Mining Genomes

Introduction to BLAST and BLAST Searching

This exercise casts you in the role of biological detective, trying to figure out the functions of newely discovered genes. The simplest way to determine what is encoded by new sequences is to compare them with information already in the databases by using

BLAST (Basic Local Alignment Search Tools). You will use the National Center for Biotechnology Information (NCBI) Web site to explore some of the strengths and weaknesses of this powerful approach.

COMPREHENSION QUESTIONS^

* 1. How does supercoiling arise? What is the difference between positive and negative supercoiling? 2. What functions does supercoiling serve for the cell?

* 3. Describe the composition and structure of the nucleosome.

How do core particles differ from chromatosomes?

4. Describe in steps how the double helix of DNA, which is 2 nm in width, gives rise to a chromosome that is 700 nm in width.

5. What are polytene chromosomes and chromosomal puffs?

* 6. Describe the function and molecular structure of the centromere.

* 7. Describe the function and molecular structure of a telomere.

8. What is the C value of an organism?

9. What is a C0t curve? Explain how C0t curves of DNA provide evidence for the existence of repetitive DNA in eukaryotic cells.

*10. Describe the different types of DNA sequences that exist in eukaryotes.

*11. What general characteristics are found in many transposable elements? Describe the differences between replicative and nonreplicative transposition.

*12. What is a retrotransposon and how does it move?

*13. Describe the process of replicative transposition through DNA intermediates. What enzymes are required?

*14. Draw and label the structure of a typical insertion sequence.

15. Draw and label the structure of a typical composite transposon in bacteria.

How are composite transposons and retrotransposons alike and how are they different?

Explain how Ac and Ds elements produce variegated corn kernels.

18. Briefly explain hybrid dysgenesis and how P elements lead to hybrid dysgenesis.

*19. Briefly summarize three hypotheses for the widespread occurrence of transposable elements.

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