Test Questions & Answers Microbial Genomics Chapter 18

Prescott's Microbiology, 11e (Willey)

Chapter 18 Microbial Genomics

1) Genomic studies of marine microorganisms has revealed that a considerable amount of the photosynthesis in the ocean is based on photopigments called proteorhodopsins.

2) The method of nucleotide sequence determination that utilizes dideoxynucleotides was developed by ________.

3) Modern automated sequencing machines detect DNA bands by measuring incorporated radioactivity.

4) Dideoxynucleotide sequencing methodologies rely on the ability of dideoxynucleotides to facilitate chain extension after incorporation by DNA polymerase.

5) Each of the four Sanger sequencing reactions include ________.

A) a combination of the four different dideoxynucleotides

B) a single dideoxynucleotide triphosphate

C) ATP

D) tRNA

6) Most automated nucleotide sequencing machines detect bands by ________.

A) laser induced fluorescence

B) measuring incorporated radioactivity

C) autoradiography

D) sizing DNA fragments produced by base specific chemical cleavage reactions

7) The Sanger sequencing approach developed in the 1970s ________.

A) has been rendered obsolete by the development of fundamentally different methodologies

B) is still the main approach used to determine nucleotide sequences

C) is useful for sequencing small DNAs but is not applicable to genome-sized DNA molecules

D) is applicable to RNA but not DNA

8) Genomics is the study of ________.

A) the molecular organization of genomes

B) the information content of genomes

C) the gene products that genomes encode

D) All of the choices are correct.

9) Automated nucleotide sequencing machines detect DNA bands by laser induced ________.

10) After completing the nucleotide sequence of a microbial genome, computer translation of the DNA sequence allows enzymes to be identified based on a short pattern of amino acid sequence called a contig that corresponds to the active site of the enzyme.

11) The whole-genome shotgun approach is useful for sequencing small bacterial genomes but has failed in the case of larger eukaryotic genomes such as those of Drosophila and human.

12) In genomic research the term contig refers to overlapping nucleotide sequences that are not adjacent in the genome and are formed from smaller fragments.

13) Clonal libraries used to determine the sequence of a microbial genome using the whole-genome shotgun approach are typically generated by ________.

A) cloning small gene-sized DNA fragments produced by breaking chromosomal DNA with ultrasonic waves

B) cloning large DNA fragments produced by breaking chromosomal DNA with ultrasonic waves

C) cloning random PCR fragments amplified from genomic DNA

D) cloning large DNA fragments produced by restriction endonuclease cleavage

14) The whole-genome shotgun approach for collecting the data used to determine the nucleotide sequence of microbial genomes uses ________.

A) adapters that are added to genomic DNA fragments

B) powerful computers and specialized software

C) automated sequencing of random fragments of genomic DNA

D) powerful computers and specialized software and automated sequencing of random fragments of genomic DNA

15) An acronym that describes sequences of a protein-coding gene that specify the amino acid sequence is ________.

16) The proteome refers to the collection of open reading frames in a genome.

17) ORF refers to ________.

A) the location of the start site of transcription

B) the region of a gene that codes for a protein or a functional RNA product

C) the region of a gene that serves as the promoter

D) the region between the ribosome binding site and translation initiation codon

18) When two or more genes from the same genome have nucleotide sequences so alike that they most probably arose from gene duplication those genes are called ________.

A) homologs

B) orthologs

C) paralogs

D) duologs

19) ________ is the field concerned with the management and analysis of biological data using computers.

20) Nucleic acids to be analyzed using microarrays are usually tagged by covalent attachment of ________ molecules.

21) ________ technology can be used to simultaneously monitor the level of expression of every gene in a cell.

22) Expressed sequence tags are nucleotide sequences derived from cDNA molecules.

23) DNA microarray technology is used to measure the ________.

A) DNA content of cells

B) levels of specific proteins expressed by cells

C) levels of specific RNAs expressed by cells

D) genetic complexity of cells of interest

24) The genome sequence of Treponema pallidum ________.

A) almost immediately provided explanations for how this organism causes syphilis

B) should ultimately help us understand the mechanism by which this organism causes syphilis

C) identified proteins that have already been used to produce the first successful vaccine for syphilis

D) has led us to be able to completely eradicate this organism

25) Treponema pallidum ________.

A) requires protein factors found in blood

B) lacks numerous biosynthetic pathways and thus has numerous nutritional requirements

C) is missing the pathway for peptidoglycan synthesis

D) is missing several important genes essential for DNA replication

26) Analysis of the genome and transcriptome of the highly radiation resistant bacterium Deinococcus radiodurans has revealed all of the following EXCEPT ________.

A) its genome consists of two circular chromosomes and two plasmids

B) it has more DNA repair genes than E. coli

C) genes whose products are involved in DNA replication and recombination are dramatically up-regulated after irradiation

D) genes whose products are involved in cell wall metabolism and cellular transport are dramatically up-regulated after irradiation

27) The proteome refers to ________.

