The segment of the bacterial TrpA gene involved in intrinsic termination of transcription is the following:
3'-TGGGTCGGGGCGGATTACTGCCCCGAAAAAAAACTTG-5'
5'-ACCCAGCCCCGCCTAATGACGGGGCTTTTTTTTGAAC-3'
Explain how a sequence of this type leads to intrinsic termination of transcription.

Verified step by step guidance

1. Intrinsic termination of transcription in bacteria relies on specific sequences in the DNA that form a hairpin structure in the RNA transcript. Begin by identifying the sequence in the given DNA that could form a complementary base-pairing region in the RNA transcript.
2. Look for a region in the DNA sequence that is rich in G and C nucleotides. These regions are important because they form strong hydrogen bonds, leading to the formation of a stable hairpin structure in the RNA transcript.
3. After the GC-rich region, identify the stretch of adenine (A) nucleotides on the template strand (3'-5' strand). This corresponds to a stretch of uracil (U) nucleotides in the RNA transcript, which forms a weak RNA-DNA hybrid due to the weaker A-U base pairing.
4. Explain that during transcription, the RNA polymerase transcribes the GC-rich region, which folds into a hairpin structure in the RNA. This structure causes the RNA polymerase to pause.
5. Finally, describe how the weak A-U base pairing downstream of the hairpin destabilizes the RNA-DNA hybrid, leading to the release of the RNA transcript and termination of transcription.

Key Concepts

Intrinsic Termination of Transcription

Intrinsic termination is a mechanism by which RNA polymerase stops transcription without the need for additional factors. It typically involves the formation of a stable hairpin structure in the RNA transcript, followed by a stretch of uracil residues. This hairpin structure disrupts the interaction between the RNA polymerase and the DNA template, leading to the release of the newly synthesized RNA.

Hairpin Structure Formation

The hairpin structure is formed when complementary sequences within the RNA transcript base-pair with each other, creating a double-stranded region. This structure is crucial for intrinsic termination as it stabilizes the RNA molecule and causes RNA polymerase to pause. The presence of a GC-rich region followed by a series of uracils is often indicative of potential hairpin formation, which is essential for signaling the end of transcription.

Role of Uracil in Termination

Uracil plays a significant role in the intrinsic termination process due to its weaker base-pairing with adenine compared to guanine-cytosine pairs. After the formation of the hairpin, the RNA polymerase encounters a stretch of uracils, which destabilizes the RNA-DNA hybrid. This instability leads to the dissociation of the RNA transcript from the DNA template, effectively terminating transcription.