3 Micro Bio - Lec 1-3 Intro

Front 1

What are some characteristics of C difficile?

Back 1

- rod shaped, spore forming, gram +

- strict anaerobe

- makes toxin proteins TcdA & TcdB

Front 2

What is the difference between prokaryotes & eukaryotes: nuclear membrane? membrane-bound organelles? Endocytosis?

Back 2

- eukaryotes have nuclear membrane, bound organelles, sample the environment, way bigger than prokaryotes

Front 3

What are the 5 different bacterial shapes?

Back 3

1) bacilli (rods)
2) cocci (spheres)
3) spiral (wavy)
4) spirochete (corkscrew)
5) vibrio (comma-shaped)

Front 4

gram positive vs. gram negative

Back 4

- gram positive: thick cell wall (retains blue purple dye)

- gram negative: thin cell wall (does not retain dye)

Front 5

What is the gram (+) envelope made out of (aka the cell wall)

Back 5

- has peptidoglycan outside of cell membrane w/ lipoteichoic & teichoic acid

- short polysaccharide chains cross-linked by amino acids

- M= N-acetylmuramic acid, G=N-acetylglucosamine

- repeating units crosslinked by D-amino acids

- excellent target for antibiotics

Front 6

How does penicillin work? This makes it only effective against _____ cells

Back 6

- inhibits cross linking of peptides (by binding to transpeptidases) --> leads to lysis

- only effective against growing cells

Front 7

What are the phases of the bacterial growth curve?

Back 7

- lag phase

- exponential phase

- stationary phase (when run out of nutrients)

- death

Front 8

why do bacteria grow so much faster in a rich medium?

Back 8

- because they don't have to spend anytime making the mediums

Front 9

How do bacteria get energy from outside sources?

Back 9

- take nutrients outside cell --> catabolic reactions then use ATP & reducing power & precursor molecules --> biosynthesis of macromolecules

Front 10

prototrophs vs auxotrophs

Back 10

- prototrophs: no requirements for organic compounds other tahn simple carbon source (sugar) - can make everything on their own

- auxotrophs: more complex nutritional requirements (amino acids, purines/pyrimidines)

Front 11

symbiotic/commensal relationships vs parasitic/pathogenic relationships

Back 11

- symbiotic means both parties are benefitting

- parasitic means that causing damage to host

- bacteria can go from commensal --> pathogenic

Front 12

normal flora & how do they protect against infection

Back 12

- helps obtain maximum value from digestion

- produces products we need (vit K)

- induce development of immune system

- protect against infection b/c secrete anti-microbial peptides, metabolism of compounds needed by C. difficult

Front 13

what do probiotics do?

Back 13

- aid in restoring normal flora after antibiotic treatment

- reduce diarrheal disease

Front 14

strict aerobes vs. anaeorbes vs facultative anaeorbes

Back 14

- strict aerobes: terminal electron acceptor = oxygen

- strict anaerobes: terminal electron acceptor = organic molecule

- facultative anaerobes = some respire aerobically & ferment anaerobically, some respire both aerobically & anaerobically

Front 15

What are the two ways that bacteria can get ATP?

Back 15

- substrate level phosphorylation (1,3BPG --> 3PG)

- electron transport chain

Front 16

Difference b/w aerobic respiration & anaerobic in terms of terminal electron acceptor?

Back 16

- aerobic: oxygen is terminal electron acceptor

- anaerobic: organic molecule (fumarate --> succinate OR nitrate --> ammonia)

Front 17

When does fermentation take place? What are some of the end products?

Back 17

- fermentation takes place when only generating energy by substrate level phosphorylation

- lactate, ethanol, acetoin, fatty acids, acetate

Front 18

What does spore formation do? Gram neg. or pos. produce these? What triggers this?

Back 18

- non-growing structures, can survive for long periods of time under conditions of extreme heat,/no water/chemicals, low water allows them to survive harsh environmental conditions

- gram positive

- triggered by nutritional limitations

Front 19

What phase of the bacterial growth curve does spore formation happen? What else happens during this phase? What is the difference b/w antibiotics & toxins and why do they secrete these?

Back 19

- stationary phase

- motility & chemotaxis

- secrete degradative enzymes so can breakdown things normaly wouldn't eat --> transport secondary nutrients

- intracellular catabolic pathways

- antibiotic & toxin production

- secrete antibiotics to prevent growth of competitors

- toxins damage eukaryotic cells to get nutrients from us

Front 20

What are the steps in spore formation? To become growing cell again, spore has to _________.

Back 20

- cell divides unevenly on one end --> larger cytoplasm engulfs smaller cytoplasm

- spore develops inside mother cell --> mother cell then lyses to release spore

- to become growing cell again, spore has to germinate

Front 21

What happens when people are reinfected with bacteria after antibiotic treatment?

Back 21

- antibiotics kill growing cells --> NO antibiotics kill spores

- once antibiotics are over, spores will germinate and reinfect you

- infectious form is the spore!

