Topic 1: Microbial World and You Microbiology – a specialized area of

biology that deals with living things

ordinally too small to be seen without
 Microorganism (microbes) are magnification
organism that requires microscope Microscopic organism, it is referred to
 Microbes are dominant organisms as microorganisms or microbes
on earth -Gr. Mikros (small) and scopein (to see)
 Bacteria, Algae, Protozoa, Fungi, microbes
Parasitic Worms, and Viruses are -Gr. Mikros (small) and bios (life)
major groups of microorganisms
 Genetics, Immunology, Several Major Groups of
Biochemistry, Epidemiology, and Microorganisms
Ecology are other areas of sciences -Bacteria, Viruses, Fungi, Protozoa, and
that are in microbiology involving helminths
cell structure.  Different biological characteristics
 Microorganisms are essential to  Nature of microorganisms can be
the operation of the earths easy or difficult
ecosystem, as photosynthesizes, Easy – reproduce rapidly and can
decomposers, and recyclers quickly grow large populations in the
 Versatility of microbes to make laboratory
improvements in the industrial Difficult – cannot be seen directly
production, agriculture, medicine
and environmental protection Microbiology
 Beneficial qualities of microbes Vs.  One of the largest and most complex
Infections diseases of the biological science
 Microorganisms are the oldest  Deals with every aspects of microbes
organisms o Genetics
 The use of Scientific Method to o Physiology
develop theories and explanation o Characteristics – disease or
 Marked with significant discoveries to benefits
and events in microscopy, culture o Interaction with
technique, and other methods of environment
handling or controlling microbes o Interaction with
 Microbes are classified into groups mammalian host
according to evolutionary o Uses industry and
relationships, provided with
agriculture
standard scientific names, and
Microbes, also called microorganisms,
identified by the specific
- tend to be associated only with
characteristics
common inconveniences such as
spoiled food, or with major diseases
- Helps maintain the balance of life in
our environment
 Marine and freshwater 3 primary concerns of Taxonomy
microorganisms form the basis of
the food chain in oceans, lakes and Classification
rivers - is an orderly arrangement of
 Soil microbes help break down organisms into groups
wastes and incorporate nitrogen gas Nomenclature
from the air intro organic - process of assigning name to the
compounds various taxonomic ranking of each
 Microbes that play important roles microbial species
in photosynthesis Identification
 Microbes in the intestines that aids - process of discovering and recording
digestions and synthesis of some the traits of organisms for overall
vitamins required in the body taxonomic scheme

Commercial applications Level of classification

 Used in the synthesis of such
chemical products as vitamins, Domain
enzymes, alcohols, and many drugs - a giant, all-inclusive category based
Food Industry on a unique cell type
 Used in producing vinegar, soy - one or few general characteristics
sauce, cheese, yogurt, bread, and
alcoholic beverages Species
- Smallest and most specific taxon
Naming and Classifying - essentially the same kind of
Microorganisms organisms
- share majority of their characteristics
Nomenclature
 A system of naming organisms In biology, relies on the degree of the
 Establish in 1735 by Carolus relatedness among organisms. This
Linnaeus, Swedish Botanist to relatedness between groups of living
prevent chaos in scientific studies things called Phylogeny
my means of naming (catalogue) for
future identification Phylogenetic Tree of life or Three
Domain System
 Scientific names are latinized
because of Latin was the language
traditionally used by scholars
Taxonomy
 Formal system for organizing,
classifying, and naming living things
Assigning Specific Names
Binomial (two-name) systems of
nomenclature
- the method of assigning the scientific,
or specific name
Scientific Name
- is always a combination of the generic
(genus) name followed by the species
name
- genetic part: capitalized
- species part: lowercase letter
- both should be italicized (or
underlined if italics are not available
- Ex: Staphylococcus aureus or S.
aureus

Type of Microorganisms
Bacteria
 Unicellular and prokaryotes
 Various shapes (cocci, bacilli, and
spirilli)
 Enclosed in cell walls that are
largely composed of a carbohydrate
and protein complex called
peptidoglycan
 Reproduce by dividing into two
equal cells; this process is called
binary fission
 For nutrition, use organic
chemicals, which is nature can be
derived from either dead or living
organisms. Some manufacture their
own food photosynthesis
 Many bacteria can swim through
flagella
 Virus
 A microscope infectious agent
 Prolific and found in almost all life
forms
 Can only replicate inside the living
cells of organism
 The study of virus virology
 Viruses infect host cells to
reproduce
 Virus infect host cells to reproduce
 Viruses can learn to adapt to
immune responses
 Viruses are much more difficult to
treat than bacteria

