Pre-lab questions

Question 1

The design of the specific primers used in a PCR is very important. What can lead to the formation of primer dimers?

Select one:

a. Primers that are too long
b. Primers that are too short
c. Complementary regions between primers in a pair
d. Annealing temperatures that are too high

Answer 1

c. Complementary regions between primers in a pair

Question 2

What is the melting temperature, in (°C) for the 5’ primer used to amplify the ACE gene?

5’ Primer: 5’ CCT GGA GAC CAC TCC CAT CCT TTC T 3’

Remember: Tm = 69.4 + 0.41(%G+C) – 650/N

Select one:

a. 43.63
b. 66.36
c. 61.36
d. 49.14

Answer 2

b. 66.36

Question 3

Isozymes are enzymes that:

Select one:

a. catalyse different reactions but have similar primary structures
b. catalyse isomerisation reactions
c. are identical but expressed in different tissues
d. catalyse the same reaction but have different primary structure

Answer 3

d. catalyse the same reaction but have different primary structure

Question 4

How does the antibiotic Rifampicin work?

Select one:

a. Inhibition of the bacterial enzyme DNA polymerase
b. Inhibition of peptidoglycan synthesis
c. Inhibition of cell wall synthesis
d. Inhibition of the bacterial enzyme RNA polymerase

Answer 4

Inhibition of the bacterial enzyme RNA polymerase

Question 5

The hospital’s senior microbiologist David wished to study the sequence of the S. aureus that infected Amy and chose to compare this sequence, using BLAST, with the NCBI database. What information did this provide him with?

Select one:

a. Whether the sequence matches to any known sequences submitted to the database
b. Whether the sequence matches to Brent ad Kristen’s sequence
c. Where Amy is likely to have contracted the infection
d. Whether the S. aureus that infected Amy would be susceptible to the antibiotic, Vancomycin

Answer 5

a. Whether the sequence matches to any known sequences submitted to the database

Question 6

Following comparisons using BLAST, David wished to study the sequence of the S. aureus that infected Amy, Kristen and Brent by using the multiple sequence alignment tool Clustal. What information did this provide him with?

Select one:

a. Regions of similarity or differences between the Amy, Brent ad Kristen’s sequence
b. Whether the sequence matches to any already known sequences
c. Whether the S. aureus that infected Amy would be susceptible to the antibiotic, Vancomycin
d. Where each patient is likely to have contracted the infection

Answer 6

a. Regions of similarity or differences between the Amy, Brent ad Kristen’s sequence

Question 7

Which property of DNA allows us to quantify it using Hoechst 33342?

Select one:

a. Complementary base pairing
b. Solubility
c. Tertiary structure/presence of DNA grooves
d. Viscosity

Answer 7

c. Tertiary structure/presence of DNA grooves

Question 8

You are setting up a dilution series for a fluorescence assay using a stock DNA solution containing 5 µg/mL DNA. How much of this stock solution is needed to make 100 µL of a 4 µg/mL standard?

Select one:

a. 80 µL
b. 60 µL
c. 40 µL
d. 20 µL

Answer 8

a. 80 µL

Question 9

You are setting up a dilution series for a fluorescence assay using a stock DNA solution containing 5 µg/mL DNA. What is the final concentration of the standard solution prepared from 25 µL of stock DNA and 75 µL of dilution buffer?

Select one:

a. 1.25 µg/mL
b. 0.33 µg/mL
c. 0.8 µg/mL
d. 1.66 µg/mL

Answer 9

d. 1.66 µg/mL

Question 10

What is the following statement best described as?

To quantify the concentration of DNA in an unknown sample utilising a calibration/standard curve from fluorescence emission data following incubation with Hoechst 33342

Select one:

a. An experimental aim
b. An experimental conclusion
c. An experimental hypothesis
d. An experimental result

Answer 10

a. An experimental aim

Question 11

You perform a fluorescence assay in a 96-well plate but observe that many of the empty wells still registered a reading from the plate reader. Which of the following best explains this?

Select one:

a. The wells weren’t empty, some solution must have spilt into them
b. Fluorescence detected from adjacent well containing samples
c. Background fluorescence detected from the dilution buffer
d. Background fluorescence detected from the 96-well plate

Answer 11

d. Background fluorescence detected from the 96-well plate

Question 12

When grown on selective media with an antibiotic and X-gal, bacteria WITH the correctly inserted gene of interest:
will form blue colonies

will form white colonies

will not grow

Answer 12

will form white colonies

Question 13

Question text
Transformation is a form of horizontal gene transfer where genetic material is:

Select one:

a. taken up from the environment
b. transferred directly from cell to cell
c. transferred via a bacteriophage intermediate

Answer 13

a. taken up from the environment

Question 14

What information does NEB cutter provide?

Select one:

a. The location of restriction enzymes sites
b. The location of mutations
c. The similarities and differences between two sequences
d. The optimum primers to amplifiy gene of interest

Answer 14

a. The location of restriction enzymes sites

Question 15

Which technique would be best suited to determine if any of the strains from Amy, Kristen or Brent harboured any other known resistance genes?

Select one:

a. Restriction Fragment Length Polymerisation
b. Cloning and expression of the recombinant protein
c. FISH with molecular probes
d. PCR

Answer 15

d. PCR

Question 16

Which technique would be best suited to identify the location of the rpoB gene within a tissue/skin biopsy infected with S. aureus?

