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Questions and Answers
What is the functional unit of genetic information in microorganisms?
What is the primary role of topoisomerases in DNA replication?
Which statement about plasmids is accurate?
How is the size of a genome typically expressed?
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What percentage of the E. coli K-12 genome is made up of protein-encoding genes?
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What type of genetic element usually carries genes for antibiotic resistance?
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Which of the following describes the structure of most bacterial chromosomes?
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What is the typical gc content of the Escherichia coli K-12 genome?
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Which element can move from one DNA molecule to another?
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What is the effect of supercoiling on DNA structure?
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What is the significance of plasmids in pathogenic bacteria?
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Which statement correctly describes the process of DNA replication?
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What role does DNA polymerase I serve during DNA replication?
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How does the DNA helicase function during DNA replication?
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What is a replisome?
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During DNA replication, how are Okazaki fragments connected?
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What dictates the direction of DNA replication?
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Which of the following statements about bidirectional replication is correct?
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What are the precursors for nucleotide synthesis in DNA replication?
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Why do Rhizobia require plasmid-encoded functions?
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Which components are part of the replisome in DNA replication?
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How do DNA polymerases I and III ensure the accuracy of DNA replication?
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What is a primary difference between prokaryotic and eukaryotic transcription?
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What role does tRNA play in the process of translation?
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What characteristic of mutation rates is generally observed in cells?
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During transcription, what must happen to eukaryotic RNAs before translation can occur?
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What is the function of primase in DNA replication?
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In what type of cells does coupled transcription and translation occur?
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Which type of RNA serves as a structural component of the ribosome?
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What statement accurately describes the process of DNA replication?
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What is the primary function of RNA polymerase in transcription?
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Which of the following statements correctly describes bacterial RNA polymerase?
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What type of RNA does RNA polymerase II primarily transcribe in eukaryotes?
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Which of the following describes the groove for template DNA binding in bacterial RNA polymerase?
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What differentiates the various RNA polymerases in eukaryotic organisms?
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What is a major difference between RNA polymerase and DNA polymerase regarding proofreading?
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Which RNA polymerase in plants is specifically responsible for generating small interfering RNAs?
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Which of the following is required for the activity of RNA polymerase during transcription?
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What is generally true about the overall structure of RNA polymerases from eukaryotes and prokaryotes?
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What is the role of the positively charged groove in bacterial RNA polymerase?
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What is the role of the sigma factor in bacterial RNA transcription?
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Which regions are recognized by the sigma factor in the transcription initiation process?
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In E. coli, what is the significance of the major sigma factor σ70?
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How many distinct sigma factors are present in E. coli?
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What might indicate a promoter sequence for transcription initiation in bacteria?
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What is a characteristic of sigma factors in bacterial species?
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What defines the -10 region in RNA transcription initiation?
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What is the relationship between sigma factors and gene function in bacteria?
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Why is the sigma factor described as not tightly bound to the core enzyme?
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What happens to the sigma factor after transcription initiation has been initiated?
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What is the primary reason that coupled transcription and translation occurs in bacteria but not in eukaryotes?
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What type of termination mechanism relies on an inverted repeat followed by a run of uracils?
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What role does the Rho protein play during Rho-dependent termination in bacteria?
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Which factor is NOT one of the termination factors associated with transcription in E. coli?
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What happens when Rho protein binds to the rut site during Rho-dependent termination?
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Which statement accurately describes a feature of factor-independent termination?
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During transcription termination, what occurs when RNA polymerase encounters a transcription terminator sequence?
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What is the primary reason that polymerase pausing can occur at terminator sequences?
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What distinguishes Rho-dependent termination from factor-independent termination?
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What triggers the release of the anti-sigma factor NepR, allowing σEcfG1 to function in the transcription process?
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During the formation of the closed complex in transcription, what happens to the DNA?
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Which aspect of the sigma factor is crucial for forming the open complex during transcription?
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What describes the composition of a polycistronic mRNA molecule?
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What occurs during the elongation phase of transcription?
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In the context of bacterial transcription, what role does the transcription bubble serve?
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What characterizes the release of the sigma factor during transcription?
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Which of the following best describes the formation of the open complex during transcription initiation?
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What defines the transcription start site in relation to the first nucleotide of mRNA?
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Which factor is crucial for transcription initiation in bacterial cells?
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What best describes the process that allows proteins to begin to form before mRNA is fully transcribed in bacteria?