A) the composite database of amino acid sequences

B) the protein complex responsible for degrading ubiquitin labeled proteins

C) all of the proteins that an organism produces

D) which proteins are secreted from the cell

28) Isoelectric focusing ________.

A) separates proteins based on the pH at which they are electrically neutral

B) separates proteins based on their size and shape

C) directly reveals the identity of unknown proteins in a complex mixture

D) focuses the data gathered onto a specific protein or ORF

29) Two-dimensional gel electrophoresis ________.

A) separates proteins based on their isoelectric pH

B) separates proteins based on their size

C) can be used to resolve thousands of proteins in a complex mixture

D) All of the choices are correct.

30) Protein spots eluted from a two-dimensional gel analysis can be identified and correlated to specific genes that code for them using ________.

A) Sanger sequencing and computer analysis

B) mass spectrometry

C) gas chromatography

D) None of the choices are correct.

31) In modern proteomic analysis the amino acid sequence of a protein can be determined by ________.

A) two-dimensional gel electrophoresis

B) mass spectrometry

C) determining its nucleotide sequence

D) analysis using protein chips with appropriate probes

32) The proteome ________.

A) is another way of referring to the array of proteins that cover the surface of some prokaryotes

B) refers to the complete amino acid sequence of a protein

C) is the entire collection of proteins that an organism can produce

D) is a proteinaceous organelle of cyanobacteria that can be used as a source of carbon and fixed nitrogen

33) Since proteins are encoded by nucleotide sequences, the proteome of a microorganism can be readily inferred from the given complete nucleotide sequence of a genome and a high-speed computer with specialized software.

34) Bioinformatic analysis of genomic nucleotide sequences using specialized software and high-speed computers make it possible to determine how proteins encoded by ORFs are post-translationally modified.

35) The term "proteome" refers to the complete amino acid sequence of a protein.

36) Research focused on determining the function of different cellular proteins, protein interactions, and protein regulation is called ________ proteomics.

37) Isoelectric focusing separates proteins based on the pH at which they are electrically ________.

38) A long-term goal(s) of the bioinformatic analysis of a pathogenic bacterium is ________.

A) assembly of accurate and complete genomic nucleotide sequences

B) identification of molecules that could be used to treat genetic disorders

C) identification of molecules that can be passed to a new host

D) identification of molecules that could be used as targets by antimicrobial agents, or develop or improve a vaccine

39) In an experiment, you have created a microbial strain in which you have deleted a single gene; to evaluate the transcriptome and the proteome, you ________.

A) run microarray analysis

B) perform DNA sequencing

C) run two-dimensional gels

D) run microarray analysis and two-dimensional gels

40) Analysis of the genome of Mycobacterium tuberculosis has revealed all the following EXCEPT ________.

A) it is significantly larger than the genome of M. leprae

B) it is more closely related to M. leprae than to M. bovis

C) it has 99.5% homology with the genome of M. bovis

D) M. tuberculosis has 11 additional genomic regions compared to M. bovis

41) The subdiscipline of genomics that seeks to identify similarities and differences between genomes of different strains and species is called ________ genomics.

42) Genome analysis has revealed that horizontal gene transfer is frequently mediated by phages.

43) Mobile genetic elements that are permanently integrated into a microbial genome are known as ________ ________.

44) Mobile genetic elements that encode proteins that contribute to or confer virulence are known as contiguous sequences.

45) Which of the following is not a required characteristic of antigens from microbial pathogens that might be used in vaccine production?

A) It must be excreted or found on the surface of the pathogen.

B) It must be found in all strains of the pathogen.

C) It must be essential for the survival of the pathogen in the host.

D) All of the choices are correct.

46) Analysis of the nucleotide sequence of the genome of microorganisms has revealed important information about their metabolic potential.

47) Environmental genomics is sometimes called metagenomics.

48) The technique of ________ ________ is used to copy the genome of a single microbial cell so there is sufficient DNA for sequencing.

49) The application called multiple strand displacement amplification is a powerful tool because ________.

A) it allows single-cell genomic sequencing that can analyze uncultivated microorganisms

B) it provides data on the pathogenic nature of the microorganism

C) it identifies the transcriptome of the microorganism

D) it provides errorless sequencing results for that microorganism

50) Microbiome sequencing requires the construction of a genomic library, while whole-genome shotgun sequencing does not. 

51) Which of the following statements is correct in comparing metagenomic (next generation) sequencing to whole-genome (shotgun) sequencing?

A) Both sequencing methods utilize overlapping sequence contigs to assemble the full sequence.

B) Metagenomic sequencing uses a bacterial artificial chromosome (BAC) genomic library as the template.

C) Whole-genome sequencing does not fragment genomic sequences, but rather utilizes adaptor molecules on the template DNA.

D) Both sequencing methods have equal depth and coverage from the polymerase "reads" on the template.

52) Genes from different organisms with similar sequences or open reading frames (ORFs) are called ________.

