Question

1. Name the cis-acting and trans-acting element that determine how a ribosome binds to just the right spot on an mRNA when it initiates translation. Explain how they interact with each other to achieve the ribosome and the mRNA

2.Explain why mRNA capping and polyadenylation are dependent upon protein interactions with the CTD of RNA polymerase II

3.Name 3 types of proteins that are needed for in vivo transcription, but not in vitro transcription by eukaryotes

4.Name the important thing that TFIIH does to dsDNA and tell me what it does to the CTD of RNA polymerase II

5.Name the elongation factor that drives eukaryotic ribosomal translocation and briefly explain how it works

Answer 1

1.Cis-acting elements that influence mRNA translation are mainly the nearly ubiquitous 5? cap structure as well as the 3? poly(A) tail.The secondary structures such as the hairpin structure along with the upstream open reading frames present in the 5? UTR function to inhibit translation.There are presence of internal ribosome entry sequences (IRES) that are known to stimulate translation independently of the cap structure. Also,PABP binds to the poly(A) tail that helps to initiate contact with the cap-binding complex resulting in a closed loop conformation of the mRNA that in turn is efficient for ribosome recruitment for translation to take place.The trans-acting elements include the RNA-binding factors and the miRNAs) that alter the translational of mRNAs.

2.mRNA capping and polyadenylation are dependent upon protein interactions with the CTD of RNA polymerase II because it is CTD that stimulates the capping and polyadenylation process.CTD independently enhances the process of splicing and 3? processing.Also, the process of stimuation of splicing by enhancers is facilitated by the CTD. 3? processing is intiated by CTD via being in contact with the cleavage stimulation factor, CstF.

3. 3 types of proteins that are needed for in vivo transcription, but not in vitro transcription by eukaryotes are transcription factors , activators and repressors.

4.TFIIH large protein complex that consists of thee CDK7/cyclin H kinase complex as well as the DNA helicase complex.The DNA helicase complex specifically binds to the template strand so that only the correct DNA strand melts ,unwinds (as it posseses DNA helicase activity) and is transcribed.The kinase activity of TFIIH phosphorylates the C-terminal domain (CTD) of RNA Pol II at the speicific amino acid and that aminoacid is serine. This helps in switching of the RNA polymerase so that it starts to produce RNA.

5.The elogation factor is eEF-2(eukaryotic elongation factor 2).It works in a way that it promotes the translocation of the ribosome and that is GTP dependent.