BLY 314 CH 9 HW - after midterm

Chromosomal islands are similar to plasmids __________. A. because both elements contain nonessential genes B. because both elements contain inverted repeats C. because both elements replicate independently of the chromosome D. because both elements are found separate from the chromosome

A

Researchers using molecular analyses, including sequencing technology, may be interested in studying horizontal gene transfer because it plays such an important role in microbial evolution. Genome sequencing has led to insights about this type of genetic transfer between a wide range of organisms, even in very different taxa. This is another area in which portable, inexpensive sequencing will expand the research that can be done. If a researcher wanted to understand whether a particular species of non-pathogenic bacteria had obtained genes via horizontal gene transfer, which of the following would be true? A. They should focus their attention on metabolic genes. B. They should focus their attention on virulence genes. C. They should focus their attention on the genes for DNA replication. D. They should focus their attention on the genes for gene expression.

A

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. chloroplast. B. plant. C. autotrophic archaeon. D. autotrophic bacterium.

A

Portable sequencers and other portable, efficient equipment for molecular analysis make genomic analyses easier to do in a wide range of conditions. These types of analyses can provide a great deal of information, from metabolic profiles to genome sizes. How would researchers accomplish this type of work?

1. isolation of genetic material 2. genome sequencing 3. genome assemble 4. genome annotation/determination of open reading frame 5. comparative genomics

RNA-Seq analysis is a method aimed at defining a(n) A. interactome. B. metagenome. C. metabolome. D. transcriptome.

D

Arrange the following genetic components in the correct order. A. genome, proteome, transcriptome, metabolome B. genome, transcriptome, proteome, metabolome C. genome, transcriptome, metabolome, proteome D. genome, metabolome, transcriptome, proteome

B

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

B

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

Mobile DNA elements are more common in the genomes of A. Archaea. B. rapidly evolving species. C. hyperthermophiles. D. pathogens.

B

You are interested in trying to determine the function of a particular gene in a common bacterium (meaning that it has a haploid genome). To do this, could you use a knockout mutation? A. Yes; the second copy of the gene would continue to function and allow the organism to live even if the gene encoded an essential gene product. B. Possibly; it would depend on whether the gene was essential for survival and on whether you could create a diploid bacteria as well. C. Yes; knockout mutations can be used for any genes. D. No, the knockout technique is not ever possible in haploid organisms.

B

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

C

Functional analysis of the genome of a prokaryote shows that 20% of the genome is for metabolism, 1 % for biosynthesis of amino acids, 8% for peptide ABC transporters, and 2% for replication. What can you determine about the environment in which this organism lives? A. The organism lives in an environment rich in lipids. B. The organism lives in an environment rich in sugars. C. The organism lives in an environment rich in organic material, particularly amino acids and proteins. D. The organism lives in an environment rich in hydrocarbons.

C

Sequencing with devices such as the MinION can be used to study individual organisms. However, researchers sometimes also study the genetics of an entire community in an environmental sample (metagenomics) without distinguishing individual organisms. Why would researchers study the metagenome of an entire community in this way rather than separating out individual species? A. The researchers may be interested in determining DNA contributions from different sources (such as viruses and dead bacteria). B. Studying the entire community is always more useful. C. The microbial community may be more complex. D. a & b

D

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. carbohydrate metabolism. C. cell membrane functions. D. energy and coenzyme production.

D

Which of these organisms is likely to have the largest genome? A. an extremophile Archaean due to the demands of surviving in harsh environments B. an autotrophic bacterium C. a chloroplast D. a yeast cell

D

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

D

the study of the entire genetic makeup of an organism.

genomics

Just by knowing that a particular organism is an archaean, it is possible to predict that its genome ___________those of most Bacteria.

may contain more unidentified genes than

the study of all of the proteins produced by an organism.

proteomics

Not suggestive of horizontal gene transfer

-identification of an unusually large genome -identification of a high number of metabolic genes -identification of a high GC content within the entire genome

Suggestive of horizontal gene transfer

- identification of genes typically found in other, distantly related species -identification of a segment with an unusual codon bias compared with the rest of the genome - identification of a DNA segment that has a distinctive GC content compared with other segments of the genome

An open reading frame (ORF) encodes for A. a polypeptide. B. a carbohydrate. C. a lipid. D. a carbohydrate or a polypeptide.

A

If a researcher wanted to compare the enzymatic capacity to degrade compounds in a water column at various depths under a specific set of conditions, which would be the most useful approach? A. metagenomics B. metaproteomics C. metabolomics D. genomics

B

In DNA replication in vivo, RNA primers are used. However, researchers used DNA primers instead in the lab because DNA primers are more stable. Why might this be the case? A. DNA has a more stable structure because the deoxyribose in DNA is a larger molecule than the ribose in RNA. B. RNA has a relatively short half-life compared with DNA and does not need to be as stable to perform its functions in the cell. C.RNA is usually single-stranded, and the double-stranded nature of DNA makes it more stable. D. RNA molecules are shorter than DNA molecules, making them more stable.

B

Researchers discover a new species of bacterium that has an unusual metabolism. However, it has biochemical and morphological similarities to other species. What is the most comprehensive and effective approach to determine how to classify these bacteria? A. Because of their unusual metabolic pathways, the bacteria should be classified in a new group. B. The bacteria should be classified by using genomic analyses to construct phylogenies. C. The bacteria should be classified with other bacteria that have the most similar morphology. D. The bacteria should be classified with the other bacteria that use the most similar biochemical pathways.

B

The pan genome of a species is the genomic content that is A. shared with all other prokaryotes. B. present in one or more strains of the same species. C. hypothetical or uncharacterized genome content of a species. D. common to all strains of the same species.

B

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. 30% C. 5% D. 90%

B

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

C

Determine why some prokaryotes have less DNA but more genes than eukaryotes. A. Eukaryotes have more exons in their chromosomes. B. Eukaryotes do not have introns in their chromosomes. C. Prokaryotes have more introns in their chromosomes. D. Eukaryotes have more introns in their chromosomes.

D

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. orthologous / gene families B. homologous / functional genes C. paralogous / functional genes D. homologous / gene families

D

Genome assembly relies on A. systems biology. B. codon bias. C. accurate gene annotation. D. overlap of a large numbers of short sequences.

D

Just by knowing that a bacterium is a autotroph, it is possible to predict that its genome _______ those of average heterotrophs.

is larger than than

Just by knowing that N. equitans is a parasite, it is possible to predict that its genome ______those of most other hyperthermophiles.

is smaller than than

the study of all intermediates and small molecules produced by reactions within an organism.

metabolomics

the study of all of the genetic material of all organisms in a particular habitat.

metagenomics

the study of all of the RNA produced by an organism.

transcriptomics