Secondary Structure of DNA and RNA

Question 1

What did wilkin and franklin’s X-ray difraction of DNA show?

Answer 1

It showed that DNA is a helical molecule and that bases form a stack of parallel rings, parallel to the fibre axis.

Question 2

What are Chagraff’s rules? (HINT: 3 rules)

Answer 2

%A = %T and %G = %C
%keto bases = %amino bases
%purines = %pyrimidines

Question 3

What is the distance between the base pairs?

Answer 3

3.4Å

Question 4

What is the length of the helical turn?

Answer 4

34Å

Question 5

What is the distance between the base pairs?

Answer 5

3.4Å (0.34nm)

Question 6

What is the length of the helical turn?

Answer 6

34Å (3.4nm)

Question 7

Describe the secondary structure of DNA?

Answer 7

The two strands running anti parallel to each other and the complimentary bases on each strand linked by hydrogen bonds.

Question 8

What does Watson-Crick base pairing state?

Answer 8

A and T are bond by 2 hydrogen bonds.
G and C are bonded by 3 hydrogen bonds.
Purines always face pyrimidines.

Question 9

Why is there a major and minor groove in DNA?

Answer 9

Because the two strands are not directly opposite each other.

Question 10

Describe the secondary structure of DNA.

Answer 10

The two strands running anti parallel to each other and the complimentary bases on each strand linked by hydrogen bonds.

Question 11

Describe how the bases are arranged in the secondary structure of DNA.

Answer 11

The bases project at a perpendicular angle to the sugar phosphate backbone (helical axis).
Bases are parallel to each other and stack, partially overlapping.
Van der waals and hydro

Question 12

Describe how the bases are arranged in the secondary structure of DNA.

Answer 12

The bases project at a roughly perpendicular angle to the sugar phosphate backbone (helical axis). (In B/Z DNA)
Bases are parallel to each other and stack, partially overlapping.
EXTRA: Van der waals and hydrophobic interactions between the planar rings of the bases stabilizes the DNA structure

Question 13

What is the ‘average’ form of DNA?

Answer 13

B DNA.

Question 14

Describe the structure of B DNA.

Answer 14

The helices are right handed. (hint: when looking a helix it goes in the right direction when going from the base up.)
Bases roughly perpendicular to backbone (6 degree tilt).
The rise between adjacent bases is 0.34nm.
The helical repeat is 3.4nm.
There 10 base-pairs per turn.
The helix is 2nm wide.
Puckering of 2’ Carbon

Question 15

Why are base pairs not directly opposite each other?

Answer 15

Due to hydrogen bonding.

Question 16

Why are base pairs not directly opposite each other and what does this result in?

Answer 16

Due to hydrogen bonding.

This results in two types of groove - the majore and minor groove.

Question 17

What does the major groove’s size allow?

Answer 17

Because it is larger it can allow intimate protein binding to the double stranded DNA.

Question 18

What is double stranded DNA also known as?

Answer 18

Duplex DNA.

Question 19

Describe the features of A DNA.

Answer 19

It is a right handed helix.
11 bases per turn (more compact than B DNA)
Its bases are tilted (rather than perpendicular in B DNA) 19 degrees away.
Rise between adjacent base pairs is 0.26nm
Helical repeat is 2.6nm
The helix is 2.6nm wide
Puckering of 3’ carbon.

Question 20

Describe the features of Z DNA.

Answer 20

It is a left handed helix.
12 bases per turn.
Has a zig zag appearance.
Roughly perpendicular to backbone (7 degree tilt)
Rise between adjacent base pairs is 0.37nm
Helical repeat is 4.5nm
The helix is 1.8nm.
Puckering of 2’ carbon for pyrimidines and puckering of 3’ carbon of purines.

Question 21

RNA is flexible and unstructured mainly, give example of the pockets of structure they do have.

Answer 21

Hairpins: when complementary base pairing forms from being very close together.
Stem-loop structures: form when complementary bases are more distant.

Question 22

Why is single stranded RNA a stable structure?

Answer 22

Because of the rigidity provided by base stacking and Van der Waals forces.

Question 23

Draw a bulge, internal loop and hairpin structure.

Answer 23

See picture on phone.

Question 24

What types of RNA are hairpin and stem loop structures important?

Answer 24

rRNA and tRNA.

Question 25

When in these structures (hairpin and stem-loop) which type of DNA does RNA resemble?

Answer 25

A DNA.

Question 26

Can hybrid DNA-RNA complex form and if so what form of DNA do they ressemble?

Answer 26

Yes they have an A DNA-like conformation.

Question 27

When can DNA-RNA hybridisation occur?

Answer 27

During transcription when mRNA is synthesised on the DNA template strand.
Also during replication when RNA primers are synthesised to initiate DNA synthesis.