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Brock Biology Of Microorganisms 14th Edition By Michael T. Madigan -Test Bank

Brock Biology of Microorganisms, 14e (Madigan et al.)

Chapter 6  Microbial Genomics

 

6.1  Multiple Choice Questions

 

1) ________ of prokaryotic genomes are now available in public databases.

  1. A) Dozens
  2. B) Hundreds
  3. C) Thousands
  4. D) Millions

Answer:  C

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.1

 

2) When comparing genes from Archaea, Bacteria, and Eukarya, which statement is TRUE?

  1. A) Almost all archaeal genes are more similar to eukaryotic genes than to bacterial genes.
  2. B) Almost all archaeal genes are more similar to bacterial genes than to eukaryotic genes.
  3. C) Genes in Archaea involved in DNA replication, transcription, and translation are more similar to those of Eukarya, while those encoding metabolic functions other than information processing are more similar to those of Bacteria.
  4. D) Archaeal genes are almost universally unique; very few are similar to either eukaryotic or bacterial genes.

Answer:  C

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.1

 

3) Based on the table of average intron frequency given below, predict the relative order of genome size for these four eukaryotic organisms.

 

Organism                                    Average Intron Frequency

Cryptosporidium parvum                                0

Plasmodium falciparum                                  1

Arabidopsis thaliana                                       5

Homo sapiens                                                 8

 

  1. A) Homo sapiens > Arabidopsis thaliana > Plasmodium falciparum > Cryptosporidium parvum
  2. B) Cryptosporidium parvum > Plasmodium falciparum > Arabidopsis thaliana > Homo sapiens
  3. C) Homo sapiens > Cryptosporidium parvum > Plasmodium falciparum > Arabidopsis thaliana
  4. D) Intron frequency cannot be used to predict genome size in eukaryotes.

Answer:  A

Bloom’s Taxonomy:  Analysis

Chapter Section:  6.6

 

 

4) The 140 kbp genome containing many short repeats, ribosomal RNA genes, one RNA polymerase gene (rpo) and one RubisCO gene (rbcL) is most likely from a(n)

  1. A) plant.
  2. B) autotrophic bacterium.
  3. C) chloroplast.
  4. D) autotrophic archaeon.

Answer:  C

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.5

5) The evolutionary origin of mitochondria is demonstrated by which of the following key genomic characteristics?

  1. A) variable numbers of protein-encoding genes
  2. B) large stretches of AT-rich DNA
  3. C) linear and circular genome structure in different organisms
  4. D) rRNA genes most closely related to Bacteria

Answer:  D

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.5

 

6) An open reading frame (ORF) encodes for

  1. A) a carbohydrate.
  2. B) a polypeptide.
  3. C) mRNA.
  4. D) a carbohydrate or a polypeptide.

Answer:  B

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.3

 

7) The pan genome of a species is the genomic content that is

  1. A) common to all strains of the same species.
  2. B) present in one or more strains of the same species.
  3. C) shared with all other prokaryotes.
  4. D) hypothetical or uncharacterized genome content of a species.

Answer:  B

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.13

 

8) Microarrays can be used to

  1. A) analyze global gene expression.
  2. B) detect pathogens.
  3. C) detect unwanted food additives or substitutes.
  4. D) detect pathogens, analyze global gene expression, and detect unwanted food additives or substitutes.

Answer:  D

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.7

 

9) Transcriptome analysis is useful in relation to genome analysis because

  1. A) it is NOT dependent on nucleic acid sequencing technology.
  2. B) it results in amino acid sequence and is, thus, easier to analyze.
  3. C) it analyzes RNA, thus it reveals which genes are expressed under different conditions.
  4. D) it reveals interactions between molecules and, thus, provides more information than genome analysis.

Answer:  C

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.7

10) The most abundant genes in prokaryotic genomes are

  1. A) those involved in metabolism.
  2. B) those involved in translation.
  3. C) those involved in transport.
  4. D) those involved in DNA replication.

Answer:  A

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.4

 

11) When compared with Bacteria, species of Archaea seem to devote a higher percentage of their genomes to genes encoding proteins involved in

  1. A) transcription.
  2. B) energy and coenzyme production.
  3. C) cell membrane functions.
  4. D) carbohydrate metabolism.

Answer:  B

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.4

 

12) The entire complement of RNA produced under a given set of conditions is called a(n)

  1. A) array.
  2. B) genome.
  3. C) proteome.
  4. D) transcriptome.

Answer:  D

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.7

 

13) The very first DNA sequencing technology called the Sanger method relies on

  1. A) nanopore technology that separates DNA molecules based on charge differences.
  2. B) the incorporation of dideoxynucleotides that terminate chain extension during DNA synthesis.
  3. C) nuclear magnetic resonance (NMR) analysis.
  4. D) the release of protons whenever a new nucleotide is added to a growing strand of DNA.

Answer:  B

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.2

 

14) The advantage(s) of second-generation DNA sequencing compared to the Sanger method are the result of

  1. A) miniaturization of reaction size.
  2. B) increased computing power.
  3. C) increased length of DNA sequences obtained.
  4. D) miniaturization of reaction size and increased computer power.

Answer:  D

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.2

15) Within Archaea and Bacteria, one megabasepairs of DNA encode about ________ open reading frames.

  1. A) 10
  2. B) 100
  3. C) 1,000
  4. D) 10,000

Answer:  C

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.4

 

16) You want to know whether the virulence genes present in Bordetella pertussis are evolutionarily related to genes in the less pathogenic species B. bronchiseptica or if the virulence genes were acquired via horizontal gene transfer. What characteristic(s) would you compare to answer this question?

