Sept 13 Flashcards
What can be “seen” by proteins for the major and minor groove?
The proteins can see the top side of the base pairs (major groove), which is the side without the glycosidic bonds.
What is a palindromic sequence?
It is a sequence that is mirrored on the other side of the same strand of DNA. The complementary strand will match the first strand such that if the sequence was 5’-AATTGGCC-3’, the complementary strand will also be 5’-AATTGGCC-3’
What on the operator sites (in this case OR1) is recognized by C1 and Cro?
It is the near perfect palindromic sequence presented.
How does the major grove fit into the C1 repressor’s ability to read it? How does it enhance binding?
The side chains on the helix 3 of the lambda repressor are guided by helix 2. Certain amino acids fit into the major groove and interact with key base pairs.
The repressor has arms that wrap around the operator to enhance binding.
When the lambda repressor dimerizes, it is an _________ dimer?
Symmetric. This means that they are the same and that the helix 3 of one will act as the other for the complementary strand of DNA.
What helices are used by Cro for interaction with DNA?
Cro has 3 helices and 3 B-sheets, it binds with helix 3 as well.
What amino acids are conserved between C1 and Cro in helix 3 and what do they do?
In helix 3 they both have a gln and ser in the same spot, targeting an A and G respectively.
It is observed that the lys on the Cro protein targets nucleotides quite far away from it as the protein is tilted in that way. Why would this still work?
The other amino acid side chains are relatively short and so protein has to tilt to interact with those nucleotides. Lys works as it has a longer side chain.
What roles does Alanine play in helix 3 when it is recognizing the operators?
The side chain has no charge but is hydrophobic, it drives away waters between the protein and DNA so allows for interactions.
