Question 1

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)

Accepted Answer

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

Question 2

Genomes of species in both Bacteria and Archaea show a strong correlation between genome size and

Accepted Answer

A)  noncoding RNA. 
B)  codon bias. 
C)  number of ORFs. 
D)  number of introns. 
A)  noncoding RNA. 
B)  codon bias. 
C)  number of ORFs. 
D)  number of introns.

Question 3

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.

Accepted Answer

Genome diversity is likely to be high du

Question 4

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

Accepted Answer

A) True 
 B)False

Question 5

Few genes in all organisms have common evolutionary roots.

Accepted Answer

A) True 
 B)False

Question 6

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

Accepted Answer

Certain proteins might not be synthesize

Question 7

The advantage(s) of second-generation DNA sequencing compared to the Sanger method are the result of

Accepted Answer

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. 
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 8

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?

Accepted Answer

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

Question 9

Explain why parasitic and endosymbiotic organisms such as Tremblaya and Hodgkinia can have unusually small genomes and what genes they may lack.

Accepted Answer

These organisms coexist with another org

Question 10

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

Accepted Answer

A) True 
 B)False

Question 11

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

Accepted Answer

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. 
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 12

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

Accepted Answer

A) True 
 B)False

Question 13

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

Accepted Answer

A) True 
 B)False

Question 14

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

Accepted Answer

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

Question 15

The most abundant genes in prokaryotic genomes are

Accepted Answer

A)  those involved in metabolism. 
B)  those involved in translation. 
C)  those involved in transport. 
D)  those involved in DNA replication. 
A)  those involved in metabolism. 
B)  those involved in translation. 
C)  those involved in transport. 
D)  those involved in DNA replication.

Question 16

The pan genome of a species is the genomic content that is

Accepted Answer

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. 
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 17

Codon usage varies from one organism to the next.

Accepted Answer

A) True 
 B)False

Question 18

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

Accepted Answer

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

Question 19

The very first DNA sequencing technology called the Sanger method relies on

Accepted Answer

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. 
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.

Question 20

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

Accepted Answer

One could grow E. coli in identical flas

Exam 9: Microbial Systems Biology

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)

Genomes of species in both Bacteria and Archaea show a strong correlation between genome size and

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.

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

Few genes in all organisms have common evolutionary roots.

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

The advantage(s) of second-generation DNA sequencing compared to the Sanger method are the result of

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?

Explain why parasitic and endosymbiotic organisms such as Tremblaya and Hodgkinia can have unusually small genomes and what genes they may lack.

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

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

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

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

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

The most abundant genes in prokaryotic genomes are

The pan genome of a species is the genomic content that is

Codon usage varies from one organism to the next.

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

The very first DNA sequencing technology called the Sanger method relies on

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

The Microbial World

Microbial Cell Structure and Function

Microbial Metabolism

Molecular Information Flow and Protein Processing

Microbial Growth and Its Control

Microbial Regulatory Systems

Molecular Biology of Microbial Growth

Viruses and Their Replication

Viral Genomics, Diversity, and Ecology

Genetics of Bacteria and Archaea

Biotechnology and Synthetic Biology

Microbial Evolution and Systematics

Metabolic Diversity of Microorganisms

Functional Diversity of Microorganisms

Diversity of Bacteria

Diversity of Archaea

Diversity of Microbial Eukarya

Taking the Measure of Microbial Systems

Microbial Ecosystems

Nutrient Cycles

Microbiology of the Built Environment

Microbial Symbioses

Microbial Symbioses with Humans

Microbial Infection and Pathogenesis

Innate Immunity: Broadly Specific Host Defenses

Adaptive Immunity: Highly Specific Host Defenses

Clinical Microbiology and Immunology

Epidemiology

Person-to-Person Bacterial and Viral Diseases

Vectorborne and Soilborne Bacterial and Viral Diseases

Waterborne and Foodborne Bacterial and Viral Diseases

Eukaryotic Pathogens: Fungi, Protozoans, and Helminths

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