Genetics Quiz: Alternative Splicing And Isoforms

What this quiz covers

This quiz focuses on Alternative Splicing And Isoforms, giving you a quick way to practice the rules, question types, and explanations that matter most for Genetics.

How to use this quiz

Try each quiz question before looking at the correct answer. Use the explanations to review missed ideas, then come back to similar questions until the pattern feels familiar.

Question 1

1. SR proteins are core catalytic components of the spliceosome, while hnRNP proteins function to shuttle mRNA out of the nucleus.
2. SR proteins typically bind to exonic splicing enhancers (ESEs) to promote exon inclusion, while hnRNPs often bind to splicing silencers to inhibit inclusion. (correct answer)
3. hnRNP proteins bind to the 5' cap and poly(A) tail to circularize the mRNA for efficient translation, while SR proteins mark introns for removal.
4. Both protein families bind exclusively to introns; SR proteins unmask splice sites, while hnRNP proteins mask them.

Explanation: This question addresses the fundamental antagonistic relationship between the two major families of splicing regulators. SR proteins are classic splicing enhancers. They bind to ESEs within exons and recruit core spliceosomal components (like U1 and U2AF) to the nearby weak splice sites, thereby promoting exon definition and inclusion. Conversely, many hnRNP family members (like hnRNP A1) act as splicing repressors by binding to exonic or intronic splicing silencers (ESS or ISS), often competing with SR proteins or looping out the exon to promote its skipping.

Question 2

1. Post-translational modifications, such as phosphorylation and ubiquitination, which create functionally distinct protein states.
2. The use of alternative translation start codons (e.g., CUG instead of AUG) within a single mRNA transcript.
3. Alternative splicing of pre-mRNA from a single gene to generate multiple, distinct mRNA molecules. (correct answer)
4. Somatic recombination events in immune cells that generate a vast repertoire of antibodies and T-cell receptors.

Explanation: While all the listed mechanisms contribute to proteomic diversity, alternative splicing is the primary driver for generating a vast number of distinct protein primary sequences (isoforms) from a limited set of genes. It is estimated that over 95% of human multi-exon genes undergo alternative splicing. Post-translational modifications alter existing proteins but don't create new primary sequences. Alternative start codons are less common. Somatic recombination is a powerful mechanism but is restricted to a small subset of genes in specific cell types.

Question 3

1. A stable, truncated SRSF2 protein with a novel function is produced from the intron-retained transcript.
2. The intron-retained mRNA is targeted for degradation by the nonsense-mediated decay (NMD) pathway. (correct answer)
3. The retained intron is spliced out by a secondary, cytoplasmic splicing mechanism prior to translation.
4. The ribosome bypasses the premature stop codon, allowing for translation of a full-length protein with an insertion.

Explanation: The presence of a premature termination codon (PTC) more than 50-55 nucleotides upstream of the last exon-exon junction is a classic signal for the nonsense-mediated decay (NMD) pathway. This mRNA surveillance mechanism recognizes and degrades such transcripts to prevent the production of potentially harmful truncated proteins. Therefore, the intron-retained isoform will be degraded, leading to reduced levels of functional SRSF2 protein.

Question 4

1. The neuronal isoform has a higher basal level of kinase activity. (correct answer)
2. The neuronal isoform is catalytically inactive due to the misfolded SH3 domain.
3. The neuronal isoform is targeted for rapid degradation by the proteasome.
4. The neuronal isoform is localized to the nucleus instead of the plasma membrane.

Explanation: The stem states that the SH3 domain is involved in an inhibitory interaction. The insertion of the 6-amino acid sequence from the microexon disrupts this autoinhibition. Relieving inhibition leads to activation. Therefore, the neuronal isoform, which includes the microexon, will be more active at baseline compared to the non-neuronal isoform, which is more tightly autoinhibited.

Question 5

1. The presence of the unspliced intron physically tethers the transcript to the spliceosome and other nuclear matrix components. (correct answer)
2. A peptide encoded by the retained intron acts as a nuclear localization signal, importing the translating ribosome back into the nucleus.
3. The retained intron sequence is recognized by cytoplasmic exosomes, which rapidly degrade the transcript upon export.
4. The poly(A) tail cannot be added until all introns are removed, and the lack of a poly(A) tail prevents nuclear export.

Explanation: Splicing is tightly coupled to mRNA export. Transcripts that retain introns are often recognized as 'incompletely processed' by the cell's quality control machinery. They can remain associated with components of the spliceosome or other nuclear proteins, which effectively anchors them within the nucleus and prevents their interaction with the export machinery (like the TREX complex) that facilitates passage through the nuclear pore.

