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Introduction
The Science of Microbiology
Microorganisms: Things too small to be seen by the human eye (bacteria,protozoa
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Requires the testing of a proper hypothesis
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Roles of Microbes
A) Positive
a) Decomposition (Nutrient recycling) helps yield nutrient molecules used by living
organisms
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c) Normal microbiota are microbes that make up the body and compete with harmful
microbes
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e) Photosynthesis
f) Food production
g) Produce medicine and vaccines through the use of biotechnology
B) Negative
a) Food spoilage
b) Disease
The Chemistry of Life
A) The Atomic Structure of Some Important Elements
Consists of a nucleus with protons inside and electrons on the outside
Surrounding the nucleus is the electrons
More complex atoms have protons and neutrons in the nucleus
The Big Four
Hydrogen

Carbon
Nitrogen
Oxygen
Atomic number refers to the number of protons
Chemical Bonds
1
...
Ionic
Charge (opposites attract)
Helps form a stable compound due to balance
3
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RNA not DNA as first genetic material
Enzymes made of RNA can catalyze certain reactions, self replicating
Under the RNA world hypothesis- the first cells may have been liposomes
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Descent with modification
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1
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Resources become limited
3
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Those individuals most suited pass helpful traits onto offspring
5
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Prokaryotes: The genetic material (DNA) is found in the cell cytoplasm
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There are two types of prokaryotic cells, the bacteria and the
archaea
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Bacteria and archaea are unicellular
organisms
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Flagella are external protein structures with rigid components and flexible components
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Sex Pili: Reproduction, Join bacteria together for DNA transfer
Glycocalyx:
Capsules and Slime Layers
Thick, slippery, or sticky substance
Attached to outside of cell wall
Functions of capsules:
Slippery capsules protect bacteria from being engulfed by immune system cells
Sticky capsules assist in bacterial attachment to surfaces
Components of bacterial cells
Outer membrane
Cell wall: Major function is to keep microbial cell from bursting, almost every species of
bacteria has a cell wall
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Forms a net like structure that
covers the entire cell
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Sometimes additional proteins, some are
toxic to hosts
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Gram negative cells
Cell membrane: The selectively permeable barrier to the cell, main function is to regulate what
substances can enter and leave the cell
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Made of the phospholipid

bilayer
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Breaks down nutrients and generates energy, jobs done by mitochondria in eukaryotic cells
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very tightly packed, dense, for bacterial cells, genetic material is
dispersed throughout the cytoplasm
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They carry special traits like antibiotic resistance genes
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Ribosomes: Make proteins, assemble amino acids, 10,000 per cell, composed of RNA and
protein
Inclusions: Stored material,
Nucleoid/chromosome
Actin cytoskeleton: recent discovery, long fibers of actin wrapped around the cell under the cell
membrane
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Formed by just 3 groups of bacteria
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Not a form of reproduction
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Eukaryotic Cells
Much larger than bacterial cells
External:
Cell wall
Cell membrane: Selectively permeable, phospholipid bilayer with embedded proteins, similar but
not identical to bacterial cell membranes
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Nucleus: membrane-bound structure that contains the cells chromosomes (DNA, genetic
material)
No nucleus in a prokaryotic cell
Ribosomes: build proteins from amino acids
Cytoskeleton: network of microtubules and microfilaments
Functions: Cell support and shape, mixing of cytoplasm, anchoring other structures, sometimes
movement of cell
The organelles:
1
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Endomembrane system, endoplasmic reticulum and golgi apparatus: membrane bound
channels and sacs in which various molecules are processed and transported
Structures Found in Most Eukaryotic Cells
Glycocalyx: protection of cell adherence to surfaces or other cells
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Carbon
dioxide is fundamental in photosynthesis
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The carbon is put into molecules to
be utilized by other living organisms
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Inorganic carbon is another term for carbon dioxide
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Organic carbon is multiple carbons attached together
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Through metabolism and decomposition, it gets cycled back into carbon dioxide
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Animals acquire organic carbon in their diets
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Microbes decompose organic molecules and the corresponding microbial respiration returns
carbon to the atmosphere as CO2
Organic molecules are not always completely decomposed to carbon dioxide
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Nitrogen Cycle
Inorganic Nitrogen has to be converted
Nitrogen has
Organic Nitrogen: Biomolecules: Nucleotides A, G, C, T, U for making RNA, DNA and all 20
amino acids
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Most of the nitrogen on earth is atmospheric nitrogen gas
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Root nodules provide housing and food to microorganisms
Plants can use ammonium as a nitrogen source and incorporate the nitrogen into amino acids
Bacteria can also produce ammonia using ammonification, which is the decomposition of
proteins, RNA, and DNA from dead plants and animals and microbes and animal waste
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Animals require amino acids in their diets as their nitrogen source
Denitrification is when certain bacteria carry out a series of reactions to convert nitrate to
nitrogen gas
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Biofilms form on moist surfaces, water is absolutely necessary
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Biofilms are organized structures
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Other bacteria can then attach
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Open channels among this bacteria allow the flow of water, nutrients and oxygen and waste
products
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History of Microbiology
Antoni van Leeuwenhook (1670’s)
Developed simple microscopes

