L3 - DNA recogntion 2 Flashcards
structure of CAP
homodimer
2 helix turn helices - 1 on each monomer
- each bind to 11 base pair sequnce
binds to a 22 base pair sequence total
helix turn helix motif
2 alpha helices held together
recognition helix fits into major groove and interacts with bases
stabilsing helix holds it in place
DAn is palnindromic. What does this mean and how does itr affect binding porteins
(think of adam cartoon)
DNA is the same on each strand but going opposite directions
the ‘feet’ of the binding proteins touch the SAME sequnce on DIFFERENT strands of DNA
reasons for dna binding proteins to dimerse
dimeric molecules bind much more tightly than indivdual monomers
dont double the affinity - they SQUARE it
+
also dimers can recgonise longer DNA binding sequnces that would appear less frequently in random DNA
more specific
direct vs indirect readout
direct - intercations with base due to chemical interactions
indirect - specificity for sequnces even though no contacts are made
preferences for shapes in strand
= some DNA is easier to bend than others
= proteins that cause beding have prefernceds ffor easy to distort/bend DNA
CAPs indirect binding
when CAP binds introduces kinks at position 6 on each strand
P6 is a T-A bp and nearly always present in sequnce = howrever never actualy touched by CAP protein
DNA ligases low specific interactions
DNA ligase must work non-specifcally so it can bhind and repair wherever needed on entire genome
BUT must bind with high enough affinity to work
- has 0 specificity
- same kd for damaged and undamaged DNA
= works by maximising surface area for max hydrogen and ionic interactions
= extensiev contact with phosphate backbone
