Molecular Biology: Translation and Transcription Quiz
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Questions and Answers

What role does the ribosome-binding site play in bacterial translation?

  • It binds to the stop codon.
  • It provides a location for ribosomes to begin translation. (correct)
  • It identifies the terminator sequence.
  • It initiates the transcription process.

Which of the following correctly describes the stop codon in translation?

  • It is always the first codon in the mRNA sequence.
  • It designates the end of polypeptide synthesis. (correct)
  • It determines the start sequence of the mRNA.
  • It signals the beginning of transcription.

During the initiation stage of transcription, what is the primary role of transcription factors?

  • They enable RNA polymerase to bind to the promoter. (correct)
  • They synthesize RNA independently of RNA polymerase.
  • They assist in denaturing the DNA duplex.
  • They degrade mRNA after synthesis.

What happens during the elongation stage of transcription?

<p>RNA polymerase synthesizes mRNA while sliding along the open complex. (B)</p> Signup and view all the answers

What is formed when the DNA strands are separated during transcription initiation?

<p>Open transcription bubble (C)</p> Signup and view all the answers

What is the outcome when RNA polymerase reaches a terminator during transcription?

<p>RNA polymerase and the primary transcript dissociate from the DNA. (A)</p> Signup and view all the answers

Which of the following statements is true regarding the start codon?

<p>It marks the beginning of the coding sequence in mRNA. (A)</p> Signup and view all the answers

Which protein complex is essential for the initiation of transcription?

<p>Transcription factors and RNA polymerase (B)</p> Signup and view all the answers

What is the primary function of TFIID in the transcription process?

<p>Recognizes the TATA box near the transcription start point (C)</p> Signup and view all the answers

How many subunits compose TFIID?

<p>12 (B)</p> Signup and view all the answers

Which general transcription factor is responsible for attracting and regulating TFIIH?

<p>TFIIE (D)</p> Signup and view all the answers

What does TFIIH primarily do at the transcription start point?

<p>Unwinds DNA (A)</p> Signup and view all the answers

What effect does the binding of the stem-loop structure have on RNA polymerase during transcription termination?

<p>It leads to a conformational change and a pause in synthesis. (C)</p> Signup and view all the answers

Which factor binds to TFIID and stabilizes its interaction with the TATA box?

<p>TFIIA (B)</p> Signup and view all the answers

What is the role of the ρ protein during transcription termination?

<p>It catches up to the stem-loop to break hydrogen bonds. (C)</p> Signup and view all the answers

How does TFIIF assist RNA polymerase II during transcription initiation?

<p>By interacting with TFIIB (A)</p> Signup and view all the answers

Which feature differentiates the ρ-independent termination from the ρ-dependent termination?

<p>The presence of the uracil-rich sequence is exclusive to ρ-independent termination. (B)</p> Signup and view all the answers

Which transcription factor is known to position RNA polymerase II at the transcription start site?

<p>TFIIB (A)</p> Signup and view all the answers

What occurs immediately after the synthesis of the RNA sequence?

<p>The stem-loop structure forms and binds to RNA polymerase. (C)</p> Signup and view all the answers

What stabilizes the pause of RNA polymerase during the ρ-independent termination?

<p>The binding of NusA protein to RNA polymerase. (B)</p> Signup and view all the answers

What role does TFIIE play in the open complex formation?

<p>It helps maintain the open complex (A)</p> Signup and view all the answers

What is a primary characteristic of the stem-loop structure formed during transcription?

<p>It results from complementary sequences within the RNA. (D)</p> Signup and view all the answers

During ρ-independent termination, what occurs to the uracil-rich sequence in the RNA transcript?

<p>It weakly attaches to the DNA template strand, causing dissociation. (B)</p> Signup and view all the answers

What is the consequence of the RNA transcript dissociating from the DNA template?

<p>Transcription is halted and the process is considered complete. (C)</p> Signup and view all the answers

What is the primary direction in which RNA polymerase synthesizes RNA during transcription?

<p>5′ to 3′ (A)</p> Signup and view all the answers

Which mechanism of termination involves an RNA-binding protein known as rho (ρ)?

<p>Rho-dependent termination (C)</p> Signup and view all the answers

What prevents the dissociation of RNA polymerase from the template strand during transcription elongation?

<p>Hydrogen bonding between RNA-DNA (C)</p> Signup and view all the answers

How does RNA polymerase connect nucleotides during transcription?

