DNA rep II

Question 1

Bacterial Helicase vs. Eukaryotic Helicase

Answer 1

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.

Question 2

SSB or RPA

Answer 2

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.

Question 3

DNA Pol III

Answer 3

Multi-subunit replicative protein that has its core activity in the alpha, omega episilon unit

Question 4

Tao protein

Answer 4

responsible for connecting different sides of the polymerase.

Question 5

B camp loader

Answer 5

Uses ATP hydrolysis to place B clamp on DNA.

Question 6

Primase in DNA polymerase III

Answer 6

Binds to DnaB, synthesizes a new primer, then dissociates (Okazaki fragments)

Question 7

B clamp loader structure

Answer 7

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.

Question 8

Where is AMP added to DNA ligase?

Answer 8

To the lysine of DNA ligase.

Question 9

Tus

Answer 9

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.

Question 10

Ter

Answer 10

20 bp-long sequence that traps replication fork

Question 11

Cantenated Chromosomes

Answer 11

DNA molecules connected together. Present in both linear and circular chromosomes.

Question 12

DNA topoisomerase IV

Answer 12

Separates cantenated chromosomes.

Question 13

Cyclins

Answer 13

Proteins that are produced in cells that determine which cyclic phase a cell is in

Question 14

Cyclin dependent kinases

Answer 14

Activated kinases in specific cycles in the cell cycle.

Question 15

Pre-RC

Answer 15

Prereplicative complex; binds to origin of replication in eukaryotes. ORC + Cdc6 and Cdt1 loads MMC2-7 on dsDNA

Question 16

MMC2-7

Answer 16

Especially active during S phase; hexameric helicase; loaded on dSDNA unlike helicases in prokaryotes that are loaded on ssDNA

Question 17

Cdt1 and Cdc6

Answer 17

Helicase loaders that cause MMC2-7 to bind to the origin of replication. Happens in G1 phase.

Question 18

Although ORC, Cdt1, Cdc6, and MMC2-7 bind during G1, why isn’t MMC2-7 active?

Answer 18

Because it isn’t activated until S phase. right before S phase, Cyclin E increases, which causes CDK2 to become activated.

Question 19

CDK2

Answer 19

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

Question 20

What happens after MMC2-7 is activated?

Answer 20

Auxiliary factors and Polymerases, epsilon and delta, recruited to helicase.

Question 21

Polymerase a/primase

Answer 21

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)

Question 22

PCNA + RF-C

Answer 22

Sliding clamp and clamp loader. associated with polymeras

Question 23

Telomeres

Answer 23

Act as protective caps on the ends of chromosomes; composed of short, tandem repeats; non-coding; 5’ TTAGGG-3’

Question 24

Telomerase

Answer 24

A protein component with reverse transcriptase activity plus an RNA component containing 1.5 copies.

Question 25

TRF1 and TRF2

Answer 25

Binds hanging regions of DNA at the ends telomeres.

Question 26

Histone Chaperones

Answer 26

Disassemble histones, especially H2A and H2B.

Question 27

Histone acetylytransferase

Answer 27

binds acetylated histone tails using bromodomain. Deposits same acetylation pattern on adjacent histones.

Question 28

CAF-I

Answer 28

Histone Chaperone.