Prokaryotic Transcription

Question 1

What is the role of RNA polymerase?

Answer 1

Catalyze the addition of nucleotides to RNA

Question 2

How are bonds formed in RNA molecule?

Answer 2

o The 3’-OH of the RNA molecule attacks the 5’P of the incoming nucleotide

Question 3

What is the notation for the start point of transcription? Which nucleotide is it?

Answer 3

 Indicated as +1

 Corresponds to the “most” 5’ nucleotide

Question 4

What is the notation for nucleotides before the start point of transcription? What term is used to describe them?

Answer 4

 Numbered -1, -2,-3…

 Referred to as upstream

Question 5

What is the notation for nucleotides before the start point of transcription? What term is used to describe them?

Answer 5

 Numbered +2, +3…

 Referred to as downstream

Question 6

To which nucleotide in transcription does 0 (zero) correspond?

Answer 6

There is no zero. It goes from -1 to +1

Question 7

Which is the template strand of DNA?

Answer 7

 Has the complementary bases to RNA

Question 8

Which is the coding strand of DNA?

Answer 8

 Has an identical sequence as RNA

Question 9

How is the terminator denoted? What is its particularity?

Answer 9

 Noted as t

 In bacteria only

Question 10

What are the elements involved in the regulation of transcription?

Answer 10

• Regulatory protein: “trans”-acting factors
o They bind on cis-acting sequence
o Cis-acting sequence is found on the DNA that is being transcribed

Question 11

What is the function of mRNA?

Answer 11

To carry codons for translation

Question 12

What are the common features in bacterial vs. eukaryotic mRNA?

Answer 12

o All mRNA is transcribed, translated, and degraded

Question 13

What are the differences in bacterial vs. eukaryotic mRNA?

Answer 13

o Coordination is different due to compartmentalization

Question 14

How does compartmentalization in bacteria affect mRNA?

Answer 14

o 1 compartment: the cytosol
o 3 processes occur more or less simultaneously
o Ribosome binds to mRNA before the termination of transcription
 Translation begins
 Degradation also begins shortly
o All 3 processes occur in the 5’ to 3’ direction
o Bacterial mRNA has a half-life of 1-3 min

Question 15

How does compartmentalization in eukaryotes affect mRNA?

Answer 15

o 2 compartments (related to gene expression)
 The nucleus and the cytosol
o mRNA is circularized in the cytosol
 Translation cannot begin before
 Degradation cannot occur while mRNA is circularized

Question 16

What are the stages of transcription?

Answer 16

1. Initiation
2. Elongation
3. Termination

Question 17

Briefly describe transcription initiation.

Answer 17

a. RNA Pol recognition and binding to promoter
b. DNA melting: formation of transcription bubble
c. Synthesis of first 8-9 nucleotide bonds
i. Series of abortive transcripts
ii. Short transcript synthesized, then “spit out”
iii. While RNA pol “sits” at the promoter

Question 18

Briefly describe transcription elongation.

Answer 18

a. RNA Pol proceeds from +1 to the end (t in the case of bacteria)
b. Pol synthesizes RNA: unwinds DNA, forms DNA-RNA hybrid i.e. synthesizes RNA, then winds DNA

Question 19

Briefly describe transcription termination.

Answer 19

a. RNA-DNA hybrid dissociation
b. The transcription bubble collapse
c. RNA Pol dissociation