BIO 220 Introduction

I.

Introduction to Microbes and Microbiology

A. Terms

1. Microbiology is the study of microbes.

2. Microbes are organisms so small that they must be viewed
with a
microscope.
a. viruses (virology)
b. bacteria (bacteriology)
c. protozoans (protozoology)
d. algae (phycology)
e. fungi (mycology)
3. Pathogens are disease-causing organisms (3% of all microbes are
pathogenic)

4. Normal Flora-normally found in or on the body

5. Opportunists-normally non-pathogenic, can become
pathogenic if in the
wrong place at the wrong time. Example: E. coli
B. Benefits of Microbes (97% of all microbes are non-pathogenic)

1. Food: yogurt (bacteria), bread & wine (yeast is a fungus),

mushroom
2. Medicines: antibiotics, penicillin is made by a fungus
3. Producers: some microbes participate in photosynthesis to
make food &
oxygen (basis of some food chains)
4. Saprophytes: break down dead materials to recycle nutrients,
decomposers

5. Nitrogen-fixers: take nitrogen out of the air & fix it into nitrates
in the soil

6. Bioremediation: using microbes to clean up the environment

like oil spills

7. Water purification: cleaning water of toxins

8. Genetic engineering: manipulating microbes to produce things
that they
would not normally produce such as insulin
9. Normal flora: microbes living in or on the body can occupy
space to
prevent us from getting sick, can synthesize vitamins, help
break
down undigested food
BIO 220 Introduction

C. Milestones in Microbiology

1. Robert Hooke (mid 1600s) Father of Microscopy coined the

term
cell when looking at cork, the empty squares reminded him of
an
empty monks cell in a monastery; wrote a book,
Micrographia, with
drawings of microbes
2. Anton van Leeuwenhoek Father of Microbiology read
Hookes book
and got interested in microscopy; made about 400 kinds of
microscopes; saw animalcules (probably protozoa and
bacteria) in
water samples.
a. The acceptance of microbes sparked a debate on their
origin.
b. Spontaneous generation-life spontaneously appeared from
non-life.
c. Biogenesis-life comes only from life
3. Francesco Redi demonstrated that flies arise from maggots
and not dead meat disproved spontaneous generation of flies
4. John Needham boiled broth to kill microbes, set flasks out,
microbes appeared in the broth for spontaneous generation
of microbes

5. Lazzaro Spallanzani suggested the microbes fell from the air

into the
broth so the flasks should be sealed no growth
6. Antoine Lavoisier discovered oxygen which is needed for life
7. Louis Pasteur
a. disproved spontaneous generation curved the neck on
the flask
so that air with oxygen could get in but the microbes
could not
b. devised aseptic techniques to prevent contamination
c. fermentation of wine yeasts convert sugar into alcohol,
bacteria
convert alcohol into vinegar
d. pasteurization heat milk & wine (beer) to kill the
bacteria
e. proposed the germ theory of disease microbes cause
disease
f. discovered how vaccines work use dead or weakened
microbe to build immunity (rabies)
BIO 220 Introduction

8. Robert Koch-proved germ theory; (anthrax); devised Kochs

Postulates-sequence of experimental steps for directly relating
a specific microbe to
a specific disease
a. The microbe must be present in all organisms suffering
from the
disease and absent in the healthy organisms.
b. The microbe must be isolated from the diseased organism
and
grown in pure culture free from other microbes.
c. When the pure culture is inoculated into a healthy
organism, it
should get the disease.

d. The microbe must be reisolated from the experimentally

infected organism and shown to be identical to the
original.
9. Edward Jenner (1796) used cowpox to vaccinate people
against
smallpox.
10. Joseph Lister first used antiseptics during surgery
11. John Snow-British physician in 1850s traced a cholera
outbreak to a
town well-pump handle
D. Types of Microorganisms (Cells)
1. Prokaryotic-without a nucleus (bacteria)
2. Eukaryotic-with a nucleus (animals, plants, fungi, protists)

