YARMOUK UNIVERSITY (2020)

By: Yousef Alzoubi

Lecture # 1
Microbiology in the biological world - indogenous microbiota (microflora) which are
harmless and live in & on our bodies and provides
 Microbiology : is the study of very small living
benefits . (10 times the # of body cells )
organisms , which cant be seen by naked eyes .
 Microbes are ubiquitous (presents everywhere) and
- opportunistic pathogens : they are non pathogenic
we use microscopes to study them .
under normal circumstances but have the
 Microbes involve ( bacteria, viruses , fungi , archaea ,
potential to cause diz in certain cases .( ex ;
protozoa , algae )
immunosuppressed patients)
 Superficially, bacteria appear to be simple forms of
 Why we Study Microbiology?
life; in fact are sophisticated and highly adaptable.
- Microbes produce oxygen more than plants (algae
 Microbes are divided according to pathogenicity (
and cyanobacteria a group of photosynthetic
causing diseases) into :
bacteria that produce oxygen)
1) Pathogens : only 3% of microbes can cause
- Microbes are involved in the decomposition of
diseases
dead organisms and the waste products of living
2) Nonpathogens : 97% of microbes cant cause
organisms into nitrates & phosphates and other
diseases .
chemicals which aid in soil fertilization ( we call
 Pathogens cause two major types of diseases :
them decomposers or saprophytes)
1) infectious diseases ; the pathogen colonizes the
- Microbes are capable of decomposing industrial
body and cause the diz
wastes (oil spills).
2) microbial intoxications ; pathogen produces
- Many microbes are involved in elemental cycles,
toxin outside the body and the ingested toxin
e.g: nitrogen cycle (nitrogen fixing bacteria )
causes the diz
- Algae and bacteria serve as food for tiny animals.
 nonpathogens include :
 - Microbes produce valuable substances to the host
e.g: E. coli produce vitamins K and B1 (thiamine)  Spontaneous generation theory (abiogenesis) ; life
- Microbes have been used as “cell models. E. coli is can arise spontaneously from nonliving material (
the most studied model of bacteria and its an this theory was believed in the past)
example of opportunistic pathogen ( normally  theory of biogenesis : life can only arise from
found in intestines but if it gain access to bladder preexisting life.
or blood it will cause an infection )  Francesco Redi try to debunk (disprove) the
- Many microbes are essential in various food and spontaneous generation theory by simple
beverage industries experiment
- Some bacteria and fungi produce antibiotics that
are used to treat patients with infectious diseases
- Microbes are essential in the field of genetic
engineering. ( inserting some genes in bacterial or
yeast cells to produce certain proteins ex; insulin)

Pioneers in the Science of Microbiology :

 Van Leeuwenhoek: first person using magnification

Glass (simple microscope) to identify bacteria and
describe their shapes but didn’t associate them
with dizs ; he is considered the father of
microbiology and bacteriology and he wasn’t a
scientist but a fabric merchant .
 Francesco redi experiment was disapproved by
another scientist due to design problem as some
maggots had pierced the mesh plate to meat
 Louise Pasteur (French chemist) father of medical
microbiology designed a valid experiment (Swann
neck) and disproved the sponateous generation
theory
 pasteur defined disease specifity (specific microbe
can cause specific disease in specific organ) , ex;
Ecoli infects urethra as it has receprtors there but
cant cause infection in lungs if it reach there .
 Pasteur introduced the terms “aerobes : microbes
which live in presence of o2 ” and “anaerobes :
microbes which live in the absence of o2 ”
 Pasteur made significant contributions to the germ
theory of disease " specific microbes cause specific
diseases"
 Pasteur discovered bacillus anthracis ( anthrax )
 Pasteur lead changes in hospital practices to
minimize the spread of disease by pathogens.
 Pasteur developed Pasteurization : sterilization
process using middle to high temp for a short time
to kill pathogens in liquids "kills only pathogens not
all microbes" ex; spore formers not killed
 Pasteur developed vaccines for prevention of:
- chicken cholera
- anthrax
- swine erysipelas ( skin disease)
- rabies
 Robert Koch :
 Koch’s Postulates: proof of the germ theory
of disease
1) The microorganism must always be found in
similarly diseased animals but not in healthy ones.
2) The microorganism must be isolated from a
diseased animal and grown in pure culture
3) The isolated microorganism must cause the
original disease when inoculated into a susceptible
animal
 4) The microorganism can be reisolated from the
experimentally infected animal.
 Koch discovered that B. anthracis produces spores
(virulence factor)
 Koch developed methods of cultivating bacteria on
solid media and grow bacteria in pure lab cultures
 Koch discovered the bacterium (M. tuberculosis) that
causes tuberculosis and the bacterium (Vibrio
cholerae) that causes cholera.
 Koch’s work on tuberculin which is a purified protein
from MTB used as skin test to diagnose TB
 Koch won a Nobel prize in 1905 for his work in TB
Medical microbiology-past triumphs :
 Golden Age of microbiology 1875-1918, most
pathogenic bacteria were identified
 10 million died of small pox ( ‫ ) الجدري‬in the past, but
as a result of vaccination no cases have been
reported since 1977
 In 1346-1350, 1/3 of the entire population of Europe
died from bubonic plague ‫الطاعون‬
 The discovery of antibiotics provided an important
weapon against bacterial diseases
 Human pathogens have existed for thousand of years
because damage caused by them has been observed
in the bones and internal organs of mummie and
early human fossils.
Medical microbiology- future challenges :
 The importance of medical microbiology as an active
field of research
 Respiratory infections and diarrheal diseases are the
leading causes of illness and deaths
 Diseases that were attributed to other causes have
now been shown to be caused by microorganisms
ex;" peptic ulcer " 90% of the causes of peptic ulcer
are from H.pylori the only microbe that survive
stomach acidity
 New diseases continue to arise ex; legionnaires
disease, AIDS, toxic shock syndrome
 Many infectious diseases started to increase again i.e
international traveler incubating a disease in his body
could theoretically circle the globe, such diseases as
malaria,cholera, plague still exist, these diseases have
been eliminated through sanitation, vaccination and
quarantine ;(
 Control the vaccination of childhood diseases
(measles,mumps, whooping cough) as lax in some
families of having their children vaccinated could
lead to dramatic increase in number of infected
people (reemergent diseases)
 TB has increased worldwide and thousands of cases
are reported annually, these new cases of TB is
resistant to the drugs that once effective in curing
the disease
 world wide top causes of death from infectious
diseases :TB, diarrheal diz , respiratory diz ,HIV
careers in microbiology :
 Medical Microbiology : This branch deals with
microbes that cause diseases in humans and animals.
Researchers examine factors that make the microbes
virulent and mechanisms for inhibiting them.
 Public Health Microbiology and Epidemiology : These
branches monitor and control the spread of diseases
in communities
 Immunology : This branch studies the complex web
of protective substances and cells produced in
response to infection. It includes such diverse areas
as vaccination, blood testing, and allergy
 Agricultural Microbiology : This branch is concerned
with the relationships between microbes and
domesticated plants and animals.
Plant specialists focus on plant diseases, soil fertility,
and nutritional interactions.
Animal specialists work with infectious diseases and
other associations animals have with
microorganisms.
 Industrial Microbiology : This branch safeguards our
food and water, and also includes biotechnology, the
use of microbial metabolism to arrive at a desired
product, ranging from bread making to gene therapy.
Microbes can be used to create large quantities of
substances such as amino acids, beer, drugs,
enzymes, and vitamins
 Environmental Microbiology :These microbiologists
study the effect of microbes on the earth’s diverse
habitats. Whether the microbes are in freshwater or
saltwater, topsoil or the earth’s crust, they have
profound effects on our planet.
Done
Questions : c. Most microbes are harmful to humans

1. Which of the following individuals is considered to be d. Pasteur conducted experiments that proved the
the “Father of Microbiology?” theory of abiogenesis

a. Anton van Leeuwenhoek b. Louis Pasteur 5. Which of the following individuals introduced the
c. Robert Koch d. Rudolf Virchow terms “aerobes” and “anaerobes?”
a. Anton van Leeuwenhoek b. Louis Pasteur

2. The microbes that usually live on or in a person are c. Robert Koch d. Rudolf Virchow
collectively referred to as:
a. germs b. indigenous microbiota 6. all are true except :
c. nonpathogens d. opportunistic pathogens a) All infectious diseases are caused by pathogens
b) Pasteurization is a process that kills all
3. Microbes that live on dead and decaying organic microorganisms present in the liquid being pasteurized
material are known as: c) Louis Pasteur and Robert Koch made significant
a. indigenous microbiota b. parasites contributions to the “Germ Theory of Disease

c. pathogens d. saprophytes d) nonPathogens greatly outnumber pathogens

E) Microorganisms are ess

4. Which of the following statements is true? ential in the field of genetic engineering

a. Koch developed a rabies vaccine

b. Microbes are ubiquitous Keys 1) a 2) b 3) d 4) b 5) b 6)b
 YARMOUK UNIVERSITY (2020)