<p>By catalyzing bonds between 3′-OH and 5′-PO42− groups (C)</p> Signup and view all the answers

Which statement about transcription directionality is correct?

<p>Genes can be transcribed in both left to right and right to left directions (A)</p> Signup and view all the answers

What role does the rut site play in rho-dependent termination?

<p>It serves as a recognition site for rho (ρ) protein binding (C)</p> Signup and view all the answers

Which of the following best describes the speed of RNA synthesis?

<p>Approximately 43 nucleotides per second (B)</p> Signup and view all the answers

In transcription termination, what occurs when the RNA-DNA hybrid region is separated?

<p>The newly synthesized RNA transcript and RNA polymerase are released (D)</p> Signup and view all the answers

What is the significance of the promoter in gene expression?

<p>It is the region where RNA polymerase binds to start transcription. (B)</p> Signup and view all the answers

What sequence is recognized at the -10 site in the E. coli promoter?

<p>5′–TATAAT–3′ (D)</p> Signup and view all the answers

How are nucleotides numbered in relation to the transcription start site?

<p>Bases to the left of the start site are in negative direction. (D)</p> Signup and view all the answers

What forms the RNA polymerase holoenzyme in E. coli?

<p>A combination of five core subunits and a sigma factor (C)</p> Signup and view all the answers

What nucleotide is designated as +1 in the conventional numbering system?

<p>The first nucleotide used as a template for transcription (A)</p> Signup and view all the answers

What is referred to as the consensus sequences?

<p>The sequences at -10 and -35 sites recognized by transcription proteins (B)</p> Signup and view all the answers

Which of the following statements is NOT true regarding the conventional numbering of nucleotides?

<p>The nucleotide immediately to the right of +1 is numbered -1. (C)</p> Signup and view all the answers

Which protein initiates the transcription process by recognizing the promoter?

<p>Sigma factor (A)</p> Signup and view all the answers

What is the primary role of TFIIB in the transcription initiation process?

<p>To promote the binding of RNA polymerase II and TFIIF (B)</p> Signup and view all the answers

Which component of the transcription machinery is specifically responsible for helicase activity?

<p>TFIIH (A)</p> Signup and view all the answers

What event occurs immediately after the transcription of the polyadenylation signal sequence?

<p>Cleavage of mRNA occurs downstream (A)</p> Signup and view all the answers

What is the main function of the carboxyl-terminal domain (CTD) of RNA polymerase II?

<p>To undergo phosphorylation and influence transcriptional elongation (C)</p> Signup and view all the answers

Which subunits are involved in forming the closed complex in eukaryotic transcription?

<p>TFIID, TFIIB, and TFIIE (A)</p> Signup and view all the answers

What is the consequence of CTD phosphorylation during transcription initiation?

<p>Promotes the release of RNA polymerase II from the promoter (C)</p> Signup and view all the answers

What sequence is crucial for directing the cleavage of mRNA during polyadenylation?

<p>The polyadenylation signal sequence (B)</p> Signup and view all the answers

Which of the following statements about TFIID is accurate?

<p>It is composed of multiple subunits known as TAFs (D)</p> Signup and view all the answers

Flashcards

Ribosome-binding site

A short sequence on mRNA that marks the starting point for ribosome binding, crucial for initiating translation.

Codon

Three consecutive nucleotides on mRNA that code for a specific amino acid.

Start codon

The first codon in mRNA that signals the start of protein synthesis.

Stop codon

A codon in mRNA that signals the end of translation.

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Transcription

The process by which DNA is used as a template to synthesize RNA. It has three stages: initiation, elongation, and termination.

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Transcription initiation

The first stage of transcription where RNA polymerase binds to the promoter region of DNA. It involves the recognition of promoter sequences by transcription factors.

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Transcription elongation

The second stage of transcription where RNA polymerase moves along the DNA template, adding nucleotides and forming the RNA molecule.

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Transcription termination

The final stage of transcription where RNA polymerase detaches from the DNA template and the newly synthesized RNA molecule is released.

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Promoter

A DNA sequence that signals the start of transcription, located upstream from the transcription start site.

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Transcription start site

The first nucleotide used as a template for transcription, denoted by +1.

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Conventional promoter numbering

The numbering system for nucleotides in a promoter, where numbers increase in the direction of transcription.

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Consensus sequences

Two important sequences within a prokaryotic promoter, typically located around -10 and -35.