  1. A) percentage of GC content and codon usage
  2. B) genome size and number of introns
  3. C) number of genes in the pan genome
  4. D) ribosomal binding site and intron sequence

Answer:  A

Bloom’s Taxonomy:  Evaluation

Chapter Section:  6.13

 

17) The science that applies powerful computational tools to DNA and protein sequences for the purpose of analyzing, storing, and accessing the sequences for comparative purposes is known as

  1. A) metagenomics.
  2. B) proteomics.
  3. C) bioinformatics.
  4. D) genomics.

Answer:  C

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.3

 

 

18) Most mobile DNA consists of

  1. A) transposable elements.
  2. B) introns.
  3. C) linear chromosomes.
  4. D) plasmids.

Answer:  A

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.12

 

19) Mobile DNA elements are more common in the genomes of

  1. A) Archaea.
  2. B) hyperthermophiles.
  3. C) rapidly evolving species.
  4. D) pathogens.

Answer:  C

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.12

20) Chromosomal islands contain clusters of genes for

  1. A) DNA repair and replication.
  2. B) virulence, biodegradation of pollutants, and symbiotic relationships.
  3. C) catabolic and anabolic reactions.
  4. D) antibiotic resistance.

Answer:  B

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.13

 

21) A computer program recognizes an ORF by looking for ribosomal binding sites, start codons, and stop codons with an appropriate number of nucleotides between each element. What is a drawback of this approach?

  1. A) Too many ORFS are identified, most of which are stretches on non-coding junk DNA.
  2. B) Codon bias causes incorrect annotations.
  3. C) Unusual, but legitimate genes and non-coding RNA may be missed.
  4. D) We lack the computing power to complete the analyses in a timely manner, thus many genomes are only partially annotated.

Answer:  C

Bloom’s Taxonomy:  Evaluation

Chapter Section:  6.3

 

22) The total genetic complement of ALL cells within a microbial community is called a(n)

  1. A) chromosomal island.
  2. B) interactome.
  3. C) metagenome.
  4. D) metabolome.

Answer:  C

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.10

 

23) Linking an ORF with a specific function is an example of gene

  1. A) annotation.
  2. B) assembly.
  3. C) codon bias.
  4. D) expression.

Answer:  A

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.3

 

24) The first genome sequenced was that of a

  1. A) virus.
  2. B) bacterium.
  3. C) eukaryote.
  4. D) archaeon.

Answer:  A

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.1

25) In general, prokaryotic genome size is correlated to lifestyle. Which type of prokaryote typically has the smallest genome?

  1. A) parasite
  2. B) endosymbiont
  3. C) autotroph
  4. D) free-living heterotroph

Answer:  B

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.2

 

26) Chloroplasts and mitochondria originated from ________ by a process known as ________.

  1. A) bacteria / chromosome reduction
  2. B) plants / gene deletion
  3. C) bacteria / endosymbiosis
  4. D) plants / endosymbiosis

Answer:  C

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.5

 

27) In addition to chromosomes, some mitochondria also contain other genetic material known as

  1. A) plasmids.
  2. B) transposons.
  3. C) proteomes.
  4. D) lysosomes.

Answer:  A

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.5

 

28) Gene function is annotated based on homology between the ORFs of a genome and proteins whose function has been proven experimentally. What “-omic” approach could help us determine the function and structure of proteins encoded by uncharacterized ORFs?

  1. A) metabolomics
  2. B) metagenomics
  3. C) transcriptomics
  4. D) proteomics

Answer:  D

Bloom’s Taxonomy:  Application

Chapter Section:  6.9

 

29) Which method is most commonly used in metabolomics?

  1. A) ion torrent semiconductor sequencing
  2. B) mass spectrometry
  3. C) 2D polyacrylamide gel electrophoresis
  4. D) Sanger method

Answer:  B

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.9

30) Many of the genes in the chloroplast genome encode proteins involved in ________, whereas mitochondrial genomes primarily encode proteins involved in ________.

  1. A) autotrophy / DNA replication
  2. B) photosynthesis / glycolysis
  3. C) autotrophy / glycolysis
  4. D) photosynthesis / oxidative phosphorylation

Answer:  D

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.5

 

31) Genome assembly relies on

  1. A) accurate gene annotation.
  2. B) overlap of a large numbers of short sequences.
  3. C) codon bias.
  4. D) systems biology.

Answer:  B

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.2

 

 

32) The core genome of a prokaryotic species is the genomic content that is

  1. A) unique compared to all other prokaryotes.
  2. B) expressed under all environmental conditions.
  3. C) shared between all other prokaryotes.
  4. D) shared between all strains of a species.

Answer:  C

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.13

 

33) Compounds such as pyruvate, acetyl-CoA, fructose-6-phosphate, oxaloacetate, and other small organic compounds could be part of a(n)

  1. A) metagenome.
  2. B) metabolome.
  3. C) interactome.
  4. D) transcriptome.

Answer:  B

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.10

 

34) Genomes of species in both Bacteria and Archaea show a strong correlation between genome size and

  1. A) noncoding RNA.
  2. B) codon bias.
  3. C) number of ORFs.
  4. D) number of introns.

Answer:  C

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.4

35) Typically ________ of ORFs in a genome cannot clearly be assigned a function. These ORFs are usually assigned and predicted to encode hypothetical proteins.

  1. A) < 1 %
  2. B) 5 %
  3. C) 30 %
  4. D) 90 %

Answer:  C

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.4

 

 

36) Fourth-generation sequencing methods no longer use ________ to detect nucleotide incorporation.