By: Yousef Alzoubi

Lecture # 2
Cell Structure and Taxonomy :
 A cell is defined as the fundamental unit of any living
organism , and contains the genetic material which can
differentiates to whole organism
 Metabolism refers to all of the chemical reactions that
occur within a cell and allow the cell to grow, reproduce
and response to stimuli
 Metabolism include both anabolism (building up) and
catabolism ( breaking down)
 Two major categories of microbes:
1- Acellular microbes (infectious particles) they are
not living organisms because they cant reproduce
by themselves so we call them particles or agents
2- Cellular microbes (microorganisms) they have
complete genetic material and can reproduce
(replicate) by themselves
 These factors must be known before one can determine
 Bacteria are the most common pathogens and
causes 80% of infectious diz
 Eukaryotic cells possess a true nucleus, whereas
prokaryotic cells do not.
 Eukaryotic cells contain membrane bound organelles
whereas prokaryotic cell doesn’t
 Bacteria and Archaea, are called prokaryotes or
prokaryotic cells.
 Viruses are composed of only a few genes(genetic
material ) protected by a protein coat, and sometimes
may contain one or a few enzymes
 Viruses depend on the energy and metabolic
machinery of a host cell to reproduce.
 Because viruses are acellular (not composed of
cells), they are placed in a completely separate
category.
 Health care professionals, should learn differences in
the structure of various cells to:
1. identify organisms and differentiate between them
2. understand differences in their metabolism , so
we can understand the way to treatment of
diseases they cause
or explain why antimicrobial agents (drugs) attack and
destroy pathogens, but do not harm human cells. (fungi
are eukaryotes like human cells so they have more
similar cellular structures unlike bacteria)
 Cell wall is not used to differentiate eukaryotic from
prokaryotic cells ; cell wall is present in : plants , algae
,fungi and most bacteria
 Cell wall is absent in animal cells , protozoa and
mycoplasma
 A typical eukaryotic animal cell picture which you
studied previously just review the organelles quickly
 Prokaryotic cells are about 10 times smaller than
eukaryotic cells
 Reproduction of prokaryotic cells is by binary fission
unlike eukaryotes ( miosis , mitosis)
 Embedded within the cytoplasm of prokaryotic cells are
a chromosome, ribosomes, and other cytoplasmic
particles
 All bacteria are prokaryotes
 Unlike eukaryotic cells, the cytoplasm of prokaryotic
cells is not filled with internal membranes (endoplasmic
reticulum, lysosomes and golgi complex) also no
mitochondria or nucleus
 The cytoplasm is surrounded by a cell membrane, a cell
wall (usually), and sometimes a capsule or slime layer.
 cell membrane also called (cytoplasmic or plasma
membrane ) chemically consists of proteins and
phospholipids and regulates passage of nutrients and
wastes in and out of the cells due to differences in conc.
In &out of the cell (selective permeability)
 Many enzymes are attached to the cell membrane
mainly (cytochrome oxidase enzyme) which is
responsible for energy production in bacteria
 Mesosomes—are inward foldings of the prokaryotic cell
membranes where cellular respiration (energy
production) takes place in bacteria
 The prokaryotic chromosome usually consists of a
single, long, supercoiled, circular DNA molecule, which
serves as the control center of the bacterial cell
 Chromosome size differs from one bacteria to another
,mycoplasma has the smallest size genome while E.coli
has 10 times larger size than it
 The chromosome is suspended or embedded in the
cytoplasm.
 The DNA-occupied space within a bacterial cell is
sometimes referred to as the bacterial nucleoid ,, but
remember no nucleus , nucleoplasm or nuclear
membranes in prokaryotes.
 Plasmids (extrachromosomal DNA) a small, circular
molecules of double-stranded DNA that are not part of
the chromosome may present in the cytoplasm of
prokaryotic cells their size is ( 0.1 to 10 )% of
chromosome size
 Plasmids are self-replicating and are not essential for
cell survival , some bacteria have no plasmids , others
have one or multiple plasmids
 Plasmids play role in antibiotic resistance and
considered as virulence factor
 The cytoplasm of prokaryotic cells consists of water,
enzymes, dissolved oxygen (in some bacteria), waste
products, essential nutrients, proteins, carbohydrates,
and lipids—a complex mixture of all the materials
required by the cell for its metabolic functions.
 Prokaryotic ribosomes (protein factory) are smaller
than eukaryotic ribosomes
 A 70S prokaryotic ribosome is composed of a 30S
subunit and a 50S subunit 50s +30s = 70s
 Eukaryotic ribosomes composed of 60s +40s = 80s
 Cytoplasmic granules occur in certain species of
bacteria & may consist of starch, lipids, sulfur, iron, or
other stored substances.
 Bacterial Cell Wall :
- The structure of bacterial cell walls is different from
the eukaryotic cell walls
- cell wall surrounds plasma membrane and functions
in rigidity , strength and protection of cell
- Peptidoglycan ( also known as murein) is the major
constituent of most bacterial cell walls & only found in
bacteria
- The thickness of the cell wall and its exact
composition vary with the species of bacteria
- the backbone of peptidoglycan composed of
N-acetylglucosamine (NaG) + N-acetylmuramic acid
(NAM) attached by peptide bone
- a set of identical tetrapeptide are attached to each
NAM
 Remember not all bacteria have cell walls mycoplasma
is a genus of bacteria that lack cell wall
 Gram-positive bacteria have a thick layer of
peptidoglycan combined with teichoic acid and
lipoteichoic acid molecules
 It has a thick cell wall about 30 layers of peptidoglycan
and single inner membrane & no outer cell membrane
 Lipoteichoic acid links to plasma membrane while
teichoic acid links to peptidoglycan
 gram- negative bacteria have a much thinner layer of
peptidoglycan, but this layer is covered with a complex
layer of lipid macromolecules , usually referred to as the
outer membrane
 Lipoproteins connect outer membrane to peptidoglycan
 Lipopolysaccharide (LPS) ,phospholipids and
lipoproteins are characteristics of gram negative
bacteria which make it more complex than gram +
 Glycocalyx (Slime Layers and Capsules)
 A thick layer of material located outside their cell wall
 Depending on the species, bacterial cells may or may
not be surrounded by glycocalyx.
 The two types of glycocalyx are slime layers and
capsules. , capsules are thicker and firmly attached to
cell wall and protects the bacteria from phagocytosis
(virulence factor) (antiphagocytic function of capsule by
WBC)
 If we remove the capsule of bacteria the new
generations still be capsuled
 and not associated with motility
 Flagella : Motile bacteria usually possess flagella
outside the cell wall which is long filamentous
appendages that propel bacteria
 The number and arrangement of flagella possessed by
a certain species of bacterium are characteristic of that
species. (may reach 200 )
 Bacteria never possess cilia
 Types of flagella :
1) Peritrichous :flagella all over entire surface
2) Lophotrichous : tuft (bundle) of flagella at one end
3) Amphitrichous: one or more flagella at each end
4) Monotrichous : single polar flagellum at one end
5) Atrichous : no flagella , nonmotile
 Pili (Fimbriae) : are hair-like structures, most often
observed on Gram-negative bacteria composed of a
protein called pilin , pili are much thinner than flagella
 There are two types of pili:
1) One type enables bacteria to adhere or attach to
surfaces of host cell called (fimbria)
2) The other type (called a sex pilus) facilitates transfer
of genetic material (plasmid) from one bacteria to
another
 The process by which one bacteria (donor) transfer
its genetic material to another bacteria (recipient)
through sex pillus is called CONJUGATION
 Spores (Endospores) :
 few bacteria are capable of forming spores as mean
of survival in adverse conditions, the process by
which the spores are formed is called sporulation
 Spores are resistant to heat, cold, drying, and most
chemicals.
 Spores have been shown to survive for many years in
soil or dust as dormant cells, and some are quite
resistant to disinfectants and boiling
 During sporulation a copy of the chromosome and
some of the surrounding cytoplasm becomes
enclosed in protein coats
 When the spore lands on a moist , nutrient rich media
it germinates to one bacterium
 Spores can form in different sites of bacteria :
 Terminal spores : produced at the end of bacterial
cell
 Subterminal spores: produced elsewhere in the cell
 central
 Prokaryotic Cell Reproduction : by a process known
as binary fission :one cell split to two identical cells
 Chromosome must be duplicated (a process known
as DNA replication)
 The length of time it takes for one bacterial cell to
split into two identical cells is referred to as the
organism’s generation time
Taxonomy :
 Taxonomy =classification of living organisms &
Consists of three separate but interrelated areas:
classification, nomenclature, and identification
1) Classification is the arrangement of organisms into
taxonomic groups (known as taxa) on the basis of
similarities or relationships either phenotypic or
genotypic
 An organism’s complete collection of genes is referred
to as the organism’s Genotype or genome.
 An organism’s complete collection of physical
characteristics is known as the organism’s phenotype.
2) Nomenclature is the assignment of names to the
various taxa according to international rules
3) Identification is the process of determining whether
an isolate belongs to one of the established, named
taxa or represents a previously unidentified species
 Microbial Classification : In the binomial system of
nomenclature, the first name (e.g., Escherichia) is the
genus, and the second name (e.g., coli) is the specific
epithet
 When used together, the first and second names (e.g.,
Escherichia coli) are referred to as a species.
 The genus name usually is the name of scientist who
discovers it while the species name is according to the
site of isolation of this bacteria
 Bacterium Disease
Bacillus anthracis Anthrax
Chlamydophila pneumoniae Pneumonia
Chlamydophila psittaci Psittacosis (“parrot fever”)
 Robert H. Whittaker proposed a Five-Kingdom System
of Classification
1) Bacteria and archaea are in the Kingdom
Prokaryotae (or Monera)
2) Algae and protozoa are in the Kingdom Protista
(protists)
3) Fungi are in the Kingdom Fungi
4) Plants are in the Kingdom Plantae
5) Animals are in the Kingdom Animalia
 Note that viruses are not included in this classification
because they are not living cells
 Three domain system classification to : bacteria ,
archae , eukarya
 Eukarya domain is divided into four kingdoms: Protista
(algae and protozoa); Kingdom Plantae; Kingdom
Fungi; Kingdom Animalia
 The first prokaryote which appears on earth is archea
from its name "ancient"
 The most widely used technique for gauging diversity
or relatedness among organisms is rRNA sequencing
 Questions 6) The site of energy production in bacteria is :
1) Which of the following combinations is NOT true: A. Mitochondria C. ribosomes
A. Algae : cellulose cell wall C. fungi : chitin cell wall B. Cell membrane D. cell wall
B. Bacteria :peptidoglycan D. archae :peptidoglycan 7) Molecules of extrachromosomal DNA are also known
as:
2) Which of the following does NOT have cell wall: a. Golgi bodies b. lysosomes
A. Plants C. fungi c. plasmids d. plastids
B. Algae D. mycoplasma
8) One way in which an archaean would differ from a
bacterium is that the archaean would possess no:
3) When the flagella is all over the bacteria its classified
as : a. DNA in its chromosome b. peptidoglycan in its cell walls
A. Monotrichous C. amphitrichous c. ribosomes in its cytoplasm d. RNA in its ribosomes
B. Lophotrichous D peritrichous 9) Some bacteria stain Gram-positive and others stain
Gram-negative as a result of differences in the structure of
their:
4) The locomotion organelle of bacteria is called :
A. Flagella C. fimbriae a. capsule b. cell membrane c. cell wall d. ribosomes
B. Cilia D. pili 10) Which one of the following is never found in prokaryotic
5) Which of the following is NOT true about eukaryotic
cells?
cells vs prokaryotic, respectively:
a- Eukaryotic size X10 of prokaryotic cells a. flagella b. capsule c. cilia d. ribosomes
b- True nucleus( DNA enclosed by nuclear
membrane) in eukaryotes vs absent membrane in
prokayotics 11) The Three-Domain System of Classification is based
c- cell wall is absent in most eukaryotes vs present in on differences in which of the following molecules?
most bacteria a. mRNA b. peptidoglycan c. rRNA d. tRNA
d- Mesosomes in bacteria vs mitochondria in
eukaryote for energy production
e- both have the same complex membrane keys: 1)D 2)D 3)D 4) A 5) E 6)B 7) c 8) b 9) c 10) c
structures and organelles with no difference 11) C
 YARMOUK UNIVERSITY (2020)

