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Science
Q:
The largest cellular genomes belong to prokaryotes that are parasitic or pathogenic.
Q:
Heterotrophs need only a few more genes than autotrophs.
Q:
The key characteristic of third-generation sequencing is the ability to sequence single molecules of DNA.
Q:
Paralogs always have the same function.
Q:
Despite having smaller genomes, the protozoans Paramecium and Trichomonas have significantly more genes than humans.
Q:
Based on the evolutionary tree shown below, RubisCO Form II and RLP beta are orthologs.
Q:
Gene families are composed of homologous genes that have different evolutionary origins but the same function.
Q:
It is generally accepted that independent mutation rather than gene duplication is the mechanism for evolution of most new genes.
Q:
Reconstructing evolutionary relationships helps in differentiating between primitive and derived characteristics.
Q:
Comparative genomics helps us to understand evolutionary relationships between organisms.
Q:
Genomic analysis led to the discovery that pathogenic organisms often lack genes for amino acid biosynthesis.
Q:
Knowledge of an organism's genome sequence yields important clues to how an organism functions and its evolutionary history.
Q:
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.
Q:
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.
Q:
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.
Q:
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
Q:
RNA-Seq analysis is a method aimed at defining a(n)
A) metabolome.
B) transcriptome.
C) interactome.
D) metagenome.
Q:
Fourth-generation sequencing methods no longer use ________ to detect nucleotide incorporation.
A) mass
B) pH
C) charge
D) light
Q:
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 %
Q:
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.
Q:
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.
Q:
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.
Q:
Genome assembly relies on
A) accurate gene annotation.
B) overlap of a large numbers of short sequences.
C) codon bias.
D) systems biology.
Q:
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
Q:
Which method is most commonly used in metabolomics?
A) ion torrent semiconductor sequencing
B) mass spectrometry
C) 2D polyacrylamide gel electrophoresis
D) Sanger method
Q:
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
Q:
In addition to chromosomes, some mitochondria also contain other genetic material known as
A) plasmids.
B) transposons.
C) proteomes.
D) lysosomes.
Q:
Chloroplasts and mitochondria originated from ________ by a process known as ________.
A) bacteria / chromosome reduction
B) plants / gene deletion
C) bacteria / endosymbiosis
D) plants / endosymbiosis
Q:
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
Q:
The first genome sequenced was that of a
A) virus.
B) bacterium.
C) eukaryote.
D) archaeon.
Q:
Linking an ORF with a specific function is an example of gene
A) annotation.
B) assembly.
C) codon bias.
D) expression.
Q:
The total genetic complement of ALL cells within a microbial community is called a(n)
A) chromosomal island.
B) interactome.
C) metagenome.
D) metabolome.
Q:
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.
Q:
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.
Q:
Mobile DNA elements are more common in the genomes of
A) Archaea.
B) hyperthermophiles.
C) rapidly evolving species.
D) pathogens.
Q:
Most mobile DNA consists of
A) transposable elements.
B) introns.
C) linear chromosomes.
D) plasmids.
Q:
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.
Q:
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
Q:
Within Archaea and Bacteria, one megabasepairs of DNA encode about ________ open reading frames.
A) 10
B) 100
C) 1,000
D) 10,000
Q:
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.
Q:
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.
Q:
The entire complement of RNA produced under a given set of conditions is called a(n)
A) array.
B) genome.
C) proteome.
D) transcriptome.
Q:
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.
Q:
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.
Q:
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.
Q:
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.
Q:
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.
Q:
An open reading frame (ORF) encodes for
A) a carbohydrate.
B) a polypeptide.
C) mRNA.
D) a carbohydrate or a polypeptide.
Q:
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
Q:
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.
Q:
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) 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.
Q:
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.
Q:
________ of prokaryotic genomes are now available in public databases.
A) Dozens
B) Hundreds
C) Thousands
D) Millions
Q:
Why are microbial doubling times in nature typically longer than those obtained in the laboratory?
Q:
Justify why clinical medicine has an interest in understanding bacterial cell division at the molecular level.
Q:
Defend and explain how FtsZ-type proteins being found in mitochondria and chloroplasts strengthens or weakens the endosymbiosis theory.
Q:
Propose a growth setup that an industrial microbiologist would create to obtain large quantities of a bacteriocidal product of secondary metabolism. Be certain to explain how temperature and dissolved oxygen parameters would be selected as well as how stationary growth phase would be maintained.
Q:
Would you expect a xerophilic organism to be halotolerant? Why or why not?
Q:
Explain our present understanding of molecular adaptations to the cytoplasmic membrane that are present in thermophiles.
Q:
Explain our present understanding of molecular adaptations to the cytoplasmic membrane that are present in psychrophiles.
Q:
Explain why a hyperthermophile is unlikely to be a human pathogen.
Q:
Enumerating the viable and total cell concentration of a population of a microbial isolate can be a really laborious task for a microbiologist. Especially when a microbiologist studies the same isolate for several years, it often becomes practical to determine the relationship between optical density (OD) and cell concentration. Once this relationship (determined by a standard curve) is determined, the OD of an isolate in a broth can be routinely used to determine the population's concentration. Why must a standard curve be prepared for each isolate when using OD measurements to determine cell concentration? Also describe an experiment that would generate this type of standard curve.
Q:
Compare and contrast the spread plate method and the pour plate method of doing plate counts. Also describe which group of organisms would not be quantifiable in the pour plate method but would still be observed in the spread plate method.
Q:
Knowing the concentration of microorganisms in a sample is often an important consideration for environmental, industrial, and medical microbiologists, yet a microscope is sometimes not used to accomplish this task. Explain five major limitations to using a light microscope to directly count microorganisms.
Q:
Explain the difference between the division rate and the generation time.
Q:
Use the formulas N = N02n and g = t/n.N = final cell number, N0 = initial cell number,n = number of generations, t = time, g = generation time.Find the generation time if N = 2 x 108, N0 = 3 x 106 and t = 3 hours.
Q:
An unpressurized autoclave would not be able to sterilize a growth medium with contaminating bacteria but could still pasteurize it.
Q:
Sterility of a laminar flow hood is accomplished by filter-sterilized air passed through the hood quickly enough that non-sterile air does not flow into the work area.
Q:
A bacterium's pH optimum reflects the optimal pH of its intracellular environment.
Q:
The sensitivity of DNA and RNA is one major reason water activity can limit microbial growth.
Q:
In principle, the chemical composition of membranes in obligate acidophiles could be distinguished from neutrophiles.
Q:
Taq polymerase was isolated from a thermophile and is used in the polymerase chain reaction (PCR) technique because it does not become inactivated at high temperatures.
Q:
Due to the relationship between the rate of enzyme catalysis and temperature, organisms living in boiling hot springs are also rapid growers with fast doubling times.
Q:
Some microbes can grow in boiling water.
Q:
A non-aerated or shaken liquid growth medium inoculated with a bacterium is one of the best ways to culture an obligate anaerobe.
Q:
A bacterium such as a snow alga that is able to survive a cold temperature is called a psychrophile.
Q:
The optimum temperature is usually closer to the minimum temperature than the maximum temperature.
Q:
One reason food is refrigerated to control microbial growth is because irreversible cell damage is more likely to occur at low rather than high temperatures.
Q:
During elongation of a cell during binary fission, small gaps caused by transglycosylases are formed before cell membrane precursors can be inserted.
Q:
Identifying bactoprenol inside the rare bacteria that lack peptidoglycan would be unexpected considering its role in membrane biosynthesis.