RNA Metabolism: Chapter 26

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Questions and Answers

What is the role of rRNA in protein synthesis?

to encode the amino acid sequence of a gene

to form the structural components of ribosomes (correct)

to transfer amino acids to a growing polypeptide chain

to read the information encoded in mRNA

What is the difference between transcription and replication in terms of the template?

Transcription uses both DNA strands as templates, while replication uses only one.

Transcription uses a primer, while replication does not.

Transcription uses only one DNA strand as a template, while replication uses both. (correct)

Transcription uses a RNA template, while replication uses a DNA template.

What is the function of the promoter in transcription?

to elongate the transcript

to unwind the DNA duplex

to terminate transcription

to initiate transcription (correct)

What is the result of changes in DNA supercoiling during transcription?

unwinding of the DNA duplex Signup and view all the answers

What is the length of the transcription 'bubble' during transcription?

17 bp Signup and view all the answers

What is the role of the 8 bp RNA-DNA hybrid in transcription?

to elongate the transcript Signup and view all the answers

What is the equation for RNA synthesis during transcription?

(NMP)n + NTP → (NMP)n+1 + PPi Signup and view all the answers

What is the role of DNA-dependent RNA polymerase in transcription?

to act as a nucleophile Signup and view all the answers

What is the length of the region of DNA that is unwound during the initiation of transcription?

12 to 15 bp Signup and view all the answers

What is the direction of movement of the Rho factor during Rho-dependent termination of transcription?

5' to 3' Signup and view all the answers

What is the characteristic of the sequence of repeated residues found in Rho-independent termination sites?

Repetition of A residues Signup and view all the answers

What is the outcome of the formation of a stem and loop structure (hairpin structure) during transcription?

Termination of transcription Signup and view all the answers

What is the nature of the AUU hybrid region at the 3' end of the new transcript during transcription termination?

Relatively unstable Signup and view all the answers

What is the role of the Rho factor during Rho-dependent termination of transcription?

ATP-dependent helicase Signup and view all the answers

What is the outcome of the unwinding of the 12 to 15 bp region of DNA during the initiation of transcription?

Commitment to elongation of RNA Signup and view all the answers

What is the location of the Rho-independent termination site in a DNA sequence?

3' end of the gene Signup and view all the answers

What is the rate of RNA polymerase transcription in E. coli?

50 to 90 nucleotides/s Signup and view all the answers

What is the function of topoisomerases in transcription?

To relieve topological problems caused by transcription Signup and view all the answers

What is the sequence of the RNA transcript compared to the nontemplate strand?

Identical in sequence with U in place of T Signup and view all the answers

What is the function of the sigma factor in RNA polymerase?

To direct the enzyme to specific binding sites on the DNA Signup and view all the answers

What is the recognition sequence at the -10 region of E. coli promoters?

Pribnow box Signup and view all the answers

What is the effect of variations in the consensus sequence of E. coli promoters?

Decreased efficiency of RNA polymerase binding Signup and view all the answers

What is the state of the promoter DNA during transcription initiation?

Stably bound but not unwound Signup and view all the answers

What is the region of the promoter that extends between positions -70 and +30?

The promoter region Signup and view all the answers

What is the primary function of RNA polymerase I in eukaryotes?

To synthesize pre-rRNA, which contains the precursor for the 18S, 5.8S, and 28S rRNAs Signup and view all the answers

What is the role of transcription factors in RNA polymerase II-mediated transcription?

To form the active transcription complex Signup and view all the answers

What is the function of the TATA box in eukaryotic promoters?

To serve as a binding site for transcription factors Signup and view all the answers

Which of the following is a subunit of RNA polymerase II?

RPB1=B' Signup and view all the answers

What is the outcome of the phosphorylation of the carboxyl-terminal domain of the Pol II subunit?

The polymerase escapes the promoter and begins elongation Signup and view all the answers

What is the role of TFIIH in RNA polymerase II-mediated transcription?

To phosphorylate the carboxyl-terminal domain of the Pol II subunit and unwind DNA at the Inr region Signup and view all the answers

What is the outcome of the transcription process at RNA polymerase II promoters?

The release of the polymerase and the recycling of transcription factors Signup and view all the answers

What is the sequence of events during transcription at RNA polymerase II promoters?

Formation of a closed complex, phosphorylation of the carboxyl-terminal domain, unwinding of DNA, and elongation Signup and view all the answers

What is the primary function of TFIIH in response to DNA lesions?

To interact with the lesion and recruit the entire nucleotide-excision repair complex Signup and view all the answers

What is the consequence of the genetic loss of TFIIH?

XP disease Signup and view all the answers

What is the primary function of the 5' cap in mRNA modification?

