DNA Structure, Synthesis and Sequencing

Question 1

What bases are pyrimidines?

Answer 1

Cytosine and Thymine

Question 2

What bases are purines?

Answer 2

Adenine and Guanine

Question 3

Describe the structure of pyrimidines?

Answer 3

One ring structure

Question 4

What carbon does DNA attach to on a ribose sugar?

Answer 4

1’ carbon

Question 5

Synthesis of DNA requires the addition of what to the growing chain?

Answer 5

A nucleotide triphosphate (NTP)

Question 6

What releases energy in the synthesis of DNA?

Answer 6

Release of the diphosphate from the NTP

Question 7

What do the bases bond via and where?

Answer 7

They bond via a phosphodiester bond between the 3’ carbon of one nucleotide and the 5’ carbon of the next

Question 8

What is the chemical energy that holds DNA strands together made up of?

Answer 8

Hydrogen bonding between base pairs and the base stacking energy between adjacent bases

Question 9

What is DNA hybridisation?

Answer 9

The balance between the bonding energy and the heat energy or entropy which is a measure of how much energy it takes to keep a molecule in a particular conformation

Question 10

What happens to DNA if the change in Gibbs Free Energy is negative?

Answer 10

The DNA will anneal and be double stranded

Question 11

What happens to DNA if the change in Gibbs Free Energy is positive?

Answer 11

DNA will melt ad become single stranded

Question 12

What will an increase in temperature do to DNA?

Answer 12

It will increase the magnitude of the entropy and drive the DNA towards melting

Question 13

What happens when there is no hydroxyl on the 3’ position?

Answer 13

You cannot attach the next nucleotide

Question 14

Does single stranded DNA have a higher absorbance in UV than double stranded DNA?

Answer 14

Yes (0.027 Au vs 0.020 AU at 1ug/ml)

Question 15

What is Tm?

Answer 15

Melting temperature

Question 16

What affect does longer DNA strands have on the Tm?

Answer 16

It increases the Tm

Question 17

If there are mismatches between two strands, what happens to the enthalpy change?

Answer 17

The enthalpy change will be less (weaker binding)

Question 18

Oligos only anneal with what?

Answer 18

Exact/extremely close to exact sequences

Question 19

Are oligonucleotides single or double stranded?

Answer 19

Single stranded

Question 20

What is an oligonucleotide?

Answer 20

a polynucleotide whose molecules contain a relatively small number of nucleotides

Question 21

What does the ‘reverse’ in reverse transcriptase refer to?

Answer 21

It refers to the reversal of synthesis from generating RNA from a DNA template to generating DNA from an RNA template.

Question 22

What happens if a dideoxy base is mixed with a normal deoxy NTP base?

Answer 22

It creates at random termination of the chain at the dideoxy base