mol. bio lecture 10

5′ GU (splice donor), branch-point A, and 3′ AG (splice acceptor).

What are the three key conserved sequences involved in pre-mRNA splicing

What enzyme complex performs pre-mRNA splicing

The spliceosome.

What type of reactions remove introns

Two transesterification reactions.

Which snRNP recognizes the 5′ splice site

U1 snRNP.

Which snRNP binds the branch-point A

U2 snRNP.

What shape does the intron form during splicing

A lariat (loop) structure.

Serine-arginine–rich proteins that mark exons and help recruit spliceosome components.

What are SR proteins and what do they do

Why is exon recognition harder in humans

Introns are much longer and contain many fake GU/AG motifs.

Average exon length vs intron length in humans

Exons ≈ 150 bp; Introns ≈ 3500 bp.

Define “alternative splicing.” Different combinations of exons joined to make different mRNA variants (isoforms).

What is an isoform

A different version of the same protein produced from the same gene by alternative splicing.

How many isoforms can the Drosophila Dscam gene produce

≈ 38 016 isoforms (12 × 48 × 33 × 2).

Why does Dscam need so many isoforms

To help neurons form unique connections and avoid self-contact.

What happens when Dscam is lost in neurons

Dendrites cross and grow abnormally (lack self-avoidance).

What triggers female vs male development in Drosophila

A cascade of sex-specific alternative splicing (Sxl → Tra → Dsx).

Which protein starts the female splicing cascade

Sex-lethal (Sxl).

What does Sxl do

Binds to intron 2–3 and blocks U2AF → skips exon 3 with stop codon → functional Sxl in females.

Why don’t males produce functional Sxl

They splice exon 2–3 → include stop codon → no functional protein.

What does Tra protein do

Promotes female-specific splicing of dsx mRNA (exon 3–4).

What dsx isoform is made in females vs males

Females: exon 4 (activator); Males: exon 5 (repressor).

What is the role of Tra2 and Rbp1

They are SR proteins that bind exonic splicing enhancers with Tra to activate female splicing.

How does the female Dsx isoform affect gene expression

Activates female-specific genes with Dsx binding sites.

How does the male Dsx isoform affect gene expression

Represses those same genes.

What is the main splicing defect linked to autism spectrum disorder (ASD)

Reduced inclusion of microexons in neuronal mRNAs.

What are microexons

Tiny exons (3–27 nt) that maintain reading frame and fine-tune protein interactions.

Which SR protein is reduced in ASD patients

SRRM4.

What disease is caused by SMN1 gene mutation

Spinal Muscular Atrophy (SMA).

What does SMN protein do

Maintains motor neuron survival.

Why can’t SMN2 fully compensate for SMN1 loss

Most SMN2 transcripts skip exon 7 → unstable protein.

What causes SMN2 to skip exon 7

C-to-T mutation reduces 3′ splice-site efficiency.

Name two SMA treatments and their approaches. Zolgensma (gene therapy adds SMN1) and Spinraza/Nusinersen (changes SMN2 splicing to include exon 7).

How does Spinraza work

Antisense oligo binds intron 7 → blocks repressors → exon 7 included.

What is an mRNP

mRNA plus associated proteins (export complex).

Which proteins form the mRNA exporter

NXF1 + NXT1 heterodimer.

What other proteins help in export

SR proteins and REF (bound to exon-junction complexes).

What ensures only mature mRNAs are exported

Pre-mRNAs still bound to spliceosomes are retained in nucleus.

What replaces CBC on the 5′ cap in the cytoplasm

eIF4E.

What replaces PABPN1 on the poly(A) tail in the cytoplasm

PABPC1.

What determines mRNA stability in the cytoplasm

Poly(A) tail length and 3′ UTR binding proteins.

Which pathway is the main route for mRNA degradation

Deadenylation-dependent pathway.

Which enzymes shorten the poly(A) tail

Deadenylase complex.

What happens after PABPC1 loss

mRNA gets decapped and degraded.

Which enzymes decap mRNA

DCP1/DCP2.

Which enzyme degrades 5′→3′ after decapping

XRN1.

Which complex degrades 3′→5′ RNAs

The exosome.

What is the deadenylation-independent pathway

mRNA is decapped first → degraded by XRN1.

What is endonuclease-mediated decay

mRNA cut internally → fragments degraded by exosome and XRN1.

What is the overall purpose of cytoplasmic mRNA control

Regulate how long mRNAs last and where they get translated.