Prokaryotic Transcription
During bacterial transcription initiation, this factor allows RNA polymerase to recognize specific promoter sequences.
Sigma factor
This eukaryotic RNA polymerase is responsible for synthesizing pre-mRNA.
RNA polymerase II.
These sequences are transcribed into pre-mRNA but are removed before translation.
Introns
This modified nucleotide is attached to the 5′ end of eukaryotic pre-mRNA through an unusual 5′–5′ linkage.
7-methylguanine.
This large complex contains five snRNAs and approximately 300 proteins and is responsible for removing nuclear pre-mRNA introns.
The spliceosome.
These two consensus sequences are recognized by the bacterial RNA polymerase holoenzyme during transcription initiation.
The −10 and −35 promoter regions.
This protein, part of TFIID, recognizes and binds the TATA box during transcription initiation.
TATA-binding protein (TBP)
Bacterial genes are generally colinear, whereas many eukaryotic genes are noncolinear. Explain the structural difference responsible.
Eukaryotic genes often contain introns that interrupt coding sequences, whereas bacterial protein-coding sequences are generally continuous.
Approximately 50–250 adenine nucleotides are added to the 3′ end of eukaryotic mRNA during this process.
Polyadenylation.
During pre-mRNA splicing, the 5′ end of an intron attaches to a branch-point adenine, forming this structure.
A lariat.
During transcription initiation, RNA polymerase transitions from a closed complex to an open complex. Describe the major change that occurs.
The DNA strands separate locally, exposing the template strand for transcription.
During eukaryotic transcription initiation, this general transcription factor helps unwind DNA and phosphorylate the CTD of RNA polymerase II.
TFIIH.
During DNA–RNA hybridization, researchers observed loops of unpaired DNA. Explain what these loops revealed about gene organization.
They demonstrated that genes contain noncoding regions absent from mature mRNA, providing evidence for introns.
A mutation prevents the addition of the 5′ cap to newly synthesized pre-mRNA. Predict two consequences for the mRNA.
Reduced mRNA stability and impaired translation initiation.
A mutation changes the conserved GU sequence at the 5′ splice site of an intron. Predict how this could affect RNA processing
The spliceosome may fail to recognize the splice site, causing abnormal splicing or intron retention.
A bacterial gene contains a GC-rich inverted repeat followed by several adenine nucleotides in the DNA template strand. Predict which termination mechanism will occur.
Rho-independent termination, because the resulting RNA can form a hairpin followed by a U-rich sequence.
A mutation prevents a SWI/SNF chromatin-remodeling complex from functioning. Explain how this could affect transcription.
Nucleosomes may not be repositioned properly, reducing DNA accessibility to transcription factors and RNA polymerase.
A mature mRNA contains a 5′ UTR and a 3′ UTR. Explain why these regions are important even though they are not translated.
They contain regulatory sequences that influence mRNA stability and translation.
A researcher inhibits polyadenylation but allows transcription and splicing to proceed normally. Predict how this would affect the mature mRNA.
The mRNA would likely have reduced stability and could undergo more rapid degradation.
A single gene produces three different mature mRNAs containing different combinations of exons. Identify the process responsible and explain its significance.
Alternative splicing, which allows one gene to produce multiple mRNA transcripts and potentially different protein isoforms.
A mutation prevents the sigma factor from associating with the RNA polymerase core enzyme. Predict how this would affect transcription initiation.
The RNA polymerase would have difficulty recognizing promoters, significantly reducing transcription initiation at promoters requiring that sigma factor.
A mutation prevents the phosphorylation of the RNA polymerase II CTD. Predict how this could affect transcription initiation and the transition into elongation.
RNA polymerase II may fail to efficiently escape the promoter and transition into productive elongation.
A researcher discovers a DNA sequence that produces a functional RNA but never produces a protein. Explain why this sequence is still considered a gene.
Genes can encode functional noncoding RNAs, such as tRNA, rRNA, and miRNA, rather than proteins.
A eukaryotic cell produces normal amounts of pre-mRNA, but very little mature mRNA reaches the cytoplasm. Identify two RNA-processing defects that could explain this observation.
Defective RNA splicing and defective 5′ capping or 3′ polyadenylation, which can interfere with proper mRNA maturation, stability, and export.
A researcher discovers an intron capable of removing itself without the assistance of a spliceosome. Identify two classes of introns capable of this process and explain how they differ from nuclear pre-mRNA introns.
Group I and Group II introns undergo self-splicing, whereas nuclear pre-mRNA introns generally require the spliceosome.