Deck 9: Microbial Systems Biology

Question 1

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.

Answer 1

A

Question 2

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

Answer 2

A

Question 3

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.

Answer 3

B

Question 4

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.

Question 5

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.

Question 6

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.

Question 7

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.

Question 8

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

Question 9

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.

Question 10

The entire complement of RNA produced under a given set of conditions is called a(n)

A) array.
B) genome.
C) proteome.
D) transcriptome.

Question 11

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

A) 10
B) 100
C) 1,000
D) 10,000

Question 12

Most mobile DNA consists of

A) transposable elements.
B) introns.
C) linear chromosomes.
D) plasmids.

Question 13

An open reading frame (ORF) encodes for

A) a carbohydrate.
B) a polypeptide.
C) a lipid.
D) a carbohydrate or a polypeptide.

Question 14

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.

Question 15

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.

Question 16

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) 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.

Question 17

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.

Question 18

Mobile DNA elements are more common in the genomes of

A) Archaea.
B) hyperthermophiles.
C) rapidly evolving species.
D) pathogens.

Question 19

________ of prokaryotic genomes are now available in public databases.

A) Dozens
B) Hundreds
C) Thousands
D) Millions

Question 20

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.

Question 21

The total genetic complement of all cells within a microbial community is called a(n)

A) chromosomal island.
B) interactome.
C) metagenome.
D) metabolome.

Question 22

Which method is most commonly used in metabolomics?

A) ion torrent semiconductor sequencing
B) mass spectrometry
C) 2D polyacrylamide gel electrophoresis
D) Sanger method

Question 23

Genome assembly relies on

A) accurate gene annotation.
B) overlap of a large numbers of short sequences.
C) codon bias.
D) systems biology.

Question 24

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.

Question 25

Fourth-generation sequencing methods no longer use ________ to detect nucleotide incorporation.

A) mass
B) pH
C) charge
D) light

Question 26

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

Question 27

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%

Question 28

Linking an ORF with a specific function is an example of gene

A) annotation.
B) assembly.
C) codon bias.
D) expression.

Question 29

The first genome sequenced was that of a(n)

A) virus.
B) bacterium.
C) eukaryote.
D) archaeon.

Question 30

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.

Question 31

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.

Question 32

In general, prokaryotic genome size is linked to its metabolism and interaction with the environment. Which type of prokaryote typically has the smallest genome?

A) parasite
B) endosymbiont
C) autotroph
D) free-living heterotroph

Question 33

Genes encoding 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.

Question 34

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.

Question 35

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.

Question 36

Gene function is annotated based on homology between the ORFs of a genome and proteins whose function has been proven experimentally. What ʺ-omicʺ approach could help us determine the function and structure of proteins encoded by uncharacterized ORFs?

A) metabolomics
B) metagenomics
C) transcriptomics
D) proteomics

Question 37

Chloroplasts and mitochondria originated from ________ by a process known as ________.

A) bacteria / chromosome reduction
B) plants / gene deletion
C) bacteria / endosymbiosis
D) plants / endosymbiosis

Question 38

RNA-Seq analysis is a method aimed at defining a(n)

A) metabolome.
B) transcriptome.
C) interactome.
D) metagenome.

Question 39

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

Question 40

In addition to chromosomes, some mitochondria also contain other genetic material known as

A) plasmids.
B) transposons.
C) proteomes.
D) lysosomes.

Question 41

Genes for DNA replication and transcription make up only a small fraction of the typical prokaryotic genome.

Question 42

Chromosomal rearrangements due to insertion sequences have apparently contributed to the evolution of several human pathogens.

Question 43

Codon usage varies from one organism to the next.

Question 44

It is generally accepted that independent mutation rather than gene duplication is the mechanism for evolution of most new genes.

Question 45

Why has research in metabolomics been slower than in genomics, transcriptomics, and proteomics?

A) Screening for metabolites is technically challenging due to their diversity.
B) Procedures have not yet been developed for studying the metabolome.
C) The molecules studied in metabolomics are too small for easy analysis.
D) Individual cells are too small to allow metabolomic analysis using existing techniques.