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What outcome typically occurs when RNA polymerase encounters a transcription terminator?
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In factor-independent termination, which sequence structure is commonly formed?
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Which statement is true about Rho-dependent termination in E. coli?
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What role does the Rho hexamer play in transcription termination?
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What consequence might arise from incorrect recognition of terminator sequences?
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Why do eukaryotes not exhibit coupled transcription and translation similar to bacteria?
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Which of the following statements about transcription termination in bacteria is correct?
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What is the function of the rut site in the context of Rho-dependent termination?
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What characterizes the distinction between prokaryotic and eukaryotic transcription processes?
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What initiates the release of the anti-sigma factor NepR in M.extorquens during stress response?
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What occurs during the formation of the open complex in transcription initiation?
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Which statement best describes the elongation phase of transcription?
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What is a characteristic feature of polycistronic mRNA?
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Which factor plays a crucial role in preventing the need for a helicase during transcription initiation?
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In which scenario can transcription occur simultaneously on the same gene?
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Which feature distinguishes the initiation of transcription at the +1 site?
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What role do anti-sigma factors serve in cellular processes?
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What dictates the directionality of transcription during gene expression?
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The transient melting of the DNA duplex during transcription is primarily facilitated by which component?
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Study Notes
DNA and Genetic Information Flow
- The functional unit of genetic information is the gene.
- Genes are part of genetic elements, which are large molecules, such as chromosomes.
- Nucleic acids contain genetic information through nucleotides, which are monomers of nucleic acids.
- DNA is the genetic blueprint, and RNA is its transcription product.
- Both DNA and RNA are polynucleotides.
- Informational macromolecules include nucleic acids and proteins.
Genetic Elements: Chromosomes and Plasmids
-
Genome size is expressed in base pairs.
- 1000 base pairs = 1 kilobase pair = 1 kbp
- 1 million base pairs = 1 megabase pair = 1 Mbp
- The E. coli genome is 4.64 Mbp and encodes around 4000 genes.
- Linear DNA is several hundred times longer than the cell, so supercoiling compacts DNA to accommodate the genome.
- Topoisomerases insert and remove supercoils.
- DNA gyrase introduces supercoils into DNA via double-strand breaks.
- Chromosomes are the main genetic element in prokaryotes.
- Most bacteria and archaea have a single circular chromosome carrying all or most of their genes.
-
Plasmids are double-stranded DNA that replicate separately from the chromosome.
- Usually circular.
- Generally beneficial for the cell (e.g., antibiotic resistance).
- Not extracellular, unlike viruses.
-
Transposable elements are segments of DNA that can move from one site to another on the same or a different DNA molecule.
- They can be inserted into other DNA molecules (e.g., chromosomes, plasmids, viral genomes).
Escherichia coli K-12 Chromosome Features
- Approximately 5 Mbp in size.
- GC content (% of G and C in the genome) is 50.8 %.
- Almost 4300 possible protein-encoding genes, comprising 88% of the genome.
Plasmid Features
- Plasmids can carry genes associated with virulence factors in pathogenic bacteria that contribute to infection.
- Bacteriocins, proteins that inhibit or kill closely related species or different strains of the same species, can be encoded on plasmids.
- Rhizobia use plasmid-encoded functions to fix nitrogen.
- Plasmids can contribute to metabolism, such as hydrocarbon degradation.
- Plasmids are crucial for conjugation, a form of horizontal gene transfer.
### DNA Replication
- DNA replication is semiconservative, meaning each new double helix consists of one original strand and one newly synthesized strand.
- Deoxynucleoside 5′-triphosphate (dNTP) serves as the precursor for each nucleotide.
- DNA replication always proceeds from the 5′ end to the 3′ end.
- DNA polymerases, specifically DNA Pol III, are the primary enzymes responsible for replicating chromosomal DNA in E. coli.
- Other DNA polymerases play roles in DNA repair.
- DNA synthesis initiates at the origin of replication in prokaryotes.
- DNA polymerases require a primer, a short stretch of RNA, which primase creates.
- The replication fork is the region of unwound DNA where replication occurs.
- DNA helicase unwinds the DNA.
- DNA synthesis occurs continuously on the leading strand and discontinuously on the lagging strand.
- Okazaki fragments are short segments of DNA synthesized on the lagging strand.
- DNA polymerase I removes the RNA primer and replaces it with DNA.
- DNA ligase seals the gaps in the DNA.
- Bidirectional replication occurs in circular chromosomes.
