Multiple Choice
1. The genomes of higher eukaryotes contain families of closely related genes. Which of the following statements offers the best explanation for the origin of these gene families:
A. were acquired through horizontal gene transfer from closely related organisms.
B. represent several rounds of whole-genome duplication.
C. arose from multiple rounds of gene duplication with subsequent divergence.
D. are the result of alternative processing patterns for introns and exons.
2. Exon shuffling facilitates gene evolution by:
A. making possible alternative splicing of introns and exons.
B. allowing entire domains to be rearranged within a protein.
C. leading to the evolution of much bigger proteins.
D. speeding up the evolution of new amino acid sequences.
3. The largest known protein, titin, contains 30,000 amino acids comprising about 120 domains arranged as shown here:
The best explanation for the origin of this structure would be:
A. the loss of stop codons.
B. a series of exon duplication.
C. fusion of many similar genes.
D. reshuffling of introns and exons.
4. A more complete representation of the genes for the globin subunits of hemoglobin is presented in the figure to the right.
It shows that a family of α-globin genes are located on chromosome 16. What is the most logical explanation for the different locations of the α-globin and β-globin genes?
A. After the first gene duplication occurred, one copy of the globin gene was translocated to a different chromosome.
B. The α-globin and β-globin genes evolved completely independent of each other.
C. After several rounds of gene duplication, much of the
β-globin gene locus was duplicated and moved to chromosome 16.
D. At some point in vertebrate evolution, either chromosome 11 or 16 was fully duplicated.
5. The α-globin gene family includes 5 pseudogenes. What is a pseudogene?
A. An unidentified gene located within a gene family
B. Mobile genetic elements that act like real genes.
C. A gene with the same sequence as another gene in the same organism.
D. A coding region that cannot be translated into a functional protein.
Biol 309 Question Bank Genome Evolution
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6. As shown in the antennapedia mutation of Drosophila , mutation of a single gene can dramatically affect developmental patterns. Why?
A. A single mutation can shift the reading frame of an entire gene.
B. Knocking out a tumor suppressor gene can lead to many other mutations.
C. Some genes regulate the expression of many other genes involved in development.
D. In eukaryotes, many genes are organized into large operons controlled by a single promoter.
7. Even though the glycolytic enzyme pyruvate kinase shows a high degree of homology between prokaryotes and eukaryotes, the eukaryotic gene is typically 5-times larger. Which of the one of the following statements would provide the best explanation for this difference?
A. The eukaryotic genes have many more domains.
B. The coding region of the eukaryotic genes is longer.
C. Insertion and expansion of introns has occurred in eukaryotes.
D. There has been a lengthening of the exons.
8. Horizontal gene transfer refers to:
A. movement of DNA between non-homologous chromosomes.
B. the evolutionary spread of a beneficial gene within a species.
C. the movement of mobile gene elements within the chromosome.
D. direct transfer of genes between unrelated organisms.
9. Why does cytosine methylation increase the rate of DNA mutation?
A. It leads to unwanted supercoiling of the chromosome.
B. Deamination yields a potentially unrepairable base mismatch.
C. DNA repair enzymes read methyl-cytosine as a mutation.
D. When the methyl group is removed, a uracil type base is created.
10. Traditionally, molecular biologists identify the position of an unknown gene within a DNA sequences by looking for an ‘open reading frame’ (ORF), which is:
A. an extended sequence that lacks stop codons.
B. a sequence downstream from a known promoter sequence.
C. a sequence from which a meaningful protein can be deduced.
D. a sequence with close homology to that of a gene in another organism.
11. A retrotransposon would be best described as
A. a mobile DNA element that can also reproduce as a virus.
B. an old-fashion transposon that is no longer in popular among geneticists.
C. a transposable element that passes through an RNA stage.
D. a transposable element that cuts and moves the DNA from one site to another.
True or false
1. In higher eukaryotes, only mutations to the germ-line cells will be transferred to the offspring.
2. Single nucleotide polymorphisms are relatively rare, single-base mutations.
3. Master regulator genes typically code for cell cycle checkpoint proteins.
4. Spread of antibiotic resistance between bacteria is often due to horizontal gene transfer.
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5. An “expressed sequence tag” is a base sequence derived from an mRNA used to locate the corresponding gene on the chromosomes.
6. DNA methylation evolved very early in the evolution of life.
7. A CpG island is a region high in un-methylated cytosine.
8. In general, housekeeping genes are not highly methylated.
9. Phylogenetic relationships between closely related species are easiest to interpret by comparing sequence homologies of highly conserved genes.
