Lesson 2 of 6 / DNA replication and gene expression
Copy both DNA strands
Why is one new strand made in fragments?
I can explain semi-conservative replication, directionality and leading/lagging synthesis.
I can explain DNA replication and the end-replication problem.Syllabus
Syllabus 9477, Core 2(b). Explain DNA replication and the end-replication problem.
About 8 min
Make a guess. You are not marked.
Both DNA strands are copied at a replication fork. Is each new strand made in one continuous piece?
Show the answer
No. One strand is made in short fragments.
DNA polymerase only extends 3-prime ends. On the lagging strand it must restart again and again, making Okazaki fragments.
The key idea
DNA polymerase extends a 3-prime end, so antiparallel templates require continuous and discontinuous synthesis.
Explore the idea
Follow the growing 3-prime end
The upper template is read 3-prime to 5-prime towards the fork. Polymerase extends the new strand at its 3-prime end, so it can follow the opening fork continuously.
Green: parental templates. Blue: new DNA; arrowheads mark extension. Orange: RNA primers. This separated, parallel view shows direction; intact DNA ahead of the fork and enzyme shapes are omitted. Helicase opens the fork, primase makes primers, polymerase extends, and ligase seals nicks.
Track old and new strands after copying
Explore the idea
Track the old strands
The two parental strands separate. Neither complete old double helix remains together in just one daughter molecule.
This model tracks strand origin, not fork movement. The connecting lines represent paired bases, not additional DNA backbones.
Explanation
Replication is semi-conservative: each daughter DNA double helix contains one parental strand and one newly synthesised strand. Helicase separates the strands at a replication fork, exposing templates. Complementary pairing selects incoming nucleotides; DNA polymerase catalyses phosphodiester-bond formation.
DNA polymerase adds to a free 3-prime OH, making new DNA in the 5-prime to 3-prime direction while reading the template in the opposite direction. It cannot initiate a strand without a primer. Primase supplies short RNA primers that provide suitable starting ends.
At each fork, the leading strand can extend continuously towards the moving fork. The other template has the opposite orientation, so the lagging strand is made as successive Okazaki fragments, each initiated near the fork and extended away from it. Both strands are still synthesised 5-prime to 3-prime.
RNA primers are removed and replaced with DNA where a suitable upstream 3-prime end exists. DNA ligase seals remaining nicks in the sugar-phosphate backbone. Do not assign ligase the role of selecting every complementary base or helicase the role of joining nucleotides.
Step by step
- 1
Mark template directions
An unlabelled fork invites direction errors.
- 2
Find extendable 3-prime ends
Polymerase requires a primer.
- 3
Finish the backbone
Replace primers and seal nicks with ligase.
Worked example
Work through the evidence
Does discontinuous synthesis mean the lagging strand is made 3-prime to 5-prime?
One way to explain it
No. Each fragment is made 5-prime to 3-prime. Discontinuity allows synthesis on the oppositely oriented template as the fork opens.
Why this answer works
- Template and new-strand directions differ.
- Fork movement is not the same as the direction of every fragment's extension.
Watch out for this
A student says: "DNA ligase unwinds the double helix." What is wrong with this?
Show the answer
Helicase separates strands. Ligase seals nicks between DNA fragments.
Check your understanding
Why are RNA primers necessary?
Show the answer
DNA polymerase requires an existing 3-prime OH to extend.
A primer supplies an extendable starting end.
Quick recall
Why is one new strand made in fragments?