Deck 12: Microbial Genomics

Question 1

Microarrays are also known as

A) introns.
B) in- silica instruments.
C) inteins.
D) gene chips.

Answer 1

D

Question 2

When comparing genes from Archaea, Bacteria, and Eukarya, which statement is TRUE?

A) 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.
B) Almost all archaeal genes are more similar to bacterial genes than to eukaryotic genes.
C) Almost all archaeal genes are more similar to eukaryotic genes than to bacterial genes.
D) Archaeal genes are almost universally unique; very few are similar to either eukaryotic or bacterial genes.

Answer 2

A

Question 3

The bacterial genome to be sequenced was

A) Bacillus subtilis.
B) Haemophilus influenzae.
C) Pseudomonas aeruginosa.
D) Escherichia coli.

Answer 3

B

Question 4

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

A) discovery.
B) identification.
C) assembly.
D) annotation.

Question 5

The haploid yeast genome contains _ chromosomes.

A) 16
B) 8
C) 32
D) variable numbers of

Question 6

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

A) interactome.
B) metagenome.
C) population genome.
D) chromosomal island.

Question 7

Microarrays allow for

A) the hybridization of cDNA (converted from mRNA with DNA affixed to a solid- state support.
B) the analysis of global gene expression.
C) a comparison of expression of different genes under different growth conditions.
D) all of the above.

Question 8

The first DNA genome to be sequenced was that of the ssDNA virus 0X174 and debuted the

A) dideoxynucleotide Sanger technique.
B) technique known as nuclear magnetic resonance (NMR) analysis.
C) technique known as high- pressure liquid chromatography (HPLC).
D) 454 pyrosequencing technique.

Question 9

Within Archaea and Bacteria, one megabase of DNA encodes about open reading frames.

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

Question 10

When compared with Bacteria, species of Archaea seem to devote a higher percentage of their genomes to genes encoding proteins involved in

A) cell membrane functions.
B) carbohydrate metabolism.
C) transcription.
D) energy and coenzyme production.

Question 11

Genetic elements that collect and express genes carried on mobile segments of DNA called cassettes are known as

A) transposable elements.
B) integrons.
C) plasmids.
D) pathogenicity islands.

Question 12

Several investigators have estimated that around genes are the minimum for a viable cell.

A) 750- 1,000
B) 250- 300
C) 500- 700
D) 100- 200

Question 13

Which type of sequence is used for a BLASTn?

A) amino acid
B) nucleotide
C) genome
D) protein

Question 14

Most known integrons carry genes for

A) DNA replication, transcription, and translation.
B) virulence.
C) antibiotic resistance.
D) metabolic functions.

Question 15

Most mobile DNA consists of

A) transposable elements.
B) integrons.
C) plasmids.
D) virus genomes.

Question 16

The use of computers to do sophisticated analyses of genomes is called working

A) in computo.
B) in silico.
C) in vivo.
D) in vitro.

Question 17

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) proteomics.
B) bioinformatics.
C) metagenomics.
D) genomics.

Question 18

The structural modules, each with characteristic functions, found in many proteins are known as

A) silica expressions.
B) amino acid sequences.
C) protein domains.
D) intron splices.

Question 19

An estimated 50- 60% of the DNA in the oceans is and is found in deep- sea sediments.

A) present in Archaea and Bacteria
B) an example of genome stability
C) encapsulated by marine viruses
D) extracellular

Question 20

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

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

Question 21

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

Question 22

Most integrons are found on or in and may collect multiple .

Question 23

At present, no available method can come close to giving as much information about gene expression as can _.

Question 24

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

Question 25

Encephalitozoon cuniculi is an intracellular pathogen that lacks _ _ and is currently the smallest genome sequenced of the .

Question 26

The mitochondrial genomes of almost all animals, including humans, encode

A) rRNA.
B) proteins.
C) tRNA.
D) all of the above.

Question 27

The total gene content of the organisms inhabiting an environment is known as the
.

Question 28

Special proteins or other molecules or structures necessary to cause disease are known as
.

