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Molecular Biology Questions

Describe how transposition can give rise to speckled maize kernels.

Breaking of the chromosome especially the short arm of chromosome 9 during transposition in maize plants yields purple-spotted kernels. An Activator (Ac) gene from the long arm chromosome controls the Dissociator (Ds) gene on the short arm chromosome. A colored gene on the dissociated short arm chromosome produces the purple or speckled maize kernels, which is passed on during cell division.

Compare and contrast the mechanism of retrovirus replication and retrotransposon transposition.

A common ground for both mechanisms is the involvement of enzyme reverse transcriptase or RNA-dependent DNA polymerase during replication and transposition. In retrovirus replication, new viral DNA strands are made from viral RNA through reverse transcriptase. Contemporary viral DNA strand or cDNA is then synthesized, which is then used to make viral RNA strands through host-cell RNA polymerase. In retrotransposon transposition, there is interaction of transposable element with the DNA target site of cleavage. One DNA strand acts a primer for DNA polymerase, and the reverse transcriptase replicates RNA into DNA. cDNA retrotransposon copy should be converted to a double stranded element to complete the transposition process.

3. What is the Alu transposable element?

The Alu transposable element is a type of jumping gene found only in primates. They are separate DNA sequences capable of self-replicating by making copies in protein-coding genes. They are significant elements in molecular genetics and forensic uses as well as human evolution (Fedoroff Web).

4. Describe the mechanism of Alu TE integration (into the genome)

The first step involves the insertion of Alu TE into the intron of a gene. The Alu TE trigger mutations in the gene causing the formation of active splice sites on one side of the Alu. This makes the Alu TE an exon, integrating it into the mRNA genome (Pray Web).

5. Describe the outcome/result when Alu TE is integrated into the coding region of a gene

When Alu TE is incorporated into the coding region of a gene, it is spliced out of the mRNA as it acts as a part of an intron. Exonization process then takes place where the Alu TE is converted into an exon in the final copy of the mRNA.

6. Describe the outcome/result when Alu TE is integrated into the promoter region of a gene

Once the Alu element is inserted into a promoter region, reverse transcriptase converts it into a double-stranded DNA because it has no ability for self-replication. They then rely on a transposon called L1 for replication and integration into new chromosomal positions (McDonald 159).

7. Describe how Alu TE serves as recombination hot spots.

Alu TE are only found in primates and they are the only elements used in molecular biology to identify human DNA sequences present in other animals through marker-rescue experiments. Because of their scarcity, they are hot spots in recombination as they are used in joining various genetic materials from different organisms.

8. Describe how Alu recombination gives rise to inherited human diseases such as insulin-resistant diabetes type II.

Alu elements have played significant roles in evolution through gene combinations or emergence of new genes. The existing genes have advanced features added onto them through the process of exonization. This process causes mutations in the genes, for example, mutations occurring in genes responsible for diabetes type II will give rise to a new type of diabetes that has resistance to insulin.

Works Cited

Fedoroff, Nina. “Transposable Elements, Epigenetics, and Genome Evolution.” Science 2012: 338. 6108 (2012): 758-767 DOI: 10.1126/science.338.6108.758

McDonald, John. Transposable Elements and Genome Evolution: Volume 1 of Georgia genetics review. New York: Springer, 2000. Print.

Pray, Leslie. Functions and Utility of Alu Jumping Genes. Nature Education, 2008. Web. 26 Oct. 2013.