- Two replication forks move in opposite directions along the circular chromosome.
- DNA Pol III adds approximately 1,000 nucleotides per second.
- The replisome, a complex of multiple proteins involved in replication, consists of two copies of DNA polymerase III, DNA gyrase, helicase, primase, and multiple single-strand DNA-binding proteins.
- DNA replication is extremely accurate due to proofreading mechanisms that ensure high fidelity.
- Mutation rates in cells are typically 10–8 to 10–11 errors per base inserted.
- DNA Pol I and Pol III can detect mismatches through incorrect hydrogen bonding and remove them via their 3'→5' exonuclease activity.
RNA Synthesis: Transcription
- Central Dogma: DNA is duplicated (replication), information is transferred from DNA to RNA (transcription), and information in RNA is used to build polypeptides (translation).
- mRNA (messenger RNA) encodes proteins.
- tRNA (transfer RNA) converts mRNA into the amino acid sequence of a protein.
- rRNA (ribosomal RNA) provides catalytic and structural components for ribosomes.
### Transcription Characteristics in Prokaryotes & Eukaryotes
- Eukaryotes: Each gene is transcribed individually into a single mRNA. Replication and transcription happen in the nucleus. RNA must be exported outside the nucleus for translation.
- Prokaryotes: Multiple genes can be transcribed in a single mRNA. Transcription and translation are coupled, maximizing protein synthesis.
Transcription in Bacteria
- Transcription is the synthesis of RNA from a DNA template.
- RNA polymerase is the enzyme that carries out transcription.
- RNA polymerase requires DNA as a template and uses ATP, GTP, CTP, and UTP as RNA precursors.
- Transcription proceeds in the 5' to 3' direction, similar to DNA replication.
- Only one strand of DNA is transcribed.
- No primer is required for RNA transcription.
Prokaryotic vs. Eukaryotic RNA Polymerases
- Most eukaryotes have three different RNA polymerases:
- Pol I: synthesizes ribosomal RNAs (rRNAs)
- Pol II: synthesizes messenger RNAs (mRNAs)
- Pol III: synthesizes 5S rRNA, transfer RNAs (tRNAs), and other small RNAs
- Plants have two additional RNA polymerases:
- Pol IV: involved in the generation of small interfering RNAs (siRNAs) from transposons and repetitive sequences, contributing to epigenetic regulation.
- Pol V: responsible for silencing (DNA and histone methylation) of transposons and repetitive sequences.
- Bacteria and Archaea only have a single RNA polymerase.
Bacterial RNA Polymerase Structure
- E. coli RNA polymerase is composed of five subunits: two α (αI and αII), β, β', and ω.
- The core enzyme consists of the β, β', and ω subunits.
- Together, the core enzyme and the sigma factor form the holoenzyme.
Key Features of Bacterial RNA Polymerase
- The DNA binding groove of RNA polymerase is positively charged, while DNA is negatively charged, facilitating the binding of DNA.
- Magnesium ions (Mg2+) are required for RNA polymerase activity.
- RNA polymerase lacks a proofreading mechanism, unlike DNA polymerase, which has 3' to 5' exonuclease activity.
Transcription Initiation in Bacteria
- Initiation is sequence-specific and occurs at the promoter sequence, located upstream of the RNA transcription start site.
- The core enzyme can catalyze transcription, but the sigma factor is needed for promoter recognition.
- Sigma factors are bacterial transcription factors that bind to the promoter sequence (-10 and -35 regions) and help RNA polymerase initiate transcription.
- The +1 site marks the transcription initiation site.
- The -10 region (also known as the Pribnow box) is a consensus sequence located about 10 base pairs upstream of the +1 site.
- The -35 region is another consensus sequence located about 35 base pairs upstream of the +1 site.
- Multiple sigma factors exist in bacteria, allowing RNA polymerase to recognize and transcribe different sets of genes.
Sigma Factor in E. coli
- E. coli has seven distinct sigma factors.
- The primary sigma factor, σ70, is responsible for the transcription of "housekeeping" genes.
- Each sigma factor typically binds to a set of genes with related functions, such as sporulation genes.
Examples of Sigma Factor Functions
- Sporulation sigma factor in Bacillus subtilis: responsible for transcribing genes involved in bacterial sporulation in response to adverse conditions.
RNA Polymerase Holoenzyme Structure
- The sigma factor is attached to the core RNA polymerase complex.
