Unit 2 Lecture Notes

September 21, 2009
• E. Coli bacteria are killed by a virus
o Virus = T4 bacteriophage
 Infection of E. Coli q/ T4 bacteriophage
 E. Coli is gram (-)
 Gram negative bacteria picture
 Proteins allow things to go in/out of cell in cell wall and outer membrane as well as plasma membrane
• Allow transport of chemicals in/out of bacterial cell
 1st step: T4 bacteriophage adheres to a protein on the outer surface of the bacteria
• Ribosomes and Enzymes used for DNA replication
• Sticks to protein in the outer membrane of the E. Coli bacterium
 2nd Step: T4 bacteriophage through that interaction pokes a hole through all of the layers of the cell envelope of the E. Coli Bacterium
• Through that hole it injects its DNA
 3rd Step: The DNA belonging to the virus that kills the E. Coli is going to be copied by the enzymes and translated by bacterial ribosomes
• Gives a whole bunch of many copies of the T4 bacteriophage inside the bacterium
 4th Step: bacterial cells bursts because its full of the viral T4 bacteriophage
• Releases viruses out into the world

• E. Coli bacteria are killed by a virus
o Virus = T4 bacteriphage
o Questions – Can E. Coli become resistant to T4?
 Assuming they do become resistant to T4: why is it?
• Are they “immune” after virus attack & able to pass that acquired immunity on to offspring
• Is it just that some E. Coli are randomly “born” resistant to T4?
 If so, is it
• “acquired immunity”
• Bacterial communication/gene sharing
• All just random who lives and dies
• Adhesins:

Are ribosomes a good target for antibacterial drugs?
1. Bacterial adhesion to surfaces
a. “Adhesins” are usually integral or peripheral membrane proteins
i. Membrane/Cell Wall proteins used by bacteria to stick to surfaces
ii. More often they are peripheral membrane proteins
1. Peripheral Membrane proteins picture
2. Protein is in part of the membrane and does not go all the way through
b. Pili
i. Attachment to surfaces and motility
ii. Use on conjugation (bacterial sex) by some species
1. How they share plasmids with abx resistance
2. Pillus extension reaches over and sticks to another bacterium plasmid is copied and the copy of the plasmid is sent across the bridge to the other bacterium
September 23, 2009
2. Motility: flagella and pili
a. Pili
i. Example: adhesions on ends of pilli:
1. Are retractable extensions from bacterial cell envelope
2. Attach to surfaces and retract
3. Use peripheral membrane proteins to attach to surfaces
ii. Twitching motility
1. Jerking motion of bacteria with pili along surface; pili attach to surface, retract
2. Stick to a surface and retract
b. Flagella (NOTe: bacterial flagella are NOT THE SAME as eukaryotic flagella)
i. Bacteria swim more smoothly through a liquid such as water
ii. Flagella act like a motor for the bacteria that have them
iii. Analogous to motor submarine
iv. Flagella on sperm/eukaryotic organisms (NOT THE SAME!!!)
1. Eukaryotic are really just cilia
2. They are much smaller on bacteria
v. Flagellar arrangements
1. Polar (ex. P aeruginosa)
a. Means the bacteria have flagella located on one end or the other or both ends; they flagella are NOT all over the bacterial cell

2. Pertirchous (ex. E. Coli)
a. “Covered in hair”
b. Have flagella all over
vi. Eukaryotic cell flagella are just glorified cilia and are flexible
a. Flexible; move like snakes
b. Made of
i. Microtubules (tubulin) and dynein
ii. Two separate proteins and completely different than bacterial flagella
iii. Accounts for snaky motion of the flagella of the eukaryotic cell
vii. Bacterial flagella are:
1. Rigid: act like propellers w/motors to move bacterial cells
2. Consequence of the proteins they are made out of
3. Smaller than eukaryotic
viii. Flagellin
1. Protein that makes flagella rigid
2. Particles come together to make a long flagellan filament that acts as propeller
3. Makes the propeller part of the flagellin of the flagella
ix. Basal body and hook
1. Flagellan filament attached to “motor”
2. Made of various integral membrane proteins
3. Whole set of integral proteins is the basal body or “motor”
4. “motor” = basal body
5. Basal body of gram positive bacteria
a. no outer membrane