  1. A) mass
  2. B) pH
  3. C) charge
  4. D) light

Answer:  D

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.2

 

37) RNA-Seq analysis is a method aimed at defining a(n)

  1. A) metabolome.
  2. B) transcriptome.
  3. C) interactome.
  4. D) metagenome.

Answer:  B

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.4

 

38) Genes from different sources that are related in sequence due to shared evolutionary ancestry are called ________ genes, and groups of such genes are known as ________.

  1. A) homologous / gene families
  2. B) paralogous / functional genes
  3. C) orthologous / gene families
  4. D) homologous / functional genes

Answer:  A

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.11

 

39) Horizontal gene transfer

  1. A) is rare and only occurs between closely related strains.
  2. B) is common and may sometime occur between unrelated organisms.
  3. C) does not provide an advantage to organisms.
  4. D) only occurs in prokaryotes.

Answer:  B

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.12

40) Horizontal gene transfer has been thoroughly documented for genes involved in

  1. A) DNA replication and repair.
  2. B) virulence and metabolic functions.
  3. C) only very few processes.
  4. D) translation.

Answer:  B

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.12

 

41) A surprising finding of environmental metagenomic studies is that a majority of genes in the environment are

  1. A) from microbes grown in the lab.
  2. B) viral in origin.
  3. C) eukaryotic in origin.
  4. D) from extinct microorganisms.

Answer:  B

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.10

 

6.2  True/False Questions

 

1) Knowledge of an organism’s genome sequence yields important clues to how an organism functions and its evolutionary history.

Answer:  TRUE

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.11

 

2) Genomic analysis led to the discovery that pathogenic organisms often lack genes for amino acid biosynthesis.

Answer:  TRUE

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.3

 

3) Comparative genomics helps us to understand evolutionary relationships between organisms.

Answer:  TRUE

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.11

 

4) Reconstructing evolutionary relationships helps in differentiating between primitive and derived characteristics.

Answer:  TRUE

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.11

 

5) It is generally accepted that independent mutation rather than gene duplication is the mechanism for evolution of most new genes.

Answer:  FALSE

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.11

6) Gene families are composed of homologous genes that have different evolutionary origins but the same function.

Answer:  FALSE

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.11

 

7) Based on the evolutionary tree shown below, RubisCO Form II and RLP beta are orthologs.

 

RLP alpha

|                                   RLP beta

Ancestral gene                              |

|                 RLP ancestor

|                 |                 |

|                 |

                  Duplicate gene

                                    |                    RubisCO Form II

                                    |                    |

                                    RubisCO ancestor                   RubisCO Form I

                                                         |                          |

                                                         RubisCO Duplicate

                                                                                    |

                                                                                    RubisCO Form III

Answer:  FALSE

Bloom’s Taxonomy:  Analysis

Chapter Section:  6.11

 

8) Despite having smaller genomes, the protozoans Paramecium and Trichomonas have significantly more genes than humans.

Answer:  TRUE

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.6

 

9) Paralogs always have the same function.

Answer:  FALSE

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.11

 

10) The key characteristic of third-generation sequencing is the ability to sequence single molecules of DNA.

Answer:  TRUE

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.2

 

11) Heterotrophs need only a few more genes than autotrophs.

Answer:  FALSE

Bloom’s Taxonomy:  Evaluation

Chapter Section:  6.4

 

12) The largest cellular genomes belong to prokaryotes that are parasitic or pathogenic.

Answer:  FALSE

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.4

13) Codon usage and even the genetic code itself varies from one organism to the next.

Answer:  TRUE

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.5

 

14) Genes for DNA replication and transcription make up only a small fraction of the typical prokaryotic genome.

Answer:  TRUE

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.4

 

15) The relative percentage of genes devoted to protein synthesis in small-genome organisms is high compared with that of large-genome organisms.

Answer:  TRUE

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.4

 

16) Few genes in all organisms have common evolutionary roots.

Answer:  FALSE

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.11

 

17) Horizontally transferred genes typically encode essential metabolic functions such as DNA replication, transcription, and translation.

Answer:  FALSE

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.12

 

18) Chromosomal rearrangements due to insertion sequences have apparently contributed to the evolution of several human pathogens.

Answer:  TRUE

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.13

 

19) Some virulence genes are carried on plasmids or lysogenic bacteriophages.

Answer:  TRUE

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.12

 

20) Microorganisms that grow in extreme environments typically contain larger genomes when compared to microbes that grow in non-extreme environments.

Answer:  FALSE

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.4

 

 

21) With modern molecular techniques, it is now possible to completely assemble a genome from a single cell.

Answer:  TRUE

Bloom’s Taxonomy:  Knowledge

Chapter Section:  6.10

6.3  Essay Questions

 

1) After transcription, mRNA may undergo significant editing. Compare and contrast RNA editing in prokaryotes and eukaryotes and connect how these differences affect genome size and gene content.

Answer:  RNA editing occurs after transcription of mRNA. Introns are pieces of RNA that are removed after transcription and before translation. Eukaryotic mRNA undergoes extensive RNA editing after transcription and in general eukaryotic genes contain many more introns than do prokaryotic genes. The number of introns per gene in eukaryotic genes ranges from 0-10, while most prokaryotic genes do not have any. The number of introns per gene is positively correlated with genome size. As the number of introns per gene increases, the genome size increases. The number of ORFs per 1000 nucleotides thus tends to decrease. In general, prokaryotic genomes encode for more genes (ORFs) per every 1000 base due to the lack of introns and less regulatory DNA.

