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Flashcards in MCB Lecture 8 Nucleotides Deck (12)
0

Be able to draw all four nucleotides

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1

Be able to draw a nucleotide

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2

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

12 kcal/mol

A lot

3

What are the two grooves in a double helix?

Major minor

4

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

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

5

What are DNA binding proteins?
What are the general features of DNA binding proteins?

These are literally proteins that bind to DNA

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

6

How does the helix turn helix motif bond with DNA?

In the major groove

H bonds
VDW
Ionic interactions

7

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

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

8

What kind of bonding is histone-DNA?

Electrostatic

9

What can destabilise nucleosomes?

Other DNA binding proteins
Unusual DNA sequences
Histone modifying complexes

10

Describe non-specific binding between protein and DNA

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

11

Describe sequence specific bonding between protein and DNA

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

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