x. Use of ATP
1. Energy currency of the cell
2. Basal body breaks down ATP into ADP into phosphate to turn the motor
3. Why do bacteria not have mitochondria?
a. Fuels the transport of the flagellar protein filaments to go through the hook and out to make the flagella; polymerize together to make the flagella
i. Energy for this is breaking ATP into ADP
b. Proton pump system spins the flagellar motor
xi. How bacterial flagella are made:
1. ATP is broken down into ADP + P (inorganic phosphate)  this provides the energy to export the flagellan filament molecules out the hook through the basal body where they polymerize spontaneously into the flagella
xii. How they move:
1. Does not use ATP
2. Uses a proton pump system
a. H+ that have lost they’re electrons
b. H+ are pumped across the plasma membrane of bacteria
i. Proteins must be pumped across the plasma membrane because the inner part of the membrane is hydrophobic and only uncharged particles can move across a hydrophobic barrier or lipid membrane
ii. If protons were pumped across the plasma membrane and get into the cell wall; they cannot come back on their own; must be pumped
iii. Protons are trapped between the cell wall and plasma membrane b/c H+ cannot cross either of the hydrophobic layers of plasma membrane
iv. Protons fall through/across gate in flagellar basal body this spins the basal body which spins the flagellum like a water wheel when water falls down a water wheel
v. Energy gets taken from electrons coming out of the electron transport change; passing electrons down the electron transport change
xiii. Similarity to type 3 secretion systems
1. Bacterial flagella are very similar to secretion systems used by bacteria
2. These secretion systems are used to pump proteins out of the bacterial cell into the surrounding environment in particular by many pathogenic bacteria to inject toxins that kill eukaryotic cells directly into the eukaryotic cell
a. EX) virulence factors (any protein used by pathogenic “disease causing” microbes that contribute to disease in a particular host): pump directly into host cells thru type 3 secretion systems by some pathogenic bacteria
xiv. Similarity to ATP synthase of eukaryotic mitochondria
1. A brief digression on mitochondria and what bacteria do not have them

September 25, 2009
Why do bacteria not have mitochondria?
Bacteria transport protons by taking energy from electrons by taking electrons from the electron transport chain and passing them down the chain they get energy
Mitochondria used to make energy (ATP) by Kreb’s Cycle
Why do eukaryotes have mitochondria?
To make ATP efficiently
How do mitochondria make ATP?
Mitochondira are able to use the power from passing electrons from point to point to pump protons out from the inside of the mitochondrion to in the space between; as electron is passed from A  B enough energy is provided to pump the proton from the space between the inside membrane and the outside membrane.
As electrons are passed from protein to protein this provides the power to pump a proton to between the inner and outer membrane
Protons cannot get back into the center of the mitochondria on their own because they are positively charged and cannot cross a hydrophobic layer
Integral membrane proteins act as water-wheel gate; as protons pass through this gate the water wheel spins and adds an inorganic phosphate
Mitochondria make ATP by: using electron passes down proteins embedded in membrane to pump protons across inner membrane to space between inner & outer membranes
Every time an electron is pumped from one protein to the next it gives the energy to pump a proton to the space between the inner and outer membrane
Since the protons are + charged, they can’t cross either membrane on their own because of their hydrophibic nature, so to equalize the gradient of protons the protons have to fall across the water-wheel like proteins in inner mitochondrial membrane to equalize H+ gradient

Everytime a proton falls across that gate this powers the addition of one inorganic phosphate to an adenosine so that for every 3 protons that fall across the gate there is 3 spins and 3 inorganic phosphates being added to one adenosine resulting in 1 ATP

