Nucleic acids: Structure and properties

Question 1

Nämn de två purinerna.

Answer 1

Adenine, Guanine.

Question 2

Nämn de två pyrimidinerna.

Answer 2

Thymine, Cytosine.

Question 3

Vilken grupp i DNA-molekylen ger den dess negativa laddning?

Answer 3

Fosfatgruppen.

Question 4

What differs between a nucleotide and a nucleoside?

Answer 4

A nucleotide has a base, sugar and phosphate group.

A nucleotide has a base and a sugar.

Question 5

What does isosterisism mean?

Answer 5

Two atoms are isosteric if they have the same amount of available valence electrons.

Question 6

How many hydrogen bonds are there between Guanine and cytosine?

Answer 6

Three

Question 7

What is base stacking?

Answer 7

Base stacking is when sequential bases stack on top of each other and create a plane.

Question 8

Are GT bonds stronger than GC bonds?

Answer 8

No, they are similar to AT-bonds.

Question 9

What are hoogsteen base pairs?

Answer 9

Non-cannonical base pairs which were found when chemists started experimenting with nucleotides outside of physiological context.

Question 10

What’s the distances between complementary bases in the minor- and major groove, respectively?

Answer 10

8.2 Å resp. 10.1 Å.

Question 11

How does the helical form of DNA/RNA contribute to stability?

Answer 11

When the helix is twisted, the length in between the phosphodiester bonds (the bonds within ssDNA) is reduced.

Question 12

Which DNA helix is the most common (A/B/Z)?

Answer 12

B

Question 13

Which one of A- and Z-DNA is more compact than B-DNA?

Answer 13

A-DNA is more compact than B-DNA.

(Z-DNA is less compact)

Question 14

Do TFs generally bind to the minor groove?

Answer 14

No. They generally bind to the major groove.

Question 15

Whys is RNA less chemically stable than DNA?

Answer 15

Ribose has an exposed 2’ OH-group.

2’deoxyribose has had it removed.

There are RNAses everywhere.

Question 16

What’s the most common form of RNA?

Answer 16

A-RNA.

RNA cannot form B-RNA due to 2’OH on ribose.

Question 17

Name four stabilising forces that act on DNA.

Answer 17

1. Hydrogen bonds between two DNA strands.
2. Base stacking within one DNA strand.
3. Hydrophobic interactions
4. Electrostatic interactions (van der waals).

Question 18

Why is the addition of positive ions to a DNA solution stabilising?

Answer 18

Because each nucleotide in DNA is negative. When positive ions are present, the negative charge from the phosphate groups are neutralized. This makes the two DNA strands less prone to repel each other.

Question 19

What is Wallace’s rule?

Answer 19

Wallace’s rule states the Tm at a certain salt concentration:

Td (celsius) = 2(n(A)+n(T)) + 4(n(G)+n(C))

Question 20

What does the degree of absorption of UV260nm tell you about nucleic acids?

Answer 20

UV260 is absorbed by nucleic acids. You can:
1. Assay the degree of denaturation (ssDNA absorbs more UV260 than dsDNA.
2. Assay the purity of nucleic acids by dividing UV260/UV280.

Question 21

How does formaldehyde affect DNA?

Answer 21

The formaldehyde gradually decreases the DNA bases’ ability to form hydrogen bonds. This happens because formaldehyde reacts with NH2 of the nucleic bases.

The DNA becomes less stable over elapsed time as less hydrogen bonds decreases the Tm.

Question 22

What’s the acceptable purity threshold (UV260 / UV280) for nucleic acids?

Answer 22

1.8

Question 23

Is UV-absorption more accurate than fluorescent markers?

Answer 23

No. Intercalating dyes are very precise. They’re used when performing qPCRs.

Question 24

Why is it preferable to have a constant voltage than a constant amperage when running gels?

Answer 24

Constant amperage leads to a rapid increase in voltage as the gel’s resistance increases over time.

Constant voltage keeps the amperage constant as well. The gel will take longer time to run toward the end.

P = I^2 * R
P = V^2 / R

I^2 * R = V^2 / R

Question 25

Why would you run a Pulsed field gel electrophoresis (PFGE)?

Answer 25

If you have very large DNA fragments to purify, the PFGE allows for effective separation. This is the case because the voltage is shifted diagonally, making the samples migrate in a zigzag fashion.

Question 26

Name four techniques which are based on nucleic acid hybridisation.

Answer 26

1. Northern blot (Nucleic acid probe for DNA)
2. Southern blot (Nucleic acid probe for RNA)
3. Microarray (DNA-cDNA)
4. FISH (Histological assay w/ nucleic acid probes)