Viral Components
 Genetic material (core)
- DNA or RNA
- Surrounded by the capsid
 Capsid
- “coat” made of proteins
- Surrounds the DNA/RNA core
 Envelope
- made of lipids (like cell
membranes)
- only on some viruses
 Spike
- made of glycoproteins
- used to attach to cells
- only on viruses with envelopes
 Parasite He constructed more than 250 small
 A parasite is an organism that lives on and powerful microscopes that could
or inside another organism to the magnify up to 300 times
detriment of the host organism The first person to record faithfully his
 Traditionally parasite referred to an observations
organisms with life stages that need Bacteria and protozoa as “animalcules”
more than one host
Parasitism
 A form of symbiosis in which one
organism (called parasite) benefits at
the expense of another organism
usually of different species (called
host)
 Parasites that lives on the surface of
host are called ectoparasites (e.g.
lice, mite)
 Parasites that live inside the host
are called Endoparasites (e.g.
Giardia lamblia, Ascaris inumbriodes The Debate over spontaneous
etc.) Generation
 Parasite usually requires more than  Spontaneous generation – forms of
one host for completion of life cycle life could arise spontaneously from
e’g plasmodium falciparum nonliving matter
 1668 Francesco Refi – disproved
History spontaneous generation of maggots
Robert Hooke: In 1665 built a by using covered jars
compound light microscope and used it  1745 John Needhams experiment
to observe thin slices of cork. Coined on chicken broth that contained
the word cell. microbes after boiling (grow
Cell theory – all living things are spontaneously
composed of cells - Lazaro Spallanzani suggested that
Anton van Leeuwenhoek: In 1673 was microorganism from the air probably
the first person to observe live entered Needham’s solutions after
microorganisms which he called they were boiled, and no microbial
“animalcules” (bacteria, protozoa), growth when fluids heated after
using single-lens microscopes that he being sealed in a flask
designed.
- rainwater from a clay pot
- scraped plaque from his teeth and
from the teeth of some volunteers

During 1600’s discovered the first ever

bacteria through his won glass lenses.
With all his discoveries and
observations, he started to send theses
to the Royal Society of London
 Robert Koch (1876): First person to
conclusively prove that a specific
bacterium caused a disease.
Germ Theory: One microbe causes
one specific disease.
Proved that Bacillus anthracis causes
anthrax in cattle.
Later identified bacterium that causes
tuberculosis.

Louis Pasteur: In 1861 finally Bacillus anthracis – bacterium from

disproved spontaneous generation disease anthrax , Koch Postulate – very
when he demonstrated that useful, discovered many causative
microorganisms in the environment agents, and used even today as a
were responsible for microbial growth in standard way of identifying pathogens
nutrient broth.
Designed swan neck flasks that allowed Human use of Microorganisms
air in, but trapped microbes in neck.
Developed aseptic technique: Practices Biotechnology – production of foods,
that prevent contamination by drugs and vaccines using living
unwanted microorganisms. organisms
Genetic Engineering – manipulating
1858 – Rudolf Virchow put forth the genes of organisms to make new
biogenesis, where living cell arise only products
from pre-existing living cells Bioremediation – using living
organisms to remedy environmental
1857-1914 The golden age problem
Pasteur’s Contributions to
Microbiology:
Fermentation: Pasteur found that Biotechnology
yeasts were responsible for converting - yeast, fungi cause bread to rise and
sugar into alcohol in the absence of air. ferment sugar into alcohol to make
– presence of heat to kill most of the wine and beers
bacteria that causes spoilage - ancient Egyptians use moldy loaves of
Germ Theory of Disease: Belief that brad for wound and lessions
microbes cause diseases. Before, most Genetic engineering
people believed diseases were caused by - thru the technique of recombinant
divine punishment, poisonous vapors, DNA
curses, witchcraft, etc. - bacteria and fungi were the first
organisms to be genetically engineered
Joseph Lister (1860): Used - has unlimited potentials in medical,
disinfectant to treat surgical wounds, industrial and agriculture uses
greatly reducing infection rates. - microbes – to synthesize desirable
Considered the father of antiseptic proteins such as drugs, hormones and
surgery. enzymes
Microbes and Human Disease
1. Everyone has microorganisms in
and on the body; theses make up
the normal microbiota, or flora
2. The disease-producing properties
of a species of microbe and the
host’s resistance are most
important factors in determining
whether a person will contract a
disease
3. Bacterial communities that form
slimy layer on surface are called
biofilms
4. An infectious disease is one in
which pathogens invade a
susceptible host
5. An emerging infectious disease
(EID) is a new or changing disease
showing an increases in incidence
in the recent past or a potential to
increase in the near future
Topic 2 Observing Microorganisms incidences/ epidemics,
through Microscopes studies/research, medicine, etc.