E. Scientific Nomenclature-system of naming organisms

1. Carolus Linnaeus-developed the naming system
2. Latin is the language used because it is a dead language
3. Binominal nomenclature-two-word name of organisms

a. genus-first name, capitalized

b. specific epithet-(species) second name, not capitalized
c. Each word is underlined separately or written in italics.
d. Example: Homo sapiens

or

Escherichia coli

BIO 220 Introduction

F. Classification-organizing organisms into related groups

1. Categories: Domain, Kingdom, Phylum, Class, Order, Family, Genus,
species
2. Three Domains of Woese

a. Archae-bacteria without peptidoglycan in their cell walls

b. Bacteria-bacteria with peptidoglycan in their cell walls

c. Eukarya-eukaryotic organisms
3. Six Kingdoms

a. Archaebacteria (in Archae Domain)- extreme bacteria

b. Eubacteria (in Bacteria Domain)-regular germ bacteria
c. Protista-algae & protozoa
d. Fungi-yeasts and mushrooms
e. Plantae-plants
f. Animalia-animals
Viruses are not classified in a kingdom because they are not cellular;
cannot reproduce on their own; do not have all the characteristics of
living organism

BIO 220 Introduction

Beside Kingdom Animalia: Draw a big circle around all the words to include every animal listed as
belonging to Animalia.
Beside Phylum Chordata: Draw a big circle around everything EXCEPT grasshopper, ant, and butterfly
(they do NOT belong to Chordata-they do not have spinal cords in a vertebral column)
Beside Class Mammalia: Draw a big circle around everything EXCEPT grasshopper, ant, butterfly, robin,
eagle, bass, and trout (they do NOT have hair and nurse their young)
Beside Order Primates: Draw a big circle around everything EXCEPT grasshopper, ant, butterfly, robin,
eagle, bass, and trout (they do NOT have opposable, grasping fingers)

Beside Family Hominidae: Draw a big circle around everything EXCEPT grasshopper, ant, butterfly, robin,
eagle, bass, trout, and monkey (they are NOT large, tail-less primates)
Beside Genus Homo: Draw a big circle around everything EXCEPT grasshopper, ant, butterfly, robin, eagle,
bass, trout, monkey, gorilla, and chimpanzee (they are not humans)
Beside species sapiens: Draw a big circle around everything EXCEPT grasshopper, ant, butterfly, robin,
eagle, bass, trout, monkey, gorilla, chimpanzee, and cavemen (they are not wise)
This lets you see visually that as you go down the classification scheme, the groups are getting more
specific and less inclusive.

BIO 220 Introduction

II.

Microscopy-staining & observing microbes with a microscope

A. Measurement of Microbes
1. Primary units

a. centimeter-1/100 of a meter (cm)

b. millimeter-1/1000 of a meter (mm)
c. micrometer- 1/1000,000 of a meter (m)

d. nanometer-1/1000,000,000 of a meter (nm)

2. Examples

a. smallest object visible to naked human eye-100

micrometers
b. red blood cell- 10 micrometers
c. bacteria-1 micrometer
d. viruses-0.1 micrometer
B. Types of Microscopes
1. Bright-field Light (1500X) uses bright light; hard to see clear
microbes
2. Dark-field Light (1500X) uses dark light, clear microbes show

up
3. Fluorescence (1500X) uses UV light and fluorescent stain
4. Phase contrast (1500X) used to observe living cells without

staining cell; cell parts are of different density than

surroundings so light
passes through them differently; good for internal detail
5. Electron Microscope (10,000-100,000X) uses a beam of

electrons instead of visible light; shorter wavelengths =

better resolution; must
be done in a vacuum; uses magnets for focusing
6. Transmission Electron Microscope (100,000X) used to see

internal cell structure; fine detail; specimens are sliced ultrathin; one cell is too thick; heavy metals are used to stain the
specimens
*Photomicrograph-electron image is focused onto a fluorescent screen &
photographed
7. Scanning Electron Microscope (10,000X) used to see detailed

surface structures; specimens coated w/ gold; 3D image

BIO 220 Microbiology

III.

Immunology Crash Course Version

A. Immunity - the ability to recognize and repel disease

B. Self from Non-self

1. Cells have groups of molecules (proteins) called major

histocompatibility complexes (MHCs) that identify each cell.

