Lecture 4: DNA Helices

Question 1

In DNA are there more a) keto bases or amino bases and b) more purines or more pyrimidines?

Answer 1

a) There are an equal number of keto and amino bases in DNA.

b) There are an equal number of purine and pyrimidine bases in DNA.

Question 2

How many hydrogen bonds are between cytosine and guanine?

Answer 2

3

Question 3

How many hydrogen bonds are between adenine and thymine?

Answer 3

2

Question 4

What leads the the major groove and the minor groove?

Answer 4

The anti-parallel strands in a DNA helix are not directly opposite each other, because the hydrogen bonding between the base pairs causes the bases to not be directly opposite each other.
The major groove is large enough to allow intimate binding of proteins to the DNA.

Question 5

What is the significance of the fact that purines always face pyrimidines and vice versa?

Answer 5

The DNA helix is of a constant width.

Question 6

Describe the consequences of the positions of the bases relative to the helical axis of the DNA molecule.

Answer 6

The bases project perpendicular to the helical axis and are parallel to each other. They stack and van der Waals and hydrophobic interactions between the planar base rings stabilise the DNA structure.

Question 7

Which form of DNA is ‘average’ DNA?

Answer 7

The B form

Question 8

Give the characteristic measurements and features of B-DNA.

Answer 8

• B-DNA is a right handed helix
• the rise between adjacent bases is 3.4 nm
• the helical repeat is 3.4 nm
• there are 10.5 base-pairs per turn
• the helix is 2 nm wide

Question 9

What is duplex DNA?

Answer 9

Double-stranded DNA

Question 10

What other forms of DNA are there (apart from B-DNA)?

Answer 10

A-DNA is a more compact right handed helix with 11 bases per turn (rather than 10.5 in the B-form) and very titled bases and a central hole.

Z-DNA is a left handed helix with 12 bases per turn (rather than 10.5 in the B-form) and a zig-zag appearance.

Question 11

What causes a DNA molecule to be in a specific form?

Answer 11

The biochemical conditions of the cell, particularly protein-DNA interactions.

Question 12

DNA forms are fairly interesting, no? Maybe you could look up some outside reading about them. Wouldn’t it be nice to get a first?
What about the cellular function of the different forms? Why is A-DNA useful? What is the function of the central hole of A-DNA? What is the functional consequence of the zig-zagness of Z-DNA? What are the consequences of the different base tilts and number of base pairs per turn? What is the significance of right handed or left handed helices?

Answer 12

Of course I will look up some extra information to count as outside reading. 
I can try:
- Alberts
- Voet and Voet
- the internet, e.g. PubMed

Because, of course, I want a first :)

Question 13

What is a right handed helix and how is it different to a left handed helix?

Answer 13

Not sure yet

Question 14

When does B-DNA form?

Answer 14

DNA fibres in an environment of very high humidity (92%) take up the B-form.

Question 15

When does A-DNA form?

Answer 15

DNA fibres in an environment of 75% humidity take up the A-form.

Question 16

When does Z-DNA form?

Answer 16

Z-DNA is formed when a sequence of DNA has alternating purine/pyrimidine bases, e.g. CGCGCGCGCG etc. This form of DNA may exists in parts of a chromosome within cells.

Question 17

What is the function of Z-DNA?

Answer 17

The function is unknown, but it might be to aid protein-DNA interactions and bending/kinking of DNA.

Question 18

Are different DNA forms adopted globally or locally?

Answer 18

Locally. Different parts of the same long DNA molecule can take up different forms depending on their environment, e.g. humidity, or the sequence of a section of the DNA molecule, e.g. alternating purine/pyrimidine gives Z-DNA.

Question 19

Give the different measurements and characteristics of A, B and Z DNA.

Answer 19

• Helical sense: A and B-DNA are right handed, but Z-DNA is left handed
• Diameter: A-DNA is 2.6 nm (26 A), B-DNA is 2 nm (20 A) and Z-DNA is 1.8 nm (18 A)
• Bases per helical turn: A-DNA has 11, B-DNA has 10.5 and Z-DNA has 12
• Helix rise per base pair: 2.6 A in A-DNA, 3.4 A in B-DNA and 3.7 A in Z-DNA
• Base tilt perpendicular to the helical axis: 20° in A-DNA, 6° in B-DNA and 7° in Z-DNA
• Sugar pucker configuration: C3’-endo for A-DNA, C2’-endo for B-DNA and C2’-endo for purines/C3’-endo for pyrimidines in Z-DNA
• Glycosyl bond formation: anti for A-DNA, anti for B-DNA and anti for pyrimidines in Z-DNA

Question 20

Describe the secondary structure of RNA.

Answer 20

RNA is flexible and unstructured with small local regions of structure where complementary base pairing allows hairpins and stem loops to form.
Hairpins are formed when the complementary sequences are close together and stem loops are formed when they are more distant, so there is a significant section between which does not base pair.
Single stranded RNA is stable because of the rigidity provided by base stacking, Van der Waals forces.

Question 21

What are hairpins and stem loops used in?

Answer 21

Ribosomal RNA and transfer RNA

Question 22

Which form of DNA is duplex RNA similar to?

Answer 22

A-DNA

Question 23

Does there have to be a perfect match for secondary RNA structures to form?

Answer 23

No, as long as there are enough matching base pairs surrounding it, a non-matching pair can base pair, e.g. G and U. In this case only 2 hydrogen bonds are formed as U cannot make 3 hydrogen bonds.

Question 24

Which form of DNA is a DNA-RNA hybrid similar to?

Answer 24

A-DNA

Question 25

When do RNA-DNA hybrids occur?

Answer 25

• During transcription, when mRNA is synthesised on a DNA template
• During replication, when RNA primers are synthesised to initiate DNA synthesis.