Secondary Structure of DNA and RNA Flashcards
What did wilkin and franklin’s X-ray difraction of DNA show?
It showed that DNA is a helical molecule and that bases form a stack of parallel rings, parallel to the fibre axis.
What are Chagraff’s rules? (HINT: 3 rules)
%A = %T and %G = %C
%keto bases = %amino bases
%purines = %pyrimidines
What is the distance between the base pairs?
3.4Å
What is the length of the helical turn?
34Å
What is the distance between the base pairs?
3.4Å (0.34nm)
What is the length of the helical turn?
34Å (3.4nm)
Describe the secondary structure of DNA?
The two strands running anti parallel to each other and the complimentary bases on each strand linked by hydrogen bonds.
What does Watson-Crick base pairing state?
A and T are bond by 2 hydrogen bonds.
G and C are bonded by 3 hydrogen bonds.
Purines always face pyrimidines.
Why is there a major and minor groove in DNA?
Because the two strands are not directly opposite each other.
Describe the secondary structure of DNA.
The two strands running anti parallel to each other and the complimentary bases on each strand linked by hydrogen bonds.
Describe how the bases are arranged in the secondary structure of DNA.
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
Describe how the bases are arranged in the secondary structure of DNA.
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
What is the ‘average’ form of DNA?
B DNA.
Describe the structure of B DNA.
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
Why are base pairs not directly opposite each other?
Due to hydrogen bonding.
Why are base pairs not directly opposite each other and what does this result in?
Due to hydrogen bonding.
This results in two types of groove - the majore and minor groove.
What does the major groove’s size allow?
Because it is larger it can allow intimate protein binding to the double stranded DNA.
What is double stranded DNA also known as?
Duplex DNA.
Describe the features of A DNA.
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.
Describe the features of Z DNA.
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.
RNA is flexible and unstructured mainly, give example of the pockets of structure they do have.
Hairpins: when complementary base pairing forms from being very close together.
Stem-loop structures: form when complementary bases are more distant.
Why is single stranded RNA a stable structure?
Because of the rigidity provided by base stacking and Van der Waals forces.
Draw a bulge, internal loop and hairpin structure.
See picture on phone.
What types of RNA are hairpin and stem loop structures important?
rRNA and tRNA.
When in these structures (hairpin and stem-loop) which type of DNA does RNA resemble?
A DNA.
Can hybrid DNA-RNA complex form and if so what form of DNA do they ressemble?
Yes they have an A DNA-like conformation.
When can DNA-RNA hybridisation occur?
During transcription when mRNA is synthesised on the DNA template strand.
Also during replication when RNA primers are synthesised to initiate DNA synthesis.