September 30, 2009

1. Why don’t’ bacteria have mitochondria
a. Most bacteria are free-living; they DO NOT live on/in a host/in a host cell
b. A definition is NOT a reason
i. Ex) Prokaryotes don’t have membrane-bounded organelles, and mitochondria are membrane-bounded organelles
c. Because use ATP as energy currency just like ALL OTHER LIVING THINGS do
d. Virtually all bacteria are free living
e. Don’t use the word because
f. Bacteria are like one big mitochondria themselves
g. 1000 nm size of bacteria
h. Mitochondria have their own DNA and replicate on their own time whenever they want to; bacteria act the same way to create ATP
i. Because:
i. Mitochondria have their own DNA
1. Replicate on their own independently of when our cells replicate using the same cell division steps that bacteria do
2. Mitochondria generate ATP like bacteria do
3. Mitochondria can be killed by many abx
4. Mitochondria most likely are descendants of bacteria that were engulfed by or invaded by eukaryotic cells in the past
ii. Biologists think mitochondria re descended from bacteria
1. Symbiotic relationship
2. Mitochondria can be seen as their own separate organisms because they have their own DNA
3. Mitochondria do not have cell walls made of peptidoglycan but are very similar to bacteria in other ways
2. Bacterial Flagellum Article
a. Structures flagellum is similar to:
i. The ATP synthesis set up of Mitochondria and the ATP synthesis of bacteria by proton being pumped by the water-wheel apparatus using electrons
ii. Virulence Factor:
1. Any protein that helps cause symptoms
iii. Type 3 Secretion Systems
1. Works like a hypodermic needle and is also very similar to the setup that spins the bacterial flagellum
2. Similar to bacterial flagellum ATPsynthase
3. Acts like a needle to inject virulence factors into the host cell
4. Need a set of proteins that can cross the envelope of the bacterial cell envelope
3. Review of Wong article:
What is evolution? What is intelligent design? What predictions does evolution make about the origins of any complicated structure? How are these different from the predictions of intelligent design? What evidence do authors of this article use to support their contention that the bacterial flagellum is the product of evolution rather than design?
a. These people are undergrad students
b. How are the predictions of evolution different from the predictions of intelligent design?
i. Intelligent design
1. Things were set up the way they already are
2. Flagellum
a. Bacteria always had the flagellum; wasn’t something that developed over time
b. If you take out the parts of the flagellum it would just fall apart
c. Separate fully functioning things cannot take things away from it or it wont work
ii. Evolution
1. Parts of cells descended from earlier parts of cells and we should see recycling of parts and repetition of parts
iii. Bacteria Flagellum
1. Is the bacterial flagellum similar to other things in the cell?
a. Yes, it is more similar to other things in the cell than just on its own

October 2, 2009
1. Exponential growth vs. logarithmic growth
a. # of bacteria at a given time = 2 X power (x=# of generations since we just had 1 bacterium)
b. Exponential Growth
i. 1 bacteria into 2; 2 bacteria into 4; 4 bacteria into 16
ii. Increase at a rate to 2 to the x power = number of bacteria at a given time in culture
iii. X = # of generation times since original bacterium
iv. Exponential multiplication does not go on forever
v. It is only exponential for part of the grow and logarithmic for the rest
c. Logarithmic Growth
i. Only PART of bacterial growth curve is exponential
2. How an individual bacterium divides
a. Replication of chromosome
i. Replicate its DNA
1. Done by DNA polymerase = enzyme that synthesizes new DNA molecules complementary to template strand
a. DNA is double-stranded interacting via complementary bases (A= T) (C- G) A and T have double hydrogen bond and C and G have triple hydrogen bonds
2. Chromosome is attached to inside of plasma membrane upon replication
a. When bacterium elongates nad makes new cell wall components in the middle of the bacterium, pulls new cell chromosomes and old chromosome that are grouped apart
3. Bacteria have a single circular chromosome
4. Need 2 copies of chromosome: 1 for each cell
b. Elongation of cell
i. Happening simultaneously along with DNA replication
ii. Chromosomes attached ot cell wall and the new cell wall components in the middle of the cell begin to pull new chromosomes apart
iii. New chromosome copies are sent off to either side of the cell
c. Formation of FtsZ ring at septum
i. FtsZ is what pinches the cell at the middle after the chromosome copies have moved to the other ends of the cell
ii. FtsZ pinching in the middle of the cell; chromosomes separate to either side of the cell
iii. Min proteins stop FtsZ from working; they bounce from one end of the cell to other
1. Min proteins bounce back and forth stopping it from working anywhere else but the center of the cell
iv. FtsZ ring begins to pinch off between the new cells
v. Similar to tubulin in eukaryotic cells
d. Building of new cell envelope components at septum
i. New cell envelope components built at the center of the cell
ii. Between two new bacterium
3. Bacteria Generation Times
a. Vary from bacterium to bacterium
b. Speediest is E. Coli
i. Generation time of 15-20 min
c. Staphylococci species
i. Generation time of about 30 min
d. Mycobacterium Tuberculosis
i. Generation time of about 23 hours
ii. Have to wait a month and a half to two months just to show some bacterial growth
e. Differences in cell wall structures is the cause as to why it takes longer for some to generate versus others
i. Mycolic acid outer layer makes if very hard to replicate; takes much longer to make the outer waxy material of the cell envelope
f. Bacterial chromosomes
i. Size range: ~1million bps (base pairs) to ~ 8-10 million bps
ii. E. Coli - ~ 5 million bps

