Bacterial Gene Regulation

Question 1

DNA binding proteins

Answer 1

-Do the regulating
-Domain containing protein-protein contacts, holding protein dimer together (2 subunit)
-DNA-binding domain fits in major groove and along sugar-phosphate backbone.
-look at notes

Question 2

Transcriptional Control

Answer 2

-repressors exert NEGATIVE control
-look at notes

Question 3

Arginine graph

Answer 3

-cell number and total protein are positive increasing lines
-when arginine is added its line goes from increasing positive to flatting out
-arginine production repressed

Question 4

Lactose graph

Answer 4

-cell number and total protein are increasing lines
-when lactose is added, it removes the repressor, and B-Galacto-sidase increases

Question 5

How do the Arg (arginine) repressors act when it binds the “corepressor” arginine?

Answer 5

-transcription is blocked

Question 6

How does the Arg (arginine) repressors act when the “corepressor” does not bind to arginine?

Answer 6

-Transcription proceeds

Question 7

Can arg operator be placed in front of arg promoters and work?

Answer 7

-No, because it is to far upstream

Question 8

What happens to the Lac repressor when a repressor binds to the lac operator with no inducer?

Answer 8

-Transcription blocked

Question 9

What happens when an inducer binds to the Lac Repressor?

Answer 9

-The inducer pulls the Lac repressor off the lac operator and transcription proceeds

Question 10

Repressors

Answer 10

-bind to sites in the DNA called “operators”
-Prevent transcription by blocking access of RNA polymerase to the promoter (steric hindrance)
-Often are turned on or off by the binding of a small molecule

Question 11

What sites of the promoter do they overlap on?

Answer 11

-They overlap on the -35, -10 or +1 site

Question 12

What are considered small molecules?

Answer 12

-corepressors
-inducer
-effector

Question 13

What do activators exert?

Answer 13

-Positive control
-look at notes

Question 14

What happens when an RNA polymerase binds weakly to a mal promoter with an activator binding site?

Answer 14

-The maltose activator protein doesn’t bind
-No transcription

Question 15

What happens when the maltose activator binds to the activator binding site?

Answer 15

-An inducer (maltose) binds)
-The RNA polymerase binds strongly
-Transcription proceeds

Question 16

Where can activators bind?

Answer 16

-near or far upstream of the promoter
-look at notes

Question 17

Can repressor bind far upstream of the promoter?

Answer 17

-No

Question 18

Activators

Answer 18

-bind to sites in the DNA called “Activator-Binding Sites”
-Activate transcription by a positive interaction with RNA polymerase binding at the promoter.
-Often are turned on or off by the binding of a small molecule “effector”

Question 19

Do activators over lap?

Answer 19

-Activators DON’T overlap

Question 20

Can the activator and RNAP polymerase bind at the same time?

Answer 20

-Yes

Question 21

Can E. Coil use many carbon sources?

Answer 21

-Yes

Question 22

Catabolite Repression in E. Coli

Answer 22

-E. Coli will use ONLY glucose until glucose is exhausted
-Once glucose is exhausted E. Coli will induce lactose utilization genes
-Same for other secondary carbon sources

Question 23

Catabolite Repression Graph

Answer 23

-positive increasing glucose line, then glucose exhausted to line flattens, then lactose and line is positively increasing but not as steep as glucose
-more B-Galactosidase with lactose

Question 24

Production of cyclic AMP (cAMP)

Answer 24

-Active transport of glucose into the cell inhibits the enzyme adenylate cyclase.
-A lack of glucose results in production of cAMP
-cAMP is the signal that the cell lacks glucose

Question 25

What inhibits adenylate cyclase?

Answer 25

-active transport of glucose into the cell

Question 26

What happens when cAMP binds to the CPR protein?

Answer 26

-activated transcription
-The lactose utilization genes are only one of the many sets of genes that can be activated by CPR.
-absence of glucose, presents of lactose
-look at notes

Question 27

When are lactose genes ecpressed?

Answer 27

-glucose is absent
-lactose is present
-look at notes

Question 28

2-Component Regulatory Systems

Answer 28

-a signaling pathway commonly found in bacteria that allows them to respond to changes in their environment
-The signal is transmitted by phosphorylation/dephosphorylation of the response regulator by the sensor kinase
-look at notes

Question 29

What is component #1 in the regulatory system?

Answer 29

-a sensory kinase protein that receives a signal, often extracellular, and transmits that signal to component #2

Question 30

What is component #2 in the regulatory system?

Answer 30

-is a response regulator that is usually a transcription regulator (a repressor or activator)

Question 31

2-Component Regulatory Systems in Bacteria

Answer 31

-Many bacterial species have 20-40 different 2-component systems encoded in their genomes
-Ex. Pho regulation = inorganic phosphate
-Porin regulation = osmotic pressure

Question 32

Sporulation

Answer 32

-Spore formation requires the cooperative action of two cells, the mother cell and the developing forespore.
-Each cell must change its pattern of gene expression several times during the sporulation process, and these changes must happen in proper order.
-The two cells communicate to activate new sigma factors to direct transcription at the proper time and in the proper cell type

Question 33

What does the forespore make?

Answer 33

-internal spore components

Question 34

What does the mother cell make?

Answer 34

-external spore wall and coat components

Question 35

How does sporulation work?

Answer 35

-signal from endospore activates sigma E, transcription of early endospore genes
-Then signal from mother cell triggers synthesis of sigma G in endospore and pro-sigma K in mother cell
-Lastly, signal from endospore activates sigma K.
-Look at notes

Question 36

What is Quorum Sensing?

Answer 36

-A mechanism for a population of bacterial cells to determine their population density and respond accordingly.
-some activates are only useful at high or low concentration

Question 37

What do all cells in the population of quorum sensing produce?

Answer 37

-a small molecule “Autoinducer” that is released from the cell

Question 38

How does Quorum Sensing work?

Answer 38

-Cells contain a regulatory protein (repressor or activator) that can bind the autoinducer ONLY when it is a high concentration
-Gene regulation is turned on or off at low or high cell density
-Look at notes

Question 39

What do various species use to regulate?

Answer 39

-Luminescence (light production), virulence, biofilm formation, transformation (DNA uptake), sporulation, and antibiotic synthesis

Question 40

What do Gram Pos use?

Answer 40

-peptides
-8-11 amino acids