Lecture 3-Transcription I (Martin)

Question 1

What are 2 other names for the nontemplate strand of DNA?

Answer 1

• plus strand

- coding strand

Question 2

What are 2 other names for the template strand of DNA?

Answer 2

• minus strand

- non-coding strand

Question 3

What is the function of Eukaryotic Pol I?

Answer 3

• synthesizes the 28s, 18s, and 5.8s rRNAs

Question 4

What is the function of eukaryotic Pol II?

Answer 4

• synthesizes mRNAs

Question 5

What is the function of eukaryotic Pol III?

Answer 5

• synthesizes tRNAs and 5s rRNA

Question 6

Rho-dependent Termination

Answer 6

• the end of the gene codes for a complimentary-w/self sequence that causes a hairpin structure to form
• the hairpin causes the Pol to pause and the rho protein (an ATP-dependent helicase) binds the end of the RNA and uses ATP to separate the RNA-DNA hybrid

Question 7

Rho-independent termination

Answer 7

• the end of the gene codes for a complimentary-w/self sequence that causes a hairpin structure to form and then multiple A’s after this
• the hairpin structure causes the Pol to pause
• due to the weaker interactions in the DNA-RNA hybrid from the multiple A-U bonds (only 2 H bonds/bp) in addition to the pausing of the Pol, the Pol falls off

Question 8

Operons

Answer 8

clustered genes associated with a metabolic process

Question 9

operator

Answer 9

repressor binding site

Question 10

Negative regulation of transcription

Answer 10

• binding of the repressor to the promotor to cause inhibition of transcription
• molecular signal can cause the repressor to be released or the signal can cause the repressor to bind the promotor

Question 11

Positive regulation of transcription

Answer 11

• bound activator recruits pol for transcription
• binding of molecular signal can cause release of the activator (inhibiting transcription) or can cause binding of the activator (promoting transcription)

Question 12

Why must glu not be available to get activation of the lac operon?

Answer 12

• low glu = high cAMP
• cAMP is required for CRP to bind CRP site upstream of lac operon
• CRP helps the sigma70 of the Pol to bind to the -35 and -10 sequences of the lac operon that do not match exactly to the consensus sequence and thus you get operon activation

Question 13

What are the 3 main differences between prokaryotic and eukaryotic gene transcription?

Answer 13

Prokaryotes:

• polycistronic DNA but NO INTRONS
• mRNAs not processed
• transcription and translation at the same time

Question 14

viruses can have ______ genes

Answer 14

overlapping

Question 15

what are the synthetic subunits of prokarytic polymerase?

Answer 15

• beta, beta prime, omega

Question 16

What gives prokaryotic pols specificity? How?

Answer 16

• sigma subunit

- recognizes consensus sequences at -35/10

Question 17

Do prokaryotes proofread their mRNA?

Answer 17

no

Question 18

Other than recognizing consensus sequences, what does the sigma factor do? When is it released?

Answer 18

• gives the pol binding affinity, on its own it has very little affinity
• after the pol has passed the promoter

Question 19

supercoiliing relieved by ______

Answer 19

topoisomerases

Question 20

Rho is a ________

Answer 20

ATP-dependent helicase

Question 21

Most transcription is regulated at the level of ______

Answer 21

Pol binding (consensus sequences)

Question 22

What is the repressor gene for lac operon? how many operator sites?

Answer 22

• gene I

- 3

Question 23

What 2 things are needed for the lac operon to be active?

Answer 23

• lactose present

- glu not available

Question 24

What are the 3 repressor sites of the ara operon? How are they oriented?

Answer 24

• O1, O2, I

- on the opposite strand going in the opposite direction

Question 25

autoregulation

Answer 25

when the genes turn themselves off by making the repressor

Question 26

when AraC repressor is bound which sites does it sequester by folding?

Answer 26

• the CRP site

- the promotor for the repressor