Lecture 3: Primary Structure of DNA

Question 1

What is the structure of a nucleotide?

Answer 1

A nucleotide is made up of 3 moieties:

• a pentose sugar (5C)
• phosphate
• organic nitrogenous base (can accept H+)

Question 2

Are the pentose sugars in DNA and RNA aromatic?

Answer 2

No. The atoms in the ring are therefore not in the same plane. The steric strain causes puckering such that the 2’ or 3’ carbon is out of the plane.

Question 3

What is the difference between ribose and deoxyribose?

Answer 3

Deoxyribose has a hydrogen on the 2’ carbon where ribose has an OH group.

Question 4

Are free nucleic acids or proteins more soluble in water?

Answer 4

Free nucleic acids are much more soluble in water than proteins, especially in ionic conditions.

Question 5

How are phosphate groups labelled in nucleotide triphosphates?

Answer 5

Alpha, beta, gamma,

where alpha is closest to the sugar and gamma is furthest from the sugar.

Question 6

Which carbon in deoxyribose is the phosphate group attached to?

Answer 6

5’ carbon, via a phosphoester bond (P-O-C)

Question 7

How are the bases joined to the sugar?

Answer 7

The base is joined to the 1’ carbon by a beta-glycosidic linkage. The beta means that the base is in the plane above the sugar ring.

Question 8

Why are atoms in the bases in a plane?

Answer 8

The bases are aromatic.

Question 9

What are the two types of base?

Answer 9

Purine (double ring) and pyrimidine (single ring)

Question 10

Which of the bases are purines?

Answer 10

Adenine and guanine are purines.

Question 11

Which of the bases are pyrimidines?

Answer 11

Cytosine, thymine and uracil are pyrimidines.

Question 12

What is a keto base?

Answer 12

A base which has a C=O group at position 4 (pyrimidine) or position 6 (purines). This includes guanine, thymine and uracil.

Question 13

What is an amino base?

Answer 13

A base which has an amino group (NH2) at position 4 (pyrimidine) or position 6 (purines). This includes cytosine and adenine.

Question 14

What are the differences between thymine and uracil?

Answer 14

Thymine is present in DNA, whereas uracil is present in RNA. They are chemically very similar: uracil has a hydrogen where thymine has a methyl group, but they are otherwise structurally the same.

Question 15

What is the difference between a nucleoside and a nucleotide?

Answer 15

A nucleoside is made up of a sugar and a base, whereas a nucleotide is made up of a sugar, base and phosphate.

Question 16

Discuss polymerisation of nucleotides.

Answer 16

During polymerisation, the alpha phosphoryl group of a free nucleotide triphosphate undergoes nucleophilic attack by the 3’C-OH group of the nucleotide at the 3’ end of the growing chain.
Electronegative oxygens pull electrons away from phosphorous in phosphate group, making it slightly positive and vulnerable to nucleophilic attack by the growing chain.
The DNA chain grows at the 3’ end.
This reaction is catalysed by DNA polymerase/RNA polymerase.
Unfavourable entropy is balanced out by high enthalpy using the releases of free energy as phosphoanhydride bonds are hydrolysed.

Question 17

Describe what is meant by ‘directionality’ of DNA and RNA.

Answer 17

Phosphodiester bonds link the 3’ and 5’ C of all the sugars within the chain.
At one end there will be a free 5’ phosphate group (we call this the 5’ end)
At the other end there will be a free 3’ –OH group (the 3’ end).
Thus DNA & RNA polymers have directionality.
Convention has it that we write nucleic acid sequences in the 5’ to 3’ direction.

Question 18

Why is DNA the hereditary molecule?

Answer 18

The presence of the 2’ –OH group in RNA makes it susceptible to base-catalysed hydrolysis.
Thus DNA is much more stable than RNA.
DNA is better suited to being the hereditary material

Question 19

What are other roles of nucleotides?

Answer 19

The high free energy of the phosphoanhydride bond in ATP is used to drive very many biochemical reactions
A lot of biochemistry is involved in making ATP
Some nucleotides are important, intracellular signaling molecules (e.g. cAMP)
Nucleotides can act as intercellular, neurotransmitters, thus regulating cell and organismal behaviour.