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TATAAT sequence

The sequence at the -10 site in a promoter, often called the Pribnow box.

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RNA polymerase

The enzyme that catalyzes the synthesis of RNA from a DNA template.

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RNA polymerase holoenzyme

The active form of RNA polymerase in prokaryotes, containing the core enzyme and a sigma factor.

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Sigma factor

A protein subunit that binds to the core enzyme, required for initiating transcription.

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Terminator

A specific sequence on DNA that signals the end of transcription and initiates the release of the newly synthesized RNA molecule.

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Rho protein

A protein that binds to a specific site on RNA and helps to terminate transcription by separating the RNA-DNA hybrid.

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Rut site

A specific sequence on RNA where a Rho protein binds to initiate termination of transcription.

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Rho-independent Termination

A mechanism of transcription termination that does not require the involvement of Rho protein.

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Rho-dependent Termination

A mechanism of transcription termination that involves the binding of Rho protein to a specific sequence on RNA.

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RNA-DNA hybrid

The region where DNA and RNA are temporarily paired within the open complex, preventing the polymerase from detaching.

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What causes RNA polymerase to pause during transcription termination?

RNA polymerase pauses transcription due to a stem-loop structure in the newly synthesized RNA.

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What is a stem-loop in transcription termination?

A sequence in RNA comprised of complementary base pairs that form a hairpin structure.

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What does the ρ protein do during transcription termination?

A protein that binds to the RNA and moves towards RNA polymerase, aiding in the termination process.

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What is ρ-dependent termination?

The termination process involving ρ protein. Requires a stem-loop and a ρ-binding site in the RNA.

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What is ρ-independent termination?

The termination process that does not require ρ protein. Requires a stem-loop and a uracil-rich sequence.

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What is the role of the uracil-rich sequence in ρ-independent termination?

A sequence of uracil nucleotides at the 3' end of the RNA molecule that helps detach the RNA from DNA during termination.

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What is the role of NusA in ρ-independent termination?

A protein that stabilizes the pause of RNA polymerase during ρ-independent termination, giving the uracil-rich sequence time to bind to DNA.

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What is a terminator sequence in transcription?

A sequence in DNA that signals the end of transcription, often containing a stem-loop and a uracil-rich sequence.

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Polyadenylation

The process of adding a tail of adenine nucleotides to the 3' end of eukaryotic mRNA, marking it for translation.

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Polyadenylation signal sequence

A specific sequence in the DNA template that signals the addition of a poly-A tail to the mRNA transcript.

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Polyadenylation signal

A specific sequence on the DNA template that signals the end of transcription.

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DNA unwinding

The process of breaking the hydrogen bonds between the two strands of DNA.

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Mediator

A complex of proteins that helps to assemble the preinitiation complex, and plays a role in phosphorylating the CTD of RNA polymerase II.

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Carboxyl-terminal domain (CTD)

A domain in RNA polymerase II that is phosphorylated during the transition from initiation to elongation.

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TFIID

A complex of proteins that helps initiate transcription in eukaryotes. It recognizes the TATA box, a DNA sequence upstream of the transcription start site, and helps position RNA polymerase II for transcription.

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TFIIA

A general transcription factor that stabilizes the binding of TFIID to the TATA box, ensuring the proper initiation of transcription.

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TFIIB

A general transcription factor that binds to TFIID and positions RNA polymerase II at the transcription start site, preparing it for transcription.

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TFIIF

A general transcription factor that binds to RNA polymerase II and stabilizes its interaction with TFIIB and the core promoter, ensuring efficient transcription.

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TFIIE

A general transcription factor that attracts and regulates TFIIH, playing a crucial role in the assembly of the transcription complex.

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TFIIH

A general transcription factor with multiple roles: It unwinds DNA at the transcription start point, phosphorylates the RNA polymerase C-terminal domain (CTD) to release RNA polymerase from the promoter, and plays a role in the initiation and elongation of transcription.

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TFIID's Role

The 12 subunits of TFIID bind the TATA box on the promoter, a region in DNA that signals the start of transcription. TFIID plays a key role in recruiting other transcription factors, including TBP and RNA polymerase II, to initiate transcription.

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Transcription Factors

Transcription factors are proteins that bind to specific DNA sequences and regulate gene expression. They can act as activators to increase transcription or repressors to decrease transcription. These factors bind to promoter regions, influencing the rate at which a gene is copied into RNA.

