Midterm 1-2

Question 1

Bactoprenol

Answer 1

undecaprenol diphosphate

hydrophobic C55 alcohol that is bonded to N-acetylglucosamine and N-acteylmuramic acid

pentapeptide PG precursor

transports the PG precursors across the cytoplasmic membrane by rendering them sufficiently hydrophobic to cross through the membrane

Question 2

Growth of the bacterial cell wall

Answer 2

1. Autolysins hydrolyze (break) the B-1,4 linkages - creates gaps in the cell wall
2. Flippase - flips single units of PG precursors across the cytoplasmic membrane
3. Once the bactoprenol units are crossed the cytoplasmic membrane, the unit interacts with transglycosylases that insert the units into the cell wall and catalyze glycosidic bond formation. TRANSGLYCOSYLATION

Question 3

transpeptidation

Answer 3

forms the peptide cross links between
- adjacent muramic acid residues in Gram+ cell walls
- DAP on one peptide and D-alanine on the adjacent strand in Gram- cell walls

exergonic - supplies the E required for the wall formation

Question 4

Transpeptidation is inhibited by:

Answer 4

Vancomycin and penicillin (beta lactam antibiotic)

Question 5

Transglycosylation inhibited by:

Answer 5

vancomycin

Question 6

Agents that destroy PG

Answer 6

lysozyme - found in tears and egg whites - hydrolyzes PG
antibiotics like vancomycin and B-lactam antibiotics (penicillin)
- inhibit formation and/or cross linking of the glycan strands

Question 7

B-lactamase

Answer 7

enzyme that breaks down B-lactam (ring) antibiotics
a common component of antibiotic resistance plasmids (R-plasmids) that are becoming increasingly prevalent in clinical settings

Question 8

Divisome

Answer 8

Forms 3/4 through cell division and is made up of Fts proteins (filamentous temperature sensitive).

Question 9

FtsZ

Answer 9

Part of the divisome
Forms a ring around the centre of the cell -
It has been found to have structural homology with tubulin in eukaryotes

COORDINATES THE CELL DIVISION PROCESS. the other components are less important

Question 10

ZipA

Answer 10

Anchor that connects FtsZ ring to the cytoplasmic membrane

Question 11

FtsL

Answer 11

A peptidoglycan biosynthesis proteiN

Question 12

FtsK

Answer 12

assists in chromosome separaton

Question 13

FtsA

Answer 13

ATPase

Question 14

DNA replication and cell division events

Answer 14

Initially MinCD inhibits formation of FtsZ ring
Then MinE oscillates from pole to pole - sweeping MinCD aside
When the cell becomes very long, there is little MinCD in the middle of the cell - why the cell divides in the middle

Question 15

crescentin

Answer 15

shape determining protein found in curved cells - causes curvature

organizes into filaments that localize on the concave face of curved cells

Question 16

MreB

Answer 16

major shape determining factor in prokaryotes. Esp rod cells (not found in coccus shaped cells)
Forms simple cytoskeleton with patch-like filaments around the inside of the cell just below cytoplasmic membrane in Bacteria and some Archaea
coordinates the breakdown of PG
Recruits other proteins for cell wall growth to group into a specific pattern

Question 17

polyhydroxyalkanoates (PHA)

Answer 17

Energy storage polymer that includes PHB

Question 18

nitrification

Answer 18

lithotrophic oxidation of ammonia to nitrate
- done by ammonia oxidizerd

Question 19

annamoxisome

Answer 19

A membrane-bound compartment packed with enzymes. Allows it to grow with NH3 under anoxic conditions

Question 20

Endospores

Answer 20

Only found in Gram+ bacteria. Resting stage is able to survive all sorts of harsh conditions

Only formed in some Firmicutes

Question 21

lophotrichous flagella

Answer 21

a tuft of flagella coming out from one region on the bacterium. Like a pony tail.

Question 22

fimbriae

Answer 22

small hair-like structures coming off of the entire body of a bacterium. These are smaller than both flagella and pili

enable organisms to stick to surfaces or form pellicles (thin sheets of cells on a liquid surface) ie biofilms

Question 23

pili

Answer 23

longer and fewer than fibriae
- conjunctive sex pili facilitate exchange between bacteria (conjugation)
- type lV pili adhere to host tissues and support twitching motility (Pseudomonas ex)

Question 24

Archaeal cell membranes

Answer 24

• can form monolayers (rather than bilayers) which decrease the fluidity of the membrane)
• monolayers have tetraethers while bilayers have diether linkages
• ether linkages are more thermostable and more resistant to hydrolytic cleavage compared to ester bonds.

