HL DNA replication

Question 1

Directionality of DNA polymerases
- Students should understand the difference between the 5’ and 3’ terminals of strands of nucleotides and that DNA polymerases add the 5’ of a DNA nucleotide to the 3’ end of a strand of nucleotides.

Answer 1

• When a new DNA strand is synthesized, the direction of replication will always occur from 5’ to 3’ direction – new nucleotides can only join at the 3’ end.
• The formation of a single stranded chain of DNA involves repeated condensation reactions between nucleotides.
• To each Carbon 3 of the previous deoxyribose molecule the phosphate group at Carbon 5 from the next nucleotide gets attached. Because the starting nucleotide of the DNA begins with a 5’end, the linkage of nucleotides is said to progress in 5’ 🡪 3’ direction.
• As a result, DNA can only be synthesized in a 5’ to 3’ direction

Question 2

where does the energy come from?

Answer 2

The energy for the attachment of a new nucleoside triphosphate comes from the hydrolysis of two phosphate groups which are located on the 5’ end of the new deoxyribose nucleoside triphosphate which is why new nucleotides cannot connect to the 5’ end of a nucleotide – the phosphate groups are simply on the «wrong» end.

Question 3

MORE!

Answer 3

• Once DNA polymerase has recognized the 3’ end of a nucleotide, it helps the formation of a covalent (phosphodiester bond) between previous nucleotide and the free one.
• DNA polymerase cannot initiate the process of DNA replication – there has to be a 3’ end to which a free nucleotide can be added.
• The covalent (phosphodiester bond) between previous nucleotide and the free one is formed in a condensation reaction.

Question 4

DNA replication process (slides 9-12)
- 3 stages (IET)

Question 5

Differences between replication on the leading strand and the lagging strand
- Include the terms “continuous”, “discontinuous” and “Okazaki fragments”. Students should know that replication has to be initiated with RNA primer only once on the leading strand but repeatedly on the lagging strand.

Answer 5

• Because of the DNA’s antiparallel arrangements, replication proceeds in two different directions from the origin and on both strands:

It is continuous on the leading strand but discontinuous on the lagging strand.

In both cases, however, replication moves in a 5’ to 3’ replication.

Leading strand:
Here, DNA polymerase adds nucleotides moving towards the replication fork. Replication is continuous on this strand.

Lagging strand:
DNA polymerase adds nucleotides moving away from the replication fork. They are added in a series of lengths (discontinously) as more of the template strand becomes exposed. These short sections are called Okazaki fragments.

Replication on the lagging strand is slower than on the leading strand. The DNA polymerase has to ”leapfrog” in order to continue replicating in 5’ to 3’ direction.

Question 6

Functions of DNA primase, DNA polymerase I, DNA polymerase III and DNA ligase in replication
- Limit to the simpler, prokaryotic system.

Answer 6

https://ib.bioninja.com.au/dna-replication-ahl/

DNA primase - DNA primase generates a short RNA primer on each of the template strands. The RNA primer provides an initiation point for DNA polymerase III, which can extend a nucleotide chain but not start one

DNA polymerase I - removes RNA primers and replaces them with DNA

DNA polymerase III - DNA pol III attaches to the 3’-end of the primer and covalently joins the free nucleotides together in a 5’ → 3’ direction

DNA ligase - joins Okazaki fragments together through covalent bonds btw. sugars and phosphates

Question 7

DNA proofreading
- Limit to the action of DNA polymerase III in removing any nucleotide from the 3’ terminal with a mismatched base, followed by replacement with a correctly matched nucleotide.

Answer 7

• DNA polymerases replicate DNA with great fidelity. When errors occur they are usually corrected, preventing mutations.
• In prokaryotes polymerase III takes over a repair and proofreading immediately after replication.