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What are the three forms of DNA? What are their characteristics?
- B - Common - Narrow(ish) diameter, major/minor grooves
- A - Fatter DNA, equal(ish) grooves
- Z - Thin, Shallow grooves, left handed
How many torsion angles shape DNA? Why is it not more flexible?
6, because of constrains from the double helix (steric inteference)
Is DNA a perfect double helix? Why?
No, local variations can induce small in the shape of the helix
What are some examples of base pair geometries? What are their properties?
- Twist - 26-43 degrees (36 degrees ave.)
- Propellor twist - (-23)-(-7) degrees
- Roll - 14-17 degrees
How does stacking affect DNA bending?
Smaller stacking makes DNA less stiff, therefore making it more bendable.
How can DNA be bent?
- - Sequence structure (AT rich)
- - Protein binding
What are some examples of DNA bending proteins?
- Catabolite gene activator protein (CAP) - 90 degree
- Lac repressor - 45 degree
How are Holliday junctions formed?
- Homologous recombination
- Nickec strands cross over
What are some properties of RNA?
- 2' OH
- Single stranded
- RNA-11 (like A-DNA)
What is a stem loop?
A single strand of RNA that has base paired with itself
What is a Ribozyme?
A catalytic RNA
What are four key types of RNA?
- Other (often catalytic)
Give an example of a stem loop RNA
What are the levels of RNA structure? What are their properties?
- Primary - Sequence
- Secondary - Base paring
- Tertiary - Long range interactions
What are the three edges of a base?
- Watson Crick
Are all RNAs coding?
No some have other functions (rRNA, tRNA etc)
Where is the riboswitch found?
The 5' UTR
How does the Riboswitch work?
TPP binds, preventing ribosome binding and therefore translation (like a snorlax on the promoter)
Give one key example of a Ribozyme. What does it do?
Hammerhead Ribozyme - Cleaves itself before cytidine-17, yields cyclic phosphodiester
What are group II introns?
Self splicing introns, possibly spliceosome precursor
What sites in the Ribosome are made of RNA (mostly)
Decoding and peptidyltransferase
What catalytic mechanisms take place in the ribosome?
Mainly Proximity and Orientation, as well as preferential transition state binding
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