October 5, 2009
4. Phases of bacterial growth curve (in culture… not in nature) assuming pure culture of bacteria
a. Lag phase
i. Due to the math of the growth
ii. Take s awhile to go from having few bacteria to having a lot
iii. Bacterial cell division getting started
iv. Generation times not as rapid as will be during Exponential Phase (b)
v. Bacteria are making:
1. ATP
2. Cell envelope components
3. Enzymes: DNA polymerase; Ftsz;
4. Need a lot of things before they can actually get cell division started
b. Exponential phase (log phase)
i. During this phase, generation time is shortest, nutrients are abundant
1. So bacteria easily able to make all components needed for cell division
c. Stationary phase
i. Growth has stopped
ii. Number of deaths may = number of new bacteria
iii. Population is not growing
iv. Bacteria starting to run out of nutrients and space
1. Much less able to make all the enzymes that are needed to make the bacteria divide ; also, lack of food  some bacteria dying
d. Death phase
i. # of new bacteria vastly outnumbered by # bacteria dying
ii. Cell division has essentially stopped b/c nearly out of food to conserve the food
iii. Because of out of food, living bacteria have nothing to eat either so they start to die
iv. Suicide at high population densities common among bacteria
1. Bacteria cells have receptors on the outside of them; signaling molecules secreted by the bacterium and diffuse down the concentration gradient
2. At some point there will be no where for the signaling molecules to go/diffuse to
a. Then they stick to the receptor and the bacterium is signaled to kill it self
b. It’s the bacteria’s own enzyme that kills them
5. Generation time = 0.301 (t-t0)/(log10N-log10N0) (don’t need to know)
6. Can T4 Phages infect human cells
a. Human cells do not have proper receptors for the Phages
7. Can E.Coli become resistant to T4 Phages
a. Yes
What are the implications of bacterial generation times on diagnosis and treatment of disease? Can humans adapt as quickly as bacteria can evolve?

