Midterm 2 study Q's

Question 1

(Quorum sensing)

1. Autoinducers for Gram positive bacteria are …

a) Peptides
b) Small molecules
c) Either peptides or small molecules depending on autoinducer
d) Molecules that can freely diffuse in and out of the cells

Answer 1

(c) peptides

Question 2

2. Autoinducers are …

a) Kinase activators
b) Gene regulators
c) Stress responses

Answer 2

(b) gene reguators

Question 3

3. Autoinducers are …

a) Expressed during a stress response
b) Always expressed
c) Expressed when bacteria are in sufficient numbers

Answer 3

b) Always expressed

(They always are ‘expressed’, but they only actually have an affect when there’s enough bacteria around expressing them. So, these molecules need to be in sufficient numbers in order to have any AFFECT. If the bacteria are in sufficient numbers, the genes will be expressed, but the autoinducers themselves are always expressed.)

Question 4

(Quorum Sensing)

1: What is an autoinducer?

Answer 4

An autoinducer is a molecule that is secreted by bacteria cells, out into their environments. The point of this molecule is so that if there are other bacteria present in the area they will receive these signaling molecules from their peers, and they will be able to communicate with each other. When autoinducers are in high enough concentration, they will have an effect on regulating gene expression for specific genes.

Question 5

(QS)

2: What is quorum sensing and what does it do?

Answer 5

Quorum sensing is the process of communication that is used by bacteria that are in groups. They use chemical signals called autoinducers to send information to each other. This is important for coordinating group behavior such as building biofilms. When bacteria are in sufficient numbers, they will be able to express certain genes.

Question 6

3: Explain the mechanism for quorum sensing in Gram-negative bacteria using the Lux system in V. fischeri. You can use a schematic representation to support your explanation, but using a schematic representation alone is not sufficient.

Answer 6

The Lux system in V. fischeri begins when the enzyme Luxl produces the autoinducer N-acyl homoserine lactone (or AHL). These autoinducer molecules are released out to the environment, and when there are enough cells present, there will be a high saturation of autoinducers. When AHL reaches a high enough saturation, it will diffuse into the cells and bind with the LuxR protein. The LuxR protein will activate the transcription of genes that code for bioluminescence, so this is why it only happens when there are enough of the bacteria species around.

Simplified:
*Luxl makes autoinducer AHL (N-acyl homoserine lactone).
*If autoinducer amount is high enough, it goes into other cells to LuxR receptor, and the receptor activates gene tranmscription for bioluminescence.

Question 7

4: Explain the mechanism for quorum sensing in Gram + bacteria. You can use a schematic representation to support your explanation, but using a schematic representation alone is not sufficient.

Answer 7

While gram(-) bacteria use AHL autoinducers, Gram(+) bacteria are different because they use peptide based autoinducers. Like gram(-) bacteria, they will secrete these into the extracellular environment. When the concentration is high enough, the peptide autoinducers will bind to receptor kinases on the cell membrane of the bacteria. Then the kinase will phosphorylate itself, and then transfers the phosphate to a response regulator protein. The response regulator protein is a transcription factor for the genes that the bacteria want to express when they’re in a large group.

Question 8

8: What is the role of LuxS in V. harveyi?

Answer 8

LuxS is an enzyme that makes DPD, and then there will be formation of a ring called S-DHMF, which the autoinducer-2 will be formed from, and autoinducer-2 is the one used to communicate with multiple different bacteria species.

Question 9

5: Is the Gram + quorum sensing described by Dr Bassler a species-specific way of communicating?

Answer 9

Yes, it is species specific because each species has a different autoinducer.

Question 9

6: What was different about the quorum sensing mechanism of V.haveyi?

Answer 9

V. haveyi is different because it has the ability to produce two different autoinducers, one to communicate within its own species, and one to communicate with other bacteria species. V. haveyi produces 2 different autoinducers: Al-1 and Al-2. Al-1 is a species specific autoinducer, while Al-2 is an autoinducer that is used for multi-species communication.

Question 10

7: How could bacteria benefit from using multiple autoinducer signals for quorum sensing? Name two possible benefits.

Answer 10

Firstly, it is beneficial because the bacteria has the ability to communicate with more cells since it can send signals to a broader range of species. Secondly, the bacteria can probably utilize the skillset of a different species for things it may not be able to do with its own species alone.

Question 11

9: Why could inhibiting quorum sensing be beneficial clinically? Give me at least 3 reasons.

Answer 11

Inhibiting quorum sensing could be beneficial in medicine because of the following:
1: Some types of bacteria use quorum sensing to figure out when they have enough ‘friends’ around to start producing virulence factors without the host (such as humans) being able to fight them off.
2: Quorum sensing is used to coordinate the formation of biofilms, and the formation of biofilms can occur in human hosts, such as in in the mucus in the lungs of a person with Cystic Fibrosis. Biofilms also form around artificially inserted tubes such as a catheter.
3: It could also be used to inhibit species-specific growth and biofilm formation of any bacteria that is causing a specific infection in the body.
Inhibiting quorum sensing in all of these 3 examples would aid in improving health of humans who have bacteria accumulating in these ways in their bodies.