Microscope – is a device used for Magnification and Microscope Design

producing a much larger view of every
small object so that they can be seen Two key characteristics of Reliable
clearly Microscope:

History 1. Magnification – the ability to

 Hand and Zacharias Janssen, make objects appear enlarged
1590, Dutch eyeglass makers, 2. Resolving Power – the ability to
inventor show detail
First compound microscope (2
lenses), tube with lenses at each end
 Robert Hooke
1635-1703, English Chemist,
Mathematician, Physicist, and
Inventor
Compound Microscope improvement
 Antoine Van Leeuwenhoek
1632-1732, wine assayer, Surveyor,
Cloth merchant, minor public
official, and inventor
Simple Microscope (1lens)

Proper care of microscope

 Always start with lowest objective to
focus
 Always store with lowest objective
locked in place
 Carry with two hands
 Cover with dust cover
 Be sire to clean oil off of oil objective
 Use fine adjustment with 100x and
oil objective

Importance of microscopy in Simple Microscopes:

microbial investigation Only have one lens, similar to a
 Exploring the existence of microbes magnifying glass.
 Structure of cells and smallest parts Leeuwenhoeck’s simple microscopes
of plants, animals and fungi, etc. allowed him to magnify images from
 Use as a tool to diagnosis illness in 100 to 300 X.
hospitals and clinics
 Opens to new discoveries about the
microorganisms related to disease,
 Compound Microscope (two-lens) Light reflected off the specimen does
- with a second magnifying lens not enter the objective lens
systems, lamp, located at the base of  Multipurpose instrument (both live,
the microscope to give off visible light unstained and stained material)
and illuminate the specimen
- with a special lens called condenser Dark-field microscope
which focuses the rays to a single - with a special disc called stop to the
point on the object condenser
- stope blocks all light from entering
the objective lens except peripheral
light from the side of the specimen
- result: brightly illuminated
specimens surrounded by a dark/black
field
- effective:
 Visualize living cells distorted
by drying or heat, or cannot be
stained
 Outline organisms shape
 Rapid recognition of swimming
cells
Resolution/ Resolving Power
Phase-Contrast Microscope
- distinguish magnified objects clearly
- transform subtle changes in light
Clarity of image
waves passing through the specimen
- the factor that limits the clarity is
into differences in light intersity
the resolving power
- amount of internal detail visibility is
greater than bright and dark-field
Variation on the Optical Microscope
microscope
- useful for observing intracellular
Optical microscope
structure
- has special adaptations in lenses,
condensers, and light sources
Differential Interference Contrast
Special types of microscopes
(DIC) Microscope
 Bright-field
- provides detailed view of unstained,
 Dark-field
live specimens by manipulating the
 Phase-contrast light
 Interference Refinement:
 Fluorescence 2 prisms – contrasting colors to the
 Confocal image
- Adaption of viewing specimens in a 2 beams of light
particular way - produce extremely well-defined images
that are vividly colored and appear as
Bright-field microscope three-dimensional
 Widely used type of light microscope
 Dark objects are visible against a Fluorescence Microscope
bright background
- is a specially modified compound - origin: for studying metals and small
microscope with and ultraviolet (UV) electronic parts
radiation source and filters - began to use it in early 1930’s
- name is based on the use of due - one of the most impressive features it
(acridine and fluorescein) and minerals provides is resolution
- specimen must be coated or place first - image forms with beam of electrons
with a source of fluorescence causes tc - magnifies in stages by means of: 2
emit visible light, produce an intense lens systems, condensing lens,
blue, yellow, orange, or red image specimen holder, and focusing
against a black field apparatus
- useful applications in diagnosing
caused by specific bacteria, protozoan, Two general Forms of EM
and viruses 1. Transmission electron microscope
- with the staining technique, it is used – for viewing the detailed structure
to detect mycobacterium tuberculosis of cells and viruses
- diagnostic procedures, fluorescent - produce its image by transmitting
dyes are bound to specific antibodies electrons through the specimen
- fluorescent antibodies – used to - specimen must be stained or
detect the causative agents in diseases coated with metals to increase image
such as syphilis, chlamydiosis, contrast and sectioned into
trichomoniases, herpes, and influenza extremely thin slice
- new technology: flurescenet nucleic 2. Scanning electron microscope
acid stains – can differentiate live and - provides some of the most
dead cell In mixtures or detect dramatic and realistic images in
uncultured cells existence
- handy for locating microbes in - can create an extremely detailed
complex mixtures because only those three-dimensional of all biological
cells targeted by the technique will -images are produced when it is
fluoresce bombards the surface of a whole,
metal-coated specimen electrons
Confocal microscope while scanning back and forth
- uses laser beams of light to scan Preparing Specimens for light
various depths in the specimen Microscopy
- delivers sharp image focusing on just - is generally prepared by mounting a
a single place sample on a suitable glass slide
- able to capture a highly focused view - mount specimens are prepared
at any level depends upon:
- most often used on fluorescently  Condition of specimen (living or
stained specimens preserved)
- used to visualize live unstained cells  Aims of the examiner
and tissues  Type of microscopy available

