6.2 DNA Replication

DNA polymerases can only synthesize new DNA in the 5' → 3' direction because of how the chemistry of bond formation works. Each incoming dNTP has a 5' triphosphate; the free 3'-OH on the growing strand performs a nucleophilic attack on that 5' phosphate to form a new phosphodiester bond. Polymerase’s active site is built to add nucleotides onto the 3' end, so synthesis can’t proceed 3' → 5'. That’s why DNA replication (EK 6.2.A.1.i) needs an RNA primer (EK 6.2.A.1.v) to provide a starting 3'-OH and why the fork has a continuously made leading strand and a discontinuous lagging strand with Okazaki fragments joined by ligase (EK 6.2.A.1.vi–vii). For review tied directly to the AP CED, see the Topic 6.2 study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ) and try practice problems (https://library.fiveable.me/practice/ap-biology).

Semiconservative replication means each new DNA molecule keeps one original (parent) strand and gets one newly made complementary strand. At an origin of replication helicase unwinds the double helix, forming a replication fork; topoisomerase relaxes supercoiling ahead of the fork. DNA polymerase builds new strands only 5'→3' and needs short RNA primers to start. Because the two parent strands run opposite directions, replication is continuous on the leading strand and discontinuous on the lagging strand (Okazaki fragments). DNA ligase then joins fragments on the lagging strand. Base-pairing rules (A–T, G–C) guide accurate copying and DNA polymerase proofreads to reduce errors. This semiconservative model is exactly what AP EK 6.2.A.1(ii) describes. For a quick review, see the Topic 6.2 study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ) and more unit resources (https://library.fiveable.me/ap-biology/unit-6). For extra practice, try the AP problems page (https://library.fiveable.me/practice/ap-biology).

Think of the replication fork like a two-lane road: the parental DNA strands run antiparallel, but DNA polymerase can only build new DNA in the 5' → 3' direction (CED EK 6.2.A.1.i). The leading strand is the lane where synthesis can go the same direction as the fork moves, so DNA polymerase makes one continuous new strand after a single RNA primer (continuous 5'→3' synthesis). The lagging strand is the other lane—because its template runs opposite the fork’s movement, polymerase must work away from the fork in short pieces (Okazaki fragments) each started by an RNA primer; ligase then joins those fragments (discontinuous synthesis; EK 6.2.A.1.vi–vii). Helicase unwinds the helix and topoisomerase relieves supercoils ahead of the fork (EK 6.2.A.1.iii–iv). For quick review and practice aligned to the CED, check the Topic 6.2 study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ) and try practice questions (https://library.fiveable.me/practice/ap-biology).

Helicase’s job is to unzip the double helix at the replication fork by breaking the hydrogen bonds between the two DNA strands so each strand can serve as a template. It moves away from the origin of replication, powered by ATP, and creates the single-stranded templates needed for DNA polymerase to synthesize new strands in the 5′→3′ direction (EK 6.2.A.1–iii). In the AP CED, helicase is one of the named enzymes you should know; it works with topoisomerase (which relaxes supercoiling ahead of the fork), primase (to lay RNA primers), and DNA polymerase (which does the actual synthesis). For a quick topic review, check the Topic 6.2 study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ). Practice problems are at (https://library.fiveable.me/practice/ap-biology) if you want to test this concept.

Good question—DNA polymerase can’t start a new strand from scratch because it can only add nucleotides onto an existing 3′-OH group. That’s why short RNA primers are laid down first: they provide the free 3′-OH that DNA polymerase needs to begin synthesizing in the 5′→3′ direction (EK 6.2.A.1.i, v). On the leading strand one primer is enough for continuous synthesis; on the lagging strand many primers are needed to make Okazaki fragments, which are later filled in and joined by DNA polymerase and ligase (EK 6.2.A.1.vi–vii). This is a core AP idea about mechanism—know that initiation requires an RNA primer and why (no usable 3′ end otherwise). For a quick CED-aligned review, see the Topic 6.2 study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ) and practice questions (https://library.fiveable.me/practice/ap-biology) to test this concept.

