Molecular Biology Practice Questions and Answers

1.DNA and RNA preparations were made and suspended in 0.5 mL and 0.2 mL, respectively. Calculate the concentrations for the following and also report the total yield for each preparations: 

a.A DNA preparation (1:100 dilutions) has an absorbance reading of 0.200 at 260nm. 

b.An RNA preparation (1:10 dilutions) has an absorbance of 0.500 at 260 nm. 

2.a. At times, patient’s sample may contain chelators that can inhibit a PCR reaction resulting in a false-negative result. How would you demonstrate the presence of an inhibitor in the sample? 

b. Suppose you are amplifying a gene by PCR with fluorescent labeled nucleotides, so that you can follow the synthesis by following the fluorescence. After three cycles, what percentage of the DNA (single stranded) is labeled? 

3.The following represents a melt curve analysis of a normal (Tm = 62 C) and mutant (Tm= 55 C) PCR products (see figure on next page).

a. Correctly label the normal, homozygous mutant and heterozygous mutant in the following figure (both in Panel A and B). 

b. Also indicate in the Fluorescence-Y-axis (on the left) of Panel A, the position of the % single strands (SS) and % double strands (DS)? 

4.Purely a Hypothetical case: A curious scientist tested the DNA from a group of individuals who are exclusively meat eaters and another group who are exclusively vegans to explore the possibility of genetic variation. After a series of PCR-RFLP experiments, he located a G to A polymorphism on exon 5 of chromosome 8 upon Rsa 1 digestion on the vegans. Provided below are the sample results of PCR-RFLP from three individuals: PCR products were digested with Rsa1. Identify the location of the polymorphic site (schematically represent),and explain the genotype for all three individuals for this marker. 

M-molecular weight standard; Lanes 1-2: Individual #1; Lanes 3-4: Individual #2;
Lanes 5-6: Individual #3. Lanes 1, 3 and 5 are uncut PCR products; Lanes 2, 4 and 6 are cut with Rsa1. 

5.The polypeptide products resulted from the in vitro (coupled transcription/translation assay of the PCR products) reaction are resolved by polyacrylamide gel electrophoresis. The samples are from the patients suffering from mild Becker form of muscular Dystrophy.

a. What type of assay is performed here? 

b. What is your diagnosis for both patients? 

c. What type of mutation is detected with this assay? 
 

6.When a DNA fragment is resolved by slab gel electrophoresis, a single sharp band is obtained. What would the equivalent observation be if this fragment had been ?uorescently labeled and resolved by capillary electrophoresis?

7.In an array CGH experiment, three test samples were hybridized to three microarray chips. Each chip was spotted with eight gene probes (Genes A – H ). The following table shows the results of this assay expressed as the ratio of test DNA to reference DNA. Are any of the eight genes consistently deleted or amplified in the test samples?  If so, which ones?

8.a. A FISH test with a centromere 13 probe is ordered for a suspected case of Patau syndrome (trisomy 13). How many signals per nucleus will result if the test is positive for Patau syndrome?
b. What would be the results if a centromere 13 probe was used on a case of Edward syndrome (trisomy 18)?

9.You wish to perform an electrophoretic resolution of your restriction enzyme– digested DNA. The sizes of the expected fragments range from 100 to 500 bp. You discover two agarose gels polymerizing on the bench. One is 0.5% agarose; the other is 2% agarose. Which one might you use to resolve your fragments?

10.After completion of the electrophoresis of DNA fragments along with the proper molecular-weight standard on an agarose gel, suppose the outcomes in (a) and (b) were observed. What might be the explanations for each outcome? 

a.The gel is blank (no bands, no molecular-weight standard).

b.Only the molecular weight standard is visible.