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Study Notes

Molecular Biology I - BIO316, Lecture 7

  • Gene Transcription Overview: Genetic material stores information for living organisms; this information is contained in genes, segments of DNA that code for functional products (RNA or polypeptide).

  • Transcription process: Transcription produces an RNA copy (mRNA) of a gene. mRNA carries the information for creating a polypeptide. A polypeptide assembles into a functional protein.

  • DNA Replication: DNA makes copies of itself, transmitting it from one cell to the next and from parent to offspring.

  • Prokaryotic vs. Eukaryotic Transcription: Gene transcription in prokaryotes is simpler than in eukaryotes. Eukaryotic cells—larger than prokaryotic—contain multiple compartments and organelles.

  • Protein-coding genes: These genes provide information for polypeptide synthesis, forming proteins essential for organismal functions. Transcription of a protein-coding gene generates mRNA as the initial product.

  • Gene Expression: Gene expression is the overall mechanism through which information encoded in a gene is utilized to produce a functional protein.

  • Promoter & Terminator: The promoter site signals the start of transcription, offering an initiation point. The terminator site marks the end of the transcription process.

  • Regulatory elements: These DNA segments control transcription rates.

  • Transcription Factors: Proteins that bind to genes and regulate the rate of transcription. Some bind directly to the promoter.

  • mRNA Structure: mRNA contains a sequence of codons (three-nucleotide units) that specify particular amino acids. Each codon encodes an amino acid.

Stages of Transcription

  • Initiation:

    • The promoter region acts as a recognition site for transcription factors.
    • Transcription factors enable RNA polymerase to bind to the promoter.
    • DNA denatures to form an open complex, facilitating RNA synthesis.

  • Elongation:

    • RNA polymerase moves along the DNA template strand.
    • RNA polymerase synthesizes a complementary RNA strand from the template DNA.
    • Synthesis occurs in the 5' to 3' direction, using nucleotides.

  • Termination:

    • RNA polymerase encounters a terminator sequence.
    • RNA polymerase and the newly formed RNA transcript detach from the DNA.

Transcription in Prokaryotes

  • Promoters: In prokaryotes, promoters have a -35 consensus and -10 consensus sequence. Promoters are upstream from the transcription start site.

  • RNA Polymerase: The enzyme that catalyzes mRNA synthesis. RNA polymerase in prokaryotes are made up of five core subunits.

  • Holoenzyme: The sigma (σ) factor associates with the RNA polymerase core enzyme to form the holoenzyme. The sigma factor helps the RNA polymerase recognize the promoter.

  • Transcription Start Site (+1): This is where transcription begins the coding strand nucleotide +1 is where the transcript starts.

Transcription in eukaryotes

  • RNA Polymerases: Eukaryotes have three RNA polymerases (I, II, and III). Each polymerase transcribes distinct types of genes.

  • TATA Box: A critical sequence within the core promoter, often found in eukaryotic genes, helps RNA polymerase recognize and bind to the promoter regions.

  • Regulatory elements (Enhancers & Silencers): DNA segments that influence transcription rates. Activators bind to enhancers to stimulate transcription; repressors bind to silencers to repress transcription.

General transcription factors (GTFs)

  • Multiple subunits: RNA polymerase II consists of several subunits.

  • TBP: The TATA binding protein is one of the protein subunits within the TFIID protein complex. It plays a critical role in recognizing the core promoter.

  • Mediator complex: Mediator is a multiprotein complex that facilitates basal transcription by interacting with RNA polymerase II, general transcription factors, and regulatory transcription factors (activators and repressors). Mediator influences transcription by affecting TFIIH's ability to phosphorylate the RNA polymerase II CTD (carboxyl terminal domain).

Transcription Termination

  • Prokaryotic Termination: Rho-dependent termination involves the rho protein and a rut site on RNA; rho-independent involves DNA/RNA stem loops.

  • Eukaryotic Termination: Termination occurs after cleavage of the transcript downstream of the polyadenylation signal and involves cleavage followed by addition of adenine nucleotides to the newly produced RNA. Two models (allosteric and torpedo) describe this process.

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Molecular Biology I BIO316 Lecture 7 PDF

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Test your knowledge on the key processes of translation and transcription in molecular biology. This quiz covers important elements like ribosome-binding sites, stop codons, and the roles of transcription factors. Assess your understanding of the initiation, elongation, and termination stages of transcription.

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