Ch. 15 - Gene Mutation, DNA Repair, and Transposition

Problem 16

Chapter 15, Problem 16

Contrast the structure of SINE and LINE DNA sequences. Why are LINEs referred to as retrotransposons?

Verified step by step guidance

Step 1: Understand the basic definitions of SINEs and LINEs. SINEs (Short Interspersed Nuclear Elements) and LINEs (Long Interspersed Nuclear Elements) are both types of non-coding DNA sequences that are repeated many times throughout the genome.

Step 2: Compare the structure of SINEs and LINEs. SINEs are typically shorter, around 100-300 base pairs in length, and do not encode proteins. LINEs are longer, usually over 1,000 base pairs, and often contain two open reading frames (ORFs) that encode proteins necessary for their own retrotransposition.

Step 3: Explore the mechanism of retrotransposition. LINEs are referred to as retrotransposons because they can copy and paste themselves into new locations in the genome through an RNA intermediate. This process involves transcription into RNA, reverse transcription into DNA, and integration into a new genomic location.

Step 4: Discuss the role of reverse transcriptase. LINEs encode a reverse transcriptase enzyme, which is crucial for converting their RNA back into DNA, allowing them to integrate into the genome. SINEs, lacking this enzyme, rely on the machinery of LINEs for their own retrotransposition.

Step 5: Summarize the functional implications. The ability of LINEs to move within the genome can lead to genetic variation and has implications for genome evolution and stability. SINEs, while not encoding proteins themselves, can also contribute to genetic diversity by utilizing LINE machinery.

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Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

SINE and LINE Sequences

SINE (Short Interspersed Nuclear Elements) and LINE (Long Interspersed Nuclear Elements) are two types of transposable elements found in eukaryotic genomes. SINEs are typically less than 500 base pairs long and do not encode proteins, relying on other elements for their transposition. In contrast, LINEs are longer, usually over 1,000 base pairs, and can encode proteins necessary for their own mobilization, including reverse transcriptase.

Retrotransposons

Retrotransposons are a class of transposable elements that replicate through an RNA intermediate. LINEs are classified as retrotransposons because they transpose via a process called retrotransposition, where their RNA is reverse transcribed back into DNA and integrated into new genomic locations. This mechanism allows them to increase their copy number within the genome.

Transposition Mechanisms

Transposition refers to the process by which transposable elements move within the genome. SINEs typically use a 'copy-and-paste' mechanism facilitated by the enzymatic activity of LINE-encoded proteins, while LINEs can utilize their own reverse transcriptase to replicate and insert themselves into new sites. Understanding these mechanisms is crucial for studying genome evolution and the role of transposable elements in genetic diversity.

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Textbook Question

The family of a sixth-grade boy in Palo Alto, California, was informed by school administrators that he would have to transfer out of his middle school because they believed his mutation of the CFTR gene, which does not produce any symptoms associated with cystic fibrosis, posed a risk to other students at the school who have cystic fibrosis. After missing 11 days of school, a settlement was reached to have the boy return to school. What ethical problems might you associate with this example?

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Textbook Question

A significant number of mutations in the HBB gene that cause human β-thalassemia occur within introns or in upstream noncoding sequences. Explain why mutations in these regions often lead to severe disease, although they may not directly alter the coding regions of the gene.

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Textbook Question

Dominant mutations can be categorized according to whether they increase or decrease the overall activity of a gene or gene product. Although a loss-of-function mutation (a mutation that inactivates the gene product) is usually recessive, for some genes, one dose of the normal gene product, encoded by the normal allele, is not sufficient to produce a normal phenotype. In this case, a loss-of-function mutation in the gene will be dominant, and the gene is said to be haploinsufficient. A second category of dominant mutation is the gain-of-function mutation, which results in a new activity or increased activity or expression of a gene or gene product. The gene therapy technique currently being used in clinical trials involves the 'addition' to somatic cells of a normal copy of a gene. In other words, a normal copy of the gene is inserted into the genome of the mutant somatic cell, but the mutated copy of the gene is not removed or replaced. Will this strategy work for either of the two aforementioned types of dominant mutations?

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Textbook Question

In 2013 the actress Angelina Jolie elected to have prophylactic double-mastectomy surgery to prevent breast cancer based on a positive test for mutation of the BRCA1 gene. What are some potential positive and negative consequences of this high-profile example of acting on the results of a genetic test?

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Textbook Question

Describe how the Ames test screens for potential environmental mutagens. Why is it thought that a compound that tests positively in the Ames test may also be carcinogenic?

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Textbook Question

It has been shown that infectious agents such as viruses often exert a dramatic effect on their host cell's genome architecture. In many cases, viruses induce methylation of host DNA sequences in order to enhance their infectivity. What specific host gene functions would you consider as strong candidates for such methylation by infecting viruses?

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