Problem : Suppose you have a 400 base pair segment of prokaryotic DNA that is transcribed into RNA. Approximately how long will it take to transcribe this region?

The rate of prokaryotic DNA transcription is 40 nucleotides per second. For each base pair present in the region, there is one nucleotide. Thus, in order to solve this problem, we simply need to divide the total number of nucleotides to be transcribed (400) by the rate of transcription in nucleotides per second (40). The answer is approximately 10 seconds.

Problem : During elongation, a small region of the newly synthesized RNA molecule remains base paired to the DNA template strand forming a _________.


Problem : What is the name of the structure that signals transcription termination in rho- independent termination? What mediates the formation of this structure?

A hairpin loop. Complementary base pairing allows the transcribed RNA chain to fold back on itself into the hairpin structure.

Problem : What key structural difference between DNA and RNA helps account for RNA chain release during rho-independent termination?

RNA bases include uracil instead of thymine. At the end of the hairpin loop DNA sequence there is a string of As. When these are transcribed, they will not pair with thymines as in DNA, but rather with uracils. This A:U pairing is weak and leads to the release of the newly synthesized RNA chain.

Problem : In which direction, 5' to 3' or 3' to 5', does the rho factor move along the RNA chain in rho-dependent termination?

The rho factor moves from the 5' end of the newly synthesized RNA chain towards the 3' end that is being formed inside the open complex bubble.