DNA

Question 1

What is the north conformation of the pentose sugar?

Answer 1

C2-exo, C3-endo

Question 2

What is the south conformation of the pentose sugar?

Answer 2

C2-endo, C3-exo

Question 3

where do the ribose sugars bind to nitrogenous bases?

Answer 3

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

Question 4

ideal/W-C DNA structure

Answer 4

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

Question 5

what forms are pyrimidines in

Answer 5

always anti

Question 6

what forms are purines in

Answer 6

usually anti, sometimes syn

Question 7

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

Answer 7

ya

Question 8

B form DNA general info

Answer 8

10.5 bps per turn, 6 degree tilt, right handed, sugars in C2 conf, propellor twisting

Question 9

A form DNA general info

Answer 9

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

Question 10

Z form DNA general info

Answer 10

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

Question 11

how can Z DNA be formed in an actual cell?

Answer 11

when it is being untwisted and if the seq permits it

Question 12

B-Z junction general info

Answer 12

between the junctions, there are likely A and T molecules sticking out–>more prone to damage or modification

Question 13

types of repeat specific structures

Answer 13

direct repeat; inverted repeat; mirror repeat

Question 14

what are direct repeats?

Answer 14

a seq that is duplicated in succession; eg AAAAA, AGAGAGA, ATGATGATG; may cause slipped strands during DNA replication

Question 15

what are inverted repeats?

Answer 15

mirrored version of cross-sections (lol idk how to explain)–>can cause cruciform structure in dsDNA or hairpin structure in ssDNA

Question 16

how and when does triplex/hoogsteen DNA form?

Answer 16

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)

Question 17

what causes Freidrichs Ataxia?

Answer 17

triplex/hoogsteen DNA

Question 18

human telomeres for tetraplexes as they shorten–inhibits telomerase–means telomeres have a lot of guanines

Answer 18

ya??

Question 19

sugar puckering affects the angles and distances of bases and phosphates

Answer 19

ya

Question 20

DNA is usually in south conformation but can adopt north conformation

Answer 20

ya

Question 21

RNA is always in north conformation

Answer 21

ya

Question 22

what is the purpose of base stacking?

Answer 22

to achieve the most thermodynamically favourable conformation of bases possible–even if it’s not favourable for H bonds