Genomes and Their Evolution

What role does the Internet play in current genomics and proteomics research?

The best estimate is that the human genome contains fewer than 21,000 genes. However, there is evidence that human cells produce many more than 21,000 different polypeptides. What processes might account for this discrepancy?

Discuss the characteristics of mammalian genomes that make them larger than prokaryotic genomes.

Describe three examples of errors in cellular processes that lead to DNA duplications.

Describe three examples of errors in cellular processes that lead to DNA duplications

Would you expect the genome of the macaque (a monkey) to be more like that of a mouse or that of a human? Explain.

Bioinformatics includes all of the following except 

(A) using computer programs to align DNA sequences. 

(B) using DNA technology to combine DNA from two different sources in a test tube. 

(C) developing computer-based tools for genome analysis. 

(D) using mathematical tools to make sense of biological systems.

Explain the advantage of the systems biology approach to studying cancer versus the approach of studying a single gene at a time.

The Genomes Online Database (GOLD) website of the Joint Genome Institute has information about genome sequencing projects. Scroll through the page at https:// gold.jgi.doe.gov/statistics and describe the information you find. What percent of bacterial genome projects have medical relevance?

VISUAL SKILLS Which of the three mechanisms described in Figures 21.8 and 21.9 result(s) in a copy remaining at the original site as well as a copy appearing in a new location?

Explain how multiple exons might have arisen in the ancestral EGF and fibronectin genes shown on the left side of Figure 21.16.

The earlier that two genes arose from a duplicated gene, the more their nucleotide sequences can have diverged, which may result in amino acid differences in the protein products. (a) Based on that premise, identify which two genes are most divergent from each other. What is the percent amino acid identity between their polypeptides? (b) Using the same approach, identify which two globin genes are the most recently duplicated. What is the percent identity between them?

DNA sequences called homeoboxes help homeotic genes in animals direct development. Given that they are common to flies and mice, explain why these animals are so different.

Homeotic genes 

(A) encode transcription factors that control the expression of genes responsible for specific anatomical structures.

(B) are found only in Drosophila and other arthropods.

(C) are the only genes that contain the homeobox domain.

(D) encode proteins that form anatomical structures in the fly.

The ENCODE pilot project found that at least 75% of the genome is transcribed into RNAs, far more than could be accounted for by protein-coding genes. Review Concepts 17.3 and 18.3 and suggest some roles that these RNAs might play.

WHAT IF? What evolutionary processes might account for prokaryotes having smaller genomes than eukaryotes?

Contrast the organizations of the rRNA gene family and the globin gene families. For each, explain how the existence of a family of genes benefits the organism.

The model of globin gene evolution shown in Figure 21.14 suggests that an ancestral gene is duplicated and mutated to become α- and β-globin genes, and then each one was further duplicated and mutated. What features of the data set to support the model?

What are three ways that transposable elements are thought to contribute to genome evolution?

WHAT IF? There are three times as many Alu elements in the human genome as in the chimpanzee genome. How do you think these extra Alu elements arose in the human genome? Propose a role they might have played in the divergence of these two species.

Two eukaryotic proteins have one domain in common but are otherwise very different. Which of the following processes is most likely to have contributed to this similarity?

(A) Gene duplication 

(B) Alternative splicing 

(C) Exon shuffling 

(D) Random point mutations

In Concept 20.2, you learned about genome-wide association studies. Explain how these studies use the systems biology approach.

Assign each DNA segment at the top of Figure 18.8 to a sector in the pie chart in Figure 21.6.

Make an ordered list of all the percent identity values from the table, starting with 100% at the top. Next to each number write the globin pair(s) with that percent identity value. Use one color for the globins from the α family and a different color for the globins from the β family. (a) Compare the order of pairs on your list with their positions in the model shown in Figure 21.14. Does the order of pairs describe the same relative “closeness” of globin family members seen in the model? (b) Compare the percent identity values for pairs within the α or β group to the values for between-group pairs.

In 2005, Icelandic scientists reported finding a large chromosomal inversion present in 20% of northern Europeans, and they noted that Icelandic women with this inversion had significantly more children than women without it. What would you expect to happen to the frequency of this inversion in the Icelandic population in future generations?

Below are the amino acid sequences (using the single-letter code; see Figure 5.14) of four short segments of the FOXP2 protein from six species: chimpanzee (C), orangutan (O), gorilla (G), rhesus macaque (R), mouse (M), and human (H). These segments contain all of the amino acid differences between the FOXP2 proteins of these species.

Use a highlighter to color any amino acid that varies among the species. (Color that amino acid in all sequences.) 

1. The C, G, R sequences are identical. Identify which lines correspond to those sequences.
2. The H sequence differs from that of the C, G, R species at two amino acids. Underline the two differences in the H sequence. 
3. The O sequence differs from the C, G, R sequences at one amino acid (having V instead of A) and from the H sequence at three amino acids. Identify the O sequence. 
4.  In the M sequence, circle the amino acid(s) that differ from the C, G, R sequences, and draw a square around those that differ from the H sequence. 
5. Primates and rodents diverged between 60 and 100 million years ago, and chimpanzees and humans about 6 million years ago. Compare the amino acid differences between the mouse and the C, G, R species with those between the human and the C, G, R species. What can you conclude?

Genes important in the embryonic development of animals, such as homeobox-containing genes, have been relatively well conserved during evolution; that is, they are more similar among different species than are many other genes. Explain why this is.

The scientists mapping the SNPs in the human genome noticed that groups of SNPs tended to be inherited together, in blocks known as haplotypes, ranging in length from 5,000 to 200,000 base pairs. There are as few as four or five commonly occurring combinations of SNPs per haplotype. Integrating what you’ve learned throughout this chapter and this unit, propose an explanation for this observation.

The continuity of life is based on heritable information in the form of DNA. In a short essay (100–150 words), explain how mutations in protein-coding genes and regulatory DNA contribute to Evolution.

Insects have three thoracic (trunk) segments. While researchers have found insect fossils with pairs of wings on all three segments, modern insects have wings or related structures on only the second and third segment. It turns out that in modern insects, Hox gene products act to inhibit wing formation on the first segment. The treehopper insect (above) is somewhat of an exception. In addition to having wings on its second segment, the treehopper’s first segment has an ornate helmet that resembles a set of thorns, which a recent study has found to be a modified, fused pair of “wings.” The thorn-like structure helps to camouflage the treehopper in tree branches, thus reducing its risk of predation. Explain how changes in gene regulation could have led to the evolution of such a structure

Describe the whole-genome shotgun approach.