New strands grow 5'→3', always. Toward the fork: one piece. Away from it: fragments. At chromosome tips: a gap.
Replication unzips DNA and builds a new partner on each old strand. Primers, Okazaki fragments, and shrinking chromosome tips all trace back to one rule: DNA polymerase can only add to an existing 3' end.
Key terms
- Semiconservative — each new double helix keeps one old strand and pairs it with one newly built strand.
- Primer — a short RNA strand, made by primase, that gives DNA polymerase a 3' end to build from.
- DNA polymerase — reads the template 3'→5' and builds the new strand 5'→3'. It also proofreads its work.
- Leading strand — the new strand built in one continuous piece, following the fork as it opens.
- Lagging strand — the new strand built away from the fork in short Okazaki fragments, later joined by DNA ligase.
How it works
- Replication starts at an origin. The helix opens both ways, making two forks. A bacterial chromosome usually has one origin; a eukaryotic chromosome has many.
- Helicase breaks the hydrogen bonds between bases, unzipping the strands. Single-strand binding proteins keep them apart. Topoisomerase eases the twisting ahead of the fork.
- Primase lays down a short RNA primer. DNA polymerase extends it, pairing A with T and G with C.
- The strands are antiparallel. So one new strand grows toward the fork and follows it continuously, while the other grows away and must restart as more template opens.
- Each RNA primer is later swapped for DNA by a polymerase extending the 3' end of the piece behind it. DNA ligase then joins the pieces.
- At a linear chromosome's tip, the last primer has no piece behind it. Once it is removed, the gap stays empty, so each round shortens the new strand.
Why it matters
Expect numbers here. With one origin, two forks run at once, each copying half the chromosome, which halves the time. For density-band experiments, track strands, not whole molecules. Old strands are never destroyed; each round adds new ones that outnumber them. Start with all-heavy DNA in light medium: after two rounds, half is hybrid and half is light.
Exam traps
| Trap | Actually |
|---|
| Polymerase reads the template 5'→3', so half of each template gets skipped. | It builds 5'→3', so it reads the template 3'→5'. Nothing is skipped: the lagging template is copied in pieces. |
| Okazaki fragments form because polymerase keeps falling off the DNA. | They form because the strands are antiparallel and polymerase only adds to a 3' end. Neither fact alone would do it. |
| Chromosome ends shrink because enzymes trim them after copying. | The last primer's gap can't be filled, since no 3' end sits behind it. Telomerase extends the ends in germ-line and stem cells. |
| Helicase cuts the DNA backbone to open the fork. | Helicase breaks only the hydrogen bonds between bases. That is why unzipped strands can snap back together unless binding proteins hold them apart. |
Worked example
A bacterial strain makes a DNA ligase that stops working at 42 °C. The cells are shifted to 42 °C and given labeled nucleotides for one minute. Researchers separate the newly made DNA into single strands and sort them by length. What will they find?
- Name ligase's job. It seals the backbone between neighboring pieces of a new strand. It adds no nucleotides of its own.
- Find which new strand is built in pieces. The lagging strand is made as Okazaki fragments; the leading strand is one long chain.
- Primase and polymerase still work at 42 °C, so both templates keep being copied. Only the joining step fails.
Two groups: long new strands from the leading side, and many short, unjoined fragments from the lagging side. Together the fragments make up about half of the new DNA.
Only the lagging strand is made in pieces, so only it depends on ligase to become continuous. The near-miss is 'no new DNA is made,' which treats ligase as a builder. Polymerase does the building and ligase only stitches, so copying continues and only the stitching goes missing.