Bloom’s Taxonomy:  Synthesis

Chapter Section:  6.6

 

2) You are interested in the minimum set of genes necessary for survival of a eukaryotic microorganism such as Saccharomyces cerevisiae. Design an experiment to systematically test which genes are essential for survival and which are not under high nutrient, aerobic conditions.

Answer:  The genome of S. cerevisiae can be either haploid or diploid. Genes can be systematically mutated or disabled (knocked out) in S. cerevisiae in the diploid state. Then each mutant can be tested for viability in the haploid state. Any mutant that dies in the haploid state had a mutation in a critical survival gene. Any mutant that survives in the haploid state had a mutation in a gene unnecessary for survival.

Bloom’s Taxonomy:  Synthesis

Chapter Section:  6.6

 

3) Explain how codon bias and GC content can be used to detect horizontal gene transfer within a genome.

Answer:  If an organism rarely uses a particular amino acid and one gene sequence has significantly more codons for the otherwise rare amino acid, this codon bias can be used to infer horizontal transfer of the gene. GC content may also be significantly different in a gene that has been transferred horizontally compared to the average GC content of the majority of the genome.

Bloom’s Taxonomy:  Application

Chapter Section:  6.12

 

 

4) Explain horizontal gene transfer and demonstrate how this phenomenon has complicated evolutionary studies using a diagram that illustrates phylogenetic relationships between organisms and genes.

Answer:  Horizontal (or lateral) gene transfer involves a gene sequence being transferred from one cell to another non-progenic cell. This mechanism explains how one cell lineage acquires genes from others but complicates phylogenetics. It is therefore difficult to determine the evolutionary relatedness of organisms when they each contain a mosaic of genes laterally transferred from several different organisms.

Bloom’s Taxonomy:  Application

Chapter Section:  6.4

5) Why are the words “about” and “approximately” used in discussing the results of genomic analysis? Predict what advances in knowledge or methods could change our understanding of a genome sequence.

Answer:  As genome sequence analysis becomes more refined, the number of predicted open reading frames (ORFs) changes. Also, a fully sequenced genome can be misleading because sometimes repetitive DNA is not completely sequenced. Therefore conservative terms are used to describe the results of genome analysis. Advances in knowledge that change our understanding of genomes include experimental determination of the protein function or structure of hypothetical proteins from uncharacterized ORFs, discovery of new types of noncoding RNA, and identification of new or unusual gene families.

Bloom’s Taxonomy:  Evaluation

Chapter Section:  6.3

 

6) Explain the terms “core genome” and “pan genome” and describe how each contributes to the genome of a bacterial species. Give an example of genes that are part of a core genome versus those that are more often in the pan genome.

Answer:  A core genome is the genome content present in all strains of a bacterial species. These are typically fundamental metabolic genes that combine to help define the bacterial species as a whole. The pan genome is the genome content that is found in only some of the strains within the species. The additional genes in the pan genome are what distinguish strains from one another. Typical genes in the pan genome may be for accessory functions such as virulence, degradation of a variety of substrates, or symbiosis. Often the pan genome contains mobile elements and plasmids.

Bloom’s Taxonomy:  Application

Chapter Section:  6.13

 

7) Interpret the genomic content of mitochondria in relation to their evolution. How is mitochondrial evolution more complicated than expected?

Answer:  Some mitochondria contain accessory plasmids in addition to chromosomal DNA. The shapes of mitochondrial genomes are not all the same; some are linear and others are circular. These fundamental differences in mitochondrial genomes further complicate even basic comparative analyses. Some mitochondrial genes have also been transferred to the nuclear genome.

Bloom’s Taxonomy:  Analysis

Chapter Section:  6.5

 

8) Design an experiment using —omic methods to test how Escherichia coli adapts to different growth temperatures.

Answer:  One could grow E. coli in identical flasks and media in two different temperatures (25 and 37 °C, for example). Then, you compare gene expression and protein content in the two cultures using transcriptomics and proteomics. Transcriptomics would require the extraction of RNA and the creation of cDNA, then sequencing and assembly of the transcripts to the genome for differential gene expression comparisons. For proteomics, the proteins would be separated from other cell components and then analyzed via 2D polyacrylamide gel electrophoresis. Quantified proteins matched to the proteome would be used to identify differentially translated proteins. (An alternative answers could describe use of a gene chip for gene expression analysis instead of sequencing of cDNA or quantifying peptides with HPLC-ESI-MS/MS instead of 2D-PAGE. Diagrams of the experiment should be encouraged.)

Bloom’s Taxonomy:  Synthesis

Chapter Section:  6.8

9) Recommend what type of data should be collected and analyzed in a systems biology approach to investigate how a non-pathogenic bacterial strain becomes pathogenic. Describe what scientific fields and methods would be involved in your recommendation.

Answer:  A systems biology approach integrates multiple methods and fields to model or analyze a problem. One approach would be to compare the genome and the proteome of non-pathogenic and pathogenic strains of a particular species to find the genes and proteins that are different and may be related to pathogenicity. This research would involve 3rd or 4th generation sequencing, 2D polyacrylamide gel electrophoresis of proteins, and bioinformatics to process and analyze all the data. Further experimentation could involve genetic manipulations to investigate the effect of removing or mutating the implicated genes and biochemical characterization of the implicated proteins. (Answers could vary significantly, but any reasonable discussion of how various “-omic” techniques and methods could be applied to this problem could be acceptable as long as the discussion is consistent and logical, linking the appropriate data types and methods to detect differences between pathogenic and nonpathogenic organisms. The answer should include the definition of systems biology.)

