L1.5 -

Question 1

Describe the chemical information displayed in the minor groove of DNA?

Answer 1

~ T-A and A-T present the same info = 2 hydrogen bond acceptor
~ G-C and C-G present the same info = hydrogen bond acceptors (2) and donors (1)
~ can’t be distinguished

Question 2

Describe the chemical information displayed in the major groove of DNA?

Answer 2

all 4 sets of base pairs present different combinations of hydrogen bond acceptors, donors and methyl groups

Question 3

Name the different types of DNA and when you would find them.

Answer 3

A-DNA = low humidity 
B-DNA = high humidity
Z-DNA = alternating pyrimidine/purines

Question 4

Describe B-DNA.

Answer 4

~ clockwise helix
~ long and thin
~ 10.5 bp/turn
~ predominant conformation in cells
~ helix diameter = 2.0nm

Question 5

Describe A-DNA.

Answer 5

~ clockwise helix
~ short and fat
~ 11 bp/turn
~ even sized grooves
~ conformation can be induced by DNA binding proteins
~ helix diameter = 2.6nm

Question 6

Describe Z-DNA.

Answer 6

~ anti-clockwise helix
~ elongated and thin
~ 12 bp/turn
~ induced by methylation of cytosine, torsional stress and high salt concentrations
~ helix diameter = 1.8nm

Question 7

Give 3 examples of non B-DNA structure formed by genomic repetitive sequences.

Answer 7

1. cruciform - cross shape + inverted repeats
2. slipped (hairpin) structure - direct repeats
3. quadruplex - pairing between Gs

Question 8

Describe supercoiled DNA.

Answer 8

~ circular DNA that is under tension and twists in on itself

~ can form constrained linear DNA

Question 9

How does supercoiling occur?

Answer 9

1. circular DNA is cut, held at one end and twisted

2. when the two ends reattach, the DNA twists to restore preferred no. of bases per turn

Question 10

Negative supercoiling

Answer 10

circle becomes negatively supercoiled to compenstate for increased twist

Question 11

Linking number (LK)

Answer 11

the no. of times one strand wraps around the other

~ for circular DNA and constrained linear molecules, this is fixed

Question 12

Twist (Tw)

Answer 12

the number of turns in a DNA fragment (+1 per 360 twist)

Question 13

Writhe (Wr)

Answer 13

the no. of supercoils

~ can be =ve or -ve

Question 14

What formula links Tw, Wr and LK together?

Answer 14

LK = Tw + Wr

Question 15

What does negative supercoiling facilitate?

Answer 15

DNA strand separation

Question 16

Topoisomerase

Answer 16

Introduce or remove supercoils from DNA by temp. breaking

Question 17

Describe Griffith’s transformation experiment.

Answer 17

1. inject mice with living, nonvirulent bacteria = mice live
2. inject mice with living virulent bacteria = mice die & bacteria recovered
3. inject mice with heat-killed, virulent bacteria = mice live
4. inject mice with living non-virulent and heat-killed virulent = mice dead

Question 18

Describe Avery’s transformation experiment.

Answer 18

1. acquire combo of DNA and RNA
2. treat sample with RNase and then add remaining DNA to bacteria and grow on medium = S transformants produced
3. treat sample with DNase and then add remaining RNA to bacteria and grow on medium = NO S transformants

Question 19

Describe the Hershey-Chase experiment.

Answer 19

~ radioactively labelled 2 types of T2 bacteriophages
1) grown in 35S-containing medium = labelled protein
2) grown in 32P-containing medium = labelled DNA
~ radioactivity was only recovered inside host and then passed on to progeny with 2)