1. Genomes and Their Evolution21
Genomes and Their Evolution
Clicker Questions by Tara Stoulig

2. Which of these criteria have been used in selecting species whose genomes have been sequenced?
The species should be relevant for human health or well-being.
The species should have a relatively small genome.
The species should have an important ecological role.
The species may yield key evolutionary insights.
all of the above
Answer: e
This is a good discussion question.

3. Which of these criteria have been used in selecting species whose genomes have been sequenced?
The species should be relevant for human health or well-being.
The species should have a relatively small genome.
The species should have an important ecological role.
The species may yield key evolutionary insights.
all of the above 3

4. Which of the following represent the shotgun approach to gene sequencing? (Choose more than one answer.)
Sequence fragments of DNA.
Purify mRNA; make DNA.
Use a computer to align the overlap regions of DNA fragments.
Combine DNA fragments with DNA ligase.
Use a computer to clone genes.
Answer: a, c 4

5. Which of the following represent the shotgun approach to gene sequencing? (Choose more than one answer.)
Sequence fragments of DNA.
Purify mRNA; make DNA.
Use a computer to align the overlap regions of DNA fragments.
Combine DNA fragments with DNA ligase.
Use a computer to clone genes. 5

6. A group of scientists is interested in analyzing the genomes of the various microbial species found in the Dead Sea. If they collect a sample from the Dead Sea and sequence the DNA in the sample, they are using the _______ approach.
dideoxy chain termination
whole-genome shotgun
sequencing by synthesis
metagenomics
transformation
Answer: d 6

7. A group of scientists is interested in analyzing the genomes of the various microbial species found in the Dead Sea. If they collect a sample from the Dead Sea and sequence the DNA in the sample, they are using the _______ approach.
dideoxy chain termination
whole-genome shotgun
sequencing by synthesis
metagenomics
transformation 7

8. Which of the following is the known size range of genomes?
1–2900 Mb
1500–40,000 Mb
100–580,000 Mb
1–149,000 Mb
100–200,000 Mb
Answer: d
Concept 18.3 8

9. Which of the following is the known size range of genomes?
1–2900 Mb
1500–40,000 Mb
100–580,000 Mb
1–149,000 Mb
100–200,000 Mb 9

10. Proteins are made up of domains that are associated with a certain function. Different proteins have similar domains. If I have a partial nucleotide sequence for a domain in my unknown protein, I can use this to search for similar known sequences. Which of the following could help me guess the function of my unknown protein?
Compare the unknown protein amino acid sequence with known amino acid sequences.
View all three-dimensional shapes of known proteins, looking for a similarity.
Use a computer program for comparing primers for PCR.
Use a computer program to predict the amino acid sequence.
Use BLAST to compare the unknown sequence to known sequences.
Answer: e
Concept 18.2 10

11. Proteins are made up of domains that are associated with a certain function. Different proteins have similar domains. If I have a partial nucleotide sequence for a domain in my unknown protein, I can use this to search for similar known sequences. Which of the following could help me guess the function of my unknown protein?
Compare the unknown protein amino acid sequence with known amino acid sequences.
View all three-dimensional shapes of known proteins, looking for a similarity.
Use a computer program for comparing primers for PCR.
Use a computer program to predict the amino acid sequence.
Use BLAST to compare the unknown sequence to known sequences. 11

12. Given the high degree of sequence similarity between the human and chimpanzee genomes, what might be the most important factor that drove hominid evolution in the past 6 million years?
small changes in proteins that affect their function or activity in important ways
changes in regulatory sequences that affect the timing and level of expression of genes
evolution of a few novel protein-coding genes that play key roles in neural development
gene duplication events that selectively expanded a set of genes favoring development of human traits
all of the above
Answer: e
Students could be challenged to either develop ways to test one of these hypotheses or search the literature to find evidence or examples to support one of these hypotheses. 12

13. Given the high degree of sequence similarity between the human and chimpanzee genomes, what might be the most important factor that drove hominid evolution in the past 6 million years?
small changes in proteins that affect their function or activity in important ways
changes in regulatory sequences that affect the timing and level of expression of genes
evolution of a few novel protein-coding genes that play key roles in neural development
gene duplication events that selectively expanded a set of genes favoring development of human traits
all of the above 13

14. What experimental technique could be used to test the hypothesis that humans and chimpanzees have significantly different patterns of gene expression?
comparison of promoter DNA sequences
hybridization of RNA from various human and chimpanzee tissues to a DNA microarray containing all 21,000 human genes
analysis of single nucleotide polymorphisms (SNPs) in human and chimpanzee populations
comparison of human disease alleles to chimpanzee homologs
Answer: b 14

15. What experimental technique could be used to test the hypothesis that humans and chimpanzees have significantly different patterns of gene expression?
comparison of promoter DNA sequences
hybridization of RNA from various human and chimpanzee tissues to a DNA microarray containing all 21,000 human genes
analysis of single nucleotide polymorphisms (SNPs) in human and chimpanzee populations
comparison of human disease alleles to chimpanzee homologs 15