Bloom’s Taxonomy:  Evaluation

Chapter Section:  6.9

 

10) Chromosomal islands are presumed to have a “foreign” origin based upon three observations. What are these observations and how do they indicate that chromosomal islands are “foreign” in origin?

Answer:  The presence of a sequence flanked by inverted repeats suggests transposition brought in the sequence. An island is also likely “foreign” when there is a dissimilar composition of bases (GC%) or a different codon bias. Lastly, chromosomal islands typically contain genes that are related in function, such as virulence or biodegradation.

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.13

 

 

11) Explain why organisms undergoing rapid evolutionary change often contain relatively large numbers of mobile DNA elements, whereas once organisms settle into a stable evolutionary niche, most of these mobile elements are lost.

Answer:  Genome diversity is likely to be high during a process of rapid evolutionary change. To obtain this high diversity, several processes, such as horizontal gene transfer and chromosomal rearrangements (e.g., deletions, inversions, translocations), are common. Organisms with a more stable niche require less diversity in their genomes and therefore tend to be less dynamic in genome content.

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.12

 

12) The intracellular parasite Nanoarchaeum equitans has one of the smallest prokaryotic genomes. Why is the genome of N. equitans so small? How is it possible that the genome of N. equitans contains more genes than that of Mycoplasma genitalium, which is actually 90 kbp larger?

Answer:  The intracellular parasite, N. equitans is a highly specialized archaeon with a very condensed genome, containing little noncoding DNA and no introns. It is well-adapted to live within its archaeon host and can hijack its host’s proteins. It therefore does not require its own genes for energy consumption. N. equitans contains more genes that M. genitalium because there is very little noncoding DNA and can thus fit more ORFs into a smaller genome. This is very efficient, although it does not allow for changes in gene expression in response to environmental changes.

Bloom’s Taxonomy:  Application

Chapter Section:  6.4

13) Explain why larger genomes contain more genes devoted to regulation than smaller genomes and why these genes increase the competitiveness of organisms.

Answer:  Answers will vary, but one explanation is an increase in regulatory networks of larger genome-containing organisms provides a much greater opportunity for the cell to be dynamic in response to environmental stimuli. For example, this can be advantageous for cells to invoke certain pathways when particular carbon substrates become available. In this way, a cell can more finely tune its metabolic activities to minimize energy consumption and maximize energy acquisition.

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.4

 

14) Explain why the proteome is NOT defined as “all the proteins encoded by an organism’s genome.”

Answer:  Certain proteins might not be synthesized under a particular condition. Gene expression changes under different environmental conditions. Recognizing that not all potential ORFs will encode for proteins, it becomes difficult to determine all of the proteins within an organism, thus the proteome is only the proteins expressed under specific conditions.

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.8

 

 

15) When analyzing the sequence of genes similar to ones already known, why is the amino acid sequence of the protein more important than the DNA sequence?

Answer:  Over evolutionary time, a nucleotide sequence can change, yet its encoded protein function can remain the same. Individual nucleotide changes especially at the third position of a codon might not change the amino acid sequence at all. Depending on the location of the amino acid, some can substitute for others and not affect the protein’s function. Therefore a nucleotide sequence could be quite different from another, yet their function could remain the same.

Bloom’s Taxonomy:  Analysis

Chapter Section:  6.11

 

16) What process allows evolution to “experiment” with genes to create novel functions? How is this manifested in extant genes (presently existing) and their relationships to each other?

Answer:  Duplication of genes through duplication of the entire genome or just parts of the genome allows the second gene to evolve and diversify into a different functional protein while still maintaining the original protein’s function. Gene duplication creates paralogs, which can further diverge through random mutations into several orthologs. Genes with shared evolutionary ancestry are called homologs (both paralogs and orthologs are homologs). Contemporary genes thus display relationships such as gene families, which are groups of homologous genes that may have different functions but share evolutionary ancestry.

Bloom’s Taxonomy:  Analysis

Chapter Section:  6.11

17) How does the FoodExpert-ID identify macroorganisms and why is this significant?

Answer:  The FoodExpert-ID is a specialized microarray chip with assorted nucleotide sequences unique to individual organisms. This chip can be used to assess whether or not particular microorganisms are present and to what extent they are present in a particular food product. This can be applied to ensure a food product lacks potentially cheaper meats acting as filler ingredients. Ultimately the FoodExpert-ID is meant to instill more confidence in the wholesomeness of food products for consumers.

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.7

 

18) Explain how mass spectrometry (MS) has aided in the progression of the field of metabolomics.

Answer:  Due to the complex nature of all possible chemical structures, metabolomics requires a highly sensitive instrument to identify each individual metabolite with high accuracy and precision. The field of metabolomics has greatly increased due to powerful MS approaches being used today. The capabilities of MS instruments such as a MALDI-TOF-MS permit the identification of many metabolites from a sample with high mass resolution when compared to older methods using NMR.

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.9

 

 

19) The Human Microbiome Project is a large research program that aims to understand all of the microorganisms on and in the human body. Which “-omic” methods could be applied directly to a sample from the human body to study the microorganisms in the sample? Propose a general experimental approach for analyzing a sample containing a complex mixture of microorganisms.

Answer:  A sample from the human body, such as stool or tooth swab, would be collected and the DNA or RNA extracted. RNA would be converted to cDNA. The cDNA would then be sequenced. This approach is metagenomics (and metatransciptomics for RNA). After sequencing, the short sequences must be assembled into longer stretches (genes or whole genomes). An alternative answer could outline the procedure of single-cell genomics from cells obtained from samples from the human body or the use of a gene chip for identification of organisms. Any answer that shows understanding of general steps and uses terms appropriately and consistently throughout the answer would be acceptable.

