Gene Expression (Transcription) Overview

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Questions and Answers

What role does polyadenylation play in the RNA lifecycle?

  • It replaces exons with introns during RNA maturation.
  • It protects the 3' end from exonuclease degradation. (correct)
  • It enhances the binding of RNA polymerase to DNA.
  • It facilitates protein synthesis by enhancing ribosome binding.

Which small nuclear RNA is not involved in the formation of spliceosomes?

  • U6
  • U1
  • U5
  • U3 (correct)

What modification is performed on tRNA during its processing?

  • Addition of a poly-A tail.
  • Incorporation of a 7-methylguanylate cap.
  • Capping with trimethylguanosine for ribosomal recognition.
  • Removal of the 5' extension and addition of CCA at the 3' end. (correct)

What is the outcome of alternative splicing in mRNA processing?

<p>It generates distinct varieties of mRNA from the same gene. (A)</p> Signup and view all the answers

What is the primary function of small nuclear ribonucleoproteins (snRNPs) in RNA splicing?

<p>To bind with snRNAs and splice introns from pre-mRNA. (C)</p> Signup and view all the answers

What characterizes the initiation phase of transcription in prokaryotes?

<p>The sigma factor recognizes the promoter at the TATA box and binds it. (D)</p> Signup and view all the answers

How does termination of transcription differ between prokaryotes and eukaryotes?

<p>Eukaryotic termination requires the dissociation of RNA polymerase by dephosphorylation. (A), Prokaryotic RNA can form a hairpin structure for termination. (D)</p> Signup and view all the answers

Which statement accurately describes eukaryotic transcription elongation?

<p>RNA polymerase unwinds the DNA and then synthesizes RNA. (C)</p> Signup and view all the answers

What is the composition of the RNA polymerase in prokaryotic transcription?

<p>It consists of one enzyme formed of 2α and 2β subunits. (B)</p> Signup and view all the answers

Which eukaryotic RNA polymerase is responsible for synthesizing mRNA?

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

Which factors are recognized during the initiation phase of transcription in eukaryotes?

<p>TFIID binds to the TATA box and other specific boxes. (D)</p> Signup and view all the answers

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

<p>It serves as the primary site for transcription factor binding. (D)</p> Signup and view all the answers

In the context of the preinitiation complex, which component directly binds to the TATA box?

<p>Transcription factor IID (TFIID) (A)</p> Signup and view all the answers

Which of the following is NOT a feature of RNA polymerase II?

<p>It directly binds to the promoter sequence. (B)</p> Signup and view all the answers

What is the primary role of transcription factors in eukaryotic transcription?

<p>To regulate which genes are transcribed. (D)</p> Signup and view all the answers

What determines the frequency of transcription in eukaryotes?

<p>The GC box located upstream of the transcription start site. (D)</p> Signup and view all the answers

What is the significance of the CAAT box in the transcription process?

<p>It enhances transcription efficiency. (A)</p> Signup and view all the answers

Which mechanism is associated with the absence of a hairpin in histone mRNAs?

<p>Processing by a specific histone mechanism. (C)</p> Signup and view all the answers

Which transcription factor is recruited after TFIIB during the formation of the transcription initiation complex?

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

What initiates the transcription process by RNA polymerase II?

<p>Phosphorylation by kinase (C)</p> Signup and view all the answers

What is the role of Polyadenylation Specificity Factor (CPSF) in transcription termination?

<p>Binds to the AAUAAA sequence (D)</p> Signup and view all the answers

Which of the following statements about capping of mRNA is true?

<p>Capping protects the RNA from ribonucleases (A), A 5'-5' triphosphate bridge is formed (C)</p> Signup and view all the answers

What is the main consequence of enhancer sequences binding during transcription initiation?

<p>Modification of initiation complex formation rate (B)</p> Signup and view all the answers

What role does Cleavage Stimulation Factor (CstF) play in transcription termination?

<p>Binds the GU-rich sequence (D)</p> Signup and view all the answers

During transcription elongation, what process must occur to allow RNA synthesis to progress?

<p>Unwinding of DNA (C)</p> Signup and view all the answers

What sequence in the emerging RNA is critical for transcription termination?

<p>AAUAAA sequence followed by GU-rich sequence (A)</p> Signup and view all the answers

What is the role of the sigma factor in prokaryotic transcription initiation?

<p>It recognizes and binds to the promoter at the TATA box. (B)</p> Signup and view all the answers

What is the significance of the TATA box in prokaryotic transcription?