October 7, 2009
Bacteria need to be in an aqueous environment; all of them need to be in this environment
Cell envelope stuff protects bacteria from osmotic pressure
1. Bacteria cell envelope stuff protects bacteria from osmotic pressure
2. Osmosis
a. Diffusion of water across a membrane down concentration gradient
3. Penicillin interferes with enzymes that make the new cell wall so when bacteria grow to divide they simply burst because they cannot form a septum to make a new cell wall
a. Some just blow up because the cell envelope stuff that protects the cell from osmotic pressure cannot recycle and make new cell wall components
b. There is some turnover in cell envelope components
4. If E. Coli were put on distilled water the bacterial cell wall would protect the cell from osmotic pressure
5. Bacteria live in an aqueous environment
a. Bacterial cell walls help make the bacterial cells much more resistant to osmotic pressure than eukaryotic cells
b. If something inhibits the production of their cell wall they will either blow up or shrivel up because the cell wall cannot protect it anymore
c. If cell wall is compromise then the bacteria are no more resistant to osmotic stress than our eukaryotic cells are
New Handout
1. Factors that influence bacterial growth rates
a. Osmotic pressure and availability of water
i. Water availability
1. Distilled water = 1.0
2. Blood = .95
3. Ocean = 0.90
4. Honey = .80
5. E.Coli is happiest at a water availability of .95 (blood) which is why it grows so well in us
a. Because of its cell wall we can drop it in something with an availability of 1.0 it will be okay and not burst
b. If dropped in sea water it will lose some of its water but will not die
c. This is true for virtually all bacteria that live in people
ii. Halophiles
1. Bacteria that can live at very low water availabilities
2. Halo = salt in Latin
3. By having very high solute concentrations inside cell, halophiles able to pull water into cell even when in very water-poor environments
4. Internal concentration of water is slightly lower than the external concentration of water which allows water to rush into the cell
iii. Why honey doesn’t spoil, and about rubbing salt in a wound
1. If you leave a steak out on the counter it will spoil because?
a. Water availability is high enough for bacteria that make us sick to live in/on the steak
2. Honey will not spoil because?
a. Honey does not have a high enough water availability for bacteria that make us sick to live in it
3. Rubbing salt into a wound
a. Actually used to be a standard medical treatment
b. It ought to work because it will move the water availability down so that most bacteria cannot grow in it
c. It will suck all the water out which will intern shrivel all the bacteria that were in it as well as shrivel up your cells which is why it hurts
d. Prevents any bacteria that could grow in there from growing

October 9th, 2009
Variances in Counts of T4-Resistant E.Coli Colonies, Tubes vs. Flask
Section 1:
Tubes: Variance = 202700.94
Flask: Variance = 2173.66
P-Value for F-test for variances = 2 x 10 ^ -49
Section 1:
p-Value for F-test for variances = 2 x 20 ^ -49
indicator of how likely you are to be wrong or showing something that is not there
The closer your p-value is to zero or the smaller it is = the more likely it is that your data is showing a real pattern
Usually, p-value < 0.05 accept our data means there is a 95% chance that the pattern we see in our data is a real patter
How many times would you have to repeat this experiment to see equal variances in the numbers of T4-resistant colonies from the flaks and tubes? A billion times
Does resistance to phages occur because of exposure to the phages, or randomly?
Randomly; there was variance in the tubes was much greater than the variance of the flask
When did T4 resistance occur in the E.Coli
Obs 1: DNA is instructions for making proteins;
Obs 2: When DNA is being copied (during cell division/replication) is when changes to DNA sequence are most likely to occur
Obs 3: changes to DNA sequences can  changes in amino acid sequences of proteins
What e the implications of this?
What other things occur randomly?
Abx resistance
If what is true of phage resistance is true of abx resistance and we stop using antibiotics would there still be resistance to abx?