Question 25

Archaeal cell walls

Answer 25

NO PG, but have PG-like polymers like pseudomurin and methanochondroitin HAVE S-LAYERS which function like PG does in bacterial cell walls - consists of protein or glycoprotein - paracrystallin structure A sheath is an S-layer that covers multiple cells

Question 26

S-LAYERS

Answer 26

function like PG does in bacterial cell walls - consists of protein or glycoprotein - paracrystallin structure A sheath is an S-layer that covers multiple cells Found mostly in Archaea, sometimes in Bacteria Act as structural support, molecular sieves, and to form a pseudoperiplasmic space.

Question 27

whICH shaPES of bacteria are flagella found on?

Answer 27

Found on rod-shaped or curved bacteria

Question 28

wHAt protein are flagella made out of?

Answer 28

flagellin - repeated in a helical pattern along the flagellum

Question 29

What is the function of the L and P rings in flagellar movement?

Answer 29

Sleeves in the peptidoglycan and outer membrane - anchors

Question 30

What is the function of the Mot proteins in flagellar movement?

Answer 30

form the slater which is where protons come through. They do not move but instead form the framework for where the flagella rotates

Question 31

What forms the rotor?

Answer 31

The MS ring and the Rod. Within the slater, the rotor rotates using the energy from the proton motive force. (protons moving from the periplasm into the cytoplasm)

Question 32

flagella biosynthesis

Answer 32

basal structures are formed first and then the filament grows from the TIP via the transport of flagellin proteins up through the hollow core of the growing structure.

Question 33

What is going on when the flagella is rotating counter clockwise?

Answer 33

THE SAME DIRECTION AS THE HELIX OF THE FLAGELLA the bacterium is in run mode and swimming STRAIGHT forward The flagella form a trailing bundle.

Question 34

What is going on when the flagella is rotating clockwise?

Answer 34

The bacterium is in tumble mode and the flagella are spread a part rotation is the opposite of the direction of the helices of the flagella.

Question 35

What does having a low Renolds number mean?

Answer 35

Bacteria have a low Renolds number and this means that the friction of water is massive compared to the momentum. Stops very quickly once it stops moving its flagellum (momentum ceases)

Question 36

What are two component-regulatory systems composed of?

Answer 36

A sensor kinase and a response regulator

Question 37

Sensor kinase

Answer 37

Usually found spanning the cytoplasmic membrane Detects the environmental signal with a chemical signal and autophosphorylates itself on a histidine residue. It transmits the signal via the phosphorylation of a response regulator which activates the RR CheA

Question 38

Response regulator

Answer 38

in the cytoplasm. Usually a DNA binding protein that regulates transcription - Has a negative feedback loops that terminates the signal The RR can also sometimes interact directly with the flagellum

Question 39

biased random walk

Answer 39

allows for directed movement Bacteria respond to temporal, not spatial, difference in concentration. length of runs changes respond to if things get better or worse

Question 40

CheA

Answer 40

Sensor kinase. Associated with MCP (transmembrane component) and CheW Phosphorylates CheY and indirectly CheB to mAKE THem active

Question 41

MCPs

Answer 41

methyl-accepting chemotaxis proteins Bind to the attractants or repellents in the environmment interact with the sensor kinase ie CheA Binding to attracting makes MCPs LESS active which promotes a longer run.

Question 42

CheW

Answer 42

the link between MCP and CheA

Question 43

CheY

Answer 43

primary response regulator. Signals the flagellar rotation to change direction and TUMBLE Interacts with Fli proteins to reverse flagellar rotation

Question 44

CheZ

Answer 44

the off switch for CheY (dephosphorylates CheY to an INACTIVE state) Reset!

Question 45

CheB

Answer 45

secondary response regulator that acts as an off switch for MCPs (making them INACTIVE) removes the methyl groups from MCPs to make them inactive meaning the promotion of RUNNING (not signalling a tumble) regulates the negative feedback CheB is activated during the signal promoting tumble. During the reset, CheB-P is removing methyl groups from MCPs so that MCPs come less active and CheY is no longer phosphorylated. time-delay switch

Question 46

CheR

Answer 46

On switch for MCPs. It methylates MCPs to make them ACTIVE/sensitive Activity of CheR promotes the signal transduction pathway - ie promotes tumbling This is what causes the tumble to happen even when the MCPs are binding attract that decreases their sensitivity

Question 47

What is happening during a 'run'

Answer 47

The response regulators are inactive (not phosphorylated) and the flagella rotate counterclockwise - however CheR is constantly adding methyl groups to MCPs (making more sensitive/active and thus more likely to signal a tumble)

Question 48

Tumble

Answer 48

Signal begins when MCP signals to CheA to be autophosphorylated CheA-P then activates CheY to CheY-P and CheB to CheB-P CheY-P interacts with Fli proteins to reverse the flagellar rotation of the motor. Cell tumbles

Question 49

Equations you need to know.

Answer 49

Nt = N0 * 2^n n = t/g Nt = population of bacteria at time T N0= population of bacteria at time 0 n = number of generations t = time passed g = generation time (amount of time required for the population to double)