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Questions and Answers
What elements are found in the prokaryotic gene structure?
Which region is directly responsible for the initiation of transcription in prokaryotic DNA?
What is the function of sigma domain 2 during transcription?
In the context of prokaryotic mRNA, what does the acronym ORF stand for?
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What term describes the region where transcription ends in a prokaryotic gene structure?
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Which sequence plays a critical role in recognizing the promoter in prokaryotic transcription?
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What is the primary function of the Open Reading Frames (ORFs) in prokaryotic mRNA?
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What characteristic distinguishes prokaryotic mRNA from eukaryotic mRNA?
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What is the primary difference between how an amateur and a professional practices?
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What components make up prokaryotic genes?
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Which of the following elements is NOT part of the consensus sequences in E. coli promoters?
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What does the UP element in bacterial promoters signify?
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Which sequence element is commonly referred to as the Pribnow box?
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During transcription initiation in E. coli, what is the first step?
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What role does the transcription terminator play in a gene's structure?
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What is the purpose of the -10 extended element in bacterial promoters?
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What role does the sigma factor play in transcription initiation?
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Which sigma domain interacts with the -10 region of the DNA during transcription initiation?
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What is the function of the GC-rich palindrome found in the terminator sequence?
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During intrinsic termination, what follows the GC-rich palindrome in the terminator sequence?
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What happens to RNA polymerase after approximately 12 nucleotides during transcription elongation?
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How does Rho-dependent termination function?
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Which sigma domain inhibits access to the RNA polymerase active site?
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At which significant sequence does sigma domain 4 bind during the transcription process?
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Study Notes
Gene Structure
- A protein coding gene contains information that encodes for the order of amino acids in a polypeptide.
- An RNA gene determines the order of ribonucleotides in an RNA molecule.
- Prokaryotic genes have a promoter, an RNA coding region, and a transcription terminator.
Transcription
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Transcription Initiation
- Promoter Recognition: The sigma factor recognizes the -35 and -10 consensus sequences in the promoter.
- Formation of Closed Complex: The RNA polymerase binds to the promoter and forms a closed complex where the DNA is still double-stranded.
- Formation of Open Complex: The sigma factor interacts with the -10 element, causing the DNA to melt, allowing the single-stranded template to enter the RNA polymerase active site.
-
Transcription Elongation
- The RNA polymerase moves along the template, adding ribonucleotides to the growing RNA chain.
- The sigma factor dissociates after about 12 nucleotides.
-
Transcription Termination
- Intrinsic termination: A GC-rich palindrome followed by a poly-A stretch on the template strand forms a hairpin loop in the mRNA, leading to dissociation of the weak U:A hybrid.
- Factor-dependent termination: Rho protein binds to the transcript at the rut site and travels in the 5' to 3' direction, removing RNA polymerase from the template.
Transcription in E. coli
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Promoter Elements:
- -35 element: TTGACA
- -10 element (Pribnow box): TATAAT
- UP element: upstream element
- EXT: -10 extended element
- DIS: discriminator
- CRE: core-recognition element
Sigma Factor Roles
- Sigma domain 1: Prevents template access to the RNA polymerase active site.
- Sigma domain 2: Interacts with the -10 element and causes DNA melting.
- Sigma domain 3: Interacts with the EXT -10 element.
- Sigma domain 4: Interacts with the -35 element.
Prokaryotic Gene Structure
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dsDNA:
- Promoter region contains regulatory sequences like the -35 element, -10 element, and the UP element.
- RNA coding region contains the open reading frame (ORF) and the 5' UTR (untranslated region) and 3'UTR.
-
ssRNA:
- The 5' UTR and 3' UTR are present, but not the promoter region.
- The ORF contains start and stop codons.
Prokaryotic mRNA
- Contains the 5' UTR and 3' UTR regions.
- Often polycistronic, meaning it can code for multiple proteins.
Additional Note:
- The text states that the DNA duplex remains double-stranded during transcription initiation and the contacts cause sigma domain 2 to be positioned adjacent to the promoter -10 element.
- The text also notes that the DNA duplex around position +1 is unwound, with sigma domain 2 making specific base contacts with the single-stranded non-template strand of the promoter -10 element.
- This allows the single-stranded template strand to enter the RNA polymerase active site.
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Description
Explore the fundamental concepts of gene structure and the transcription process. This quiz covers the specifics of coding genes, RNA gene orders, and the steps involved in transcription initiation, elongation, and termination. Test your knowledge on these essential molecular biology topics.