Electron Microscope (EM)

- said to be the window on the tiniest
details of the microscope world
Fresh, Living preparations - cells do not stain because the dyes
- live samples are used to prepare wet applied are negatively charged and are
mounts for near observation of their repelled by the negatively charged
natural state surface of the cells
- cells are suspended in a suitable fluid - value: relative simplicity and reduced
(water, broth or saline) for temporary shrinkage or distortion of cells, as the
maintenance of viability, space, and smear is not hear fixed
locomotion - quick assessment for cellular size,
shape, and arrangement
Fixed, stained smears (smear - used to accentuate the capsule of
technique) bacteria and yeasts
- for permanent mount for long-term
study Method classifications of positive
- developed by Robert Koch staining
- involves air-drying and heat fixation 1. Simple Stains
- it kills the specimen and secures it to Aqueous or alcohol solution of a single
the slide basic dye.
- preservation of various cellular Primary purpose is to stain entire
component performed with chemicals microorganism to view cell shape and
basic structures.
Staining: coloring the microbe with a Procedure:
dye that emphasizes certain structures Stain is applied for a certain time, and
Smear: a thin film of a solution of then washed off.
microbes on Slide is dried and examined.
a slide Mordant: May be used to increase
A smear is usually fixed to attach the stain intensity. Increases affinity of
microbes to the slide and to kill the stain for specimen.
microbes Examples: Safranin, methylene blue,
Stains consist of a positive and crystal violet, and carbolfuchsin.
negative ion Single dye used
In a basic dye, the chromophore is a Dye sticks to specimen
cation 2. Differential Stains
In an acidic dye, the chromophore is React differently to different types of
an anion bacteria.
Staining the background instead of the Can be used to distinguish among
cell is called negative staining different groups of bacteria.
There are two important differential
Positive Staining stains used in microbiology:
- the dye sticks to cells and give them A. Gram stain
color B. Acid-Fast stain
Negative staining Two dyes used
- dye does not stick but dries around its  Primary dye
outer boundary, forming a silhouette  Counterstain
- commonly used dues are Nigrosin
(blue-blakc) and India Ink (black
suspension of carbon particle)
1. Simple Stains Provides useful information for disease
- Aqueous or alcohol solution of a single treatment.
basic dye. - basis of several important
- Primary purpose is to stain entire bacteriological topics (taxonomy, cell
microorganism to view cell shape and wall structure, identification, and drug
basic structures. therapy)
Examples: Safranin, methylene blue, Acid-Fast Stain (Ziehl-Nielsen Stain)
crystal violet, and carbolfuchsin. Modification of a method developed in
- with methylene blue, it is used to 1882 by Paul Ehrlich.
stain granules in bacteria such as Used to detect tuberculosis and leprosy
Corynebacterium causing organisms of the genus
- may appear same color, regardless of Mycobacterium and pathogens of the
type, but can still reveal bacterial genus Nocardia.
characteristics such as shape, size, and These bacteria have waxy cell walls,
arrangement. which makes them difficult to stain.
- acid-fast bacteria (pink) from non-
acid-fast bacteria (blue)
- origin: detecting mycobacterium
tuberculosis
- impervious outer wall that hold fast to
the dye, carbol fuchsin, even when
wash with a solution containing acid or
acid alcohol
2. Differential Stains
- used to detect myobacterium from
React differently to different types of
Hansen’s disease (leprosy) bacillus and
bacteria.
for Nocardia (an agent of lung or skin
Can be used to distinguish among
infections)
different groups of bacteria.
There are two important differential
Endospore Stain
stains used in microbiology:
Endospores are extremely resistant,
A. Gram stain
dormant structures that are formed by
B. Acid-Fast stain
some gram-positive bacteria to protect
- use different-colored dyes, primary
them from harsh environmental
dye and counterstain, to distinguish
conditions: heat, drought, chemicals,
between cell types or parts
radiation, etc.
Preparation of Specimens for
Ordinary staining methods cannot
Microscopy
penetrate the thick endospore wall.
2. Differential Stains
Most commonly used method is
Gram Stain
Schaeffer-Fulton endospore stain.
- Developed in 1884 by Hans Gram, a
- forced by heat into resistant survival
Danish microbiologist.
cells called spores
- The most useful staining procedure
- designed to distinguish between
in medical microbiology.
spores and the vegetative cellsthat
- Distinguishes bacteria of two large
make them
and medically important groups:
- significant in medical microbiology
Gram-positive bacteria
- bacillus - caused of anthrax
Gram-negative bacteria
- clostridium – cause of botulism and
tetanus

