Flashcards in Lecture 4: DNA Helices Deck (25):
In DNA are there more a) keto bases or amino bases and b) more purines or more pyrimidines?
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.
How many hydrogen bonds are between cytosine and guanine?
How many hydrogen bonds are between adenine and thymine?
What leads the the major groove and the minor groove?
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.
What is the significance of the fact that purines always face pyrimidines and vice versa?
The DNA helix is of a constant width.
Describe the consequences of the positions of the bases relative to the helical axis of the DNA molecule.
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.
Which form of DNA is 'average' DNA?
The B form
Give the characteristic measurements and features of B-DNA.
- 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
What is duplex DNA?
What other forms of DNA are there (apart from B-DNA)?
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.
What causes a DNA molecule to be in a specific form?
The biochemical conditions of the cell, particularly protein-DNA interactions.
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?
Of course I will look up some extra information to count as outside reading.
I can try:
- Voet and Voet
- the internet, e.g. PubMed
Because, of course, I want a first :)
What is a right handed helix and how is it different to a left handed helix?
Not sure yet
When does B-DNA form?
DNA fibres in an environment of very high humidity (92%) take up the B-form.
When does A-DNA form?
DNA fibres in an environment of 75% humidity take up the A-form.
When does Z-DNA form?
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.
What is the function of Z-DNA?
The function is unknown, but it might be to aid protein-DNA interactions and bending/kinking of DNA.
Are different DNA forms adopted globally or locally?
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.
Give the different measurements and characteristics of A, B and Z DNA.
- 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
Describe the secondary structure of RNA.
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.
What are hairpins and stem loops used in?
Ribosomal RNA and transfer RNA
Which form of DNA is duplex RNA similar to?
Does there have to be a perfect match for secondary RNA structures to form?
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.
Which form of DNA is a DNA-RNA hybrid similar to?