Question 1

How are the positions of codons determined in a genomic sequence, as illustrated in Figure 14-11?

Accepted Answer

By aligning cDNA sequences with the genomic DNA and identifying the regions that are translated into protein.

Question 2

Which method is primarily used to determine the positions of transcriptional regulatory elements in a genome, as shown in Figure 14-11?

Accepted Answer

By identifying conserved non-coding sequences upstream of the gene.

Question 3

How are expressed sequence tags (ESTs) helpful in genome annotation, as shown in Figure 14-12?

Accepted Answer

They help identify the locations of exons and gene boundaries by aligning with genomic DNA.

Question 4

Why are cDNA sequences more important for eukaryotic genome annotation than for bacterial genome annotation?

Accepted Answer

Eukaryotic genes contain introns and exons, so cDNA helps identify exon-intron boundaries.

Question 5

If you injected a reporter-gene construct containing the rat ortholog of the ISL1 ultraconserved element into fertilized mouse oocytes, what would you expect to observe in the developing embryo?

Accepted Answer

Reporter gene expression in specific tissues where the ultraconserved element acts as an enhancer.

Question 6

Based on the gene tree in Figure 14-17, did the duplication that created the A and B genes occur before or after the speciation of the common ancestor of frogs, humans, and mice?

Accepted Answer

Before speciation.

Question 7

According to the phylogenetic tree in Figure 14-18, are humans more closely related to mice or to dogs?

Accepted Answer

Mice.

Question 8

What do syntenic regions between mouse chromosome 11 and human chromosome 17, as shown in Figure 14-20, reveal about the genome of their last common ancestor?

Accepted Answer

Large blocks of genes were conserved, indicating shared ancestry and limited chromosomal rearrangement.

Question 9

Based on Figure 14-22, what percent of Denisovan ancestry would you predict to find in modern Western Europeans?

Accepted Answer

Approximately 0%.

Question 10

Which of the following is a direct application of comparing genome sequences between different species?

Accepted Answer

Providing evidence that predicted open reading frames represent real exons.

Question 11

In a BLAST search, you find four non-overlapping open reading frames within a 3 kb region, and two ESTs from a muscle cDNA library map to this region. Which question can you answer definitively?

Accepted Answer

Whether the gene is expressed in muscle tissue.

Question 12

Which of the following best describes an ultraconserved element in the genome?

Accepted Answer

A DNA sequence that is identical across multiple species and likely has an important regulatory function.

Question 13

Which of the following is NOT a function of expressed sequence tags (ESTs) in genome annotation?

Accepted Answer

Identifying the methylation status of DNA.

Question 14

Which equation would you use to calculate the percent identity between two aligned DNA sequences?

Accepted Answer

$$	ext{Percent Identity} = \frac{	ext{Number of Identical Matches}}{	ext{Total Number of Aligned Positions}} 	imes 100$$

Question 15

Which of the following best explains why cDNA is used to annotate eukaryotic genomes?

Accepted Answer

cDNA represents the spliced mRNA, allowing identification of exons and exon-intron boundaries.

Question 16

Which of the following is a likely outcome of a gene duplication event, as shown in Figure 14-17?

Accepted Answer

The creation of paralogous genes that may evolve new functions.

Question 17

Which of the following statements about synteny is correct?

Accepted Answer

Synteny refers to the conservation of blocks of gene order between different species.

Question 18

Which of the following is NOT a use of comparative genomics?

Accepted Answer

Determining the rate of translation of a specific mRNA.

Question 19

Which of the following best describes the relationship between orthologs and paralogs?

Accepted Answer

Orthologs are genes in different species that evolved from a common ancestral gene, while paralogs are genes related by duplication within a genome.

Genomes and Genomics: Key Concepts and Problem-Solving Guidance

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