Proteins: Molecular Machines Flashcards
What is a replisome?
An assembly of enzymes, DNA polymerase and primase, and molecular motors, helicase and polymerase, that are involved in DNA replication.
What does the replisome do?
Coordinates the synthesis of the leading and lagging strand at equal speed. Several processes require coordination.
What does DNA polymerase do?
Adds nucleotides to the 3’ OH using nucleotide triphosohates as substrates. Moves in a 3’-5’ direction, catalysing the nucleophilic attack of 3’ OH on the alpha phosphate of NTP aligned, releasing pyrophosphate.
What cofactor does polymerase require?
Magnesium.
What is the structure of the polymerase?
Like a hand with a finger, thumb and palm. The space between the fingers and thumb is the catalytic site.
How is fidelity maintained by the polymerase?
Allosteric conformational changes where the finger domain clamps the aligned active site with a complementary nucleotide and the template helps to ensure fidelity.
What happens if a mismatched nucleotide is incorporated?
It is transferred to eh exonuclease site for removal by a 3nm swivelling if the thumb domain.
What processivity does the polymerase have?
Has the ability to stay associated with template for ~15 nucleotides and longer thanks to the association with helicase.
What is an RNA polymerase?
The molecular engine for transcription, DNA dependent as it uses DNA as a template and produces RNA.
What chemistry does the RNA polymerase active site have?
2 magnesium ion chemistry: MgA is for activation of the 3’ OH and MgB is brought in with the incoming nucleotide.
By what model is the RNA polymerase driven along the template?
Bownian Ratchet Model: the newly added nucleotide acts as a pawl and biases motion in the forward direction. However backtracking is possible and has been observed at single molecule level.
What does helicase do?
Splits the nucleic acid duplex into individual strands, also removes proteins associated with nucleic acid and remodels nucleoprotein complexes.
How are helicases classified?
By substrate specificity and directionality, can be DNA or RNA specific and can go in either the 3’-5’ or 5’-3’ direction.
How many helicase super families are there?
6
Give some differences of the helicase families?
1 and 2 are monomeric and most abundant whereas 3-6 are hexameric.
