RNA Synthesis and Processing - Foundations of Medicine

100 practice flashcards covering RNA synthesis, processing, and related concepts from the lecture notes.

What are the four well-understood roles of ribonucleic acids in eukaryotic cells and their primary functions?

mRNA carries protein-coding messages; snRNA participates in splicing hnRNA; tRNA matches amino acids to codons during translation; rRNA forms the ribosome.

What is the role of mRNA in the cell?

mRNA encodes the amino acid sequences of all polypeptides in the cell.

What is the role of snRNA in RNA processing?

snRNA forms small nuclear RNA particles that splice hnRNA into mRNA.

What is the role of tRNA during protein synthesis?

tRNA matches specific amino acids to triplet codons in mRNA.

What is the role of rRNA in the cell?

rRNA is a constituent of the ribosome and helps form the ribosome's catalytic center.

What does hnRNA stand for and how is it related to mRNA?

hnRNA stands for heterogeneous nuclear RNA; it is the precursor transcribed from DNA that is spliced into mature mRNA.

Approximately what percentage of total RNA is mRNA?

About 5% of total RNA.

Approximately what percentage of total RNA is tRNA?

About 15% of total RNA.

Approximately what percentage of total RNA is rRNA?

About 80% of total RNA.

Where does RNA synthesis (transcription) occur in the cell?

In the nucleus, using DNA as the template.

What template is used for RNA synthesis?

DNA serves as the template for transcription.

Why is transcription tightly regulated in cells?

To control the concentration of each protein by controlling RNA production.

Why can RNA fold into compact structures more readily than DNA?

RNA is mainly single-stranded, allowing intramolecular base pairing and folding into functional structures.

What additional catalytic capability can some RNA molecules have?

Some RNA molecules can act as ribozymes (catalysts).

When are most eukaryotic RNAs processed?

During synthesis or after synthesis (co-transcriptional capping and post-transcriptional processing).

What processing events occur during transcription vs after transcription?

Capping at the 5' end occurs during synthesis; polyadenylation of the 3' end and intron removal occur after synthesis.

What is added to the 3' end of RNA during processing?

A poly-A tail is added (polyadenylation).

What is added to the 5' end of pre-mRNA to form the 5' cap?

A cap of 7-methylguanosine (m7G cap) is added.

Which enzyme adds the 5' cap and what other enzymes modify the cap?

Guanylyltransferase adds the cap; methyltransferases add methyl groups to riboses.

What are the main functions of the 5' cap?

It increases mRNA stability and enhances translation efficiency.

What signals the start and end of the 3' end processing to add the poly-A tail?

The AAUAAA hexamer and a GU-rich element guide the 3' processing complex.

What is the typical length of the poly-A tail?

Up to about 200 adenosine residues.

Why is the poly-A tail important?

It improves mRNA stability and aids in translation.

What does splicing accomplish?

Removal of introns and joining of exons to produce mature mRNA.

What are splice junction donor and acceptor sequences?

Donor (5' end) is GU; acceptor (3' end) is AG.

Which complex recognizes splice junctions during splicing?

The spliceosome.

What components form the spliceosome?

Small nuclear RNAs (snRNAs) and associated proteins (snRNPs) U1-U6.

Which proteins initiate spliceosome assembly at the 5' splice site?

U1 snRNP binds the 5' splice site.

Which snRNP binds the branch point and helps align splice sites?

U2 snRNP.

How is the intron removed during splicing?

The intron is excised as a lariat through two transesterification reactions.

What are the two transesterification steps in splicing?

(i) 2'OH attacks the 5' splice site; (ii) 3'OH attacks the 3' splice site, joining exons.

What structure is released after intron removal in splicing?

A lariat intron is released; exons are joined.

What is alternative splicing?

Process that generates multiple mRNA transcripts and protein isoforms from a single gene.

What is the biological significance of alternative splicing?

It increases protein diversity and allows cell-type specific expression.

What percentage of human genetic diseases may be due to splicing defects?

Approximately 15%.

Name a disease associated with splicing defects involving autoantibodies blocking splicing.

Systemic lupus erythematosus (anti-U1 antibodies block proper splicing).

Name two diseases caused by splicing defects.

Spinal muscular atrophy (SMA) and Becker muscular dystrophy (BMD) among others.

What is mature mRNA composed of?

5' cap, 5' UTR, coding sequence (starts with AUG, ends with a stop codon such as UGA), 3' UTR, and poly-A tail.

What is the untranslated region at the 5' end called?

5' UTR (untranslated leader).

Where does the coding region of mRNA begin and end?

Begins with the start codon AUG and ends at the stop codon (e.g., UGA in the notes).

What is the untranslated region at the 3' end called?

3' UTR.

Where does mature mRNA go after processing?

It leaves the nucleus and enters the cytosol for translation.

What is the start site of transcription called?

+1 region.

What promoter element is mentioned as important for transcription initiation in the notes?

The -10 region (TATA box).

What is a TATA box used for in transcription?

Promoter element important for transcription initiation.

What is an enhancer?

A regulatory DNA sequence that increases transcription when bound by transcription factors.

What is transcription termination region?

A region downstream of genes involved in termination signaling.

What is a transcription termination signal for RNA polymerase II?

A termination sequence downstream of the poly(A) site leading to cleavage and polyadenylation.

What are 5' and 3' UTRs?

Untranslated regions at the ends of mRNA that regulate stability and translation.

Which RNA polymerase transcribes rRNA?

RNA Polymerase I.

Which RNA polymerase transcribes mRNA?

RNA Polymerase II.

Which RNA polymerase transcribes tRNA?

RNA Polymerase III.

