DNA Flashcards
What is the north conformation of the pentose sugar?
C2-exo, C3-endo
What is the south conformation of the pentose sugar?
C2-endo, C3-exo
where do the ribose sugars bind to nitrogenous bases?
the 1’ C of the pentose sugar binds with the 1’ nitrogen forming an N-glycosydic bond with pyrimidine or the 9’ nitrogen with purines
ideal/W-C DNA structure
right-handed helix, 10 bp per turn, 36 degrees per bp; bases held in plane and adjacent parallel to one another; uniform external backbone shape
what forms are pyrimidines in
always anti
what forms are purines in
usually anti, sometimes syn
C-G pairs have the strongest base-stacking energies, that’s why it’s tough to break GC pairs–not bc of extra H-bond
ya
B form DNA general info
10.5 bps per turn, 6 degree tilt, right handed, sugars in C2 conf, propellor twisting
A form DNA general info
found in RNA:DNA hybrids or RNA:RNA or in dsDNA in less than 75% humidity; righthanded helix with 11 bp per turn, shape largely due to C3 endo sugar pucker–>makes DNA shorter and wider: major and minor groove relatively the same size; bases 20 degrees tilted
Z form DNA general info
zig-zag appearance to sugr-phos backbone; left-handed helix with 12 bp per turn; can occur when sequence contains an alternating pyr-pur seq, especially lots of (GCGCGCGCGC) etc; purines have a north pucker and syn rotation; pyr have a south and anti; major groove is wide and flat, minor almost inaccessible
how can Z DNA be formed in an actual cell?
when it is being untwisted and if the seq permits it
B-Z junction general info
between the junctions, there are likely A and T molecules sticking out–>more prone to damage or modification
types of repeat specific structures
direct repeat; inverted repeat; mirror repeat
what are direct repeats?
a seq that is duplicated in succession; eg AAAAA, AGAGAGA, ATGATGATG; may cause slipped strands during DNA replication
what are inverted repeats?
mirrored version of cross-sections (lol idk how to explain)–>can cause cruciform structure in dsDNA or hairpin structure in ssDNA
how and when does triplex/hoogsteen DNA form?
forms when there’s a long run of alternating pur:pyr and mirror repeats; and third strand peels away from its complementary strand and wraps back around, forming H-bonds with the already-double stranded segment (which is also complementary to it)
what causes Freidrichs Ataxia?
triplex/hoogsteen DNA
human telomeres for tetraplexes as they shorten–inhibits telomerase–means telomeres have a lot of guanines
ya??
sugar puckering affects the angles and distances of bases and phosphates
ya
DNA is usually in south conformation but can adopt north conformation
ya
RNA is always in north conformation
ya
what is the purpose of base stacking?
to achieve the most thermodynamically favourable conformation of bases possible–even if it’s not favourable for H bonds
