In this animation, towards the end (about three quarters) the process of transcription termination is shown. It states that the transcribed RNA forms a hairpin loop (or stem-loop), which halts the transcription process.
My question is, why does it halt the transcription process, considering that the RNA polymerase moves in the opposite direction of where the stem loop is created? Does it somehow change the RNA conformation such that no further bases can be added? Interpreting it as a physical obstacle doesn't seem to make any sense here.
Answer
There are two mechanisms of transcriptional termination in prokaryotes. The one shown here is "rho-dependent" because it involves rho, a DNA-RNA helicase that loads on and unwinds the RNA from the DNA, terminating the elongation by the polymerase. Check out [1] which shows a model for how rho multimers move through the RNA.
The other mechanism involves just a hairpin. The paper [2], especially Page 23, part C, shows how "rho-independent" or "intrinsic" termination works. Basically, the hairpin slows down the polymerase and destabilizes the transcription bubble, allowing the intrinsically-weaker A:U bonds to fall apart.
There is no requirement for a hairpin in rho-dependent termination, and I think the movie is mixing them up.
Geiselmann J, Wang Y, Seifried SE, von Hippel PH. 1993. A physical model for the translocation and helicase activities of Escherichia coli transcription termination protein Rho. Proceedings of the National Academy of Sciences of the United States of America 90: 7754–8. [pdf]
Datta K, von Hippel PH. 2008. Direct spectroscopic study of reconstituted transcription complexes reveals that intrinsic termination is driven primarily by thermodynamic destabilization of the nucleic acid framework. The Journal of biological chemistry 283: 3537–49. [pdf]
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