By: Yousef Alzoubi

Lecture # 3
Microbial Diversity :
 Acellular Microbes :
1) Viruses :
 Viruses are extremely small (measured in
nanometer)
 They are observed using electron
microscopes.
 Viruses are not alive ( must invade live host
cells to replicate )
 Viruses infect humans, animals, plants, fungi,
protozoa, algae, and bacterial cells
 Many human diseases are caused by viruses
 Oncogenic viruses or oncoviruses— cause
specific types of cancer, including human
cancers such as lymphomas, carcinomas, and
some types of leukemia.
 Viruses have five specific properties :
1) The vast majority of viruses possess either
DNA or RNA
2) They are unable to replicate (multiply) on their
own
3) They do not divide by binary fission, mitosis, or
meiosis.
4) They lack the genes and enzymes necessary
for energy production.
5) They depend on the ribosomes, enzymes, and
metabolites(“building blocks”) of the host cell
for protein and nucleic acid production.
 The complete virus particle is called "virion" :
which is DNA or RNA genome surrounded by
protein capsid (coat)
 The capsid is composed of many small
proteins called capsomere
 Some viruses are enveloped with outer
membrane composed of lipids or polysaccride
or both
 Viruses classification:
type of genetic material (either DNA or RNA)
shape of the capsid
number of capsomeres
size of the capsid
presence or absence of an envelope
type of host that it infects
type of disease it produces
target cell
immunologic or antigenic properties.
 Origin of viruses :
1) Coevolution theory : viruses originated in
the primordial soap & coevolved with bacteria
an archaea
2) Retrograde evolution theory : viruses
evolved from free living prokaryotes that
invaded other organisms
3) Escaped gene theory: viruses are pieces of
host cell RNA or DNA that escaped from
living cells & no longer under cellular control
Bacteriophage:
 The viruses that infect bacteria are known as
bacteriophages or simply phages
 They are obligate intracellular pathogens, in
that they must enter a cell to replicate
 Bacteriophages can only attach to bacteria that
possess surface molecules (receptors) that
can be recognized by molecules on the phage
surface.
 Categories of bacteriophages :
1) icosahedron (spherical shape)
2) filamentous (helical structure)
3) complex bacteriophage
(icosahedral head attached to
helical tails ) (most common)
 Bacteriophages can be categorized by the
events that occur after invasion of the bacterial
cell ( Some are virulent phages, whereas
others are temperate phages)
 Virulent bacteriophages : Once it enters a
host cell, a virulent bacteriophage always
initiates the lytic cycle, which results in the
destruction of the cell.
 Steps of lytic cycle :
1. Attachment (adsorption)
2. Penetration ( the phage injects its genome
(DNA) into the bacterial cell , the capsid
remains out)
3. Biosynthesis (expression of viral genes ,
protein synthesis (viral pieces) & genome
replication)
4. Assembly (virus pieces assemble to create
complete virion )
5. Release of complete phage &bacterial lysis
 Temperate phages (lysogenic phages):
 Temperate bacteriophages do not immediately
initiate the lytic cycle. Their DNA can remain
integrated into the host cell’s chromosome for
generation after generation.
 Bacteriophages are involved in two of the four
major ways in which bacteria acquire new
genetic information.
 These processes— called lysogenic
conversion and transduction
 The remaining 2 are transformation &
conjugation
 Animal Viruses:
 Viruses that infect humans and animals
 Animal viruses can only attach to and invade
cells bearing appropriate surface receptors.
 Animal viruses escape from their
host cells by either lysis of the cell or
budding.
 Viruses that escape by budding
become enveloped viruses.
 Steps of lytic cycle in animal viruses
:
1. Attachment (adsorption)
2. Penetration (The entire virus enters the
host cell because in some cases it was
phagocytized by the cell)
3. Uncoating (the viral nucleic acid escapes
from the capsid)
4. Biosynthesis
5. Assembly (virus pieces assemble to create
complete virion )
6. Release by cell lysis or budding
 Inclusion bodies, (remenants or collection of
viruses) are often seen in infected cells and are
used as a diagnostic tool to identify certain viral
diseases
 Inclusion bodies may be found in the cytoplasm
(cytoplasmic inclusion bodies) or within the
nucleus (intranuclear inclusion bodies),
depending on the particular disease.
 In rabies, the cytoplasmic inclusion
bodies in nerve cells are called Negri
bodies
 In herpes & poliomyelitis
(intranuclear inclusion bodies)
 Latent Virus Infections : like
herpes virus infections although the infected
person is always harboring the virus in nerve
cells, the cold sores (fever blisters) come and go
 Latent viral infections are usually limited by the
defense (immune) systems of the human body
 Antiviral Agents : Chemicals have been
developed to interfere with virus-specific
enzymes and virus production by either
disrupting critical phases in viral cycles or
inhibiting the synthesis of viral DNA, RNA, or
proteins
 Antibiotics are not effective against viral
infections.
 Oncogenic Viruses :
 Viruses that cause cancer are called oncogenic
viruses or oncoviruses
 Viruses were shown to be the cause of various
types of cancers in rodents, frogs, and cats.
 Epstein–Barr virus = causes nasopharyngeal
carcinoma, Burkitt lymphoma, and B-cell
lymphoma
 Human papillomaviruses (HPV) = cancers of the
cervix (cervical cancer) and other parts of the
genital tract.
 HIV( Human Immunodeficiency Virus) : is an
enveloped, single-stranded RNA virus.
 It is a member of a genus of viruses called
lentiviruses, in a family of viruses called
Retroviridae (retroviruses)
 AIDS is caused by HIV.
 Mimivirus and Megavirus :
 An extremely large double-stranded DNA virus
can be observed using a standard compound
light microscope called Mimivirus, was recovered
from amebas.
 The virus was given the name Mimivirus
because it “mimics” bacteria
 Mimivirus may be the cause of some cases of
human pneumonia
 Megavirus, Discovered in 2010 off the coast of
Chile , Its genome is larger than that of some
bacteria
 Megavirus was isolated in a French laboratory
by co-cultivation with amebas ,, Its natural host is
not known.
 Plant Viruses : More than 1,000 different viruses
cause plant diseases
 Plant viruses are usually transmitted via insects
mites ,nematodes (round worms); and
contaminated tools
 These diseases result in huge economic losses
 Viroids and Prions :
 Viroids are infectious RNA molecules that cause
a variety of plant diseases.
 Viroids consist of short, naked fragments of
single-stranded RNA (about 300–400
nucleotides)
 Prions are infectious protein molecules that
cause a variety of animal and human diseases.
 cause fatal neurological diseases in animals,
such as : - scrapie in sheep and goats
- bovine spongiform encephalopathy
 In humans, causes
- kuru,
- Creutzfeldt–Jakob (C–J) disease,
- Gerstmann–Strussler–Scheinker (GSS) disease
- fatal familial insomnia.
 Kuru, C–J, and GSS diseases involve loss of
coordination and dementia
 Dementia, a general mental deterioration, is
characterized by disorientation and impaired
memory, judgment, and intellect
 The 1997 Nobel Prize for Physiology or Medicine
was awarded to Stanley B. Prusiner, the scientist
who coined the term prion and studied the role of
these proteinaceous infectious particles in
disease
 Bacteria ;
 Bacteria vary in size from 0.1 μm in diameter to
10.0-μm-long
 The size, shape, and morphologic arrangement
of various bacteria are easily observed using
compound light microscope.
 The three general shapes of bacteria are round
(cocci), rod- shaped (bacilli), and spiral-shaped
(spirochete)
 Bacteria reproduce by binary fission.
 Generation time= The time it takes for one
bacterial cell to split into two
 Bacteria are divided into three phenotypic
categories (categories based on their physical
characteristics)
(a)Gram-negative
 some CWD bacteria regain its cell wall when
place in favorable growth conditions whereas
others do not ( genetically determined CWD)
 Most bacteria are colorless, transparent, and
difficult to see without staining
 A simple stain is sufficient to determine bacterial
shape and morphologic arrangement

(b)Gram-positive
(c) Cell walless
 Cocci may be seen singly or in pairs (diplococci),
chains (streptococci), clusters (staphylococci),
packets of four (tetrads), or packets of eight
(octads),
 Cell wall–deficient (CWD) bacteria or L-forms are
pleomorphic (have different shapes)

 Fixation serves three purposes:

1. It kills the organisms.
2. It preserves their morphology.
3. It anchors the smear to the slide.
 The procedures used to observe bacterial 4) counterstain or secondary stain (safranin) +
capsules, spores, and flagella are collectively purple - pink (red)
referred to as structural staining procedures.
 The Gram and acid-fast staining procedures are
referred to as differential staining procedures
 The Gram stain differentiates between “Gram
positive” and “Gram-negative” bacteria
 Gram-variable bacteria = M. tuberculosis and M.
leprae ( contain mycolic acid in their cell wall)
 The acid-fast stain is of value in the diagnosis of
tuberculosis.

Acid fast stain : differentiates acid fast from non

1) Primary stain (carbofuchsin) = both acid fast &
non red
2) Mordant (heat) = both red
3) Decolorizer (acid alcohol) = acid fast remain blue
but non become colorless
4) Counterstain (methylene blue) = acid fast still red
1) primary stain (crystal violet) both +- purple
but non acid fast become blue
2) mordant (iodine solution) both +- purple (blue)
3) decolorizer (ethanol) + purple - colorless
 Determining bacterial motility
 Motile bacteria swim due to flagella or axial
filaments
 A flagella stain = demonstrate the presence,
number, and location of flagella on bacterial
cells.
 Motility test : stabbing the bacteria into a tube
of semisolid agar or by using the hanging drop
technique

 Bacterial Colony Morphology:
 Colony morphology includes the size, color,
overall shape, elevation, and the appearance
of the edge or margin of the colony.
 Colony features serve as important “clues” in
the identification of bacteria
 Atmospheric Requirements :
 Obligate aerobes require an atmosphere
containing about 20% to 21% oxygen (room)
 Microaerophiles require reduced oxygen
concentrations (usually around 5% oxygen).
 Obligate anaerobe grow only in anaerobic
environment ( 0% Oxygen)
 Facultative anaerobes capable of living in either
presence or absence of oxygen ( 0 – 20 oxygen)
 Aerotolerant anaerobes grows better in the
absence of oxygen , but can tolerate ( survive)
atmosphere containing oxygen
 Capnophiles require an atmosphere containing
5% to 10% carbon dioxide.
 Nutritional Requirements : All bacteria need the
elements carbon, hydrogen, oxygen, sulfur,
phosphorus, and nitrogen for growth.
 Certain microbes have specific vitamin
requirements and need some organic
substances secreted by other living MOs
 Fastidious organisms = especially demanding
nutritional requirements
 Bacteria can produce many waste products and
secretions enable them to invade their host and
cause disease.
 The pathogenic strains like staphylococci and
streptococci, can be identified by the enzymes
they secrete.
 Some bacteria are characterized by the
production of certain gases, such as carbon
dioxide, hydrogen sulfide, oxygen, or methane
 Pathogenicity factors : capsules, pili, or
endotoxins, exotoxins and exoenzymes
 The composition of the genetic material (DNA) of
an organism is unique to each species.
 16S rRNA sequencing can determine the degree
of relatedness between two different bacteria.
 Unique Bacteria :
 Rickettsia, chlamydia, and mycoplasmas are
atypical bacteria, (they do not possess all the
attributes of typical bacterial cells)
 Rickettsias and chlamydias are bacteria with a
Gram negative– type cell wall.
 Rickettsias and chlamydias are obligate
intracellular pathogens that cause diseases in
humans and other animals
 Mycoplasmas are the smallest of the cellular
microbes.
 Because Mycoplasma spp. do not possess cell
walls, they are pleomorphic
 Most bacteria are microscopic , coccus (ex:  Archaea ;
staphylococcus aureus) is 1 μm in diameter ,  Archae means “ancient,” vary widely in shape
whereas typical bacillus (E.coli) is about 1 μm (cocci, bacilli, and long filaments)
width ×3.0 μm long  All archaea possess cell walls, their cell walls
 The largest bacteria is Thiomargarita contain no peptidoglycan.
namibiensis, which is coloreless ,marine ,sulfide-  Some live at the bottom of the ocean in and
oxidizing bacteria , Single spherical cells are 100 near thermal vents, (heat , salinity , pressure)
to 300 μm,  Other archaea, called methanogens, produce
 Nanobacteria. Their sizes are expressed in methane
nanometers less than 1 μm in diameter found in  Many archaea are extremophiles = live in
soil, minerals, ocean water, extreme environments very hot or very cold or
human and animal blood, human dental calculus dry
(plaque),arterial plaque, and even rocks.
 Photosynthetic Bacteria : include purple
bacteria, green bacteria, and cyanobacteria
(blue-green algae) "“pond scum”
 Capable of converting light energy into chemical
energy.
 Cyanobacteria played a major part in the
oxygenation of the atmosphere
 Convert nitrogen gas (N2) from the air into
ammonium ions (NH4) in the soil or water; this
process is known as nitrogen fixation
 Some cyanobacteria produce toxins (called
cyanotoxins)= neurotoxin and hepatotoxin
Questions : 5) At the end of the Gram staining procedure,
1) Which one of the following steps occurs during Gram-positive bacteria will be:
a. blue to purple b. green
the multiplication of animal viruses, but not
c. orange d. pink to red
during the multiplication of bacteriophages?
a. assembly b. biosynthesis 6) Which one of the following statements about
c. penetration d. uncoating cyanobacteria is false?
2) Which one of the following diseases or groups of a. Although cyanobacteria are photosynthetic, they
diseases is not caused by prions? do not produce oxygen as a result of photosynthesis
b. At one time, cyanobacteria were called bluegreen
a. certain plant diseases
algae
b. chronic wasting disease of deer and elk
c. Some cyanobacteria are capable of nitrogen
c. Creutzfeldt–Jacob disease of humans fixation
d. “mad cow disease” d. Some cyanobacteria are important medically
3) Most prokaryotic cells reproduce by: because they produce toxins
a. binary fission b. budding 7) An organism that does not require oxygen, grows
better in the absence of oxygen, but can survive in
c. gamete production d. spore formation atmospheres containing some molecular oxygen is
4) The group of bacteria that lack rigid cell walls and known as a(n):
take on irregular shapes is: a. aerotolerant anaerobe b. capnophile
a. chlamydias b. mycobacteria c. facultative anaerobe d. microaerophile
c. mycoplasmas d. rickettsias

keys 1)d 2) a 3) a 4) c 5) a 6) a 7) a
 YARMOUK UNIVERSITY (2020)

