Intrinsic terminator

Intrinsic terminator refers to a mechanism in molecular biology that allows for the termination of transcription in prokaryotes. It is a specific sequence of nucleotides in the DNA that signals the RNA polymerase to stop transcription. The intrinsic terminator consists of a palindromic sequence that forms a stable hairpin structure in the newly synthesized RNA molecule, followed by a sequence of adenine nucleotides. This structure causes the RNA polymerase to pause and eventually dissociate from the DNA, thus ending the transcription process.

Mechanism

The mechanism of intrinsic termination involves two key elements: the formation of a hairpin structure and a sequence of uracil nucleotides in the RNA (corresponding to adenine in the DNA). When the RNA polymerase transcribes the palindromic sequence, the complementary bases within the RNA transcript pair with each other, forming a stable hairpin loop. This loop structure causes the polymerase to slow down or pause. Following the hairpin, a series of uracil bases (U-rich region) makes the RNA-DNA hybrid in the transcription bubble weak due to the weaker RNA-DNA base pairing between uracil and adenine. This weakness, combined with the pausing induced by the hairpin, facilitates the dissociation of the RNA polymerase from the DNA template, thereby terminating transcription.

Function and Significance

Intrinsic terminators play a crucial role in the regulation of gene expression in prokaryotes. They ensure that transcription stops at the appropriate point, preventing the synthesis of unnecessary RNA and allowing the cell to conserve energy. Moreover, intrinsic terminators are involved in the termination of transcription for a wide range of genes, including those coding for proteins, rRNA, and tRNA, highlighting their versatility and importance in cellular processes.

Comparison with Rho-dependent Termination

In addition to intrinsic termination, prokaryotes also use a Rho-dependent termination mechanism, which relies on the Rho protein to terminate transcription. Unlike intrinsic termination, Rho-dependent termination does not require a specific nucleotide sequence to form a hairpin loop. Instead, it depends on the Rho protein recognizing specific RNA sequences and actively moving along the RNA to displace the RNA polymerase. Both mechanisms are essential for the proper regulation of gene expression in prokaryotes, but they operate independently of each other.