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What are the principal structures of RNA that students need to reproduce?
The structures of the principal nucleotides present in RNA.
What is the primary structure of RNA composed of?
The chemical monomeric and polymeric structure of the genetic material RNA.
What are the secondary and tertiary structures of RNA?
The secondary structure involves base pairing and folding, while the tertiary structure is the three-dimensional conformation of RNA.
What is the mechanism of RNA synthesis?
RNA synthesis involves the transcription cycle, which includes initiation, elongation, and termination.
How do eukaryotic RNA polymerases transcribe genomic DNA?
They can differentially transcribe genomic DNA to produce specific RNAs.
What is RNA splicing?
RNA splicing is the process of removing intronic RNA to generate functional mRNAs from precursor molecules.
What are the steps involved in mRNA splicing?
The steps include recognition of splice sites, cutting of the RNA, and joining of exons.
What type of bonds link successive nucleotide units in RNA?
Phosphodiester bonds.
What is the backbone composition of RNA?
The backbone consists of alternating pentose and phosphate groups.
How does the structure of RNA differ from DNA?
RNA is unbranched, polymeric, and typically single-stranded, while DNA is double-stranded.
What happens to RNA when it is exposed to ribonucleases?
RNA can be hydrolyzed by ribonucleases.
What is a hairpin structure in RNA?
A hairpin structure forms when a single RNA strand folds into a secondary structure with intrastrand base pairing.
What is the general structure of paired regions in RNA secondary structure?
They generally have an A-form right-handed helix.
What is the initial product of RNA transcription?
The primary transcript.
What is the direction of RNA synthesis?
RNA synthesis occurs in the 5' to 3' direction.
What is the transcriptome?
The complete set of RNA transcripts expressed by a genome.
What role does Mg2+ play in RNA synthesis?
Mg2+ is required for the activity of RNA polymerase during transcription.
What is the relationship between the RNA transcript and its DNA template?
The RNA transcript is complementary to its DNA template (antisense strand) and identical to the coding strand (sense strand).
What are posttranscriptional modifications?
Changes made to RNA after transcription, including capping, polyadenylation, and splicing.
What factors influence transcription?
Various factors can influence transcription, including transcription factors, enhancers, and repressors.
What is the significance of accurately removing intronic RNA?
Accurate removal of intronic RNA is crucial for generating functional mRNAs.
What is the role of RNA polymerase in transcription?
RNA polymerase catalyzes the synthesis of RNA from a DNA template.
What are the three major types of RNA involved in protein synthesis?
Ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA).
What percentage of total RNA is ribosomal RNA (rRNA)?
Close to 80%.
What is the role of transfer RNA (tRNA) in protein synthesis?
tRNA carries specific amino acids to the ribosome, with at least one type of tRNA for each of the 20 amino acids.
What is the function of messenger RNA (mRNA)?
mRNA serves as the coding RNA that carries genetic information from DNA to the ribosome for protein synthesis.
What are noncoding RNAs (ncRNAs)?
ncRNAs perform specialized structural, catalytic, and regulatory functions and are not translated into proteins.
How many RNA polymerases are present in bacteria, and what is their function?
One multisubunit RNA polymerase synthesizes all types of RNA except for short RNA primers.
What are the main steps of transcription in E. coli?
Initiation, elongation, and termination.
What is the role of RNAP (RNA polymerase) during transcription initiation?
RNAP binds to DNA, locates a promoter, and melts the DNA strands to form an open promoter complex.
What happens after the RNA chain reaches 10 to 20 nucleotides during transcription?
The polymerase undergoes a conformational change, allowing it to move away from the promoter.
What is the transcription termination process?
Upon encountering a termination sequence, RNAP undergoes a conformational change that releases the completed RNA chain, the DNA template, and itself.
What is the structure of the prokaryotic promoter region?
The promoter region contains consensus sequences recognized by RNA polymerase holoenzyme's σ factor.
What are the components of the bacterial RNA polymerase (RNAP) core complex?
The core complex consists of two β subunits (β and β′) and two α subunits.
What is the transcription bubble?
An approximately 20-bp area of melted DNA during transcription.
How does RNA polymerase relieve supercoiling during transcription?
Supercoils generated by unwinding are relieved by DNA topoisomerases.
What occurs to the σ factor during the elongation phase of transcription?
The σ factor is released after the RNA transcript exceeds 10 nucleotides.
What is the role of additional proteins during the transcription cycle?
Additional proteins facilitate the transcription steps and regulate the process through positive and negative factors.
What is the significance of the Pribnow box in prokaryotic transcription?
The Pribnow box is the initial site of melting that converts the closed initiation complex to a transcription bubble.
What happens to short RNA pieces made during transcription?
Several short pieces of RNA are first made and discarded before elongation starts.
What is the function of the core enzyme in bacterial transcription?
The core enzyme leaves the promoter and moves along the template, serving as its own sliding clamp.
What is the approximate length of DNA covered by the transcription complex?
The entire complex covers 30 to 75 bp of DNA.
What is the primary nucleotide that typically starts the RNA transcript?
The transcript typically starts with a purine.
What is a key difference between RNA polymerase and DNA polymerase regarding primer requirement?
RNA polymerase does not require a primer.
What proofreading capability is absent in RNA polymerase?
RNA polymerase does not have a 3' to 5' exonuclease domain for proofreading.
What may cause RNA polymerase to pause during transcription?