By: Yousef Alzoubi

Lecture # 4
Microbial Diversity (Eukaryotic Microbes):
 Eukaryotic microbes include some species of algae and
fungi and all protozoa, lichens, and slime moulds.
 Algae :
 Algae are photosynthetic, eukaryotic organisms
 Algae and protozoa are referred to as protists because
they are in the kingdom Protista.
Photosynthetic protists = algae
 If the organism enters the lymphatic system, it may
Nonphotosynthetic protists = protozoa.
cause a debilitating, sometimes fatal infection,
 Although they are not plants, algae are more plantlike
especially in immunosuppressed individuals.
than protozoa
 Algae in several other genera secrete substances
 Most algal cell walls contain cellulose
(phycotoxins) that are poisonous to humans, fish, and
 A few species use organic nutrients, and others survive other animals
with very little sunlight.
 Protozoa :
 Depending on pigments they possess ; algae are
 Most protozoa are single-celled free-living
classified as green, golden (or golden brown), brown, or
microorganisms found in soil and water
red.
 Diatoms algae live in both freshwater and seawater  Protozoal cells are more animal-like than plantlike
 Medical Significance of algae :  All protozoa are eukaryotes
 Structures and organelles = cell membranes, nuclei,
 One genus of algae (Prototheca) is a very rare cause of
human infections (causing a disease known as endoplasmic reticulum, mitochondria, Golgi bodies,
lysosomes, centrioles, and food vacuoles
protothecosis).
 Protozoa do not have cell walls, but some, including
 Prototheca lives in soil and can enter wounds,
some flagellates and some ciliates, possess a pellicle
especially those located on the feet
(thickened cell membrane ) , which serves the same
 It produces a small subcutaneous lesion that can
purpose as a cell wall—protection.
progress to a crusty, warty-looking lesion.
 Some flagellates and some ciliates ingest food through
a primitive mouth or opening, called a cytostome.
 A typical protozoan life cycle consists of two stages:
1) motile trophozoite stage
2) nonmotile cyst stage.
 Many parasitic protozoa are pathogens, causing
malaria, giardiasis, African sleeping sickness, and
amebic dysentery
 Classification of protozoa : classified taxonomically
by their mode of locomotion.
 Some move by pseudopodia, others by flagella
(flagellates) others by cilia (ciliates) , and some are
nonmotile (sporozoan)
 Amebae (amebas), move by means of
cytoplasmic extensions called pseudopodia (false
feet).
Examples on mediacally important amebas :
- Entamoeba histolytica causes amebic dysentery
(amebiasis) and extraintestinal amebic abscesses
- Acanthamoeba spp causes eye infections
- Naegleria fowleri causes primary amebic
meningoencephalitis
 Ciliates, move by means of large numbers of
hairlike cilia on their surfaces
Examples on ciliates
- Balantidium coli causes dysentery in
underdeveloped countries
- Paramecium
- Stentor
- Vorticella
 Flagellated protozoa (flagellates), move by
means of whiplike flagella.
Examples on flagellates :
- Trypanosoma brucei subspecies gambiense
cause African sleeping sickness
- Trypanosoma cruzi causes Chagas desease
- Trichomonas vaginalis cause trichomoniasis
- Giardia lamblia causes giardiasis
 Sporozoan protozoa are nonmotile.
Examples on sporozoan that causes human
infections
- Plasmodium spp. Causes malaria
- Cryptosporidium parvum causes cryptosporidiosis
- Toxoplasma gondii causes toxoplasmosis
- Babesia
- Cyclospora
 Fungi :
 Fungi are a diverse group of eukaryotic organisms
that include yeasts, moulds, and mushrooms.
 The study of fungi is called mycology.
  Characteristics of fungi (differ from plants & algae)
- not photosynthetic
- no chlorophyll or other photosynthetic pigments.
- no cellulose (a polysaccharide) in fungal cell wall
- Fungal cell walls do contain a polysaccharide
called chitin (polysaccharide)
 Yeasts are unicellular, whereas moulds are
multicellular.
 Moulds grow as filament called hyphae (septate or
aseptate )
 hyphae which intertwine to form a mass called a
mycelium
 Septate or aseptate hyphae is an important “clue”
when attempting to identify a fungus that has been
isolated from a clinical specimen
 Fungi reproduction :
 Fungi reproduce by spore production (sexual or
asexual spores)
 Sexual spores are produced by the fusion of two
gametes (thus, by the fusion of two nuclei).
 Fungi are classified by the sexual spore that they
produce or the type of structure on which the spores
are produced
Asexual spores (conidia) = NO fusion of gametes
 Fungal spores are very resistant to heat, cold, acids,
bases, and other chemicals.
 Many people are allergic to fungal spores
 Yeasts:
 Yeasts are microscopic, single-celled organisms that
usually reproduce by budding. (can be seen under
microscope as germ tube )
 Yeasts are found in soil and water and on the skins
of many fruits and vegetables.
 Pasteur discovered that naturally occurring yeasts on
the skin of grapes and other fruits and grains were
responsible for these fermentation processes.
 Saccharomyces cerevisiae (“baker’s yeast”) ferments
sugar to alcohol under anaerobic conditions.
 Yeast breaks down simple sugars to carbon dioxide
and water aerobically, it has long been used as a
leavening agent in bread production
 Yeasts are also a good source of nutrients for
humans because they produce many vitamins and
proteins
  Medically important Yeast :
 C. albicans and Cryptococcus neoformans are
examples of yeasts that cause human infections.
 C. Albicans is the yeast most frequently isolated from
human clinical specimens (oral thrush , yeast
vaginitis)
 In the laboratory, yeasts colonies = quite similar in
appearance to bacterial colonies
 A wet mount can distinguish between a yeast colony
and a bacterial colony
 Yeasts are usually larger than bacteria, usually oval
shaped;may be observed in the process of budding
 Moulds :
 Moulds are the fungi often seen in water and soil and
on food
 They grow in the form of cytoplasmic filaments or
hyphae that make up the mycelium of the mould
 Aerial hyphae = extend above
the surface
 Vegetative hyphae = beneath
the surface
 Many antibiotics are produced by moulds. =
Penicillium and Acremonium
 Some moulds produce = large quantities of enzymes
(such as amylase, which converts starch to glucose),
citric acid, and other organic acids that are used
commercially.
 The flavor of cheeses such as bleu cheese and
limburger is the result of moulds that grow in them.
 Fleshy Fungi :
 Mushrooms, toadstools, puffballs, and bracket fungi
(collectively referred to as fleshy fungi) are examples of
fungi that are not microorganisms.
 Many mushrooms are delicious to eat, but others are
extremely toxic and may cause permanent liver and
brain damage or death
 Some moulds and fleshy fungi produce mycotoxins,
which can cause human diseases called microbial
intoxications.
 A variety of yeasts and moulds cause human infections
(known as mycoses).
 Many diseases of crop plants, grains, corn, and
potatoes are caused by moulds.
 Fungal Infections of Humans (mycoses) :
 Superficial, cutaneous, subcutaneous, or systemic
mycoses.
 Superficial mycoses = hair, fingernails, toenails, and the
dead, outermost layers of the skin (the epidermis).
 Cutaneous mycoses = fungal infections of the living
layers of skin (the dermis)
 Subcutaneous mycoses are fungal infections of the
dermis and underlying tissues
 Systemic mycoses are fungal infections of internal
organs of the body (e.g., simultaneous infection of the
respiratory system and the bloodstream, or
simultaneous infection of the respiratory tract and the
central nervous system).
 Dermatophytes cause = tinea infections, which are often
referred to as “ringworm” infections
 C. albicans lives harmlessly on the skin and mucous
membranes of the mouth, gastrointestinal tract, and
genitourinary tract.
 Reduction in the number of indigenous bacteria at these
anatomic locations, C. albicans flourishes, leading to
yeast infections of the mouth (thrush), skin, and vagina
(yeast vaginitis).
 Madura foot (a type of eukaryotic mycetoma), in which
the patient’s foot becomes covered with large, unsightly,
fungus- containing bumps
 Spores of some pathogenic fungi may be inhaled with
dust from contaminated soil or dried bird and bat feces
(guano), or they may enter through wounds of the
hands
 Inhalation of spores of bread moulds like Rhizopus and
Mucor spp. by an immunosuppressed patient can lead
to a respiratory disease called zygomycosis or
mucormycosis.
 The mould can then become disseminated throughout
thepatient’s body and can lead to death
 In the mycology laboratory, yeasts are identified
(speciated) by determining which substrates they are
able to use as nutrients.
 Yeasts are identified (speciated) by inoculating them
into a series of biochemical tests.
 Moulds are identified by a combination of macroscopic
and microscopic observations and the speed at which
they grow.
 Dimorphic Fungi : Dimorphic fungi can live either as
yeasts or as moulds depending on growth conditions.
 Dimorphic fungi that cause human diseases include:
- Histoplasma capsulatum (histoplasmosis)
- Sporothrix schenckii ( sporotrichosis)
- Coccidioides immitis ( coccidioidomycosis)
- Blastomyces dermatitidis ( blastomycosis)
  Within the human body (in vivo 37C), dimorphic fungi Questions :
exist as yeasts. However, when grown in vitro at
1) Which of the following statements about algae and fungi
room temperature (25°C), dimorphic fungi exist as is (are) true?
moulds, producing mould colonies (mycelia)
a. Algae are photosynthetic, whereas fungi are not
 When grown in vitro at body temperature (37°C), b. Algal cell walls contain cellulose, whereas fungal
dimorphic fungi exist as unicellular yeasts and cell walls do not
produce yeast colonies c. Fungal cell walls contain chitin, whereas algal cell
walls do not
 Lichens : lichen is a combination of two organisms: d. All of the above
an algae (or a cyanobacterium) and a fungus.
 Lichens are classified as protists. 2) All of the following are algae except:
 They are not associated with human disease a. desmids b. diatoms
 Some substances produced by lichens shown to
have antibacterial properties c. dinoflagellates d. sporozoan
 Slime Moulds : found in soil and on rotting logs, 3) All of the following are fungi except:
have both fungal and protozoal characteristics and
a. moulds b. Paramecium
very interesting life cycles
 Some taxonomists classify slime moulds as fungi, c. Penicillium d. yeasts
whereas others classify them as protists. 4) A protozoan may possess any of the following except:
 not known to cause human disease
a. cilia b. flagella
c. hyphae d. pseudopodia
some notes from last lecture :
5) Which one of the following is not a fungus?
 fastidious organism : (needy organism) require
complex nutritional media to grow no basic media a. Aspergillus b. Candida
 cyanobacteria in ponds or lakes create water bloom c. Penicillium d. Prototheca
(pond scum) bluish green layer (turquoise)
 global warming increase cyanobacteria which
produce cyanotoxins (neurotoxin & hepatotoxin)
6) Which one of the following terms is not associated with 10) all of the following are true about fungi except:
fungi?
a) Fungi can cause both infectious diseases and microbial
a. conidia b. hyphae intoxications
c. mycelium d. pellicle b) Asexual spores are also known as conidia
7) If a dimorphic fungus is causing a respiratory infection, c) Classification of fungi is based on the type of conidia
which of the following might be seen in a sputum specimen that they produce
from that patient?
d) Diseases caused by fungi are called mycoses
a. amebae b. conidia
c. hyphae d. yeasts
11) all of the following are true about protozoa except:
8) A lichen usually represents a symbiotic relationship
a) cause diseases such as African sleeping sickness,
between which of the following pairs?
babesiosis, cryptosporidiosis, malaria, and toxoplasmosis
a. a fungus and an ameba b. a yeast and an ameba
b) protozoa are classified by their means of locomotion
c. an alga and a cyanobacterium d. an alga and a fungus
c) Toxins produced by protozoa are called phycotoxins
9) choose the true statements from the following :
d) protozoa don’t have cell wall
a) A Paramecium cell moves by means of flagella
b) A dimorphic fungus would exist as a mould inside the
human body
c) Protozoa that move by means of pseudopodia are in a
category known as sporozoan
d) Slime moulds possess characteristics of both fungi and keys : 1) d 2) d 3) b 4) c 5) d 6) d 7) d 8) d 9)d
protozoa 10) C 11) C
 YARMOUK UNIVERSITY (2020)

