Question 1

Which of the following best describes the discipline of genomics?

Accepted Answer

The mapping, sequencing, analyzing, and comparing of entire genomes.

Question 2

In the Sanger dideoxy sequencing method, what is the role of dideoxynucleotides (ddNTPs)?

Accepted Answer

They prevent further extension of the DNA chain by lacking a 3'-OH group.

Question 3

During gel electrophoresis, why do nucleic acids migrate toward the positive electrode?

Accepted Answer

Because their phosphate groups are negatively charged.

Question 4

Which equation best represents the exponential amplification of DNA during PCR cycles?

Accepted Answer

$$N = N_0$ 	imes 2^n$$

Question 5

What is the main advantage of second-generation DNA sequencing over the Sanger method?

Accepted Answer

It generates data 100 times faster using massively parallel methods.

Question 6

Which modern sequencing technique measures the release of protons to detect nucleotide incorporation?

Accepted Answer

Ion torrent semiconductor sequencing

Question 7

What is the primary function of microarrays in functional genomics?

Accepted Answer

To measure patterns of gene expression by hybridizing DNA segments with mRNA.

Question 8

Which of the following statements about the correlation between genome size and gene content in prokaryotes is correct?

Accepted Answer

Gene content increases proportionally with genome size.

Question 9

Which of the following is a key insight gained from RNA-seq analysis?

Accepted Answer

The amount of expressed mRNA and noncoding RNA in a cell.

Question 10

A researcher is using mass spectrometry to analyze the metabolome of a bacterial sample. Which technique is most likely being used?

Accepted Answer

MALDI-TOF (Matrix Assisted Laser Desorption Ionization - Time of Flight)

Question 11

Which hypothesis explains the origin of eukaryotic cells by the symbiotic association of prokaryotes?

Accepted Answer

Endosymbiotic hypothesis

Question 12

What is the primary molecule used by Carl Woese to establish the three domains of life?

Accepted Answer

Small subunit ribosomal RNA (SSU rRNA)

Question 13

Which of the following is NOT a mechanism for genetic change in microbial evolution?

Accepted Answer

Genetic drift

Question 14

According to the phylogenetic species concept for prokaryotes, which criterion is most important for defining a new species?

Accepted Answer

Greater than 70% DNA-DNA hybridization and less than 3% difference in 16S rRNA gene sequence

Question 15

Which taxonomic method uses the analysis of DNA fragments generated from restriction enzyme digestion of SSU rRNA genes?

Accepted Answer

Ribotyping

Question 16

Which of the following is a reason why functional traits are widely distributed among Bacteria and Archaea?

Accepted Answer

Horizontal gene flow allows genes to be exchanged between distantly related species.

Question 17

Which group of bacteria is responsible for the production of antibiotics and the earthy odor of soil?

Accepted Answer

Streptomyces

Question 18

What is the main adaptation of extremely halophilic archaea to maintain water balance?

Accepted Answer

Pumping large amounts of K$$^+$$ ions into the cell.

Question 19

Which metabolic process was most likely used by primitive cells on early anoxic Earth?

Accepted Answer

Chemolithotrophy

Question 20

Which equation would you use to estimate the number of genes in a prokaryotic genome of 5 Mbp, given the average gene length?

Accepted Answer

$$	ext{Number of genes} = \frac{5,000,000}{1,000}$$

Microbial Genomics, Evolution, and Systematics: Study Notes

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