2. Before a person is born, lymphocytes (white blood cells)

roam the
body and learn to identify the bodys own cells as self.
3. When a person is born and exposed to other foreign

particles, the
lymphocytes are able to recognize them as non-self.
4. Non-self particles that are pathogenic initiate the bodys

immune
responses.
C. Two types of immunity
1. Innate nonspecific aimed at all pathogens

a. first line of defense surface barriers: skin, tears,

saliva,
mucus, sweat, vaginal secretions, urine
b. second line of defense fever, inflammation,
phagocytes,
interferon, complement proteins
2. Adaptive - specific aimed at specific pathogens respond

to
surface structures called antigens (antibody generating)
a. humoral initiates the production of antibodies (B
cells)
b. cell-mediated activates cells that destroy the
invaders (T cells)
IV.

Vaccines
A. is a dead, weakened, or part of the microbe that will illicit an

immune
response (production of antibodies)
B. are sometimes multivalent aimed at more than one microbe

C. contain preservatives (mercury thimerosal is no longer used

since 1997)
D. some people do have side effects to vaccines
E. There is/was concern that vaccines are/was linked to autism.
F. Should vaccines be required for everyone?
BIO 220 Microbiology

V.

Viruses
A. General Virology Information
1. are much smaller than most bacteria (exceptions:
mycoplasmas,
rickettsias, and chlamydias) 25 nm to 250 nm
2. cannot be seen with a light microscope ( must use electron
microscope)

3. are not filterable as most bacteria are

4. infections range from trivial warts to extremely serious
AIDS
5. are not considered living organisms because of their
inability to
reproduce, grow, or make energy on their own
a. a group of molecules that invade living cells, take over
the cells, & use the cell resources to make copies of
themselves
replication
b. Outside of a living cell, a virus is inactive temperate
virus.
c. Viruses are obligate intracellular parasites: infectious
particles
that parasitize all types of organisms. i f disease-causing:
virulent.

d. A single infectious virus is called a virion. Virus is

plural
referring to lots of a particular virion. Viruses is plural
referring to lots of different kinds of viruses.

6. The host range for viruses include:

a. plants and animals including humans
b. algae and protozoans (protists)
c. fungi
d. bacteria- a virus that invades a bacterium is called a
bacteriophage (phage)
7. Plaque Assay-used to count the number of bacteriophages to

determine
the number of viruses (bacteriophages-viruses that infect bacteria)

a. Dilutions of phages are put on plates of bacteria.

b. The plates are incubated to allow viruses to invade the
cells.
c. There will be clear areas called plaques around the
bacterial
colonies that were invaded by the virus. (#plaques = # of
viruses)
BIO 220 Microbiology

8. Laboratories grow viruses to make vaccinations. To be

cultured in a
laboratory, viruses require living cells.
a. Fertilized (embryonated) eggs are used. (A person
allergic to
eggs should be cautious when getting a viral
vaccination.)
b. The current preferred culture method uses living cell
cultures
of bacteria or those made of slices of animal tissue.
c. Living animals such as mice, rabbits, and guinea pigs
are used
to study the immune response to the virus.
B. Viral Structure
1. The inner core is composed of nucleic acid-either DNA or
RNA-

which contains the genes or coded instructions for making

more
copies of the virus.
a. DNA viruses include the herpesviruses.
b. RNA viruses include the ones that cause the measles,
flu, and
rabies.
2. The protein shell is called the capsid, which is composed of
subunits
called capsomeres.
3. Viruses can be classified into several different
morphological types
based on the shape of their capsid.
a. Helical viruses resemble long rods that may be flexible
or rigid.
The viral nucleic acid is inside the hollow, cylindrical,
helical
capsid.
b. Polyhedral viruses have a many-sided capsid.
c. Complex viruses have both a helical & a polyhedral
capsid.
4. Enveloped viruses have a capsid that is covered with a
protective envelope.
a. Helical and polyhedral viruses can be enveloped.
b. The envelopes may have spikes, which help the virus
attach.
5. Naked or non-enveloped viruses lack the protective
envelope.

BIO 220 Microbiology

C. Viral Taxonomy

10

1. is determined by the

International Committee on the Taxonomy of Viruses

ICTV

2. The categories of domain, kingdom, phylum, class are not

used.
3. Viruses are classified based on their nucleic acid type,
morphology,
replication method, host, and disease.
* A man named Baltimore also has a seven group classification scheme using Roman
numerals I: double stranded DNA, II: single stranded DNA, III: double stranded RNA, IV:
+single stranded
RNA; V: -single stranded RNA; VI: single stranded RNA Retro; VII: double stranded
DNA Retro

4. Orders: There are 5 viral orders whose names end in ales.

a. Caudovirales

b. Herpesvirales

c. Picornavirales

d. Nidovirales

e.