By: Yousef Alzoubi

Lecture # 5
Microbial physiology : 2) Photoheterotroph: Light & Organic compounds
e.g. some bacteria
 The study of vital life processes of microorganisms
 Living protoplasm contains 6 major chemicals 3) Chemoautotroph: Chemicals & CO2
C, H, O, N, P, S e.g. certain bacteria
 Other : Na, K, Cl, Mg, Ca, Fe, I
4) Chemoheterotroph: Chemicals & Organic
 These chemicals are needed for Make up of
macromolecules (CHO , lipids , proteins , nucleic acids) e.g. All (animal, fungi, protozoa); most bacteria
 Essential amino acids, and Essential fatty acid are not
 Ecology: Is the study of the interaction between
synthesized by cells , but supplied from the environment
organisms and the world around them, e.g. photoauto-
 Terms related to an organism’s energy source :
trophs produce food and O2 for Chemoheterotroph
1) Phototrophs : Light as energy source by
 Metabolism : Chemical reactions (metabolic reactions)
Photosynthesis (means conversion of light to energy)
 Metabolic enzymes: Control metabolic reactions and
2) Chemotrophs: Inorganic or organic chemicals as
are under gene control
energy source
 Enzymes (biological catalysts) are Specific; act on
- Chemoorganotrophs (Organotrophs): Organic
one substrate (Lock-Key) & Unchanged during the
chemicals as energy source
- Chemolithotrophs (Lithotrophs): Inorganic reaction ( used in multiple reactions)
chemicals as energy source
 Terms relating to an organism’s carbon source :
1) Autotroph : Use CO2 as the sole source of carbon,
e.g. plants, cyanobacteria
2) Heterotroph : Use organic compounds other than
CO2 as a carbon source, e.g. human cells, fungi,
protozoa, most bacteria
 Terms combined energy & carbon source :
1) Photoautotroph: Light & CO2
e.g. plants, algae, Cyanobacteria
 Endo-enzymes: found & act Within the cell
 Exo-enzymes: Produced within a cell & then released
outside e.g Cellulase, Pectinase of saprophytic fungi
remember exo-enzymes may act as virulence factor
 Factors that affect the efficiency of enzymes :
1) pH
2) Temperature
3) Concentration of enzyme and substrate
4) Metals: Some enhance (Calcium, Magnesium), some
inhibit (Lead (pb), Zinc Zn , Mercury Hg)
 Some enzymes Bind to a similar substrate (mimic the
original one) so block/stop reaction, e.g.
chemotherapeutics drugs
 Metabolism include both anabolism ( require energy for
binding of small molecules ) & catabolism ( releasing
energy from breaking bonds of large molecules )
 Catabolism & anabolism are in balance ( equal) and
ATP is used in energy transfer
 Remember ATP contains 3 phosphate molecules , ADP
contains 2 , and AMP contain 1
 Biochemical reactions has : 1) starting material
3) intermediate products (intermediary) 3) end product
Common metabolic processes :
1) Aerobic respiration
2) Fermentation (Anaerobic) reaction
 Aerobic respiration of glucose include ;
1) Glycolysis
2) Krebs cycle
3) Electron transport chain
1) Glycolysis (glycolytic pathway or Embden- Meyerof
pathwayor Embden- Meyerof-Parnas pathway)
 Occurs in cytoplasm of Prokaryotes & Eukaryotes
 9 steps; each requires a specific enzyme
 Glucose (6C) is converted into 2 pyruvic acid molecules
( pyruvate) (3C)
 Little energy is released (2 ATP only)
2) Krebs cycle (Citric Acid Cycle; Tricarboxylic
Cycle)
 At the mitochondria in eukaryotes , but in bacteria at the
inner surface of the cell membrane (mesosomes).
 8 steps; each with an enzyme (note the details of each
step are not required)
 Generate little energy (only 2 ATP molecules)
 Starts with Acetyl-CoA combines with Oxaloacetate to
produce citric acid (tricarboxylic acid) that’s why its
name like that
3) Electron transport chain
 Series of oxidation- reduction reactions ( redox)
 Energy is released by electrons transfer
 The End product is oxygen (final / terminal electron
acceptor)
 The Enzyme involved is Cytochrome oxidase
(cytochrome c, or oxidase) - transfer electrons to
oxygen, some bacteria are classified according to the
presence of the enzyme ex; oxidase positive gram
negative bacilli
 Involve 10 NADH (from glycolysis & Krebs cycle) &
2 FADH (from Krebs cycle) to produce 34 ATP
 10 NADH produce 30 ATP , 2 FADH produce 4 ATP
 In conclusion, as many as 38 ATP molecules are
produced by oxidative-phosphorylation (ADP to ATP)
from glucose catabolism including glycolysis, Krebs
cycle and electron transport chain in prokaryotic cells
 Aerobic respiration is 18 fold more efficient in releasing
energy (ATP) then anaerobic ( fermentation)
 Phosphorylation: Conversion of ADP to ATP
 Oxidation is loss of electrons while reduction is
gaining electrons
 Dehydrogenation reactions (loss of hydrogen ) occurs
in krebs cycle to produce NADH & FADH
 Chemical equation of aerobic respiration
Substrates : C6H12O6 + 6O2 + 38 ADP + 38 (P)
Products : 6H2O + 6 CO2 + 38 ATP
Fermentation of glucose : (anaerobic)
 Oxygen is NOT involved (anaerobic)
 First step: Glycolysis to produce 2 pyruvate
 Then pyruvic acid to End product , release only 2 ATP
 Examples:
- Yeast (Saccharomyces) and bacteria
(Zymomonas) Convert pyruvic acid to ethyl
alcohol
- Lactobacilli : convert pyruvic acid to lactic acid
(e.g. Yogurt)
- Streptococcus: convert pyruvic acid To lactic acid
(damage enamel of teeth)
Anabolism/Anabolic reactions
 Require energy; bonds are formed
 Energy provided by simultaneous catabolic reactions
 Example: 2 Monosaccharides will form Disaccharide ;
Similarly for Proteins & Nucleic Acids
 Organic anabolic reactions like photosynthesis &
chemosynthesis
Photosynthesis CO2+ Water Glucose + Oxygen
 Light energy will be converted to chemical energy
 Examples ; Photoautotroph, e.g. Cyanobactia
Photoheterotroph, e.g. some bacteria
 Photosynthesis is the reverse of aerobic respiration
 Oxygenic photosynthetic bacteria (Produce O2) 2-) Most ATP molecules are produced during which phase
 Anoxygenic purple/green sulfur bacteria (obligate of aerobic respiration?
anaerobic photoautotrophs), e.g. Bacteria produce S or a. electron transport chain b. fermentation
H
 If no light: organism will Survive Anaerobically by c. glycolysis d. Krebs cycle
fermentation 3) Saprophytic fungi are able to digest organic molecules
 If no CO2 Become Photoheterotroph outside of the organism by means of:
a. apoenzymes b. coenzymes
Chemosynthesis c. endoenzymes d. exoenzymes
 Chemoautotrophs: use CO2 e.g.,Archaea 4) Which of the following does (do) not occur in
(methanogens) produce methane CH4 anaerobes?
4H2 + CO2 CH4 + 2H2O
a. anabolic reactions b. catabolic reactions
 Chemoheterotrophs: Organics (other than CO2 )e.g.,
Most bacteria, Fungi Protozoa, Animals Humans c. electron transport chain d. fermentation reactions
extra note : holoenzyme is the complete active enzyme 5) . Proteins that must link up with a cofactor to function as
consist from apoenzyme ( protein part cant function alone) an enzyme are called:
+ coenzyme (cofactor) mostly mineral
a. apoenzymes b. coenzymes
Questions
c. endoenzymes d. holoenzymes
1) Which of the following characteristics do animals, fungi,
6) most bacteria are :
and protozoa have in common?
a) chemoautotroph b) photoheterotroph
a. They obtain their carbon from carbon dioxide
c) chemoheterotroph d) photoautotroph
b. They obtain their carbon from inorganic compounds
c. They obtain their energy and carbon atoms from
chemicals keys : 1)C 2) A 3) d 4) c 5) a 6) c
d. They obtain their energy from light
 YARMOUK UNIVERSITY (2020)

By: Yousef Alzoubi

Lecture # 6
 Bacterial Genetics :  Mutant (an organism with mutation), e.g. Sabin live
vaccine is a mutant strain- for poliomyelitis discovered
 Genetics: The study of heredity
by “Albert Sabin”
 Genotype (genome): Complete collection of genes
 Ames Test (1960): Mutagen may also be carcinogen
 Phenotype: Physical traits, attributes, characteristics;
(cause cancer)
(manifestations) e.g., Bacterial enzymes, capsule, flagella
Dictated by genotype Plasmid :
 Chromosome: A circular strand of linked genes compared to
 Extra-chromosomal DNA in the cytoplasm , carries
human chromosome which is linear bacterial Genes (many or few)
 Genes: Direct all functions of cell, e.g. mRNA (used In protein
 New genetic information can be acquired through
production
plasmid
Bacterial mutations :  The DNA of the plasmid which can integrate to bacterial
chromosome (called episome ) Can replicate alone
 DNA of gene may get altered,, result in Alter gene
independently (autonomous) or without chromosomal
product & Trait Transmissible to offspring
 Categories:
1. Beneficial to bacteria , e.g. resistance to antibiotic
2. Harmful to bacteria (sometimes Lethal)
e.g. Non-functioning enzyme (Lethal), not common
3. Silent: Most bacterial mutations
 Spontaneous mutations of bacteria are
(Random/Natural) & Some genes are More prone to DNA (integrated plasmid)
these mutations than others Bacterial new genetic information by :
 Rate of these mutations are 1 Per 10,000 (10^4) – 1
1 .Lysogenic conversion
Trillion (10^9) DNA replication rounds (average 1
million) 2 .Transduction
 Mutagens: chemical or physical agents with the ability
3 .Transformation
to induce mutations and increase the mutation rate
4. Conjugation
 1) Lysogenic conversion :
 Remember bacteriophages ( phages ) is the virus that
infects bacteria and it could be virulent ( initiates lytic
cycle of the bacteria ) or temperate (lysogenic) which
doesn’t cause lysis of bacteria and instead integrate its
genome with bacterial genome
 Lysogeny : injection of the viral DNA into the bacteria
without lysis
 Prophage: Remaining phage DNA in bacteria
 Lysogenic bacteria (Cell): Bacteria with the viral
prophage
 The phage DNA replicate with the bacterial genome
and transferred to the new generations (offspring)
 Phage conversion: A lysogenic bacterium is capable
of producing one or more new gene products (toxins)
and exhibit new properties may transform from
nontoxigenic bacteria to toxigenic
 Examples of microorganisms that are lysogenic
converted with prophage & become pathogenic :
1) Corynebacterium diphtheriae: Diphtheria; tox gene
2) Streptococcus pyogenes: Scarlet fever
3) Clostridium botulinum: Botulism
4) Vibrio cholerae: Cholera
2) Transduction : (“to carry across”)
 Definition: the carrying of genetic material
from one bacterial cell to another one by
bacterial virus (bacteriophage)
 Involves temperate bacteriophages
 Two types: General & Specialized
3) Transformation :
 It is the uptake of a disintegrated cell’s extracellular
naked DNA fragments by recipient (competent )
bacterial cell from environment.
 Examples:
- DNA extract of Capsulated S. pneumoniae + non-
capsulated broth will result in growing of
Capsulated M.O
- Indigenous bacterial microbiota + some latent viral
genes (in human) may be the cause of Parkinson
disease (theory!!)
 4) Conjugation :
 unidirectional transfer of the DNA from donor to
recipient cells by direct physical contact & through
donor’s hollow conjugation bridge (sex pilus = Fertility/ F
pilus).
 Donor (F+) attaches Recipient (F-) bacteria by F pilus
 Is not reproduction or Bacterial mating (male &
female) , it occur between 2 different bacteria
Examples: Enteric bacilli, Pseudomonas
 Can Transfer antibiotic resistance (R Factor= multiple
drug resistance = “superbug”) & Fertility “F” factor
(delivered by F+ & high frequency of recombination
“Hfr+”
 Relaxase splits plasmid dsDNA into ssDNA
Genetic engineering (vs. Recombinant DNA
Technology) :

 rDNA : human genes are transferred to plasmid ( vector

or vehicle ) which ca carry these genes
 (Genetic Engineering): is the insertion of this rDNA to
manufactures ex: ( E. coli, Yeast, human macrophages
and fibroblasts) to produce certain products ex:
 Growth hormone (GH)
 Somatostatin (Inhibitor)
 •Insulin • Interferon
 Resistant plants in “agriculture”
 Marine bacterium to break oil down for clearance
 Gene Therapy : Insertion of normal human gene into 3) he process whereby naked DNA is absorbed
cells:
into a bacterial cell is known as:
 Viral delivery (e.g. adenoviruses, retroviruses)
 Bacterial (Bacto-infection, e.g., Salmonella) a. transcription b. transduction
c. transformation d. translation
 Prescribe genes (considered as drugs) to treat:
• Autoimmune diseases 4) In lysogenic conversion, bacteria acquire new
• Sickle cell anaemia genetic information in the form of:
• Immunodeficiency disorders
a. bacterial genes b. naked DNA
• Cancers
• Many other conditions c. R-factors d. viral genes
5) The process by which a nontoxigenic C. diphtheriae
Questions : cell is changed into a toxigenic cell is called:
1) Which of the following processes does not a. conjugation b. lysogenic conversion
involve bacteriophages?
c. transduction d. transformation
a. lysogenic conversion b. lytic cycle
c. transduction d. transformation

