7 - Structure Of DNA Flashcards
Two types of nucleotide
Pyrimidines
Purines
What makes up a nucleoside
Base and sugar
What makes up a nucleotide
- what can nucleotides be seen as
The nucleoside (base and sugar) and the phosphate
- phosphorylated nucleosides
Difference between ribose and deoxyribose sugars
- Ribose has three OH groups - (on Carbon 1, 2 and 3)
- where deoxyribose has two (Carbon 2 and 3)
- hence the deoxy
Why we have purines and pyrimidines
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
DNA info
- 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
Phosphodiester bond in DNA info
- what does this give DNA
- 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.
Chargsff Levenes predictions of DNA
Percentage of A and T, and C and G, are around the same in DNA of any organism
X-ray fibre diffraction info
- 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
Fresnel work on light - info
Hight of one helical turn
3.4 nm
Hight of each stacking of bases
0.34 nm
- so 10 bases for each helical turn
Why the triple helix model from Pauling wouldn’t work
- 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
Key features of Watson-Crick model of DNA
- 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
How many hydrogen bonds between different complementary bases
A-T - 2 H bonds
C-G - 3 H bonds
Which parts of nucleotides act as electron acceptors and donors
Oxygen and nitrogen as electron acceptors
Hydrogen as electron donor
nucleotide vs nucleoside
nucleoside is sugar and base
- nucleotide is sugar, base and phosphate attached
where are the glycosidic bonds in nucleotides located (for purines and pyrimidines)
between sugar C-1’ and:
- N-9 (purine)
- N-1 (pyrimidine)
difference between purines and pyrimidines
purine - N1, N3 and N9
- pyrimidines - N1 and N3
what technique used to determine shape of DNA
X-ray fibre diffraction
other structural variants of DNA and how they arise
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
