Question

1. What is a primer? What are they made out of during DNA replication? Why does the process of DNA replication require the use of a primer?

2. When an agarose gel is set up, the DNA samples are put at one end of the gel and the pieces of DNA migrate toward the other end. a. At what end are the DNA samples put? (1 point) b. Toward what end do the DNA samples migrate? (1 point) c. What is it about DNA’s structure that allows this migration to occur?

3.Answer the following questions about agarose gel electrophoresis: (2 points each) a. Which will travel farther through the gel, large pieces of DNA or small pieces of DNA? Why? b. Which gel would be better at separating tiny pieces of DNA, a 2% gel (more agarose) or a 0.5% gel (less agarose)? Why?

Answer 1

1. What is a primer? What are they made out of during DNA replication? Why does the process of DNA replication require the use of a primer?

Primer is a small nucleotide sequence of 18-22 bp length. It is usually of RNA sequence made by DNA polymerase α in eukaryotes. Replication involves doubling of one DNA into two daughter DNAs. Parental DNA is unwound and each acts as a template for the synthesis of one daughter (complementary) strand. The synthesis of new strands by DNA polymerases require a primer to extend the nucleotide. Most of the DNA polymerases can only add nucleotides to the existing small polynucleotide (primer). Only DNA Pol α can synthesize RNA primer and initiate polymerisation.

2. When an agarose gel is set up, the DNA samples are put at one end of the gel and the pieces of DNA migrate toward the other end.

a. At what end are the DNA samples put?

DNA samples will be put at the cathode (negatively charged) end.

b. Toward what end do the DNA samples migrate?

DNA samples migrate towards the anode (positively charged) end.

c. What is it about DNA’s structure that allows this migration to occur?

DNA is negatively charged molecule. That is why it moves towards anode (positively charged end) from cathode (negatively charged end) in the agarose gel. Phosphate groups present in the nucleotides (phosphodiester bond) gives net negative charge to DNA.

3.Answer the following questions about agarose gel electrophoresis:

a. Which will travel farther through the gel, large pieces of DNA or small pieces of DNA? Why?

Small pieces of DNA travel farther through the gel. Agarose gel electrophoresis of DNA is based on the size of DNA molecules. Small molecules move faster than the large molecules. Large molecules face hindrance (retardation) through pores of the agarose gel and hence move slowly.

b. Which gel would be better at separating tiny pieces of DNA, a 2% gel (more agarose) or a 0.5% gel (less agarose)? Why?

2% agarose gel would be better at separating tiny pieces of DNA. This is because 2% gel will have smaller pores than 0.5% gel. Smaller sized pores are enough for tiny pieces of DNA to migrate through the gel.