October 12, 2009

b. Hydrostatic pressure/atmospheric pressure
i. Limitation on bacterial growth
ii. All of the weight of the air/water that is pushing down on us right now
iii. Bacteria we usually come into contact with best adapted to ~ 1 atm (pressure at sea level)
iv. some bacteria live at bottom of ocean, etc. – these adapted to MUCH greater hydrostatic pressures
c. Oxygen
i. Limiting factor for bacterial growth
ii. Our atmosphere on planet earth is about 20% oxygen
1. Toxic! Why is oxygen toxic?
a. Inhibits growth of many kinds of bacteria
b. Antioxidant is any material that “soaks up” free electrons
i. This helps prevent damage to DNA proteins caused by electrons bouncing around & breaking DNA strands/altering protein structure
2. Oxygen is very attracted to electrons so is very electronegative
a. If oxygen is present then a lot of electrons are attracted to it and the electrons bounce around and break stuff in the cell
b. So cell in environment w/ lots of oxygen is also in presence of lots of electrons
i. Electrons bounce around, break DNA, proteins
iii. Anaerobes
1. Cannot live in presence of ANY oxygen
2. Strict vs. facultative
3. Faculative:
a. can live with or without oxygen E. Coli
4. Strict:
a. C. Dificile cannot live in oxygen at all!!
b. Environments where they can live would be:
i. Bottom of the ocean possibly
ii. Deep in the soil
iii. Intestines
iv. Vagina
v. Many are in the human body
iv. Aerobes
1. Oxygen is the terminal electron acceptor
2. Oxygen is very attracted to electrons
3. Have to have specific mechanisms to deal w/ all the problems oxygen causes by attracting electrons and therefore destroying their DNA proteins
4. Environment cells (e.g. ours, ALL bacterial cells that live in normal oxygen ~20%), must have mechanisms for fixing DNA & protein damage caused by e-‘s and oxygen
5. Like our cells; require oxygen to grow
a. Use aerobic respiration as their primary means for generating ATP
b. Use identical ATP-generating mechanisms (w/ oxygen as terminal electron acceptor) as our mitochondria do
c. Cannot live in anaerobic environments
d. Most skin normal flora are aerobes
i. Staphylococci (gm +)
v. Other atmospheric requirements
1. Microaerophiles
a. Require a little bit of oxygen (5% or less) to grow but die w/ more oxygen than that
b. If very much is there at all they cannot deal w/ the damage done to their DNA
2. Capnophiles
a. Bacteria that must have some amount of oxygen to grow and have 5-10% of carbon dioxide to grow
i. Lungs are an example of an environment
b. Almost all pneumonia causing bacteria are an example
Why does oxygen inhibit the growth of many kinds of bacteria? Why do other kinds of bacteria (and your mitochondria) and oxygen?
d. Temperature
i. Psychrophiles
1. Bacteria that grow the best where it is very cold
2. ~-5C to about 10C
3. If any warmer than this they will die
a. Denatures proteins
4. Lots unsaturated fats in membrane
a. Better 4 u
b. Olive oil
c. Liquid at room temperature
d. More flexible at lower temperatures
e. Must have these so they ar flexible enough to divide
5. Little G&C, lots of A&T in DNA
ii. Mesophiles
1. Bacteria that grow best at ~20C-35C
2. All bacteria that live in/on our bodies
iii. Thermophiles & hyperthermophiles
1. Any bacteria that live the best at 60C
2. Hot enough to give a burn
3. Bacteria that live best at a little above 100C
4. Saturated fat in membrane
a. Butter
b. Stays solid at room temperature
c. Worries more about how to keep cell membrane together rather than if it is flexible
5. Lots of G&C and little A&T in DNA
iv. G and C have triple bond ant herefore more energy to break their bond and A and T have 2 bonds
v. G and C are more stable at higher temperatures and is why thermophiles and hyperthermophiles use more of these in DNA
e. pH
i. Acidophiles
1. Bacteria that live best at low pH (1.0-3.0)
2. Cause of stomach ulcers in H pylori
ii. Alkalophiles
1. Live best a high pH (10.0)
iii. Internal pH of cells is always 7 no matter what pH the environment they live in is
f. competition from other microbes; predation by phages and by other bacteria
Note: As long as there’s liquid water, some kind of prokaryote can thrive in practically any environment
Note: For bacteria to case disease in humans, that kind of bacteria must be able to grow in the human body
Do you have to worry about an epidemic caused by bacteria from Mars?

October 14 & 16, 2009
Very high fever; low blood pressure; nausea, dizziness, fainting; generalized pain; can result in organ failure
Same as inflammation but it is everywhere
Septic shock – caused by bacteria growing in blood stream; bacteria growing in the blood = septicemia; GM (–)bacteria in patients’ blood; Lipid A of LPS cause inflammation
Antibiotics will not make the person get better they will get worse; ABx the antibiotic will kill cell releasing cell components (lipid A) which will increase the immune system response
Inflammation = generalized response to injury; trying to get a lot of immune system components to the site of injury; goal = get immune system cells to injury site
1) blood vessel cells shrink, making vessels in area of injury leaky; WBC can get out because they are flexible; RBC too rigid
2) Increase blood flow to site of injury
3) Pain signal  stop re-injury
Bacterial components that  inflammation:
Lipid A of LPS
Superantigens – bacterial proteins that kick off VERY aggressive inflammatory response
Ex) Toxic Shock Syndrome or Toxin 1- (TSST-1); superantigen produced by some staph aureaus; staph aureus needs to have oxygen to grow
Toxic Shock Syndrome; tampons cause this because they make the vaginal anaerobic environment aerobic which gives staph aureus the opportunity to grow in this environment
Causes shock symptoms because the superantigen kicks off the immune system response

