Midterm Exam

Question 1

Which nucleotide database would be the best tool to compare a DNA sequence query against a DNA query database?

A. blastn
B. blastp
C. blastx
D. tblastx
E. tblastn

Answer 1

A. blastn

Question 2

Which nucleotide database would be the best tool to compare a protein sequence query against a protein query database?

A. blastn
B. blastp
C. blastx
D. tblastx
E. tblastn

Answer 2

B. blastp

Question 3

Which nucleotide database would be the best tool to compare the six-frame conceptual translation products of a nucleotide query against a protein database?

A. blastn
B. blastp
C. blastx
D. tblastx
E. tblastn

Answer 3

C. blastx

Question 4

Which nucleotide database would be the best tool to translate a query nucleotide sequence in all 6 possible reading frame translations and compare it against the six-frame translations of a nucleotide database?

A. blastn
B. blastp
C. blastx
D. tblastx
E. tblastn

Answer 4

D. tblastx

Question 5

Which nucleotide database would be the best tool to compare a protein query against all six reading frames of a nucleotide sequence?

A. blastn
B. blastp
C. blastx
D. tblastx
E. tblastn

Answer 5

E. tblastn

Question 6

What is the order of a PCR reaction and what are the temperatures for each cycle?

Answer 6

Denaturation at 94
Annealing at 55
Extension at 72

Question 7

The annealing temperatures of primers for PCR…
A. Are dependent on GC content of the primer sequence
B. Can be estimated using several calculation methods
C. Should be empirically determined in reactions with the target DNA
D. all of the above
E. A and C

Answer 7

D. All of the above

Question 8

To amplify a target molecule from the preparation of mRNA; involves the use of Reverse Transcriptase to make cDNA which is amplified in PCR

Answer 8

Reverse Transcriptase PCR (RT-PCR)

Question 9

To amplify and quantify DNA through the use of a fluorescent reporter such as an intercalating dye or probe.

Answer 9

Quantitative PCR or Real-Time PCR (qPCR)

Question 10

As the _____ is distanced from the _____ by the addition of NTPs fluorescence increases.

Answer 10

quencher; reporter

Question 11

The phenomenon whereby one species feeds off the byproducts (waste) of another organism (often occurring in consortia, or in host relationship with its symbiotic microbes)

Answer 11

Synthropy

Question 12

The phrase to describe when the number of bacteria in an environment that are culturalable does NOT equal the actual number of bacteria present.

Answer 12

The “great plate anomaly”

Question 13

Which of the below methods require that you set up a dilution series of DNA sample with known copy numbers of the target molecule?
A. Digital PCR method of absolute quantification
B. Standard curve method of absolute quantification
C. Neither of the above

Answer 13

B. Standard curve method of absolute quantification

Question 14

In a qPCR with ideal conditions, Ct value
A. Increases with increasing amount of template target molecules
B. Decreases with increasing amount of template target molecules
C. Is independent of target template molecules
D. Increases with decreasing concentrations of PCR inhibitors in the reaction

Answer 14

B. Decreases with increasing amount of template target molecules

Question 15

The 2^^Ct method (delta delta Ct, aka comparative Ct method)
A. Is used to compare the relative value of one target gene to another, such as a reference housekeeping gene
B. Is used to determine absolute quantities of the gene of interest
C. Is used to determine the sequence of a PCR product
D. Is used to estimate copy number concentration of the target sequence, taking into account the statistics of the binomial distribution

Answer 15

A. Is used to compare the relative value of one target gene to another, such as a reference housekeeping gene

Question 16

To determine the efficiency of a qPCR product, which of the below numbers is used in the efficiency calculation?
A. The number of pPCR replicates
B. The concentration of magnesium chloride in the qPCR
C. The lowest analyte concentration that can be distinguished from zero, with a specified level of confidence
D. The Ct difference between two successive concentrations in a serial dilution of a known template DNA

Answer 16

D. The Ct difference between two successive concentrations in a serial dilution of a known template DNA

Question 17

A good R2 value means that the plot represents data points that demonstrate a strong relationship (regression) between samples. T or F?

Answer 17

True

Question 18

Which standard curve diction series would provide you with more accurate estimate of PCR efficiency and accurate quantification of the target in samples with unknown quantities, (A) five 2fold dilutions of the known standard (B) or five 10fold dilutions of the known standard?

Answer 18

B. five 10fold dilutions of the known standard

Question 19

The qPCR threshold must be set in the \_\_\_\_ phase of the amplification plot?
A. Exponential 
B. Lag 
C. Linear or geometric 
D. Plateau

Answer 19

C. Linear or geometric

Question 20

T or F? Phylogenetic trees are hypothesis regarding ancestral relationships.

Answer 20

True

Question 21

T or F? Enterotype is a term referring to a particular taxon (species) found in the guts of animals.

Answer 21

True

Question 22

Which of the below techniques could be used to analyze microbial consortia genomic DNA for the presence of different types of microbes?
A. T-RFLP
B. RT-PCR
C. DGGE
D. PCR clone libraries followed by Sanger sequencing
E. A, C, and D only

Answer 22

E. A, C, and D only

Question 23

Barcoding refers to…

Answer 23

The practice of determining phylogeny among eukaryotic organisms, often by examining the sequences of the CO1 gene

Question 24

T or F? Operational Taxonomic Unit can be a synonym for species.

Answer 24

True

Question 25

Which of the following refers to Sequencing all the active message RNA, as well as other RNA molecules from all organisms in a particular environment or tissue? 
A. RFLP
B. OTU
C. Syntrophy
D. Metatranscriptomics

Answer 25

D. Metatranscriptomics