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Questions and Answers List

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Question	Answer
________ of prokaryotic genomes are now available in public databases. A) Dozens B) Hundreds C) Thousands D) Millions	C) Thousands
When comparing genes from Archaea, Bacteria, and Eukarya, which statement is TRUE? A) Almost all archaeal genes are more similar to eukaryotic genes than to bacterial genes. B) Almost all archaeal genes are more similar to bacterial genes than to eukaryotic genes. 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. D) Archaeal genes are almost universally unique; very few are similar to either eukaryotic or bacterial genes.	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.
Based on the table of average intron frequency given below, predict the relative order of genome size for these four eukaryotic organisms. A) Homo sapiens > Arabidopsis thaliana > Plasmodium falciparum > Cryptosporidium parvum B) Cryptosporidium parvum > Plasmodium falciparum > Arabidopsis thaliana > Homo sapiens C) Homo sapiens > Cryptosporidium parvum > Plasmodium falciparum > Arabidopsis thaliana D) Intron frequency cannot be used to predict genome size in eukaryotes.	A) Homo sapiens > Arabidopsis thaliana > Plasmodium falciparum > Cryptosporidium parvum
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) A) plant. B) autotrophic bacterium. C) chloroplast. D) autotrophic archaeon.	C) chloroplast.
The evolutionary origin of mitochondria is demonstrated by which of the following key genomic characteristics? A) variable numbers of protein-encoding genes B) large stretches of AT-rich DNA C) linear and circular genome structure in different organisms D) rRNA genes most closely related to Bacteria	D) rRNA genes most closely related to Bacteria
An open reading frame (ORF) encodes for A) a carbohydrate. B) a polypeptide. C) mRNA. D) a carbohydrate or a polypeptide.	B) a polypeptide.
The pan genome of a species is the genomic content that is A) common to all strains of the same species. B) present in one or more strains of the same species. C) shared with all other prokaryotes. D) hypothetical or uncharacterized genome content of a species.	B) present in one or more strains of the same species.
Microarrays can be used to A) analyze global gene expression. B) detect pathogens. C) detect unwanted food additives or substitutes. D) detect pathogens, analyze global gene expression, and detect unwanted food additives or substitutes.	D) detect pathogens, analyze global gene expression, and detect unwanted food additives or substitutes.
Transcriptome analysis is useful in relation to genome analysis because A) it is NOT dependent on nucleic acid sequencing technology. B) it results in amino acid sequence and is, thus, easier to analyze. C) it analyzes RNA, thus it reveals which genes are expressed under different conditions. D) it reveals interactions between molecules and, thus, provides more information than genome analysis.	C) it analyzes RNA, thus it reveals which genes are expressed under different conditions.
The most abundant genes in prokaryotic genomes are A) those involved in metabolism. B) those involved in translation. C) those involved in transport. D) those involved in DNA replication	A) those involved in metabolism.
When compared with Bacteria, species of Archaea seem to devote a higher percentage of their genomes to genes encoding proteins involved in A) transcription. B) energy and coenzyme production. C) cell membrane functions. D) carbohydrate metabolism.	B) energy and coenzyme production.
The entire complement of RNA produced under a given set of conditions is called a(n) A) array. B) genome. C) proteome. D) transcriptome.	D) transcriptome.
The very first DNA sequencing technology called the Sanger method relies on A) nanopore technology that separates DNA molecules based on charge differences. B) the incorporation of dideoxynucleotides that terminate chain extension during DNA synthesis. C) nuclear magnetic resonance (NMR) analysis. D) the release of protons whenever a new nucleotide is added to a growing strand of DNA.	B) the incorporation of dideoxynucleotides that terminate chain extension during DNA synthesis.
The advantage(s) of second-generation DNA sequencing compared to the Sanger method are the result of A) miniaturization of reaction size. B) increased computing power. C) increased length of DNA sequences obtained. D) miniaturization of reaction size and increased computer power.	D) miniaturization of reaction size and increased computer power.
Within Archaea and Bacteria, one megabasepairs of DNA encode about ________ open reading frames. A) 10 B) 100 C) 1,000 D) 10,000	C) 1,000
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? A) percentage of GC content and codon usage B) genome size and number of introns C) number of genes in the pan genome D) ribosomal binding site and intron sequence	A) percentage of GC content and codon usage
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 A) metagenomics. B) proteomics. C) bioinformatics. D) genomics.	C) bioinformatics.
Most mobile DNA consists of A) transposable elements. B) introns. C) linear chromosomes. D) plasmids.	A) transposable elements.
Mobile DNA elements are more common in the genomes of A) Archaea. B) hyperthermophiles. C) rapidly evolving species. D) pathogens.	C) rapidly evolving species.
Chromosomal islands contain clusters of genes for A) DNA repair and replication. B) virulence, biodegradation of pollutants, and symbiotic relationships. C) catabolic and anabolic reactions. D) antibiotic resistance.	B) virulence, biodegradation of pollutants, and symbiotic relationships.
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? A) Too many ORFS are identified, most of which are stretches on non-coding junk DNA. B) Codon bias causes incorrect annotations. C) Unusual, but legitimate genes and non-coding RNA may be missed. D) We lack the computing power to complete the analyses in a timely manner, thus many genomes are only partially annotated.	C) Unusual, but legitimate genes and non-coding RNA may be missed.
The total genetic complement of ALL cells within a microbial community is called a(n) A) chromosomal island. B) interactome. C) metagenome. D) metabolome.	C) metagenome.