Anti-sigma Factors
- Inhibit sigma factor function by binding to them
- Regulate stress response in M.extorquens
- Phosphorylation of PhyR releases anti-sigma factor (NepR) from σEcfG1
- Allows σEcfG1 to associate with RNA polymerase and transcribe stress genes
Transcription Start and Elongation
- Closed Complex: DNA is double-stranded, RNA polymerase is bound to the promoter
- Open Complex: Sigma factor unwinds DNA at the promoter region, no helicase or ATP required
- Initiating Ribonucleotides: Transcription usually starts at +1 with a nucleotide triphosphate, resulting in a triphosphate at the 5' end of the newly synthesized RNA
-
Elongation:
- Sigma subunit detaches from the polymerase
- Transcription bubble forms (18 base long DNA opening)
- RNA/DNA hybrid forms, helping keep the polymerase attached to the DNA
Transcription Features
- Transcription can occur on either DNA strand
- Multiple RNA polymerases can transcribe the same gene simultaneously
Polycistronic mRNA
- Single mRNA molecule containing multiple genes
- Transcribed from the same promoter upstream of a cluster of genes with related functions (operon)
Ribosomal RNA
- Polycistronic
Coupled Transcription and Translation in Bacteria
- Ribosomes attach to the 5' end of mRNA before transcription is complete
- Ribosomes move along the mRNA towards the 3' end as transcription continues
- Allows protein synthesis to begin before mRNA is fully transcribed
- Not possible in eukaryotes due to separate compartments for transcription and translation
Transcription Termination
- RNA polymerase detaches from the template when it encounters a terminator sequence
- Two types: factor-independent and Rho-dependent
Factor-Independent Termination
- Inverted repeat sequence with a central non-repeating segment forms a hairpin structure
- Followed by a run of U nucleotides
- Destabilizes RNA/DNA binding, leading to RNA dissociation
Rho-Dependent Termination
- Requires Rho factor - an RNA-dependent ATPase and RNA/DNA helicase
- Recognizes rut sites in RNA
- Rho binds to rut and acts as a helicase, moving 5' to 3' along the transcript
- This pulls apart the RNA/DNA hybrid, releasing the RNA polymerase when it's paused at the terminator sequence
Anti-sigma Factors
- Anti-sigma factors are proteins that bind to sigma factors, inhibiting their function.
- Phosphorylation of PhyR in Mycobacterium extorquens triggers the release of the anti-sigma factor NepR from the sigma factor σEcfG1.
- This release allows σEcfG1 to associate with RNA polymerase, leading to transcription of genes involved in stress response.
Transcription Initiation and Elongation
- Closed Complex: RNA polymerase bound to the promoter region, DNA is double-stranded.
- Open Complex: DNA unwinds at the promoter region, catalyzed by the sigma factor.
- Initiating Ribonucleotides: Transcription starts at the +1 site with a nucleotide triphosphate, creating a triphosphate at the 5' end of RNA.
- Elongation: Sigma subunit dissociates, forming a transcription bubble with an 18 base pair RNA/DNA hybrid.
- Transcription Features: Transcription can occur in either DNA strand depending on the gene, and multiple RNA polymerases can transcribe a single gene simultaneously.
Polycistronic mRNA
- One mRNA molecule contains multiple genes transcribed from the same promoter upstream of a gene cluster.
- These clusters, called operons, usually contain genes with related functions.
Coupled Transcription and Translation in Bacteria
- Ribosomes attach to the 5' end of mRNA even before transcription is complete.
- Ribosomes move along the mRNA towards the 3' end as transcription continues.
- This coupling allows protein synthesis to start before mRNA is fully produced, reducing the delay between transcription and protein expression.
Transcription Termination
-
Factor-Independent Termination:
- Inverted repeat sequence (high G+C content) forms a hairpin structure through intramolecular base-pairing.
- Run of U residues following the inverted repeat destabilizes RNA/DNA binding, leading to RNA dissociation.
-
Rho-Dependent Termination:
- Rho protein is an RNA-dependent ATPase and RNA/DNA helicase.
- Rho binds to rut (rho utilization) sequences in RNA, moving along the transcript in a 5' to 3' direction.
- Rho unwinds the RNA/DNA hybrid, causing RNA polymerase to disengage when paused at the terminator sequence.
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Description
Explore the fundamental concepts of DNA, genes, and genetic elements in this quiz. Understand how nucleic acids function in genetic information transfer and the structure of genomes. Test your knowledge on key topics such as supercoiling and the E. coli genome.
