MCB Lecture 8 Nucleotides Flashcards
Be able to draw a nucleotide
.
Be able to draw all four nucleotides
.
How much energy is harnessed from the cleavage of one phosphate group from a nucleotide?
12 kcal/mol
A lot
What are the two grooves in a double helix?
Major minor
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
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
How does the helix turn helix motif bond with DNA?
In the major groove
H bonds
VDW
Ionic interactions
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
What kind of bonding is histone-DNA?
Electrostatic
What can destabilise nucleosomes?
Other DNA binding proteins
Unusual DNA sequences
Histone modifying complexes
Describe non-specific binding between protein and DNA
Arginine and lysine (+) bind to the phosphate backbone (-)
Describe sequence specific bonding between protein and DNA
Hydrogen bonding between the protein and the exposed base pairs in the major groove
