Nucleic acids Flashcards
phosphate group
charge of -2 as H+ dissociates at physiological pH, hydrophyllic
pentose sugar
exist as either straight chains or furan rings, furan rings for nucleotide
naming: 1’ C is the one bonded to the base
deoxy - only has one hydroxyl group
nitrogenous bases classification
pyrimidine rings: single ring made of 6 atoms (CTU)
purine rings: 2 rings made of 9 atoms (AG)
nitrogenous base properties
resonance occurs, electrons are no longer localised over 2 atoms, spread over more atoms –> very stable, absorbs UV light
resonance results in bonds having a partial double bond character
due to double bonds, very planar or almost planar
nitrogenous base naming
purines: -osine, -ylate
pyrimidines: -idine, idylate
add deoxy in front for DNA
function of nucleic acids and derivatives
storage and retrieval of genetic information for determining AA sequence during protein synthesis
RNA is either structural or functional
ATP: storage of energy
NAD+ : important co factor for cellular processes
cAMP: signalling molecule
other bases
minor bases in cells, even cyclic nucleotides
nucleoside
base and sugar bonded together via glycosidic bond (N)
nucleotide
phsophate group bonded to other nucleoside via phosphoester bond
DNA structure
double helix, 2 strands running anti-parallel (5’ to 3’ and 3’ to 5’)
phosphate group of 1 nucleotide joins with ribose sugar at 3’ carbon via phosphodiester bond
H bonding between bases
hydrogen bonding between bases occurs, strongest when all 3 molecules are in a straight line, hence AT (2 H bond) CG (3 H bond)
other base pairings H bonding are not as strong
2 purines or 2 pyrimidines cause overlaps or gaps
hydrophobic effect in DNA
bases are hydrophobic, project inside the double helix to reduce contact area with water, more energetically favourable
planar bases –> stacking very efficient packing
meanwhile hydrophyllic sugar phosphate backgbone is on the outside of the helix
primary and secondary structure
primary: sequence of nucleotides 5’ to 3’
secondary: 2 strands running antiparallel : double helix with complete turn every 3.4 nm, diameter of 2nm
what did Chargaff discover
DNA contains same amount of phosphate and pentose, different base sequence varies across species
sum purines = sum pyrimidines
A=T, C=G
same species has identical DNA in different cells, does not change
X ray measurements discoveries
regular structure of a helix,
density measurements: helix must have 2 chains
Griffith 1928 experiment
S strain has polysaccharide capsules, R does not
S strain live cells: mouse dies
R strain live cells: mouse lives
heat killed S strain cells, mouse lives
R strain and heat killed S strain, mouse dies
S strain DNA was taken up by the R strain cells –> transformation
Avery 1944 experiment
mouse lives when S strain DNA is destroyed, hence DNA carries genetic information
1952 phage experiment procedure
- grow bacteria in either radioactive 35S or 32P
- infect bacteria with phage to get phage with hot (radioactive) proteins or DA
- infect fresh bacteria with phage that have hot proteins or DNA
- protein coat of phage is sheared off, phages separated from cells
- 35S not found in new phage, 32P found in bacterial cells and new phages –> DNA passed down
fundamental features of DNA double helix
right handed helix
major and minor grooves to allow proteins and ions to interact with DNA
3 forms of helices, most common is B form, 10 base pairs per full turn
denaturation annealing hybridisation
denaturing - separating double helix into single strands of DNA
annealing - 2 single strands of DNA rewind to form double helix spontaneous process if more than 10 base pairs are still intact
hybridisation - when strands from different species that have similar bases anneal
how can DNA be denatured
break H bonds –> high temperature, extreme pH
how to measure % denaturation
viscosity, increase denaturation, decrease viscosity
hyperchromism, single stranded DNA absorbs UV light more readily than double stranded DNA
Tm definition
temperature at which DNA has reached half total max denaturation
base composition and Tm
CG 3 H bonds, AT 2 H bonds, increase CG content, increase Tm
ionic strength and Tm
repulstion between sections of sugar phosphate backbone is the main destabilising force for helix
increase salt concentration, increase interactions with phosphate ions, decrease repulsion, stabilisation of helix
Tm and pH
large change in protonisation states, decrease H bonding, decrease Tm
mildly alkaline pH is preferred for denaturation
Tm and in vitro H bonds
decrease Tm, forms H bonds with bases, prevents reannealing
needs high concentrations though
DNA palindromes and hairpin formation
sequence of bases that reads the same forwards and backwards
self-complimentary bases within each strand –> intrastrand H bonding occurs, forming hairpin structures
nuclear vs mitochondrial DNA
linear vs circular
When does DNA replication occur and what it relies on
S phase of cell cycle
complementary base pairing