1. Bacterial Genetics
a. The discovery of DNA and the Griffith experiment (Draw Pictures!)
b. Experiment to find out what the molecule of in heritance is: DNA or proteins
i. Proteins are made out of Amino Acids
1. Very complex = made of 20 amino acids
2. Mainly what living organisms r made out of
3. I have the characteristics that I do because my parents passed down their proteins to me
a. This is why proteins should be molecule of inheritance (chemical containing instructions for how to make new org)
4. Proteins denature w/ heat
5. Can kill bacteria by heating them and denaturing their proteins
ii. DNA is not what we are mainly made out of we are made out of proteins
1. DNA is super simple it only had 4 bases
a. All this complexity is made of only 4 chemicals
b. A TINY minority of stuff organisms are made of
2. DNA is needed to make proteins however
3. Heat denatures proteins not DNA
iii. Obsv: Heat destroys protein but not DNA
iv. Obsv: S. pneumonia bacteria can  pneumonia, blood infections in people & mice
1. Some s. pneumonia have capsule, some don’t; made out of polysaccharide
2. S. pneumonia w/ capsule which is made out of polysaccharide which absorb water to keep the bacteria from drying out; they look very shiny and glossy when they grow on agar
a. Capsule protects from being phagocytized or engulfed by immune cells so they aren’t killed as effectively by the immune system
b. Because of capsule as a result if you inject the ones w/ a capsule into a mouse their immune system will not handle it and they will die
c. If mouse injected w/ boiled glossy bacteria mouse will be okay because proteins denatured and biofilm/capsule cannot be made and mouse can fight it off
3. S. pneumonia w/o capsule look more rough or matte on agar; don’t look glossy
a. mice immune system mice would get sick but be able to fight off the bacterium
b. inject mouse w/ live rough bacteria and boiled glossy bacteria
i. live rough bacteria on their own cannot kill the mouse and boiled glossy bacteria on their own cannot kill the mouse
v. Hypothesis:
1. Molecule of inheritance is protein
a. If mouse dies, NOT protein
b. Does not say DNA is the molecule of inheritance but does say that protein is not
2. Molecule of inheritance is DNA
a. Mouse would live, could still be protein
vi. DNA is the molecule of life
1. Mouse is dead
2. Take blood from dead mouse, mouse is filled w/ bacteria, and if u plate the blood on an agar plate, you see a lot of colonies of glossy bacteria.
3. Rough bacteria acquired the ability to made a capsule from the DNA from the dead glossy boiled bacteria and kill the mouse
2. What is the moral of the Griffith experiment? Does it show that DNA is the “Molecule of Inheritance”?
3. Properties of DNA
a. Supercoiled
i. Coiled up on itself over and over so it fits in the cell
ii. Enzymes who’s job is to uncoil the DNA (DNA Gyrase)
b. Double-stranded with antiparallel strands
i. Means the orientation of the strands is the opposite of eachother
c. Complementary base pairing  smeiconservative replication
i. DNA made of completmentary bases
ii. sugar-phosphate background hooks them together and is the backbone
1. deoxyribose
4. Steps of DNA replication (Draw Pictures!!)
a. Ori C: Where DNA replication begins on the bacterial chromosome
5. Repair to errors in DNA replication
a. Spontaneous mutation rateabout 1 mutant base pair per 10 billion base pairs copied
i. Size of bacterial genomes
b. Mismatch repair system
i. Find mismatched bases
iii. Methylated DNA is older
6. How many mutant bacteria are there in a colony of 1 billion E. Coli
7. Protection of the bacterial chromosome from degradation
a. Methylation of adenines and cytosines
b. Restriction enzymes

Amy Blass

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