RNA Polymerase Quiz

Learning Outcomes

• Students should be able to describe the universal features of transcription.
• Students should be able to discuss the steps and factors involved in prokaryotic and eukaryotic transcription.
• Students should be able to discuss the major processing events undergone by eukaryotic mRNA molecules.
• Students should be able to describe common processing events for tRNA and rRNA molecules.
• Students should be able to explain how mature RNA molecules are transported from the nucleus into the cytosol.

Central Dogma of Molecular Biology

• DNA replicates to DNA.
• DNA transcribes to RNA.
• RNA translates to polypeptides/proteins.
• Polypeptides are modified to form traits.

Gregor Mendel's Experiment

• This section includes a table from the image. It is a summary of Mendel's experiments, which shows how traits are passed from one generation to the next. The image details different traits (Height, Shape, Color) and their corresponding dominant (Tall, Round, Yellow) and recessive (Short, Wrinkled, Green) forms.

Molecular Basis for Seed Shape

• The Sbe1 gene is responsible for seed shape.
• The gene codes for an enzyme that is involved in starch branching.
• Round seeds have functional Sbe1 genes, while wrinkled seeds do not.
• Even if the Sbe1 gene exists, if the glucose isn't polymerized, it will not produce round seeds.

Molecular Basis for Plant Height

• The Le gene is responsible for plant height.
• The gene codes for gibberellin 3β hydroxylase.
• Tall plants produce functional gibberellin 3β hydroxylase, while short plants do not.

Transmission of Genetic Information

• DNA is transcribed into mRNA.
• mRNA is translated into polypeptides (NH2-Methionine-Arginine).
• Post-translational modifications occur, resulting in traits.

Universal Features of Transcription

• It is DNA-dependent RNA synthesis.
• It involves only certain regions of the DNA template (coding regions).
• Non-coding regions have critical roles in gene regulation.
• It uses RNA polymerase as the main enzyme.
• Transcription has three general steps: Initiation, Elongation, and Termination.

Transcription: Universal Features

• Template DNA is the anti-coding/antisense strand.
• RNA is complementary to the template strand.
• RNA polymerase uses DNA as a template to make RNA.
• Products of transcription are mRNA, rRNA, tRNA, miRNA, siRNA, and other regulatory RNAs.

Transcription: Universal Features

• The steps of transcription are initiation, elongation, and termination.
• Major control points are at the initiation step.
• RNA polymerase (the main enzyme) aids the process.

Some Terminologies

• Transcript Unit - Region from start to termination site.
• Gene - A segment of DNA.
• Promoter - A region that facilitates transcription initiation.
• Terminator - A region that signals transcription termination.
• Primary Transcript - The unaltered RNA product.

Some Terminologies

• Proximal - Close to the promoter.
• Distal - Farther from the promoter.

Consensus Sequence

• A sequence of nucleotides that are found frequently at certain positions across genes.

Basic Gene Structure

• Genes consist of a promoter, transcribed region, and terminator.
• Upstream and downstream sequence locations are also indicated.

RNA Polymerase

• DNA-directed enzyme used to make RNA according to a DNA template.
• Adds ribonucleotides to the 3' end of the RNA.
• Proceeds in the 5' to 3' direction.
• Has low error rate.

Bacterial RNA Polymerase

• Composed of subunits including α, β, β', σ, and ω.
• Core enzyme is 2αββ''.
• Holoenzyme is 2αββ'Σσ.

Eukaryotic RNA Polymerases

• Eukaryotic cells have three types of RNA polymerases (I, II, and III).
• Each has specific functions for different types of RNA.

Rifampicin

• An antibiotic that targets prokaryotic RNA polymerase.
• Prevents RNA elongation.

The Transcriptome

• The complete set of RNA transcripts in a cell.
• RNA molecules, including mRNA (coding), ncRNA (non-coding), and regulatory RNAs are all part of the transcriptome.

Different Types of RNA

• RRNAs, mRNAs, and tRNAs are common in cells and differ according to their structure.

RNA Polymerase: 6 sites of Activity

• RNA polymerase transcribes DNA and has several functions for transcription.

The Transcription Process

• Specific sequences (promoters) initiate transcription.
• RNA polymerase binds to these areas.
• Transcription factors assist RNA polymerase binding.

