2. DNA structure Flashcards

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1
Q

How many turns in B helix?

A

10

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2
Q

How many turns in A helix?

A

11

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3
Q

How is DNA B helix defined?

A

Average structure of DNA in solution

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4
Q

How does A helix differ from B helix?

A

More compressed, shorter, wider

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5
Q

When is Z helix formed?

A

Transiently during transcription, also for specific sequences

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6
Q

Which DNA structure does dsRNA commonly adopt?

A

A helix

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7
Q

Which non-covalent interactions form between bases?

A

Hydrogen bonds and Van der Waals interactions

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8
Q

What drives helix formation?

A

The hydrophobic effect

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9
Q

Which parts of the DNA are hydrophobic and hydrophillic?

A

Bases are hydrophobic, the backbone is hydrophillic

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10
Q

What is the distance between two sugars in the DNA backbone?

A

6 Angstrom

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11
Q

What is the typical with of a nucleotide base?

A

3.3 Angstrom

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12
Q

Why do bases stack on top of each other?

A

Because otherwise there would be a water-filled hole between bases, which is energetically discouraged

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13
Q

Why do bases twist with respect to each other?

A

To maximise exposure of hydrophillic parts to water and to maximise H-H bonds between bases

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14
Q

Which bases are purines?

A

A and G

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15
Q

Which bases are pyrimidines?

A

C and T

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16
Q

Why were AT and GC pairings favoured?

A

Because their width is nearly the same, therefore can form a helix without disrupting its structure

17
Q

What are the two Hoogsten base pairs?

A

Flipped A + T (disrupts regular structure of the helix)

Flipped G + C (only in acidic pH)

18
Q

What bases, other than cytosine, make good H-bonds with guanine?

A

Thymine and uracil

19
Q

What technique is most widely used for DNA structural studies?

A

High resolution X-ray crystallography

20
Q

What are the 4 terms used to describe changes in DNA structure?

A

Twist, Roll, Slide and Propeller twist

21
Q

What is the difference between major and minor groove?

A

Minor groove is where sugars are closest together

22
Q

What is the definition of angle of twist?

A

Rotation of one base pair with respect to the next

23
Q

What is the typical range and mean for the twist angle in B helices?

A

Range 24-40 degrees, typically 32 degrees

24
Q

What is the difference between twist and propeller twist?

A

Twist occurs between base pairs, propeller twist occurs within a base pair

25
Q

What is a typical propeller twist angle at which H-bonds are still maintained?

A

10-15 degrees

26
Q

What is the function of propeller twist?

A

Allows neighbouring base pairs to interact with a larger surface area

27
Q

Why are twist, slide and roll properties dependent on each other?

A

Change in one property must be accommodated by a change in the other properties

28
Q

Which base pair can form an additional H-bond upon propeller twisting?

A

AT

29
Q

Upon propeller twist, a clash between two countering purine bases can occur. What are the two ways in which it can be resolved and what are the consequences?

A

1) Negative slide

2) Positive slide and roll, allows for additional purine-purine interactions

30
Q

Which two properties of the DNA helix remain constant despite twist, slide and roll transformations?

A

Direction and vertical axis

31
Q

What is the function of helix untwisting/underwinding?

A

To destabilise and separate the strands, making them more accessible

32
Q

Rank GC-rich, AT-rich, poly-A/T and mixed regions in terms of decreasing stability

A

GC-rich, mixed, poly-A/T, AT-rich

33
Q

Give an example of an AT-rich region

A

TATA box

34
Q

What does gradual change in roll angle result in?

A

Curvature of DNA

35
Q

Why is gradual change in roll angle more common that stepwise?

A

It is easier to accommodate by the backbone

36
Q

In protein-binding regions of DNA, what is the importance of the regions flanking the recognition sequence?

A

They must accommodate a bend in DNA for the recognition sequence to bind to a protein

37
Q

What technique was used to prove intrinsic DNA sequence susceptibility to bending?

A

Electron microscopy