Topoisomerase prevents DNA from getting too twisted by relieving the torsional stress that builds up ahead of the replication fork. As helicase unwinds the double helix, the DNA ahead becomes overwound (positive supercoils). Topoisomerases cut the DNA backbone (Type I makes a single-strand nick; Type II makes a transient double-strand break), let the helix unwind or pass strands through, and then reseal the cut. That relaxation stops supercoiling from stalling helicase and DNA polymerase, so replication can continue smoothly (remember: replication is semi-conservative and synthesis runs 5'→3'). This function is exactly what the CED lists for EK 6.2.A.iv. For a quick review of replication proteins and practice Qs, check the Topic 6.2 study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ) and practice problems (https://library.fiveable.me/practice/ap-biology).

Okazaki fragments are short stretches of DNA synthesized on the lagging strand during replication. Because DNA polymerase can only add nucleotides in the 5'→3' direction (EK 6.2.A.1.i), the strand whose template runs 5'→3' away from the replication fork can’t be made continuously. Helicase unwinds the fork (EK 6.2.A.1.iii) and primase lays multiple short RNA primers; DNA polymerase then extends each primer to make short DNA pieces—those are the Okazaki fragments. Replication is therefore discontinuous on the lagging strand (EK 6.2.A.1.vi). Finally, DNA ligase joins the fragments into one continuous strand (EK 6.2.A.1.vii). This semiconservative, directional process is exactly the AP-level mechanism you should know for LO 6.2.A (refer to the Topic 6.2 study guide for a quick review: https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ). For more practice, check the AP-style problems (https://library.fiveable.me/practice/ap-biology).

Semiconservative means each new DNA double helix keeps one original (parental) strand paired with one newly synthesized complementary strand. That matches EK 6.2.A.1–2: DNA is copied by using each strand as a template (5'→3' synthesis by DNA polymerase), so daughter molecules are half old/half new. A conservative model would leave the parental duplex intact and make a completely new duplex—so you’d get one all-old and one all-new molecule. A dispersive model would produce daughter helices made of interspersed old and new segments on both strands. Experimental support (Meselson–Stahl density-gradient results) showed daughters are half-heavy then resolve into hybrid + light bands, which fits semiconservative replication, not conservative or dispersive. For quick review, see the Topic 6.2 study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ) and the Unit 6 overview (https://library.fiveable.me/ap-biology/unit-6). For extra practice, try problems at (https://library.fiveable.me/practice/ap-biology).

DNA polymerase and ligase do different jobs during replication. DNA polymerase reads a template strand and synthesizes new DNA in the 5'→3' direction, but it can’t start from scratch—it needs an RNA primer (EK 6.2.A.1.v). It works continuously on the leading strand and discontinuously on the lagging strand, making Okazaki fragments (EK 6.2.A.1.vi). Ligase doesn’t build nucleotides; it seals the sugar-phosphate backbone by joining adjacent Okazaki fragments (and any remaining nicks) into one continuous strand (EK 6.2.A.1.vii). So: polymerase = makes new DNA (requires primer), ligase = links fragments into an intact strand. For a quick CED-aligned review, see the Topic 6.2 study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ) and practice >1,000 AP-style problems at (https://library.fiveable.me/practice/ap-biology).

Start at an origin of replication: helicase unwinds the double helix while topoisomerase relaxes supercoils ahead of the fork (CED EK 6.2.A.iii–iv). Short RNA primers are laid down by an RNA polymerase to give a free 3′ end (EK 6.2.A.v). DNA polymerase then extends from those primers, adding nucleotides only in the 5′ → 3′ direction and using each parental strand as a template (semiconservative replication; EK 6.2.A.i–ii). On the leading strand synthesis is continuous toward the fork; on the lagging strand synthesis is discontinuous, producing Okazaki fragments away from the fork (EK 6.2.A.vi). DNA polymerase also proofreads and corrects many errors during synthesis (keyword: proofreading). After replacement of RNA primers with DNA, ligase seals the sugar–phosphate backbone between fragments (EK 6.2.A.vii). Together these steps ensure accurate copying of genetic information for transmission to daughter cells. For a concise AP-aligned review, check the Topic 6.2 study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ) and try practice questions (https://library.fiveable.me/practice/ap-biology).

