Quiz 2

Question 1

DNA duplexes at physiological conditions form…

Answer 1

B-form DNA

Question 2

What types of duplexes have A-form SS?

Answer 2

DNA duplexes below 75% humidity, RNA duplexes, DNA/RNA hybrids

Question 3

What types of duplexes have Z-form DNA?

Answer 3

Alternating purine-pyrimidine, high salt

Question 4

Describe the basic features of the A family.

Answer 4

3’ endo, bases off axis (tilted), 3 ang. hollow core, high roll - negative slide

Question 5

Describe the basic features of the B family

Answer 5

2’ endo, bases on axis (perpendicular), ~14 water molecules per bp, little roll - small positive slide

Question 6

Describe the basic features of the Z family

Answer 6

dC - C2’ endo - anti

dG - C3’ endo - anti

Question 7

What drives B-form conformational changes?

Answer 7

maximizing base stacking - patterns of h-bond donors and acceptors in groove altered

Question 8

A van der Waals interaction can be described as…

Answer 8

dipole-dipole interaction (r^-6), London forces (r^-4)

Question 9

What interactions are involved in pi/pi stacking?

Answer 9

van der Waals interaction and electrostatic interaction

Question 10

What is the average energy per stacked base pair?

Answer 10

8.2 kcal/mol

Question 11

What is the high end of the energy of stacked base pairs?

Answer 11

GC:GC - 14.6 kcal/mol

Question 12

What is the low end of the energy of stacked base pairs?

Answer 12

3.8 kcal/mol

Question 13

Do DNA sequences unwind at AT rich regions?

Answer 13

yes

Question 14

Where do repulsive interactions between bases and sugars come from?

Answer 14

thymine methyl groups, guanine amino groups, step clashes

Question 15

How are sequence dependent repulsive interactions in B-form DNA minimized?

Answer 15

flattening propeller twist, rolling clashing base pairs, sliding base pairs, twist; unwinding helix

Question 16

Does the DNA bend at A-tract and mixed sequence junctions?

Answer 16

yes

Question 17

What are the biological roles of DNA bending?

Answer 17

DNA replication, transcription, DNA repair

Question 18

True or False: The rate of migration is inversely proportional to the log of MW.

Answer 18

True

Question 19

True of False: The rate of migration does not depend on the conformation of DNA.

Answer 19

False

Question 20

Describe the wedge model.

Answer 20

AA contains a wedge angle that deflects DNA axis. There is a bend every 10.5 base pairs. Conflicts with x-ray data.

Question 21

Describe the junction model.

Answer 21

There is a bend at the junction of B-form DNA and A-tracts. The greatest bend occurs at the 3’ end of A-tracts phased by 10.5 base pairs.

Question 22

Describe the writhing model.

Answer 22

General sequence DNA is writhing. Consists of A-tracts that alternate with general sequence DNA containing a writhing turn bend. DNA writhing is produced by rolling of base pairs. Continuous curved distortion of helix.

Question 23

What is a hairpin?

Answer 23

formed by oligonucleotide single strands which have a segment of inverted complimentary sequence

Question 24

What is a cruciform?

Answer 24

involve intra-strand base pairing and generate two stems from two hairpin loops from single unwound region

Question 25

What are palindromes?

Answer 25

have a given DNA duplex sequence followed after a short break by the same duplex sequence in the opposite direction

Question 26

What is TW?

Answer 26

``` topological winding # # of 360 degree turns ```

Question 27

What is Wr?

Answer 27

writhing # coiling of helical axis +2 lefthanded crossovers -2 righthanded crossovers

Question 28

How is relaxed, circular DNA strained?

Answer 28

by changing the pitch of its helical turns

Question 29

How does circular DNA relieve torsional strain?

Answer 29

by winding itself to form a super helix whose axis is the diameter of the original circle

Question 30

How many base pairs are required for H-DNA to form?

Answer 30

15 bp

Question 31

What is a junction?

Answer 31

regions with three or more stems?

Question 32

What is a nucleosome?

Answer 32

DNA duplex wrapped around 8 histone proteins

Question 33

What is a solenoid?

Answer 33

thought to be a right-handed or left-handed helix made up of close-packed nucleosomes

Question 34

Who came up with the wedge model?

Answer 34

Ulanovsky

Question 35

Who came up with the junction model?

Answer 35

Crothers

Question 36

Who came up with the writhing model?

Answer 36

Dickerson

Question 37

How many base pairs could be expected to identify and bind to a unique human DNA target?

Answer 37

17-mer

Question 38

What is silencing RNA (siRNA)?

Answer 38

Double-stranded RNA, 20-25 bp in length and operating within the RNA interference pathway

Question 39

What is the role of siRNA?

Answer 39

interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, preventing translation

Question 40

Who discovered siRNA?

Answer 40

Discovered in plants by David Baulcombe

Question 41

What is antisense RNA?

Answer 41

short RNA transcript that lacks coding capacity

Question 42

What is the function of antisense RNA?

Answer 42

can act as a repressor of the normal function or expression of the targeted RNA