Module 2 - DNA replication

Question 1

DNA Topoisomerase I

Answer 1

“Nicks” a single strand which allows the other strand to move through the gap. The single strand then rejoins after the other strand has moved through

Question 2

DNA Topoisomerase II

Answer 2

“Nicks” both strands and then the DNA strands uncoil themselves

Question 3

Helicase

Answer 3

Helicase breaks the hydrogen bonds between bases.

This is different to Topoisomerase which just relieves the stress in the supercoiling.

Question 4

Replication fork

Answer 4

Point where DNA is being separated and synthesised.

Question 5

Exonuclease activity

Answer 5

Degrading of DNA on the outside of DNA (i.e. at the end of Okazaki fragments), it occurs in two ways:

3’ to 5’ exonuclease activity

5’ to 3’ exonuclease activity

Question 6

3’ to 5’ exonuclease activity

Answer 6

Used to go back and remove any incorrect nucleotides.

This is why there are rarely any mistakes in DNA replication - proofreading occurs.

Question 7

5’ to 3’ exonuclease activity

Answer 7

tbc

Question 8

Leading strand replication (Bacteria)

Answer 8

Primase creates a primer that is around 4 to 15 nucleotides in length and DNA polymerase III creates a new strand

Question 9

Leading strand replication (Eukaryotes)

Answer 9

DNA polymerase alpha adds around 20 nucleotides to the primer and then DNA polymerase delta continues the replication

Question 10

DNA Polymerase I (B)
Subunits:
5’ to 3’ exonuclease activity:
3’ to 5’ exonuclease activity:
Function:

Answer 10

One
Yes
Yes
DNA repair, replication

Question 11

DNA Polymerase III (B)
Subunits:
5’ to 3’ exonuclease activity:
3’ to 5’ exonuclease activity:
Function:

Answer 11

At least ten
No
Yes
Main replicating enzyme

Question 12

DNA Polymerase alpha (E)
Subunits:
5’ to 3’ exonuclease activity:
3’ to 5’ exonuclease activity:
Function:

Answer 12

Four
No
No
Priming during replication

Question 13

DNA Polymerase delta (E)
Subunits:
5’ to 3’ exonuclease activity:
3’ to 5’ exonuclease activity:
Function:

Answer 13

Two/three
No
Yes
Main replicating enzyme

Question 14

Okazaki fragments in bacteria

Answer 14

At the replication fork, fragments are made in the 5’ to 3’ direction.

As DNA Polymerase III reaches the following primer for the following Okazaki fragment, it must detach as it has no 5’ to 3’ exonuclease activity. DNA Polymerase then attaches and degrades the primer and makes it into DNA.

DNA ligase then links both Okazaki fragments, forming one continuous DNA strand.

Question 15

Okazaki fragments in eukaryotes

Answer 15

DNA Polymerase delta reaches the next primer and then, along with helicase to break the bonds, it moves the next primer and the first few nucleotides of the next Okazaki fragments out of the way.

The Okazaki fragment that has been lifted is still attached so FEN1 (an endonuclease) degrades the DNA so that all extra nucleotides are removed from the strand.

DNA ligase then forms a phosphodiester bond between the two nucleotides.

Question 16

Endonuclease activity

Answer 16

The degrading of DNA within the DNA strand (i.e. the breaking of a primer and part of an Okazaki fragment that has been moved by DNA Polymerase delta and helicase)

Question 17

The end replication problem

Answer 17

The final Okazaki fragment cannot be made

because its priming site would be after the end of the parent molecule.

Therefore, as replication occurs, DNA molecules become shorter and shorter.

Question 18

Telomerase

Answer 18

In eukaryotes, a special enzyme called telomerase prevents the ends of chromosomes from being shortened by adding telomeres to the end of DNA molecules.

By adding the sequence TTAGGG several times, the final Okazaki fragment can now be primed as the primer attaches far enough away that DNA Polymerase III can create the last Okazaki fragment.

Question 19

Tetrahymena thermophila

Answer 19

Single-cell ciliated organisms with 40,000 chromosomes need a lot of telomerase.

Telomeres in Tetrahymena have the sequence TTGGGG while we have TTAGGG

Question 20

Senescence

Answer 20

The process of cells without Telomerase getting shorter and dying.

In culture, cells can divide only around 50 times before senescence occurs.

Question 21

Telomerase in all cells?

Answer 21

Telomerase is only present in stem cells.

The reason is unclear. However, in cancer cells, telomerase is switched on and chromosomes are longer than usual. Possible explanation?

Question 22

S phase of the cell cycle

Answer 22

This is when DNA replication occurs. At this point, modified nucleotides can be incorporated into DNA and then detected with fluorescently labelled antibodies.

This is how we visualise sites of DNA replication.

Question 23

Heterochromatin

Answer 23

Highly condensed, gene-poor, and transcriptionally silent.

Although it is gene-poor, it still has a significant effect as it is used to keep stability within chromosomes.

Question 24

Euchromatin

Answer 24

Less condensed, gene-rich, and more easily transcribed.

Euchromatin is very often under transcription.