Bloom’s Taxonomy:  Synthesis

Chapter Section:  6.10

 

20) Summarize the evolution of sequencing technology beginning with the Sanger method.

Answer:  The first generation of DNA sequencing used the Sanger method to determine the DNA sequence. The Sanger method required that labeled dideoxynucleotides were added to a reaction so that the elongation of new DNA chains would terminate when the dideoxynucleotides were incorporated. In first generation sequencing, the detection of the terminated chains was not very sensitive. Second generation sequencing used similar chemistry, but miniaturized the reactions and improved detection methods and computation so that more sequence information could be collected very rapidly. Third generation sequencing improved detection such that single molecules could be detected, thus even more sequence could be generated. Fourth generation sequencing has moved beyond optical or light detection by using pH or charge changes to detect single molecules.

Bloom’s Taxonomy:  Comprehension

Chapter Section:  6.2

 

rBrock Biology of Microorganisms, 14e (Madigan et al.)

Chapter 7  Metabolic Regulation

 

Multiple Choice Questions

 

1) Regulation of an enzyme’s activity occurs

  1. A) transcriptionally.
  2. B) translationally.
  3. C) posttranslationally.
  4. D) at any point on the enzymatic production pathway.

Answer:  C

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.18

 

2) When arginine is added to a culture growing exponentially in a medium without arginine, what occurs?

  1. A) All cellular growth ceases.
  2. B) Growth continues, but the production of enzymes required for the synthesis of arginine ceases.
  3. C) Growth continues, but the production of enzymes required for the synthesis of arginine increases.
  4. D) The cell returns to the lag stage of growth to synthesize the proteins necessary for the metabolism of arginine.

Answer:  B

Bloom’s Taxonomy:  Application

Chapter Section:  7.3

 

3) Regulatory proteins

  1. A) are influenced by small molecules.
  2. B) bind to specific DNA sites.
  3. C) regulate transcription.
  4. D) regulate transcription, bind specific DNA sites, and can be influenced by small molecules.

Answer:  D

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.2

 

4) A protein region with a specific function and structure is called a

  1. A) conserved site.
  2. B) domain.
  3. C) locale.
  4. D) motif.

Answer:  B

Bloom’s Taxonomy:  Knowledge

Chapter Section:  7.2

 

5) Transcriptional regulators bind most frequently at the ________ site of DNA.

  1. A) major groove
  2. B) minor groove
  3. C) histone complex
  4. D) primary supercoil

Answer:  A

Bloom’s Taxonomy:  Knowledge

Chapter Section:  7.2

 

6) Which type of regulator(s) specifically bind to operator regions of DNA?

  1. A) activators
  2. B) activators and inducers
  3. C) repressors
  4. D) repressors and corepressors

Answer:  C

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.3

 

7) The lac operon is an example of ________ control in which the presence of an ________ is required for transcription to occur.

  1. A) negative / activator
  2. B) negative / inducer
  3. C) positive / activator
  4. D) positive / inducer

Answer:  B

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.4

 

8) Enzyme induction occurs

  1. A) when the substrate is present.
  2. B) when the organism is environmentally stressed.
  3. C) continuously.
  4. D) when the substrate is depleted.

Answer:  A

Bloom’s Taxonomy:  Knowledge

Chapter Section:  7.3

 

9) Considering the catabolite repression mechanism, which observation would make you suspect it is NOT occurring?

  1. A) CRP bound to promoter sites
  2. B) elevated levels of transcripts for maltose and sucrose catabolism
  3. C) relatively low intracellular cyclic AMP levels
  4. D) RNA polymerase bound to biosynthetic promoter sequences

Answer:  C

Bloom’s Taxonomy:  Evaluation

Chapter Section:  7.5

10) During a growth curve of Aliivibrio fischeri, when would you expect to see the strongest bioluminescence?

  1. A) lag phase
  2. B) early to middle log phase
  3. C) late log to early stationary phase
  4. D) middle to late stationary phase

Answer:  C

Bloom’s Taxonomy:  Analysis

Chapter Section:  7.9

 

11) What occurs when an inducer is added to an environment containing an organism with a metabolic pathway controlled by a repressor?

  1. A) The inducer combines with the repressor and activates the pathway.
  2. B) The inducer combines with the repressor and inactivates the pathway.
  3. C) The inducer combines with the substrate and blocks induction.
  4. D) The inducer does not combine with, but functions as a chaperone molecule for, the enzyme-substrate complex.

Answer:  B

Bloom’s Taxonomy:  Analysis

Chapter Section:  7.3

 

12) Which of the following do NOT bind to the promoter sequence during regulation?

  1. A) activators
  2. B) inducers
  3. C) repressors
  4. D) activators, inducers, and repressors

Answer:  D

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.4

 

13) Cyclic AMP is synthesized from ATP by an enzyme called ________ which is involved in ________.

  1. A) adenylate cyclase / catabolite repression
  2. B) adenylate cyclase / transcriptional activation
  3. C) cAMP receptor protein (CRP) synthase / catabolite repression
  4. D) cAMP receptor protein (CRP) synthase / transcriptional activation

Answer:  A

Bloom’s Taxonomy:  Knowledge

Chapter Section:  7.5

 

 

14) In negative control of transcription, how does the presence of an inducer affect transcription?

  1. A) The inducer binds to the operator.
  2. B) The inducer does not bind to the operator.
  3. C) The inducer causes the repressor to bind to the operator.
  4. D) The inducer prevents the repressor from binding to the operator.

Answer:  D

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.3

15) Which type of regulatory protein(s) is/are present in Archaea?