Structural stains
- used to emphasized special parts such
as capsules, endospores, and flagella
Capsules staining
- a method of observing the microbial
capsule, an unstructured protective
layer surrounding the cell of some
bacteria and fungi
- Cryptococcus (fungal meningitis in
AIDS patients)

Capsule Stain
Capsules are gelatinous covers on top
of the cell wall, which are important
virulence (disease) factors.
Capsules are difficult to stain because
they repel most stains, are water
soluble, and are easily disrupted with
harsh treatment.
Negative stain is used to obtain a dark
background (E.g.: India ink or nigrosin).
Cell is stained with a basic dye (E.g.:
safranin).
Capsule appearance: Light halo around
stained cell, dark background.
- revealing flagella which is used for
locomotion of the bacteria
- contributes to the determination of
the presence, number and arrangement
of flagella can be helpful in
identification of bacteria
 Origin of Viruses
1st Theory- Viruses existed before the
cells
2nd Theory- Cells came first that viruses
represent ancient derivatives of
degenerate cells or cell fragments.

Most Scientist agree viruses lack most

of the basic featues of cells; thus, they
consider viruses to be nonliving
entities. Because they are not
composed of cells, viruses are not
MICROBIAL DIVERSITY considered to be living organisms. They
(Acellular and Prokaryotic Microbes) are referred to as Acellular microbes
or Infectious Particles.
Acellular Microbes
Virus
- Virions- Extremely small- needs
electrons microscope
- Size from 10 to 300 nm in diameter
- Infect humans’ cells as living host
cells
- Can be called as oncogenic viruses or
oncoviruses- cause specific types of
cancer, including human cancers such
as lymphomas, carcinomas, and some
types of leukemia

Properties that distinguish them from

others:
 Posses either DNA or RNA, unlike
living cells, which possess both
 Unable to replicate (multiply) on
their own; their replication is
directed by the viral nucleic acid
once it has been introduced into a
host cell
 They do not divide by binary fission, Major Parts
mitosis, or meiosis 1. Capsid – protein coat that makes up
 Lack the genes and enzymes most of a virus and gives it shape
necessary for energy production 2. Nucleic Acid- genetic information in
 Depend on the ribosomes, enzymes, the form of DNA or RNA
and metabolites (“building block”) of 3. Envelope- an additional protective
the host cell for protein and nucleic coating usually made of lipids,
acid production proteins and carbs.
Found only in some viruses that infect o Rod-shaped capsomers that bind
animal cells together form a series of hollow
discs resembling a bracelet
Capsid o During the formation of
- Protective outer shell nucleocapsid, these discs link
- Most prominent geometric feature together and form a continuous
- Constructed with identical protein helix into which the nucleic acid
subunits called capsomers strand is coiled
Capsomers  Naked helical nucleocapsids
- It can be spontaneous self-assemble - are very rigid and tightly wound
into the finished capsid into a cylinder-shaped package
- Depending on how they are shaped - several viruses of this type infects
and arranged, this results on two plants
different types: helical and icosahedral  Enveloped helical nucleocapsids
Functions of the Viral Capsid - are more flexible and tend to be
- are responsible for helping to arranged as a looser helix within the
introduce the viral DNA or RNA into a envelope
suitable host cell - if found in several enveloped
- binding to the cell surface human viruses, including those of
- assisting in penetration of the viral influenza, measles, and rabies
nucleic acid
- stimulate the immune system to
produce antibodies that can neutralize
viruses and protect the host’s cells
against future infections

Envelope
o When releases from the host cell,
the virus may take with them a bit
of its membrane system
o Some viruses bud off the cell
membrane or leave via nuclear
envelope or the endoplasmic
reticulum
o Contains viral protein molecules
called Spikes or Peplomers for
attachment of viruses to the host
cell
o Is more supple than the capsid;
therefore, viruses are more
pleomorphic and shape from
spherical to filamentous in shape