<p>It determines the frequency of transcription initiation. (B)</p> Signup and view all the answers

Which enzyme is responsible for relieving positive supercoiling during RNA transcription?

<p>Gyrase (C)</p> Signup and view all the answers

What characterizes the Rho factor in prokaryotic transcription termination?

<p>It binds at C-rich G-poor regions and moves towards RNA polymerase. (C)</p> Signup and view all the answers

What is the composition of prokaryotic RNA polymerase?

<p>One sigma factor and two alpha and two beta subunits. (C)</p> Signup and view all the answers

Which statement about the palindromic GC-rich region at transcription termination is true?

<p>It forms a hairpin structure in RNA due to base pairing. (B)</p> Signup and view all the answers

What is the function of topoisomerase during transcription in prokaryotes?

<p>To relieve negative supercoiling behind RNA polymerase. (D)</p> Signup and view all the answers

What distinguishes Rho-independent termination of transcription from Rho-dependent termination?

<p>Rho-independent termination does not require any protein. (D)</p> Signup and view all the answers

Flashcards

Prokaryotic RNA Polymerase

In prokaryotes, this enzyme is responsible for creating all three types of RNA: mRNA, rRNA, and tRNA.

Sigma Factor (σ)

A protein subunit of prokaryotic RNA polymerase that recognizes and binds to the promoter region.

TATA Box

A specific DNA sequence located around 10 bases upstream of the start point of transcription in prokaryotes.

TTGACA Box

In prokaryotes, it's a DNA sequence located around 35 bases upstream of the start point, influencing the frequency of transcription.

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Elongation in Transcription

A process in transcription where RNA polymerase moves along the DNA template, adding nucleotides to the growing RNA strand.

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Rho Factor

A specific termination protein that binds to the newly synthesized RNA and helps end transcription in prokaryotes.

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Rho-Independent Termination

A type of transcription termination in prokaryotes where a specific DNA sequence forms a hairpin structure in the RNA, causing RNA polymerase to detach.

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Palindromic GC-Rich Region

A specific DNA sequence that forms a hairpin structure in the RNA, aiding rho-independent termination.

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Histone mRNA Hairpin Element

A special RNA sequence that acts like a hairpin, helping to signal the end of a histone mRNA. This ensures the histone mRNA doesn't get too long.

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Promoter

The starting point for RNA polymerase II to begin transcribing a gene. Think of it as the address on the DNA where transcription starts.

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Preinitiation Complex (PIC)

A group of proteins that help RNA polymerase II bind to the promoter and initiate transcription. It's like a team of workers preparing the DNA for the transcription process.

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GC Box

A DNA sequence that helps regulate how often a gene is transcribed. It affects the frequency of transcription, controlling how many mRNA copies are made from a gene.

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TATA box-binding protein (TBP)

A protein that binds to the TATA box helping to bring RNA polymerase II to the right spot on the DNA to initiate transcription.

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Transcription Factor IID (TFIID)

A transcription factor involved in initiating transcription. It helps assemble the preinitiation complex.

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Transcription

The process of making a copy of a gene's DNA sequence into RNA. This is the first step in gene expression.

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Basal Transcription Apparatus

The initial complex formed during transcription initiation, consisting of RNA polymerase II and various transcription factors (TFIIA, TFIIB, TFIIF, TFIIE, and TFIIH).

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Enhancer Sequences

DNA sequences located upstream or downstream of the gene that can bind regulatory proteins to enhance or repress the rate of transcription.

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DNA Unwinding

The process of unwinding a short region of DNA to expose the template strand for RNA polymerase.

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Capping

The addition of a 7-methylguanosine cap to the 5' end of a pre-mRNA molecule, protecting it from degradation and facilitating ribosome binding.

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Polyadenylation

The process of adding a string of adenine nucleotides (poly-A tail) to the 3' end of a pre-mRNA molecule, increasing stability and facilitating export from the nucleus.

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Splicing

The process of removing introns (non-coding regions) from pre-mRNA, leaving behind only the exons (coding regions) to form mature mRNA.

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Elongation

The process of RNA polymerase moving along the DNA template strand, synthesizing a complementary RNA strand.

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Termination

The termination of transcription occurs when the RNA polymerase encounters a specific sequence in the DNA (AAUAAA followed by a GU-rich sequence).

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Sigma Factor

A protein complex in prokaryotes that recognizes the promoter region of DNA and facilitates the binding of RNA polymerase.

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TATA Box (Pribnow Box) & TTGACA Box

A sequence of DNA located upstream of the start codon in prokaryotes, serving as a binding site for RNA polymerase.