Mononegavirales

5. Family names end in viridae. (subfamilies virinae)

6. Genus names end in virus.
7. Species names are common descriptive names: (disease)virus.
a. A viral species is a group of viruses sharing the same
genetic
background and ecological niche.
b. Subspecies or types are designated by 1, 2, 3 or A, B, C.
c. Subtypes or serotypes are designated using letters and
numbers indicating the types of proteins found on the
surface:
H - hemaglutinin (16 types) and N - neuraminadase (9
types)

Example: H1N1
d. Strains occur due to mutations in the genetic code.
Strains are
identified by the viral species name & type, (host)
geographic

region of origin, strain#, year of isolation, and

subtype/serotype.

Examples: Influenza A/Puerto Rico/8/34 (H1N1)

Influenza A/mallard/Memphis/123/95
(H5N1)

*Note: If the year is in the 1900s, 2 #s are used. If the year is 2000, 4 #s
are used

6. Viral Classification Example

a. Order: Mononegavirales

b. Family: Herpesviridae

c. Genus: Simplexvirus

d. Species: human herpes

simplex virus 2
BIO 220 Microbiology

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D. Replication
1. Viral replication is the reproduction of viruses in a host cell.
2. Bacteriophage replication-The Lytic Cycle-ends with the
lysis and
death of the host cell (like a bacterium).
a. There are five basic steps to the lytic cycle of a virus.
(1)

Attachment viral tail fibers bind to the cell

receptors

(2)

Entry the tail releases an enzyme (lysozyme)

to break down a portion of the cell wall; then
the tail
injects the viral genes into the cell

(3)
when

Replication the viral nucleic acid is replicated

the viral genes take over and use the host cells
components to make new viruses
(a) Viral nucleic acid is made.
(b) Viral protein capsids are made.
*Note the host cells parts are prevented from being made

(4)
the

Assembly complete virions are assembled as

viral nucleic acid is put into the capsids

(5)

Release viral lysozyme breaks down the cell

wall, the
cell membrane bursts to release the new
viruses,
which can go and infect more cells
b. Eclipse period-is the time in which the viruses are
multiplying
but complete, infective virions are not yet present.
(1)

It lasts from entry until the beginning of release.

(2)

The complete virus is not detected in the host

body.

c. Burst time-is the amount of time from attachment to

release
(1)

It averages about 20-40 minutes in bacteria.

(2)

It can last anywhere from 8 to 40 hours in animal

cells.

d. Burst size-refers to the number of newly synthesized

viral particles released from a single host cell. (It can be
anywhere from 50 to 200.)
BIO 220 Microbiology

12

e. Animal Cell Differences

(1)

Animal viruses lack the bacteriophage tail; they

attach using spikes. The spikes attach to
receptors on the hosts cells. These receptors
are inherited. Therefore, the receptor sites for a
specific virus can differ from person to person
and account for differences in
susceptibility. Understanding the attachment
process of viruses could lead to the
development of drugs that prevent viral
infections.

(2)

Animal viruses do not inject their nucleic acid;

they
enter by endocytosis.

(3)

They usually do not rupture the cell; they

release new viruses by cell budding, which
usually does not kill the
cell.

3. The Lysogenic Cycle-a latent period-a delay between

infection and
the appearance of symptoms
a. Upon entry, the viral genes become incorporated into
the
chromosome of the host cell creating a prophage.
b. No new viruses are being made in the cell at this time.
c. Each time the cell copies its chromosome in preparation
for cell
division, the viral genes are also copied and passed to
the
daughter cells.
d. The cell does not die from this and the virus can remain
in this
dormant state for a long time. (temperate-not causing
disease)
a. This state continues indefinitely, until some
spontaneous event
causes the viral genes to pop out of the chromosomean event
called induction. Induction could be caused by
(1) the presence of a toxin; stress; colds; fever;
period
(2) a lack of nutrients or sleep
(3) radiation or sunlight
f. Then, the lytic cycle begins.
BIO 220 Microbiology