Question 46

The key characteristic of third-generation sequencing is the ability to sequence single molecules of DNA.

Question 47

Knowledge of an organism's genome sequence yields important clues to how an organism functions and its evolutionary history.

Question 48

Which "omic" is most directly involved in identifying molecules as possible drug targets that can be used to develop new medications?

A) proteomics
B) genomics
C) transcriptomics
D) metabolomics

Question 49

The largest cellular genomes belong to prokaryotes that are parasitic or pathogenic.

Question 50

Comparative genomics helps us to understand evolutionary relationships between organisms.

Question 51

Few genes in all organisms have common evolutionary roots.

Question 52

Despite having smaller genomes, the protozoans Paramecium and Trichomonas have significantly more genes than humans.

Question 53

Some virulence genes are carried on plasmids or by lysogenic bacteriophages.

Question 54

Genomic analysis led to the discovery that pathogenic organisms often lack genes for amino acid biosynthesis.

Question 55

Reconstructing evolutionary relationships helps in differentiating between primitive and derived characteristics.

Question 56

Horizontally transferred genes typically encode essential metabolic functions such as DNA replication, transcription, and translation.

Question 57

Paralogs always have the same function.

Question 58

Gene families are composed of homologous genes that have different evolutionary origins but the same function.

Question 59

The relative percentage of genes devoted to protein synthesis in small-genome organisms is high compared with that of large-genome organisms.

Question 60

Based on the evolutionary tree shown below, RubisCO Form II and RLP beta are orthologs.

Question 61

Microorganisms that grow in extreme environments typically contain larger genomes when compared to microbes that grow in non-extreme environments.

Question 62

Most chloroplast genes are those responsible for photosynthesis and other demands of autotrophy.

Question 63

Explain the terms ʺcore genomeʺ and ʺpan genomeʺ and describe how each contributes to the genome of a bacterial species. Give an example of genes that are part of a core genome versus those that are more often in the pan genome.

Question 64

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

Question 65

Explain how mass spectrometry (MS) has aided in the progression of the field of metabolomics.

Question 66

Why are the words ʺaboutʺ and ʺapproximatelyʺ used in discussing the results of genomic analysis? Predict what advances in knowledge or methods could change our understanding of a genome sequence.

Question 67

Recommend what type of data should be collected and analyzed in a systems biology approach to investigate how a non-pathogenic bacterial strain becomes pathogenic. Describe what scientific fields and methods would be involved in your recommendation.

Question 68

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.

Question 69

Explain why organisms undergoing rapid evolutionary change often contain relatively large numbers of mobile DNA elements, whereas once organisms settle into a stable evolutionary niche, most of these mobile elements are lost.

Question 70

The intracellular parasite Nanoarchaeum equitans has one of the smallest prokaryotic genomes. Why is the genome of N. equitans so small? How is it possible that the genome of N. equitans contains more genes than that of Mycoplasma genitalium, which is actually 90 kbp larger?

Question 71

Explain horizontal gene transfer and demonstrate how this phenomenon has complicated evolutionary studies using a diagram that illustrates phylogenetic relationships between organisms and genes.

Question 72

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.

Question 73

With modern molecular techniques, it is now possible to completely assemble a genome from a single cell.

Question 74

Explain why larger genomes contain more genes devoted to regulation than smaller genomes and why these genes increase the competitiveness of organisms.

Question 75

Explain how codon bias and GC content can be used to detect horizontal gene transfer within a genome.

Question 76

Explain why the proteome is NOT defined as ʺall the proteins encoded by an organismʹs genome.ʺ

Question 77

Chromosomal islands are presumed to have a ʺforeignʺ origin based upon three observations. What are these observations and how do they indicate that chromosomal islands are ʺforeignʺ in origin?

Question 78

Interpret the genomic content of mitochondria in relation to their evolution. How is mitochondrial evolution more complicated than expected?

Question 79

What process allows evolution to ʺexperimentʺ with genes to create novel functions? How is this manifested in extant genes (presently existing) and their relationships to each other?

Question 80

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?