Because DNA polymerase can only add nucleotides in the 5'→3' direction (EK 6.2.A.1.i), synthesis has to match the template orientation. At the replication fork the two template strands are antiparallel: one template runs 3'→5' so DNA polymerase can make a new strand continuously toward the fork (the leading strand). The opposite template runs 5'→3', so a polymerase moving 5'→3' cannot follow the fork in the same direction. The cell solves that by making short 5'→3' stretches (Okazaki fragments) on the lagging strand, each started with an RNA primer (EK 6.2.A.1.v). DNA ligase then joins those fragments (EK 6.2.A.1.vii). So it’s a physical/chemical constraint of polymerase directionality and strand polarity, not a design choice. Review Topic 6.2 in the study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ) and try practice problems (https://library.fiveable.me/practice/ap-biology).

At the replication fork the double helix is opened and copied: helicase unwinds the two DNA strands, creating a Y-shaped fork (that shape comes from the two single-stranded templates diverging as they’re separated). Ahead of the fork topoisomerase relaxes supercoiling. Each original strand serves as a template (semiconservative replication) and DNA polymerase synthesizes new DNA in the 5'→3' direction. On the template that runs 3'→5' relative to fork movement, synthesis is continuous (leading strand). On the template that runs 5'→3' relative to fork movement, synthesis is discontinuous: short Okazaki fragments are made after RNA primers are laid down, and ligase later joins those fragments. DNA polymerase needs RNA primers to start and also proofreads. These are the exact CED points you’ll be asked about on AP Bio (EK 6.2.A. i–vii). For a concise study guide and practice questions, check the Topic 6.2 replication study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ) and Unit 6 overview (https://library.fiveable.me/ap-biology/unit-6); Fiveable also has 1,000+ practice problems (https://library.fiveable.me/practice/ap-biology).

The cell copies both strands accurately by using complementary base pairing plus multiple enzyme checks. Replication is semiconservative: each original strand is a template for a new 5'→3' strand. Helicase unwinds the fork and topoisomerase relaxes supercoils. RNA primers start synthesis, and DNA polymerase adds nucleotides continuously on the leading strand and discontinuously as Okazaki fragments on the lagging strand; ligase joins those fragments. Crucially, DNA polymerase proofreads (removes mismatches as it adds bases) and post-replication mismatch-repair systems fix any remaining errors, so both strands end up copied with very high fidelity. These are the mechanisms the AP CED expects you to know (semiconservative replication, 5'→3' synthesis, replication fork, leading/lagging strands, primers, polymerase proofreading, ligase)—review Topic 6.2 study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ) and try practice questions (https://library.fiveable.me/practice/ap-biology) to cement this.

Because replication is semiconservative, each daughter DNA molecule contains one original (parental) strand and one newly made complementary strand. That matters for passing genes to offspring because the parental strand serves as a precise template for complementary base pairing (A–T, G–C), which preserves the exact sequence of genes generation to generation (EK 6.2.A.1.ii). Semiconservative replication plus 5'→3' polymerization and DNA polymerase proofreading (EK 6.2.A.1.i, v, vii) lowers copying errors so offspring inherit accurate genetic information. Having an original strand also helps repair systems distinguish and correct recent mistakes in the new strand, further protecting genetic continuity. This idea is explicitly listed in the AP CED as a core mechanism you should know for Topic 6.2. For a focused review, see the Topic 6.2 study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ) and more practice problems (https://library.fiveable.me/practice/ap-biology).

If ligase didn’t work properly, Okazaki fragments on the lagging strand couldn’t be joined into a continuous 3'→5' complementary strand. You’d end up with lots of nicks/gaps between short DNA pieces, leaving the newly made strand incomplete and structurally unstable. That causes increased chance of strand breaks, replication fork collapse, activation of cell-cycle checkpoints, and either DNA repair pathways (if possible) or apoptosis if damage is severe. Over time, persistent ligase failure raises mutation rates and genome instability, which can impair cell function or viability. This ties directly to EK 6.2.A (lagging-strand discontinuous synthesis and ligase joining fragments) and LO 6.2.A from the CED. For a quick refresher on replication steps and enzymes, check the Topic 6.2 study guide (https://library.fiveable.me/ap-biology/unit-6/replication/study-guide/dWnyvQBkJXbdCZAXGCfQ). For more practice on related AP-style questions, try the practice set (https://library.fiveable.me/practice/ap-biology).