Question 6

1. The short 3' UTR isoform would produce higher levels of BDNF protein because it escapes miRNA-mediated repression. (correct answer)
2. The long 3' UTR isoform would produce higher levels of BDNF protein because it contains additional translational enhancer elements.
3. Both isoforms would produce identical amounts of protein, as the 3' UTR is not part of the coding sequence.
4. The choice of PAS alters the C-terminus of the BDNF protein, affecting its stability rather than its rate of translation.

Explanation: This process is known as alternative polyadenylation. The 3' UTR of an mRNA is a critical hub for post-transcriptional regulation, containing binding sites for microRNAs and RNA-binding proteins. By choosing a proximal polyadenylation signal, the resulting mRNA has a shorter 3' UTR and lacks the miRNA binding sites found in the longer version. This allows the shorter transcript to escape miRNA-mediated translational repression and/or degradation, generally leading to higher protein output compared to the longer isoform.

Question 7

1. A series of point mutations that weakened the 3' and 5' splice sites of exon 4, making its inclusion dependent on a neuronal-specific splicing enhancer. (correct answer)
2. A frameshift mutation within exon 4 that made the resulting protein toxic in all non-neuronal cells, selecting for its exclusion.
3. A synonymous mutation within exon 4 that created a strong exonic splicing silencer (ESS) recognized by a ubiquitous repressor protein.
4. An insertion of a retrotransposon into the promoter of gene Z, creating a new transcription start site used only in neurons.

Explanation: The transition from a constitutive to an alternatively spliced exon often involves the weakening of its splice sites. When the splice sites are weak, the core spliceosome requires assistance from enhancer elements and their associated factors (like SR proteins) for efficient recognition. If these helper factors are tissue-specific (e.g., expressed only in neurons), the exon's inclusion becomes restricted to that tissue. The other options are less likely: a toxic product would select against the gene, a ubiquitous silencer would cause skipping everywhere, and a promoter change affects transcription initiation, not splicing of a downstream exon.

Question 8

1. The kidney protein will be shorter than the liver protein by 33 amino acids, and their C-terminal sequences will be identical. (correct answer)
2. The kidney protein will be shorter than the liver protein, and a frameshift will result in a completely different C-terminal amino acid sequence.
3. No functional protein will be produced in kidney cells, as exon skipping invariably triggers nonsense-mediated decay.
4. The two proteins will have the same number of amino acids, but the kidney isoform will have a different internal sequence.

Explanation: The key information is the length of the skipped exon: 99 base pairs. Since this length is an exact multiple of 3 (99 / 3 = 33), skipping this exon will remove exactly 33 codons from the mRNA. This maintains the reading frame for all downstream exons. Therefore, the protein produced in the kidney (where the exon is skipped) will be 33 amino acids shorter than the liver protein, but the amino acid sequence encoded by the exons downstream of the cassette exon will be the same in both isoforms, resulting in identical C-termini.

Question 9

1. Alternative splicing that includes a single-nucleotide exon containing a guanine.
2. Allelic variation where the organism is heterozygous (CAG/CGG) at the GluR2 locus.
3. Post-transcriptional RNA editing of the CAG codon to CGG by an adenosine deaminase (ADAR) enzyme. (correct answer)
4. Somatic mutation of the GluR2 gene in a subset of neurons, creating cellular mosaicism.

Explanation: This is a classic example of RNA editing, not alternative splicing. The fact that the genomic DNA only contains the CAG sequence rules out allelic variation and somatic mutation as the primary source of the CGG variant found in mRNA. Alternative splicing involves the ligation of entire exons, not the alteration of a single nucleotide within an exon. The mechanism is post-transcriptional editing by ADAR enzymes, which deaminate adenosine (A) to inosine (I). In the context of the CAG codon, the A is converted to I. The translational machinery and reverse transcriptase (used for cDNA cloning) interpret inosine as guanosine (G), resulting in a CAG-to-CIG change in RNA, which is read as CGG.

Question 10

1. An increase in the total amount of FGFR2 transcription without a change in the IIIc isoform's predominance.
2. A shift in splicing from the proximal to the distal 3' splice site, increasing the proportion of the 'IIIb' isoform. (correct answer)
3. A shift in splicing from the distal to the proximal 3' splice site, reinforcing the production of the 'IIIc' isoform.
4. The complete skipping of exon 9 in both cell types due to interference with the core splicing machinery.

