Sept 18 Flashcards
Do cells have R or L handed DNA? What bond makes it like that?
We have R handed helices. It is the glycosidic bond, if it is the anti form with the base pointing away from the sugar it is right handed. If it is Syn with the base above/below the sugar, then it is left handed.
What is the most common form of DNA? What are the other 2 types and basic qualities of each?
A and B form are R handed. B is most common. A is similar to B but more compact nucleotides, has a hollow inside. Z form is left handed, looks more disordered
What are tautomers?
They are isomers that interconvert by moving a hydrogen atom.
How does tautomerization affect the nigrogenous bases? What is the process called?
Tautomeric shifts. When bases are mismatched they tautomerize to allow hydrogen bonding. Usually this causes two of the nitrogen atoms to switch roles (from H bond donor to acceptor for one and vice versa for the other)
Standard base pairing occurs when bases are not mismatched, what is it called when tautomeric shifts happen due to mismatch? What are the new BPs and how many H bonds between them?
Anomalous base pairing. Have CA with 2 H bonds and GT with 3 H bonds
What form are pyrimidines and purines predominantly in, and less common?
Pyrimidines usually in amino form, other is imino form. Purines usually in keto form, tautomer is enol form
How does DNA’s flexible nature allow enxymes to repair mismatched base pairs?
Base flipping occurs so the nucleotide base is outside the helix, and enzyme can get to it. Enzyme disrupts H bonds between BPs first to allow base to flip out.
What is the Mica experiment?
DNA helices were isolated on a mica surface. Restriction enxymes were added, but too bulky to cut the DNA helices anywhere except from the top side (furthest away from the mica surface). The polyacrylamide gel showed lengths of multiples of 10.5. This means that every 10 or so BP a full helical turn is made. So 36 degrees per BP as well.
Does the A form of DNA have more or less BP’s per turn and how many degrees per BP?
It is more compact nucleotides with hollow center so more BP’s per turn (11 instead of 10.5) and 33 degrees
Diffraction pattern lines are _______ to the actual lines.
Perpendicular
Why was the 4th point on the diffraction pattern missing?
It is from destructive interference, as it has the 3rd and 5th point. This proves DNA is double helix as destructive interference from other strand.
How can you tell if GC or CG base pair from major groove?
From Major groove, can see top side of BP. For example see left to right non polar H, then H donor, then 2 H bond acceptors. If it were a GC pair it would be the opposite left to right.
What is helical pitch and rise?
Pitch is how far apart DNA is from a full turn (so if you put it against ruler while it was twisted. a full turn would happen every 34 Angstroms). Rise is how many angstroms of rise contributed by each BP. Each ladder rung is about 3.4 A rise as there are 10.5 BPs per turn. Get periodicity of DNA.