Question 29

Genomes from the animal , the plant , and the fungus have been sequenced.

Question 30

The most abundant genes in prokaryotic genomes are

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

Question 31

The three mechanisms for horizontal gene transfer in prokaryotes are _ , , and .

Question 32

A functional open reading frame (ORF) encodes for

A) a carbohydrate.
B) DNA or RNA.
C) a protein.
D) all of the above.

Question 33

The study of the structure, function, and regulation of all the proteins present in an organism is called .

Question 34

Which statement is TRUE?

A) Mitochondrial genomes may be circular or linear.
B) Restriction genomes may be circular or linear.
C) Chloroplast genomes may be circular or linear.
D) All of the above are true.

Question 35

The proteins present in a cell at any given time are known as a(n) _ _.

Question 36

DNA replication in vivo uses primers composed of , but primers are most commonly used in molecular biology due to their increased stability.

Question 37

The is the complete set of metabolic intermediates and other small molecules produced in an organism.

Question 38

Bioinformatics is a field of study that .

Question 39

An uncharacterized ORF shares with a known protein- encoding gene a(n) of reasonable length and _ and codons.

Question 40

DNA sequences of prokaryotic genomes are now available in public databases.

A) millions
B) hundreds
C) thousands
D) dozens

Question 41

Heterotrophs need only a few more genes than autotrophs.

Question 42

Comparisons of genes and gene families can be done easily. The results are generally quite predictable, although occasionally there is a surprising find.

Question 43

The number of genes whose role can clearly be identified in a given genome is or less of the total number of ORFs detected.

Question 44

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

Question 45

Gene sequencing requires high- throughput sequencing as well as powerful computational capacities.

Question 46

Many of the genes in the chloroplast genome encode proteins involved in _ and
, whereas mitochondrial genomes primarily encode proteins involved in
.

Question 47

Comparative genomics helps us to understand evolutionary relationships between organisms.

Question 48

Introns are common in chloroplasts, and they are primarily of the self- splicing type.

Question 49

An ortholog is not always a paralog, but a paralog is always an ortholog.

Question 50

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

Question 51

With modern molecular techniques, it is now possible to completely assemble a genome de novo.

Question 52

Genomic analysis led to the discovery that the organism that causes syphilis lacks recognizable genes for amino acid biosynthesis.

Question 53

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

Question 54

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 _.

Question 55

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

Question 56

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

Question 57

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

Question 58

The proteome- wide determination of the 3- D structures of proteins is known as .

Question 59

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

Question 60

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

Question 61

Describe the types of information that can be gleaned by coupling proteomics with genomics.

Question 62

Discuss how DNA chips can be used to identify organisms.

Question 63

The protozoans Paramecium and Trichomonas have significantly more genes than humans have.

Question 64

Explain horizontal gene transfer and discuss how this phenomenon has complicated evolutionary studies.

Question 65

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

Question 66

Explain why large- genome organisms might be strongly selected for in a soil habitat.

Question 67

Explain why the absence of genes that encode proteins involved in anabolism or catabolism in Nanoarchaeum equitans is unsurprising.

Question 68

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

Question 69

Genome sequencing is an expensive endeavor, so the needs of the biomedical and biotechnology industries are important drivers for selecting genomes to be sequenced.

Question 70

Some virulence genes are carried on plasmids or lysogenic bacteriophages.

Question 71

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?

Question 72

Explain the terms "core genome" and "pan genome" and describe how each contributes to the genome of a bacterial species.

Question 73

Explain how evolution can "experiment" with duplicated genes.

Question 74

Explain why the proteome is not defined as "all the proteins encoded by an organism's genome."

Question 75

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 76

Explain why the words "about" and "approximately" are used in discussing certain genomes that have been fully sequenced.

Question 77

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

Question 78

Explain how codon bias can be used to detect horizontal gene transfer.

Question 79

Explain how genomics has shown mitochondrial evolution to be far more complicated than expected.

Question 80

Few genes in all organisms have common evolutionary roots.