Deck 16: Microbial Genomics

Question 1

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.

Answer 1

B

Question 2

Well equipped genomic sequencing laboratories can determine the sequence of a genome of a particular bacterial species in a time frame of approximately

A) 1 day.
B) 4 months.
C) 4 years.
D) 8 to 10 years.

Answer 2

B

Question 3

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.

Answer 3

False

Question 4

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

Question 5

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 6

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 7

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

Question 8

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 9

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

Question 10

Each of the four Sanger sequencing reactions include

A) a combination of the four different dideoxynucleotides.
B) a single dideoxynucleotide triphosphate.
C) ATP.
D) both a combination of the four different dideoxynucleotides and ATP

Question 11

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

Question 12

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

Question 13

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

Question 14

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.

Question 15

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

Question 16

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

Question 17

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 18

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.

Question 19

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

Question 20

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

Question 21

In modern proteomic analysis the amino acid sequence of a protein can be determined by

A) 2D gel electrophoresis.
B) mass spectrometry.
C) determining its nucleotide sequence.
D) analysis using protein chips with appropriate probes.

Question 22

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 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

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

Question 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.

Question 26

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) all of the above are characteristics of M. tuberculosis.

Question 27

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

Question 28

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) none of the choices

Question 29

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 30

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 develop or improve a vaccine.
C) identification of molecules that can be targeted by antimicrobial agents.
D) identification of molecules that could be used to develop or improve a vaccine and identification of molecules that can be targeted by antimicrobial agents

Question 31

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

Question 32

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

Question 33

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

Question 34

Protein spots eluted from a 2 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

Question 35

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) none of the choices

Question 36

Expressed sequence tags are nucleotide sequences derived from cDNA molecules.

Question 37

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 38

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) Both almost immediately provided explanations for how this organism causes syphilis and identified proteins that have already been used to produce the first successful vaccine for syphilis are correct.

Question 39

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 40

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 41

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 required characteristics.

Question 42

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

Question 43

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

Question 44

Environmental genomics is sometimes called metagenomics.

Question 45

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

Question 46

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

Question 47

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

Question 48

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 49

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

Question 50

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