nucleic acids p2

Question 1

what are some characteristics of nucleotide nitrogeneous bases

Answer 1

weakly basic and aromatic

Question 2

what is the 3D structure of a pyrimidine

Answer 2

planar because single ring

Question 3

what is the 3D structure of a purine

Answer 3

puckered because of double ring

Question 4

what sort of equilibrium do nitrogeneous bases have?

Answer 4

keto-enol tautomerization

Question 5

which is favored at a neutral pH, ketos or enol tautomers

Answer 5

keto

Question 6

how was the structure of dna determined

Answer 6

Rosalin Franklin’s contributions of X-ray crystallography revealed the helical structure

Chargaffs rule revealed that base pairs pair with eachother, which supported the double helix formation of antiparallel complementary strands

Watson and Crick put it together in a full model

Question 7

how does the diameter of an adenine thymine base pair compare with a guanine cytosine base pair

what does this mean for the overall structure

Answer 7

they have the same diameter of 1.0nm

it means the DNA has the same diameter throughout

Question 8

which carbon are the nitrogenous bases connected to in the pentose sugar

Answer 8

carbon 1

Question 9

what is the endo form? which carbons use this?

Answer 9

the endo form is when either C 2’ or C3’ are flipped up (cupped inwards) to the pentose sugar ring

Question 10

what is the orientation of the sugar to the phosphate backbone

Answer 10

perpendicular

Question 11

which pentose carbon is endo in B DNA

Answer 11

C2’ is endo

Question 12

what are some features of B DNA

Answer 12

20Å diameter
10 base pairs per turn
C2’ carbon is endo
glycosyl bond is anti

Question 13

what is the glycosyl bond conformation in B DNA

Answer 13

anti

Question 14

is hydrogen bonding in base-pairs the cause of DNA stability

Answer 14

no, base stacking is why they are more stable. the base pairs are stacked close enough that their van der waals radius can interact and form temporary dipoles that stabilize the structures

Question 15

true or false, complementary strands have the same sequence

Answer 15

false, they complement eachother but are different

Question 16

why do non-watson crick basepairs form? are they common?

Answer 16

Hydrogen bonding will occur wherever possible, so these base pairs will form regardless due to the hydrogen bonds that form between them.

they are not common because they have lower energy associations than the traditional watson-crick base-pairs

Question 17

how would a different ribose pucker (C2 to C3) affect DNA structure?

Answer 17

A C3 pucker would tilt the ribose 45° to the backbone, everything would shift and the phosphate groups would bebrought closer together

Question 18

what happens to the overall DNA structure when c3’ is endo instead of c’2

Answer 18

the base pairs are more off to the side and tilted while the phosphate background is more linear, this creates more base pairs per turn and a wider A DNA structure

Question 19

when does A DNA form?

Answer 19

in low humidity/ dehydrated environments

Question 20

what helix does A DNA have?

Answer 20

a right handed helix

Question 21

what carbon is endo in A DNA

Answer 21

carbon 3’

Question 22

what orientation is the glycosidic bond in the A DNA

Answer 22

anti

Question 23

what is syn conformation

Answer 23

it regards the conformaitonabout the glycosidic bond where the base is on the same side as the sugar

Question 24

what is anti conformation

Answer 24

the base is turned out base the sugar and they are not on the same side

Question 25

what glycosidic bond conformation does Z DNA have

Answer 25

pyrimidines are anti while purines are syn in alternating fashion

Question 26

what helix does Z DNA have

Answer 26

it is a left handed helix

Question 27

what structural differences do A and Z DNA have when compared to B DNA

Answer 27

A DNA is wider and shorter with 11 base pairs per turn while Z DNA is zig-zag and left handed in a longer and more slender conformation

Question 28

how is Z DNA involved in gene regulation

Answer 28

DNA can be twisted into the Z DNA form to make certain sequences inaccessible to proteins for expression

Question 29

whatdoes it mean to denature DNA

Answer 29

it means the hydrogen bonds have been melted or broken either by pH changes or by heating

Question 30

what does the denaturation temperature of DNA depend on

Answer 30

it depends on the number of GC bases (3 H-bonds), the length of the DNA strand, and the pH and ionic strength

Question 31

what is annealinge

Answer 31

annealing is the process where double-stranded DNA comes back together

Question 32

what is the formula for annealing temperature

Answer 32

4 °C ( number of G and Cs) + 2°C (number of As and Ts)

Question 33

how many base pairs per turn in B DNA

Answer 33

10

Question 34

how big is each helix rise per base pair in B DNA

Answer 34

3.4 Å or 0.34 nm

Question 35

how many base pairs per turn in A DNA

Answer 35

11

Question 36

how big is each helix rise per base pair in A DNA

Answer 36

2.6 Å or 0.26 nm

Question 37

how many base pairs per turn in Z DNA

Answer 37

12

Question 38

how big is each helix rise per base pair in A DNA

Answer 38

3.7Å or 0.37 nm

Question 40

what is the conformation of the penrose sugar in Z DNA

Answer 40

C2’ endo for pyramidines c3’ endo for purines