Question 12

(QS)

10: Could there also be drawbacks for our health in inhibiting quorum sensing in multi-species environments?

Answer 12

Yes, because if we try to inhibit quorum sensing across all species for example, then there are a lot of good bacteria that are naturally found in the gut or oral cavity, and inhibiting quorum sensing for these bacteria could stop them from communicating and functioning properly. Gut bacteria are important in absorption of nutrients and breakdown of certain substances in the digestive system.

Question 13

11: How might you develop an anti-quorum sensing, or quorum quenching, strategy?

Answer 13

One possibility is to create an enzyme that can hydrolyze or break down or inhibit the bacteria’s autoinducer molecules so that they cannot travel into other bacteria effectively. Another possibility is to have a molecule that has a higher affinity to the bacteria’s autoinducer receptors, so that the receptor sites will be blocked and the bacteria cell will not be able to receive the autoinducer signal.

Question 14

(Spatial Organisation)

1: What is FtsZ and what is its role?

Answer 14

FtsZ is an important protein in bacteria, that is found in almost all bacterial cells. It is essential for cell division. The FtsZ protein is very similar in structure to the eukaryotic cell’s Tubulin proteins. FtsZ is the protein that forms a ring around the cite where cytokinesis needs to occur, and it constricts and pulls the membrane together to separate the cells.

Question 15

2: If FtsZ is mutated, what happens during cell division?

Answer 15

If a cell’s FtsZ protein is not functioning properly, then the cell will not be able to finish dividing and perform cytokinesis, so it will just grow really long into a worm-looking cell filament that will die.

Question 16

3) What is MreB and what is its role?

Answer 16

While FtsZ is the equivalent of Tubulin in eukaryotes, the MreB protein is the equivalent of actin in eukaryotes. It is another protein that is important for bacterial cell division, and it mediates the width of the cell, so that even though it will of course increase in length, the width will stay constant, and the cell will keep its proper form. This is because MreB is part of the cytoskeleton, just like actin is in eukaryotes. It holds the cell’s structure especially right around the membrane to stop it from expanding in width. It forms filaments directly under the cell membrane.

Question 17

4) If MreB function is inhibited, what happens during cell division?

Answer 17

If the MreB function is inhibited, then during cell division, the cells will expand in width and they will become round. If the cells become round, they will die because they are too wide to allow for the polymerization of the FtsZ ring.

Question 18

5) What is Crescentin and what is its role?

Answer 18

Crescentin was the first intermediate filament to be discovered in bacteria. It has similar properties to the intermediate filaments in eukaryotic cells. If you purify this protein in vitro, it will assemble itself into intermediate filament-like shapes. Inside of C. Crescentus cells, the crescentin will form along one side of the cell, and it will bend along that side to form the cell into a crescent shape.

Question 19

6) If the Crescentin gene is deleted, what happens during cell division?

Answer 19

If the cell does not have crescentin, it will lose its curvature and become straight and rod-like. This doesn’t necessarily stop the cells from being able to divide.

Question 19

8) What do we mean by spatial organization?

Answer 19

Spatial organization is where different organelles are encased in their own membranes and are found in specific locations in the cell. Eukaryotes tend to have more spatial organization than bacteria, as bacteria do not have membrane-bound organelles. Spatial organization encompasses the location of all the different organelles, and they are not placed randomly.

Question 20

2) So, starting with a culture of 1000 E. coli, how many would I obtain after 16h of ideal growth conditions?

Answer 20

16h = 16x60mins = 960mins 960mins/20mins = 48 divisions per cell
1000cells x 248 = 2.81x1017 cells after 16h.
Therefore, there will be 248 = 2.81x1017 cells after 16h.

Question 20

9) What is cell polarity?

Answer 20

Symmetric cell polarity is when the bacterium has an accumulation of proteins at either end (the poles) of the cell. And asymmetric cell polarity is when a cell has different structures or accumulations of different proteins at opposite ends of the cell, allowing for different specialized functions at each end.

Question 21

1) How quickly can E. coli divide?

a) 2min
b) 20min
c) 1h
d) 24h

Answer 21

(b) 20 mins

Question 22

10) Describe two functional examples of bacterial cell polarity or spatial patterning (from the video). One example of symmetric polarity and one of asymmetric polarity.

Answer 22

An example for symmetric cell polarity are the chemoreceptors in the bacteria E. Coli which allow the bacteria to detect chemicals and swim toward things they like, and away from things they don’t like.
An example for Asymmetric cell polarity is in Caulobacter crescentus, where one end of the cell has a flagella and a phosphatase, and one end has a kinase and an extension of the cell membrane. When this cell divides, the two daughter cells will have different ‘fates’, one will have the kinase end, one will have the phosphatase end.

Question 23

3) Why would passive diffusion not always be a good means of segregating cytoplasmic material in dividing cells?

