Lecture 08

Question 1

How do cells maintain homeostasis? What parts of their cell are they using?

Answer 1

They are using their cell membranes to maintain homeostasis through processes of diffusions (there are different types)

Question 2

What is the difference between gram negative and gram positive bacteria and why is that important to understanding homeostasis?

Answer 2

Gram negative bacteria have an outer membrane, peptidoglycan layer, and the inner membrane. Gram positive bacteria only have the peptidoglycan layer and the cytoplasmic membrane. This means that anything entering or exit the cell has to get across 2 OR 3 “membranes”

Question 3

Gram negative bacteria mechanisms

Answer 3

ATP-binding cassette (ABC) transporters
TonB-dependent Transporters (TBDT)

Question 4

ATP-binding cassette (ABC) transporters

Answer 4

1. Solute enters porin and crosses outer membrane
2. Solute binds to a solute binding protein and to cross the periplasm
3. The complex will bind to the membrane transporter and pass through the cell membrane via conformational change of the transporter powered by ATP
4. ATP hydrolysis occurs and the dimer opens to release the solute into the cytoplasm

Question 5

TonB-dependent Transporters

Answer 5

These transporters are used when the solutes are too large to cross the outer-membrane nonspecifically. Only found in the outer membrane!

Question 6

TonB-dependent Transporters

Answer 6

1. TonB box attatched to the TBDT’s interacts with the corresponding IM proteins (TonB, ExbB, ExbD)
2. The IM proteins use the proton motive force to power the movement of the solute across the OM.
3. ABC transporters can bring the substrate across the IM. Still requires a periplasmic binding protein.
   Fe 3+ is used here!

Question 7

Sec YEG complex

Answer 7

A type of transporter that moves proteins into the outer membrane. Used for lipoproteins and periplasmic proteins and OM proteins.

Question 8

SEC YEG complex mechanism

Answer 8

SecB will recognize a site on the protein and bind to it preventing it from folding. It will move it to the Sec EYG complex where Sec A will power the transporter to open and move the unfolded protein across the inner membrane.

Question 9

What happens if SecB is not used?

Answer 9

Sometimes Sec B is not used because there are IM proteins that are too hydrophobic for SecB to maintain in a conformation to be exported

Question 10

Mechanisms of the Signal Recognition Particle

Answer 10

1. Signal recognition particle binds to the signal part of the peptide as it emerges from ribosome. Translation pauses!
2. This allows the SRP receptor to bind to the SRP complex
3. The SRP receptor will transfer the unfolded protein to the Sec YEG complex
4. Translation resumes and GTP hydrolysis is used to push the protein across the membrane

Question 16

Do all secretion systems occur in both Gram-negative and Gram-positive bacteria? What about archaea and eukaryotes?

Question 17

How else do bacterial cells maintain homeostasis?

Answer 17

1. Control of gene expression (which proteins are made)
   This starts with transcription
2. Enzyme activity (which proteins are on/off)

Question 18

Cell regulates global gene expression by controlling which sigma factors are present and active

Answer 18

True!

Question 19

Other methods to stop transcription

Answer 19

1. Repressors
2. Corepressors
3. Accessory transcription factors (activate or repress) these determine when protein is active.

Question 20

How can we regulate global gene expression?

Answer 20

By controlling which sigma factors are present and active!