1
Q
Nucleotide
A
base + pentose sugar + phosphate group
2
Q
Pentose Sugar
A
- ribose or deoxyribose
- deoxyribose is missing the C2 hydroxyl group
- 5 membered ring with C1 linked to C4 via oxygen
- C5 attached as side chain
- planar ring is subject to steric clash, which is relieved by puckering such that either the 2 or 3 C is out of the plane
- puckering governs relative orientations of phosphate substituents to each ribose residue
- pentose sugars contribute to the polar character of the molecules but most importantly render RNA susceptible to base
catalyzed hydrolysis
3
Q
Phosphate
A
- free nucleotides have phosphate groups attached via phosphodiester bonds to C5
- negative charges are neutralized by divalent cations
- divalent cation preferred due to their specific binding to phosphate groups
4
Q
Nitrogenous Base
A
The planar (delocalized electrons) of the aromatic bases allowing temporary dipoles contributing to chemical reactivity and van der Waals interactions in helices.
- C1 joined to base in the plane above the sugar ring
- forms planar rings
- anti conformation: faces away
- syn conformation: faces towards
5
Q
Base Types/Structures
A
Purines: double ring structure (A,G)
Pyrimidines: single ring structure (C,T,U)
Keto base: carbonyl group (G,U,T)
Amino base: amine group (C,A)
6
Q
Properties of DNA
A
- highly soluble in aqueous solution
- resistant to organic solvents from sugar/phosphate groups
- resistant to organic solvents from sugar/phosphate groups
- temperature stability from H bonding, hydrophobic effects, and VDW interactions
- light absorbance due to base aromaticity
- ph disrupts H bonding and hydrolyzes bonds
7
Q
Base Stabilizing Effects
A
- bases are aromatic and are planar/delocalised rings of electrons
- allows temporary dipole formation contributing to chemical reactivity and VDW interactions
- hydrophobic effect of base interactions
- sugar puckering determines structural alterations
- pyrimidines only have anti conformation because of steric clash
- ring substituents are eclipsed when ring is planar causing puckering
8
Q
Nomenclature
A
nucleoside: base and sugar without phosphate
- sine ending
9
Q
DNA directionality
A
5’ phosphate end
3’ hydroxyl end
10
Q
Nucleotide Addition
A
- catalysed by polymerase enzymes
- need deoxynucleoside triphosphates, DNA template, primer with free 3’ OH
- synthesis in 5’-3’ direction
11
Q
Polymerization
A
- alpha phosphoryl of a free nucleotide triphosphate undergoes nucleophilic attack by the 3’C hydroxyl group of the nucleotide at the 3’ end of the growing chain
- addition of a nucleotide to the 3’ C via a phosphodiester bond (C-O-P-O-C) with the eliminatino of pyrophosphate
- release is reversible and the hydrolysis of PPi provides energy that drives polymerization (energy coupling of reactions)
12
Q
Base Catalysed Hydrolysis
A
- explains why DNA is the hereditary material
- 2’ OH group of RNA is susceptible to base catalysed hydrolysis
- nucleophilic attack of hydroxyl group on 2’ hydroxyl
- attack on phosphate atom and electron flow onto oxygen
- oxygen and attached groups leave
13
Q
Duplex DNA structure
A
- 2 helical polynucleotide strands are coiled around an axis in the right hand direction
- backbone is outside/bases face inwards
- bases perpendicular to helix axis
- hydrophobic effect of aromatic non-polar bases being away from water
- VDW interactions and sugar ring conformations favor stacked base apirs
14
Q
DNA Statistics (B DNA)
A
- The helices are right handed
- The rise between adjacent bases is 0.34 nm.
- The helical repeat is 3.4 nm.
- There are 10 base-pairs per turn.
- The helix is 2 nm wide.
- because the glycosidic bonds are not exactly opposite each other, grooves form
- anti conformation
- 3.4 angstrom helix rise
- wide and deep major groove
- narrow and deep minor groove
15
Q
Evidence used to Deduce DNA structure
A
- Chargaff's Rules %A=%T and %G=%C %purines=%pyrimidines %amino=%keto - X Ray Diffraction Images DNA is helical and bases form stacks of parallel rings
16
Q
Stability of DNA structure
A
- energetically favorable because hydrophobic bases are away from solvent
- polar backbone is stabilised by cation bonding and solvation
- VDW and hydrophobic interactions between planar base rings stabilises structure
- aromatic ring electron delocalisation aids VDW force formation
- base stacking is enthalpy driven
17
Q
Watson Crick Base Pairing
A
- 2 antiparallel strands with H bonds between complementary bases (amino and keto groups)
- G-C forms three bonds and A-T forms two bonds
- bases project perpendicular to helical axis
- bases are parallel and stack partially overlapping
18
Q
A DNA
A
- formed from crystallisation of B DNA at lower humidity
- base pairs tilted relative to the axis
- C3’ end puckering (C3 above axis)
- 11 degree tilt of base pairs away from axis
- 11 bases per turn
- narrow and deep major groove
- wide and shallow minor groove
- anti conformation
- right hand helix
- 2.9 angstrom helix rise
19
Q
Z DNA
A
- formed by B DNA stabilisation at high salt concentration, as the high electrostatic repulsions between nearby phosphate groups on opposite strands are reduced
- left hand helix
- 12 base per turn
- flat major groove
- narrow and deep minor groove
- alternate C2 and C3 sugar puckering
- purine base syn conformation
- pyrimidine base anti conformation
- repeating unit of a dinucleotide, phosphate groups create a zigzag
20
Q
RNA Structure
A
- form similar to A DNA, as in B form there is steric clash involving the 2’ OH group and the phosphate group
- A DNA has the 2’ O projecting out so this is favored
21
Q
RNA Secondary Structure
A
- rna is flexible and unstructured but has pockets of structure where complementary base pairing forms hairpin and stem loop structures
- hairpin: complementary sequences are close together
- stem loops: complementary sequences are distant
- found in tRNA, rRNA, etc
22
Q
RNA Hybrid
A
Hybrid DNA-RNA duplexes have A like conformation
- transcription (mRNA and DNA)
- translation (RNA primer and DNA)
