Lecture Notes From First Exam Aug 26-Sept 4

August 26
Reasons why Bacteria are Awesome
-Dominant form of life on planet earth
-Bacteria are much more genetically diverse
Evolution (Reasons why bacteria are genetically diverse)
-Population of organisms
-Environment that population lives in changes
-Individuals with best traits in a given environment survive best, other die
Numerical and Mass Dominance
-Bacteria outweigh everything else put together
Longevity dominance
-Bacteria pre-date other kinds of life by approx 2 billion years
Environmental Dominance
-Bacteria are more adaptable to changing environment than any other kinds of living things
-At least a few bacteria can survive virtually all environmental assaults: high temperatures,
pressures, and radiation
-Plants got their ability to produce oxygen through bacteria
Infectious Diseases (Spread from person to person)
-Caused by bacteria or viruses symptoms from organisms growing in host
-They kill us better than we kill them
Normal Flora
-Bacteria in your body that live there normally
-Necessary for life Ex: E. Coli Produces Vitamin K Clotting factors in blood
Another Example: Gut Bacteria digest food
Maintain healthy Skin

August 28
“A great discussion of spontaneous generation, humors, and the germ theory of disease follows a brief chat about what you hope to get out of this class. Good times!!”

Article: Ignaz Semmelweis and the conquest of Puerperal Sepsis
Moral of the Story:
1. Wash your hands when going from person to person
2. Don’t chop up on dead people and then going to deliver babies without washing your hands
My Notes
-Semmelweis postmortems showed pathology suggestive of “blood poisoning” in mothers and their dead babies
-Semmelweis determined that medical students coming to the First Clinic were transmitting cadaveric matter into the pregnant women by failing to wash their hands in between performing vaginal and postmortem examinations
-Found that women in labor should never be attended by physicians/students who had been conducting postmortem examinations or who were attending patients with puerperal fever, Semmelweis recognized puerperal fever as blood poisoning or septicemia
-No one believed his diagnosis and he became mentally deranged and was placed in an asylum; he died of blood poisoning and his works didn’t become accepted until years after his death
Spontaneous Generation
Hypothesis: Life can come from non-living material
Support: Stuff grows in broth and I didn’t put it there
An experiment to disprove the hypothesis (Spontaneous Generation)
1. Bottle that’s sealed tightly and boiled broth in it and nothing grows in it
*Doesn’t disprove spontaneous generation because no oxygen is able to get to it
2. Louis Pasteur Swan-necked Flask (1850s)
*Takes a glass flask and puts the neck of it in a flame and bends the neck of the flask and they put boiled broth in it
*Air can get into the flask, but bacteria cannot
*Bacteria cannot get into the flask because they are heavier then oxygen and because of that, bacterium fall into the neck of the flask at the S-trap as long as the liquid from the flask does not get to it
The Germ Theory of Disease (Ways people get sick)
1. Blood
2. Phlegm
3. Bio
Previous Ideas about disease Causation: Humors
-People have too much blood in their bodies and as a result they feel very sick; blood gets out of balance
-People get sick
-Bleeding will fix it
Previous Ideas about disease Causation: Miasmas
-Bad Air Poisons
-People lose the bad air
-People will be well
John Snow and the Broad Street Pump
There was this city in England in 1849 and there was a terrible outbreak of cholera that caused massive diarrhea and made you lose three gallons of water a day and a lot of people were dying. No body new for sure what was causing it. There was a river that people were getting the water out of. To get a handle on this they started mapping the places where people had died of cholera. And clearly this is evidence of a Miasma. The one area of town smells horrible and most of the deaths are in that part of town

Death from Cholera
Air Smells
John Snow came up with a hypothesis that stated besides bad air there must be another reason for the outbreak. He realized that water being used was coming from the same water company
Article-Pasteur-Koch: Distictive Ways of Thinking about Infectious Diseases
Pasteur Contributions: Pasteurizing milk, Fermentation, Vaccinations, Molecular Asymmetry
Koch Contributions: Spores, Anthrax
August 31