Do mitochondria have their own RNA polymerase and transcription machinery?

Yes, mitochondria possess their own RNA polymerase.

What is the speed range for transcription by RNA polymerase II?

About 500–1000 nucleotides per second.

What are the three stages of transcription?

Initiation, elongation, and termination.

What happens during the initiation stage of transcription?

Binding phase forms the closed complex; DNA unwinds to open complex; promoter clearance occurs after phosphorylation.

What happens during the binding phase of initiation?

RNA polymerase II forms a pre-initiation complex (PIC) with the promoter, creating a closed complex.

What happens when the DNA unwinds during initiation?

An open complex is formed, enabling transcription to begin after promoter clearance.

What must occur for promoter clearance during initiation?

Phosphorylation of RNA polymerase II.

When does capping of the 5' end occur during transcription?

During transcription elongation.

What term describes the RNA produced by transcription before processing?

hnRNA (heterogeneous nuclear RNA).

What is the term for RNA polymerase II's termination process?

Termination involves cleavage of the nascent RNA and polyadenylation, with release of Pol II.

What is meant by the coding strand in transcription terminology?

The non-template strand that has the same sequence as the RNA transcript (T instead of U). Regulatory sequences are listed by this strand.

What is the term for the non-template DNA strand?

Coding strand (sequence matches the RNA transcript; the reverse is the template strand).

What direction does RNA synthesis occur in?

5' to 3' direction.

What happens to the DNA during RNA elongation?

The DNA is transiently unwound to expose the template strand.

What is the difference between a template strand and a coding strand?

Template strand is used by RNA pol to synthesize RNA; coding strand has the same sequence as RNA (T in place of U). All regulatory sequences are described by the coding strand.

What is the function of the 7-methylguanosine cap?

Stabilizes the RNA and enhances translation initiation.

What enzyme adds the 5' cap?

Guanylyltransferase (with methyltransferases for methylation of the cap).

What marks the 3' end of the pre-mRNA for processing?

The AAUAAA signal and a GU-rich element guide cleavage and polyadenylation.

What enzyme adds the poly-A tail after cleavage?

Poly(A) polymerase (PAP) adds adenosines.

What is the functional outcome of splicing defects manifesting as diseases?

Impaired production of functional proteins; examples include SMA, BMD, FTDP-17, and SLE-related splicing issues.

Which disease involves a mutation in SMN1 exon 7?

Spinal muscular atrophy (SMA) with decreased motor neuron survival.

Which disease involves a dystrophin exon mutation in exon 27?

Becker muscular dystrophy (BMD).

Which disease is associated with a Tau exon 10 mutation affecting stability?

Frontotemporal dementia with Parkinsonism-17 (FTDP-17).

What is the stop codon mentioned in the mature mRNA description?

UGA (along with other stop codons, UAA/UAG, not all listed in notes).

What is the role of the mature mRNA cap in translation initiation?

The cap helps recruit the ribosome via eIF4E and promotes translation initiation.

What happens to the intron after splicing is complete?

The intron is released as a lariat and degraded.

What are U1 and U2 snRNPs primarily responsible for in splicing?

U1 binds the 5' splice site; U2 binds the branch point and facilitates splice-site juxtaposition.

What does the term 'lariat' refer to in RNA splicing?

The looped intron intermediate formed during two transesterification steps.

What type of RNA forms most of the ribosome?

rRNA.

Which RNA type carries amino acids to the ribosome?

tRNA.

What is the function of mRNA's 5' UTR and 3' UTR?

Untranslated regions that regulate translation efficiency, stability, and localization.

What is the main outcome of transcription termination by Pol II?

Cleavage of nascent RNA, polyadenylation, and release of RNA polymerase II.

What is the significance of the GU-rich element in polyadenylation?

It is part of the 3' end processing signals guiding cleavage and tail addition.

What is the implication of having multiple RNA polymerases in eukaryotes?

Distinct polymerases transcribe different RNA types: Pol I for rRNA, Pol II for mRNA, Pol III for tRNA.

Which molecule forms the catalytic center during splicing?

snRNPs, particularly U2 and U6, assemble the catalytic core.

What is the 'pre-initiation complex' (PIC)?

A multi-protein complex including RNA polymerase II and transcription factors that forms before transcription starts.

Which region is defined as the start site of transcription in the notes?

+1 region.

What does 'polyadenylation' accomplish for mRNA?

It stabilizes the transcript and aids in translation.

What is the speed of RNA polymerase II transcription?

Approximately 500–1000 nt per second.

Which antibiotic inhibits bacterial RNA polymerases and is used to treat tuberculosis?

Rifampicin.

What does Actinomycin D do to DNA and RNA polymerases?

Intercalates between G-C base pairs, blocking both eukaryotic and prokaryotic RNA polymerases.

Which chemotherapy agent intercalates DNA to inhibit transcription?

Daunorubicin.

What is Cordycepin and how does it affect transcription/translation?

A chain terminator lacking a 3'OH, derived from mushrooms, with anti-tumor activity.

What is the primary consequence of capping on RNA stability?

Increased resistance to nucleases and enhanced translation efficiency.

What is the main product of post-transcriptional processing?

Mature mRNA that is ready for export to cytosol for translation.

What is the term for the RNA that is transcribed and later processed into mRNA?

Pre-mRNA (precursor mRNA).

What is the key difference between the coding and template strands?

The template strand is used for RNA synthesis; the coding strand has the same sequence as the RNA (with T replacing U) and defines regulatory sequences.

How does alternative splicing impact protein diversity?

By using different splice sites, a single gene can generate multiple mRNA variants and protein isoforms.