Lecture 11 - DNA structure, synthesis, and sequencing

Question 1

How do purines differ from pyrimidines?

Answer 1

• Purines have a two ring structure

- Pyrimidines have a one ring structure

Question 2

Purine bases

Answer 2

A and G

Question 3

Pyrimidine bases

Answer 3

T and C

Question 4

To which carbon in the ribose sugar does DNA attach to?

Answer 4

1’ carbon, the one with the R group attached

Question 5

How is deoxyribose formed?

Answer 5

Loss of the 2’ hydroxyl from ribose yields deoxyribose

Question 6

Oligomer

Answer 6

Polymer of nucleotides

Question 7

Explain synthesis of DNA in vivo

Answer 7

1. Requires addition of nucleotide triphosphate (NTP) to the growing chain
2. Release of the pyrophosphate (diphosphate) from the NTP releases energy
3. Bases bond via a phosphodiester bond between the 3’ carbon of one nucleotide and the 5’ carbon of the next

Question 8

What chemical energy holds DNA strands together?

Answer 8

1. Hydrogen bonding between base pairs

2. Base stacking energy, through the interaction of the aromatic rings, between adjacent bases

Question 9

Explain DNA hybridization in terms of energy

Answer 9

• It is a balance between the bonding energy and the heat energy.
• If the change in Gibbs free energy is negative, the DNA will anneal and be double stranded
• If the change is positive then the DNA will melt and become single stranded

Question 10

How do GC affect Tm?

Answer 10

GC pairs form three hydrogen bonds compared to two for AT pairs, the enthalpic energy is greater. Therefore a higher temperature is required to achieve sufficient entropy to counter act this and melt the DNA