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TATA & CAAT & GC Boxes

A DNA sequence located upstream of the start codon in eukaryotes, serving as a binding site for transcription factors.

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Gyrase Enzyme

An enzyme in prokaryotes that unwinds DNA ahead of RNA polymerase, allowing for transcription.

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RNA Splicing

The removal of introns (non-coding regions) from pre-mRNA and the joining of exons (coding regions) to create mature mRNA. This process ensures only the necessary genetic information is translated into protein.

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snRNAs (small nuclear RNAs)

Specialized RNA molecules that, along with proteins, form complexes called snRNPs (small nuclear ribonucleoproteins) involved in splicing. These complexes recognize and remove introns from pre-mRNA.

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Alternative Splicing

A process that allows the same pre-mRNA to be spliced in different ways, creating multiple protein isoforms from a single gene. This adds complexity to gene expression and allows for diverse functions.

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tRNA (transfer RNA)

A type of RNA molecule that carries amino acids to the ribosomes for protein synthesis. It has a cloverleaf structure and undergoes processing steps including 5' end removal, 3' CCA addition, and intron excision.

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Study Notes

Gene Expression (Transcription) in Prokaryotes

  • Prokaryotes use only one RNA polymerase for synthesizing three types of RNA.
  • This polymerase is composed of a sigma factor and two alpha and two beta subunits.
  • The sigma factor recognizes and binds to the promoter region (TATA box).
  • RNA polymerase then binds to the start point (of transcription).
  • Rifampicin, an antibiotic inhibits RNA synthesis by binding to the beta subunit of the polymerase.
  • Two key sequences identify the start site for transcription:
    • TATA box (10 bases upstream of start point)
    • TTGACA box (35 bases upstream of start point). This sequence determines the frequency of transcription.

Gene Expression (Transcription) in Eukaryotes

  • Eukaryotes have three RNA polymerases (I, II, and III).
  • Each polymerase is involved in the synthesis of different types of RNA:
    • RNA polymerase I synthesizes rRNA
    • RNA polymerase II synthesizes mRNA
    • RNA polymerase III synthesizes tRNA

Transcription Initiation in Eukaryotes

  • Preinitiation complex (PIC) formation is crucial for initiating transcription in eukaryotes.
  • The PIC comprises RNA polymerase II and general transcription factors.
  • TBP (TATA-box binding protein) of TFII D binds to the TATA box (-10 sequence)
  • The other transcription factors TFII A, TFII B, TFII F, TFII E, TFII H bind to the other factors to form the complete PIC.
  • These factors facilitate the unwinding of the DNA double helix.
  • The initiation complex forms in the promoter region, but RNA polymerase II does not bind directly to the promoter sequence itself, rather to the PIC.

Other Transcription Factors

  • CAAT box (CCAAT) is 40 bases from the initiation of transcription
  • GC box (GGGCGG) is 200 bases away from the initiation of transcription. Both affect transcription frequency.
  • TBP and TAFs (collectively known as TFIID) bind to the TATA box to initiate transcription.
  • Other transcription factors (TFII A, TFII B, etc.) then bind to the complex, leading to the unwinding of the DNA double helix.
  • Enhancer sequences can modify the initiation complex and affect the rate of transcription.

Transcription Elongation

  • RNA polymerase unwinds DNA and creates a new strand of RNA.
  • The process of making the new strand begins by phosphorylation of the RNA polymerase enzyme by a kinase.

Transcription Termination

  • The "end" of the RNA transcript is determined by a specific sequence (AAUAAA) followed by a GU-rich sequence. Proteins then bind to this sequence and a poly(A) polymerase adds a poly-A tail (100-200 adenine nucleotides) to the 3' end of the mRNA.
  • Polyadenylation is important to protect the 3' end of the mRNA (from enzyme degradation) and to initiate translation.
  • Capping and polyadenylation are post-transcriptional modifications to mRNA.

RNA Splicing

  • Splicing removes non-coding intron sequences and joins coding exon sequences from the primary RNA transcript.
  • Small nuclear ribonucleoproteins (snRNPs) are essential in splicing
  • Different splicing patterns result in multiple protein products from a single gene (alternative splicing). RNA polymerase III processes tRNA and RNA polymerase I processes rRNA.

Processing of other RNA molecules

  • tRNA is processed by removing extensions, adding CCA to the 3' end, removing introns, and modifying bases (methylation of uracil) for proper function.
  • rRNA is processed and cleaved (split into distinctive segments) in the nucleus to form functioning ribosomal subunits.

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