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Biocheem > Lecture 8 > Flashcards

Lecture 8 Flashcards

1
Q

What is the secondary structure of DNA?

A

Double helix

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2
Q

What is each chain in the double helix connected to each other by?

A

Hydrogen bonds between the bases (non-covalent)

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3
Q

Which residues would be found in equal numbers in DNA?

A

[A and T] and [G and C] and Purines and Pyrimidines

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4
Q

What are Hydrogen bonds?

A

Polar non-covalent interactions where a hydrogen is being shared within a hydrogen bond between two electronegative atoms

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5
Q

What atoms form the hydrogen bonds in DNA?

A

Nitrogen and Oxygen

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6
Q

Why is it necessary for hydrogen bond interactions to be weak interactions?

A

In order to unwind it to carry out processes like replication or transcription

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7
Q

How many hydrogen bonds between A and T?

A

Two

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8
Q

How many hydrogen bonds between G and C?

A

Three

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9
Q

What is DNA (B-form) stabilized by?

A

Base stacking interactions and hydrogen bonds

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10
Q

What is the primary stabilizing force for DNA in B-form?

A

Base stacking

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11
Q

What are the components of base stacking?

A
  • Van der waals

* Hydrophobic forces

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12
Q

Which direction are the strands of DNA going?

A

They are in an antiparallel orientation. On is going 5’ to 3’ and one is going 3’ to 5’

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13
Q

Which direction is the twist of DNA?

A

Right handed twist

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14
Q

When is the B-form usually found?

A

In aqueous environments

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15
Q

Which portions of the bases are hydrophobic?

A

The faces of the bases, so the flat portion of them

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16
Q

What are base stacking interactions?

A

When we have one flat base pair and another flat base pair within in the duplex structure and those base pairs are associated with each other though van der waals and hydrophobic forces

17
Q

What are the general features of B-form DNA?

A
  • Hydrophobic core/polar exterior
  • Bases largely excluded from H2O
  • Ribose/deoxyribose exposed to H2O
  • H-bonds in pairing interactions
  • ~10 BP per turn
18
Q

Why is the major groove important?

A

Because proteins can recognize base pairs within the DNA through the major groove

19
Q

Why is the core of DNA hydrophobic?

A

Because that is where base pairs are present

20
Q

What is the benefit of bases largely being excluded from water in DNA strucutre?

A

This stabilizes H-bonds between base pairs

21
Q

Which part of DNA is exposed to water?

A

The sugars and phosphates

22
Q

Where are the other hydrogen bonding groups (the ones that don’t bind the nucleotides) open?

A

At the major and minor grooves where they can interact with solvent

23
Q

What is Complementarity in DNA strucuture?

A

When an A pairs with a T and a G pairs with a T

24
Q

What does Chargaff’s rule only apply to?

A

Duplex DNA with complementary strands

25
Q

What is DNA Denaturation?

A

The separation of double-stranded DNA to single-stranded DNA

26
Q

What bonds does denaturation disrupt?

A

The non-covalent forces of base-stacking and hydrogen bonding

27
Q

What is DNA denaturation essential for?

A
  • Energy-dependent process

* Replication and transcription require strand separation

28
Q

How is absorption at 260 nm affected during denaturation?

A

Absorption increases when DNA goes from double stranded to single stranded DNA

29
Q

Which bonds can be disrupted by increasing the thermal energy of DNA molecules?

A

The weka H-bond and base-stacking forces

30
Q

What does the sigmoidal relationship during DNA denaturation suggest?

A

That there is something cooperative occurring in the process

31
Q

What is a cooperative process?

A

Something that is very easy to continue and once it begins it propagates very rapidly through the structure

32
Q

Which form of DNA has a higher absorbance?

A

Single stranded DNA has a higher absorbance

33
Q

What does Tm reflect?

A

The temperature at which we’ve got 50% double stranded and 50% single stranded

34
Q

What does Hyperchromicity reflect?

A

The increase in absorbance as we go from double stranded to single stranded structures

35
Q

What does Hypochromicity reflect?

A

The reduction in absorbance when going from single stranded to double stranded

Biocheem (38 decks)

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