Answer 23

Passive diffusion is not a good strategy when there are not a lot of copies of the material, because then chances are higher that one daughter cell could end up with not enough or even no copies.

Question 23

4) The Par or ParABS system evolved as mechanism to partition low copy numbered cellular material, such as chromosomal DNA. Explain how this system works, in a sequential manner, for segregating chromosome during cell division of Caulobacter crescentus. Use a schematic representation to support your explanation if you wish.

Answer 23

There is a DNA sequence near the ori site of the cell at the ‘old pole’ that we call ParS, that will be duplicated early on in DNA replication, this spot at the ori site is held onto the cell by the PopZ matrix. There is a dimer protein called ParB that will bind to this ParS sequence, and then more ParB will bind along the DNA adjacent to the ParS sequence. There will be a gradient of the ATPase called ParA along the length of the cell, with the highest concentration being toward the opposite pole (so toward the ‘new pole). ParA is an ATPase that binds to ATP and attaches also onto DNA, and when interacting with the protein ParB, then ParA will hydrolyze ATP and It will pull/ ‘walk’ the newly synthesized chromosome to the opposite end of the cell. The ParA will bind to ParB on the DNA and eventually, the strand will end up at the opposite end of the cell, where it then will become attached to the PopZ matrix on the other side of the cell, and now they are separated properly for cell division.

Question 24

(lec. 7)

Autotroph vs heterotroph?

Answer 24

An Autotroph will Fix CO2, and assemble that into organic molecules.

A heterotroph will acquire pre-existing organic molecules and rearrange them for stuff.

Question 24

5) What is an ATPase activity?

Answer 24

An ATPase is an enzyme that hydrolyzes ATP, and the term ‘ATPase activity’ is referring to the ability of the ATPase to hydrolyze ATP molecules into ADP, which is used to generate energy for many reactions. So, an ATP molecule gets hydrolyzed into ADP plus a phosphate.

Question 24

(lect. 7 ~ Microbial growth)

Define:

(1) Essential Nutrients

(2) Macronutrients

(3) Micronutrients

Answer 24

(1) Essential Nutrients: Nutrients that MUST be supplied from the environment.

(2) Macronutrients:
* Major elements in cell macromolecules, so C, H, O, N, P, S.
* Cations that are necessary for protein function, so Mg2+, Ca2+, Fe2+, K+.

(3) Micronutrients: trace elements that are necessary for enzyme function, so Co, Cu, Mn, Zn.

Question 24

6) Are you surprised at how similar or dissimilar are certain aspects of cell biochemistry between eukaryotes and prokaryotes? Discuss your thoughts on the matter.

Answer 24

I am not super surprised about the similarities between the two because I know that bacteria would of course also have cell division and whatnot. I am a little surprised about how differently they do certain things like how they can partition their cellular material like their circular chromosome, whereas eukaryotes have the mitotic spindles for chromosome segregation instead. But I also know that bacteria would obviously have to do things differently since their DNA is condensed differently than eukaryotes.

Question 25

(lec. 7)

What are the 3 ways that selective permeability is achieved in the cell membrane (the 3 types of things that intake or export substances).

Answer 25

(1) Permeases ~ Substrate-specific carrier proteins.

(2) Periplasmic Nutrient Binding Proteins ~ binds nutrients in the periplasm (space between inner and outer membranes).

(3) Porins ~ channels in outer membrane that allow larger or polar molecules to pass through the cell.

Question 26

(lect. 7)

What are secretion systems?

Answer 26

Secretion systems are specialized structures bacteria use to transport molecules, like proteins or toxins, from inside the cell to the outside environment or into other cells. These systems help bacteria interact with their surroundings, defend themselves, or infect host cells.

SO basically, the bacteria will have these tube things that it pokes into other cells, and secretes it’s stuff into them.

Question 27

(lec. 7)

ABC transporters are what?

Answer 27

-ABC transporters are the largest family of energy driven transport proteins.
(so, active transport)

-Found in all 3 domains of life!

-Gram-negatives employ periplasmic binding proteins,
and Gram-positives and Archaea employ substrate-binding proteins on the external surface of the cytoplasmic membrane.

Question 28

NOTE CARD: Below this point are cards i’ve added for the FINAL EXAM.

I am starting with LECTURE 7 here!!:

.

Question 28

(slide 4) Macro vs micro nutrients?

Answer 28

Macronutrients: major elements in macromolecules CHONPS, and cations for protein function: Mg2+, Fe2+, Ca2+, ect.

Micronutrients: trace elements for enzyme function: Zn, Co, Cu, etc.

(so, if CHONPS or cation, it’s prob macro.)

Question 29

(slide 10)

1) Quick recap on ABC transporters?

2) uptake vs efflux transport?

Answer 29

1) ATP-Binding-Casette.
they are membrane transporters that are powered by ATP.
found in all 3 domains of life.

2) Uptake: bringing nutrients into the cell.
Efflux: discarding waste out of the cell.