2) in transduction, bacteria acquire new genetic

keys : 1) d 2) a 3) c 4) d 5) b
information in the form of:
a. bacterial genes b. naked DNA
c. R-factors d. viral genes
 YARMOUK UNIVERSITY (2020)

By: Yousef Alzoubi

Lecture # 7
Sterilization & disinfection :  Microbicidal Agents : The suffix cide or cidal refers to
“killing”
 Sterilization : the destruction or elimination of all
 Examples:
microbes, including cells, spores, and viruses.
• Bactericidal = Kill bacteria
 When something is sterile, it is devoid of microbial life.
• Sporicidal = Kill bacterial spores
 sterilization of objects can be accomplished by physical
• Viricidal = Kill viruses
or chemical methods :
• Fungicidal = Kill fungi
•Dry heat
• Pseudomonicidal= Kill Pseudomonas
• Autoclaving (steam under pressure)
• Tuberculocidal = Kill M. tuberculosis
• Ethylene oxide gas
 Microbiostatic agents : Drugs or chemicals that inhibit
• Formaldehyde liquid
reproduction and metabolism of microorganisms (NOT
• Radiation (UV, gamma rays)
necessarily kill them)
 Disinfection : the elimination of most or all pathogens
 Freeze-drying (lyophilization) and rapid freezing are
(except bacterial spores) from nonliving objects using :
microbistatic techniques that are used to preserve
1. Liquid chemicals (disinfectants)
microbes for future use or study
2. Wet pasteurization
 Lyophilization : is a process that combines dehydration
 Antiseptics: Disinfectants used on living tissues as the
(drying) and freezing , a good method of preserving
skin.
microorganisms for future use.
 Sanitization: Reduction of the microbial population to
 Sepsis : refers to the presence of pathogens in blood or
safe levels, e.g. in restaurants
tissues.
 Pasteurization : a method to disinfect liquids , is used
 Asepsis means the absence of pathogens.
today to eliminate pathogens from milk and most other
 Aseptic techniques : various medical or surgical
beverages.
techniques, used to eliminate and exclude pathogens.
 pasteurization is not a sterilization procedure, because
e.g, hand hygiene, sterile gloves, masks, and gowns
not all microbes are destroyed
 Antisepsis : is the prevention of infection
 pasteurization methods (important) :
63 C for 30 minutes  Antiseptic technique: Use of antiseptics
72 C for 15 seconds
140 C for 4 seconds
Physical Methods to Inhibit Microbial Growth :
1) Heat :
 the most common type of sterilization for inanimate
(non-living) objects able to withstand high temperatures.
 Two factors—temperature and time—determine the
effectiveness of heat for sterilization.
 pathogens are usually more susceptible to heat than
nonpathogens.
 thermal death point (TDP) : is the lowest temperature
that will kill all the organisms in a standardized pure
culture within a specified period.
 thermal death time (TDT) : is the length of time
necessary to sterilize a pure culture at a specified
temperature.
Dry heat :
 Dry-heat baking in a controlled oven provides effective
sterilization of metals, glassware, some powders, oils,
and waxes
 160 – 165 C for 2 hours or 170 – 180 C for 1 hour
 Incineration (burning) : is an effective means of
destroying contaminated disposable materials.
 An incinerator must NOT be overloaded with moist or
protein laden materials, such as feces, vomitus, or pus,
because the contaminating microorganisms within these
moist substances may not be destroyed if the heat does
not penetrate and burn them.
 Flaming: by Bunsen burner flame or electrical heat
device is an effective way to kill microorganisms for
forceps, wires, or loops
Moist heat :
 Heat applied in the presence of moisture, as in boiling,
is faster and more effective than dry heat
 The vegetative forms of most pathogens are quite easily
destroyed by boiling for 30 minutes. (needles , metal or
glass)
 Not effective against spores, viruses and
Mycobacterium
 An autoclave : is a large metal pressure cooker that
uses moist heat and pressure to completely destroy all
microbial life (Kills spores, viruses, and vegetative form)
 Autoclaves should be set to run 20 minutes at a
pressure of 15 psi and a temperature of 121.5 C.
 rubber, which may be damaged by high temperatures,
can be autoclaved .
 Cans should remain open, bottles covered loosely with
cotton, Sealed containers should not be autoclaved.
 Indicators for Autoclave completion :
Autoclave tape or Solutions of bacterial spores

2) Cold :
 Most microorganisms are not killed by cold
temperatures and freezing .
 Refrigeration cannot be relied upon to kill
microorganisms; it merely slows their metabolism and
their rate of growth
 Slow freezing causes ice crystals to form within cells
and may rupture the cell walls of some bacteria; hence,
slow freezing should not be used as a way to preserve
or store bacteria.
 Rapid freezing, using liquid nitrogen, is a good way to
preserve food, and bacterial cultures
 Freeze-thawing foods allow bacterial spores in the
foods to germinate and microorganisms to resume
growth. Consequently, refreezing of thawed foods is an
unsafe practice, because it preserves the millions of
microbes that might be present.
3) Desiccation (Drying) :
 Desiccation doesn’t kill microorganisms.
 In the hospital or clinical environment, healthcare
professionals should keep in mind that dried viable
pathogens may be present in dried matter and clinical
specimens, including blood, pus, fecal material, and
dust that are found on floors, in bedding, on clothing.
4) Radiation :
 Many biologic materials, such as sera, antisera,
toxins, and vaccines, are sterilized with UV rays
 UV rays penetrate cells and, thus, can cause damage
to DNA (skin cancer, eye damage)
 X-rays and gamma and beta rays of certain
wavelengths may be lethal or cause mutations in
microorganisms and tissue cells because they damage
DNA and proteins within those cells
 Gamma ray sterilizes food as meat
from Salmonella & Campylobacter.
 International symbol for irradiated
food.
5) Ultrasonic US waves :
 In hospitals, medical clinics, and dental clinics,
ultrasonic waves are frequently used to clean delicate
equipment (glassware) .
 Ultrasonic cleaners consist of tanks filled with liquid
(water) ,the short sound waves are then passed through
the liquid. The sound waves mechanically dislodge
organic debris on instruments and glassware.
Glassware then must be washed to remove the
dislodged particles then sterilized by another method
before they are used.
6) Filtration:
 Filters of various pore sizes are used to filter or
separate cells, larger viruses, bacteria, and other
microorganisms from the liquids or gases
 High-Efficiency Particulate Air (HEPA) filters used in
operating rooms or patient room to filter air and remove
pathogens.
 positive pressure isolation room for bone marrow
transplantation
 negative pressure isolation room for contagious
diseases
 7) gaseous atmosphere :
 it is possible to inhibit growth of microorganisms by
altering the atmosphere in which they are located
 Because aerobes and microaerophiles require oxygen,
they can be killed by placing them into an atmosphere
devoid of oxygen.
 obligate anaerobes can be killed by placing them into
an atmosphere containing oxygen
 wounds likely to contain anaerobes are lanced (opened)
to expose them to oxygen
 gas gangrene, a deep wound infection that causes rapid
destruction of tissues. Gas gangrene is caused by
various anaerobes mainly Clostridium perfringens.
gas gangrene can be treated by placing the patient in a
hyperbaric (increased pressure) oxygen chamber to
kill the microorganisms.
Chemical Agents to Inhibit Microbial Growth :
1) disinfectants :
 inhibit the growth of pathogens, either temporarily or
permanently.
 Factors affecting disinfectants:
• Prior cleaning of the object or surface to be
disinfected.
• The organic load that is present, meaning the
presence of organic matter (e.g., feces, blood, vomitus,
pus)
• The bioburden, meaning the type and level of
microbial contamination.
• The concentration of the disinfectant.  Never use disinfectant if physical sterilization is possible
• The contact time, meaning the amount of time that the because disinfectants cant destroy all bacteria and
disinfectant must remain in contact with the organisms bacterial spores.
in order to kill them
 Formaldehyde (fumigation) and ethylene oxide, when
• The physical nature of the object being disinfected
properly used, are highly destructive to spores,
(e.g., smooth or rough surface)
mycobacteria, and viruses. (sterilizers)
• Temperature and pH
 Disinfectants characteristics (broad, fast-acting, stable,
 Almost all bacteria in the vegetative state, as well as
nontoxic, soluble in water, inexpensive, odorless, not
fungi, protozoa, and most viruses, are susceptible to
affected by organic material and leave residual
many disinfectants
microbial film)
 Some Resistant microbes to disinfectants :
 Antiseptics : chemical agents that can safely be
Mycobacteria, Pseudomonas spp, bacterial endospore, applied to human skin e.g., alcohol, iodine, H2O2
fungal spores, hepatitis viruses
 Reduce numbers of organisms on surface & Used at
surgical incisions, and folds of the skin.
Questions: 7-) which of the following not sterilized by dry heat:
1) Pasteurization is an example of what kind of technique? a- Metals b- glassware
a. antiseptic technique b. disinfection
c- oils d- waxes e- anti-sera
c. sterilization d. surgical aseptic technique
8-) Vaccines are sterilized by:
2) It would be necessary to use a tuberculocidal agent to
kill a particular species of: a- radiation b- formaldehyde
a. Clostridium b. Mycobacterium c- dry heat d- ultrasonic waves e- moist heat
c. Staphylococcus d. Streptococcus 9-) which of the following not used for sterilization:
3) The combination of freezing and drying is known as: a- autoclave b- ethyl oxide
a. desiccation b. lyophilization c- formaldehyde d- desiccation e- incineration
c. pasteurization d. tyndallization 10) Sterilization of delicate dental equipment can be
achieved efficiently by using one of the following
4) To prevent Clostridium infections in a hospital setting,
procedures:
what kind of disinfectant should be used?
a) Ultrasonic waves. b) desiccation
a. fungicida l b. pseudomonicidal
c) gamma rays d) UV- light
c. sporicidal d. tuberculocidal
11) The optimal conditions to achieve proper autoclaving
5) Sterilization can be accomplished by use of:
is by applying one of the following settings regarding
a. an autoclave b. antiseptics pressure (psi), temperature ( C) and time (minutes)
respectively:
c. alcohol d. pasteurization
a) 30 - 63 – 30 b) 15 – 121.5 – 30
6) Which of the following eliminate all microbes:
c) 15 – 121.5 – 20 d) 30 – 121.5 – 20
a- antiseptics b- disinfectants
keys : 1) b 2) b 3) b 4) c 5) a 6) e 7) e 8) a
c- sanitization d- Pasteurization
9) d 10 ) a 11) c
e- none of above
 YARMOUK UNIVERSITY (2020)