53) One of the first sequenced genomes was for the bacterium Haemophilus influenzae. Once the genes were annotated, a(n) ________ was constructed to represent the entire genome visually.

A) physical genome map

B) color-code map

C) metagenomic map

D) ORF map

54) Which of the following is a technology that can be used to identify the DNA to which a protein binds?

A) ChIP-Seq analysis

B) RNA-seq and microarray analysis

C) PCR and RT-PCR analysis

D) Isoelectric focusing and 2D gel electrophoresis analysis

55) One reason to study DNA-protein interactions is because many proteins (e.g., regulatory proteins and proteins involved in replication and transcription) directly interact with DNA, and by understanding those interactions, we may be able to inhibit microorganism pathways in the future.

56) One area where genomics has been applied to systems biology is the study of metabolism, by using genome sequencing and annotation to lead to predictions that can be tested by transcriptomics, proteomics, and metabolomics.

57) As systems biology matured, genomics led to understanding cellular regulatory systems and a new level of metabolic engineering, called ________, such that a microbe could be constructed with novel genetic networks (e.g., rerouting amino acid biosynthetic pathways in E. coli to produce biofuels).

A) synthetic biology

B) functional proteomics 

C) metaprotein genetics

D) "parts listing"

58) Genome sequencing and annotation of metabolic pathways has led to predicted interactions that can be tested by transcriptomics, proteomics, and metabolomics. These interactions between the individual products can then be linked in a predictive network and used to construct testable hypotheses. The field best suited to investigate these statements would be ________.

A) systems biology

B) synthetic biology

C) adaptive biology

D) pathway-predictive biology

59) The field of (systems, synthetic, adaptive, descriptive) biology seeks to integrate the "parts list" of cells with the molecular interactions that become pathways, while (systems, synthetic, adaptive, descriptive) biology is interested in the development of artificial regulatory pathways to yield specific products. 

A) systems

B) synthetic

C) adaptive

D) descriptive

60) Proteins that do not align with known amino acid sequences fall into two classes: (1) (conserved hypothetical, unknown function, mystery, non-critical) proteins are encoded by genes that have matches in the database but no function has yet been assigned to any of the sequences; (2) Proteins of (conserved hypothetical, unknown function, mystery, non-critical) function are the products of genes unique to that organism. 

A) conserved hypothetical

B) unknown function

C) mystery

D) non-critical

61) The difference between Sanger sequencing and NGS is that ________.

A) Sanger sequencing is expensive and time consuming whereas NGS is faster and cheaper

B) Sanger uses a chain termination method whereas NGS uses parallel sequencing of identical fragments

C) Sanger uses dideoxynucleotide triphosphates in solution whereas NGS uses oligonucleotide adapters

D) All of the choices are correct.

62) One advantage to using NGS genome assembly over the Sanger method is that ________.

A) NGS avoids the need to insert fragments into cloning vectors, using oligonucleotide adapters that bind to a solid surface instead

B) NGS involves inserting the genomic fragments into vectors, which is an efficient process compared to using the oligonucleotide adapters employed in the Sanger method

C) NGS involves the construction of a genomic library, giving extra depth of coverage compared to the Sanger method

D) NGS sequences the same fragment no more than 10 times, avoiding wasteful processes compared to the Sanger method

63) Which of the following describes the construction of a metagenomic library?

A) A sample of ocean water is collected, the DNA is extracted and fragmented, then next-generation sequencing leads to the alignment of the 100-300 bp sequences to known microbial genomes.

B) A sample of ocean water is collected, the microbes are cultured on saline agar, then their DNA is extracted and sequenced using the Sanger method before constructing a library.

C) A sample of ocean water is collected, the DNA is extracted and fragmented, then inserted into plasmid vectors before sequencing using the Sanger chain termination method.

D) A sample of ocean water is collected and the organisms present are sequenced, which allows construction of a library containing the whole genome.

64) Bioinformatics provides database information to align proteins from novel sequences with known proteins.  If a new amino acid sequence does not match an existing sequence ________.

A) it is either a conserved hypothetical protein, i.e., the DNA matches genes in the database but they have no known function, or it is a protein of unknown function; the genes are unique to that organism

B) it is either a protein of unknown function, i.e., the DNA matches genes in the database but they have no known function, or it is a conserved hypothetical protein; the genes are unique to that organism

C) it is called an orthologue; the DNA that codes the ORF does not match any other organism in the database and the function is not known

D) it is called an paralogue; the DNA that codes the ORF does not match any other organism in the database and the function is not known

65) Which statement best reflects the main difference between the genomes of bacteria, archaea, and eukaryotes?

A) Intracellular parasites have the smallest genomes since they have evolved to lack genes that code for the synthesis of essential metabolites.

B) Eukaryotes have a high gene density compared to bacteria and archaea since their genes contain introns.

C) Eukaryotes have larger genomes than bacteria and archaea since they are larger cells.

D) Pathogens have larger genomes than non-pathogenic microbes since genome size is generally dependent on the presence of pathogenicity islands.