Question 1

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

Accepted Answer

Answers will vary, but one explanation i

Question 2

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

Accepted Answer

Due to the complex nature of all possibl

Question 3

The first genome sequenced was that of a(n)

Accepted Answer

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

Question 4

Comparative genomics helps us to understand evolutionary relationships between organisms.

Accepted Answer

A) True 
 B)False

Question 5

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.

Accepted Answer

The genome of S. cerevisiae can be eithe

Question 6

Most mobile DNA consists of

Accepted Answer

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

Question 7

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?

Accepted Answer

The intracellular parasite, N. equitans

Question 8

Microarrays can be used to

Accepted Answer

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. 
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 9

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

Accepted Answer

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

Question 10

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

Accepted Answer

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

Question 11

Horizontal gene transfer has been thoroughly documented for genes involved in

Accepted Answer

A)  DNA replication and repair. 
B)  virulence and metabolic functions. 
C)  only very few processes. 
D)  translation. 
A)  DNA replication and repair. 
B)  virulence and metabolic functions. 
C)  only very few processes. 
D)  translation.

Question 12

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

Accepted Answer

A) True 
 B)False

Question 13

Paralogs always have the same function.

Accepted Answer

A) True 
 B)False

Question 14

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?

Accepted Answer

The presence of a sequence flanked by in

Question 15

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?

Accepted Answer

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. 
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 16

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 ________.

Accepted Answer

A)  homologous / gene families 
B)  paralogous / functional genes 
C)  orthologous / gene families 
D)  homologous / functional genes 
A)  homologous / gene families 
B)  paralogous / functional genes 
C)  orthologous / gene families 
D)  homologous / functional genes

Question 17

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?

Accepted Answer

Duplication of genes through duplication

Question 18

Based on the table of average intron frequency given below, predict the relative order of genome size for these four eukaryotic organisms. $\begin{array}{lc}
\text { Organism } & \text { Average Intron Frequency } \
\hline \text { Cryptosporidium parvum } & 0 \
\text { Plasmodium falciparum } & 1 \
\text { Arabidopsis thaliana } & 5 \
\text { Homo sapiens } & 8
\end{array}$

Accepted Answer

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. 
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 19

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

Accepted Answer

A) True 
 B)False

Question 20

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

Accepted Answer

If an organism rarely uses a particular

Exam 9: Microbial Systems Biology

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

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

The first genome sequenced was that of a(n)

Comparative genomics helps us to understand evolutionary relationships between organisms.

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.

Most mobile DNA consists of

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?

Microarrays can be used to

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

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

Horizontal gene transfer has been thoroughly documented for genes involved in

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

Paralogs always have the same function.

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?

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?

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 ________.

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?

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

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

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

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

Filters

Chloroplasts and mitochondria originated from by a process known as .

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 .