Flashcards in DNA rep II Deck (28):
Bacterial Helicase vs. Eukaryotic Helicase
BH- unwinds 5' to 3'/ EH- unwinds 3' to 5'; ATP dependent helicases, binds to phosphodiester bonds; As ATP hydrolysis occurs, helicase slides down and opens up hydrogen bonds between bases.
SSB or RPA
No ATP used; bind to phosphodiester backbone; protect DNA, keeps it from forming secondary structures. DNA polymerase cannot interact with secondary structures. SSB acts as substrate for DNA polymerase.
DNA Pol III
Multi-subunit replicative protein that has its core activity in the alpha, omega episilon unit
responsible for connecting different sides of the polymerase.
B camp loader
Uses ATP hydrolysis to place B clamp on DNA.
Primase in DNA polymerase III
Binds to DnaB, synthesizes a new primer, then dissociates (Okazaki fragments)
B clamp loader structure
5 subunit protein, binds 2 ATP molecules. When ATP binds, b-clamp is loaded non-covalently in the open conformation of the clamp (Clamp loader opens b-clamp), DNA loaded, 1st ATP hydrolysis causes b-clamp closure around DNA, 2nd ATP hydrolysis causes clamp loader and clamp w/DNA to disassociate.
Where is AMP added to DNA ligase?
To the lysine of DNA ligase.
Terminus utilization substance; protein binds to Ter sequence and helps to stall replication fork; Terminator regions run in the same direction of the polymerase they are trying to stop.
20 bp-long sequence that traps replication fork
DNA molecules connected together. Present in both linear and circular chromosomes.
DNA topoisomerase IV
Separates cantenated chromosomes.
Proteins that are produced in cells that determine which cyclic phase a cell is in
Cyclin dependent kinases
Activated kinases in specific cycles in the cell cycle.
Prereplicative complex; binds to origin of replication in eukaryotes. ORC + Cdc6 and Cdt1 loads MMC2-7 on dsDNA
Especially active during S phase; hexameric helicase; loaded on dSDNA unlike helicases in prokaryotes that are loaded on ssDNA
Cdt1 and Cdc6
Helicase loaders that cause MMC2-7 to bind to the origin of replication. Happens in G1 phase.
Although ORC, Cdt1, Cdc6, and MMC2-7 bind during G1, why isn't MMC2-7 active?
Because it isn't activated until S phase. right before S phase, Cyclin E increases, which causes CDK2 to become activated.
cyclin dependent kinase-2; Kinase that complexes with Cyclin E; activates kinase, which in turn phosphorylates helicase loaders (Cdc6 and Cdt1 which dissociate) and helicase MMC2-7, which makes a transition to activation on ssDNA
What happens after MMC2-7 is activated?
Auxiliary factors and Polymerases, epsilon and delta, recruited to helicase.
Activated and recruited by CDK2. Causes synthesis of RNA primer. After primer, deoxynucleotides are added specifically by polymerase a. Has no exonuclease activity (prone to error)
PCNA + RF-C
Sliding clamp and clamp loader. associated with polymeras
Act as protective caps on the ends of chromosomes; composed of short, tandem repeats; non-coding; 5' TTAGGG-3'
A protein component with reverse transcriptase activity plus an RNA component containing 1.5 copies.
TRF1 and TRF2
Binds hanging regions of DNA at the ends telomeres.
Disassemble histones, especially H2A and H2B.
binds acetylated histone tails using bromodomain. Deposits same acetylation pattern on adjacent histones.