Nucleotides and DNA Flashcards
Nucleotides in the monomer form are used for?
Metabolism (ATP), enzyme cofactors (NAD+) and signal transduction (cAMP).
Nucleoside
Nitrogenous base and pentose.
PO4 is what a neutral pH?
Negative.
PO4 is typically attached to which position?
5’
Nitrogenous bases are…
Derivative of pyrimidine or purine, planar or almost planar, absorb UV light around 250-270nm.
Difference between ribo and deoxyribo
Deoxyribo has no O at 2’ carbon.
N-glycosidic bond
Pentose is attached to the nitrogenous base. Quite stable towards hydrolysis.
Where does the N-glycosidic bond form in pyrimidines?
N1 position of N base.
Where does the N-glycosidic bond form in purines?
N9 position of N base.
Syn conformation
Angle near 0 in N-glycosidic bond.
Anti conformation
Angle near 180 in N-glycosidic bond. Normal B-DNA.
Ring pucker limits what?
The angle of torsion possible for the N-glycosidic bond.
How do nucleotides connect to one another?
Phosphodiester bonds, connected from 3’ carbons to 5’ carbons.
How are DNA/RNA strands held together?
Hydrogen bonding.
What was the waston and crick model of B-form DNA?
10.5 base pairs, or 3.6nm, per turn of helix.
RNA is unstable under…
Alkaline conditions. The OH at the 2’ position acts as a nucleophile.
What remains intact during DNA denaturation?
Covalent bonds and genetic code.
What is lost during DNA denaturation?
Hydrogen bonds and base stacking.
What induces denaturation?
High temperature or change in pH.
Tm
Mid point of melting
What increases Tm (DNA denaturation)?
High CG composition, longer DNA and high salt.
Deamination
Cytosine to uracil, very slow reactions.
Depurination
N-glycosidic bond is hydrolyzed, significant for purines.
UV light induces…
Dimerization of pyrimidines.
cAMP
Second messenger, activates protein kinase A activity.
What ends are new nucleotides added to?
3’ end (to the 3’-OH).
How are trinucleotides added in DNA elongations?
The nucleophilic OH group at the 3’ end of the growing chains attacks the alpha phosphate of the incoming trinucleotide.
How is the 3’ OH made a more powerful nucleophile?
By near by Mg+ ions.
Primer
Contains 3’ - OH to begin the first DNA polymerase catalyzed reaction, commonly made of RNA.