“We revisit the Pasteur/Koch article, and chat about Koch’s postulates and exceptions thereto. Also we discuss chapters 1 & 2 in Revenge of the Microbes. And a cricket invades the classroom.”
Koch’s Postulates
Trying to show that a specific microbe causes a specific set of symptoms because he wants to show that at least some diseases are caused by microbes and not other things like miasmas
Hes going to set out a specific set of steps for a particular microbe for a particular set of symptoms and if you can do the set of 4 things unambiguously your microbe causes your disease
1. Microbe must be found in all hosts with the set of symptoms (and be absent in everyone else)
2. Isolate microbe and grow it in a pure culture; streak plate technique; Microbe must be gathered/taken from sick host and grown in pure culture
3. Get pure Culture of Microbe from (2) put in new, healthy host, =same symptoms
4. Microbe must be gathered from new sick host and confirm it was the same microbe from step 1
Are there diseases caused by microorganisms that are exceptions to Koch’s Postulates? Why?
*Any Microbe that causes different effects in different hosts/people
*Any microbe that can’t be grown in pure culture (viruses)
*Any microbe that only causes symptoms in humans
Revenge of the Microbes: Chapter 1 & 2
Alexander Fleming-what allowed him to discover penicillin
-Bacteria is on the plate; he did a streak plate technique
-He originally did not put penicillin on the plate
-There’s a zone where there is no bacteria growing
Antiseptic-Safe for outside of the body; kills generally (not just bacteria, but you too)
Dininfectant-Not safe for your body because concentration of toxic ingredients too high; kills generally (not just bacteria, but you too)
Antibiotic-Attacks structure present in bacteria, absent in us (so we aren’t harmed at all, but bacteria are killed)
Definition of Microbes: Any organism so small it can’t be seen with naked eye
Nucleated Cells
Nucleus: Membrane bag surrounds the DNA
Most kinds of eukaryotes on earth are microscopic
Most are single-celled
All eukaryotes very genetically similar to each other
No Nucleus
Thought to have not changed much for a billion years
Live in extreme environments: Geysers, ocean vents, other water, dead sea, lots of others with very high or low 100 degree Celsius temps

Robert Koch believed that bacteria would never change and Pasteur believed that they would

Sept 2
“We conclude our chat about Koch and Pasteur, visit the differences between vaccines and antibiotics, and then discuss archaea in some depth. Also there is discussion of RNA polymerases and peptidoglycan cell walls in bacteria, and how gram stains differentiate bacteria with thin and thick cell walls.”
Vaccines: Make your body make a specific immune response against a particular kind of pathogen (Any organism that causes a disease)
Antibiotics: Drug that you injest (not made by you) that kills bacteria generally
Attacks target in bacteria cells necessary for cell survival that our cells don’t have
Eukaryotes have a membrane bound nucleus but prokaryotes do not have a membrane bound nucleus
No Membrane bound nucleus
Have chemical characteristics that make us think they have been unchanged for billions of years
Much more closely related to each other than eukaryotes, but they have more in common with eukaryotic cells than bacterial cells, except for the thing of not have a nucleus
RNA Polymerase used by Archaea in which the enzyme does transcription (DNA is copied into an RNA copy and has to happen because you cant make the proteins that your cells are made out of)
Similarities between archaea and eukaryotic cells:
Their RNA polymerase is virtually the same as eukaryotic RNA polymerase
Similar to eukaryotes than archea are to prokaryotes is that the chemistry of their cell membranes is very much like the cell membranes of eukaryotic cell membranes and not like bacterial cell membranes
Plasma Membrane Drawing (Phospholipid bilayer)
-Circles represent Hydrophilic phosphate
-wiggly lines represent hydrophobic tails
*Archaea have been found in extreme temperatures
*Geysers, dead sea, ocean vents
Represent Prokaryotes
Much more closely related to each other
Distinct Cell Wall
Cell membrane structures not found in Archaea or Eukaryotes
Distinct RNA Polymerase
A semi-synthetic drug that is bacterialcidal because it inhibits the bacteria RNA polymerase
A small minority of bacteria on earth, but important clinically