Explanation: ESRP1 is an epithelial-specific splicing factor that promotes the use of the distal 3' splice site to produce the IIIb isoform. Mesenchymal cells normally lack ESRP1 and default to the proximal site (IIIc isoform). Overexpressing ESRP1 in these cells introduces the factor that actively promotes the distal site. This will cause the splicing pattern to switch from the mesenchymal default to the epithelial pattern, resulting in a shift from IIIc to IIIb production.

Question 11

1. It allows for the production of one catalytically active isoform and one inactive isoform that acts as a competitive inhibitor.
2. It provides a mechanism for differential transcriptional regulation of glucokinase in response to the distinct metabolic signals of liver and beta-cells. (correct answer)
3. It ensures that the glucokinase protein has a different subcellular localization in the liver compared to beta-cells.
4. It is a form of gene dosage compensation, ensuring that both tissues produce an identical total amount of glucokinase enzyme.

Explanation: The use of alternative promoters is a key mechanism for achieving tissue-specific gene expression. By having separate promoters, the GCK gene can be regulated independently in the liver and pancreatic beta-cells, allowing each tissue to control glucokinase expression according to its specific physiological role and signaling environment (e.g., response to insulin vs. glucose). While the N-terminal difference can slightly alter kinetic properties, the primary consequence of having distinct promoters is differential transcriptional control.

Question 12

1. The mutation will result only in a single amino acid change (missense) but will not affect splicing.
2. The entire exon 12 will be skipped as the spliceosome cannot resolve the two competing 5' splice sites.
3. The new cryptic 5' splice site within exon 12 will be preferentially used, resulting in a truncated exon 12. (correct answer)
4. The mutation will prevent the splicing of intron 11 (upstream), causing its retention in the mature mRNA.

Explanation: The creation of a new, strong consensus 5' splice site (often called a cryptic splice site) within an exon can cause the spliceosome to recognize and use this site instead of the authentic one at the exon-intron boundary. This leads to the premature termination of the exon, resulting in a transcript with a truncated version of exon 12. This event almost always causes a frameshift, leading to a non-functional protein. A mutation that creates a strong splicing signal is very likely to affect splicing and not just be a simple missense mutation.

Question 13

1. The short 3' UTR isoform would produce higher levels of BDNF protein because it escapes miRNA-mediated repression. (correct answer)
2. The long 3' UTR isoform would produce higher levels of BDNF protein because it contains additional translational enhancer elements.
3. Both isoforms would produce identical amounts of protein, as the 3' UTR is not part of the coding sequence.
4. The choice of PAS alters the C-terminus of the BDNF protein, affecting its stability rather than its rate of translation.

Explanation: This process is known as alternative polyadenylation. The 3' UTR of an mRNA is a critical hub for post-transcriptional regulation, containing binding sites for microRNAs and RNA-binding proteins. By choosing a proximal polyadenylation signal, the resulting mRNA has a shorter 3' UTR and lacks the miRNA binding sites found in the longer version. This allows the shorter transcript to escape miRNA-mediated translational repression and/or degradation, generally leading to higher protein output compared to the longer isoform.

Question 14

1. The DNA of the Fas gene is permanently rearranged upon T-cell activation, deleting exon 6 in resting cells.
2. The overall transcription rate of the Fas gene increases in activated T-cells, which favors the inclusion of exon 6.
3. The expression level or activity of a key splicing regulatory protein is altered upon T-cell activation. (correct answer)
4. The core spliceosome machinery (U1, U2, U4/U6, U5 snRNPs) is fundamentally different in activated versus resting T-cells.

Explanation: Regulated, tissue- or cell-state-specific alternative splicing is primarily controlled by the differential expression or activity of trans-acting splicing factors (e.g., SR proteins, hnRNPs). T-cell activation involves a major signal transduction cascade that changes the expression of many genes, including those encoding splicing regulators. A change in the concentration or phosphorylation state of a specific factor that binds to regulatory elements near Fas exon 6 is the most direct cause of the observed splicing shift. The core splicing machinery is generally invariant.

Question 15

1. Post-translational modifications, such as phosphorylation and ubiquitination, which create functionally distinct protein states.
2. The use of alternative translation start codons (e.g., CUG instead of AUG) within a single mRNA transcript.
3. Alternative splicing of pre-mRNA from a single gene to generate multiple, distinct mRNA molecules. (correct answer)
4. Somatic recombination events in immune cells that generate a vast repertoire of antibodies and T-cell receptors.

