1. Bacterial transcription termination VS . Eukaryotic transcription initiation
ID: 256961 • Letter: 1
Question
1. Bacterial transcription termination VS. Eukaryotic transcription initiation
a. What is required for Rho-independent termination? How does each sequence feature contribute to the mechanism of termination?
b. What is required for Rho-dependent termination?
c. How does Rho differ from other helicases we discussed in Chapter 28? How is it similar?
d. Do you understand the difference between core promoter elements and regulatory elements? Do you understand the difference between core transcription factors and regulatory transcription factors?
e. What are the major features of the TATA-binding protein-DNA interaction? How does this interaction lead to dsDNA destabilization?
Explanation / Answer
Ans
a The Rho-independent termination required palindromic GC rich sequences followed by a stretch of 6 uracils. the palindromic region folds to form a hairpin or intrinsic loop terminator. The moving RNA polymerase pause after the hairpin has been reached at the AU base pair between the template strand and RNA dissociate between template strand and RNA dissociate because A=U base pair weakest. this termination method is very common in eukaryotes.
B. Rho-dependent termination is a common mode of transcription in prokaryotes. rho-dependent termination required rho factor which is encoded by rho gene that is a homohexameric protein with helicase activity i.e. responsible for digestion of hydrogen bond between DNA-RNA hybrid. Rho required SS RNA as a binding region.
C. As discussed in Chapter 28 the Rho protein differs from DNA helicase because rho protein promote transcription termination by binding to RNA and breaking bonds of RNA-DNA hybrids. DNA helicase helps in replication of DNA by binding to DNA and breaking hydrogen bonds that connect DNA to each other. however, the rho protein and DNA helicase have the similarity that both bind with a single stand nucleotide and move 5` to 3` breaking hydrogen bond.
d. The core promoter elements are the part of RNA polymerase which is essential for transcription initiation while regulatory elements regulate the transcription process. Transcription factors are proteins that regulate the transcription of genes—that is, their copying into RNA, on the way to making a protein. the core transcription factors are part of the core unit of a transcription factor that is responsible for initiation of transcription while regulatory TFs are responsible for the regulation of transcription.
e. The TATA-binding protein (TBP) is a general transcription factor that binds to a DNA sequence called TATA box. This TATA box found about 30 base pair upstream of transcription start site. TBP with various TBP associated factors formed a TFIID, a general transcription factor which is the part of RNA polymerase II. It is also involved in DNA melting by bending the DNA. TBP has a long string of glutamine in the N-terminus of protein. The TBP binds to a TATA box in the DNA and distorts the DNA by inserting Amino acid side chains between base pairs and partially unwinding the helix and doubling kinking it. TBP binds with positively charged lysine and arginine amino acid residues to negatively charged phosphate in the DNA backbone. The sharp bend in the DNA is produced through the projection of 4 phenylalanine residue in the minor groove. As the DNA bends and its attachment increase with TBP which enhances the DNA-protein interaction.
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