To stabilize the mRNA molecule Signup and view all the answers

What is the consequence of alternative splicing in mRNA modification?

Regulatory significance Signup and view all the answers

What is the primary function of polyadenylation in mRNA modification?

To add a poly(A) tail to the 3' end of mRNA Signup and view all the answers

What is the mechanism of action of intercalating agents, such as actinomycin?

By intercalating into the double-helical DNA and deforming the DNA Signup and view all the answers

What is the mechanism of action of rifampicin in bacterial RNA synthesis?

By preventing the promoter clearance step of transcription Signup and view all the answers

What is the consequence of RNA polymerase II halting at the site of a DNA lesion?

The DNA lesion is repaired by the nucleotide-excision repair complex Signup and view all the answers

Study Notes

RNA Metabolism

RNA plays three roles in protein synthesis: mRNA encodes amino acid sequence, tRNA reads mRNA and transfers amino acids, and rRNA is a constituent of ribosomes.

RNA Synthesis

RNA synthesis is carried out by DNA-dependent RNA polymerase, which acts as a nucleophile attacking the phosphate of incoming rNTPs.
Transcription resembles replication in its fundamental chemical mechanism, with polarity, template use, and initiation, elongation, and termination phases.
Transcription differs from replication in not requiring a primer and involving only limited segments of a DNA molecule.

Initiation of Transcription

Initiation starts at a promoter, where the DNA duplex unwinds, forming a transcription "bubble" of about 17 bp.
The RNA-DNA hybrid occurs in this unwound region, and the transcription bubble moves along the DNA, generating waves of positive supercoils ahead and negative supercoils behind.

Elongation of Transcription

Elongation of a transcript proceeds at a rate of 50-90 nucleotides/s.
Movement of the transcription bubble requires considerable strand rotation of the nucleic acid molecules.
Topological problems caused by transcription are relieved by topoisomerases.

RNA Polymerase

RNA polymerase holoenzyme consists of five core subunits and a sigma factor, which directs the enzyme to specific binding sites on the DNA.
The enzyme lacks 3'>5' proofreading activity.

Promoters

E. coli promoters have several recognition sequences, including the -10 and -35 regions, and the UP element.
The promoter region extends between positions -70 and +30.
Variations in the consensus sequence affect the efficiency of RNA polymerase binding and transcription initiation.

Termination of Transcription

Termination occurs in two ways: Rho-independent and Rho-dependent.
Rho-independent termination occurs at characteristic sequences, including a stem and loop structure.
Rho-dependent termination involves the Rho factor, which is an ATP-dependent helicase that associates with the RNA and migrates in the 5'>3' direction.

Eukaryotic RNA Polymerases

There are three eukaryotic RNA polymerases: RNA pol I, RNA pol II, and RNA pol III.
RNA pol I synthesizes pre-rRNA, which contains the precursor for the 18S, 5.8S, and 28S rRNAs.
RNA pol II synthesizes mRNAs and requires an array of transcription factors.
RNA pol III synthesizes tRNAs, the 5S rRNA, and some other small specialized RNAs.

Promoters in Eukaryotes

Promoters in eukaryotes have a TATA box and an Inr region.
The TATA box is a pyrimidine-rich sequence that is recognized by the TBP protein.
The Inr region is a sequence that is recognized by the RNA polymerase.

RNA Polymerase II

RNA pol II is a huge enzyme consisting of 12 subunits.
The carboxyl-terminal domain (CTD) of the RPB1 subunit is phosphorylated by TFIIH during transcription initiation.

Transcription at RNA Polymerase II Promoters

Transcription at RNA polymerase II promoters involves the sequential assembly of transcription factors, including TBP, TFIIB, TFIIF, and TFIIH.
The DNA is unwound at the Inr region by the helicase activity of TFIIH, and the polymerase then escapes the promoter and begins elongation.

mRNA Modification in Eukaryotes

mRNA modification in eukaryotes involves three steps: capping, splicing, and polyadenylation.
Capping occurs before the synthesis of the primary transcript is complete.
Splicing involves the removal of introns and the joining of exons to form a continuous sequence.
Polyadenylation involves the addition of 80-250 A residues to the 3' end of the mRNA.

Modified RNA

RNA polymerase can undergo selective inhibition by certain agents, including intercalating agents and rifampicin.
Intercalating agents, such as actinomycin, intercalate into the double-helical DNA, deforming the DNA and inhibiting RNA elongation.
Rifampicin inhibits bacterial RNA synthesis by binding to the B subunit of bacterial RNA polymerases, preventing the promoter clearance step of transcription.

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Explore the three roles of RNA in protein synthesis, including mRNA, tRNA, and rRNA. Learn about the functions of each type of RNA in this crucial biological process.