Lecture 8 Flashcards
What is the secondary structure of DNA?
Double helix
What is each chain in the double helix connected to each other by?
Hydrogen bonds between the bases (non-covalent)
Which residues would be found in equal numbers in DNA?
[A and T] and [G and C] and Purines and Pyrimidines
What are Hydrogen bonds?
Polar non-covalent interactions where a hydrogen is being shared within a hydrogen bond between two electronegative atoms
What atoms form the hydrogen bonds in DNA?
Nitrogen and Oxygen
Why is it necessary for hydrogen bond interactions to be weak interactions?
In order to unwind it to carry out processes like replication or transcription
How many hydrogen bonds between A and T?
Two
How many hydrogen bonds between G and C?
Three
What is DNA (B-form) stabilized by?
Base stacking interactions and hydrogen bonds
What is the primary stabilizing force for DNA in B-form?
Base stacking
What are the components of base stacking?
- Van der waals
* Hydrophobic forces
Which direction are the strands of DNA going?
They are in an antiparallel orientation. On is going 5’ to 3’ and one is going 3’ to 5’
Which direction is the twist of DNA?
Right handed twist
When is the B-form usually found?
In aqueous environments
Which portions of the bases are hydrophobic?
The faces of the bases, so the flat portion of them
What are base stacking interactions?
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
What are the general features of B-form DNA?
- Hydrophobic core/polar exterior
- Bases largely excluded from H2O
- Ribose/deoxyribose exposed to H2O
- H-bonds in pairing interactions
- ~10 BP per turn
Why is the major groove important?
Because proteins can recognize base pairs within the DNA through the major groove
Why is the core of DNA hydrophobic?
Because that is where base pairs are present
What is the benefit of bases largely being excluded from water in DNA strucutre?
This stabilizes H-bonds between base pairs
Which part of DNA is exposed to water?
The sugars and phosphates
Where are the other hydrogen bonding groups (the ones that don’t bind the nucleotides) open?
At the major and minor grooves where they can interact with solvent
What is Complementarity in DNA strucuture?
When an A pairs with a T and a G pairs with a T
What does Chargaff’s rule only apply to?
Duplex DNA with complementary strands
