Nucleic Acids Flashcards
(27 cards)
Nucleoside
Lacking phosphate group.
Sugar + base
Can be mono, di, tri-phosphate
A nucleoside monophosphate = a nucleotide.
What’s soluble?
Nucleotide > nucleoside > bases
pyrimidine > purine
Where is the OH group on ribose sugar?
At the 2’C
dNTP
deoxynucleotide-triphosphate
Lesch-Nyhan
an accumulation in tissues of purines. This forms uric acid in kidneys and other body tissues.
Purine
Pure as gold. A and G.
Gout
Defect in phosphoribosyl synthetase, accumulation in tissues of purines. Low solubility. Uric acid in joints.
Why the 5’-3’ polarity?
This is because the 3’ end has a spare OH group.
5’ end has spare phosphate group.
Phosphodiester linkage
Strong covalent bonds. OR (R is akyl group). Between phosphate group and 2 5-C ring carbs.
Link between 3’ carbon of one sugar and the 5’ C of another.
Pyrophosphate breaks away (can be 1 or 2 P’s) to provide the catalyzing energy for the bond formation.
Where is the P?
On the 5’ C because it is the most partially positive.
Avery, McCloud, and McCarty
They transformed pneumococcus serotype R to S, showed that DNA causes bacterial transformation. Before they thought it was protein.
Living R + heat-killed S –> dead mouse.
Chargaff’s rules
In DNA there is always equality in quantity between bases A and T, C and G. (every organism has diff G+C/A+T)
Watson-Crick
Discovered definitive double-helical structure and that DNA semi-conservatively replicates
B form DNA
2 strands in a right-handed helix
Strands backbones are oriented anti-parallel
Sugar phosphate backbone is on OUTSIDE of helix (hydrophilic)….
Chemical basis for stability of double helix DNA
Hydrophobic interactions b/w adjacent base pairs
H bonding between complementary bases in a base pair are imp for DNA stability (to compensate for the neg charged P which want to repel).
In sol’n: Mg (cations in sol’n) stabilize negative P. Base pair linkages & adjacent base pairs stack via hydrophobic interactions.
Backbone is phosphodiester, it binds with water, negative.
Increased salt concentration
Increases the Tm.
Salt stabilizes the P groups with na and Mg. Exposed negatives would force strands apart.
Extremes of pH
alter ionization of groups on bases that provide and accept the H bonds.
Really acidic, really positive.
Increased chain length
Increased length stabilizes the molecule, and increases the Tm
Increased GC content?
Increases the Tm. 3 bonds b/w G and C.
Linear DNA
Can be relaxed or supercoiled.
Relaxed is the NORMAL, straight ribbon of proper twisting.
Supercoiled: torsional strain that becomes contorted into shapes like a Figure 8.
Important for DNA packaging in eukaryotes.
Circular DNA
is in prokaryotes
Methylation
Occurs at CpG sites. 5’ end on cytosine. Converts cytosine to 5-methyl-cytosine. DNA methyltransferase facilitates this.
Human DNA has 80-90% methylated CpG sites… often associated with promoters of 56% of genes.
CpG can often be seen around genes that DO get transcribed (bizarre thought).
Can be epigenetically inherited.
Deamination
C can lose an amine to become U (results in mutated DNA).
MAJOR cause of mutated DNA. Repair enzymes should catch this.
5’ methylcytosine can be deaminated to THYMINE (so this becomes A-T and is harder to catch).
Nitrous acid, tobacco, speeds this up.
Depurination
A or G is removed by hydrolysis of the beta-N-glycosidic link (b/w base and first sugar)… leaves HYDROXIDE in its place
Lower pH promotes the hydrolysis of this.
The phosphate backbone is now prone to breakage.
Base excision repair??
