Gene 366 Study Questions- Chapter 9-10-11

1. What is the function of the Min system in bacterial divisions?

Controls the location of the septum formation and it composed of 3 proteins Min C-D-E. Min C
prevents the ring formation while incorporating the Min D proteins because MinC is not moving
itself, it moves with MinD. MinD can bind itself to the membrane. On the other hand, MinE can
inhibit the MinC-D complex.

2. If bacterial chromosomes are catenated (interlinked) following replication, how are they
separated?
1- Topoisomerases (Muk Proteins[like condensin help separation])
2- Site specific recombination (FtsK- Xer-C[can bind dif sequence to form holliday junction and
FtsK can resolve this holliday junction, Xer-D)

3. When can a “multiforked” bacterial chromosome form?

It is formed when bacteria divide more often than every 60minutes

4. How can a eukaryotic cell enter the cell cycle and initiate genome replication?
Licensing factors (Cdt1, Cdc6) enter the nucleus then bind to ORC in ARS region.
Cdc6 binds to ORC and allows MCM proteins to bind
Cdt1 facilitates MCM loadings on origins
Mcm[similar to DnaB]  helicase activity
Prereplication [The complex contains the ORC complex, Cdc6, and the MCM proteins]
and postreplication complexes [consists of the ORC complex bound to the origin.]

5. What are the major functions of p53?

P53 protein is kind of decision maker. Normally, the level of the p53 is low because of constantly
degradation of p53 by MDM2 proteins, but in the case DNA damage, some elements [ATM, ATR]
can block the MDM2 activity, so the p53 level gets increasing over time

If there is a damage in a dna strand, p53 comes into account and decides whether it will be
repaired or will go under apoptosis.

6. In a) prokaryotes and in b) eukaryotes, how does the cell prevent re-replication of a site?
Eukaryotes- Cyclin/Cdk activity is very important. For example, Rb- E2f interaction. That is, the Rb
is normally block the E2F, while the cyclin level is up, the Rb is hyperphosphorylated ,so it cannot
bind the E2F and with this releasing. E2F can bind to DNA and start transcription to some
Trancription factors for initiation of the S phase.
Also, the Geminin protein can inhibit Cdt1, so no more licensing factor

cdk activity, RB- E2F binding should be maintained

Prokaryotes
SeqA- binds to DnaA and blocks DnaA binding to Dna boxes in oriC
Dat locus compete the binding of DnaA against the oriC – DnaA binds to dat locus instead of
binding to oriC
Hda protein (Hydrolysis of ATPase) – inhibits licensing factors[DnaA] / prevents the further activity
of DnaA
Prevent the binding of Dam methylases to the DNA - prevent DNA methylation (hemi-methylated)

7. What kind of a phenotype would you expect in a temperature mutant for the following genes
 a. DnaA mutant – no initiation bcs DnaA should bind to the DnaA boxes in oriC to initiate
replication
b. DnaC mutant – premature initiation bcs DnaB cannot be inhibited, and it undergoes initiation
process
c. HU mutant – DNA cannot be opened up so fork formation failed

8. Why is it that DNA can only be synthesized in one direction?

Free 3’ OH end

9. What are the differences between prokaryotic and eukaryotic replication mechanisms?
Prokaryotes have one origin of replication because they only have the one circular/single
chromosome
- Eukaryotes have multiple origins of replication because they multiple linear chromosomes

Replication also happens at a much faster rate in prokaryotic cells, than in eukaryotes
10. Lagging strand is synthesized in pieces. Do you think this will delay the synthesis of the lagging
strand? In addition, if so how is the rep. fork affected?

11. What happens when DNA polymerase replicating DNA encounters RNA polymerase transcribing
DNA in the same direction?

DNA polymerase is able to move 10× faster than RNA polymerase, so DNA polymerase normally
overtakes RNA polymerase. It appears that DNA polymerase bypasses RNA polymerase without
disrupting transcription, but the mechanism is unknown.

12. Describe the two-state assembly model of DnaA at oriC

DnaA-ATP monomers bind to the 13-mers sequences of oriC in an extended state. As the 9-mers
begins to melt, DnaA- ATP monomers change to a compact state which stabilizes the single
strands.
(10.5)

13. Name four mechanisms that may be involved in controlling reinitiation in bacteria.

SeqA- binds to DnaA and blocks DnaA binding to Dna boxes in oriC
Dat locus compete the binding of DnaA against the oriC – DnaA binds to dat locus instead of
binding to oriC
Hda protein (Hydrolysis of ATPase) – inhibits licensing factors[DnaA] / prevents the further activity
of DnaA
Prevent the binding of Dam methylases to the DNA - prevent DNA methylation (hemi-methylated)

14. A replicon: C

A) may or may not have an origin.

 B) must include the gene for the protein that regulates initiation of replication.

C) must “fire” only once during the cell cycle.

D) must have a terminus.

E) is trans-acting.

15. Single-copy replication control means that: D

A) only one DNA molecule can be present in a cell at a time.

B) there can be only one origin of replication in the entire genome.

C) only one DNA molecule can be replicated in a cell at a time.

D) a DNA molecule can only be replicated once during the cell cycle.

E) there can be only one origin of replication on each DNA molecule.