L1 Flashcards
pyrimidine
big name, small molecule -> cytosine and thymine and uracil
purines
small name, big molecule _> adenine guanine
nucleobase
just nitrogenous base
nucleoside
base + sugar
nucleotide
base + sugar + phosphate
base deamination
It’s a spontaneous hydrolysis reaction wherein a NH2 group in a base gets
replaced by an oxygen with a double bond, and every lone N attached gains a
hydrogen to become NH. C becomes U
base tautomerization
Basically, when pH changes, the bases change too, for example in Uracil, when
pH is below 7, one of its oxygens gains a hydrogen.
pentose puckering
A carbon atom is not completely flat compared to other carbons in the same
molecules, it sticks out. In DNA, the C-2 and C-3 stick out. If it’s in the same axis
as C-5 it’s endo pucker, if not it’s exo pucker.
flagging
when a nucleoside forms it can be in two syn and anti
syn
base hangs on the same side as the sugar
anti
base hangs on the opposite side to the sugar, looks like flag (pyrimidines are alwayls like this)
base stacking
this forms rna and dna, major and minor groove, a dna, b dna, z dna, relies on vd waals interactions and dipole dipole interactions (N-H, C=O) between bases, C=-G -15 kj/mol, A=T -6kj/mol
a dna
rna only in this form, dna often too, spins to the right, narrow but deep major groove
b dna
dna takes this form if little water, wide major groove
z dna
spins left, only with CGTACAGC