Helical Capsids
 Viruses are classified by the
following characteristics:
1. Types of genetic material (either
DNA or RNA)
2. Shape of capsid
3. Number of capsomers
4. Size of capsid
5. Presence or absence of an
envelope
6. Type of host that it infects
7. Type of disease it produces
8. Target cell
9. Immunologic or antigenic
properties
Four categories of viruses based on
the type of genome they possess: In addition to shape, bacteriophages
1. Genome- DNA (double-stranded) or can be categorized by the type of
RNA (Single-stranded) nucleic acid that they possess:
2. Capsids- various shapes and  Single-stranded DNA phages
symmetry.  Double- stranded DNA phages
3. Envelope- derived either from the  Single-stranded RNA phages
host’s nuclear membrane or cell  Double-stranded RNA phages
membrane
4. Viral disease Bacteriophages can be categorized by
the events that occur after invasion of
Bacteriophage or phage the bacterial cell:
- viruses that infect bacteria  Virulent phages
- must enter a bacterial cell to replicate  Temperate phages
- 3 categories based on their shape
 Icosahedron bacteriophages: an Virulent Bacteriophages- always
almost spherical shape, with 20 because what is known as the lytic
triangular facets; the smallest cycle, which ends with the destruction
icosahedron phages are about 25 (lysis) of the bacterial cell. For the most
nm in diameter. phages, the whole process (from
 Filamentous bacteriophages: long attachment to lysis) takes less than 1
tubes formed by capsid proteins
assembled into a helical structure;
they can be up to about 900 nm
long.
 Complex bacteriophages:
icosahedral heads attached to
helical tail; may also posses plates
and tail fibers
hour

Latent Virus infection

Temperate Bacteriophage  are usually limited by the defense
o Also known “lysogenic phages” systems of the human body-
o Do not immediately initiate the lytic phagocytes and antiviral proteins
cycle, but rather, their DNA remains called interferons that are
integrated into the bacterial cell produced by the virus infect cells
chromosome, some generation after  Herpes such as cold sores (fever
generation blisters)- a fever, stress, or excessive
sunlight can trigger the viral genes
to take over the cells and produce
more viruses; in them process, cells
are destroyed and a cold sore
develops
 Shingles, a painful nerve disease
that is also caused by a herpes
virus. After a chickenpox infection,
Animal Viruses the virus remain latent in the
 Collectively referred to as viruses human body for many years. Then,
that infect humans and animals when the body’s immune defense
 DNA or RNA viruses become weakened by old age or
 May consist solely of nucleic acid disease, the latent chickenpox virus
surrounded by a protein coat resurfaces to cause shingles
(capsid), or they may be more
complex Antiviral Agents -drugs used to treat
viral infections

Antibiotics function by inhibiting

certain metabolic activities within
cellular pathogens, and viruses are not
cells. However, for certain patients with
colds and influenza, antibiotics may be
prescribed in an attempt to prevent
secondary bacterial infections that  All of the mentioned oncogenic
might follow virus infection. viruses, except HTLV-1, are DNA
viruses, HTLV-1 is an RNA virus.
It has been developed to interfere with
virus-specific enzymes and virus Viroid and Prions
production by either disrupting critical - smaller and less complex infectious
phases in viral cycles or inhibiting the agents
synthesis of viral DNA, RNA, or
proteins. Viroid
 Consists of short, naked fragments
Oncogenic Viruses or oncoviruses of single-stranded RNA (about 300-
 Virus that causes cancer 400 nucleotides in length) that can
 Conducted several experiments to interfere with the metabolism of
other animals to prove various types plant cells and stunt the growth of
of cancers plants, sometimes killing the plants
 Epstein-Barr virus (a type of herpes in the process.
virus) causes infections  Potato spindle tuber (producing
mononucleosis (not a type of small, cracked, spindle shaped
cancer), but also causes three types potatoes), citrus exocortis (stunting
of human cancers: nasopharyngeal of citrus tress), and disease of
carcinoma, Burkitt lymphoma, and chrysanthemums, coconut palms
B-cell lymphoma. and tomatoes
 Kaposi sarcoma, a type of cancer Prions
common in AIDS patients, is cause  Are small infectious proteins that
by human herpesvirus apparently cause fatal neurological
disease in animal, such as Scrapie
in sheep and goat
 Bovine spongiform encephalopathy
(BSE) “mad cow disease”
 Kuru – ate human brains as part of
Oncogenic Viruses or oncoviruses a traditional burial custom
 Human papillomaviruses (HPV)- (ritualistic cannibalism)
like wart viruses can cause different  Kuru, Creutzfeldt-Jakob (C-J)
types of cancer, including cancer of disease, Gertsmann-Straussler-
the cervix and other parts of the Scheinker (GSS) disease involve loss
genital tract of coordination and dementia
 Fatal familial insomnia in humans –
 a retrovirus that is closely related follow difficulty to sleeping
to human immunodeficiency virus
 Kuru, Creutzfeldt-Jakob (C-J)
(HV) the cause of acquired
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which the brain becomes riddled
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Cell extensions and surface
structures