On outside-

Cell wall is made up out of peptidoglycan which is composed of carbohydrate sugar component and a protein component
The cell wall is thick with 30+layers of peptidoglycan
Is crosslinked with lipoteichoic acid (LTA) which is a fatty acid
Gram negative bacteria also has a cell wall but does not contain lipoteichoic acid, they have a cell membrane and there cell wall is a lot smaller with only about five layers of peptidoglycan
The crystal violet and iodine clumps inside the bacteria staining the slide purple and the you decolorize with ethanol which dissolves the clumps and the bacteria stays purple then you add pink safranin

Sept 4
-Archaea are prokaryotes and do not have a nucleus
-Archaea are more similar to eukaryotes than bacteria because they have a distinct RNA Polymerase, and cell membranes are more similar to our cell membranes’ than bacteria cell membranes
-Could you use Rifampin to treat a hypothetical infection with archaea?

  • 19 people said yes and a total of 22 said no, and of the 22, 9 had weird reasoning for that

*No because Rifampin destroys RNA polymerase and RNA polymerase is necessary to do transcription
Correct Answer: No because archaea have the same RNA polymerase as our Karyote cells do, therefore if you had a drug that did destroy RNA polymerase of Archaea, it would also destroy the RNA polymerase of us
-Antibiotics attack targets that are specific to bacteria and that the bacteria needed to survive are absent from our cells
-The mechanism of antiseptics and disinfectants is that they are necessary for all things to continue living, including our cells which is why we can’t drink a bottle of bleach
-Antibiotics are attacking products that are unique to a bacteria
-Scientific data either supports a hypothesis or disproves a hypothesis
-Antibiotics tend not to work in the future because bacteria adapt to resist them and bacteria become immune to them and not because you become immune to them
-Antibiotics kill your normal flora bacteria
(Does the antibiotic kill the thing that’s the disease)?
Cross section of parts of the cell membrane (Drawing on board)Gram (+) bacteria
*Phospholipid Bilayer
*Bacillus shapes (Tubular)
*Cell Wall (Made out of peptidoglycan Made out of 30+ layers and Crosslinked with component called LTA)
*Thick Cell wall
*Coccus (round)

Components of Gram (-) bacteria (Stain Pink)
*Plasma Membrane which is made out of phospholipid bilayer
*Cell wall layer made of peptidoglycan has fewer layers approx 5 layers that are attached to each other but are not linked with LTA
*Bonus layer that is called the outer membrane which has an additional component LPS (lipid poly-saccharide)
*Chemical components of LPS-Fat and Sugar (hydrophilic and hydrophobic parts)
(Two leaflets-the outside and inside)
Inside side made out of regular phospholipids
Outside side made out of lipo polysaccharide
*A space called the periplasmic space-space btw the cell wall and the outer membrane
For LTA and LPS Your immune response acts violently against ingrediences that are never found in human cells
Inflammatory Response reacts violently against non-eukaryotic chemical components
Too much Lps or lta in blood=violent inflammation resulting often in death
Acid-fast bacteria (drawing)
-outer membrane with mycolic acid
-Mycolic acid is very dense, waxy molecules; is very resistant to drying out-can survive for a long
time in dry environments
It prevents gram stains from penetrating bacteria cell envelope

  • The gram stain technique does not work on acid fast bacteria because it prevent the acid from getting into the bacteria

-Have no cell wall
-Plasma Membrane
-Don’t have clearly defined shapes (ex. Chlamydia-almost all are asymptomatic (an infection with no symptoms))
Consequences of cell wall that’s made out of peptidoglycan
*Clearly defined shapes:
-Spirochetes (spiral/Corkscrew)

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