Question 1

Which of the following best describes the mechanism by which Alu elements are retrotransposed in the human genome?

Accepted Answer

Alu elements use the ORF2 protein from LINE-1 elements for target-primed reverse transcription.

Question 2

What is the primary structural feature at the 3' end of Alu elements that is essential for their retrotransposition?

Accepted Answer

A long A-tail

Question 3

Which proteins are essential for the formation of Alu ribonucleoprotein particles, facilitating their retrotransposition?

Accepted Answer

SRP9/14 and polyA-binding protein (PABP)

Question 4

Alu elements are most commonly found in which regions of the human genome?

Accepted Answer

Gene-rich regions

Question 5

Which of the following diseases is associated with Alu-mediated insertional mutagenesis in the NF1 gene?

Accepted Answer

Neurofibromatosis

Question 6

How do Alu elements contribute to alternative splicing in human genes?

Accepted Answer

By introducing new exons (exonization) that may require ADAR editing for proper splicing

Question 7

Which enzyme is responsible for editing Alu-containing RNAs, and what is the consequence of this editing?

Accepted Answer

ADAR; conversion of adenosine to inosine, potentially leading to nuclear retention or alternative splicing

Question 8

A new Alu insertion is detected in the BRCA2 gene of a patient. Which of the following is the most likely consequence?

Accepted Answer

Disruption of coding sequence or splicing, increasing risk for breast cancer

Question 9

Which of the following best explains why most Alu elements in the human genome are no longer active?

Accepted Answer

They accumulate mutations and lose their A-tail, reducing retrotransposition capability.

Question 10

Which process is illustrated by the formation of direct repeats flanking Alu elements at their insertion sites?

Accepted Answer

Target-primed reverse transcription

Question 11

A researcher finds that a particular Alu element has a sequence nearly identical to the consensus and a long A-tail. What can be inferred about this element?

Accepted Answer

It is likely to be retrotranspositionally active.

Question 12

Which of the following best describes the role of methylation in Alu element regulation?

Accepted Answer

Methylation generally represses Alu transcription, but is reduced in tumors, potentially increasing Alu expression.

Question 13

Which of the following is a plausible outcome of Alu-mediated non-allelic homologous recombination?

Accepted Answer

Large genomic deletions, duplications, or inversions

Question 14

What is the significance of Alu elements being found in both orientations within primary nuclear transcripts (hnRNAs) and mature mRNAs?

Accepted Answer

It allows for the formation of double-stranded RNA regions, which can be substrates for ADAR editing.

Question 15

Which of the following best explains why authentic Alu RNAs are rare and difficult to detect in cells?

Accepted Answer

Most Alu sequences in transcripts are produced by RNA polymerase II and are not involved in retrotransposition.

Question 16

A patient with hemophilia B is found to have an Alu insertion in the HEMB (IX) gene. Which Alu subfamilies are most likely involved?

Accepted Answer

Ya5 and Yb8

Question 17

Which of the following equations best represents the probability $$P of a $$new Alu insertion occurring in a human birth, given that there is approximately one new insert per 20 births?

Accepted Answer

$$P = \frac{1}{20}$$

Question 18

Which of the following is a direct consequence of Alu exonization in a gene?

Accepted Answer

Introduction of a novel exon, potentially altering the protein product

Question 19

Which of the following best explains why Alu elements are considered a major force in primate genome evolution?

Accepted Answer

Their high copy number and frequent insertion/recombination events drive genetic diversity and genome instability.

Question 20

A mutation shortens the A-tail of an Alu element. What is the most likely effect on its retrotransposition activity?

Accepted Answer

Retrotransposition activity will decrease.

Transposable Elements: Alu Elements in the Human Genome

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