First to observe microbes that were present in food, water and everywhere we look
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(How did microbes come into the environment)
Spontaneous generation is the idea that living organisms can arise from nonliving matter
Biogenesis is how living organisms can arise only from preexisting living organisms
Louis Pasteur (1850’s-1860’s)
Swan neck flask experiment
Experiment to investigate spontaneous generation
Put broth into flasks and the flasks contained microorganisms
Sterilization
Three Key Conclusions: Spontaneous generation is ruled out, Microbes can be present in
non-living matter, including broth and on particles in the air
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Development of the Germ Theory of Disease
As recently as the mid to late 1800’s:
Most diseases were thought to be caused by “miasmas”
No understanding that microbes were the cause of disease
Ignaz Semmelweis (1840’s)
50% of mothers who gave birth in his hospital got childbed fever
Instituted mandatory hand washing in a chlorine solution
Caused the death rate to drop
John Snow (1850’s)
London
“Mapped” the distribution of cholera, tried to determine the causes
No indoor plumbing or running water, concluded that it came from the broad street pump, where
everyone got their water
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Developed Koch’s postulates: steps for determining the cause of any infectious disease (still in
use today)
Discovered the bacteria that causes tuberculosis
Discovery and Development of the first Vaccines
Edward Jenner (late 1700’s)
Smallpox/Cowpox
Tested on humans
Vaccination that led to a steady decline in cases
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Created vaccines to prevent anthrax, cholera, rabies
Alexander Fleming (1928)
Discovered fungi produced penicillin, which killed bacteria
Sloppy in his research
Was unable to purify penicillin for further testing
Ernst Chain and Howard Florey (late 1930’s-1941)
Demonstrated penicillin was effective against bacterial infection in patients
Began the antibiotic era
Gerhard Domagk (1930’s)
Demonstrated antibacterial properties of sulfanilamide (first “sulfa” drug)
Discovery of Viruses
Dmitri Ivanowski and Martinus Beijerinck (early 1890’s)
Characterized the cause of tobacco mosaic disease as a “filterable virus” or a “contagious living
fluid” because the cause of the disease passed through filters that trapped bacteria
Friedrich Loeffler and Paul Forsch (late 1890’s)
Wendell Stanley (1930’s)

Made crystals of the filterable virus of tobacco mosaic disease and suggested that the virus was
not living, but was actually a chemical molecule
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Chain of Transmission: How diseases move throughout a population
Pathogen in Reservoir- (pathogen exits reservoir)- Mode of Transmission-(portal of entry into
target)- New susceptible host
John Snow is the father of epidemiology (conducted the study of broad street pump, cholera)
Important Terminology
Epidemic: Sudden increase in the number of cases of a disease
Pandemic: Worldwide epidemic
Endemic: A disease that is always present in a particular geographic area
Common Source vs
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Tracking a New Disease
First is the identification of an unusual amount of cases of a disease
Notify the health care providers
Interview the suspected patients
Epidemiological parameters that help define an outbreak (characteristics)
-Time (when are people getting sick?) (why does it look like this?)
-Place (where do affected individuals live?) (where do they work?)

