Question

What will be an ideal response?

Answer 1

Answer: Answers should refer to the fact that E. coli is gram negative and thus has both a cytoplasmic and outer membrane. In order to secrete the protein a translocase that can move the protein through the outer membrane will be necessary. The protein folds after it has left the cell, thus the Sec system would work better than the Tat system, because the Tat system is specialized for proteins that fold in the cytoplasm and then cross the cytoplasmic membrane. Together these properties dictate that a two-step mechanism, such as a type II secretion system would work best for this project.

Answer 2

Answer: A theme to this answer should be how several different RNA molecules catalyze the formation of bonds in the process of protein synthesis (translation) and/or mRNA processing. Specifically, the peptidyl transferase reaction is catalyzed by 23S rRNA, rather than by ribosomal proteins. Catalytic RNAs are also involved in splicing the introns of mRNA in Archaea and Eukarya.

Answer 3

Answer: The RNA polymerase holoenzyme initiates transcription without the need for a primer. The sigma factor component of RNA polymerase easily dissociates from the holoenzyme to first recognize the promoter region by specifically binding to the Pribnow box and consensus sequence, which are both upstream of the transcriptional start site.

Answer 4

Answer: Intrinsic terminators occur at the nucleotide (DNA) level and require no additional protein involvement. They can develop into secondary structures such as loops, which freely form through base pairing with itself to ultimately halt transcription of RNA. Rho-dependent termination also stops RNA transcription but requires the protein Rho, which interacts with the DNA template-RNA polymerase complex to dissociate the complex at specific nucleotide sequences.

Answer 5

Answer: Answers should describe Figure 4.36 in the textbook where initiation involves a complex formation of the ribosome, initiation proteins, formylmethionine-tRNA, GTP, and mRNA. Elongation uses elongation factors, GTP, and tRNAs to extend a peptide, and termination occurs when release factors are recruited to a nonsense codon that breaks apart the tRNA and polypeptide to release the newly synthesized protein.