bacterial gene expression

Question 1

transcription unit

Answer 1

• a sequence of DNA bases that is transcribed to give a single, discrete complementary RNA
• In bacteria, multiple genes can be in the same transcriptional unit, this is termed an operon

Question 2

promoter site

Answer 2

-a special region of DNA where RNA pol binds for the purpose of initiating transcription (-35 and -10 regions are two key elements of most promoters)

Question 3

termination site

Answer 3

-a site within the DNA or RNA product at which RNa synthesis stops

Question 4

inhibitors of RNA synthesis

Answer 4

• bind to beta subunit of RNA pol
• rifamycin: blocks elongation (rifampicin)
• lipiarmycins: blocks initiation (fidaxomicin)

Question 5

sigma subunit of RNA pol

Answer 5

-necessary for recognition of the promoter region of a gene

Question 6

two forms of RNA pol

Answer 6

• holoenzyme and core enzyme
• holoenzyme releases the sigma subunit upon binding the promoter, transcription is initiated, and becomes the core enzyme

Question 7

the role of the sigma subunit

Answer 7

• causes very stable binding at promoter regions
• reduces binding at non-promoter regions of DNA (specificity)
• removal of gama allows escape from the promoter (translocation) and elongation of the transcript
• only one type of RNa pol, but many types of gama subunit which recognize promoters with different sequences

Question 8

holoenzyme composition

Answer 8

• 2 alpha
• 2 beta
• 1 sigma

Question 9

core enzyme composition

Answer 9

• 2 alpha

- 2 beta

Question 10

how does transcription stop

Answer 10

• factor dependent termination

- factor independent termination

Question 11

factor independent termination

Answer 11

-site is encoded in the DNA sequence appearing as a region of dyad symmetry

Question 12

factor dependent termination

Answer 12

-Rho factor binds directly to RNa polymerase and causes the polymerase to stop and release when reaching the factor dependent terminator

Question 13

regulation of transcription

Answer 13

• positive regulators bind upstream of the promoter

- negative regulators can overlap the promoter or be downstream

Question 14

organization of toxin genes, pathogenicity locus

Answer 14

tcdR, tcdB, tcdE, tcdA, tcdC

Question 15

tcdR

Answer 15

positive regulator

Question 16

tcdB

Answer 16

toxin B

Question 17

tcdE

Answer 17

holin

Question 18

tcdA

Answer 18

toxin A

Question 19

tcdC

Answer 19

negative regulator

Question 20

operon of toxin genes

Answer 20

toxin B and holin

Question 21

when is the toxin produced

Answer 21

during stationary phase

Question 22

CodY

Answer 22

• represses the toxin gene by binding to the promoter of tcdR
• Ile dependent activation
• active during exponential growth phase due to abundant Ile
• inactive during stationary phase

Question 23

toxin regulation: nutrient excess and nutrient limitation

Answer 23

• excess: cody is active and inhibits the RNA pol from binding, tcdC is synthesized which inhibits tcdR
• limitation: CodY is inactive, bacteria are in the stationary phase, and TcdR is promoting the

Question 24

what causes high toxin production?

Answer 24

-mutation in tdcC that inactivates the protein

Question 25

tcdR is inactive when

Answer 25

associated with tcdC

Question 26

codY active when

Answer 26

associated wiht Ile

• in the active state, CodY represses toxin expression
• this is a negative regulator active in nutrient excess

Question 27

rifamycin

Answer 27

ex: rifampycin: blocks elongation by the RNa pol

Question 28

lipiarmycins

Answer 28

ex: fidaxomycin, blocks initiation