-Personal (Sex, Age, Cultural background)
The Nature of Diseases
Virulence: Capacity of organisms to cause harm, range of effects, adaptations acquired to affect
virulence, typically aid access to nutrients
Commensalism: One organism benefits, the other is unaffected
Mutualism: Both organisms benefit
Disease: Disruption in some way of normal host function
Infection: Entry, establishment and replication of microbes within or on a host
Pathogen: Parasitic microorganism able to cause disease
Pathogenesis: Ability of microbes to cause disease
Normal Flora: Microbes that colonize a host without causing disease (largely benign microbes
typically found in or on body surfaces)
Opportunistic infection:
Process of Infectious Disease
1
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Transmission to Host
3
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Adherence
5
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Evasion of Host defenses
7
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The virulence of a particular bacterial species depends on its particular arsenal of
virulence factors
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pyogenes is confirmed
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This is because
certain strains make Erythrogenic toxin: Red Skin rash, high fever, strawberry tongue
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gonorrhoeae can infect the eye, throat, anus

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Possible complications if untreated: Men: Scarred, partially blocked urethra, infected
tissue, possible infertility
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Bacteria prefer cells commonly found on the
adolescent cervix
- Treatment: Antibiotics
- Prevention: Abstinence, condoms
- If transmitted to infants, can cause eye infections, pneumonia
Bacterial Diseases of the Gastrointestinal System
Enterohemorrhagic E
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coli O157:H7 (and its close relatives)
- There are many different strains of E
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coli strains do not cause disease
- E
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coli
O157:H7
- Some people get mild diarrhea and a fever, others get bloody diarrhea
- 10% develop Hemolytic Uremic Syndrome (HUS) which can lead to: kidney damage and
failure, seizure, stroke, blindness
- Sources: Contaminated meat, unpasteurized apple juice, untreated water, raw fruit and
vegetables, direct contact with farm animals
- Treatment: Rehydration theory, dialysis
- Antibiotics actually make the disease worse by causing higher levels of toxin release
- Prevention: Thorough cooking of meat, washing fruits and vegetables, hand washing
- Vaccine for cattle is in development

Physical Barriers to infection: Skin, Mucus

Mucous membranes
Mucous membranes consist of tightly packed epithelial cells that secrete mucus
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These cells sweep
trapped microbes upward (away from the lungs) to the throat, where they are eventually
swallowed
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Lysozyme: An enzyme found in mucus, secretions, tears, sweat, and saliva that kills certain
bacteria by destroying their cell walls
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Allow your body to
recognize invading organisms
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Adaptive Response
Antigens: ​Foreign molecules that stimulate an immune response by T and B lymphocytes
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APC job is to take the antigen and deliver it to the cell surface, then it tells other immune cells
that there is an infection, and it tells them the antigen they need to target
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Have a more specialized function
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Memory T cells
Remain in body long term following Ag presentation by macrophages
Provide larger, faster cell mediated response to a particular Ag upon repeated (secondary)
exposure
Memory cells are the foundation of immunity
Antibody Mediated Immune Responses
Antibodies- primary purpose is to recognize antigens
Antibodies are proteins that are made by plasma B cells in response to an Ag that will recognize
and bind to that specific Ag
(humoral response)
Ag-Ab binding “tags” cells/molecules for destruction by various mechanisms, for example, Ab
binding makes phagocytosis more efficient
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Cause bacteria to clump together- easy target for phagocytes

