Lecture 15

Question 1

Purines vs pyrimdines

Answer 1

Purines have 2 rings while pyrimidines have 1 ring.

Question 2

Thymine vs uracil

Answer 2

Extra methyl group on thymine. Thymine is on DNA while uracil is only on RNA

Question 3

Chargaff’s Rule

Answer 3

Quantified ratios between bases. A:T, G:C and purines:pyrimidines are equal.

Question 4

Base properties

Answer 4

Electronegative groups like O and N will be electron acceptors. In protonation state where lots of H+ around, some will associate with bond acceptor, preventing it from being able to bond with other base. In higher pH, some groups will be deprotonated preventing bonding.

Question 5

Sugar

Answer 5

1’: N-glycosidic bond attaches (N of base)

2’: OH for RNA and H for DNA

3’: OH (where nucleotides attach for extending DNA)

4’: Nothing

5’: Phosphate attaches here

Question 6

Phosphodiester bond

Answer 6

Formed through a condensation reaction where a phosphate group from one nucleotide reacts with the hydroxyl group (–OH) on the 3′ carbon of the adjacent nucleotide’s sugar molecule

Question 7

Double helix

Answer 7

Sugar-phosphate backbone with bases on inside due to hydrophobic nature. Backbone is covalent phosphodiester bonds. In the helix, you’ve got H bonds, ionic interactions, Van Der Waals interaction and hydrophobic interactions which can be broken.

Question 8

H bonds

Answer 8

Between complementary bases (2 between A and T, 3 between G and C). 3H bonds makes it harder to separate.

Question 9

Ionic interactions

Answer 9

Repulsive as backbone is full of negatively charged ions. Hence, they twist. Against interactions that follow base pairings.

Question 10

Hydrophobic interactions

Answer 10

Bases have aromatic ring. Therefore, hydrophobic AF

Question 11

Van der Waals

Answer 11

Distance-dependent where it is favourable for attraction.

Question 12

Base stacking

Answer 12

Favours formation of double helix.

Question 13

Spectrophotometry

Answer 13

Useful for determining if the sample is contaminated and what with. RNA absorbs more due to single-strand feature. Base-stacking causes lower abs. (hyperchromatic effect).

Question 14

Major and minor grooves

Answer 14

Comes from the fact the N-glycosidic bonds are angled. This causes a difference in the space on DNA surface. Different interactions as major grooves have more functional groups sticking out. When proteins wish to bind, they recognise specific grooves. How you get sequence specific interactions with transcriptions (often in major grooves). Small molecules go into minor grooves. Though, they are less sequence specific and may prefer particular sequence. But not picky.

Question 15

Storing info in DNA

Answer 15

Backbone outside is hydrophilic. Hydrophobic bases contain info. between the bases are more polar groups. One strand can be used to check accuracy of replication.

Question 16

RNA less stable than DNA

Answer 16

1. RNA is places in solution with high pH where it is deprotonated.
2. The O will ‘attack’ the P
3. Backbone is split and RNA is split.

Question 17

cytosine deamination

Answer 17

Spontaneous. Occurs ~100-500 times/cell/day. This mutation is recognised and removed via basic excision repairs as its in DNA.