Microbiology Final - chp 9
An open reading frame (ORF) encodes for
a polypeptide.
Chromosomal islands are similar to plasmids __________.
because both elements contain nonessential genes
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 by using genomic analyses to construct phylogenies.
A surprising finding of environmental metagenomic studies is that a majority of genes in the environment are
viral in origin.
Chromosomal islands contain clusters of genes for
virulence, biodegradation of pollutants, and symbiotic relationships.
Typically ________ of ORFs in a genome cannot clearly be assigned a function. These ORFs are usually assigned and predicted to encode hypothetical proteins.
30%
When analyzing the sequence of genes similar to ones already known, why is the amino acid sequence of the protein more important than the DNA sequence?
Analyzing the amino acid sequence is more important because it leads to more concise results. There are less options for amino acids than for codons. Grading comment: Not quite but you're on the right track. Some nt changes don't change the amino acid sequences and will thus have no effect on protein function. Looking at changes in amino acid sequence means you're looking at changes that could lead to a change in function and therefore may be subject to natural selection.
Determine why some prokaryotes have less DNA but more genes than eukaryotes.
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
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?
Legitimate genes and non-coding RNA may be missed.
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.
After transcription, mRNA may undergo significant editing. Compare and contrast RNA editing in prokaryotes and eukaryotes and connect how these differences affect genome size and gene content.
RNA editing does not occur in prokaryotes; however, in eukaryotes, RNA editing includes the addition of a polyA tail and capping and the process of splicing. Genes in eukaryotes contain introns which are removed during splicing. This means that the genome of the eukaryote is larger and contains noncoding genes that the prokaryote genome does not.
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 has a relatively short half-life compared with DNA and does not need to be as stable to perform its functions in the cell.
Design an experiment using -omic methods to test how Escherichia coli adapts to different growth temperatures.
The E. coli would need to be grown in each of the temperatures to be studied. The different cultures would then need to be tested with the different -omic methods to determine what processes change with a change in temperature. RNA-seq could be used to determine the how the expression of different genes changes in the different environments (temperatures). Also, mass spectrometry could be used to determine what metabolites are present at the different temperatures.
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 organic material, particularly amino acids and proteins.
Which of these organisms is likely to have the largest genome?
a yeast cell
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)
chloroplast
When compared with Bacteria, species of Archaea seem to devote a higher percentage of their genomes to genes encoding proteins involved in
energy and coenzyme production.
Arrange the following genetic components in the correct order.
genome, transcriptome, proteome, metabolome
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 ________.
homologous / gene families
Transcriptome analysis is useful in relation to genome analysis because
it analyzes RNA, thus it reveals which genes are expressed under different conditions.
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?
metaproteomics
Genome assembly relies on
overlap of a large numbers of short sequences.
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?
percentage of GC content and codon usage
The pan genome of a species is the genomic content that is
present in one or more strains of the same species.
Mobile DNA elements are more common in the genomes of
rapidly evolving species.
RNA-Seq analysis is a method aimed at defining a(n)
transcriptome.