Deck 10: Genome Evolution

Question 1

What is the source of DNA acquired by a bacterial cell during conjugation?

A) the environment
B) bacteriophage and other viral pathogens
C) other bacteria
D) the eukaryotic host cell

Answer 1

C

Question 2

Which of the following tends to contribute to an overall increase in genome size over evolutionary time?

A) small genetic elements capable of self-catalyzing their movement
B) selection on cell size
C) selection on replication speed
D) the cell's energetic efficiency as it relates to cell volume

Answer 2

A

Question 3

Telomeres are necessary because

A) without them, the ends of a chromosome would grow by approximately 100 base pairs with each replication.
B) Okazaki fragments no longer need a binding region.
C) they aid in the replication of prokaryotic genomes.
D) without them, the ends of a chromosome would shorten by approximately 100 base pairs with each replication.

Answer 3

D

Question 4

Eukaryotic genome size is

A) tightly correlated with organismal complexity.
B) not well correlated with organismal complexity.
C) approximately the same in all eukaryotes.
D) typically smaller than prokaryotic genome size.

Question 5

Bacteriophage MS2 was the first organism to have its entire genome sequenced, and this was facilitated by

A) the bacteriophage's long and complex genome.
B) the bacteriophage's exceptionally small genome.
C) previous sequencing of bacterial genomes.
D) the bacteriophage's role as a human pathogen.

Question 6

The exon theory of genes states that

A) genomes consist solely of exons.
B) introns are deleterious and are purged from the genome.
C) introns lead to recombination errors.
D) many current genes arose through the rearrangement of exons into new combinations.

Question 7

Transposons can be deleterious to a host genome because they can

A) translate a coding sequence into protein.
B) act as regulatory elements.
C) prevent beneficial mutations.
D) cause recombination errors.

Question 8

A researcher discovers a new prokaryote whose genome is ~8 Mb in size. Based on the figure shown, what type of organism is this likely to be?

A) free-living bacterium
B) obligate parasitic bacterium
C) obligate symbiontic bacterium
D) Archaean

Question 9

Which of the following is NOT a type of horizontal gene transfer?

A) transcription
B) transduction
C) transformation
D) conjugation

Question 10

Which of the following statements regarding mutational bias and its influence on GC content is true?

A) G is more likely to mutate to A.
B) C is less likely to mutate to T.
C) G is more likely to mutate to C.
D) A is more likely to mutate to T.

Question 11

For the syntenic dot plot below, what does the shorter line in between and perpendicular to the two longer lines represent?

A) matching gene sequences
B) a chromosomal inversion
C) a synonymous mutation
D) a region with high mutation rates

Question 12

Most prokaryotic genomes are structured as ________ chromosome(s).

A) one single circular
B) many circular
C) one single linear
D) many linear

Question 13

The nematode Caenorhabditis elegans and humans have nearly identical numbers of protein-coding genes, yet humans have much more complex organismal features. This is an example of

A) the C-value paradox.
B) the G-value paradox.
C) cell size paradox.
D) linkage disequilibrium.

Question 14

Transposons

A) are genetic elements that move within and between genomes.
B) all use a DNA intermediate while making duplicates.
C) are composed of RNA.
D) represent a small fraction of the genomes of multicellular eukaryotes.

Question 15

The G-value paradox states that

A) genome size does not correlate with organismal complexity.
B) the number of protein-coding sequences does not correlate with organismal complexity.
C) genome size does not correlate with the number of protein-coding sequences.
D) organismal complexity does not correlate with the number of chromosomes.

Question 16

What does the figure convey about genome size in prokaryotes?

A) The number of protein-coding genes decreases with genome size.
B) There is strong evidence of G-value paradox in prokaryotes.
C) Bacteria have larger genomes than Archaeans.
D) Free-living bacteria generally have larger genomes than do obligate symbionts.

Question 17

Viral genomes

A) consist only of DNA.
B) consist only of RNA.
C) may consist of DNA or RNA.
D) are always found as a single circular chromosome.

Question 18

GC content refers to the

A) G-value paradox.
B) C-value paradox.
C) fraction of G and C nucleotides in the genome.
D) number of genes on a chromosome.

Question 19

The C-value paradox is

A) the lack of correlation between genome size and organismal complexity.
B) unresolved due to the presence of noncoding DNA.
C) resolved by the discovery of linkage disequilibrium.
D) the strong correlation between genome size and organismal complexity.

Question 20

For which of the following would a syntenic dot plot NOT be useful?

A) when comparing gene orders among prokaryotes
B) when identifying chromosomal inversions
C) when examining genomic evolution in bacteria
D) when only fragments of DNA are available for sequencing

Question 21

What was the first multicellular organism to have its entire genome sequenced?

A) the yeast Saccharomyces cerevisiae
B) the nematode Caenorhabditis elegans
C) a human, Homo sapiens
D) the fruit fly Drosophila melanogaster

Question 22

Which of the following makes up the smallest fraction of the human genome?