Appendages (sprouting from surfaces)

 Motility- flagella and axial
filaments
 Attachments or channels-
fimbriae and pili
Flagella
 Provides power of motility or self-
propulsion
 Allows a cell to swim freely
Parts Flagella according to number
 Filaments -helical structure arrangement:
with protein called flagellin
- inserted into a curved, tubular 1. Polar Arrangement (flagella are
hook attached at one or both ends of the
 Hook- is anchored to the cell by cell)
the basal body  Monotrichous (single flagellum)
 Basal Body- a stack of rings  Lophotrichous (small bunch or
firmly anchored through the tuffs flagella emerging from the
cell wall to the cell membrane same time)
 Amphitrichous (flagella at both
Flagella poles of the cell
 Some prokaryotic cells have 2. Peritrichous (flagella are dispersed
flagellum or flagella (plural) randomly over the surface of the
- Outside cell wall cell)
- Different arrangement  Presence of mobility – used in
 Made of chains of proteins flagellin the laboratory for identification
 Attached to a protein hook of bacteria
 Anchored to the wall and membrane  Special stains or electron
by the basal body microscope preparations –
 used to see the arrangement of
the flagella

Flagella responses
Flagellated bacteria can move in
response to chemical signals, this type
of behavior is called chemotaxis Fimbriae and Pili
 Positive chemotaxis – - refer to bacterial surface appendages
movement of cell in the direction - involved in interactions with other
of favorable chemical stimulus cells but do not provide locomotion,
except for some specialized pili
 Negative chemotaxis –
movement away from a repellent
Fimbriae
(potentially harmful) compound
- small, bristle like fibers emerging from
Flagella guides bacteria in a certain
the surface of many bacterial cells
direction due to detecting chemicals in
the environment where clusters of
Pilus/ Sex pilus
receptors located at the cell membrane
- an elongate, rigid tubular structure
binds specific molecules. These
made of a special protein called pilin
molecules transmit signals to the
- linked to “mating” process between
flagellum and sets rotary motion.
called conjugation
Run – counterclockwise, smooth linear
Bacterial Conjugation
direction towards the stimulus, and
interrupted at various intervals by  It is involved transfer of DNA from
tumbles one cell to another
Tumbles – caused by flagellum  A pilus from a donor cell, unites
reversing direction with a recipient cell, thus, providing
connection for making the transfer
 Genetically produced
 Takes place only between
compatible gram-negative cells
Cell Envelope: the boundary later of
bacteria
- chemically complex external covering
of most bacteria that lies outside of the
cytoplasm
Main layers
 Cell wall – stacked together, tightly
bound into a unit
 Cell membrane – maintain cell
integrity
Basic Types Structure of cell walls
 Structure of cell walls  Helps determine the shape of a
- Gram+ and gram – (Gram bacterium
staining)  Provides kind of strong structural
 Cell Membrane structure support (Osmotic Pressure)
 Gain its strength and stability from
a unique macromolecule called
peptidoglycan (PG), composed of
repeating fragments of long glycan
crossed-linked by short peptide
fragments
1. Gram-Positive Cell Wall
 Thick, homogenous sheath of
peptidoglycan from 20-80nm in
thickness
  Contains acidic polysaccharides
o Teichoic acid – is a polymer
of ribitol or glycerol and
phosphate embedded in the
PG sheath
o Lipoteichoic acid – similar
in structure to teichoic acid
but is attached to the lipids
in the plasma membrane
2. Gram-Negative Cell Wall
- is more complex in morphology
due to outer membrane (OM) and a
thinner shell of peptidoglycan
- OM- lipopolysaccharides (LPS)
and lipoproteins