Select one:

a. Gene Sequencing
b. FISH with molecular probes
c. Restriction Fragment Length Polymorphism
d. PCR
e. Cloning and expression of the recombinant protein

Answer 16

b. FISH with molecular probes

Question 17

You perform a cloning experiment and transform bacteria with a plasmid containing a gene for ampicillin (antibiotic) resistance and a gene of interest inserted into the the LacZ gene. To confirm the transformation you perform blue-white screening and grow your bacteria on medium containing ampicillin and X-gal. You observe your results and note that all colonies are blue. What can be concluded?

Select one:

a. The gene of interest was inserted into the antibiotic resistance gene
b. The gene of interest was correctly inserted into the LacZ gene
c. None of the bacteria took up the plasmid
d. The gene of interest was not inserted into the LacZ gene

Answer 17

a. The gene of interest was inserted into the antibiotic resistance gene

Question 18

Microarray analysis

Answer 18

Microarray analysis involves breaking open a cell, isolating its genetic contents, identifying all the genes that are turned on in that particular cell, and generating a list of those genes.

DNA microarray analysis is a technique that scientists use to determine whether genes are on or off.

Scientists know a gene is on in a cell if its mRNA is present.

Question 19

DNA micorarray allows scientists to perform an experiment on thousands of genes at the same time.

Answer 19

Each spot on a microarray contains multiple identical strands of DNA.
The DNA sequence on each spot is unique.
Each spot represents one gene.
Thousands of spots are arrayed in orderly rows and columns on a solid surface (usually glass).
The precise location and sequence of each spot is recorded in a computer database.
Microarrays can be the size of a microscope slide, or even smaller.

Question 20

Which of the following might be an advantage for genetic testing of individuals via microarrays?

Many different potential mutations in a single gene could be tested at once
Expression patterns of many different genes can be analyzed simultaneously
Microarray analysis can provide information on relative levels of expression of particular genes
All of these
None of these

Answer 20

All of these

Question 21

Which of the following is INCORRECT about a microarray?

It is a slide attached with a high-density array of immobilized DNA oligomers that can represent the entire genome of the species under study
It is the most commonly used global gene expression profiling method
It is an array of immobilized mRNA that serve as multiple probes for binding to a unique complementary DNA (cDNA)
Each DNA oligomer is spotted on the slide and serves as a probe for binding to a unique complementary DNA (cDNA)

Answer 21

It is an array of immobilized mRNA that serve as multiple probes for binding to a unique complementary DNA (cDNA)

Question 22

What properties of DNA are exploited in setting up and running a microarray?

Solubility
Viscosity
Double-stranded helix
Complementary base pairing
Check

Answer 22

Complementary base pairing

Question 23

Number the steps in a microarray workflow below in the correct order from 1 to 6:

Hybridisation

Isolate RNA

Generate labelled cDNA

Collect samples

Scan and Analyse Microarray

Remove tRNA and rRNA

Answer 23

5
Hybridisation

2
Isolate RNA

4
Generate labelled cDNA

1
Collect samples

6
Scan and Analyse Microarray

3
Remove tRNA and rRNA

Question 24

Which feature of mRNA is exploited to separate it from tRNA and rRNA?

Uracil
Physical conformation
5’ cap
3’ Poly-A tail

Answer 24

3’ Poly-A tail

Question 25

Using a Microarray to determine Breast Cancer Treatment

Answer 25

Microarray technology can assist us in understanding the differences between healthy cells and cancer cells. It can also be used to help identify a tailored course of treatment for individual patients based on the specific genes expressed.

Question 26

What feature makes the different types of cells in our body different from each other?

Select one:

a. The same genes are turned on in all cells but proteins that are not required are degraded giving rise to different cell types
b. The same genes are turned on in all cells but the protein they encode is different in depending on the cell type
c. Only certain genes are turned on in a particular cell, depending on its specific function
d. Each cell only contains the genes it needs for its specific function

Answer 26

c. Only certain genes are turned on in a particular cell, depending on its specific function

Question 27

What is the origin of the sequences of the oligonucleotides on the chip used in the virtual microarray tutorial?

Select one:

a. Derived from DNA in healthy cells from another individual
b. Derived from the human genome
c. Derived from DNA in the cancer cells
d. Derived from DNA in the healthy cells

Answer 27

b. Derived from the human genome

Question 28

Which step in the experiment specifically allows us to compare gene expression from two different cell samples?

Select one:

a. Hybridising cDNA from two different samples sequentially, as opposed to simultaneously
b. Hybridising cDNA from two different samples simultaneously, as opposed to sequentially
c. Ensuring the immobilised, single stranded DNA oligonucleotides have incorporated different coloured fluorescent labels
d. Labelling the cDNA synthesised from the two cell types with different coloured fluorescent labels

Answer 28

d. Labelling the cDNA synthesised from the two cell types with different coloured fluorescent labels

Question 29

What has been immobilised onto the surface of the Microarray chip?

Select one:

a. double stranded DNA
b. single stranded DNA
c. single stranded mRNA
d. double stranded mRNA

Answer 29

b. single stranded DNA