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Inquiry Questions

Sequencing DNA. DNA is replicated, and fluorescent nucleotides that halt replication are randomly inserted into different sequences. An automated sequencer determines the base-pair sequence.
Why is it important to know whether or not your primer hybridizes to the template strand in the replication step?
Answer: If your primer copies the template strand, your result will be the sequence of the gene in the 5' to 3' direction. Remember, the newly synthesized sequence will be the complement of the template strand. The complement of the template strand is the coding (gene) sequence. You may want to look at Figure 15.8 and review transcription.
FIGURE 17.14
Corn crop productivity well below its genetic potential due to drought stress. Corn production can be limited by water deficiencies due to the drought that occurs during the growing season in dry climates. Global climate change may increase drought stress in areas where corn is the major crop.
The corn genome has not been sequenced. How could you use information from the rice genome sequence to try to improve drought tolerance in corn?
Answer: You may be able to take advantage of synteny between the rice and corn genome (see Figure 17.9). Let's assume that a drought tolerant gene has already been identified and mapped in rice. Using what is known about synteny between the rice and corn genomes, you could find the region of the corn genome that corresponds to the rice drought tolerance gene. This would narrow down the region of the corn genome that you might want to sequence to find your gene. A subsequent step might be to modify the corn gene that corresponds to the rice gene to see if you can increase drought tolerance.

Self Test

1). Researchers from many labs collaborated to determine the sequence of the human genome. How did labs avoid sequencing the same fragments multiple times?
    a). Each lab could isolate DNA from one particular chromosome to divide the sequencing projects.
    b). Using restriction fragment length polymorphisms, labs could ensure that they were not sequencing the same fragments.
    c). Using short sequences from their respective clones, sequence-tagged sites (STSs), researchers could check to make sure their fragments were not already being sequenced by another group.
    d). By comparing sequences from collaborating labs, researchers could ensure that they were not sequencing the same fragments.
Answer: c

2). Some of your friends are trying to make sense of their genome. To help them out, you draw an analogy between our chromosomes and the interstate highway system. In this analogy, every interstate represents a single chromosome. How could you describe the relationship between chromosomes and genes to your friends using this analogy?
    a). Every mile marker would represent a gene.
    b). Every town would represent a gene.
    c). Every state would represent a gene.
    d). Genes would be defined by the twists and turns on the highway.
Answer: b

3). Imagine that you broke your mother's favorite vase and had to reconstruct it from the shattered pieces. To do this, you would have to look for pieces with similar ends to join and then progressively glue every piece together. What sequencing strategy does this most closely represent?
    a). shotgun sequencing
    b). contig sequencing
    c). clone-by-clone sequencing
    d). manual sequencing
Answer: a

4). Knowing the sequence of an entire genome
    a). completes our understanding of every gene's function in the organism.
    b). allows us to predict the genetic cause of every disease in the organism.
    c). provides a template for constructing an artificial life-form.
    d). provides the raw data that can then be used to identify specific genes.
Answer: d

5). If you were to look at the sequence of an entire chromosome, how could you identify which segments might contain a gene?
    a). You could identify large protein-coding regions (open reading frames).
    b). You could look for a match with an expressed sequence tag (EST).
    c). You could look for consensus regulatory sequences that could initiate transcription.
    d). All of these strategies could be used to identify possible genes.
    e). It is impossible to predict genes from sequence data alone.
Answer: d

6). You have been hired to characterize the genome of a novel organism, Undergraduatus genomicus. After fully sequencing the 106 base-pairs in the genome, you predict that this organism has approximately 10,000 genes. You have a collaborator on this project, however, who has identified 20,000 different expressed sequence tags from this organism. How can you resolve this conflict?
    a). You suggest that your collaborator is an idiot who counted every gene twice!
    b). You suggest that your collaborator may have identified multiple isoforms of the same gene that could arise by alternative splicing.
    c). You fear that you may have underestimated the number of genes, because you forgot that the organism is diploid and you did not count both copies of every gene in your total.
    d). You only identified genes with open reading frames, but most genes do not encode proteins, so your number will be low.
Answer: b

7). In addition to coding sequences, our genome contains
    a). noncoding DNA within genes (i.e., introns).
    b). structural DNA involved in telomeres and centromeres.
    c). simple repetitive DNA.
    d). DNA from transposable elements that have jumped around in the genome.
    e). All of these are present in genomic DNA.
Answer: e

8). Natural variation in the length of tandem repeat sequences (VNTRs) found in the genome can be used to identify individual people by their DNA fingerprint. Why is this possible?
    a). The statement is not true; such variability prevents this from being a useful identification tool.
    b). The changes in repeat length change the DNA synthesis pattern, so the cell cycles have different lengths, making the cells of different people different sizes.
    c). The changes in repeat length occur very infrequently, so there is only one pattern that everybody shares.
    d). The changes in repeat length occur very frequently, so everybody has a unique pattern of different lengths when several repeats are examined.
Answer: d

Test Your Visual Understanding

1). From the information given in the above diagram, construct a contig map of the region presented.
Answer: Review figure 17.3. Your completed contig map should match that shown in Step 3 of figure 17.3.

Apply Your Knowledge

1). Every cell in your body contains the same genomic DNA, yet the proteome of different tissues is unique. How can you explain this?
Answer: The proteome is comprised of the proteins present in any given cell at a specific time.

2). Chromosomes are much like interstate highways. Develop this analogy by assigning a chromosomal counterpart to the following:
    a). the beginning and end of a particular highway
    b). towns along the highway
    c). stretches of highway that pass through wilderness
2a). These are analogous to the telomeres.
2b). These are analogous to genes.
2c). These are analogous to the intervening regions of DNA between genes.

3). If you are given a sample of DNA from an unknown organism, how could you determine the origin of the DNA sample?
Answer: Comparing the sequence from the unknown organism with sequences deposited in public sequence databases will allow you to identify likely relatives based on the degree of sequence identity.

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