Molecular Biology Lecture 13

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Questions and Answers

What is a key difference between DNA replication and transcription in terms of chain growth?

DNA replication and transcription both involve rapid chain growth at many sites.

DNA replication involves slower growth at few intracellular sites, while transcription involves rapid chain growth at many sites.

DNA replication involves rapid chain growth at few intracellular sites, while transcription involves slower growth at many sites. (correct)

DNA replication involves slower growth at many sites, while transcription involves rapid chain growth at few intracellular sites.

What is a characteristic of RNA polymerase subunits in the three domains of life?

Homologous subunits are not color coded.

Subunits are arranged by size rather than function.

Subunits are arranged by function rather than size. (correct)

Subunits marked with an asterisk are not conserved among the three eukaryotic RNA polymerases.

What is shown in the crystal structures of RNA polymerases?

Core enzyme structures with bound proteins.

Bound proteins that aid in template recognition.

Core enzyme structures without bound proteins. (correct)

Only the promoter site of the DNA.

What is the first step in the transcription process by bacterial RNA polymerase?

Sequence-specific interaction between RNA polymerase and a promoter site. Signup and view all the answers

What is a feature of the open-promoter complex formed by Taq RNA polymerase?

A sharp bend in the template strand. Signup and view all the answers

What is the function of the RNA polymerase subunits marked with an asterisk?

They are conserved among the three eukaryotic RNA polymerases. Signup and view all the answers

What is a difference between DNA replication and transcription in terms of RNA accumulation?

More RNA accumulates than DNA. Signup and view all the answers

What is the characteristic of the promoter site in transcription?

It is where transcription begins. Signup and view all the answers

What is the consequence of backtracking in an elongation complex?

The transcript terminus is cleaved, creating a new base-paired 3' terminus. Signup and view all the answers

What determines the frequency of transcription of E. coli genes?

The similarity between the gene's promoter sequence and the consensus sequence. Signup and view all the answers

What is the function of the protein in factor-dependent termination?

It acts as an RNA-DNA helicase. Signup and view all the answers

What is the composition of the GC-rich region in factor-independent termination?

A region with high GC content. Signup and view all the answers

What happens to the RNA-RNA duplex in factor-independent termination?

It is stabilized by G-C base pairs. Signup and view all the answers

What is the consequence of the RNA-RNA duplex formation in factor-independent termination?

The transcription is terminated. Signup and view all the answers

What is the role of the A-rich segment in factor-independent termination?

It is transcribed into a U-rich mRNA segment. Signup and view all the answers

What is the purpose of the run of four to eight A residues in factor-independent termination?

To facilitate release of the transcript. Signup and view all the answers

What is the purpose of phosphorylation in transcription initiation?

To release the enzyme from the initiation site Signup and view all the answers

What is the function of the AATAAA sequence near the end of most eukaryotic genes?

It provides a signal for endonuclease cleavage and poly(A) tail addition Signup and view all the answers

What is the location of acetylation in core histones?

In the N-terminal domain Signup and view all the answers

What is the purpose of DNA looping in transcriptional regulation?

To bring enhancer-bound activator proteins into contact with TAFs associated with the core complex Signup and view all the answers

Which of the following is NOT a step in post-transcriptional processing in bacteria?

Splicing of exons Signup and view all the answers

What is the function of the TFIIA–TBP–TFIIB complex?

To initiate transcription by binding to the promoter Signup and view all the answers

Which of the following is a step in post-transcriptional processing in eukaryotes?

Addition of a poly(A) tail Signup and view all the answers

What is the structure of the core histones?

A helical domain plus a highly basic N-terminal domain Signup and view all the answers

What is the primary function of alanyl-tRNA synthetase?

To aminoacylate tRNA Signup and view all the answers

What is the characteristic of the cleft in the glutaminyl-tRNA synthetase?

It accommodates both ATP and the amino acid Signup and view all the answers

What is the difference between bacterial and eukaryotic ribosomes?

Size of the ribosomal subunits Signup and view all the answers

What is the method used to determine the shape of the ribosomal subunits?

Electron microscopy Signup and view all the answers

What is the characteristic of the assembly pathway of the 30S subunit?

It is an obligatory process Signup and view all the answers

What is the function of the 3' acceptor stem of the tRNA?

To accommodate the amino acid Signup and view all the answers

What is the class of the glutaminyl-tRNA synthetase?

Monomeric class I Signup and view all the answers

What is the component of the tRNA that is represented by a detailed atomic model?

The entire tRNA molecule Signup and view all the answers

What is the function of SF3b in post-transcriptional processing?

To act as a protein splicing factor Signup and view all the answers

What is the significance of alternative splicing in gene expression?