16. Most of the human genome sequence is made up of exons from different genes.
True
False
Answer: false 16

17. Most of the human genome sequence is made up of exons from different genes.
True
False
Answer: false 17

18. Most of the human genome is made up of
introns.
repeats of DNA sections (e.g., Alu).
nonrepeated noncoding DNA.
promoters and regulatory sequences such as enhancers.
repeats of DNA that do not jump to different chromosome locations.
Answer: b 18

19. Most of the human genome is made up of
introns.
repeats of DNA sections (e.g., Alu).
nonrepeated noncoding DNA.
promoters and regulatory sequences such as enhancers.
repeats of DNA that do not jump to different chromosome locations. 19

20. Many pseudogenes (which no longer produce functional proteins) in vertebrate genomes lack introns. What process may account for such pseudogenes? Remember mRNA processing.
gene duplication followed by DNA splicing to remove introns
recombination between duplicated copies of genes
reverse transcription of a processed mRNA and insertion of the cDNA copy to a new chromosomal location
duplication events that involve just the exons
unequal crossing over between duplicated copies of genes
Answer: c
Concept 18.4 20

21. Many pseudogenes (which no longer produce functional proteins) in vertebrate genomes lack introns. What process may account for such pseudogenes? Remember mRNA processing.
gene duplication followed by DNA splicing to remove introns
recombination between duplicated copies of genes
reverse transcription of a processed mRNA and insertion of the cDNA copy to a new chromosomal location
duplication events that involve just the exons
unequal crossing over between duplicated copies of genes 21

22. The human genome has about 7,000 Alu elements not found in chimpanzees, whereas the chimpanzee genome has about 2,300 Alu elements not found in humans. How might the Alu elements influence human evolution?
They may affect levels of expression of adjacent genes.
They may create new alternative splicing variants of a protein.
They may promote recombination events that induce chromosomal rearrangements, deletions, and duplications.
all of the above
none of the above: Alu elements are “junk” DNA
Answer: d 22

23. The human genome has about 7,000 Alu elements not found in chimpanzees, whereas the chimpanzee genome has about 2,300 Alu elements not found in humans. How might the Alu elements influence human evolution?
They may affect levels of expression of adjacent genes.
They may create new alternative splicing variants of a protein.
They may promote recombination events that induce chromosomal rearrangements, deletions, and duplications.
all of the above
none of the above: Alu elements are “junk” DNA 23

24. To build a model of the evolutionary history of the globin genes, researchers compared the amino acid sequences of the polypeptides they encode. In this exercise, you will analyze comparisons of the amino acid sequences of globin polypeptides to see how scientists shed light on their evolutionary relationships.
Scientists obtained the DNA sequences for each of the eight globin genes and “translated” them into amino acid sequences. They then used a computer program to align the sequences and calculate a percent identity value for each pair. The percent identity reflects the number of positions with identical amino acids relative to the total number of amino acids in a globin polypeptide.
The table to the right shows an example of a pairwise alignment--that of the α1-globin (alpha- 1 globin) and ζ-globin (zeta globin) amino acid sequences—using the standard single-letter symbols for amino acids. To the left of each line of amino acid sequence is the number of the first amino acid in that line.

25. The percent identity value for the α1- and ζ-globin amino acid sequences was calculated by counting the number of matching amino acids (87), dividing by the total number of amino acid positions (143), and then multiplying by 100. This resulted in a 61% identity value for the α1- ζ pair.

26. The more recently that two genes arose from a single duplicated gene, the more identical their nucleotides are, which results in few amino acid differences in the protein products. Based on that premise, identify which two globin genes are the most recently duplicated. What is the percent amino acid identity between them?
β and ζ, with 38% amino acid identity
δ and , with 73% amino acid identity
Aγ and Gγ, with 99% amino acid identity
α1 and α2, with 100% amino acid identity
Answer: d

27. The more recently that two genes arose from a single duplicated gene, the more identical their nucleotides are, which results in few amino acid differences in the protein products. Based on that premise, identify which two globin genes are the most recently duplicated. What is the percent amino acid identity between them?
β and ζ, with 38% amino acid identity
δ and , with 73% amino acid identity
Aγ and Gγ, with 99% amino acid identity
α1 and α2, with 100% amino acid identity

28. The earlier that two genes arose from a single duplicated gene, the more divergent their nucleotides can become, which may result in amino acid differences in the protein products. Which two globin genes are most divergent from each other? What is the percent amino acid identity between them?
β and ζ, with 38% amino acid identity
α2 and ε, with 39% amino acid identity
α1 and Gγ, with 42% amino acid identity
α1 and α2, with 100% amino acid identity
Answer: A

29. The earlier that two genes arose from a single duplicated gene, the more divergent their nucleotides can become, which may result in amino acid differences in the protein products. Which two globin genes are most divergent from each other? What is the percent amino acid identity between them?
β and ζ, with 38% amino acid identity
α2 and ε, with 39% amino acid identity
α1 and Gγ, with 42% amino acid identity
α1 and α2 , with 100% amino acid identity