  1. A) Activators that stimulate RNA polymerase activity are present in Archaea.
  2. B) Repressors that block RNA polymerase activity are present in Archaea.
  3. C) Both activators and repressors are present in Archaea.
  4. D) Similar to regulation in Eukarya, Archaea lack bacterial-like regulators such as activators and repressors and use transcription factors instead.

Answer:  B

Bloom’s Taxonomy:  Knowledge

Chapter Section:  7.6

 

16) The function of a kinase is

  1. A) methylation.
  2. B) response regulation.
  3. C) phosphorylation.
  4. D) glycosylation.

Answer:  C

Bloom’s Taxonomy:  Knowledge

Chapter Section:  7.7

 

17) The promoters of positively controlled operons require activator proteins, because

  1. A) RNA polymerase easily recognizes the consensus sequence.
  2. B) they are required to inactivate the repressor proteins.
  3. C) the promoters have nucleotide sequences that bind RNA polymerase weakly, which are not close matches to the consensus sequence.
  4. D) they are needed to bind to the allosteric site of RNA polymerase.

Answer:  C

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.4

 

18) To be most sensitive to a repellant, a methyl-accepting chemotaxis protein must be ________ methylated to initiate a ________.

  1. A) fully / run
  2. B) fully / tumble
  3. C) not / run
  4. D) not / tumble

Answer:  B

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.8

 

19) The most frequent way in which regulatory RNA molecules exert their effects is by

  1. A) base pairing with other RNA molecules that have regions of complementary sequence.
  2. B) binding to a repressor and repressing enzyme transcription.
  3. C) acting as an inducer that then binds to an activator protein to allow transcription to proceed.
  4. D) signal transduction.

Answer:  A

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.14

20) When a Bacillus anthracis population suddenly must form spores to survive a harsh nutrient poor environment, how do the cells obtain energy?

  1. A) Cells in a growth phase that have not used up all of their energy will be the only ones to make endospores, which is why relatively few endospores are often made from a large population.
  2. B) Intracellular energy reserves are quickly made available to produce endospores.
  3. C) Slow responding cells are cannibalized by others that already began spore formation.
  4. D) Global regulation is initiated to minimize energy waste in biosynthetic pathways and catabolic pathways are increased to consume remaining usable substrates to fuel spore formation.

Answer:  C

Bloom’s Taxonomy:  Knowledge

Chapter Section:  7.11

 

21) Interpret the results to the following experiment. Transcriptional activity of chemotactic genes showed a high expression level during the following conditions: repelling away from compound 1, moving towards compound 2, and remaining sessile when presented compounds 3 and 4.

  1. A) Activity during movement in any direction led to high measurements observed, and the sessile population responded equally to both a chemoattractant and a chemorepellant but remained in the same location for their net movement.
  2. B) Gene expression by itself cannot distinguish between cells responding to both an attractant and repellent, so this ambiguity makes transcriptomics unfavorable but nonetheless indicates activity.
  3. C) The activity observed during a sessile existence suggests the molecular probe was targeting a chemotactic gene that is also involved in other non-chemotactic functions due to the activity observed.
  4. D) Transcriptomics as a whole cannot be used for chemotaxis genes because they are not regulated at the transcriptional level (i.e., they are constitutive), which is why activity is observed on all three conditions.

Answer:  D

Bloom’s Taxonomy:  Analysis

Chapter Section:  7.8

 

 

22) Based on their abundance and location in bacterial genomes, deduce which is LEAST likely to horizontally transfer into another bacterium while maintaining its identical function and regulatory roles.

  1. A) heat shock protein-encoding gene
  2. B) lac operon
  3. C) catabolic regulon
  4. D) quorum sensing operon

Answer:  C

Bloom’s Taxonomy:  Evaluation

Chapter Section:  7.4

23) In Bacteria, sensor kinases that respond to extracellular signals transfer this signal to the cytoplasmic machinery by typically phosphorylating the ________ residues.

  1. A) histidine
  2. B) serine
  3. C) threonine
  4. D) tyrosine

Answer:  A

Bloom’s Taxonomy:  Knowledge

Chapter Section:  7.7

 

24) Which enzyme would be BEST to include in a protein extract to refold and denature improperly folded proteins?

  1. A) DnaK
  2. B) RepA
  3. C) RpoH
  4. D) Spo0A

Answer:  C

Bloom’s Taxonomy:  Application

Chapter Section:  7.10

 

25) Bacteria from the genus Caulobacter are used to model cellular differentiation in eukaryotes. The abundance of CtrA, DnaA, and GcrA separately control activity of other genes necessary for differentiation in Caulobacter. Thus, these three proteins can be classified as

  1. A) activating sensors.
  2. B) heterologous regulators.
  3. C) differentiating regulons.
  4. D) transcriptional regulators.

Answer:  D

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.12

 

 

26) Which statement is TRUE of two separate regulators controlling one individual operon?

  1. A) The two regulators themselves must respond to different signals, which enables both to control the operon differently.
  2. B) One regulator will likely control the transcription of one section of the operon, whereas the other regulator will control the other component.
  3. C) One regulator will bind to the operator region whereas the other will bind to the promoter region so they can co-occur and co-regulate the operon.
  4. D) Two regulators trying to control the same operon will likely result in only one being maintained after several generations.

Answer:  A

Bloom’s Taxonomy:  Analysis

Chapter Section:  7.4

 

27) How would you design an sRNA to bind to a sequence?

