MCB Lecture 8 Nucleotides Flashcards

0
Q

Be able to draw a nucleotide

A

.

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1
Q

Be able to draw all four nucleotides

A

.

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2
Q

How much energy is harnessed from the cleavage of one phosphate group from a nucleotide?

A

12 kcal/mol

A lot

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3
Q

What are the two grooves in a double helix?

A

Major minor

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4
Q

How many reisdues associate with nucleotide bases to form a strong and sequence specific bond?

A

10-20 need to form bonds to give a strong interaction

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5
Q

What are DNA binding proteins?

What are the general features of DNA binding proteins?

A

These are literally proteins that bind to DNA

In general, the protein has a helix-turn-helix motif that binds to the major groove

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6
Q

How does the helix turn helix motif bond with DNA?

A

In the major groove

H bonds
VDW
Ionic interactions

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7
Q

Do helix-turn-helix motifs have high affinity for DNA?

A

Yes, because the motif is always present in a dimer, so there is double the free energy change and squared Km

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8
Q

What kind of bonding is histone-DNA?

A

Electrostatic

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9
Q

What can destabilise nucleosomes?

A

Other DNA binding proteins
Unusual DNA sequences
Histone modifying complexes

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10
Q

Describe non-specific binding between protein and DNA

A

Arginine and lysine (+) bind to the phosphate backbone (-)

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11
Q

Describe sequence specific bonding between protein and DNA

A

Hydrogen bonding between the protein and the exposed base pairs in the major groove

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