DNA Flashcards
DnaB
helicase, ATP-dependent unwinding of DNA
DnaG
primase (RNA polymerase) synthesizes primers
TopA
topoisomerase, detangles DNA
PolA
DNA polymerase 1. replaces RNA primers
LigA
ligates 3’OH of strand with 5’P of okazaki fragments
DARS1 (site in the genome)
DnaA activation
DARS2 (site in the genome)
reactivation of DnaA. free ATP bind to DnaA and now DnaA has high affinity for the nucleotide binding site.
-Fis and IHF bind to DARS2 in order to facilitate and activate this exchange of ADP to ATP.
factors involved in replication initiation
HU, IHF, Fis
HU
nucleoid associated protein that helps destabilize double-stranded DNA at the origin.
IHF
integration host factor, bends DNA
Fis
factor for inversion stimulation. helps stabilize initial initiation complex.
where does DnaA bind in the OriC?
between the duplex unwinding element and the IHF binding site
SeqA-oriC regulates?
prevents binding of DnaA at the oriC. SeqA fxns when hemimethylated DNA is present. methylation occurs on the A of GATC motifs in the DNA.
ATP-DnaA regulates?
prevents dnaA gene transcription
steps for initiation
- DnaA is activated with ATP
- DnaA binds to DnaA binding box (between DUE and IBS) - DnaA oligomerizes
- DnaB is recruited
- DnaG is recruited
- DnaA is inactived and dissociates, priming by DnaG
- DNA polymerase III holoenzyme will bind and replication starts.
DNA polymerase I
removes primers and replaces them with nucleotides
DNA polymerase III
has 3-5 exonuclease activity as proofreading
Tus
binds to ter sequences
interferes with DnaB function.
(terminus utilization substance)
regulation of DnaA-ATP
- ATP-DnaA inhibits its own transcription
- seqA inhibits ATP-DnaA from binding to the oriC
- datA hydrolyzes the ATP
Negative controls - Dna replication
- ppGpp: shows up when the cells are low on energy (nutrient limitation). down regulates the DnaA in the cell
- Arc: senses O2 concentration and redox potential. binds to the TATA box (DUE) repressing replication
- Ici: binds at DUE region. present in cells in stationary phase growth, so replication is not initiated.