By: Yousef Alzoubi

Lecture # 8
Antimicrobial Agents :
 chemotherapeutic agent : is any drug used to treat any
condition or disease.
 antimicrobial agents : chemotherapeutic agents used to
treat infectious diseases ex: Anti-Bacterial , Anti-Viral , Anti-
Fungal , Anti-Protozoal
 Antibiotic : is a substance produced by a microorganism that
is effective in killing or inhibiting the growth of other
microorganisms. Antibiotics are primarily antibacterial
agents
Examples: Mould-produced: Penicillin, Cephalosporin
Bacteria (mainly soil bacteria) produced:
Erythromycin, Chloramphenicol
 Types of Antibiotics/Antimicrobials  Characteristics of an ideal antimicrobial agent :
1. Natural AB e.g. Peniciilin G
2. Semisynthetic AB, e.g. Modified AB (Ampicillin, • Kill or inhibit the growth of pathogens
Carbenicillin) • Cause no damage to the host (selective toxicity)
3. Synthetic Antimicrobials e.g. Monobactam (Aztreonam)
• Cause no allergic reaction in the host
 In 1928, Alexander Fleming , a Scottish bacteriologist,
accidentally discovered the first antibiotic when he noticed • Be stable when stored in solid or liquid form
that growth of contaminant Penicillium notatum mould
• Remain in specific tissues in the body long enough to be
colonies on his culture plates was inhibiting the growth of
effective
Staphylococcus bacteria .
 Fleming gave the name “penicillin” to the inhibitory • Kill the pathogens before they mutate and become resistant
substance being produced by the mould to it
 Selective toxicity: The drug affects microorganisms but NOT
human cells.
How antimicrobial agents work :  Extended spectrum Antibiotics : Broad spectrum antibiotics
with extended activity against certain microbes such as
 an antimicrobial agent must inhibit or destroy the pathogen
certain resistant gram negative bacteria, Pseudomonas, or
without damaging the host (the infected person).
others.
 To accomplish this, the agent must target a metabolic
 Competitive inhibitors drugs :
process or structure possessed by the pathogen but not
 Example: sulfonamide (sulfa drugs)
possessed by the host.
 sulfonamide drugs inhibit production of folic acid (a vitamin)
 The five most common mechanisms of action of
in those bacteria that require p-aminobenzoic acid (PABA) to
antimicrobial agents are as follows:
synthesize folic acid. Because the sulfonamide molecule is
• Inhibition of cell wall synthesis
similar in shape to the PABA molecule .
• Damage to cell membranes
• Inhibition of nucleic acid synthesis (either DNA or RNA)  the enzymes that convert PABA to folic acid cannot produce
• Inhibition of protein synthesis folic acid from the sulfonamide molecule.
• Inhibition of enzyme activity  Without folic acid, bacteria cannot produce certain essential
 Bacteriostatic drugs inhibit growth of bacteria, whereas proteins and its growth will be inhibited (bacteriostatic)
bactericidal agents kill bacteria .  Cells of humans and animals do not synthesize folic acid
 Bacteriostatic agents Should NOT be used in from PABA ; they get folic acid from the food they eat.
immunocompromised or leukopenic patients. Consequently, they are unaffected by sulfa drugs.
 Bacteriostatic agents should be used only in patients whose
host defense mechanisms are functioning properly
(immunocompetent)
 Narrow-spectrum antibiotic: Destroy (affect) either gram
positive or gram negative bacteria
, Examples: Vancomycin: G+ Colistin : G -
 Broad spectrum antibiotic: Destroy (affect) both gram
positive and gram negative bacteria
Examples: Ampicillin , Chloramphenicol , Tetracycline
 Beta lactam drugs include : penicillin's , cephalosporins ,
carbapenems , monobactams all work by inhibiting cell
synthesis & all are bactericidal
1) Penicillin's :
 β-lactam drugs because their molecular structure includes a
four-sided ring structure known as a β-lactam ring
 MOA: inhibit cell wall synthesis.
 have maximum effect on bacteria that are actively dividing.
 They are bactericidal drugs.
 Natural penicillins (penicillin G & penicillin V)
are effective against some G + bacteria (especially
Streptococcus spp.), anaerobic bacteria, and spirochetes &
few Gram-negative bacteria (e.g., N. meningitidis and
Haemophilus influenzae)
 aminopenicillin and Extended penicillin:
e.g. Ampicillin, Amoxicillin 5. Fifth generation: e.g., Ceftaroline
• Against G- and G+ bacteria G+ as methicillin-resistant Staph.aureus (MRSA) & weaker on
2) Cephalosporins : G-
 β-lactam antibiotics , produced by moulds like penicillin , NOTE : staph aureus is divided according to susceptibility to
inhibit cell wall synthesis and are bactericidal. methicillin (penicillin type) to MSSA & MRSA
 Divided into 5 generations : 3) Monobactam :
1. First generation: e.g., cephalexin cover G+ bacteria  Beta-lactam drug, inhibits cell wall synthesis.
2. Second generation: e.g., cefuroxime  Example: Aztreonam (synthetic drug)
Increased activity against G- (besides G+)  Active against gram negative rods (bacilli)
3. Third generation: e.g., cefotaxime.  Not active against gram positive bacteria
More G- & Pseudomonas (besides G+, but less)  Not active against anaerobes
4. Fourth generation: e.g., cefepime
More G- & Pseudomonas & G+
 4) carbapenems : 2) Aminoglycosides :
 Beta lactam drug, inhibit cell wall synthesis  Broad-spectrum drug (e.g. Gentamicin, Amikacin)
 Active against most G+, G-, and anaerobes  Bactericidal (Inhibit protein synthesis)
 Examples :  Effective against:
• Imipenem: Inactivated by dihydropeptidase enzyme •Many G- and some G+ bacteria
(DHP) secreted from renal tubules ; so protected by • Enterobacteriaceae
Cilastatin (inhibit DHP) • V. cholera • P. aeruginosa
• Meropenem: Not inactivated by DHP enzyme  NOT effective against anaerobes (Anaerobic bacteria is
• Ertapenem: Not active against P. aeruginosa, is long acting naturally resistant to aminoglycosides)
 Ototoxic (damage to 8th nerve responsible for hearing)
Drugs acting by disruption of cell membrane : Nephrotoxic (damage to kidney )
 Examples : polymyxin B , polymyxin E (colistin) and bacitracin
 Bactericidal drugs & active against gram negative bacteria 3) Macrolides :
 Examples : Erythromycin, Clarithromycin
Drugs acting by inhibition of protein synthesis:
 Inhibit protein synthesis
1) Tetracyclines :  Bacteriostatic (at low doses) & Bactericidal (at Higher doses)
 Broad-spectrum drug (e.g. Tetracycline, Doxycycline)  Effective against:
 Action on ribosome in cytoplasm (inhibit protein synthesis) •Many G+ and some G- bacteria
 Bacteriostatic • Atypical bacteria (Chlamydia , Mycoplasma)
 Effective against: • treponema pallidum (syphilis)
• G+ and G- bacteria • legionella
• Atypical bacteria (Chlamydia , Mycoplasma , Rickettsia)
• Vibrio cholerae 4) Linezolid
• Spirochete bacteria (Borrelia, Treponema pallidum which 5) chloramphenicol
causes syphilis)
just know that these 2 drugs work by inhibiting protein
synthesis
 Drugs acting by inhibition of nucleic acid synthesis:
1) Rifampin : bactericidal , cover G+ and some G- bacteria
2) Quinolones & fluoroquinolones (e.g. ciprofloxacin ) they
inhibit DNA synthesis & are bactericidal broad spectrum
drug effective against: Enterobacteriaceae &
Pseudomonas. Aeruginosa
3) Metronidazole : bactericidal drug works by destruction of
DNA & effective against Anaerobes
Drugs acting by inhibition of enzyme activity :
1) Sulfonamide : bacteriostatic drug covers primarily G+ &
some G- bacteria
2) Trimethoprim : bacteriostatic drug covers mainly gram
negative & some gram positive
Synergism : the use of two antimicrobial agents produces a
degree of pathogen killing that is far greater than that achieved
by either drug alone or the sum of both. 1+1 >2
Example: Co-trimoxazole (Trimethoprim + sulfamethoxazole) ,
(Jordanian name : Balkatrin)
(TMP : SMX ratio is 1:5 ) e.g. 40/200 or 80/400
Antagonism : the use of two drugs produces pathogen killing
that is less than that achieved by either drug alone 1+1 < 1
Example: Penicillin (bactericidal) + Tetracycline (static) ,
These two drugs actions antagonize each other because
tetracycline is bacteriostatic and inhibit bacterial growth and
division & penicillin works effectively against the actively
dividing bacteria .
In general don’t give bacteriostatic agent with bactericidal
Multidrug therapy : Using two or more drugs simultaneously to
kill all the pathogens and to prevent resistant mutant pathogens
from emerging.
Example: Mycobacterium tuberculosis treatment usually
requires 3 or 4 drugs : (isoniazid + rifampin + pyrazinamide +
ethambutol)
Questions : 6-) All of the following antimicrobial agents can inhibit nucleic
acid synthesis, EXCEPT:
1-) Which of the following is not a common mechanism by
which antimicrobial agents kill or inhibit the growth of bacteria? a. Rifampin b. quinolone
a. damage to cell membranes b. destruction of capsules
C. linezolid d. ciprofloxacin
c. inhibition of cell wall synthesis
7-) One of the following antibiotics is a narrow spectrum
d. inhibition of protein synthesis antibiotic, which one is it?
2-) Multidrug therapy is always used when a patient is a. Vancomycin b. cefotaxime
diagnosed as having:
C . gentamicin d . imipenem
a. an infection caused by MRSA b. diphtheria
8-) Good synergism can be achieved by all of the following
c. strep throat d. tuberculosis antimicrobial agent combinations, EXCEPT:
3-)Which of the following scientists discovered penicillin? A . penicillin + gentamicin b. penicillin + doxycycline
a. Alexander Fleming b. Paul Ehrlich C . trimethoprim + sulfamethoxazole
c. Selman Waksman d. Sir Howard Walter Florey D . cefotaxime + amikacin
4-) All the following antimicrobial agents work by inhibiting 9-) One of the following antibiotics can cause nephrotoxicity
protein synthesis except: and ototoxicity :
a. chloramphenicol b. erythromycin A . ampicillin b. rifampin
c. imipenem d. tetracycline C . gentamicin d . clarithromycin
5-) All the following antimicrobial agents work by inhibiting cell
wall synthesis except:
Keys : 1) b 2) d 3) a 4) c 5) b 6) c 7) a 8) b 9) c
a. cephalosporins b. polymyxin
c. penicillin d. aztreonam
 YARMOUK UNIVERSITY (2020)

By: Yousef Alzoubi

Lecture # 9+10
Antifungal agents :
 Antifungal and antiprotozoal drugs tend to be more toxic to
the patient because, like the infected human, they are
eukaryotic organisms.
 Most antifungal agents work in one of three ways:
• By binding with cell membrane sterols (e.g., nystatin and
Amphotericin B)
• By interfering with sterol synthesis (e.g., miconazole)
• By blocking mitosis or nucleic acid synthesis (e.g.,
Griseofulvin )
Antiprotozoal Agents :
 Toxic to the host and work by:
• Interfere with DNA and RNA synthesis e.g. Chloroquine
(anti-malarial drug)
•Interfere with protozoal metabolism and DNA destruction:
e.g. Metronidazole (Flagyl) also against anaerobic bacteria
Antiviral agents :
 Antiviral agents are particularly difficult to develop and use
because viruses are produced within host cells
 The first antiviral agent effective against (HIV) was
introduced in 1989 Zidovudine (AZT)
Drug resistant :
 Drug resistant bacteria are called (Superbugs)
 Superbugs USUALLY are Multidrug Resistant (resistant to
more than one antimicrobial)
 Although the term superbug most often refers to multidrug-
resistant bacteria, other types of microbes (e.g., viruses,
fungi, protozoa and helminths) have also become multidrug-
resistant.
 Examples on Especially Troublesome “Superbugs”
(important resistant bacteria) :
• MRSA (methicillin resistant staph aureus) , MRSE
(methicillin resistant staph epidermidis)
• VISA (vancomycin-intermediate S. aureus) , VRSA
(vancomycin-resistant S. aureus)
• VRE (Vancomycin-resistant Enterococcus) (causes UTI)
• P. aeruginosa
• Clostridium difficile (which causes pseudomembranous
colitis)
• Acinetobacter baumanni
• Klebsiella pneumonia
• Multidrug-resistant M. tuberculosis (MDR-TB) = Resistant
to rifampin and isoniazid.
 Mechanisms of bacterial resistance :
Intrinsic resistance: Natural
Acquired resistance: Acquired (4 mechanisms in the table )