Explanation: While all the listed mechanisms contribute to proteomic diversity, alternative splicing is the primary driver for generating a vast number of distinct protein primary sequences (isoforms) from a limited set of genes. It is estimated that over 95% of human multi-exon genes undergo alternative splicing. Post-translational modifications alter existing proteins but don't create new primary sequences. Alternative start codons are less common. Somatic recombination is a powerful mechanism but is restricted to a small subset of genes in specific cell types.

Question 16

1. The ASO uses the SMN2 transcript as a template to repair the SMN1 gene via reverse transcription.
2. The ASO sterically blocks a splicing repressor from binding to the ISS, thereby promoting the inclusion of exon 7. (correct answer)
3. The ASO binds to and activates the mutated ESE on exon 7, overriding the effect of the silencer.
4. The ASO directly binds to the faulty SMN protein produced from SMN2, restoring its normal function.

Explanation: Nusinersen is designed to interfere with the splicing regulation of SMN2. By binding to the ISS in intron 7, the ASO physically prevents repressor proteins (like hnRNPs) from binding to this silencing element. Removing this repressive signal tips the balance of splicing regulation in favor of exon 7 inclusion. This leads to an increased production of full-length, functional SMN protein from the SMN2 gene, compensating for the lack of SMN protein from the missing SMN1 gene.

Question 17

1. Overexpression of the hnRNP protein that binds to the ISS.
2. A mutation that strengthens the weak 5' splice site to a consensus sequence. (correct answer)
3. Deletion of the entire exon from the gene.
4. A mutation that disrupts the ESE sequence without changing the amino acid code.

Explanation: The inclusion level (50%) reflects a balance between positive and negative signals. To shift this balance strongly towards inclusion, one must either enhance a positive signal or remove a negative one. The strength of the core splice sites is a dominant factor. Changing a weak 5' splice site to a strong, consensus sequence would dramatically increase its recognition by the U1 snRNP component of the spliceosome, making its inclusion much more favorable and less dependent on enhancer elements. Overexpressing an ISS-binding repressor or disrupting the ESE would decrease inclusion. Deleting the exon is not a form of splicing modulation.

Question 18

1. An increase in the ratio of exon 3a-containing transcripts to exon 3b-containing transcripts. (correct answer)
2. A decrease in the ratio of exon 3a-containing transcripts to exon 3b-containing transcripts.
3. The exclusion of both exon 3a and exon 3b, leading to a direct ligation of the flanking exons.
4. A general decrease in the transcriptional rate of the Nrxn1 gene due to splicing feedback.

Explanation: hnRNP H acts as a splicing repressor for exon 3a by binding to an ISS. Knocking down this repressor protein with siRNA will alleviate the repression on exon 3a. As a result, the splicing machinery will be more likely to include exon 3a. Since exons 3a and 3b are mutually exclusive, the increased inclusion of 3a will come at the expense of 3b, thus increasing the ratio of 3a-containing to 3b-containing transcripts.

Question 19

1. It will cause the complete skipping of exon 16, potentially maintaining the reading frame depending on exon length.
2. It will have no effect on the mRNA sequence because the mutation is located within a non-coding intron.
3. It will cause the retention of the entire intron 15 sequence, leading to a frameshift and premature termination.
4. It will cause the inclusion of the 5 terminal nucleotides of intron 15 in the mature mRNA, leading to a frameshift. (correct answer)

Explanation: The mutation creates a new AG dinucleotide, which is the consensus sequence for a 3' splice site. Because this new (cryptic) site is upstream of the authentic site, the spliceosome may recognize and use it instead. This would result in the inclusion of the last 5 base pairs of intron 15 in the mature mRNA. The inclusion of 5 nucleotides, which is not a multiple of three, will shift the reading frame, likely leading to a premature stop codon and a truncated, non-functional dystrophin protein.

Question 20

1. A stable, truncated SRSF2 protein with a novel function is produced from the intron-retained transcript.
2. The intron-retained mRNA is targeted for degradation by the nonsense-mediated decay (NMD) pathway. (correct answer)
3. The retained intron is spliced out by a secondary, cytoplasmic splicing mechanism prior to translation.
4. The ribosome bypasses the premature stop codon, allowing for translation of a full-length protein with an insertion.

Explanation: The presence of a premature termination codon (PTC) more than 50-55 nucleotides upstream of the last exon-exon junction is a classic signal for the nonsense-mediated decay (NMD) pathway. This mRNA surveillance mechanism recognizes and degrades such transcripts to prevent the production of potentially harmful truncated proteins. Therefore, the intron-retained isoform will be degraded, leading to reduced levels of functional SRSF2 protein.