What happens when the immune system is compromised?
Drug induced: chemotherapy, anti-rejection meds for transplants, steroids for autoimmune
disorders
Microbe induced: Secondary infections, HIV
Vaccines and Vaccine Preventable Disease Examples
Before 1900, vaccines existed to prevent smallpox, rabies, anthrax, and cholera
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MMR, Varicella (chicken pox,) Zostavax)
Flu Mist: (Nasal influenza)
Inactivated Whole Agent Vaccines
Vaccine contains: Inactivated “killed” microbes (incapable of infecting the host)
Positives: Safe
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(ex
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No chance of disease
Negatives: Immunity to toxoids is short lived
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(ex
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)
Acellular or Subunit Vaccines
Vaccine contains: Purified microbial antigens
Positives: No chance of infection
(ex
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Positives: Safe
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(ex
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Contaminates others that come in contact with those feces, since feces contain the infected
particles
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Can lead to
paralysis
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Paralytic polio often results in flaccid
paralysis of the leg, back, and abdominal muscles
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Damage is permanent
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Recombinant DNA
Review of Genetic Terms
DNA: double stranded nucleotides linked together by covalent bonds forming a double helix
structure
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Genome: All the genetic information (DNA) in a cell (includes gene and non gene regions)
Plasmids: Small replicating circular pieces of DNA
Transformation: Bacteria take up DNA from their surroundings ]
DNA can be exchanged vertically (through natural environments ) parents to offspring
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Recombinant DNA is the basis for genetic engineering
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Microbial Tools for applied genetics: Restriction enzymes (discovered in bacteria, gene cloning,)
Polymerase chain reaction
Electrophoresis
Separates DNA pieces by size in a gel mix
Overall charge of DNA is negative due to phosphate groups
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In a given period of time, smaller DNA pieces will move farther down the gel
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There was that time in winter when the roads were so bad I was too terrified to drive so Lauren
did it and I thought we would die until she said “it’s really nothing like it’s just snow” and we
didn’t
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I remember when Claudia asked Zoe how she would react if people judged her for what she put
online- Zoe said “if it’s weird- unfollow me then” someone might have thought she cared- but
she didn’t
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There was one day where me and Lauren were in the library and we got yelled at for wearing a
sweatshirt out of uniform
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” and
I thought we were going to get in trouble again, but we didn’t
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And I thought I would get in trouble- But I didn’t
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And I guess I
thank God every day that we didn’t
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There are so many things that can turn a
person hateful in this world but when I think about them I think about Maggie and I remember
that she didn’t
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I remember when I got mad and tried to make myself hate Mitchell as much as I hated myself for
hating Mitchell
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I remember when he told me how much I hurt him
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But he didn’t
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I
thought I would get angry and give up on everything
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It felt scary and wrong and like it did not belong
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But
I didn’t
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But we didn’t
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5 hours
home he liked me he did I know it even though I deleted the text messages because I told my
sister and I was so excited he liked me he did even though he said he wouldn’t like me which I
thought was beautiful and so did he because he always told me I was beautiful and I was what he
liked and what he liked was beautiful
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He had said we would be together
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It was easy to pretend his lies weren’t there
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He
said we would be friends
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But it was still okay because I knew his heart was
always good
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I was fine
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It was easy because I loved him
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I say that but I shouldn’t because now I’m
the one that’s lying
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When I was in 11th grade I got my license
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When I started driving I would go to see Julia who was with Mitchell and
he loved me again
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He wanted me back
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And despite him lying to me, taking him back
was so easy
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And he loved me
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And we went to the movies and we saw Star Wars
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On Valentines Day
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And I know I did because I still have the glasses
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He lied
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But I understood his lies
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It was easy because I loved him
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And it’s so painfully easy for
me not to
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He broke up with me again
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1 day
before Spring Break
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He said his 1 biggest reason was that he was 5
months away from going 480 miles and 7 hours and 41 minutes away from Cleveland to college
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I almost cried
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He still wanted to be friends
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I did not want to be his friend
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It hurt more because I understood his reasoning
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It was easy because I loved him
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That was my second

lie
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For a
while I thought he was also lying when he said that
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The truth is that we end there
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This is where my story clings to
whatever it can, whatever metaphor or simile, just so I can keep it going because I could never
bear to see it stop
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I was numb to it, but I wasn’t unaware
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We would do it so that we wouldn’t have to run and we could just pretend we weren’t
there instead
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And that has to be an analogy for the
way I feel and maybe it is and now I don’t actually know what to say because I feel like I’m
running into a brick wall because this sounds like the same love poem a hundred times written
over and over again
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And the
only thing I know is that I miss Mitchell so much, even though the whole point of doing this was
to stop missing him at all
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It can’t just be that time and time again we ran
into these stupid difficulties
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But maybe there's not
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I hated not being the one in control and I hated not feeling loved and I just
wanted him to like me but I knew that he wouldn’t and I’m so sick of feeling so fucking stupid
no matter what I do I just want this to end

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