DNA Structure and Replication
General Biology · Section 2.1 · 17 study cards
The experiments that identified DNA, the chemistry of the double helix, and the enzymes that copy it semiconservatively.
Practice this set → Spaced repetition, card by card. No account needed.
Method
Two halves, taught for two different reasons
The experimental history is tested for reasoning, not dates. For each classic experiment, be able to say what was manipulated, what was measured, and which alternative the result eliminated. That is the form the exam question takes.
Structure first, then the machine
Every mechanism in replication follows from three structural facts, so learn those three and derive the rest.
- The backbone has polarity, with a free phosphate at the 5ʹ end and a free hydroxyl at the 3ʹ end.
- The two strands are antiparallel and complementary, so knowing one strand tells you the other exactly.
- DNA polymerase can only add to a 3ʹ hydroxyl, so new strands grow 5ʹ to 3ʹ and templates are read 3ʹ to 5ʹ.
Fact three plus fact two is the entire explanation for leading and lagging strands, and fact three alone explains why a primer is needed and why telomeres shorten.
How to walk through a fork
- Draw the parental duplex and label both ends of both strands. Do not skip this; unlabelled diagrams are where marks disappear.
- Mark the direction the fork is opening.
- Find the template whose 3ʹ end faces into the fork. Its new strand is the leading strand and runs continuously.
- The other template gives the lagging strand, made as Okazaki fragments pointing back away from the fork.
- Add the support crew in order: helicase unwinds, single-strand binding proteins hold, topoisomerase relieves strain ahead, primase starts, polymerase III extends, polymerase I swaps RNA for DNA, ligase seals.
Accuracy is a theme, not a footnote
Base pairing, proofreading and mismatch repair are three separate layers of fidelity, and questions often ask what happens when one layer fails. A cell with no proofreading is alive but mutates heavily; that is the answer shape examiners want.
Definitions and theorems
Worked example
A replication bubble opens in a bacterial chromosome. One parental strand in the region reads 5ʹ-GGCATTACGCTAGCTA-3ʹ. Write out the other parental strand, identify which new strand at the rightward-moving fork is leading and which is lagging, write the daughter strand made on the given strand, and state in order the enzymes needed to finish the lagging strand.
Write the complement with polarity. Pairing A with T and G with C, and running the second strand in the opposite direction, the parental duplex is 5ʹ-GGCATTACGCTAGCTA-3ʹ paired with 3ʹ-CCGTAATGCGATCGAT-5ʹ.
Fix the rule. Every new strand grows 5ʹ to 3ʹ, so each polymerase must read its template 3ʹ to 5ʹ. The only question at any fork is which template presents its 3ʹ end to the advancing fork.
Assign leading and lagging. At the rightward fork, the template that runs 3ʹ to 5ʹ from left to right can be copied continuously in the direction the fork is opening, so its new strand is the leading strand. The other template is copied in short pieces that point back, away from the fork, giving the lagging strand.
Write the daughter strand on the given template. Reading 5ʹ-GGCATTACGCTAGCTA-3ʹ as a template means reading it 3ʹ to 5ʹ, that is from right to left, and the new strand is 5ʹ-TAGCTAGCGTAATGCC-3ʹ. Check it by pairing the two sequences end to end: it is simply the complement written in the opposite orientation.
List the lagging strand enzymes in order. Helicase unwinds, single-strand binding proteins keep the strands apart, topoisomerase relieves the supercoiling ahead of the fork, primase lays an RNA primer for each fragment, DNA polymerase III extends each primer into an Okazaki fragment, DNA polymerase I removes each RNA primer and fills the gap with DNA, and DNA ligase seals the nicks.
Say why the asymmetry exists at all. Both strands are made at the same fork on antiparallel templates, while polymerase can only work in one direction. That single constraint, and not any difference in the enzymes used, is what forces one strand to be discontinuous.
Common mistakes
- Saying helicase breaks the bonds between nucleotides. Helicase breaks the hydrogen bonds between the two strands, not the covalent phosphodiester bonds along a strand. Breaking the backbone would destroy the template, and it is topoisomerase, not helicase, that cuts the backbone and then immediately reseals it.
- Writing a complementary strand without reversing the polarity. If a template is given as 5ʹ-ATGC-3ʹ, the answer is 5ʹ-GCAT-3ʹ, not 5ʹ-TACG-3ʹ. Students who write the complement base by base in the same left-to-right order get an antiparallel strand labelled backwards and lose the mark even though every base is right.
- Thinking the lagging strand is made 3ʹ to 5ʹ. Every Okazaki fragment is built 5ʹ to 3ʹ like everything else. What runs the other way is the overall direction in which the fragments are laid down, and stating that clearly is usually what the mark is for.
- Forgetting that the primer is RNA. If the primer were DNA there would be nothing to remove and no job for DNA polymerase I. The RNA identity is also why a primer cannot simply be left in place in the finished chromosome.
- Muddling the two Meselson-Stahl generations. The first generation rules out the conservative model, and only the second generation rules out the dispersive model. Answers that claim one round of replication proves semiconservative replication are incomplete.
Practice it
Reading the method is not the same as being able to recall it under pressure. This set drills 17 cards one at a time and schedules each card separately, so the ones you keep missing come back sooner.