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