Lipopolysaccharides (LPS)
 are composed of lipid molecules
bound to the polysaccharides
 projects from the lipid surface
 polysaccharides give rise to the
stomatic antigen in gram-
negative pathogens use for
identification
Lipoproteins
 the lipid from the matrix of the
top layer of the OM
 the lipid may become toxic when
release during infections
Porins
 a protein inserted in the upper
later of OM
 selective permeability over
molecules
Fluid mosaic model
- proposed by S.J Singer and G.L
Nicolson
- describes the following:
o a membrane as a continuous
bilayer formed by lipids with polar
heads (outside) and nonpolar
heads (center of the membrane)
o embedded globular proteins
o dynamic and constantly changing
due to the lipids and present
 o fluidity serve as engulfment of food
and discharge or secretion by cells
o selective permeability
o capacity to regulate transport of
molecules
Functions of Cell Membrane
1. Provides site for energy rection,
nutrient processing, and synthesis
2. Regulates transport – passage of
nutrients into the cell and the
discharge of wastes
3. Selective permeability – Passage of
molecules
4. Involves in secretion – release of a
metabolic product into the
extracellular environment

Prokaryotic Groups with Unusual

Characteristic

Photosynthetic Bacteria
 Are independent cells that contain
special light-trapping pigments
 Use energy of sunlight to synthesize
all required nutrients
Types
 Produce oxygen during
photosynthesis
 Produce other substance like
sulfur granules or sulfates
Cyanobacteria: blue green bacteria
- 1 um to 10 um bacterial size and
unicellular
- are among the oldest types of bacteria
on earth
- grows in freshwater and seawater –
algal bloom
- some membranes are pollution-
resistant
- serve as biological indicators of
polluted
- special adaption – thylakoids which
contain granules of chlorophyll and
other photosynthetic pigments
-
features: o Endemic typhus
 Gas inclusions permits them to -Rickettissia Typhi
float on the water surface and - lice
increase their light exposure
 Cysts convert gaseous nitrogen into
a form usable by plants
 Phycocyanin – blue green pigment

Green and Purple sulfur bacteria

 Are also photosynthetic and
contains pigments
 Chlorophyll- bacteriochlorophyll
 It does not give off oxygen as a
product of photosynthesis
 Live in sulfur springs, freshwater Chlamydia Rickettsia
lakes, and swaps Chlamydia is Rickettsia is
group of gram- group of gram-
Gliding, Fruiting Bacteria negative bacteria negative bacteria
and obligate and obligate
 mixed collection of gram-negative
intracellular intracellular
bacteria that live in water and soil
parasite that parasites that
 bacteria glides over moist surfaces transmits from transmits by
 gliding property – involves rotation person to person arthropod vectors
of filaments or fibers just under the Cannot produce Can produces
outer membrane of the cell wall ATP some ATP
 no flagella
 slime bacteria also called Chlamydia
myxobacteria - bacteria – Chlamydia and
 fruiting body – survival structure Chlamydophila
- require host cell for growth and
Unusual forms of medically metabolism
significant bacteria - Chlamydia trachmatis – cause of sever
eyes infection that can lead to
Rickettsia blindness and on of the most common
 distinctive, very tiny, gram-negative STD
bacteria - Chlamydophila pneumonia – an agent
 cannot survive multiply outside a in lung infection
host cell
 cannot carry out metabolism
completely on their own, so they are
closely attached to their host
 Diseases:
o Rocky mountain spotted
fever
- Rickettsia rickettsii
- ticks
  Found in exteme environments, oral
cavity, and human large intestine

Extreme Halophiles
o Requires salt to grow
o High salt tolerance – can
multiple in NaCl solutions
that would destroy most cells
o Exist in the saltiest places on
earth
o “halobacteria” used red
pigments to synthesize ATP in
Archaea: the other prokaryotes the presence of light
 Single-celled, simple organisms
 Archaea or archaeon
 Domain archaea
 Genetic sequences found only in
their rRNA
 Most primitive of all life forms
 “extremophiles” – they love
extreme conditions in the
environment
 Metabolically exhibits incredible
adaptions that would be deadly to
another organism
 Multiple adaption combinations: Hyperthermophiles
temperature, salt, acid, pH, - flourish at temperature between 80
pressure, and atmosphere degrees and 121 degrees and cannot
grow at 50 degrees
 Included in this group: methane
Habitat: volcanic waters and soils and
producers, hyperthermophiles,
submarines vents
extreme halophiles, and sulfur
- salt and acid tolerant
reducers
- psychrophilic - archaea at very low
Methanogens
temperatures
 Converts CO2 and H2 into methane
- hyperthermophilic
gas
 Common inhabitants of anaeorganic
mud and the bottom sediments of
lakes and oceans
 Gas produced may become a source
of fuel
 Contributes to the “greenhouse
effect” – maintains the earths
temperature and contributes to
global warming