EMQ 4. Theme: Binding partners of DNA and RNA

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Identify the specific binding partners of each of the macromolecules or molecule domains listed below.

A A complementary region on mRNA
B A complementary region on ribosomal RNA (rRNA)
C MicroRNAs (miRNAs)
D A mismatched base pair (G:T or A:C) in double stranded DNA
E The DNA sequence 5’TATATT3’, often called the Pribnow box
F The palindromic DNA sequence 5’AGAACANNNTGTTCT3’ where N means that any nucleotide is acceptable.

1. A region rich in guanosine and cytosine at the 3’ end of a newly synthesized prokaryotic mRNA.
Your Answer:
Answer: A, a complementary region on mRNA. Towards the end of transcription, the GC rich region base pairs with a second GC rich region on the same mRNA, forming an RNA hairpin loop and thereby weakening the attachment of the mRNA to the DNA strand. The newly synthesized mRNA can therefore leave the DNA template. See book page 84.
2. The DNA repair enzyme MutS.
Your Answer:
Answer: D, a mismatched base pair (G:T or A:C) in double stranded DNA. This is part of the mismatch repair system that can replace an incorrect base pair if it is detected soon after DNA synthesis. See book page 71.
3. The glucocorticoid hormone receptor.
Your Answer:
Answer: F, the palindromic DNA sequence 5’AGAACANNNTGTTCT3’. You may not remember the specific sequence to which the glucocorticoid hormone receptor binds, but you should know that since the active transcription factor is a dimer, the sequence to which it binds will be palindromic (that is, contain two identical sequences, one running in one direction on one DNA strand, the other running in the opposite direction on the other DNA strand). See book page 95.
4. Transfer RNA (tRNA).
Your Answer:
Answer: A, a complementary region on mRNA. The anticodon on the tRNA base pairs with the corresponding codon on the mRNA. See book page 123.
5. σ factor (sigma factor).
Your Answer:
Answer: E, the DNA sequence 5’TATATT3’, often called the Pribnow box. During the initiation of transcription in prokaryotes, the &signma; factor binds to the promoter sequence on the DNA strand, which includes the Pribnow box, and then recruits the other components of RNA polymerase. See book page 83.
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