Nucleic Acids Flashcards
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??
Oxidative damage
Reactive O2 free radicals generated in mitochondria can damage DNA.
Leads to OH groups on bases.
UV light
covalently bonds thymines (distorts DNA helix) and can block replication enzymes.
Occurs between thymines (get cyclobutane thymine dimers). PYRIMIDINE DIMERS.
Transcription factor IIH human (repair)… nucleotide excision repair.
Alkylating agents and chemo
Alkylating agents are used as chemo to damage the DNA of cancer cells (prevents proper DNA replication/transcription and thus cell growth).