Front 22

Explain toxin gene locus in C. difficile

Back 22

- tcdA & tcdB are toxin genes - flank tcdE (holin - punches hole in membrane for toxins to escape cell)

- regulators flanking tcd A & B = tcdR & tcdC

- tcdR: positive regulator --> codes for alternative sigma subunit only expressed during stationary phase (will go bind toxin gene promoters) --> negatively regulated by CodY-Ile (ie when low nutrients - neg. regulator (repression) of tcdR turned off & tcdR (pos regulator) turned on)

- tcdC: negative regulator, keeps tcdR in inactivate state (b/c CodY is not 100% efficient) --> makes protein that inhibits tcdR

Front 23

What are the 5 subunits of RNA polymerase? What are the special sites it recognizes?

Back 23

- 2 alpha

- beta, beta'

- sigma

- recognizes -35 & -10

Front 24

holoenzyme vs core enzyme

Back 24

- holoenzyme: 2 alpha, beta, beta', sigma

- core enzyme: 2 alpha, beta, beta'

- core enzyme cannot recognize promoter b/c doesn't have sigma

Front 25

What are the different functions of the different subunits of the RNA polymerase?

Back 25

- beta: catalytic activity, holds alpha subunits on, target of rifamycins

- beta': allows RNA polymerase to stay bound to DNA

- alpha: important role with regulatory proteins

- sigma: necessary for recognition of promotor region

Front 26

The _____ subunit allows escape from the promoter (translocation) & elongation of the transcript

Back 26

- sigma

- this is because sigma causes very stable binding at promoter regions, reduces binding at non-promoter regions of DNA

Front 27

____ is an alternative sigma subunit expressed only during stationary phase. How is it repressed during non-stationary phase? Because repression isn't 100% efficient how else it it blocked?

Back 27

- tcdR

- CodY-Ile - blocks transcription of tcdR gene

- tcdC is protein that binds to little amount of tcdR produced to inactivate it --> goes away in nutrient limited state

Front 28

how it CodY regulated?

Back 28

- inactive without any amino acid bound to it (in nutrient limited state)

- active when sufficient Ile

Front 29

Gram + vs - : thickness of PG layer? outer membrane? LPS?

Back 29

- gram +: thick PG layer no outer membrane, no LPS

- gram - : thin PG layer, outer membrane, LPS

Front 30

______ is the area in between the inner and outer membranes of gram - bacteria where the peptidoglycan layer is. There are _____ in the outer membrane that allow the cell to take up nutrients. LPS is in the _______ leaflet and phospholipid in the _____ leaflet. LPS is also known as ______.

Back 30

- periplasm

- pores

- outer

- inner

- endotoxin (O-antigen)

Front 31

______ are found on surface or tip of pili & bind to sugar molecule on host cell surface. What are the 3 types of adhesins?

Back 31

- adhesins

1) pili (fimbriae)
2) capsules
3) flagella

Front 32

What are pili (fimbriae)?

Back 32

- extensions from cell surface

- can adhere to surfaces & conjugate b/w bacteria

- mainly for adhesion to almost anything

Front 33

What do capsules do?

Back 33

- loose network of polymers around cell (polysaccharide/protein) - mucoid layer

- anti-phagocytic

- mucoid layers cause them to be encapsulated & hides from immune systems

- adherence to surfaces

Front 34

______ is the most common agent of motility. _____ allows bacteria to penetrate mucous layer. _____ movement towards food or away from poisons (specific receptors direct this motility).

Back 34

- flagellum (linked to membrane by basal bodies)

- motility

- chemotaxis

Front 35

How does chemotaxis work?

Back 35

- membrane bound protein senses something outside cell

- transmits it to sensor histidine kinase

- phosphorylates flagellar motor

Front 36

Bacteria also secrete mucous layers (capsule possibly made of alginate) because they help protect them from ______. Explain regulation of alginate?

Back 36

- antibiotics

- alginate production depends on AlgU (alternative sigma factor) for transcription of alginate genes

- AlgU in inactive state by interaction with MucA

- when cell sense stress MucA is degraded by protease in periplasm & AlgU can direct transcription of alginate genes

Front 37

What are the steps in biofilm formation?

Back 37

- reversible adsorption of bacteria --> irreversible attachment of bacteria

- growth & division of bacteria --> as grow signal to own species & others to attract more bacteria

- signaling process turns on production of exopolymer (alginate) production & biofilm formation (matrix of polysaccharides & free DNA)

- attachment of other organisms to biofilm

Front 38

What is intercellular signaling in a biofilm? What are the 2 signaling compounds & which types of bacteria do what?

Back 38

- associated with population crowding

- within species or across species

1) acylated homoserine lactones (gram -)

2) peptides (gram +)

Front 39

For gram - bacteria, the acylated homoserine lactones are secreted _____ of the time, however the concentration _____ when in a closed environment. Once it reaches a critical concentration, it activates pathways more sensitive to it, _____ sensing. AHL or peptide (gram +) signal to ______ kinase that phosphorylates response regulators involved in ________. These phosphorylated regulators bind DNA & stabilize RNA polymerase to bind to promoter.

Back 39

- all

- increases

- quorom sensing

- sensor histidine kinase

- biofilm gene expression

Front 40

What adaptive benefits do bacterial populations derive from multi-cellular cooperation?

Back 40

- work better in community than they can as individuals --> ex. metabolism: need more degrading enzyme than they have in 1 bacteria so like to have lots