Linking an ORF with a specific function is an example of gene A) annotation. B) assembly. C) codon bias. D) expression.	A) annotation.
The first genome sequenced was that of a A) virus. B) bacterium. C) eukaryote. D) archaeon.	A) virus.
In general, prokaryotic genome size is correlated to lifestyle. Which type of prokaryote typically has the smallest genome? A) parasite B) endosymbiont C) autotroph D) free-living heterotroph	B) endosymbiont
Chloroplasts and mitochondria originated from ________ by a process known as ________. A) bacteria / chromosome reduction B) plants / gene deletion C) bacteria / endosymbiosis D) plants / endosymbiosis	C) bacteria / endosymbiosis
In addition to chromosomes, some mitochondria also contain other genetic material known as A) plasmids. B) transposons. C) proteomes. D) lysosomes.	A) plasmids.
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? A) metabolomics B) metagenomics C) transcriptomics D) proteomics	D) proteomics
Which method is most commonly used in metabolomics? A) ion torrent semiconductor sequencing B) mass spectrometry C) 2D polyacrylamide gel electrophoresis D) Sanger method	B) mass spectrometry
Many of the genes in the chloroplast genome encode proteins involved in ________, whereas mitochondrial genomes primarily encode proteins involved in ________. A) autotrophy / DNA replication B) photosynthesis / glycolysis C) autotrophy / glycolysis D) photosynthesis / oxidative phosphorylation	D) photosynthesis / oxidative phosphorylation
Genome assembly relies on A) accurate gene annotation. B) overlap of a large numbers of short sequences. C) codon bias. D) systems biology.	B) overlap of a large numbers of short sequences.
The core genome of a prokaryotic species is the genomic content that is A) unique compared to all other prokaryotes. B) expressed under all environmental conditions. C) shared between all other prokaryotes. D) shared between all strains of a species.	C) shared between all other prokaryotes.
Compounds such as pyruvate, acetyl-CoA, fructose-6-phosphate, oxaloacetate, and other small organic compounds could be part of a(n) A) metagenome. B) metabolome. C) interactome. D) transcriptome.	B) metabolome.
Genomes of species in both Bacteria and Archaea show a strong correlation between genome size and A) noncoding RNA. B) codon bias. C) number of ORFs. D) number of introns.	C) number of ORFs.
Typically ________ of ORFs in a genome cannot clearly be assigned a function. These ORFs are usually assigned and predicted to encode hypothetical proteins. A) < 1 % B) 5 % C) 30 % D) 90 %	C) 30 %
Fourth-generation sequencing methods no longer use ________ to detect nucleotide incorporation. A) mass B) pH C) charge D) light	D) light
RNA-Seq analysis is a method aimed at defining a(n) A) metabolome. B) transcriptome. C) interactome. D) metagenome.	B) transcriptome.
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 ________. A) homologous / gene families B) paralogous / functional genes C) orthologous / gene families D) homologous / functional genes	A) homologous / gene families
Horizontal gene transfer A) is rare and only occurs between closely related strains. B) is common and may sometime occur between unrelated organisms. C) does not provide an advantage to organisms. D) only occurs in prokaryotes.	B) is common and may sometime occur between unrelated organisms.
Horizontal gene transfer has been thoroughly documented for genes involved in A) DNA replication and repair. B) virulence and metabolic functions. C) only very few processes. D) translation.	B) virulence and metabolic functions.
A surprising finding of environmental metagenomic studies is that a majority of genes in the environment are A) from microbes grown in the lab. B) viral in origin. C) eukaryotic in origin. D) from extinct microorganisms.	B) viral in origin.
Knowledge of an organism's genome sequence yields important clues to how an organism functions and its evolutionary history.	TRUE
Genomic analysis led to the discovery that pathogenic organisms often lack genes for amino acid biosynthesis.	TRUE
Comparative genomics helps us to understand evolutionary relationships between organisms.	TRUE
Reconstructing evolutionary relationships helps in differentiating between primitive and derived characteristics.	TRUE
It is generally accepted that independent mutation rather than gene duplication is the mechanism for evolution of most new genes.	FALSE
Gene families are composed of homologous genes that have different evolutionary origins but the same function.	FALSE
Based on the evolutionary tree shown below, RubisCO Form II and RLP beta are orthologs.	FALSE
Despite having smaller genomes, the protozoans Paramecium and Trichomonas have significantly more genes than humans.	TRUE
Paralogs always have the same function.	FALSE
The key characteristic of third-generation sequencing is the ability to sequence single molecules of DNA.	TRUE
Heterotrophs need only a few more genes than autotrophs.	FALSE
The largest cellular genomes belong to prokaryotes that are parasitic or pathogenic.	FALSE
Codon usage and even the genetic code itself varies from one organism to the next.	TRUE
Genes for DNA replication and transcription make up only a small fraction of the typical prokaryotic genome.	TRUE
The relative percentage of genes devoted to protein synthesis in small-genome organisms is high compared with that of large-genome organisms.	TRUE
Few genes in all organisms have common evolutionary roots.	FALSE
Horizontally transferred genes typically encode essential metabolic functions such as DNA replication, transcription, and translation.	FALSE
Chromosomal rearrangements due to insertion sequences have apparently contributed to the evolution of several human pathogens.	TRUE
Some virulence genes are carried on plasmids or lysogenic bacteriophages.	TRUE
Microorganisms that grow in extreme environments typically contain larger genomes when compared to microbes that grow in non-extreme environments.	FALSE
With modern molecular techniques, it is now possible to completely assemble a genome from a single cell.	TRUE