A) protein-coding genes
B) LINE elements
C) SINE elements
D) introns

Question 23

A researcher collects a soil sample and sequences the entire genomes of two prokaryotes found in the sample. In these genomes, he finds identical prophage DNA located in different areas of the two genomes. Based on the similarity of the sequences of the prophages and their placement in the prokaryotes' genomes, what could he conclude about the relatedness of the two prokaryotes?

Question 24

Which of the following is FALSE regarding viral genomes?

A) The remarkable diversity that viruses exhibit in their genetic material suggests that they may be evolutionarily ancient.
B) Many viral genes lack orthologs in cellular life-forms.
C) RNA viruses tend to have larger genomes than DNA viruses.
D) Viral genomes tend to be extremely compact.

Question 25

Which of the following statements is FALSE regarding viral genomes?

A) Viral genomes tend to be extremely compact and compressed.
B) DNA-based viruses have genomes comparable in size to most prokaryotes.
C) Because viruses replicate many times within a host cell, their capsules must be very small, which constrains the amount of genetic material that can be contained inside.
D) Most viruses undergo strong natural selection for rapid replication.

Question 26

List three ways in which horizontal gene transfer is different from sexual reproduction.

Question 27

When examining recombination rates across a chromosome, a researcher detects an area of high recombination rates. What could he or she infer based on this observation?

A) This region is likely the centromere.
B) This region is likely a telomere.
C) This region is likely a recombination hotspot.
D) This region is within a protein-coding gene.

Question 28

Consider two species, one of which has an effective population size that is five orders of magnitude greater than the other. In which species would you expect to see a smaller genome size? Explain your reasoning.

Question 29

Which of the following are NOT mobile genetic elements that you could expect to find associated with a prokaryotic genome?

A) telomeres
B) transposons
C) prophages
D) plasmids

Question 30

Recombination rates across a chromosome

A) are highly variable.
B) are negligible at recombination hotspots.
C) are nearly equal at all positions.
D) do not affect linkage disequilibrium.

Question 31

Which of the following statements regarding haplotype blocks is FALSE?

A) Within haplotype blocks, there is minimal genetic diversity.
B) Within haplotype blocks, recombination is rare.
C) Within haplotype blocks, linkage disequilibrium is high.
D) Within haplotype blocks, recombination hotspots break down disequilibrium.

Question 32

Viral genomes exhibit extreme compression in size, and this is possible because multiple genes may be packed in the same region of the genome. Which of the following is NOT a way in which this can occur?

A) Multiple genes can be packed in the same reading frame but only partially overlapping.
B) Multiple genes can be located in the same region but with different reading frames.
C) Proteins can be produced by reading in the same reading frame but with genes starting in different places using different start codons.
D) Certain genes are located on multiple chromosomes.

Question 33

What are transcription factors and how do they address the G-value paradox?

Question 34

Which of the following are NOT a vehicle for horizontal gene transfer?

A) plasmids
B) bacteriophages
C) endosymbiosis
D) centromeres

Question 35

A group of scientists sequence and identify various regions of an organism's genome and find that 92% of the genome (a circular chromosome and a plasmid) is comprised of protein-coding genes. The organism is most likely a

A) unicellular eukaryote.
B) multicellular eukaryote.
C) bacterium.
D) bacteriophage.

Question 36

What was the first eukaryotic organism to have its entire genome sequenced?

A) the bacteriophage MS2
B) the bacterium Haemophilus influenzae
C) the yeast Saccharomyces cerevisiae
D) the nematode Caenorhabditis elegans

Question 37

Certain single-celled amoeba have a genome that is 1,000 times the size of the genome of a complex multicellular puffer fish. This is an example of what phenomenon?

A) the C-value paradox
B) the G-value paradox
C) GC skew
D) codon usage bias

Question 38

Which of the following would you expect to have the largest diploid cell size?

A) Siamese fighting fish, genome size 630 Mb
B) African clawed toad, genome size 3,080 Mb
C) Yellow-spotted salamander, genome size 29,300 Mb
D) Red-spotted newt, genome size 39,100 Mb

Question 39

In the syntenic dot plot of E. coli K-12 strains A and B, there are two circled dots in the lower-right corner of the plot. How do you interpret the position of these two dots in terms of the gene orders of the two strains?

Question 40

In the figure shown, what is the range of genome size for protozoa? What does this tell us about the relationship between genome size and organismal complexity?

Question 41

In the figure shown, a double crossing-over event occurs between the Alu elements. How does this event illustrate a means by which introns generate genetic diversity?

Question 42

When comparing recombination rates between a dog, with a genome size of 2,410 Mb, and a mustard weed, with a genome size of 100 Mb, which would you expect to have a larger recombination rate per kilobase? Explain your answer.

Question 43

Summarize the composition of the human genome as it relates to various molecular functions.

Question 44

Describe the characteristics of a haplotype block.

Question 45

While sequencing a bacterial genome, a researcher notes that G is more common on the leading strand than the lagging strand. This is an example of what phenomenon? Explain.

Question 46

What general patterns of recombination have been observed in eukaryotic genomes?

Question 47

In what ways do prokaryotic and eukaryotic genomes differ?

Question 48

Describe the field of evolutionary genomics.

Question 49

Why are transposons considered selfish genetic elements?