Deck 18: Microbial Genomics

Question 1

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

Answer 1

C

Question 2

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.

Answer 2

B

Question 3

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.

Answer 3

False

Question 4

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.

Question 5

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

A)Maxam Gilbert sequencing of cloned restriction 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.

Question 6

The method of nucleotide sequence determination that utilizes dideoxynucleotides was developed by _________.

Question 7

Automated nucleotide sequencing machines detect DNA bands by laser induced _________.

Question 8

_______________ is the field concerned with the management and analysis of biological data using computers.

Question 9

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.

Question 10

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

Question 11

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

Question 12

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

Question 13

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

Question 14

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

Question 15

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.

Question 16

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.

Question 17

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

Question 18

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

Question 19

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.

Question 20

After completing the nucleotide sequence of a microbial genome,computer translation of 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.

Question 21

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.

Question 22

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.

Question 23

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.

Question 24

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.

Question 25

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.

Question 26

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

Question 27

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

Question 28

Expressed sequence tags are nucleotide sequences derived from cDNA molecules.

Question 29

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.

Question 30

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.

Question 31

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.

Question 32

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.

Question 33

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.

Question 34

Isoelectric focusing separates proteins based on the pH at which they are electrically _________.

Question 35

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.

Question 36

The proteome

A)is another way of referring to the paracrystaline 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.

Question 37

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.

Question 38

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
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.
E)coli.

Question 39

______________ technology can be used to simultaneously monitor the level of expression of every gene in a cell.
or

Question 40

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.

Question 41

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.

Question 42

The combination of all the genes present in the human genome and those present in the trillions of microbes living in and on adults is known as the human __________.

Question 43

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.

Question 44

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

Question 45

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

Question 46

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

Question 47

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

A)physical genome map
B)color-code map
C)metagenomic map
D)ORF map

Question 48

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.

Question 49

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

Question 50

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

Question 51

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

Question 52

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

Question 53

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.

Question 54

The _____ is the collection of microorganisms (and their genes)that are normally present in and on an organism.

Question 55

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.

Question 56

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

A)ChIP-Chip and ChIP-Seq analysis
B)RNA-seq and microarray analysis
C)PCR and RT-PCR analysis
D)Isoelectric focusing and 2D gel electrophoresis analysis

Question 57

Mobile genetic elements that are permanently integrated into a microbial genome are known as _________ _________.

Question 58

The microbiome represents all the genes present in the trillions of microbes living on and in adult humans.

Question 59

Metagenomics has helped us to understand that the composition of the microbiome may be connected to many aspects of human health.

Question 60

Environmental genomics is sometimes called metagenomics.

Question 61

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

Question 62

The field of biology is interested in the development of artificial regulatory pathways to yield specific products.

Question 63

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

A)synthetic biology
B)functional proteomics
C)metaprotein genetics
D)"parts listing"
E)coli to produce biofuels).

Question 64

Proteins that do not align with known amino acid sequences fall into two classes: (1)function are the products of genes unique to that organism.