Beta-Lactamases :
 Some bacteria produce enzymes that destroy the β-lactam
ring; these enzymes are known as β-lactamases
 Thus, an organism that produces a β-lactamase is resistant to
antibiotics containing the β-lactam ring
 There are two types of β-lactamases Penicillinases and
cephalosporinases they destroy the β-lactam ring in
penicillin's and cephalosporins, respectively.
 Some bacteria produce 1 or both types of β-lactamases.
 Prevention of Beta-lactamase action is by Combining :
beta-lactamase Inhibitors + antibiotics; examples :
• Clavulanic acid + Amoxicillin = Augmentin
• Sulbactam + Ampicillin = Unasyn
• Clavulanic Acid + Ticarcillin = Timentin
• Tazobactam + Piperacillin = Zosyn
 Strategies against drug resistance :
• Education of both patients & doctors , Prudent (wise) use of
drugs
• Proper prescription of drugs
• Starting Firstly with : Narrow spectrum & inexpensive drug
• Complete the full course of drug as prescribed
• No need for prophylactic drug taking unless prescribed by
clinician
• Good infection control and prevention of infections
Empiric therapy :
 In some cases, a clinician must start therapy before
laboratory culture & tests are available. This is referred to as
empiric therapy
 clinician “guess” the most likely pathogen and the drug most
likely to be effective
 Clinician can refer to a “pocket chart” or Antibiogram that is
available in most hospitals & Clinical Microbiology Lab
 If the patient is allergic to any antimicrobial agents like
penicillin it would be unwise to prescribe it
 age of the patient is important when prescribing drug , some
drugs are contraindicated in children like tetracycline in <7 y
 pregnancy , Certain drugs are known to be teratogenic
 Inpatients VS. outpatient treatment
 Site of infection, e.g. Brain, bladder, etc.
 What other medications is the patient taking or receiving , to
prevent (Drug cross-reaction)
 Toxic side effects of some drugs , e.g. Chloramphenicol
causes Aplastic Anemia
Streptomycin (aminoglycoside) causes Deafness (ototoxic)
 immune status of patient & drug cost
 Prolonged antibiotic use can lead to population explosions
of microorganisms that are resistant to the antibiotic(s) .
Such overgrowths are known as “superinfections.”
For example, the prolonged use of oral antibiotics (e.g.
lincomycin) can result in a superinfection of Clostridium
difficile in the colon, which can lead to antibiotic-associated
diarrhea and pseudomembranous colitis.
Yeast vaginitis often follows antibacterial therapy (e.g.
tetracycline) because many bacteria of the vaginal microbiota
were destroyed, leading to a superinfection of the indigenous
yeast, Candida albicans
Normal flora :
 Microbial ecology : is the study of the numerous
interrelationships between microbes and the world around
them.
 The most intimate association that we have with microbes is
the presence of microflora both on and within our bodies.
 Symbiosis : is the living together or close association of two
dissimilar organisms (usually two different species)
 Various symbiotic relationships involving microbes :
• Neutralism : different microorganisms occupy the same
ecologic place, but have no effect on each other
• Commensalism : is a relationship that is beneficial to one
symbiont and of no consequence (neither beneficial nor
harmful) to the other
• Mutualism : is a relationship that is beneficial to both
symbionts
• Parasitism : is a relationship that is beneficial to one
symbiont (the parasite) and harmfull to the other symbiont
(the host).
 indigenous microbiota (human microbiome or human
bioneme) includes all of the microbes (bacteria, fungi,
protozoa, and viruses) that reside on and within that person.
 During pregnancy, the human fetus lives in a remarkably
protected & sterile environment from microflora
 The first exposure of microflora to the baby is during labor
when the baby is delivered through the birth canal , he will
gains some microflora
 Over the next few years of life , communities of organisms
(microbiota or normal flora) form on the surfaces of the skin,
nares, oral cavity, intestines, and genitourinary tract.
 The child gets the normal flora from the surrounding
environment (most importantly by exposure to soil ) ,
exposure to microflora will strengthen & increase the child
immunity.
 The Human Microbiome Project : 5-year multinational study
to analyze the genetic composition (microbiome) of the
microbial populations that live in and on healthy adults by
the collection of samples from different body organs.
 It is estimated that bacterial cells outnumber human cells in
the host by 10 : 1 ratio
 Bacteria colonizing the gut are different from those in the
mouth, skin, and other body sites
 The greatest taxonomic and genetic diversity of microflora
was in the large intestine (colon) , and the vagina was the
least complex.
 different regions of the mouth, gut, skin surface, and vagina
also had their own unique microbiome
 Most individuals share a core microbiome, defined as the
species that are present at a specific site in 95% or more of
individuals. (e.g. staphylococcus on skin )
 Secondary microbiome consists of small numbers of many
species that may not be widely shared by individuals . (e.g.
Propionibacterium on skin)
 The greatest numbers of shared species are present in the
mouth, followed by the nose, intestine, and skin, and the
fewest shared species are found in the vagina
Microbiota of the Skin :
 The resident microbiota of the skin consists primarily of
bacteria and fungi—as many as 300 different species,
depending on the anatomical location.
 the most common bacteria on the skin are species of
Staphylococcus (especially S. epidermidis and other
coagulase-negative staphylococcia), Corynebacterium, and
Propionibacterium
 The number and variety of microorganisms present on the
skin depend on many factors, such as:
 Anatomical location
 Amount of moisture present
 pH  Temperature  Salinity
 Presence of chemical wastes such as urea and fatty acids
 Presence of other microbes, which may be producing toxic
substances to other microbes
Microbiota of the Ears and Eyes:
 The middle ear and inner ear are usually sterile, whereas the
outer ear and the auditory canal contain the same types of
microbes as are found on the skin.
Microbiota of the Respiratory Tract :
 The upper respiratory tract consists of the nasal passages
and the throat (pharynx), which have an abundant and
varied population of microbes.
 The lower respiratory tract consists of the larynx (voice box),
trachea, bronchi, bronchioles, and lungs, usually free of
microbes and the presence of microbes may indicate
infection
Microbiota of the Oral Cavity (Mouth) :
 The anatomy of the oral cavity (mouth) affords shelter for
numerous anaerobic and aerobic bacteria.
 The list of microbes that have been isolated from healthy
human mouths include Gram-positive and Gram negative
bacteria (both cocci and bacilli), spirochetes, and sometimes
yeasts, mould-like organisms, protozoa, and viruses.
 The bacterium most often associated with formation of
dental plaque is Streptococcus mutans.
Microbiota of the GI Tract :
 Excluding the oral cavity and pharynx, which have already
been discussed, the GI tract includes the esophagus,
stomach, small intestine, large intestine (colon), and anus.
 Accessory glands and organs of the GI system include the
salivary glands, pancreas, liver, and gallbladder.
  gastric enzymes and the extremely acidic pH (pH <3) of the
stomach usually prevent growth of indigenous microbiota
 There is one bacterium—a Gram-negative bacillus named
Helicobacter pylori— which produces urease enzyme that
increase the PH around it to 5.5 & lives in some people’s
stomachs and is a common cause of ulcers.
 When the amount of acid is reduced in the course of
diseases (increase PH) such as stomach cancer, certain
bacteria may be found in the stomach.
 The colon contains the largest number and variety of
microorganisms in the body as many as 500 to 600 different
species— primarily bacteria.
 Bacteria found in the GI tract include: Actinomyces,
Bacteroides, Clostridium, Enterobacter, Enterococcus,
Escherichia, Klebsiella, Lactobacillus, Proteus, Pseudomonas,
Staphylococcus, and Streptococcus. Also, many fungi,
protozoa, and viruses can live in the colon
Microbiota of the GU Tract (genito-urinary) :
 The GU tract consists of the urinary tract (kidneys, ureters,
urinary bladder, and urethra) and the various parts of the male
and female reproductive systems
 The healthy kidney, ureters, and urinary bladder are sterile.
 the distal urethra (the part of the urethra farthest from the
urinary bladder) and the external opening of the urethra harbor
many microbes, including bacteria, yeasts, and viruses.
 The reproductive systems of both men and women are usually
sterile, with the exception of the vagina here , the microbiota
varies with the stage of sexual development.
 Before puberty and after menopause, vaginal secretions are
alkaline, supporting the growth of various diphtheroids,
streptococci, staphylococci, and coliforms (E. coli)). Through the
childbearing years, vaginal secretions are acidic (pH 4.0–5.0),
encouraging the growth mainly of lactobacilli
Beneficial and Harmful Roles of Indigenous Microbiota :
 Some of our intestinal bacteria are beneficial to us in that
they produce useful vitamins and other nutrients
 Microorganisms of the normal flora may aid the host (by
competing for microenvironments & prevent pathogens as
Salmonella spp)
 May harm the host (by causing dental caries, abscesses, or
other infectious diseases)
 May exist as commensals (inhabiting the host for long
periods without causing detectable harm or benefit).
Microbial Antagonism :
 means “microbes versus microbes” or “microbes against
microbes by preventing other microbes from becoming
established in or colonizing a particular anatomic location.
1. Competition for nutrition
2. Competition for space
3. Production of antibiotics and bacteriocins.
 Opportunistic Pathogens : Many members of the indigenous Synergism (Synergistic Infections) : Sometimes, two (or more)
microbiota waiting for the opportunity to cause infections microorganisms may “team up” to produce a disease that
 Biotherapeutic Agents (probiotics) : Bacteria and yeasts that neither could be caused by one of them. This is referred to as
are ingested to reestablish and stabilize the microbial synergism or a synergistic relationship.
balance within our bodies .
 The diseases are referred to as synergistic infections,
 Prebiotics : giving supplements to enhance growth of polymicrobial infections, or mixed infections.
microflora
 A variety of human pathogens live in soil, including:
 Fecal transplant : to extract normal flora from feces and
 Various Clostridium species (spore former bacteria)
giving them to patient which has completely lost all his
 The spores of Bacillus anthracis
microflora
 Various yeasts
 indigenous microbiota is upset by antibiotics, other types of
 The types and amounts of microorganisms living in soil
chemotherapy, or changes in pH .
depend on many factors, including: The amount of decaying
 Cultures of Lactobacillus in yogurt or in medications may be
organic material, Available nutrients, Moisture content,
prescribed to reestablish and stabilize the microbial balance
Amount of oxygen available, pH, temperature, The presence
 Disruption of the normal microflora (commonly referred to
of waste products of other microbes.
as dysbiosis) can lead to disease by the elimination of
 Zoonotic diseases (zoonosis) : diseases of farm animals, wild
needed organisms or allowing the growth of inappropriate
animals, zoo animals, and domestic pets which is transmitted
bacteria
to humans (making 70 % of diseases)
 Shifts in the skin microbiome may cause wound infections
and dermatitis
 Alteration in the vaginal microbiome may cause vaginitis.
Microbial Communities (Biofilms) : In nature, microbes are
often organized into complex and persistent communities of
assorted organisms
 Biofilms have been implicated in diseases such as
endocarditis, cystic fibrosis, middle ear infections, kidney
stones, periodontal disease, and prostate infections.
Questions: 6) The term that best describes a symbiotic relationship in
which two different microorganisms occupy the same ecologic
1-) The greatest number and variety of indigenous microbiota of
place, but have absolutely no effect on each other is:
the human body live in or on the:
a. commensalism b. mutualism
a. colon b. genitourinary tract
c. neutralism d. parasitism
c. mouth d. skin
7) Which of the following is least likely to be taken into
2) Which of the following sites of the human body does not
consideration when deciding which antibiotic to prescribe for a
have indigenous microbiota?
patient?
a. bloodstream b. colon
a. patient’s age
c. distal urethra d. vagina
b. patient’s underlying medical conditions
3) Which of the following would be present in highest numbers
c. patient’s weight
in the indigenous microbiota of the skin?
d. other medications that the patient is taking
a. C. albicans b. coagulase-negative staphylococci
8) Which of the following is least likely to lead to drug resistance
c. Enterococcus spp. d. E. coli
in bacteria?
4) The indigenous microbiota of the external ear canal is most
a. A chromosomal mutation that alters cell membrane
like the indigenous microbiota of the:
permeability
a. colon b. mouth
b. A chromosomal mutation that alters the shape of a particular
c. skin d. distal urethra drug-binding site
5) Which of the following is not a common mechanism by which c. receiving a gene that codes for an enzyme that destroys a
antifungal agents work? particular antibiotic
a. by binding with cell membrane sterols d. receiving a gene that codes for the production of a capsule
b. by blocking nucleic acid synthesis
keys : 1) a 2) a 3)b 4) c 5) c 6) c 7) c 8) d
c. by dissolving hyphae d. by interfering with sterol synthesis