BIO 220 Introduction

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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. coliB. 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, decomposers5. 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 spills7. 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 foodBIO 220 Introduction

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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 life3. Francesco Redi demonstrated that flies arise from maggots and not dead meat disproved spontaneous generation of flies4. 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 life7. Louis Pasteur

a. disproved spontaneous generation curved the neck on the flask

so that air with oxygen could get in but the microbes could notb. devised aseptic techniques to prevent contamination

c. fermentation of wine yeasts convert sugar into alcohol, bacteria

convert alcohol into vinegard. pasteurization heat milk & wine (beer) to kill the bacteriae. 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

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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 handleD. 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 organisms1. Carolus Linnaeus-developed the naming system2. Latin is the language used because it is a dead language3. Binominal nomenclature-two-word name of organismsa. genus-first name, capitalizedb. 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

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F. Classification-organizing organisms into related groups1. Categories: Domain, Kingdom, Phylum, Class, Order, Family, Genus, species2. Three Domains of Woese

a. Archae-bacteria without peptidoglycan in their cell walls

b. Bacteria-bacteria with peptidoglycan in their cell wallsc. Eukarya-eukaryotic organisms3. Six Kingdoms

a. Archaebacteria (in Archae Domain)- extreme bacteriab. Eubacteria (in Bacteria Domain)-regular germ bacteriac. Protista-algae & protozoad. Fungi-yeasts and mushroomse. Plantae-plantsf. 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 organismBIO 220 Introduction

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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

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II. Microscopy-staining & observing microbes with a microscopeA. 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 micrometersb. red blood cell- 10 micrometersc. bacteria-1 micrometerd. viruses-0.1 micrometerB. Types of Microscopes

1. Bright-field Light (1500X) uses bright light; hard to see clear microbes2. 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 detail5. 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 focusing6. Transmission Electron Microscope (100,000X) used to see internal cell structure; fine detail; specimens are sliced ultra-thin; 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 imageBIO 220 Microbiology

7III. 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

8V. 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. if 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

98. 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

10C. Viral Taxonomy

1. is determined by the International Committee on the Taxonomy of Viruses ICTV2. 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. Mononegavirales5. 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 used6. Viral Classification Example

a. Order: Mononegavirales b. Family: Herpesviridaec. Genus: Simplexvirus d. Species: human herpes simplex virus 2 BIO 220 Microbiology

11D. 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) Replication the viral nucleic acid is replicated when

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) Assembly complete virions are assembled as the

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

12e. 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 chromosome-an 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

134. 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 oncogenes-permanently

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 viruses-

genital warts/cervical cancer, Burkitts lymphoma-Epstein-Barr

virus (prevalent in African children)

BIO 220 Microbiology

14VI. 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 mutation4. 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

15VII. 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