive immunity:

Components of adaptive
immunity

Antibody mediated
Cell mediated immunity
(cellular immune response)
immunity
(Humoral immune response)

Cell mediated immunity Antibody mediated immunity

(cellular immune response) (Humoral immune response)

• It is the main function of T-lymphocytes. • It is the main function of B-lymphocytes.

• T-cells produce their effect either directly through • B cells interact with antigen then differentiate into
cell to cell contact via cytotoxic T lymphocytes antibody-secreting plasma cells. The secreted
(CTLS) or indirectly through the secretion of antibody are dissolved in the body fluids (blood,
chemical signals (cytokines from TH cells) to lymph, .etc).
control other immune cells.
• Antibodies defend the body primarily against
• The cell-mediated immune response is most bacteria, bacterial toxins, and viruses present in
effective against bacterial and viral infections body fluids (i.e. extracellular infection).
located within cells (i.e. intracellular infection).
 ➢ Main events in adaptive immune response:
1) Antigen processing & presentation: Antigen presenting
cells (as macrophages) take up Ag & breaks it into
small fragments to present them with MHC-I & MHC-II
2) Activation of helper T-cells: When they recognize Ag
presented with MHC-II they secret cytokines (IL-2, IL-4,
IL-6) to activate other immune cells.
3) Activation of cytotoxic T-cells: When they recognize Ag
presented with MHC-I, they secret cytokines that kill
target cells.
4) Activation of B-cells & their differentiation into plasma
cells that secrete Igs.

❖ Comparison between humoral and cellular immunity

❖ Comparison between Innate and Adaptive immunity:
 Chapter (3)
Organs and cells of immune system

o The immune system consists of a number of organs and different

cell types which have evolved to accurately and specifically
recognize 'non-self' antigens found on microorganisms or foreign
cells to eliminate them.

❖ Organs of immune system are classified into:

Classification of organs of
immune system

Peripheral or secondary
Central or primary lymphoid tissue
lymphoid tissue (lymph nodes, spleen and
(bone marrow, thymus) mucosa-associated lymphoid
tissue "MALT")

❖ Cells of immune system:

o All the cells of the immune system and RBCS arise from
haemopoietic stem cells, which differentiate into three main
lines:
1) Common lymphoid progenitor: producing lymphocytes &
NK cells.
2) Common myeloid progenitor: producing granulocytes and
phagocytes.
3) Common erythroid progenitor: producing RBCS.
❖ Cells of the immune system can be differentiated
according to the presence of cytoplasmic granules into:
 Granulocytes: Neutrophils, Eosinophils, Basophils, mast cells
and NK cells.
 Agranulocytes: Monocyte, Macrophage and lymphocytes.

❖ Cells of the immune system can be divided according to

their function into:

Cells of the immune

system
(according to their function)

Cells involved in innate

immunity Cells involved in acquired
(Phagocytic cells, immunity
Inflammatory cells, Natural (APC, B-cells, T-cells)
Killer Cells)
  Cells involved in innate immunity:

Phagocytic cells Inflammatory cells Natural Killer Cells

Monocyte Mast cells NK cells

•The largest nucleated cell of the •Round central nucleus surrounded by •A small, distinct group of large
blood, developing into a macrophage large darkly stained granules. granular lymphocytes.
when it migrates into the tissues. • They reside in connective tissues
and mucous membranes. •They represent a first line of
•They are most often associated with defense to infections, tumor growth
Macrophage allergy and anaphylaxis by releasing and other pathogenic alterations of
•The main phagocytic cells fixed cells histamine. tissue homoeostasis because they
in tissues and serous cavities such as non-specifically kill any cancerous or
the pleura and peritoneum. virus-infected cells by releasing
• They have different names in Eosinophils perforins & cytolytic chemicals.
different tissues e.g. Kupffer cells in •Cells with multi-lobed nuclei and
liver, Langerhans cells in skin and eosinophilic (red) cytoplasmic •They do not express antibodies or T
mucosa, osteoclasts in bone, granules. cell receptors at their cell surface.
microglia in CNS, ...etc. •They are involved in allergic
• They are important link between reactions and killing of larger • MHC I inhibits their killing
innate and acquired immune parasites including helminthes. functions.
responses.

