Prokaryotic Transcription 3

Question 1

factor independent termination

Answer 1

• When RNA leaves exit pore, sometimes there is complementarity and forms a hairpin
• The hairpin and polymerase has affinity and will bind to RNA polymerase and cause it to cause momentarily
• If it pauses over a stretch of A’s (U’s) will be he compliment and is the least stable, this will cause termination and fall apart (stretch of 7 Us)

Question 2

what do intrinsic terminators consists of?

Answer 2

• GC rich hairpin in the RNA product
• followed by a U rich region in which termination occurs

Question 3

true/false: the mechanism for intrinsic terminators only relies on the DNA sequence

Answer 3

false
- intrinsic terminators also require that the nascent RNA form a hairpin structure

Question 4

what are the three termination factors in e. coli and which is the best understood?

Answer 4

• rho (best understood)
• tau
• nusA

Question 5

how does rho factor work?

Answer 5

• rho factor is a 6 member helicase that moves along the RNA 5’ to 3’ activity
• initially rho is an open ring, but forms a close ring when RNA is bound
• binds to a rut site on nascent RNA
• it must move faster than RNA polymerase and catch up to it, a pause site (hairpin) is also necessary so that rho can catch RNA pol
• moves along the RNA to release it from the RNA-DNA hybrid structure within the RNA polymerase
• single stranded RNA that burns ATP
• when it binds to the rut site after the polymerase has paused, it pulls the RNA transcript out of the active site

Question 6

in an intrinsic terminator, where is the string of A’s?

Answer 6

in the template strand

Question 7

what does the rut site consists of?

Answer 7

• the rut site is rich in C residues and poor in G residues
• rut sites have no secondary structure
• the efficiency of the rut site increases as the length of the c rich region increases in length

Question 8

what are the two components of the rho-dependent terminator?

Answer 8

• a rut site on the RNA to bind Rho
• a hairpin downstream of rut to cause RNA pol to pause

Question 9

what will cause a rho-dependent terminator to not function?

Answer 9

• the rut site has to accessible for rho binding and movement
• this means that no ribosomes should be between it and RNA polymerase

Question 10

under what conditions would you expect no ribosomes to bind to the RNA?

Answer 10

• under stress conditions when translation is slowed down
• if a nonsense mutation appears upstream to cause ribosomes to release early

Question 11

rho-dependent termination requires a hairpin but not at the rut sire?

Answer 11

• true
• the rut site is C rich and G poor and has no secondary structure

Question 12

polycistronic

Answer 12

single mRNA molecule can encode more than one polypeptide
- many coding regions
- include multiple translation initiation regions that signal ribosomes to begin translation

Question 13

cistron

Answer 13

the coding region for each polypeptide

Question 14

polarity

Answer 14

• some mutations in one coding region of polycistronic gene can block transcription of the next cistron
• Occurs if at least one Rho-dependent termination site is located between the point where translation was blocked and the ribosome binding site of the next.
• Rho will have access to the rut site on the mRNA and stop transcription of next gene.

Question 15

in order for the polarity effect to occur what condition must exist?

Answer 15

the rut site must not be in the last cistron, and it should be free of ribosomes