Chapter 9 Homework Questions

Within Archaea and Bacteria, one megabase pair (Mbp) of DNA encodes about ________ open reading frames. 100 10 1,000 10,000

1,000

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

Eukaryotes have more introns in their chromosomes

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

Homo sapiens > Arabidopsis thaliana > Plasmodium falciparum > Cryptosporidium parvum

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

Legitimate genes and non-coding RNA may be missed.

An open reading frame (ORF) encodes for a carbohydrate or a polypeptide. a lipid. a polypeptide. a carbohydrate.

a polypeptide.

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

a yeast cell

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

because both elements contain nonessential genes

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

it analyzes RNA, thus it reveals which genes are expressed under different conditions.

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

present in one or more strains of the same species.

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? transcriptomics metagenomics proteomics metabolomics

proteomics

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

rapidly evolving species.

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) autotrophic bacterium. chloroplast. plant. autotrophic archaeon.

chloroplast.

A surprising finding of environmental metagenomic studies is that a majority of genes in the environment are from microbes grown in the lab. from extinct microorganisms. eukaryotic in origin. viral in origin.

viral in origin.

Chromosomal islands contain clusters of genes for antibiotic resistance. virulence, biodegradation of pollutants, and symbiotic relationships. catabolic and anabolic reactions. DNA repair and replication.

virulence, biodegradation of pollutants, and symbiotic relationships.

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? Possibly; it would depend on whether the gene was essential for survival and on whether you could create a diploid bacteria as well. No, the knockout technique is not ever possible in haploid organisms. Yes; knockout mutations can be used for any genes. 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.

Possibly; it would depend on whether the gene was essential for survival and on whether you could create a diploid bacteria as well.

Design an experiment using -omic methods to test how Escherichia coli adapts to different growth temperatures.

Proteomics studies the structure, function, and activity of proteins within an organism. As the environment changes, the number and types of proteins varies. The proteome of an organism can be analyzed using mass spectrometry or high pressure liquid chromatography. Metabolomics studies the complete set of metabolic intermediates produced by an organism. NMR can be used, but is not as successful as MALDI-TOF mass spectrometry. Transcriptomics studies the total RNA produced in an organism under a specific set of conditions. This can be analyzed through microarrays and RNA-Seq. All of these -omic methods can be tested at various temperatures to see how a microorganism, like E. coli, would survive with changing conditions.

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? RNA is usually single-stranded, and the double-stranded nature of DNA makes it more stable. DNA has a more stable structure because the deoxyribose in DNA is a larger molecule than the ribose in RNA. RNA molecules are shorter than DNA molecules, making them more stable. 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.

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.

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? The bacteria should be classified with the other bacteria that use the most similar biochemical pathways. The bacteria should be classified with other bacteria that have the most similar morphology. The bacteria should be classified by using genomic analyses to construct phylogenies. Because of their unusual metabolic pathways, the bacteria should be classified in a new group.

The bacteria should be classified by using genomic analyses to construct phylogenies.

You are interested in the minimum set of genes necessary for survival of a eukaryotic microorganism such as Saccharomyces cerevisiae. Design an experiment to systematically test which genes are essential for survival and which are not under high nutrient, aerobic conditions.

The genome of S. cerevisiae should first be sequenced with a next-generation sequencing method since the genome is larger than 800 nucleotides. The genome should then be assembled by putting fragments in the right order and deleting overlaps. Next, the genome should be annotated to identify genes and other significant regions. The various interactions, proteins, etc essential for survival under these conditions should be analyzed. It may be useful to remove genes to see if the bacteria can survive without it. If it is unable to survive, then that gene is essential for survival. This process can be repeated for every gene.

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? The organism lives in an environment rich in lipids. The organism lives in an environment rich in sugars. The organism lives in an environment rich in organic material, particularly amino acids and proteins. The organism lives in an environment rich in hydrocarbons.

The organism lives in an environment rich in organic material, particularly amino acids and proteins.

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? metabolomics metagenomics metaproteomics genomics

metaproteomics

The advantage(s) of second-generation DNA sequencing compared to the Sanger method are the result of miniaturization of reaction size and increased computer power. increased length of DNA sequences obtained. increased computing power. miniaturization of reaction size.

miniaturization of reaction size and increased computer power.

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

percentage of GC content and codon usage

In Sanger sequencing and in many newer sequencing techniques, labeled precursors are used. What are these precursors? Hints DNA polymerase fluorescent dyes primers or nucleotides that will be incorporated into the newly synthesized DNA RNA

primers or nucleotides that will be incorporated into the newly synthesized DNA

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

transcriptome.