Neutrophil Basophils
•Cells with heavily stained blue
•Known as polymorphonuclear
(basophilic) granules that contain
leukocytes.
heparin and vasoactive amines,
• The commonest leukocytes of the important in the inflammatory
blood. response.
• A short-lived phagocytic cell whose •They also secrete the chemicals
granules contain numerous responsible for immediate
bactericidal substances. hypersensitivity.
  Cells involved in acquired immunity:
Antigen presenting cells
B-cells (B-lymphocytes) T-cells (T-lymphocytes)
(APCS)

•As dendritic cells and macrophages. •30% of circulating lymphocytes. •70% of circulating lymphocytes.
•They mature completely in the bone •They arise in bone marrow but
•Dendritic cells are located mainly in marrow in mammals or Bursa of mature in the thymus
the skin, nose, lungs, stomach, and Fabricius in birds (thus, designation "T").
intestines. (hence, the designation "B"). •They are responsible for
•They have antibody molecules on cell-mediated immunity.
•They are the most potent and their surface. •They recognize peptide fragments of
efficient antigen presenting cells •They are concentrated in lymph antigen complexed with cell surface
(APCS). nodes cortex where they can contact Major Histocompatibility Complex
Ags. (MHC) glycoproteins on
•They serve as a link between the neighbouring cells.
innate and adaptive immune.
Types of B-cells
(after antigen exposure( Types of T-cells
•Plasma cells (Ab-secreting cells): •Helper T (Th) Cells: CD4+ T cells
• They are seldom seen in the blood •They recognize antigen complexed
since they live for only several with MHC-II molecule.
days but are found in spleen and •Helper T-cells also release a variety
lymph nodes. of cytokines (lymphokines). These
cytokines important in regulating
•Memory cells: the function of lymphocytes.
•They are long-lived and may •Cytotoxic T (Tc) Cells: CD8+ T cells
remain in the cortical area for •Cytotoxic T-cells recognize
years. antigens bound to MHC-I. Once
•They are responsible for activated, Tc cell secretes a protein
immunological memory, on called perforin, which makes a
re-stimulation with Ag, memory hole in the cell membrane, causing
cells quickly proliferate to produce the cell to lyse and die.
more memory cells and plasma •Cytotoxic T-cells kill cells that have
cells. been infected with viruses or
intracellular bacterial pathogens,
and some tumor cells.
•Regulatory T (Treg) Cells:
•Once an immune response is
initiated, it is important that it not
be continued beyond the point
where it is of use to the host.
•Overproduction of antibodies
could cause great damage to the
body. Thus, some means of
regulation must be available.
•Regulatory T-cells help to regulate
the immune response by inhibiting
the conversion of B-cells to plasma
cells and suppressing the activity
of T cells.
•Delayed Hypersensitivity T (TD)
Cells:
•They participate in cell-mediated
reactions but do not interact with
B-cells.
•TD cells are responsible for
recruiting and activating
nonspecific effector cells such as
phagocytes.
 Chapter (4)
Cytokines
o The cells in the immune system must communicate, and one
method for doing this is through a number of soluble
proteins known as cytokines.
o Cytokines are a group of soluble proteins that regulate
cellular functions.
o Specialized cytokines produced by lymphocytes are
sometimes known as lymphokines.
o Many of the cytokines are designated interleukins (ILs)
because they are molecules that mediate interactions
between leukocytes. For example:
a) IL-1 is secreted by macrophages (which are responsible
for antigen uptake, processing, and presentation) and
acts on several cell types including Th cells.
b) IL-4 and IL-6 act primarily on B-cells.
c) Interferons (IFN-α and IFN-) are produced by leukocytes
and inhibit viral replication in nearby cells.
d) Tumor necrosis factors (TNF-α and TNF-β) are capable of
destroying tumors.
 Complement system
o It is a biochemical cascade which helps to clear pathogens.
o It belongs to the innate immune system.
o Over 25 proteins and protein fragments make up the
complement system, found in the blood, normally
circulating as inactive components.
o When stimulated by one of several triggers, proteases in the
system cleave specific proteins to release cytokines and
initiate amplifying cascade of further cleavages.
o The end result of this activation cascade is activation of the
cell-killing membrane attack complex.

❖ Functions of the complement:

1. Opsonization: They coat foreign organisms to enhance their
phagocytosis by means of binding to specific complement
receptors.
2. Inflammation: The C5a, C4a and C3a fragments are
important inflammatory activators inducing vascular
permeability, recruitment and activation of phagocytes.
3. Lysis: by the Membrane Attack Complex (MAC).
4. Immune complex clearance: Complement solubilize and
remove immune complexes from the circulation.