Prokaryotic Promoters

• Pribnow box (consensus sequence: 5'-TATAAT-3') is 10 bases upstream from the transcription start site.
• In prokaryotic cells, a -35 sequence of consensus sequence 5'-TTGACA-3' is also involved in transcription regulation.

Eukaryotic Promoters

• Eukaryotic promoters for RNA polymerase II typically include a TATA box or a Goldberg-Hogness box.

Strong vs Weak Promoters

• Strong promoters have sequences identical or similar to the consensus sequence.
• Weak promoters have deviated sequences.

General Transcription Factors

• Protein factors that are essential for transcription initiation.
• Direct RNA polymerase to target promoters.
• Transcription initiation is dependent on these protein factors.

Eukaryotic TIC Assembly

• The transcription initiation complex (TIC) assembles and facilitates the initiation step.

Gene-specific Transcription Factors

• Protein factors bind to specific sequences in DNA.
• They assist in the transcription regulation of specific gene groups in cell types.

Events in Transcription Initiation

• RNA polymerase binds to the promoter region.
• The DNA unwinds.
• The first RNA molecule is added.
• The polymerase remains stationary until phosphorylation.
• It incorporates the first ribonucleotide.

Transcription Elongation, Termination

• RNA polymerase synthesizes RNA in a 5' to 3' direction.
• Polymerization occurs ~15 nts/sec in bacteria.
• Terminator sequence guides termination.

Transcription Termination, Rho

• Termination can be Rho (p)-dependent or independent in bacteria.

Reverse Transcription

• A process that produces cDNA from RNA.
• Often found in retroviruses or for telomere elongation.
• Reverse transcriptases are involved in this process.

Reverse Transcription and HIV

• Retroviruses such as HIV use reverse transcriptase to produce DNA from their RNA genome.
• Reverse transcriptase is essential for retroviral replication.

RT-PCR, qRT-PCR

• RT-PCR is used for detecting and quantifying RNA.
• qRT-PCR is a quantitative method to monitor RNA levels during transcription regulation.

Pre-mRNA Processing Events

• A process that transforms precursor RNA into mature RNA.
• Involved in capping, tailing, splicing, editing, export.

Major mRNA Processing Events

• Capping, Tailing, and Splicing are the key mRNA processing stages.

5' Capping

• 7-methylguanosine (7mG) cap added to the 5' end.
• Enzyme: guanylyl transferase then methyl transferases add methyl groups to the cap.
• Stabilizes and enhances translation.

3' Poly-A Tailing

• Addition of a polyadenine (A) tail to the 3' end
• Catalyzed by polyadenylation; enzyme: PolyA polymerase.

Alternative Tailing

• Some transcripts have more than one polyadenylation site.
• The tailing "choice" varies depending on developmental stage, location, protein factors.

Splicing

• Removal of introns and ligation of exons.
• Occurs in eukaryotes.
• This step generates mature mRNA.

Intron Distribution in Human Genes

• Different genes have different intron numbers, sizes, and proportions.

Splicing Signals: Chambon's Rule

• Contains a 5' splice site, a branch point, and a 3' splice site.
• This method is used in eukaryotes.

Spliceosomes

• Large RNA-Protein complexes.
• U1, U2, U4, U5, and U6 snRNPs are involved in splicing.

Roles of snRNPs in Splicing

• Several types of snRNPs aid splicing efficiency.

Two-Step Splicing Reaction

• Two transesterification reactions take place in the splicing process.
• A lariat intermediate forms during this.

Alternative Splicing

• Different protein products are created from a single gene.
• Variations in gene products occur through variation in splicing.

RNA Transport in Eukaryotes

• Export of RNA from the nucleus to the cytoplasm is critical for translation.
• Karyopherins are involved in transporting RNA between nucleus and cytoplasm.

Coupled Transcription-Translation

• Bacteria can perform transcription and translation simultaneously since both occur in the cytoplasm.

Test your knowledge on key characteristics of RNA polymerase compared to DNA polymerase. This quiz explores concepts such as promoter regions, consensus sequences, the processivity of RNA polymerase, and the role of Mg2+ in its function.