Nucleic acids: Structure and properties Flashcards

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1
Q

Nämn de två purinerna.

A

Adenine, Guanine.

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2
Q

Nämn de två pyrimidinerna.

A

Thymine, Cytosine.

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3
Q

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

A

Fosfatgruppen.

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4
Q

What differs between a nucleotide and a nucleoside?

A

A nucleotide has a base, sugar and phosphate group.

A nucleotide has a base and a sugar.

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5
Q

What does isosterisism mean?

A

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

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6
Q

How many hydrogen bonds are there between Guanine and cytosine?

A

Three

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7
Q

What is base stacking?

A

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

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8
Q

Are GT bonds stronger than GC bonds?

A

No, they are similar to AT-bonds.

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9
Q

What are hoogsteen base pairs?

A

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

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10
Q

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

A

8.2 Å resp. 10.1 Å.

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11
Q

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

A

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

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12
Q

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

A

B

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13
Q

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

A

A-DNA is more compact than B-DNA.

(Z-DNA is less compact)

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14
Q

Do TFs generally bind to the minor groove?

A

No. They generally bind to the major groove.

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15
Q

Whys is RNA less chemically stable than DNA?

A

Ribose has an exposed 2’ OH-group.

2’deoxyribose has had it removed.

There are RNAses everywhere.

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16
Q

What’s the most common form of RNA?

A

A-RNA.

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

17
Q

Name four stabilising forces that act on DNA.

A
  1. Hydrogen bonds between two DNA strands.
  2. Base stacking within one DNA strand.
  3. Hydrophobic interactions
  4. Electrostatic interactions (van der waals).
18
Q

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

A

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.

19
Q

What is Wallace’s rule?

A

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

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

20
Q

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

A

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.

21
Q

How does formaldehyde affect DNA?

A

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.

22
Q

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

A

1.8

23
Q

Is UV-absorption more accurate than fluorescent markers?

A

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

24
Q

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

A

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

25
Q

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

A

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.

26
Q

Name four techniques which are based on nucleic acid hybridisation.

A
  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)