7 - Structure Of DNA

Question 1

Two types of nucleotide

Answer 1

Pyrimidines
Purines

Question 2

What makes up a nucleoside

Answer 2

Base and sugar

Question 3

What makes up a nucleotide
- what can nucleotides be seen as

Answer 3

The nucleoside (base and sugar) and the phosphate
- phosphorylated nucleosides

Question 4

Difference between ribose and deoxyribose sugars

Answer 4

• Ribose has three OH groups - (on Carbon 1, 2 and 3)
• where deoxyribose has two (Carbon 2 and 3)
• hence the deoxy

Question 5

Why we have purines and pyrimidines

Answer 5

2 purines in a double helix would be too wide,
and 2 pyrimidines wouldnt reach each other
- one of each were just the right length (2nm) to bond together via H bond

Question 6

DNA info

Answer 6

• A polynucleotide, with polarity (directionality)
• read by convention from 5’ to 3’ end
• 5’ end has a phosphate group
• 3’ end has hydroxyl group
• phosphodiester bonds from 5’ to 3’ end

Question 7

Phosphodiester bond in DNA info
- what does this give DNA

Answer 7

• links the 3’ C of one nucleotide to the 5’ C of the next
• This means that DNA strands have POLARITY: a 5’ end and a 3’ end.

Question 8

Chargsff Levenes predictions of DNA

Answer 8

Percentage of A and T, and C and G, are around the same in DNA of any organism

Question 9

X-ray fibre diffraction info

Answer 9

• crystalline molecule diffracts X-rays and causes exposed patches (‘reflections’) on exposed films
• resulting diffraction pattern is a unique ‘signature’ of the molecule
• helped find shape of DNA and proteins

Question 10

Fresnel work on light - info

Question 11

Hight of one helical turn

Answer 11

3.4 nm

Question 12

Hight of each stacking of bases

Answer 12

0.34 nm
- so 10 bases for each helical turn

Question 13

Why the triple helix model from Pauling wouldn’t work

Answer 13

• The nitrogenous bases faced out
• sugar-phosphate backbones faced inwards

Wouldn’t work as:
- negative charges on the stacked phosphate groups would repel each other and destabilise this molecule

Question 14

Key features of Watson-Crick model of DNA

Answer 14

• two polynucleotide chains are wound in a right-handed (clockwise) helix
• nucleotide chains are anti-parallel - one strand reads 5’ to 3’, other reads 3’ to 5’
• sugar-phosphate backbones are on outside of double helix, and bases are oriented towards central axis
• complementary bases from opposite strands bound together by weak hydrogen bonds
• base pair distance is 3.4nm apart, helix turn
  distance is 3.6nm
• sugar-phosphate backbones are not equally-spaced, resulting in major and minor grooves

Question 15

How many hydrogen bonds between different complementary bases

Answer 15

A-T - 2 H bonds
C-G - 3 H bonds

Question 16

Which parts of nucleotides act as electron acceptors and donors

Answer 16

Oxygen and nitrogen as electron acceptors
Hydrogen as electron donor

Question 17

nucleotide vs nucleoside

Answer 17

nucleoside is sugar and base
- nucleotide is sugar, base and phosphate attached

Question 18

where are the glycosidic bonds in nucleotides located (for purines and pyrimidines)

Answer 18

between sugar C-1’ and:
- N-9 (purine)
- N-1 (pyrimidine)

Question 19

difference between purines and pyrimidines

Answer 19

purine - N1, N3 and N9
- pyrimidines - N1 and N3

Question 20

what technique used to determine shape of DNA

Answer 20

X-ray fibre diffraction

Question 21

other structural variants of DNA and how they arise

Answer 21

A-DNA: occurs in low hydration conditions
- unsure whether this occurs in cells
B-DNA: most structurally stable form under physiological conditions
Z-DNA: taken up physiologically by stretches of alternating pyrimidines and purines
- helix is left-handed