10. Alu and L1 are genetic elements that can be copied and move to different places in a chromosome
Matching:
1. Evolutionary mechanism
__ mutation to gene promoter
__ gene duplications
__ horizontal gene transfer
__ exon/intron shuffling
Possible consequence
A. a rearranged amino acid sequence within a protein
B. acquisition of entirely new metabolic capabilities
C. change to a specific amino acid in the coding region
D. a family of functionally related genes
E. a modified pattern of gene expression/reproession
2. The human genome consists of: (approximately)
___ % Reptitive sequences
___ % Non-repetitive sequences
___ % Gene coding sequences
___ % Mobile elements
___ % Non repetitive, non-coding sequences
Fill in, etc
1. All of the following would normally result in a silent mutation, EXCEPT:
A. Deletion of a stop codon.
B. Modification of the 3’ UTR of a gene.
C. A short deletion in the non-coding intergene region.
D. An altered base in the wobble position of a codon.
E. A short deletion in the center of an intron.
For each of the answers not selected above, give an example of a situation where that mutation could affect gene expression.
2. As described in a MC question above, humans possess 5 different genes for the β-globin subunit for hemoglobin, and 7 α-globin genes. This number of genes could be accounted for by _____ gene duplication events. The two functional α-globin genes have identical coding sequences, yet all of the β-globin genes have different sequences; how would you explain this difference?
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3. Comparison of DNA sequences can be used to determine ____________________ relationships between different species.
4. A gene that controls the expression of many other genes is called a
________________________ gene, and an example would be ______________________.
5. Coding sequences account for about ____% of the human genome, whereas mobile genetic elements and other repetitive DNA represents ____%.
6. A high density of methylation of cytosines will lead to ________________ of the genes in that region.
7. Most of the variation between individuals of a species occurs as point mutations that create single-nucleotide _____________________.
8. Transposable elements include a gene that encodes a __________________, an enzyme that mediates movement of a DNA. Retrotransposons, also require the action of an enzyme called
______________________ which creates DNA from an RNA template.
9. In the following sequence:
A. Circle all of the cytosines that would be potentially methylated:
3’- A G G T C C G T A A A G C T T A A G C C G G C T A T A -5’
5’- T C C A G G C A T T T C G A A T T C G G C C G A T A T -3’
B. Explain how does cytosine methylation leads to loss of cytosines in the genome. If all of the methyl-cytosines you circled were to lead to DNA mutations, how would the DNA sequence change?
10. Consider a protein (A) consisting of 3 copies of a particular domain called the ‘hst’ domain, and another protein (B) that contains 5 copies of that same domain. Proteins A and B have a different but related functions, and the amino acids of their hst domains show slight differences as well.
A. Which of these evolutionary processes most likely contributed to the evolution of these proteins? point mutations exon/intron shuffling exon duplication gene duplications horizontal gene movment intron expansion
B. Describe a plausible evolutionary sequence involving these mechanisms, that explains the origin of proteins ‘A’ and ‘B’ from a precursor protein with only one hst domain.
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11. Dong et al (J. Mol. Biol. (1996) 260, 649–663) compared the frequency of codon usage in mRNA translation to the abundance of the cognate tRNAs (tRNA concentration) in E. coli . A part of their Table 2 is shown to the right. (‘molecules per cell’ refers to number of each type of tRNA.)
A.
Do all types of tRNAs occur in the same abundance? Among the Leu tRNAs, which have the greatest and lowest abundances?
B.
How would you explain the functions of tRNAs labeled as “Met f”, vs
“Met m”?
C.
How would the abundance of a tRNA affect the rate of translation?
D.
Suppose you were to create a synthetic peptide with the sequence of:
Val -Leu-Ser-Thr
Which codon sequence would yield the fastest translation; which would yield the slowest?
E.
Which of the following base sequence changes would cause a misense mutation (change in amino acid), which would cause only a change in translation rate, and which would be essentially silent?
GUA

GUC : __________________________
ACC  ACU : __________________________
UGA

UGC : __________________________
In the chart to the right, the authors plotted the abundance (concentration) of each tRNA vs the frequency of its corresponding codon(s) in the E.coli
genome.
F.
Describe the relationship shown in the chart.
G.
Explain how this relationship helps to assure efficient rates of mRNA translation.
Biol 309 Question Bank Genome Evolution
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