Misincorporation of nucleotides.
What are the two major mechanisms of transcription termination in bacteria?
Intrinsic termination and rho-dependent termination.
What characterizes rho-independent termination in bacterial transcription?
It involves a self-complementary sequence forming a GC-rich hairpin followed by a string of Us.
How does rho-dependent termination occur?
Rho binds to a C-rich rut site, moves along the RNA using ATPase activity, and separates the RNA-DNA hybrid helix.
What are the three types of eukaryotic RNA polymerases?
RNA polymerase I, II, and III.
What does RNA polymerase I synthesize?
The precursor of the 28S, 18S, and 5.8S rRNA in the nucleolus.
What is the function of RNA polymerase II?
It synthesizes the nuclear precursors of mRNA and certain non-coding RNAs.
What types of RNA does RNA polymerase III synthesize?
tRNA, 5S rRNA, and some snRNA and snoRNA.
What role do transcription factors play in eukaryotic transcription?
They bind to DNA and are required for the assembly of the initiation complex and determining which genes are transcribed.
What is chromatin remodeling?
The interconversion of DNA between condensed and decondensed forms, affecting transcription accessibility.
What is the TATA box and where is it located?
The TATA box (TATAAA) is located ~25 nucleotides upstream of the transcription start site.
What is the function of general transcription factors (GTF)?
They recruit RNA polymerase II to the promoter and form the preinitiation complex.
What is the role of TFIIH in transcription?
TFIIH melts the DNA and phosphorylates RNA polymerase II, allowing it to clear the promoter.
What is the significance of the Inr and DPE elements in eukaryotic promoters?
Inr is the initiator, and DPE is the downstream promoter element, both crucial for transcription initiation.
What is the role of histone acetyltransferases in gene transcription?
They acetylate lysine residues on histones, decreasing histone-DNA interaction and facilitating transcription.
What is the function of small nucleolar RNA (snoRNA)?
snoRNA primarily guides chemical modifications of other RNAs.
What is the function of small nuclear RNA (snRNA)?
snRNA is involved in splicing and other RNA processing.
What is the role of microRNA (miRNA)?
miRNA functions in RNA silencing and post-transcriptional regulation.
What is the difference between cis-acting and trans-acting elements in gene regulation?
Cis-acting elements are on the same DNA, while trans-acting elements, like GTFs, are synthesized in the cytosol.
What are CAAT and GC boxes in gene regulation?
Proximal regulatory elements located within ~200 nucleotides.
What role do enhancers play in gene regulation?
Enhancers are distal/proximal regulatory elements that specific transcription factors bind to.
What is the function of specific transcription factors (STF)?
STFs bind to regulatory elements to regulate transcription initiation frequency and mediate gene expression in response to signals.
What are the two main domains of specific transcription factors?
A transcription activating domain and a DNA-binding domain.
What is the significance of the cap structure on eukaryotic mRNA?
The cap structure at the 5′ terminal is a 7-methylguanosine that protects mRNA from nucleases.
What are the components of eukaryotic pre-mRNA?
Eukaryotic pre-mRNA is part of heterogeneous nuclear RNA (hnRNA) and undergoes extensive modifications.
What type of mRNA do eukaryotes produce?
Eukaryotes produce monocistronic mRNAs, which carry information from one gene.
What is the difference between monocistronic and polycistronic mRNA?
Monocistronic mRNA carries information from one gene, while polycistronic mRNA carries information from more than one gene.
How is prokaryotic mRNA different from eukaryotic mRNA?
Prokaryotic mRNA is generally identical to its primary transcript and can be polycistronic.
What is the process of posttranscriptional modification of rRNA?
Both prokaryotic and eukaryotic rRNAs are modified by cleavage and further processing by enzymes.
What are the rRNA species found in prokaryotic cells?
Prokaryotic cells contain 23S, 16S, and 5S rRNA species.
What are the rRNA species found in eukaryotic cells?
Eukaryotic cells contain 28S, 18S, 5.8S, and 5S rRNA species.
What percentage of total RNA do rRNAs make up?
rRNAs make up approximately 80% of the total RNAs.
What modifications occur to tRNAs posttranscriptionally?
tRNAs undergo cleavage, removal of sequences, and further modifications such as the addition of a -CCA to the 3'-terminal.
What is splicing in the context of mRNA processing?
Splicing is the process of removing introns and joining exons by a spliceosome.
What is the role of small nuclear ribonucleoprotein particles (snRNPs) in splicing?
snRNPs facilitate splicing by forming base pairs with intron ends and aligning neighboring exons.
What happens to introns during the splicing process?
Introns are excised and released as a lariat.
What can mutations at splice sites lead to?
Mutations at splice sites can produce aberrant proteins and are linked to genetic diseases.
What is an example of a genetic disease related to splicing mutations?
β-thalassemia, which involves incorrect splicing of β-globin mRNA.
What is alternative splicing?
Alternative splicing allows pre-mRNAs from over 90% of human genes to be spliced in different ways, producing multiple mRNA variations.
Do all primary transcripts contain introns?
No, some primary transcripts, such as those for histones, do not contain introns.
What is the role of Mediator in gene regulation?
Mediator binds to enhancers and helps in the regulation of transcription.
What is the significance of the Svedberg unit (S) in rRNA?
The Svedberg unit indicates the sedimentation rate, which is determined by the particle's size and shape.