PROBLEM SET
Chapter 10 -- Gene Expression: Transcription

P. 267, #2 Given that RNA polymerase does not proofread, do you expect high or low levels of error in transcription as compared with DNA replication? Why is it more important for DNA polymerase to proofread compared with RNA polymerase?
You would expect high levels of error in transcription as compared to DNA replication. Proofreading is important in DNA replication because mistakes in DNA replication will be passed to offspring (either as daughter cells or through gametes) as mutations. However, RNA's are short lived in the cytoplasm and thus mistakes are not permanent. It is better to not proofread and thus speed up transcription.

P. 267, #3 What are the transcription start and stop signals in eukaryotes and prokaryotes? How are they recognized? Can a transcriptional unit include more than one translational unit (gene)?
The transcription start signals for both prokaryotes and eukaryotes are promoters. In prokaryotes the promoters are at -10 (Pribnow Box, TATAAT) and at -35 (-35 sequence, TTGACA). In eukaryotes the promoters are at -25 (Hogness Box, TATA) and at -70 (CAAT Box, GG(C/T)CAATCT).
The promoters in prokaryotes are recognized by the RNA polymerase when it is bound to the sigma factor. In eukaryotes the promoters are also recognized by the RNA polymerases in conjunction with transcriptional factors that are similar in function to the sigma factor of prokaryotes.
In prokaryotes a transcriptional unit (mRNA) can contain more that one translational unit (protein coding region). This is called polycistronic. However, this can not occur in eukaryotes.

P. 267, #6. What would the effect be on transcription if a prokaryotic cell had no sigma factors? No rho protein?
Without sigma factors the RNA polymerase would not bind at the correct site on the DNA. You would get random starts of transcription and thus mis-transcribed genes. If the rho protein was missing then transcription would not terminate in those systems that require rho protein to terminate (rho-dependant termination).

P. 267, #9. Would introns be more or less likely than exons to accumulate mutations through evolutionary time?
Introns would be more likely to accumulate mutations over time because the bases in introns are not translated into protein. Thus a mutation within an intron would, for the most part, have no effect on the function of the protein and thus not be subject to removal by selection. Thus, selection would tend to remove deleterious mutations from exons but selection would not affect the presence of mutation in introns.

P. 265, #15 What is the function of each of the following sequences: TATAAT, TTGACA, TATA, CAAT, TACTAAC? What is a Pribnow box? A Hogness box?
TATAAT -- Pribnow Box, -10 promoter sequence in prokaryotes
TTGACA -- -35 promoter sequence in prokaryotes
TATA -- Hogness Box, -25 promoter sequence in eukaryotes
CAAT -- -70 promoter sequence in eukaryotes
TACTAAC -- branch point in the lariat sequence of an intron

P. 267, #25. For the RNA sequence below, determine the sequence of both strands of the DNA from which it was transcribed. Indicate the 5' and 3' ends of the DNA and, with an arrow, which strand was transcribed.
5'-C C A U C A U G A C A G A C C C U U G C U A A C G C-3' original


3'-G G T A G T A C T G T C T G G G A A C G A T T G C G-5' template

5'-C C A T C A T G A C A G A C C C T T G C T A A C G A-3' coding

The template strand was the strand read by the RNA polymerase and thus is the strand that is transcribed. The coding strand and the RNA will have the same base sequence, except that RNA has U's instead of T's.

P. 265, #26. Below is a DNA fragment isolated from the beginning of a gene. Determine which strand is transcribed, indicate the polarity of the two DNA strands, and then give the sequence of bases in the resultant mRNA and its polarity.
C C G T A C G C C T T T C A G G T T
G G C A T G C G G A A A G T C C A A
First write out the complementary RNA molecule to both strands
5'-G G C A U G C G G A A A G U C C A A upper
3'-C C G U A C G C C U U U C A G G U U lower
Notice that in the upper strand there is an AUG sequence, which must occur in 5'-AUG-3' direction at the beginning of all mRNAs. Thus the upper sequence is the appropriate mRNA. The top strand of the DNA molecule is the template strand (the strand that was transcribed), while the lower strand is the coding strand.
3'-C C G T A C G C C T T T C A G G T T-5' template
5'-G G C A T G C G G A A A G T C C A A-3' coding

P. 265, #27. The following DNA fragment represents the beginning of a gene. Determine which strand is transcribed and indicate polarity of both strands in the DNA.
A T G T A C A T C T A C A T T T A C A T T
T A C A T G T A G A T G T A A A T G T A A

First write out the complementary RNA molecule to both strands.
3'-U A C A U G U A G A U G U A A A U G U A A
5'-A U G U A C A U C U A C A U U U A C A U U
Notice that in the lower strand there is an AUG sequence at the very beginning, which must occur in 5'-AUG-3' direction at the beginning of all mRNAs. Thus the lower sequence is the appropriate mRNA. There is an AUG sequence in the upper strand, but the codon next to it is a stop codon, thus the upper strand is not the mRNA. As the bottom strand of the RNA is the mRNA, then the bottom strand of the DNA molecule is the template strand (the strand that was transcribed), while the lower strand is the coding strand.
5'-A T G T A C A T C T A C A T T T A C A T T-3' coding
3'-T A C A T G T A G A T G T A A A T G T A A-5' template

Last updated on 22 August 1996.
Provide comments to Dwight Moore at mooredwi@esumail.emporia.edu.
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