It allows one gene to specify several proteins Signup and view all the answers

What is the function of NTC in post-transcriptional processing?

To act as a multiprotein complex called Prp19 Signup and view all the answers

What is the purpose of the smooth (SM) and striated (STR) exons?

To encode amino acid residues 39-80 Signup and view all the answers

What is the process by which the ribosome selects specific aminoacyl-tRNAs during translation?

By matching the trinucleotide anticodon on the tRNA to the trinucleotide codon on the RNA message Signup and view all the answers

What is the result of alternative 3'-terminal exons in the tropomyosin gene?

Production of different mRNAs with the same coding sequence Signup and view all the answers

What is the term for the process of selecting specific splice sites during alternative splicing?

Splice-site selection Signup and view all the answers

What is the outcome of the tropomyosin gene organization?

Production of multiple proteins with different functions Signup and view all the answers

Study Notes

Enzymology of RNA Synthesis: RNA Polymerase

RNA polymerase is responsible for transcription, which involves slower growth at many sites, resulting in more RNA accumulation than DNA
The functions of RNA polymerase subunits can be determined by reconstitution
RNA polymerase subunit structures vary in the three domains of life (bacteria, archaea, and eukarya), with homologous subunits color-coded and conserved subunits marked with an asterisk

Mechanism of Transcription

Transcription begins with sequence-specific interaction between RNA polymerase and a promoter site, involving duplex unwinding and template strand selection
DNA bending occurs in the open-promoter complex, with a sharp bend in the template strand
Backtracking can occur in the elongation complex, where the enzyme slips backward, leaving the transcript terminus at the end of a non-base-paired RNA tail
Transcription can resume either by forward sliding of the polymerase back to the original structure or by cleavage of the non-base-paired part of the transcript, creating a new base-paired 3' terminus
The frequency of gene transcription in E. coli is largely determined by the similarity between the gene's promoter sequence and the consensus sequence
Conserved sequences in promoters recognized by E. coli RNA polymerase include the -10 and -35 regions, with lengths of spacer sequences also shown

Mechanism of Transcription (continued)

DNA sequences that promote factor-independent termination include a run of four to eight A residues and a GC-rich region that forms a stem-loop
In factor-dependent termination, a protein acts as an RNA-DNA helicase, unwinding the template-transcript duplex and facilitating release of the transcript
A model for factor-independent termination of transcription involves an A-rich segment of the template being transcribed into a U-rich mRNA segment, followed by RNA-RNA duplex formation and elimination of some base pairing between the template and transcript

Transcription and its Control in Eukaryotic Cells

A model of the TFIIA-TBP-TFIIB-promoter complex based on crystal structures of TBP-TFIIB-TATA and TFIIA-TBP-TATA complexes
DNA looping (perhaps mediated by nucleosomes) can bring enhancer-bound activator (or repressor) proteins into contact with TAFs associated with the core complex
Acetylation of core histones occurs exclusively in the N-terminal domains, at highly conserved sites

Termination of Transcription in Eukaryotes

Termination of transcription in eukaryotes involves the addition of poly(A) tails, which is signaled by the AATAAA sequence near the end of most eukaryotic genes

Post-transcriptional Processing

Bacterial transcripts undergo post-transcriptional processing, involving both endonucleolytic and exonucleolytic cleavage
Post-transcriptional processing in bacteria involves cleavage of the primary transcript, modification of bases, non-transcriptive nucleotide addition, and intron splicing (in a few cases)
Alternative splicing allows one gene to specify several proteins, as seen in the tropomyosin gene organization (rat) and its seven alternative splicing pathways

Post-transcriptional Processing (continued)

Possible mechanisms for alternative splicing by splice-site selection include the use of different splice sites, the presence of splicing enhancers or silencers, and the role of RNA-binding proteins

Translation

Translation of an RNA message into a protein involves the ribosome moving along the message, accepting specific aminoacyl-tRNAs in succession, and selecting them by matching the trinucleotide anticodon on the tRNA to the trinucleotide codon on the RNA message

The Major Participants in Translation

Major "identity elements" in tRNAs include the acceptor stem, the D stem, the anticodon stem, and the variable loop
A model of the E. coli glutaminyl-tRNA synthetase coupled with its tRNA and ATP shows the tRNA fitting into a deep cleft in the synthetase, with the ATP and 3' acceptor stem of the tRNA binding to the synthetase
Components of bacterial and eukaryotic ribosomes include the 30S and 50S subunits, with eukaryotic ribosomes being somewhat larger and more complex

The Major Participants in Translation (continued)

Assembly map for the 30S subunit shows the obligatory nature of some protein-binding events

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Description

This quiz covers the transcription and post-transcriptional processing, translation and post-translational protein processing, and enzymology of RNA synthesis.