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4. Prophage Presence Complications-the presence of a

prophage can
alter the properties of the host cell

a. Corynebacterium diphtheriae a bacterium

(1) prophage - harmless
(2) + prophage diphtheria
b. Streptococcus pyogenes a bacterium
(1) prophage - strept throat
(2) + prophage - strept throat and scarlet fever
c. Staphylococcus aureus a bacterium
(1) prophage - skin infections
(2) + prophage - toxic shock syndrome (TSS)
E. Viruses and Cancer
1. Cancer-is the uncontrolled growth of cells
2. Cancer results when the genes that regulate cell division
are altered.
3. Proto-oncogenes are normal genes that are found in all
cells that
regulate the onset of cell division and promote cell growth.
4. If altered, proto-oncogenes become oncogenespermanently
activated cells that divide without control.
5. Alterations may result from
a.carcinogens-materials that promote cancer like Xrays,
UV
radiation, asbestos, benzenes, and tobacco smoke
b.oncogenic viruses-viruses that insert their genes into the
cells
chromosome
6. Examples of virus-caused cancers
a.RNA viruses: human T-cell leukemia (HTLV-1)
b.DNA viruses: hepatitis B-liver cancer, human papilloma
virusesgenital warts/cervical cancer, Burkitts lymphomaEpstein-Barr

virus (prevalent in African children)

BIO 220 Microbiology

VI.

14

Smaller Infectious Agents

A. Viroids
1. are infectious fragments of RNA
2. were discovered in 1971
3. interfere with the cells ability to make protein
4. cause plant diseases
B. Prions
1. are infectious proteins (proteinaceous infectious particles)
2. are 1/10 the size of a virus
3. consist of a protein molecule that has folded incorrectly from a
mutation

4. cause other proteins to fold improperly and stick together

inside
cells-killing the cells.
5. cause slow neurological deterioration diseases.
a. Kuru occurs in cannibalistic tribes of New Guinea
b. sheep scrapie
(1) The diseased sheep scrapes against walls/fences until
body is raw.

(2) The sheep loses motor control and dies.

(3) The prion is passed to other animals by injection of brain
tissue.

c. Creutzfeldt-Jakob disease (CJD) rare, affects humans

d. Bovine spongiform encephalopathy (BSE)
(1) is called mad cow disease
(2) The animals become unmanageable & must be
killed.

(3) The disease is probably transmitted in feed

supplements
that are derived from sheep.
(4) There is concern that CJD may be acquired from
eating
infected beef.

BIO 220 Microbiology

15

VII. Sources of Microbiological Information

A. WHO World Health Organization
B. NIH National Institute of Health
C. CDC Center for Disease Control
D. ADPH Alabama Department of Public Health
VIII. Levels of Biosafety (Level 1 - lowest level of concern to Level 4
highest)
A. Level 1 - E. coli, chicken pox virus; open lab, handwashing
B. Level 2 influenza virus, hepatitis virus, measles virus; limited
access to
lab, professionally trained personnel
C. Level 3 Mycobacterium tuberculosis, Bacillus anthracis, SARS;
clinical,
diagnostic, teaching facilities; highly trained personnel, double
door entry,
filtered air exhaust
D. Level 4 Ebola virus, Marburg virus; Hazmat clothes, multiple
showers,
vacuum room, UV light room, air lock doors
VIII. Disease Terms
A. Symptoms & Signs
1. Symptoms are subjective changes felt by the patient like pains
& aches.
2. Signs are measureable objective changes like fever.

B. Carriers, Vectors, Zoonoses, Fomites

1. Carriers have the microbe but no signs or symptoms of the
disease.
2. Vectors are animals that carry the microbe and transmit it to
others.
3. Arthropods are insects like

ticks, mosquitos, fleas, & lice that can be vectors.

4. Zoonoses are animal diseases that humans can get like rabies.
5. Fomites are inanimate objects like

straws & utensils that transmit disease

agents.

C. Contagious, Communicable, Non-communicable

1. Communicable diseases are spread from host to host. STDs,
mumps
2. Contagious diseases are easily spread from host to host.
Chicken pox
3. Non-communicable diseases are not spread from host to host. Food
poisoning