  1. A) select six continuous nucleotides from the sequence
  2. B) take the complementary sequence of six continuous nucleotides
  3. C) select 200 continuous nucleotides from the sequence
  4. D) take the complementary sequence of 200 continuous nucleotides

Answer:  D

Bloom’s Taxonomy:  Application

Chapter Section:  7.14

28) Which of the following mechanisms leads to INCREASED transcriptional activity?

  1. A) An sRNA binds to the ribosome binding site.
  2. B) Ribonuclease activity is blocked by sRNA complementary binding to the end of a transcript.
  3. C) The ribosome binding site is made available from sRNA binding to part of it.
  4. D) Recruitment of RNA polymerase is enhanced when sRNA binds to and removes a repressor.

Answer:  C

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.14

 

29) When the nontemplate strand of a gene is transcribed into RNA, what is likely to result?

  1. A) A complementary sRNA will bind to it and form a functional ribozyme with secondary structure.
  2. B) It will complementary bind to the gene sequence, form a hairpin loop, and transcriptionally repress the gene.
  3. C) The complementary mRNA also transcribed from the template strand will bind to it and halt its translation.
  4. D) A global regulator will identify this as a stress, respond by inducing ribonuclease production, and it will degraded.

Answer:  C

Bloom’s Taxonomy:  Synthesis

Chapter Section:  7.14

 

 

30) How could you identify potential riboswitches with bioinformatics tools?

  1. A) Advanced 3D modeling techniques of mRNA folding would be necessary because complementary nucleotide binding predictions would not be useful.
  2. B) Locate short regions of an individual transcript with several complementary sites.
  3. C) Identify homologous sRNAs in other organisms.
  4. D) Identify several complementary mRNAs encoded in the genome.

Answer:  A

Bloom’s Taxonomy:  Application

Chapter Section:  7.15

 

31) Based on our understanding of the early stages of life, ________ is/are thought to be one of the earliest forms of metabolic regulation that evolved.

  1. A) attenuation
  2. B) feedback inhibition
  3. C) riboswitches
  4. D) transcription factors

Answer:  C

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.16

 

32) Attenuation is a type of regulation that can control

  1. A) allosteric enzyme activity.
  2. B) transcriptional activity exclusively.
  3. C) translational activity exclusively.
  4. D) both transcriptional and translational activity.

Answer:  B

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.16

33) Post-translational regulation of an enzyme’s activity, such as glutamine synthetase, can be finely controlled at varied levels due to

  1. A) the varied strengths metabolite-regulating compounds can have with the enzyme such as hydrogen bonding, covalent bonding, and van der Waals attractions.
  2. B) having multiple independently functional subunits.
  3. C) the structural strength enzymes have once properly folded compared to short-lived and easily degradable transcripts during translational regulation.
  4. D) weak chemical modifications of the enzyme rather than harsh protein-protein or protein-DNA interactions.

Answer:  B

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.18

 

 

34) Which of the following IS a characteristic of an isoenzyme?

  1. A) More than one enzyme is regulated by the same mechanism.
  2. B) The same reaction can be catalyzed by multiple enzyme variants.
  3. C) Multiple binding sites on the same enzyme enable multiple regulation mechanisms.
  4. D) More than one gene makes the same enzyme.

Answer:  B

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.17

 

35) Which regulatory mechanism does NOT depend on a conformational change in protein/enzyme structure to change activity?

  1. A) attenuation
  2. B) catabolite repression
  3. C) feedback inhibition
  4. D) negative control

Answer:  A

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.17

 

36) An organism grown in a high nutrient liquid broth to high turbidity always appears to produce a blue pigment and even when a large inoculum is transferred to a nutrient rich agar plate it appears blue. When the researcher noticed it never appears blue when very small colonies were grown in low nutrient agar plates. What is the most plausible conclusion?

  1. A) Large populations enabled the differentiation of a subpopulation of cells that created the blue pigment.
  2. B) Only high nutrient conditions provide enough energy for cells to produce this secondary metabolite that appears blue.
  3. C) The blue pigment production is linked to quorum sensing.
  4. D) The strong gradient from very high to low nutrient bioavailability induces production of the blue metabolite.

Answer:  C

Bloom’s Taxonomy:  Synthesis

Chapter Section:  7.9

37) A bacterium that either partially or fully catabolizes an acyl-homoserine lactone will likely disrupt

  1. A) attenuation.
  2. B) chemotaxis.
  3. C) endospore formation.
  4. D) quorum sensing.

Answer:  D

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.9

 

 

38) Phosphorylation of ________ regulates which direction a flagellum rotates, thus controlling whether an organism runs or tumbles.

  1. A) CheAW
  2. B) CheB
  3. C) CheY
  4. D) CheZ

Answer:  C

Bloom’s Taxonomy:  Knowledge

Chapter Section:  7.8

 

39) What are the primary regulator units that control endospore formation?

  1. A) allosteric proteins
  2. B) antisense RNAs
  3. C) riboswitches
  4. D) sigma factors

Answer:  D

Bloom’s Taxonomy:  Comprehension

Chapter Section:  7.11

 

40) During the biotransformation of a large molecular weight compound, two major products are formed. While one of the products is catabolized, the other compounds accumulation represses the biotransformation of the large compound. Which approach is MOST likely to artificially enhance the biotransformation beyond this point in a batch culture?

  1. A) addition of an isoenzyme for the biotransformation route to increase its transcription
  2. B) addition of inducer molecules into the medium to increase transcriptional repression
  3. C) inclusion of more of an intermediate compound in the catabolic pathway
  4. D) spike in additional activator proteins that control the transcription of this pathway

Answer:  A

Bloom’s Taxonomy:  Synthesis

Chapter Section:  7.17

 

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