Week 1 - Structure and Properties of Nucleic Acids

Question 1

bases in nucleic acids

Answer 1

• attached to 1’C sugar

purines have two bases:

• adenine
• guanine

pyrimidines have three bases:

• cytosine
• thymine
• guanine

Question 2

nucleotide charge

Answer 2

negative

Question 3

primary structure of nucleic acids

Answer 3

base stacking

Question 4

base stacking

Answer 4

• bases stack on top of each other

- interactions result from hydrophobic effect

Question 5

phosphodiester bonds

Answer 5

joins sequence of nucleotides

Question 6

secondary structure of nucleic acids

Answer 6

pentoses have a puckered conformation

• either C-2’ or C-3’ can be puckered
• puckered can be endo (towards 5’C) or exo (away 5’C)

Question 7

key features of secondary structure of double stranded nucleic acids

Answer 7

• two nucleic acid molecules
• anti-parallel
• helical
• complementary

Question 8

common hydrogen bonding patterns in DNA

Answer 8

• adenine bonded to thymine (1 pi bond)

- guanine bonded to cytosine (2 pi bonds)

Question 9

different helical structures in double stranded nucleic acids

Answer 9

precise atomic positions can differ due to:

• sugar pucker
• rotation around bonds in nucleotides

Question 10

rotation around 7 bonds in double helix

Answer 10

• theoretically, 1, 2, 3, 5, and 6 have free rotation
• 4 (delta) belongs in a sugar ring, therefore rotation is harder
• 7 (chi) is near a bulky base, therefore rotation is restricted

Question 11

purine conformations

Answer 11

• anti-adenosine is the normal conformation

- syn-adenosine is a possible conformer but rarer

Question 12

pyrimidine conformations

Answer 12

only anti-cytidine is possible as the =O causes steric hindrance

Question 13

forms of helical double stranded nucleic acids

Answer 13

• a form
• b form
• z form

Question 14

A form

Answer 14

• helical: right handed
• bp per helical turn: 11
• length: 2.6 A
• base tilt: 20 degrees
• sugar pucker: C-3’ endo
• glycosidic bond: anti

Question 15

B form

Answer 15

• helical: right handed
• bp per helical turn: 10.5
• length: 3.4 A
• base tilt: 6 degrees
• sugar pucker: C-2’ endo
• glycosidic bond: anti

Question 16

Z form

Answer 16

• helical: left handed
• bp per helical turn: 12
• length: 3.7 A
• base tilt: 7 degrees
• sugar pucker: C-2’ endo for pyrimidines; C-3’ endo for purines
• glycosidic bond: anti for pyrimidines; syn for purines